Skip to main content

Genomic Improvement of Rice for Drought, Aluminum, and Iron Toxicity Stress Tolerance

  • Chapter
  • First Online:
Genomic Designing for Abiotic Stress Resistant Cereal Crops

Abstract

The opportunity of plants to escape from unwanted environments is almost nonexistent due to their sessile characteristic. Drought, aluminum (Al), and iron (Fe) toxicity under acid soil conditions are the major constraints as abiotic stresses in rice cultivation, particularly in tropical areas. These abiotic stress tolerance mechanisms are contributed by morphological, physiological, biochemical, and anatomical alterations that affect yield. The level of tolerance to these abiotic stresses is inherited quantitatively and controlled by several genes as quantitative trait loci. The objectives of this review were to highlight the current progress in investigating genes responsible for the drought, Al, and Fe toxicity, and their utilization for genomic improvement in rice. The mechanisms at the levels of morphology, physiology, biochemistry, anatomy, and particularly at the molecular level were discussed in the review. Overall, this review presents a systemic brief of drought, Al, and Fe tolerance mechanisms, recent progress in exploring genes responsible for these traits to the latest innovation in the genomic improvement of high-yielding multi-tolerant rice variety. This review could assist as guidelines for researchers and rice breeders.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 189.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 249.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 249.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  • Abdoul KC (2006) Testing and developing tolerant rice varieties to iron toxicity in lower guinea (CRA Kilissi and Koba). In: Audebert A, Narteh LT, Kiepe P, Millar D, Beks B (eds) Iron toxicity in rice-based system in West Africa. WARDA, Cotonou

    Google Scholar 

  • Abifarin AO (1989) Progress in breeding rice for tolerance to iron toxicity. In: WARDA (ed) WARDA annual report for 1990. West Africa Rice Development Association, Bouaké

    Google Scholar 

  • Aboa K, Dogbe SY (2006) Effect of iron toxicity on rice yield in the Amou-Oblo lowland in Togo. In: Audebert A, Narteh LT, Kiepe P, Millar D, Beks B (eds) Iron toxicity in rice-based system in West Africa. WARDA, Cotonou

    Google Scholar 

  • Adiningsih J, Sudjadi M (1993) The role of alley cropping systems in increasing soil fertility on acid dryland. Bogor: Indonesian Center for Soil and Agro-climate Research and Development [in Indonesian]

    Google Scholar 

  • Adjao RT, Staatz JM (2015) Asian rice economy changes and implications for Sub-Sharan Africa. Glob Food Secur 5:50–55

    Article  Google Scholar 

  • Ahmed CB, Rouina BB, Sensoy S, Boukhris M, Abdallah FB (2009) Changes in gas exchange, proline accumulation and antioxidative enzyme activities in three olive cultivars under contrasting water availability regimes. Environ Exp Bot 67:345–352

    Article  Google Scholar 

  • Ali M, Pathan MS, Zhang J, Bai G, Sarkarung S, Nguyen HT (2000) Mapping QTLs for root traits in a recombinant inbred population from two indica ecotypes in rice. Theor Appl Genet 101:756–766

    Article  CAS  Google Scholar 

  • Ali M, McClung AM, Jia MH, Kimball JA, McCouch SR, Eizenga GC (2011) Rice diversity panel evaluated for genetic and agro-morphological diversity between subpopulations and its geographic distribution. Crop Sci 51:2021–2035

    Article  Google Scholar 

  • Aniol A, Gustafson JP (1984) Chromosome location of genes controlling aluminum tolerance in wheat, rye and triticale. Can J Genet Cytol 26:701–705

    Article  Google Scholar 

  • Anjum SA, Xie X, Wang L (2011) Morphological, physiological and biochemical responses of plants to drought stress. Afr J Agric Res 6:2026–2032

    Google Scholar 

  • Arenhart RA, Yang B, Oliveira LF, Neto LB, Schunemann M, Maraschin FS, Margis-Pinheiro M (2014) New insights into aluminum tolerance in rice: the ASR5 protein binds the STAR1 promoter and other aluminum-responsive genes. Mol Plant 7:709–721

    Article  CAS  PubMed  Google Scholar 

  • Arenhart RA, Margis R, Margis-Pinheiro M (2016) Rice ASR1 and ASR5 are complementary transcription factors regulating aluminium responsive genes. Plant Cell Environ 39:645–651

    Article  CAS  PubMed  Google Scholar 

  • Arunin S, Hillerislambers D (1984) Rice cultivation in the tidal swamps of Thailand. In: International Rice Research Institute (ed) The workshop on research priorities in tidal swamp rice; 22–25 June 1981; Banjarmasin, South Kalimantan, Indonesia. International Rice Research Institute, Manila, pp 79–88

    Google Scholar 

  • Asch F, Becker M, Kpongor DS (2005) A quick and efficient screen for resistance to iron toxicity in lowland rice. J Plant Nutr Soil Sci 168(6):764–773

    Article  CAS  Google Scholar 

  • Atwell S, Huang YS, Vilhjalmsson BJ, Willems G, Horton M, Li Y, Meng D, Platt A, Tarone AM, Hu TT, Jiang R, Muliyati NW, Zhang X, Amer MA, Baxter I, Brachi B, Chory J, Dean C, Debieu M, de Meaux J, Ecker JR, Faure N, Kniskern JM, Jones JD, Michael T, Nemri A, Roux F, Salt DE, Tang C, Todesco M, Traw MB, Weigel D, Marjoram P, Borevitz JO, Bergelson J, Nordborg M (2010) Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines. Nature 465:627–631

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Audebert A (2006) Iron toxicity in rice—environmental conditions and symptoms. In: Audebert A, Narteh LT, Kiepe P, Millar D, Beks B (eds) Iron toxicity in rice-based system in West Africa. WARDA, Cotonou

    Google Scholar 

  • Audebert A, Sahrawat KL (2000) Mechanisms for iron toxicity tolerance in lowland rice. J Plant Nutr Soil Sci 23(11–12):1877–1885

    CAS  Google Scholar 

  • Audebert A, Fofana M (2009) Rice yield gap due to iron toxicity in West Africa. J Agron Crop Sci 195(1):66–76

    Article  CAS  Google Scholar 

  • Aung MS, Masuda H (2020) How does rice defend against excess iron? Physiological and molecular mechanisms. Front Plant Sci 11:1102

    Article  PubMed  PubMed Central  Google Scholar 

  • Aung MS, Masuda H, Kobayashi T, Nishizawa NK (2018) Physiological and transcriptomic analysis of responses to different levels of iron excess stress in various rice tissues. J Soil Sci Plant Nutr 64(3):370–385

    Article  CAS  Google Scholar 

  • Babu RC, Zhang J, Blum A, Ho THD, Wu R, Nguyen HT (2004a) HVA1, a LEA gene from barley confers dehydration tolerance in transgenic rice (Oryza sativa L.) via cell membrane protection. Plant Sci 166:855–862

    Article  CAS  Google Scholar 

  • Babu RC, Zhang J, Blum A, Ho THD, Wu R, Nguyen HT (2004b) HVA1, a LEA gene from barley confers dehydration tolerance in transgenic rice (Oryza sativa L.) via cell membrane protection. Plant Sci 116:855–862

    Article  Google Scholar 

  • Bae H, Kim SK, Cho SK, Kang BG, Kim WT (2011) Overexpression of OsRDCP1, a rice RING domain-containing E3 ubiquitin ligase, increased tolerance to drought stress in rice (Oryza sativa L.). Plant Sci 180:775–782

    Article  CAS  PubMed  Google Scholar 

  • Barik SR, Pandit E, Pradhan SK, Mohanty SP, Mohapatra T (2019) Genetic mapping of morpho-physiological traits involved during reproductive stage drought tolerance in rice. PLoS ONE 14:e0214979

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Barik SR, Pandit E, Mohanty SP, Nayak DK, Pradhan SK (2020) Genetic mapping of physiological traits associated with terminal stage drought tolerance in rice. BMC Genet 76:1471–2156

    Google Scholar 

  • Bashir K, Nozoye T, Ishimaru Y, Nakanishi H, Nishizawa NK (2013) Exploiting new tools for iron bio-fortification of rice. Biotech Adv 31(8):1624–1633

    Article  CAS  Google Scholar 

  • Bauer H, Ache P, Lautner S, Fromm J, Hartung W, Al-Rasheid KAS et al (2013) The stomatal response to reduced relative humidity requires guard cell-autonomous ABA synthesis. Curr Biol 23:53–57

    Article  CAS  PubMed  Google Scholar 

  • Becker M, Asch F (2005) Iron toxicity in rice: conditions and management concepts. J Plant Nutr Soil Sci 168:558–573

    Article  CAS  Google Scholar 

  • Behnam B, Iuchi S, Fujita M, Fujita Y, Takasaki H, Osakabe Y et al (2013) Characterization of the promoter region of an Arabidopsis gene for 9-cis-epoxycarotenoid dioxygenase involved in dehydration-inducible transcription. DNA Res 20:315–324

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bernier J, Kumar A, Ramaiah V, Spaner D, Atlin GN (2007) A large-effect QTL for grain yield under reproductive-stage drought stress in upland rice. Crop Sci 47:507–518

    Article  Google Scholar 

  • Bian M, Zhou M, Sun D, Li C (2013) Molecular approaches unravel the mechanism of acid soil tolerance in plants. Crop J 1(2):91–104

    Google Scholar 

  • Bihani P, Char B, Bhargava S (2011) Transgenic expression of sorghum DREB2 in rice improves tolerance and yield under water limitation. J Agr Sci 149:95–101

    Article  CAS  Google Scholar 

  • Briat JF, Lobréaux S (1997) Iron transport and storage in plants. Trends Plant Sci 2(5):187–193

    Article  Google Scholar 

  • Brumbarova T, Bauer P (2008) Plant membrane and vacuolar transporters. CAB International, London

    Google Scholar 

  • Budzianowski G, Wos H (2004) The effect of single D-genome chromosomes on aluminum tolerance of triticale. Euphytica 137:165–172

    Article  CAS  Google Scholar 

  • Burr B, Burr FA (1991) Recombinant inbreds for molecular mapping in maize: theoretical and practical considerations. Trends Genet 7:55–60

    CAS  PubMed  Google Scholar 

  • Burr B, Burr FA, Thompson KH, Albertson MC, Stuber CW (1988) Gene mapping with recombinant inbreds in maize. Genetics 118:519–526

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Byrne A, Cole C, Volden R, Vollmers C (2019) Realizing the potential of full-length transcriptome sequencing. Phil Trans Roy Soc B 374:20190097

    Article  CAS  Google Scholar 

  • Campo S, Peris-Peris C, Montesinos L, Peñas G, Messeguer J, San Segundo B (2012) Expression of the maize ZmGF14-6 gene in rice confers tolerance to drought stress while enhancing susceptibility to pathogen infection. J Exp Bot 63:983–999

    Article  CAS  PubMed  Google Scholar 

  • Campo S, Baldrich P, Messeguer J, Lalanne E, Coca M, San Segundo B (2014) Overexpression of a calcium-dependent protein kinase confers salt and drought tolerance in rice by preventing membrane lipid peroxidation. Plant Physiol 165:688–704

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Caniato F, Guimaraes C, Schaffert R, Alves V, Kochian LV (2007) Genetic diversity for aluminum tolerance in sorghum. Theor Appl Genet 114:863–876

    Article  CAS  PubMed  Google Scholar 

  • Capell T, Escobar C, Liu H, Burtin D, Lepri O, Christou P (1998) Over-expression of the oat arginine decarboxylase cDNA in transgenic rice (Oryza sativa L.) affects normal development patterns in vitro and results in putrescine accumulation in transgenic plants. Theor Appl Genet 97:246–254

    Article  CAS  Google Scholar 

  • Capell T, Bassie L, Christou P (2004) Modulation of the polyamine biosynthetic pathway in transgenic rice confers tolerance to drought stress. Proc Natl Acad Sci USA 101:9909–9914

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Carew BP (1984) Large-scale farming bordering the Musi River tidal swamps: the P. T. Patra Tani Project. In: International Rice Research Institute (ed) The workshop on research priorities in tidal swamp rice; 22–25 June 1981; Banjarmasin, South Kalimantan, Indonesia. International Rice Research Institute, Manila, pp 29–36

    Google Scholar 

  • Chatterjee C, Gopal R, Dube BK (2006) Impact of iron stress on biomass, yield, metabolism and quality of potato (Solanum tuberosum L.). Sci Hort 108(1):1–6

    Google Scholar 

  • Che J, Tsutsui T, Yokosho K, Yamaji N, Ma JF (2018) Functional characterization of an aluminum (Al)-inducibletranscription factor, ART2, revealed a different pathway for Altolerance in rice. New Phytol 18:1–10

    CAS  Google Scholar 

  • Chen JQ, Meng XP, Zhang Y, Xia M, Wang X-P (2008) Over-expression of OsDREB genes lead to enhanced drought tolerance in rice. Biotechnol Lett 30:2191–2198

    Article  PubMed  Google Scholar 

  • Chen LS, Qi YP, Jiang HX, Yang LT, Yang GH (2010) Photosynthesis and photoprotective systems of plants in response to aluminum toxicity. Afr J Biotechnol 9:9237–9247

    CAS  Google Scholar 

  • Chen ZC, Yamaji N, Motoyama R, Nagamura Y, Ma JF (2012a) Up-regulation of a magnesium transporter gene OsMGT1 is required forconferring aluminum tolerance in rice. Plant Physiol 159:1624–1633

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chen H, Chen W, Zhou J, He H, Chen L, Chen H et al (2012b) Basic leucine zipper transcription factor OsbZIP16 positively regulates drought resistance in rice. Plant Sci 193–194:8–17

    Article  PubMed  Google Scholar 

  • Ching A, Caldwell K, Jung M, Dolan M, Smith O, Tingey S, Morgante M, Rafalski AJ (2002) SNP frequency, haplotype structure and linkage disequilibrium in elite maize inbred lines. BMC Genet 3:1–19

    Article  Google Scholar 

  • Conte SS, Walker EL (2011) Transporters contributing to iron trafficking in plants. Mol Plant 4(3):464–476

    Article  CAS  PubMed  Google Scholar 

  • Crestani M, Da Silva JAG, de Souza VQ, Hartwig I, de Souza Luche H, de Sousa RO, De Carvalho FIF, De Oliveira AC, Luche HDS, de Sousa RO, de Carvalho FIF, de Oliveira AC (2009) Irrigated rice genotype performance under excess iron stress in hydroponic culture. Crop Breed Appl Biotechnol 9:85–93

    Google Scholar 

  • Cui M, Zhang W, Zhang Q, Xu Z, Zhu Z, Duan F et al (2011) Induced over-expression of the transcription factor OsDREB2A improves drought tolerance in rice. Plant Physiol Biochem 49:1384–1391

    Article  CAS  PubMed  Google Scholar 

  • Cutler SR, Rodriguez PL, Finkelstein RR, Abrams SR (2010) Abscisic acid: emergence of a core signaling network. Annu Rev Plant Biol 61:651–679

    Article  CAS  PubMed  Google Scholar 

  • Da Silveira VC, de Oliveira AP, Sperotto RA, Espindola LS, Amaral L, Dias JF, da Cunha JB, Fett JP (2007) Influence of iron on mineral status of two rice (Oryza sativa L.) cultivars. Braz J Plant Physiol 19(2):127–139

    Google Scholar 

  • Daly M, Rioux J, Schaffner S, Hudson T, Lander E (2001) High-resolution haplotype structure in the human genome. Nat Genet 29:229–232

    Article  CAS  PubMed  Google Scholar 

  • Datta K, Baisakh N, Ganguly M, Krishnan S, Yamaguchi-Shinozaki K, Datta SK (2012) Overexpression of Arabidopsis and rice stress genes’ inducible transcription factor confers drought and salinity tolerance to rice. Plant Biotechnol J 10:579–586

    Article  CAS  PubMed  Google Scholar 

  • de Oliveira Jucoski G, Cambraia J, Ribeiro C, de Oliveira JA, de Paula SO, Oliva MA (2013) Impact of iron toxicity on oxidative metabolism in young Eugenia uniflora L. plants. Acta Physiol Plant 35:1645–1657

    Google Scholar 

  • Delhaize E, Ryan PR, Randall PJ (1993) Aluminum tolerance in wheat (Triticum aestivum L.): II. Aluminum stimulated excretion of malic acid from rootapices. Plant Physiol 103:695–702

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Delhaize E, Hebb DM, Ryan PR (2001) Expression of Pseudomonas aeruginosacitrate synthase gene in tobacco is not associated with either enhanced citrate accumulation of efflux. Plant Physiol 125:2059–2067

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Devi AG, Yadav GS, Devi HL, Ngachan SV (2016) Effect of acute iron toxicity on key antioxidative enzymes in contrasting rice (Oryza sativa L.) cultivars of North-East India. IJBSM 7(3):388–392

    Google Scholar 

  • Ding ZJ, Yan JY, Xu XY, Li GX, Zheng SJ (2013) WRKY46 functions as a transcriptional repressor of ALMT1, regulating aluminum-induced malate secretion in Arabidopsis. Plant J 76:825–835

    Article  CAS  PubMed  Google Scholar 

  • Dixit S, Swamy BPM, Vikram P, Ahmed HU, Sta Cruz MT, Amante M, Atri D, Leung H, Kumar A (2012) Fine mapping of QTLs for rice grain yield under drought reveals sub-QTLs conferring a response to variable drought severities. Theor Appl Genet 125:155–169

    Google Scholar 

  • Dobermann A, Fairhurst T (2000) Mineral toxicities. In: Dobermann A, Fairhurst A (eds) Rice: nutrient disorders & nutrient management. Potash & Phosphate Institute (PPI), Potash & Phosphate Institute of Canada (PPIC) and International Rice Research Institute

    Google Scholar 

  • Dramé KN, Saito K, Koné B, Chabi A, Dakouo D, Annan-Afful E, Monh S, Abo E, Sié M (2010) Coping with iron toxicity in the lowlands of sub-Saharan Africa: experience from Africa rice center. In: AfricaRice (ed) Innovation and partnerships to realize Africa’s rice potential. Proceedings of 2nd Africa rice congress, 22–26 March 2010, Bamako

    Google Scholar 

  • Du H, Wang N, Cui F, Li X, Xiao J, Xiong L (2010) Characterization of a β-carotene hydroxylase gene DSM2 conferring drought and oxidative stress resistance by increasing xanthophylls and ABA synthesis in rice. Plant Physiol 154:1304–1318

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Duan J, Cai W (2012) OsLEA3-2, an abiotic stress induced gene of rice plays a key role in salt and drought tolerance. PLoS ONE 7:e45117

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Dufey I, Hakizimana P, Draye X, Lutts S, Bertin P (2009) QTL mapping for biomass and physiological parameters linked to resistance mechanisms to ferrous iron toxicity in rice. Euphytica 167:143–160

    Article  CAS  Google Scholar 

  • Dufey I, Hiel MP, Hakizimana P, Draye X, Lutts S, Koné B, Dramé KN, Konaté KA, Sie M, Bertin P (2012) Multienvironment quantitative trait loci mapping and consistency across environments of resistance mechanisms to ferrous iron toxicity in rice. Crop Sci 52(2):539–550

    Article  CAS  Google Scholar 

  • Dufey I, Mathieu AS, Draye X, Lutts S, Bertin P (2015a) Construction of an integrated map through comparative studies allows the identification of candidate regions for resistance to ferrous iron toxicity in rice. Euphytica 203:59–69

    Article  Google Scholar 

  • Dufey I, Draye X, Lutts S, Lorieux M, Martinez C, Bertin P (2015b) Novel QTLs in an interspecific backcross Oryza sativa × Oryza glaberrima for resistance to iron toxicity in rice. Euphytica 204:609–625

    Article  CAS  Google Scholar 

  • Elec V, Quimio CA, Mendoza R, Sajise AGC, Beebout SEJ, Gregorio GB, Singh RK (2013) Maintaining elevated Fe2+ concentration in solution culture for the development of a rapid and repeatable screening technique for iron toxicity tolerance in rice (Oryza sativa L.). Plant Soil 372(1):253–264

    Google Scholar 

  • Engel K, Asch F, Becker M (2012) Classification of rice genotypes based on their mechanisms of adaptation to iron toxicity. J Plant Nutr Soil Sci 175(6):871–881

    Article  CAS  Google Scholar 

  • Ereful NC, Liu L, Greenland A, Powell W, Mackay I, Leung H (2020) RNA-seq reveals differentially expressed genes between two Indica inbred rice genotypes associated with droughty yield QTLs. Agronomy 10:1–19

    Article  Google Scholar 

  • Fahramand M, Mahmoody M, Keykha A, Noori M, Rigi K (2014) Influence of abiotic stress on proline, photosynthetic enzymes and growth. Intl Res J Appl Basic Sci 8:257–265

    Google Scholar 

  • Famoso A, Clark R, Shaff J, Craft E, McCouch S (2010) Development of a novel aluminum tolerance phenotyping platform used for comparisons of cereal aluminum tolerance and investigations into rice aluminum tolerance mechanisms. Plant Physiol 153:1678

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Famoso AN, Zhao K, Clark RT, Tung CW, Wright MH, Bustamante C, Kochian LV, McCouch SR (2011) Genetic architecture of aluminum tolerance in rice (Oryza sativa) determined through genome-wide association analysis and QTL mapping. PLoS Genetics 7:1–16

    Google Scholar 

  • Fang H, Meng Q, Xu J, Tang H, Tang S, Zhang H, Huang J (2015) Knock-down of stress inducible OsSRFP1 encoding an E3 ubiquitin ligase with transcriptional activation activity confers abiotic stress tolerance through enhancing antioxidant protection in rice. Plant Mol Biol 87:441–458

    Article  CAS  PubMed  Google Scholar 

  • Farooq M, Wahid A, Kobayashi N, Fujita D, Basra SMA (2009) Plant drought stress: effects, mechanisms and management. Agron Sustain Dev 29:185–212

    Article  Google Scholar 

  • Fendiyanto MH, Satrio RD, Suharsono S, Tjahjoleksono A, Miftahudin M (2019a) Correlation among Snpb11 markers, root growth, and physiological characters of upland rice under aluminum stress. Biodiversitas 20:1243–1254

    Article  Google Scholar 

  • Fendiyanto MH, Satrio RD, Suharsono S, Tjahjoleksono A, Miftahudin M (2019b) QTL for aluminum tolerance on rice chromosome-3 based on root length characters. SABRAO J Breed Genet 51:451–469

    Google Scholar 

  • Finatto T, de Oliveira AC, Chaparro C, da Maia LC, Farias DR, Woyann LG, Mistura CC, Soares-Bresolin AP, Llauro C, Panaud O, Picault N (2015) Abiotic stress and genome dynamics: specific genes and transposable elements response to iron excess in rice. Rice 8(13):1–18

    Google Scholar 

  • Foy CD, Chaney RL, White MC (1978) The physiology of metal toxicity in plants. Annu Rev Plant Physiol 29:51l–566

    Article  Google Scholar 

  • Frei M, Tetteh RN, Razafindrazaka AL, Fuh MA, Wu LB, Becker M (2016) Responses of rice to chronic and acute iron toxicity: genotypic differences and biofortification aspects. Plant Soil 408:149–161

    Google Scholar 

  • Fukuda A, Shiratsuchi H, Fukushima A, Yamaguchi H, Mochida H, Terao T, Ogiwara H (2012) Detection of chromosomal regions affecting iron concentration in rice shoots subjected to excess ferrous iron using chromosomal segment substitution lines between Japonica and Indica. Plant Prod Sci 15(3):183–191

    Article  Google Scholar 

  • Furukawa J, Yamaji N, Wang H, Mitani N, Murata Y (2007) An aluminum-activated citrate transporter in barley. Plant Cell Physiol 48:1081–1087

    Article  CAS  PubMed  Google Scholar 

  • Ganal MW, Polley A, Graner EM, Plieske J, Wieseke R, Luerssen H, Durstewitz G (2012) Large SNP arrays for genotyping in crop plants. J Biosci 37:821–828

    Article  CAS  PubMed  Google Scholar 

  • Gao T, Wu Y, Zhang Y, Liu L, Ning Y, Wang D, Xie Q (2011) OsSDIR1 overexpression greatly improves drought tolerance in transgenic rice. Plant Mol Biol 76:145–156

    Article  CAS  PubMed  Google Scholar 

  • Garris AJ, McCouch SR, Kresovich S (2003) Population structure and its effect on haplotype diversity and linkage disequilibrium surrounding the xa5 locus of rice (Oryza sativa L.). Genetics 165:759–769

    Article  PubMed  PubMed Central  Google Scholar 

  • Ghimire KH, Quiatchon LA, Vikram P, Swamy BPM, Dixit S, Ahmed HU, Hernandez JE, Borromeo TH, Kumar A (2012) Identification and mapping of a QTL (qDTY1.1) with a consistent effect on grain yield under drought. Field Crops Res 131:88–96

    Article  Google Scholar 

  • Gomez SM, Boopathi NM, Kumar SS, Ramasubramanian T, Chengsong Z, Jeyaprakash P, Senthil A, Babu RC (2010) Molecular mapping and location of QTLs for drought-resistance traits in indica rice (Oryza sativa L.) lines adapted to target environments. Acta Physiol Plant 32:355–364

    Google Scholar 

  • Gridley HE, Efisue A, Tolou B, Bakayako T (2006) Breeding for tolerance to iron toxicity at WARDA. In: Audebert A, Narteh LT, Kiepe P, Millar D, Beks B (eds) Iron toxicity in rice based system in West Africa. WARDA, Cotonou

    Google Scholar 

  • Guerinot ML, Ying Y (1994) Iron: nutritious, noxious, and not readily available. Plant Physiol 104(3):815–820

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Guo JH, Liu XJ, Zhang Y, Shen JL, Han WX, Zhang WF et al (2010) Significant acidification in major Chinese croplands. Science 327:1008–1010

    Article  CAS  PubMed  Google Scholar 

  • Guo P, Qi YP, Cai YT, Yang TY, Yang LT, Huang ZR et al (2018) Aluminum effects on photosynthesis, reactive oxygen species and methylglyoxal detoxification in two Citrus species differing in aluminum tolerance. Tree Physiol 38:1548–1565

    Article  CAS  PubMed  Google Scholar 

  • Hamid MA, Islam MR (1984) Rice cultivation in the tidal swamps of Bangladesh. In: International Rice Research Institute (ed) The workshop on research priorities in tidal swamp rice; 22–25 June 1981; Banjarmasin, South Kalimantan, Indonesia. International Rice Research Institute, Manila, pp 69–78

    Google Scholar 

  • Harushima Y, Yano M, Shomura A et al (1998) A high-density rice genetic linkage map with 2275 markers using a single F2 population. Genetics 148:479–494

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hayes M, Svoboda M, Wall N, Widhalm M (2010) The Lincoln declaration on drought indices: universal meteorological drought index recommended. Bull Amer Meteorol Soc 92:485–488

    Article  Google Scholar 

  • Hemamalini GS, Shashidhar HE, Hittalmani S (2000) Molecular marker assisted tagging of morphological and physiological traits under two contrasting moisture regimes at peak vegetative stage in rice (Oryza sativa L.). Euphytica 112:69–78

    Article  CAS  Google Scholar 

  • Ho SL, Huang LF, Lu CA, He SL, Wang CC, Yu SP et al (2013) Sugar starvation- and GA-inducible calcium-dependent protein kinase 1 feedback regulates GA biosynthesis and activates a 14-3-3 protein to confer drought tolerance in rice seedlings. Plant Mol Biol 81:347–361

    Article  CAS  PubMed  Google Scholar 

  • Hoekenga O, Vision T, Shaff J, Monforte A, Lee G, Howell SH, Kochian LV (2003) Identification and characterization of aluminum tolerance loci in Arabidopsis (Landsberg erecta × Columbia) by quantitative trait locus mapping. A physiologically simple but genetically complex trait. Plant Physiol 132:930–936

    Article  Google Scholar 

  • Hu H, Dai M, Yao J, Xiao B, Li X, Zhang Q et al (2006) Overexpressing a NAM, ATAF, and CUC (NAC) transcription factor enhances drought resistance and salt tolerance in rice. Proc Natl Acad Sci USA 103:12987–12992

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Huang C, Yamaji N, Mitani N, Yano M, Nagamura Y, Ma JF (2009a) A bacterial-type ABC transporter is involved in aluminum tolerance in rice. Plant Cell 21:655–667

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Huang XY, Chao DY, Gao JP, Zhu MZ, Shi M, Lin HX (2009b) A previously unknown zinc finger protein, DST, regulates drought and salt tolerance in rice via stomatal aperture control. Genes Dev 23:1805–1817

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Huang J, Sun SJ, Xu DQ, Yang X, Bao YM, Wang ZF et al (2009c) Increased tolerance of rice to cold, drought and oxidative stresses mediated by the over expression of a gene that encodes the zinc finger protein ZFP245. Biochem Biophys Res Commun 389:556–561

    Article  CAS  PubMed  Google Scholar 

  • Huang C, Yamaji N, Chen Z, Ma JF (2012a) A tonoplast-localized half-size ABC transporter is required for internal detoxification of aluminum in rice. Plant Cell 69:857–867

    CAS  Google Scholar 

  • Huang J, Sun S, Xu D, Lan H, Sun H, Wang Z et al (2012b) A TFIIIA-type zinc finger protein confers multiple abiotic stress tolerances in transgenic rice (Oryza sativa L.). Plant Mol Biol 80:337–350

    Article  CAS  PubMed  Google Scholar 

  • Huang X, Wei X, Sang T, Zhao Q, Feng Q, Zhao Y, Li C, Zhu C, Lu T, Zhang Z, Li M, Fan D, Guo Y, Wang A, Wang L, Deng L, Li W, Lu Y, Weng Q, Liu K, Huang T, Zhou T, Jing Y, Li W, Lin Z, Buckler ES, Qian Q, Zhang QF, Li J, Han B (2010) Genome-wide association studies of 14 agronomic traits in rice landraces. Nat Genet 42:926–927

    Google Scholar 

  • Inoue H, Kobayashi T, Nozoye T, Takahashi M, Kakei Y, Suzuki K, Nakazono M, Nakanishi H, Mori S, Nishizawa NK (2009) Rice OsYSL15 is an iron-regulated iron (III)-deoxymugineic acid transporter expressed in the roots and is essential for iron uptake in early growth of the seedlings. J Biol Chem 284(6):3470–3479

    Article  CAS  PubMed  Google Scholar 

  • IRRI (2006) Bringing hope, improving lives-strategies. Plan 2007–2015. International Rice Research Institute, Los Banos, p 61

    Google Scholar 

  • Ishimaru Y, Suzuki M, Tsukamoto T, Suzuki K, Nakazono M, Kobayashi T, Wada Y, Watanabe S, Matsuhashi S, Takahashi M, Nakanishi H, Mori S, Nishizawa NK (2006) Rice plants take up iron as an Fe3+-phytosiderophore and as Fe2+. Plant J 45(3):335–346

    Article  CAS  PubMed  Google Scholar 

  • Ishizaki T, Maruyama K, Obara M, Fukutani A, Yamaguchi-Shinozaki K, Ito Y et al (2012) Expression of Arabidopsis DREB1C improves survival, growth, and yield of upland new rice for Africa (NERICA) under drought. Mol Breed 31:255–264

    Article  Google Scholar 

  • Ismunadji M, Partohardjono S (1985) Program hasil penelitian pengapuran tanah masamuntuk peningkatan produksi tanaman pangan. Balai Penelitian Tanah, Bogor

    Google Scholar 

  • Ito Y, Katsura K, Maruyama K, Taji T, Kobayashi M, Seki M, Yamaguchi-Shinozaki K (2006) Functional analysis of rice DREB1/CBF-type transcription factors involved in cold-responsive gene expression in transgenic rice. Plant Cell Physiol 47:141–153

    Article  CAS  PubMed  Google Scholar 

  • Iuchi S, Kobayashi M, Taji T, Naramoto M, Seki M, Kato T et al (2001) Regulation of drought tolerance by gene manipulation of 9-cis-epoxycarotenoid dioxygenase, a key enzyme in abscisic acid biosynthesis in Arabidopsis. Plant J 27:325–333

    Article  CAS  PubMed  Google Scholar 

  • Iuchi S, Koyama H, Iuchi A, Kobayashi Y, Kitabayashi S (2007) Zinc finger protein STOP1 is critical for proton tolerance in Arabidopsis and coregulates a key gene in aluminum tolerance. Proc Natl Acad Sci USA 104:9900–9905

    Article  PubMed  PubMed Central  Google Scholar 

  • Jang IC, Oh SJ, Seo JS, Choi WB, Song SI, Kim CH, Kim JK (2003) Expression of a bifunctional fusion of the Escherichia coli genes for trehalose-6-phosphate synthase and trehalose-6-phosphate phosphatase in transgenic rice plants increases trehalose accumulation and abiotic stress tolerance without stunting growth. Plant Physiol 131:516–524

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Jayawardena SDG (1984) Rice cultivation in the tidal swamps of Sri Lanka. In: International Rice Research Institute (ed) The workshop on research priorities in tidal swamp rice; 22–25 June 1981; Banjarmasin, South Kalimantan, Indonesia. International Rice Research Institute, Manila, pp 107–114

    Google Scholar 

  • Jeffreys A, Kauppi L, Neumann R (2001) Intensely punctate meiotic recombination in the class II region of the major histocompatibility complex. Nat Genet 29:217–222

    Article  CAS  PubMed  Google Scholar 

  • Jeong J, Connolly EL (2009) Iron uptake mechanisms in plants: functions of the FRO family of ferric reductases. Plant Sci 176(6):709–714

    Article  CAS  Google Scholar 

  • Jeong JS, Kim YS, Baek KH, Jung H, Ha SH, Do Choi Y et al (2010) Root-specific expression of OsNAC10 improves drought tolerance and grain yield in rice under field drought conditions. Plant Physiol 153:185–197

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Jeong JS, Kim YS, Redillas MCFR, Jang G, Jung H, Bang SW et al (2013) OsNAC5 over expression enlarges root diameter in rice plants leading to enhanced drought tolerance and increased grain yield in the field. Plant Biotechnol J 11:101–114

    Article  CAS  PubMed  Google Scholar 

  • Johannes F, Porcher E, Teixeira FK, Saliba-Colombani V, Simon M, Agier N, Bulski A, Albuisson J, Heredia F, Audigier P, Bouchez D, Dillmann C, Guerche P, Hospital F, Colot V (2009) Assessingthe impact of transgenerational epigenetic variation oncomplex traits. PLoS Genet 5:100–105

    Article  Google Scholar 

  • Johnson L, Andrade F, Salvador JC, Penafiel W, Vergara BS (1984) Rice cultivation in the tidal swamps of Samborondon, Ecuador. In: International Rice Research Institute (ed) The workshop on research priorities in tidal swamp rice; 22–25 June 1981; Banjarmasin, South Kalimantan, Indonesia. International Rice Research Institute, Manila, pp 89–106

    Google Scholar 

  • Joo J, Choi HJ, Lee YH, Kim YK, Song SI (2013) A transcriptional repressor of the ERF family confers drought tolerance to rice and regulates genes preferentially located on chromosome 11. Planta 238:155–170

    Article  CAS  PubMed  Google Scholar 

  • Jumiati (2016) Physiological characteristics of aluminum sensitive mutant-rice roots and their inheritance patterns. IPB Press, Bogor

    Google Scholar 

  • Jung M, Ching A, Bhattramakki D, Dolan M, Tingey S, Morgante M, Rafalski A (2004) Linkage disequilibrium and sequence diversity in a 500-kbp region around the adh1 locus in elite maize germplasm. Theor Appl Genet 109:681–689

    Article  CAS  PubMed  Google Scholar 

  • Kang J, Choi H, Im M, Kim SY (2002) Arabidopsis basic leucine zipper proteins that mediate stress-responsive abscisic acid signaling. Plant Cell 14:343–357

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kanneganti V, Gupta AK (2008) Overexpression of OsiSAP8, a member of stress associated protein (SAP) gene family of rice confers tolerance to salt, drought and cold stress in transgenic tobacco and rice. Plant Mol Biol 66:445–462

    Article  CAS  PubMed  Google Scholar 

  • Karaba A, Dixit S, Greco R, Aharoni A, Trijatmiko KR, Marsch-Martinez N et al (2007) Improvement of water use efficiency in rice by expression of HARDY, an Arabidopsis drought and salt tolerance gene. Proc Natl Acad Sci USA 104:15270–15275

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kasuga K, Liu Q, Miura S, Yamaguchi-Shinozaki K, Shinozaki K (1999) Improving plant drought, salt, and freezing tolerance by gene transfer of a single stress-inducible transcription factor. Nat Biotechnol 17:287–291

    Article  CAS  PubMed  Google Scholar 

  • Kawahara Y, de la Bastide M, Hamilton JP, Kanamori H, McCombie WR (2013) Improvement of the Oryza sativa nipponbare reference genome using next generation sequence and optical map data. Rice 6:4

    Article  PubMed  PubMed Central  Google Scholar 

  • Khowaja FS, Norton GJ, Courtois B, Price AH (2009) Improved resolution in the position of drought-related QTLs in a single mapping population of rice by meta-analysis. BMC Genom 10:276

    Article  Google Scholar 

  • Kidd PS, Lugany M, Poschenrieder C, Gunse B, Barcelo J (2001) The role of root exudates in aluminium resistance and silicon-induced amelioration of aluminium toxicity in three varieties of maize (Zea mays L.). J Exp Bot 52:1339–1352

    CAS  PubMed  Google Scholar 

  • Kim S, Plagnol V, Hu TT, Toomajian C, Clark RM, Ossowski S, Ecker JR, Weigel D, Nordborg M (2007) Recombination and linkage disequilibrium in Arabidopsis thaliana. Nat Genet 39:1151–1155

    Article  CAS  PubMed  Google Scholar 

  • Kim H, Hwang H, Hong JW, Lee YN, Ahn IP, Yoon IS et al (2012) A rice orthologue of the ABA receptor, OsPYL/RCAR5, is a positive regulator of the ABA signal transduction pathway in seed germination and early seedling growth. J Exp Bot 63:1013–1024

    Article  CAS  PubMed  Google Scholar 

  • Kim H, Lee K, Hwang H, Bhatnagar N, Kim DY, Yoon IS et al (2014) Over expression of PYL5 in rice enhances drought tolerance, inhibits growth, and modulates gene expression. J Exp Bot 65:453–464

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kinraide TB (1991) Identity of the rhizotoxicaluminium species. Plant Soil 134:167–178

    Article  CAS  Google Scholar 

  • Kobayashi T, Nishizawa NK (2012) Iron uptake, translocation, and regulation inhigher plants. Annu Rev Plant Biol 63:131–152

    Article  CAS  PubMed  Google Scholar 

  • Kobayashi Y, Ohyama Y, Kobayashi Y, Ito H, Iuchi S (2014) STOP2 activates transcription of several genes for Al- and low pH-tolerance that are regulated by STOP1 in Arabidopsis. Mol Plant 7:311–322

    Article  CAS  PubMed  Google Scholar 

  • Kochian LV (1995) Cellular mechanisms of aluminum toxicity and resistance in plants. Annu Rev Plant Physiol Plant Mol Biol 46:237–260

    Article  CAS  Google Scholar 

  • Kochian LV (2000) Molecular physiology of mineral nutrient acquisition, transport and utilization. American Society of Plant Physiologists, Maryland

    Google Scholar 

  • Kochian LV, Hoekenga OA, Piñeros MA (2004) How do crop plants tolerant acid soils? Mechanisms of aluminum toxicity and phosphorus efficiency. Annu Rev Plant Biol 55:459–493

    Article  CAS  PubMed  Google Scholar 

  • Kochian LV, Pineros MA, Hoekenga OA (2005) The physiology, genetics and molecular biology of plant aluminum tolerance and toxicity. Plant Soil 274:175–195

    Article  CAS  Google Scholar 

  • Kochian LV, Piñeros MA, Liu J, Magalhaes JV (2015) Plant adaptation to acid soils: the molecular basis for crop aluminum resistance. Annu Rev Plant Biol 66:1–28

    Google Scholar 

  • Koskeroglu S, Tuna AL (2010) The investigation on accumulation levels of proline and stress parameters of the maize (Zea mays L.) plants under salt and water stress. Acta Physiol Plant 32:541–549

    Article  CAS  Google Scholar 

  • Koswara O, Rumawas F (1984) Tidal swamp rice in Palembang region. In: International Rice Research Institute (ed) The workshop on research priorities in tidal swamp rice; 22–25 June 1981; Banjarmasin, South Kalimantan, Indonesia. International Rice Research Institute, Manila, pp 37–48

    Google Scholar 

  • Krohling CA, Eutrópio FJ, Bertolazi AA, Dobbss LB, Campostrini E, Dias T, Ramos AC (2016) Ecophysiology of iron homeostasis in plants. Soil Sci Plant Nutr 62(1):39–47

    Article  CAS  Google Scholar 

  • Kumar R, Venuprasad R, Atlin GN (2007) Genetic analysis of rain-fed lowland rice drought tolerance under naturally-occurring stress in eastern India: heritability and QTL effects. Field Crops Res 103:42–52

    Article  Google Scholar 

  • Kumar VVS, Verma RK, Yadav SK, Yadav P, Watts A, Rao MV, Chinnusamy V (2020) CRISPR-Cas9 mediated genome editing of drought and salt tolerance (OsDST) gene in indica mega rice cultivar MTU1010. Physiol Mol Biol Plants 26:1099–1110

    Article  Google Scholar 

  • Kuromori T, Sugimoto E, Shinozaki K (2014) Intertissue signal transfer of abscisic acid from vascular cells to guard cells. Plant Physiol 164:1587–1592

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lafitte HR, Courtois B, Arraudeau M (2002) Genetic improvement of rice in aerobic systems: progress from yield to genes. Field Crops Res 75:2–3

    Article  Google Scholar 

  • Lafitte HR, Price AH, Courtois B (2004) Yield response to water deficit in an upland rice mapping population: associations among traits and genetic markers. Theor Appl Genet 109:1237–1246

    Article  CAS  PubMed  Google Scholar 

  • Lanceras CJ, Pantuwan G, Jongdee B, Toojinda T (2004) Quantitative trait loci associated with drought tolerance at reproductive stage in rice. Plant Physiol 135:384–399

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Larsen PB, Geisler MJB, Jones CA, Williams KM, Cancel JD (2005) ALS3 encodes a phloem-localized ABC transporter-like protein that is required for aluminum tolerance in Arabidopsis. Plant J 41(3):353–363

    Google Scholar 

  • Larsen PB, Cancel J, Rounds M, Ochoa V (2007) Arabidopsis ALS1 encodes a root tip and stele localized half type ABC transporter required for root growth in an aluminum toxic environment. Planta 225(6):1447–1458

    Google Scholar 

  • Lenka S, Katiyar A, Chinnusamy V, Bansal K (2011) Comparative analysis of drought-responsive transcriptome in Indica rice genotypes with contrasting drought tolerance. Plant Biotechnol J 9:315–327

    Article  CAS  PubMed  Google Scholar 

  • Li Xf, Ma JF, Matsumoto H (2000) Pattern of aluminum-induced secretion oforganic acids differs between rye and wheat. Plant Physiol 123:1537–1543

    Google Scholar 

  • Li Z, Mu P, Li C, Zhang H, Li Z, Gao Y, Wang X (2005) QTL mapping of root traits in a doubled haploid population from a cross between upland and lowland japonica rice in three environments. Theor Appl Genet 110:1244–1252

    Article  CAS  PubMed  Google Scholar 

  • Lynch JP, Saint-Clair SB (2004) Mineral stress: the missing link in understanding how global climate change will affect plants in real world soils. Field Crops Res 90(1):101–115

    Google Scholar 

  • Li HW, Zang BS, Deng XW, Wang XP (2011) Overexpression of the trehalose-6-phosphate synthase gene OsTPS1 enhances abiotic stress tolerance in rice. Planta 234:1007–1008

    Article  CAS  PubMed  Google Scholar 

  • Li JY, Liu J, Dong D, Jia X, McCouch SR, Kochian LV (2014) Natural variation underlies alterations in Nramp aluminum transporter (NRAT1) expression and function that play a key role in rice aluminum tolerance. Proc Natl Acad Sci USA 111:6503–6518

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Li GZ, Wang ZQ, Yokosho K, Ding B, Fan W, Gong QQ, Li GX, Wu YR, Yang JL, Ma JF, Zheng SJ (2018a) Transcription factor WRKY22 promotes aluminum tolerance via activation of OsFRDL4 expression and enhancement of citrate secretion in rice (Oryza sativa). New Phytol 219:149–162

    Article  CAS  PubMed  Google Scholar 

  • Li Y, Xiao J, Chen L, Huang X, Cheng Z, Han B, Zhang Q, Wu C (2018b) Rice functional genomics research: past decade and future. Mol Plant 11:359–380

    Article  CAS  PubMed  Google Scholar 

  • Li B, Sun L, Huang J, Gösch C, Shi W, Chory J, Busch W (2019) GSNOR provides plant tolerance to iron toxicity via preventing iron-dependent nitrosative and oxidative cytotoxicity. Nat Commun 10(1):3896

    Article  PubMed  PubMed Central  Google Scholar 

  • Liang X, Zhang L, Natarajan SK, Becker DF (2013) Proline mechanisms of stress survival. Antioxid Redox Signal 19:998–1011

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Liao S, Qin X, Luo L, Han Y, Wang X, Usman B et al (2019) CRISPR/Cas9-induced mutagenesis of semi-rolled leaf 1, 2 confers curled leaf phenotype and drought tolerance by influencing protein expression patterns and ROS scavenging in rice (Oryza sativa L.). Agronomy 9:728

    Google Scholar 

  • Lilley JM, Ludlow MM, McCouch SR, O’toole JC (1996) Locating QTL for osmotic adjustment and dehydration tolerance in rice. J Exp Bot 47:1427–1436

    Google Scholar 

  • Lister C, Dean C (1993) Recombinant inbred lines formapping RFLP and phenotypic markers in Arabidopsis thaliana. Plant J 4:745–750

    Article  CAS  Google Scholar 

  • Liu K, Wang L, Xu Y, Chen N, Ma Q, Li F, Chong K (2007) Overexpression of OsCOIN, a putative cold inducible zinc finger protein, increased tolerance to chilling, salt and drought, and enhanced proline level in rice. Planta 226:1007–1016

    Article  CAS  PubMed  Google Scholar 

  • Liu C, Mao B, Ou S, Wang W, Liu L, Wu Y et al (2014) OsbZIP71, a bZIP transcription factor, confers salinity, and drought tolerance in rice. Plant Mol Biol 84:19–36

    Article  CAS  PubMed  Google Scholar 

  • Liu X, Li M, Liu K, Tang D, Sun M, Li Y, Shen Y, Du G, Cheng Z (2016) Semi-Rolled Leaf2 modulates rice leaf rolling by regulating abaxial side cell differentiation. J Exp Bot 67:2139–2150

    Google Scholar 

  • Long A, Zhang J, Yang LT, Ye X, Lai NW, Tan LL et al (2017) Effects of low pH on photosynthesis, related physiological parameters and nutrient profile of Citrus. Front Plant Sci 8:185–190

    Article  PubMed  PubMed Central  Google Scholar 

  • Lou D, Wang H, Liang G, Yu D (2017) OsSAPK2 confers abscisic acid sensitivity and tolerance to drought stress in rice. Front Plant Sci 8:993

    Article  PubMed  PubMed Central  Google Scholar 

  • Lu G, Gao C, Zheng X, Han B (2009) Identification of OsbZIP72 as a positive regulator of ABA response and drought tolerance in rice. Planta 229:605–615

    Article  CAS  PubMed  Google Scholar 

  • Lum MS, Hanafi MM, Rafii YM, Akmar ASN (2014) Effect of drought stress on growth, proline and antioxidant enzyme activities of upland rice. J Anim Plant Sci 24:1487–1493

    Google Scholar 

  • Ma JF, Furukawa J (2003) Recent progress in the research of external Al detoxification in higher plants: a minireview. J Inorg Biochem 97:46–51

    Article  CAS  PubMed  Google Scholar 

  • Ma JF, Shen R, Zhao Z, Wissuwa M, Takeuchi Y, Ebitani T, Yano M (2002) Response of rice to Al stress and identification of quantitative trait loci for Al tolerance. Plant Cell Physiol 43(6):652–659

    Article  CAS  PubMed  Google Scholar 

  • Ma JF, Chen ZC, Shen RF (2014) Molecular mechanisms of Al tolerance in gramineous plants. Plant Soil 381:1–12

    Article  CAS  Google Scholar 

  • Magalhaes J, Garvin D, Wang Y, Sorrells M, Klein P (2004) Comparative mapping of a major aluminum tolerance gene in sorghum and other species in the Poaceae. Genetics 167:1905–1914

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Magalhaes JV, Liu J, Guimara CT, Lana UGP, Wang Y, SchaVert RE, Hoekenga OA, Shaff JE, Klein PE, Carneiro NP, Coelho CM, Trick HN, Kochian LV (2007) A gene in the multidrug and toxic compound extrusion (MATE) family confers aluminum tolerance in sorghum. Nat Genet 39:1156–1161

    Article  CAS  PubMed  Google Scholar 

  • Mahender A, Swamy BPM, Anandan A, Ali J (2019) Tolerance of iron deficient and -toxic soil conditions in rice. Plants 8:31

    Article  CAS  PubMed Central  Google Scholar 

  • Marschner H (1995) Mineral nutrition of higher plants. Academic Press, San Diego, CA

    Google Scholar 

  • Maruyama K, Todaka D, Mizoi J, Yoshida T, Kidokoro S, Matsukura S et al (2012) Identification of cis-acting promoter elements in cold- and dehydration-induced transcriptional pathways in Arabidopsis, rice, and soybean. DNA Res 19:37–49

    Article  CAS  PubMed  Google Scholar 

  • Maruyama K, Urano K, Yoshiwara K, Morishita Y, Sakurai N, Suzuki H et al (2014) Integrated analysis of the effects of cold and dehydration on rice metabolites, phytohormones, and gene transcripts. Plant Physiol 164:1759–1771

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Mather K, Caicedo A, Polato N, Olsen K, McCouch S, Purugganan MD (2007) The extent of linkage disequilibrium in rice (Oryza sativa L.). Genet 177:2220–2223

    Article  Google Scholar 

  • Matsukura S, Mizoi J, Yoshida T, Todaka D, Ito Y, Maruyama K et al (2010) Comprehensive analysis of rice DREB2-type genes that encode transcription factors involved in the expression of abiotic stress-responsive genes. Mol Genet Genom 283:185–196

    Article  CAS  Google Scholar 

  • Matsumoto H (2000) Cell biology of aluminum toxicity and tolerance in highe plants. Int Rev Cytol 200:1–46

    Article  CAS  PubMed  Google Scholar 

  • Matthus E, Wu LB, Ueda Y, Höller S, Becker M, Frei M (2015) Loci, genes, and mechanisms associated with tolerance to ferrous iron toxicity in rice (Oryza sativa L.). Theor Appl Genet 128(10):2085–2098

    Google Scholar 

  • McCouch SR, Teytelman L, Xu Y, Lobos KB, Clare K, Walton M, Fu B, Maghirang R, Li Z, Xing Y, Zhang Q, Kono I, Yano M, Fjellstrom R, DeClerck G, Schneider D, Cartinhour S, Ware D, Stein L (2002) Development and mapping of 2240 new SSR markers for rice (Oryzasativa L.). DNA Res 9:199–207

    Google Scholar 

  • McCouch SR, Zhao K, Wright M, Tung C-W, Ebana K, Thomson M, Reynolds A, Wang D, DeClerck G, Ali ML, McClung A, Eizenga G, Bustamante C (2010) Development of genome-wide SNP assays for rice. Breed Sci 60:524–535

    Article  Google Scholar 

  • McNally KL, Childs KL, Bohnert R, Davidson RM, Zhao K, Ulat VJ, Zeller G, Clark RM, Hoen DR, Bureau TE, Stokowski R, Ballinger DG, Frazer KA, Cox DR, Padhukasahasram B, Bustamante CD, Weigel D, Mackill DJ, Bruskiewich RM, Rätsch G, Buell CR, Leung H, Leach JE (2009) Genome-wide SNP variation reveals relationships among landraces and modern varieties of rice. Proc Natl Aced Sci USA 106:12273–12278

    Article  CAS  Google Scholar 

  • Meng L, Li H, Zhang L, Wang J (2015) QTL IciMapping: integrated software for geneticlinkage map construction and quantitative traitlocus mapping in biparental populations. Crop J 3:269–283

    Article  Google Scholar 

  • Miftahudin, Scholes GJ, Gustafson JP (2002) AFLP markers tightly linked to the aluminum-tolerance gene Alt3 in rye (Secale cereal L.). Theor Appl Genet 104:626–631

    Google Scholar 

  • Miftahudin, Scoles GJ, Gustafson JP (2004) Development of PCR-based codominant markers flanking the Alt3 gene in rye. Genome 47:231–238

    Google Scholar 

  • Miftahudin, Chikmawati T, Ross K, Scoles GJ, Gustafson JP (2005) Targeting the aluminum tolerance gene Alt3 region in rye, using rice/rye microcolinearity. Theor Appl Genet 110:906–913

    Google Scholar 

  • Miftahudin, Nurlaela, Juliarni (2007) Uptake and distribution of aluminum in rootapices of two rice varieties under aluminum stress. HAYATI J Biosci 14(3):110–114

    Google Scholar 

  • Miftahudin, Putri RE, Chikmawati T (2020) Vegetative morphophysiological responses of four rice cultivars to drought stress. Biodiversitas 21:3727–3734

    Google Scholar 

  • Miftahudin M, Roslim DI, Fendiyanto MH, Satrio RD, Zulkifli A, Umaiyah EI, Chikmawati T, Sulistyaningsih YC, Suharsono S, Hartana A, Nguyen HT, Gustafson JP (2021) OsGERLP: a novel aluminum tolerance rice gene isolated from a local cultivar in Indonesia. Plant Physiol Biochem 162:86–99

    Google Scholar 

  • Minella E, Sorrells M (1992) Aluminum tolerance in barley: genetic relationships among genotypes of diverse origin. Crop Sci 32:593–598

    Article  CAS  Google Scholar 

  • Mishra KK, Vikram P, Yadaw RB, Swamy BM, Dixit S, Cruz MTS, Maturan P, Marker S, Kumar A (2013) qDTY12.1: a locus with a consistent effect on grain yield under drought in rice. BMC Genetics 14:12

    Google Scholar 

  • Mitra GN (2015) Regulation of nutrient uptake by plants: a biochemical and molecular approach. Springer, New Dehli, India

    Book  Google Scholar 

  • Miyakawa T, Fujita Y, Yamaguchi-Shinozaki K, Tanokura M (2013) Structure and function of abscisic acid receptors. Trends Plant Sci 18:259–266

    Article  CAS  PubMed  Google Scholar 

  • Miyasaka SC, Buta JG, Howell RK, Foy CD (1991) Mechanisms of aluminum tolerance in snapbean. Root exudation of citric acid. Plant Physiol 96:737–743

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Mizoi J, Shinozaki K, Yamaguchi-Shinozaki K (2012) AP2/ERF family transcription factors in plant abiotic stress responses. Biochim Biophys Acta 1819:86–96

    Article  CAS  PubMed  Google Scholar 

  • Moncada P, Martinez CP, Borrero J, Châtel M, Gauch H Jr, Guimarães E, Tohme J, McCouch SR (2001) Quantitative trait loci for yield and yield components in an Oryza sativa × Oryza rufipogon BC2F2 population evaluated in an upland environment. Theor Appl Genet 102:41–52

    Article  CAS  Google Scholar 

  • Morimoto K, Mizoi J, Qin F, Kim JS, Sato H, Osakabe Y et al (2013) Stabilization of Arabidopsis DREB2A is required but not sufficient for the induction of target genes under conditions of stress. PLoS ONE 8:e80457

    Article  PubMed  PubMed Central  Google Scholar 

  • Mossor-Pietraszewska TM (2001) Effect of aluminium on plant growth and metabolism. Acta Biochim Pol 48(3):673–686

    Article  CAS  PubMed  Google Scholar 

  • Mulyani A, Hikmatullah, Subagyo, H (2004) Characteristics and potential of dryland acid soils in Indonesia. Bogor: Indonesian Center for Soil and Agro-climate Research and Development [in Indonesian]

    Google Scholar 

  • Muthu V, Abbai R, Nallathambi J, Rahman H, Ramasamy S, Kambale R et al (2020) Pyramiding QTLs controlling tolerance against drought, salinity, and submergence in rice through marker assisted breeding. PLoS ONE 15:e0227421

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Muthurajan R, Rahman H, Muthukumar M, Ramanathan V, Selvam J (2018) Drought responsive transcriptome profiling in roots of contrasting rice genotypes. Indian J Plant Physiol 23:393–407

    Article  CAS  Google Scholar 

  • Myers SS, Smith MR, Sarah G, Golden CD, Bapu V, Mueller ND, Dangour AD, Peter H (2017) Climate change and global food systems: potential impacts on food security and undernutrition. Annu Rev Publ Health 38:259–277

    Article  Google Scholar 

  • Nakashima K, Tran LSP, Van Nguyen D, Fujita M, Maruyama K, Todaka D et al (2007) Functional analysis of a NAC-type transcription factor OsNAC6 involved in abiotic and biotic stress-responsive gene expression in rice. Plant J 51:617–630

    Article  CAS  PubMed  Google Scholar 

  • Nakashima K, Takasaki H, Mizoi J, Shinozaki K, Yamaguchi-Shinozaki K (2012) NAC transcription factors in plant abiotic stress responses. Biochim Biophys Acta 1819:97–103

    Article  CAS  PubMed  Google Scholar 

  • Nelson GCD, Mensbrugghe V, Ahammad H (2014) Agriculture and climate change in global scenarios: why don’t the models agree. Agric Econ 45:85–101

    Article  Google Scholar 

  • Nguyen VT, Burow MD, Nguyen HT, Le BT, Le TD, Paterson AH (2001) Molecular mapping of genes coffering aluminum tolerance in rice (Oryza sativa L.). Theor Appl Genet 102:1002–1010

    Article  CAS  Google Scholar 

  • Nguyen VT, Nguyen BD, Sarkarung S, Martinez C, Paterson AH, Nguyen HT (2002) Mapping of genes controlling aluminum tolerance in rice: comparison of different genetics background. Mol Genet Genom 267:772–780

    Article  CAS  Google Scholar 

  • Nguyen BD, Brar DS, Bui BC, Nguyen TV, Pham LN, Nguyen HT (2003) Identification and mapping of the QTL for aluminum tolerance introgressed from the new source, Oryza rufipogon Griff. into indica rice (Oryza sativa L.). Theor Appl Genet 106:583–593

    Article  CAS  PubMed  Google Scholar 

  • Nijhawan A, Jain M, Tyagi AK, Khurana JP (2008) Genomic survey and gene expression analysis of the basic leucine zipper transcription factor family in rice. Plant Physiol 146:333–350

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ninamango-Cardenas F, Teixeira Guimarães C, Martins P, NettoParentoni S, Carneiro NP, Lopes MA, Moro JR, Paiva E (2003) Mapping QTLs for aluminum tolerance in maize. Euphytica 130:223–232

    Google Scholar 

  • Ning Y, Jantasuriyarat C, Zhao Q, Zhang H, Chen S, Liu J, Liu L, Tang S, Park CH, Wang X, Liu X, Dai L, Xie Q, Wang GL (2011) The SINA E3 ligase OsDIS1 negatively regulates drought response in rice. Plant Physiol 157:242–255

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ningsih RD, Yasin M, Noor A (2020) Rice productivity on tidal swampland in the agricultural assisitance area program in Barito Kuala Regency South Kalimantan. IOP conference series: Earth Environ Sci 484:012123. https://doi.org/10.1088/1755-1315/484/1/012123

  • Noor A, Lubis I, Ghulamahdi M, Chozin MA, Anwar K, Wirnas D (2012) Pengaruh konsentrasi Fe dalam larutan hara terhadap gejala keracunan Fe dan pertumbuhan tanaman padi. J Agron Indonesia 40(2):91–98

    Google Scholar 

  • Noorsyamsi H, Anwarhan H, Soelaiman S, Beachell HM (1984) Rice cultivation in the tidal swamps of Kalimantan. In: International Rice Research Institute (ed) The workshop on research priorities in tidal swamp rice; 22–25 June 1981; Banjarmasin, South Kalimantan, Indonesia. International Rice Research Institute, Manila, pp 17–28

    Google Scholar 

  • Nordborg M, Borevitz JO, Bergelson J, Berry CC, Chory J, Hagenblad J, Kreitman M, Maloof JN, Noyes T, Oefner PJ, Stahl EA, Weigel D (2002) The extent of linkage disequilibrium in Arabidopsis thaliana. Nat Genet 30:190–193

    Article  CAS  PubMed  Google Scholar 

  • Nozoe T, Agbisit R, Fukuta Y, Rodriguez R, Yanagihara S (2008) Characteristics of iron tolerant rice lines developed at IRRI under field conditions. Jarq-Jpn Agric Res Q42(3):187–192

    Article  Google Scholar 

  • Nozoye T, Nagasaka S, Kobayashi T, Takahashi M, Sato Y, Uozume N, Nakanishi H, Nishizawa NK (2011) Phytosiderophore efflux transporters are crucial for iron acquisition in graminaceous plants. J Biol Chem 286(7):5446–5454

    Article  CAS  PubMed  Google Scholar 

  • Nugraha Y, Rumanti IA (2017) Breeding for rice variety tolerant to iron toxicity. Iptek Tan Pangan 12(1):9–24

    Google Scholar 

  • Nugraha Y, Rumanti IA, Guswara A, Ardie SW, Ghulammahdi M, Suwarno, Aswidinnoor H (2016) Response of selected rice varieties under excess iron condition. J Pen Pert Tan Pangan 35(3):181–190

    Google Scholar 

  • Nugroho K, Alkasuma, Paidi, Wahdini W, Abdulrachman, Suhardjo H, Widjaja-Adhi IPG (1991) Final Report: Determination of potential areas for tidal lands, swamps, and beaches at a scale of 1: 500,000 (Laporan Teknik No. 1/PSRP/1991). Bogor: Indonesian Center for Soil and Agro-climate Research and Development [in Indonesian]

    Google Scholar 

  • Nuruzzaman M, Sharoni AM, Kikuchi S (2013) Roles of NAC transcription factors in the regulation of biotic and abiotic stress responses in plants. Front Microbiol 4:248

    Article  PubMed  PubMed Central  Google Scholar 

  • Oh S, Song SI, Kim YS, Jang H, Kim SY, Kim M et al (2005) Arabidopsis CBF3/DREB1A and ABF3 in transgenic rice increased tolerance to abiotic stress without stunting growth. Plant Physiol 138:341–351

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Oh SJ, Kwon CW, Choi DW, Song SI, Kim JK (2007) Expression of barley HvCBF4 enhances tolerance to abiotic stress in transgenic rice. Plant Biotechnol J 5:646–656

    Article  CAS  PubMed  Google Scholar 

  • Oh SJ, Kim YS, Kwon CW, Park HK, Jeong JS, Kim JK (2009) Overexpression of the transcription factor AP37 in rice improves grain yield under drought conditions. Plant Physiol 150:1368–1379

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Oladosu Y, Rafii MY, Samuel C, Fatai A, Magaji U, Kareem I, Kamarudin ZS, Muhammad I, Kolapo K (2019) Drought resistance in rice from conventional to molecular breeding. Intl J Mol Sci 20:3519

    Article  CAS  Google Scholar 

  • Olsen K, Caicedo A, Polato N, McClung A, McCouch S, Purugganan MD (2006) Selection under domestication: evidence for a sweep in the rice Waxy genomic region. Genetics 173:975

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Onaga G, Edema R, Asea G (2013) Tolerance of rice germplasm to iron toxicity stress and the relationship between tolerance, Fe2+, P and K content in the leaves and roots. Arch Agron Soil Sci 59(2):213–229

    Google Scholar 

  • Onaga G, Dramé KN, Ismail AM (2016) Understanding the regulation of iron nutrition: can it contribute to improving iron toxicity tolerance in rice? Func Plant Biol 43(8):709–726

    Article  CAS  Google Scholar 

  • Osakabe Y, Osakabe K, Shinozaki K, Tran LP (2014) Response of plants to water stress. Plant Physiol 5:1–8

    Google Scholar 

  • Ouedraogo S, Ouedraogo M (2003) Evaluation économique de l’impact de la recherche et de la vulgarisation sur le riz au Burkina Faso. Mini-report, Institut de l’Environnement et des Recherches Agricoles (INERA), Ouagadougou

    Google Scholar 

  • Ouyang Y, Zeng F, Zhuang J, Yu S, Zhu L, Jin Q, Zhang G (2007) Genetic analysis of genotype × iron nutrition interaction on coleoptile elongation rate in rice (Oryza sativa L.). Euphytica 156:311–318

    Article  Google Scholar 

  • Ozga JA, Kaur H, Savada RP, Reinecke DM (2016) Hormonal regulation of reproductive growth under normal and heat-stress conditions in legume and other model crop species. J Exp Bot 68:1885–1894

    Google Scholar 

  • Palanog AD, Swamy BM, Shamsudin NAA, Dixit S, Hernandez JE, Boromeo TH, Cruz PCS, Kumar A (2014) Grain yield QTLs with consistent-effect under reproductive-stage drought stress in rice. Field Crop Res 161:46–54

    Article  Google Scholar 

  • Phung T, Jung HI, Park J, Kim JG, Back K, Jung S (2011) Porphyrin biosynthesis control under water stress: sustained porphyrin status correlates with drought tolerance in transgenic rice. Plant Physiol 157:1746–1764

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Pineros M, Shaff J, Manslank H, Carvalho Alves V, Kochian L (2005) Aluminum resistance in maize cannot be solely explained by root organic acid exudation, a comparative physiological study. Plant Physiol 137:220–231

    Article  Google Scholar 

  • Praba ML, Cairns JE, Babu RC, Lafitte HR (2009) Identification of physiological traits underlying cultivar differences in drought tolerance in rice and wheat. J Agron Crop Sci 195:30–46

    Article  Google Scholar 

  • Prince SJ, Beena R, Gomez SM, Senthivel S, Babu RC (2015) Mapping consistent rice (Oryza sativa L.) yield QTLs under drought stress in target rainfed environments. Rice 8:25

    Article  PubMed Central  Google Scholar 

  • Pulver E, Jaramillo S, Moreira S, Zorilla G (2010) Catching the rains. Rice Today 9(3):14–16

    Google Scholar 

  • Qin F, Sakuma Y, Tran LSP, Maruyama K, Kidokoro S, Fujita Y et al (2008) Arabidopsis DREB2A-interacting proteins function as RING E3 ligases and negatively regulate plant drought stress-responsive gene expression. Plant Cell 20:1693–1707

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Qu P, Shi J, Chen T, Chen K, Shen C, Wang J, Zhao X, Ye G, Xu J, Zhang L (2020) Construction and integration of genetic linkage maps from three multi parent advanced generation intercross populations in rice. Rice 13:13

    Article  PubMed  PubMed Central  Google Scholar 

  • Quan R, Hu S, Zhang Z, Zhang H, Zhang Z, Huang R (2010) Overexpression of an ERF transcription factor TSRF1 improves rice drought tolerance. Plant Biotechnol J 8:476–488

    Article  CAS  PubMed  Google Scholar 

  • Raghavendra AS, Gonugunta VK, Christmann A, Grill E (2010) ABA perception and signalling. Trends Plant Sci 15:395–401

    Article  CAS  PubMed  Google Scholar 

  • Rakshit S, Rakshit A, Matsumura H, Takahashi Y, Hasegawa Y, Ito A, Ishii T, Miyashita NT, Terauchi R (2007) Large-scale DNA polymorphism study of Oryza sativa and O. rufipogon reveals the origin and divergence of Asian rice. Theor Appl Genet 114:731–743

    Article  CAS  PubMed  Google Scholar 

  • Ramírez LM, Claassen N, Ubiera AA, Werner H, Moawad AM (2002) Effect of phosphorus, potassium and zinc fertilizers on iron toxicity in wetland rice (Oryza sativa L.). Plant Soil 239:197–206

    Article  Google Scholar 

  • Ratnasari T, Tjahjoleksono A, Miftahudin (2016) Transgene insertion stability and aluminum tolerance candidate gene expression in T3 generation of transgenic tobacco. Int J Agric Biol 18:607–614

    Google Scholar 

  • Redillas MCFR, Jeong JS, Kim YS, Jung H, Bang SW, Choi YD et al (2012) The overexpression of OsNAC9 alters the root architecture of rice plants enhancing drought resistance and grain yield under field conditions. Plant Biotechnol J 10:792–805

    Article  CAS  PubMed  Google Scholar 

  • Reich D, Cargill M, Bolk S, Ireland J, Sabeti P, Richter DJ, Lavery T, Kouyoumjian R, Farhadian SF, Ward R, Lander ES (2001) Linkage disequilibrium in the human genome. Nature 411:199–204

    Article  CAS  PubMed  Google Scholar 

  • Remington D, Thornsberry J, Matsuoka Y, Wilson L, Whitt S, Doebley J, Kresovich S, Goodman MM, Buckler ES (2001) Structure of linkage disequilibrium and phenotypic associations in the maize genome. Proc Natl Acad Sci USA 98:11470–11479

    Article  Google Scholar 

  • Reyes-Díaz M, Inostroza-Blancheteau C, Rengel Z (2015) Physiological and molecular regulation of aluminum resistance in woody plant species. In: Panda SK, BaluÅ¡ka F (eds) Aluminum stress adaptation in plants. Springer, Cham, Switzerland, pp 187–202

    Chapter  Google Scholar 

  • Ricachenevsky FK, Sperotto RA (2014) There and back again, or always there? The evolution of rice combined strategy for Fe uptake. Front Plant Sci 5:189

    Article  PubMed  PubMed Central  Google Scholar 

  • Ricachenevsky FK, Sperotto RA, Menguer PK, Fett JP (2010) Identification of Fe-excess-induced genes in rice shoots reveals a WRKY transcription factor responsive to Fe, drought and senescence. Mol Biol Rep 37(8):3735–3745

    Article  CAS  PubMed  Google Scholar 

  • Ritung S, Suryani E, Subardja D, Sukarman Nugroho K, Suparto Hikmatullah, Mulyani A, Tafakresnanto C, Sulaeman Y, Subandiono RE, Wahyunto P, Prasodjo N, Suryana U, Hidayat H, Priyono A, Supriatna W (2015) Indonesian agricultural land resources: size, distribution, and potential availability. Indonesian Agency for Agricultural Research and Development Press, Jakarta (in bahasa)

    Google Scholar 

  • Roca-Paixão JF, Gillet FX, Ribeiro TP, Bournaud C, Lourenco-Tessutti T, Noriega DD, Melo B, Almeida-Engler J, Grossi-de-Sa MF (2019) Improved drought stress tolerance in Arabidopsis by CRISPR/dCas9 fusion with a histone acetyl transferase. Sci Rep 9:8080

    Google Scholar 

  • Rohila JS, Jain RK, Wu R (2002) Genetic improvement of basmati rice for salt and drought tolerance by regulated expression of a barley HVA1 cDNA. Plant Sci 163:525–532

    Article  CAS  Google Scholar 

  • Roslim DW (2011) Isolasi dan Karak terisasi Gen Toleran aluminium dari Tanaman Padi. IPB Press, Bogor

    Google Scholar 

  • Ruengphayak S, Ruanjaichon V, Saensuk C, Phromphan S, Tragoonrung T, Kongkachuichai R, Vanavichit A (2015) Forward screening for seedling tolerance to Fe toxicity reveals a polymorphic mutation in ferric chelate reductase in rice. Rice 8:3

    Article  PubMed Central  Google Scholar 

  • Ryan PR, Delhaize E, Randall PJ (1995) Characterization of Al-stimulated effluxof malate from the pices of Al-tolerant wheat roots. Planta 196:103–110

    Article  CAS  Google Scholar 

  • Ryan PR, Tyerman SD, Sasaki T, Furuichi T, Yamamoto Y, Zhang WH, Delhaize E (2011) The identification of aluminium-resistance genes provides opportunities for enhancing crop production on acid soils. J Exp Bot 62(1):9–20

    Article  CAS  PubMed  Google Scholar 

  • Sahebi M, Hanafi MM, Rafii MY, Mahmud TMM, Azizi P, Osman M, Abiri R, Taheri S, Kalhori N, Shabanimofrad M, Miah G, Atabaki N (2018) Improvement of drought tolerance in rice (Oryza sativa L.): genetics, genomic tools, and the WRKY gene family. Bio Med Res Intl 2018:2314–6133

    Google Scholar 

  • Sahrawat KL, Singh BN (1998) Seasonal differences in iron toxicity tolerance of lowland rice cultivars. Intl Rice Res Notes 23(1):18–19

    Google Scholar 

  • Saijo Y, Hata S, Kyozuka J, Shimamoto K, Izui K (2000) Over-expression of a single Ca2+-dependent protein kinase confers both cold and salt/drought tolerance on rice plants. Plant J 23:319–327

    Article  CAS  PubMed  Google Scholar 

  • Saikumar S, Gouda PK, Saiharini A, Varma CMK, Vineesh O, Padmavathi G, Shenoy VV (2014) Major QTL for enhancing rice grain yield under lowland reproductive drought stress identified using an O. sativa/O. glaberrima introgression line. Field Crop Res 163:119–131

    Article  Google Scholar 

  • Sakuma Y, Maruyama K, Osakabe Y, Qin F, Seki M, Shinozaki K (2006a) Functional analysis of an Arabidopsis transcription factor, DREB2a, involved in drought-responsive gene expression. Plant Cell 18:1292–1309

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sakuma Y, Maruyama K, Qin F, Osakabe Y, Shinozaki K, Yamaguchi-Shinozaki K (2006b) Dual function of an Arabidopsis transcription factor DREB2A in water-stress-responsive and heat-stress-responsive gene expression. Proc Natl Acad Sci USA 103:18822–18827

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sandhu N, Singh A, Dixit S, Cruz MTS, Maturan PC, Jain RK, Kumar A (2014) Identification and mapping of stable QTL with main and epistasis effect on rice grain yield under upland drought stress. BMC Genet 15:63

    Google Scholar 

  • Sandhu M, Sureshkumar V, Prakash C, Dixit R, Solanke AU, Sharma TR, Mohapatra T, Mithra SVA (2017) RiceMetaSys for salt and drought stress responsive genes in rice: a web interface for crop improvement. BMC Bioinformatics 18:432

    Google Scholar 

  • Sasaki T, Yamamoto Y, Ezaki E, Katsuhara M, Ryan PR, Delhaize E, Matsumoto H (2004) A gene encoding an aluminum-activated malate transporter segregates with aluminum tolerance in wheat. Plant J 37:645–653

    Article  CAS  PubMed  Google Scholar 

  • Sasaki T, Ryan P, Delhaize E, Hebb D, Ogihara Y (2006) Sequence upstream of the wheat (Triticum aestivum L.) ALMT1 gene and its relationship to aluminum resistance. Plant Cell Physiol 47:1339–1343

    Article  Google Scholar 

  • Satrio RD, Fendiyanto MH, Supena EDJ, Suharsono S, Miftahudin M (2019) Identification of drought-responsive regulatory genes by hierarchical selection of expressed sequence tags and their expression under drought stress in rice. Intl J Agric Biol 22:1524–1532

    Google Scholar 

  • Satrio RD, Fendiyanto MH, Supena EDJ, Suharsono S, Miftahudin M (2020) Genome-wide SNP discovery, linkage mapping, and analysis of QTL for morpho-physiological traits in rice during vegetative stage under drought stress condition. Euphytica (in press)

    Google Scholar 

  • Schneider K (2005) Mapping populations and principles of genetic mapping in the handbook of plant genome mapping, genetic and physical mapping. WILEY-VCH Verlag, Weinheim

    Google Scholar 

  • Sellamuthu R, Liu GF, Ranganathan CB, Serraj R (2011) Genetic analysis and validation of quantitative trait loci associated with reproductive-growth traits and grain yield under drought stress in a doubled haploid line population of rice (Oryza sativa L.). Field Crops Res 124:46–58

    Article  Google Scholar 

  • Seo JS, Joo J, Kim MJ, Kim YK, Nahm BH, Song SI et al (2011) OsbHLH148, a basic helix-loop-helix protein, interacts with OsJAZ proteins in a jasmonate signaling pathway leading to drought tolerance in rice. Plant J 65:907–921

    Article  CAS  PubMed  Google Scholar 

  • Serraj R, McNally KL, Slamet-Loedin I, Kohli A, Haefele SM, Atlin G, Kumar A (2011) Drought resistance improvement in rice: an integrated genetic and resource management strategy. Plant Production Sci 1–14

    Google Scholar 

  • Shen H, Liu C, Zhang Y, Meng X, Zhou X, Chu C et al (2012) OsWRKY30 is activated by MAP kinases to confer drought tolerance in rice. Plant Mol Biol 80:241–253

    Article  CAS  PubMed  Google Scholar 

  • Shimizu A (2009) QTL analysis of genetic tolerance to iron toxicity in rice (Oryza sativa L.) by quantification of bronzing score. J New Seeds 10(3):171–179

    Google Scholar 

  • Shimizu A, Guerta CQ, Gregorio GB, Ikehashi H (2005) Improved mass screening of tolerance to iron toxicity in rice by lowering temperature of culture solution. J Plant Nut 28(9):1481–1493

    Article  CAS  Google Scholar 

  • Sikirou M, Saito K, Achigan-Dako EG, Dramé KN, Ahanchédé A, Venuprasad R (2015) Genetic improvement of iron toxicity tolerance in rice—progress, challenges and prospects in West Africa. Plant Prod Sci 18(4):423–434

    Article  CAS  Google Scholar 

  • Sikirou M, Saito K, Dramé KN, Saidou A, Dieng I, Ahanchédé A, Venuprasad R (2016) Soil-based screening for iron toxicity tolerance in rice using pots. Plant Prod Sci 19(4):489–496

    Article  CAS  Google Scholar 

  • Simpson SP (1989) Detection of linkage between quantitative trait loci and restriction fragment length polymorphisms using inbred lines. Theor Appl Genet 77:815–819

    Article  CAS  PubMed  Google Scholar 

  • Sinclair TR (2011) Challenges in breeding for yield increase for drought. Trends Plant Sci 16(6):289–293

    Article  CAS  PubMed  Google Scholar 

  • Sinha TS, Bandyopadhyay AK (1984) Rice in coastal saline land of West Bengal, India. In: International Rice Research Institute (ed) The workshop on research priorities in tidal swamp rice; 22–25 June 1981; Banjarmasin, South Kalimantan, Indonesia. International Rice Research Institute, Manila, pp 115–118

    Google Scholar 

  • Siska DM, Hamim, Miftahudin (2017) Overexpression of B11 gene in transgenic rice increased tolerance to aluminum stress. HAYATI J Biosci 24:96–104

    Google Scholar 

  • Sivamani E, Bahieldin A, Wraith JM, Al-Niemi T, Dyer WE, Ho THD, Qu R (2000) Improved biomass productivity and water use efficiency under water deficit conditions in transgenic wheat constitutively expressing the barley HVA1 gene. Plant Sci 155:1–9

    Article  CAS  PubMed  Google Scholar 

  • Soepardi HG (2001) Land resource-based agribusiness farming strategy. Bogor: Indonesian Center for Soil and Agro-climate Research and Development [in Indonesian]

    Google Scholar 

  • Song SY, Chen Y, Chen J, Dai XY, Zhang WH (2011) Physiological mechanisms underlying OsNAC5-dependent tolerance of rice plants to abiotic stress. Planta 234:331–345

    Article  CAS  PubMed  Google Scholar 

  • Srividya A, Vemireddy LR, Ramanarao PV, Sridhar S, Jayaprada M, Anuradha G, Srilakshmi B, Reddy HK, Hariprasad AS, Siddiq EA (2011) Molecular mapping of QTLs for drought related traits at seedling stage under PEG induced stress conditions in rice. Amer J Plant Sci 2:190

    Article  Google Scholar 

  • Stein RJ, Lopes SIG, Fett JP (2014) Iron toxicity in field-cultivated rice: contrasting tolerance mechanisms in distinct cultivars. Theor Exp Plant Physiol 26(2):135–146

    Article  Google Scholar 

  • Subagyo H, Widjaja-Adhi IPG (1998) Opportunities and constraints for swampland development for agricultural development in Indonesia. Bogor: Indonesian Center for Soil and Agro-climate Research and Development [in Indonesian]

    Google Scholar 

  • Subagyo H, Suharta N, Siswanto AB (2000) Agricultural lands in Indonesia. Bogor: Indonesian Center for Soil and Agro-climate Research and Development [in Indonesian]

    Google Scholar 

  • Suhartini T, Suwarno, Safaruddin (1996) Genetic parameters of iron toxicity tolerance in rice using diallel analysis. Zuriat 7(1):33–40 [in Indonesian]

    Google Scholar 

  • Su J, Wu R (2004) Stress-inducible synthesis of proline in transgenic rice confers faster growth under stress conditions than that with constitutive synthesis. Plant Sci 166:941–948

    Article  CAS  Google Scholar 

  • Suhartini T, Makarim AK (2009) Teknik seleksi genotipe padi toleran keracunan besi. J Penelit Pertan Tanam Pangan 28:125–130

    Google Scholar 

  • Takahashi F, Kuromori T, Urano K, Yamaguchi-Shinozaki K, Shinozaki K (2020) Drought stress responses and resistance in plants: from cellular responses to long-distance intercellular communication. Front Plant Sci 11:1–14

    Article  Google Scholar 

  • Takasaki H, Maruyama K, Kidokoro S, Ito Y, Fujita Y, Shinozaki K et al (2010) The abiotic stress-responsive NAC-type transcription factor OsNAC5 regulates stress-inducible genes and stress tolerance in rice. Mol Genet Genom 284:173–183

    Article  CAS  Google Scholar 

  • Tang Y, Sorrells ME, Kochian LV, Garvin DF (2000) Identification of RFLP markers linked to the barley aluminum tolerance gene Alp. Crop Sci 40:778–782

    Article  CAS  Google Scholar 

  • Tang N, Zhang H, Li X, Xiao J, Xiong L (2012) Constitutive activation of transcription factor OsbZIP46 improves drought tolerance in rice. Plant Physiol 158:1755–1768

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tenaillon M, Sawkins M, Long A, Gaut R, Doebley J, Gaut BS (2001) Patterns of DNA sequence polymorphism along chromosome 1 of maize (Zea mays ssp. mays L.). Proc Natl Acad Sci USA 98:9155–9161

    Article  Google Scholar 

  • Thomson MJ, Tai TH, McClung AM, Lai XH, Hinga ME, Lobos KB, Xu Y, Martinez CP, McCouch SR (2003) Mapping quantitative trait loci for yield, yield components and morphological traits in an advanced backcross population between Oryza rufipogon and the Oryza sativa cultivar Jefferson. Theor Appl Genet 107:479–493

    Google Scholar 

  • Timmer P (2010) Food security in Asia and the changing role of rice. The Asia Foundation Occasional Paper No. 4

    Google Scholar 

  • Todaka D, Shinozaki K, Yamaguchi-Shinozaki K (2015) Recent advances in the dissection of drought-stress regulatory networks and strategies for development of drought-tolerant transgenic rice plants. Front Plant Sci 6:1–20

    Article  Google Scholar 

  • Tripathy JN, Zhang J, Robin S, Nguyen TT, Nguyen HT (2000) QTLs for cell-membrane stability mapped in rice (Oryza sativa L.) under drought stress. Theor Appl Genet 100:1197–1202

    Article  CAS  Google Scholar 

  • Tsutsui T, Yamaji N, Ma JF (2011) Identification of a cis-acting element ofART1, a C2H2-type zinc-finger transcription factor for aluminum tolerancein rice. Plant Physiol 156:925–931

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tung C-W, Zhao K, Wright M, Ali M, Jung J, Kimball J, Tyagi W, Thomson MJ, McNally K, Leung H, Kim H, Ahn SN, Reynolds A, Scheffler B, Eizenga G, McClung A, Bustamante C, McCouch SR (2010) Development of a research platform for dissecting phenotype–genotype associations in rice (Oryza spp.). Rice 1:1–13

    Google Scholar 

  • Turhadi T, Hamim H, Ghulamahdi M, Miftahudin M (2018) Morpho-physiological responses of rice genotypes and its clustering under hydroponic iron toxicity conditions. Asian J Agri Biol 6(4):495–505

    Google Scholar 

  • Turhadi T, Hamim H, Ghulamahdi M, Miftahudin M (2019) Iron toxicity-induced physiological and metabolite profile variations among tolerant and sensitive rice varieties. Plant Signal Behav 14(12):1682829

    Google Scholar 

  • Turhadi T, Hamim H, Ghulamahdi M, Miftahudin M (2020) Morpho-physiological and anatomical character changes of rice under waterlogged and water-saturated acidic and high Fe content soil. Sains Malaysiana 49(10):2411–2424

    Google Scholar 

  • Umezawa T, Nakashima K, Miyakawa T, Kuromori T, Tanokura M, Shinozaki K et al (2010) Molecular basis of the core regulatory network in ABA responses: sensing, signaling and transport. Plant Cell Physiol 51:1821–1839

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Usman MG, Rafii MY, Martini MY, Yusuff OA, Ismail MR, Miah G (2017) Molecular analysis of Hsp70 mechanisms in plants and their function in response to stress. Biotechnol Genet Eng Rev 33:26–39

    Article  CAS  PubMed  Google Scholar 

  • Utami DW, Hanarida I (2014) Evaluasi lapang dan identifikasi molekuler plasma nutfah padi terhadap keracunan Fe. Agro Biogen 10(1):9–17

    Google Scholar 

  • Varshney RK, Pandey MK, Chitikineni A (2018) Plant genetics and molecular biology: an introduction. In: Varshney RK, Pandey MK, Chitikineni A (eds) Plant genetics and molecular biology. Advances in biochemical engineering/biotechnology, vol 164. Springer, pp 1–9

    Google Scholar 

  • Venuprasad R, Shashidhar HE, Hittalmani S, Hemamalini GS (2002) Tagging quantitative trait loci associated with grain yield and root morphological traits in rice (Oryza sativa L.) under contrasting moisture regimes. Euphytica 128:293–300

    Article  CAS  Google Scholar 

  • Verma SK, Saxena RR, Saxena RR, Xalxo MS, Verulkar SB (2014) QTL for grain yield under water stress and non-stress conditions over years in rice (Oryza sativa L.). Aus J Crop Sci 8:916–926

    Google Scholar 

  • Vikram P, Swamy BM, Dixit S, Cruz MT, Ahmed HU, Singh AK, Kumar A (2011) qDTY1.1, a major QTL for rice grain yield under reproductive-stage drought stress with a consistent effect in multiple elite genetic backgrounds. BMC Genetics 12:89

    Google Scholar 

  • Vinod KK, Krishnan SG, Thribhuvan R, Singh AK (2019) Genetics of drought tolerance, mapping QTLs, candidate genes and their genetics of drought tolerance, mapping QTLs, candidate genes and their utilization in rice improvement. In: Rajpal VR, Sehgal D, Kumar A, Raina SN (eds) Genomics assisted breeding of crops for abiotic stress tolerance, vol II, sustainable development and biodiversity 21. Springer, pp 145–186

    Google Scholar 

  • Virmani SS (1977) Varietal tolerance of rice to iron toxicity in Liberia. Intl Rice Res Newsl Int Rice Res Inst 2:4–5

    Google Scholar 

  • von Uexkuell HR, Mutert E (1995) Global extent, development and economic impact of acid soils. Plant Soil 171:1–15

    Article  Google Scholar 

  • Wahyuningtyas W, Miftahudin Widyastuti U, Tjahjoleksono A (2016) Construction of RNA interference vector to silence aluminumtolerance gene candidate in rice cv HawaraBunar. HAYATI J Biosci 23:79–84

    Article  Google Scholar 

  • Wailes EJ, Chavez EC (2012) World rice outlook-international rice baseline with deterministic and stochastic projections 2012–2021. Department of Agricultural Economics and Agribusiness, University of Arkansas, Fayetteville

    Google Scholar 

  • Wallace JG, Rodger-Melnick E, Buckler ES (2018) On the road to breeding 4.0: unraveling the good, the bad, and the boring of crop quantitative genomics. Annu Rev Genet 52:26.1–26.24

    Google Scholar 

  • Wan JL, Zhai HQ, Wan JM, Ikehashi H (2003) Detection and analysis of QTLs for ferrous iron toxicity tolerance in rice, Oryza sativa L. Euphytica 131:201–206

    Article  CAS  Google Scholar 

  • Wan JL, Zhai HQ, Wan JM, Yasui H, Yoshimura A (2004) Detection and analysis of QTLs associated with resistance to ferrous iron toxicity in rice (Oryza sativa L.), using recombinant inbred lines. Zuo Wu Xue Bao 30:329–333

    Google Scholar 

  • Wan JL, Zhai HQ, Wan JM (2005) Mapping of QTLs for ferrous iron toxicity tolerance in rice (Oryza sativa L.). Yi Chuan Xue Bao 32(11):1156–1166

    Google Scholar 

  • Wan L, Zhang J, Zhang H, Zhang Z, Quan R, Zhou S et al (2011) Transcriptional activation of OsDERF1 in OsERF3 and OsAP2-39 negatively modulates ethylene synthesis and drought tolerance in rice. PLoS ONE 6:e25216

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wang Q, Tang J, Han B (2020a) Advances in genome-wide association studies of complex traits in rice. Theor Appl Genet 133:1415–1425

    Article  PubMed  Google Scholar 

  • Wang F, Itai RN, Nozoye T, Kobayashi T, Nishizawa NK, Nakanishi H (2020b) The bHLH protein OsIRO3 is critical for plant survival and iron (Fe) homeostasis in rice (Oryza sativa L.) under Fe-deficient conditions. Soil Sci Plant Nutr. https://doi.org/10.1080/00380768.2020.1783966

  • WARDA (1998) Annual Report 1997: West Africa Rice Development Association, Bouaké

    Google Scholar 

  • Watanabe T, Osaki M (2001) Influence of aluminum and posphorus on groTLhand xylem sap composition in Melastomamala batricum L. Plant Soil 237:63–70

    Article  CAS  Google Scholar 

  • Watson GA (1984) Utility of rice cropping strategies in Semuda Kecil village, Central Kalimantan, Indonesia. In: International Rice Research Institute (ed) The workshop on research priorities in tidal swamp rice; 22–25 June 1981; Banjarmasin, South Kalimantan, Indonesia. International Rice Research Institute, Manila, pp 49–68

    Google Scholar 

  • Wan JL, Zhai HQ, Wan JM, Yasui H, Yoshimura A (2003a) Mapping QTL for traits associated with resistance to ferrous iron toxicity in rice (Oryza sativa L.), using japonica chromosome segment substitution lines. Yi Chuan Xue Bao 30(10):893–898

    Google Scholar 

  • Wan JL, Zhai HQ, Wan JM, Ikehashi H (2003b) Detection and analysis of QTLs for ferrous iron toxicity tolerance in rice, Oryza sativa L. Euphytica 131:201–206

    Google Scholar 

  • Weiner JJ, Peterson FC, Volkman BF, Cutler SR (2010) Structural and functional insights into core ABA signaling. Curr Opin Plant Biol 13:495–502

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Widjaja-Adhi IPG, Suriadikarta DA, Sutriadi MT, Subiksa IGM, Suastika IW (2000) Management of swamp utilization and development. Bogor: Indonesian Center for Soil and Agro-climate Research and Development [in Indonesian]

    Google Scholar 

  • Wijayanto A (2013) Aplikasi Marka Molekulerdalam Seleksi Populasi Silang Balik IR64/Hawara Bunaruntuk Mendapatkan Galur Padi Toleran aluminium. IPB Press, Bogor

    Google Scholar 

  • Wood S, Sebastian K, Cherr SJS (2000) Pilot Analysis of Global Ecosystems Agroecosystems. United States of America: World Resources Institute

    Google Scholar 

  • Wu P, Hu B, Liao CY, Zhu JM, Wu YR, Senadhira D, Paterson AH (1998) Characterization of tissue tolerance to iron by molecular markers in different lines of rice. Plant Soil 203:217–226

    Article  CAS  Google Scholar 

  • Wu P, Liao CY, Hu B, Yi KK, Jin WZ, Ni JJ, He C (2000) QTLs and epistasis foraluminum tolerance in rice (Oryza sativa L.) at different seedling stages. Theor Appl Genet 100:1295–1303

    Article  CAS  Google Scholar 

  • Wu LB, Shhadi MY, Gregorio G, Matthus E, Becker M, Frei M (2014) Genetic and physiological analysis of tolerance to acute iron toxicity in rice. Rice 7(1):1–8

    Article  Google Scholar 

  • Wu LB, Ueda Y, Lai SK, Frei M (2016) Shoot tolerance mechanisms to iron toxicity in rice (Oryza sativa L.). Plant Cell Environ 40(4):570–584

    Google Scholar 

  • Xia JX, Yamaji N, Kasai T, Ma JF (2010) Plasma membrane localized transporterfor aluminum in rice. Proc Natl Acad Sci USA 107:18381–18385

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Xia J, Yamaji N, Ma JF (2011) Further characterization of an aluminum influx transporter in rice. Plant Signal Behav 6:160–173

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Xia JX, Yamaji N, Ma JF (2013) A plasma membrane-localized smallpeptide is involved in Al tolerance in rice. Plant J76:345–355

    Google Scholar 

  • Xia J, Yamaji N, Che J, Shen RF, Ma JF (2014) Differential expression of Nrat1 is responsible for Al-tolerance QTL on chromosome 2 in rice. J Exp Bot 65(15):4297–4304

    Google Scholar 

  • Xiang Y, Huang Y, Xiong L (2007) Characterization of stress-responsive CIPK genes in rice for stress tolerance improvement. Plant Physiol 144:1416–1428

    Google Scholar 

  • Xiang Y, Tang N, Du H, Ye H, Xiong L (2008) Characterization of OsbZIP23 as a key player of the basic leucine zipper transcription factor family for conferring abscisic acid sensitivity and salinity and drought tolerance in rice. Plant Physiol 148:1938–1952

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Xiao B, Huang Y, Tang N, Xiong L (2007) Over-expression of a LEA gene in rice improves drought resistance under the field conditions. Theor Appl Genet 115:35–46

    Article  CAS  PubMed  Google Scholar 

  • Xiao BZ, Chen X, Xiang CB, Tang N, Zhang QF, Xiong LZ (2009) Evaluation of seven function-known candidate genes for their effects on improving drought resistance of transgenic rice under field conditions. Mol Plant 2:73–83

    Article  CAS  PubMed  Google Scholar 

  • Xu D, Duan X, Wang B, Hong B, Ho THD, Wu R (1996) Expression of a late embryogenesis abundant protein gene, HVA1, from barley confers tolerance to water deficit and salt stress in transgenic rice. Plant Physiol 110:249–257

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Xu JL, Lafitte HR, Gao YM, Fu BY, Torres R, Li ZK (2005) QTLs for drought escape and tolerance identified in a set of random introgression lines of rice. Theor Appl Genet 111:1642–1650

    Article  CAS  PubMed  Google Scholar 

  • Xu DQ, Huang J, Guo SQ, Yang X, Bao YM, Tang HJ et al (2008) Over-expression of a TFIIIA-type zinc finger protein gene ZFP252 enhances drought and salt tolerance in rice (Oryza sativa L.). FEBS Lett 582:1037–1043

    Article  CAS  PubMed  Google Scholar 

  • Xue Y, Wan JM, Jiang L, Liu LL, Su N, Zhai HQ, Ma JF (2006) QTL analysis of aluminum resistance in rice (Oryza sativa L.). Plant Soil 287:375–383

    Article  CAS  Google Scholar 

  • Xue Y, Jiang L, Su N, Wang JK, Deng P, Ma JF, Zhai HQ, Wan JM (2007) The genetic basic and fine-mapping of a stable quantitative-trait loci for aluminum tolerance in rice. Planta 22(7):255–262

    Article  Google Scholar 

  • Yadira OC, Reyes JL, Alejandra AC (2011) Late embryogenesis abundant proteins. Plant Signal Behav 6:586–589

    Article  Google Scholar 

  • Yamaguchi-Shinozaki K, Shinozaki K (2006) Transcriptional regulatory networks in cellular responses and tolerance to dehydration and cold stresses. Annu Rev Plant Biol 57:781–803

    Article  CAS  PubMed  Google Scholar 

  • Yamaji N, Huang CF, Nagao S, Yano M, Sato Y, Nagamura Y, Ma JF (2009) A zing finger transcription factor ART1 regulates multiple genes implicated in aluminum tolerance in rice. Plant Cell 21:3339–3349

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Yamauchi M (1989) Rice bronzing in Nigeria caused by nutrient imbalances and its control by potassium sulfate application. Plant Soil 117:275–286

    Article  CAS  Google Scholar 

  • Yang A, Dai X, Zhang WH (2012) A R2R3-type MYB gene, OsMYB2, is involved in salt, cold, and dehydration tolerance in rice. J Exp Bot 63:2541–2556

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Yang LT, Qi YP, Jiang HX, Chen LS (2013) Roles of organic acid anion secretion in aluminium tolerance of higher plants. Biomed Res Int 13:173682

    Google Scholar 

  • Yin K, Gao C, Qiu JL (2017) Progress and prospects in plant genome editing. Nat Plants 3:1–6

    Article  Google Scholar 

  • Yokosho K, Yamaji N, Ma JF (2011) An Al-inducible MATE gene is involved inexternal detoxification of Al in rice. Plant Cell 68:1061–1069

    CAS  Google Scholar 

  • Yokosho K, Yamaji N, Fujii-Kashino M, Ma JF (2016) Retrotransposon-mediated aluminum tolerance through enhanced expression of the citrate transporter OsFRDL4. Plant Physiol 172:2327–2336

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Yoshida S (1981) Fundamentals of rice crop science. International Rice Research Institute, Los Banos, Manila, Philippines

    Google Scholar 

  • Yoshida S, Forno DA, Cock JH, Gomez KA (1976) Laboratory manual for physiological studies of rice. The International Rice Research Institute, Manila, Philippines

    Google Scholar 

  • You J, Hu H, Xiong L (2012) An ornithine δ-aminotransferase gene OsOAT confers drought and oxidative stress tolerance in rice. Plant Sci 197:59–69

    Article  CAS  PubMed  Google Scholar 

  • You J, Zong W, Li X, Ning J, Hu H, Li X, Xiong L (2013) The SNAC1-targeted gene OsSRO1c modulates stomata closure and oxidative stress tolerance by regulating hydrogen peroxide in rice. J Exp Bot 64:569–583

    Article  CAS  PubMed  Google Scholar 

  • Yu J, Pressoir G, Briggs W, Bi I, Yamasaki M, Doebley JF, McMullen MD, Gaut BS, Nielsen DM, Holland JB, Kresovich S, Buckler ES (2005) A unified mixed model method for association mapping that accounts for multiple levels of relatedness. Nat Genet 38:203–208

    Article  PubMed  Google Scholar 

  • Yu CS, Chen YC, Lu CH, Hwang JK (2006) Prediction of protein subcellular localization. Proteins Struct Funct Bioinf 64:643–651

    Article  CAS  Google Scholar 

  • Yue B, Xue W, Luo L, Xing Y (2008) Identification of quantitative trait loci for four morphologic traits under water stress in rice (Oryza sativa L.). J Gene Genom 35:569–575

    Article  Google Scholar 

  • Zhang J, Zheng HG, Aarti A, Pantuwan G, Nguyen TT, Tripathy JN, Sarial AK, Robin S, Babu RC, Nguyen BD, Sarkarung S (2001) Locating genomic regions associated with components of drought resistance in rice: comparative mapping within and across species. Theor Appl Genet 103:19–29

    Article  CAS  Google Scholar 

  • Zhang H, Liu W, Wan L, Li F, Dai L, Li D et al (2010a) Functional analyses of ethylene response factor JERF3 with the aim of improving tolerance to drought and osmotic stress in transgenic rice. Transgen Res 19:809–818

    Article  CAS  Google Scholar 

  • Zhang Z, Li F, Li D, Zhang H, Huang R (2010b) Expression of ethylene response factor JERF1 in rice improves tolerance to drought. Planta 232:765–774

    Article  CAS  PubMed  Google Scholar 

  • Zhang L, Xiao S, Li W, Feng W, Li J, Wu Z, Shao M (2011) Overexpression of a Harpin-encoding gene hrf1 in rice enhances drought tolerance. J Exp Bot 62:4229–4238

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhang H, Zhang J, Quan R, Pan X, Wan L, Huang R (2013) EAR motif mutation of rice OsERF3 alters the regulation of ethylene biosynthesis and drought tolerance. Planta 237:1443–1451

    Article  CAS  PubMed  Google Scholar 

  • Zhang P, Zhong K, Tong H, Shahid MQ, Li J (2016) Association mapping for aluminum tolerance in a core collection of rice landraces. Front Plant Sci 7(1415):1–11

    Google Scholar 

  • Zhang J, Chen K, Pang Y, Naveed SA, Zhao X, Wang X, Wang Y, Dingkuhn M, Pasuquin J, Li Z (2017) QTL mapping and candidate gene analysis of ferrous iron and zinc toxicity tolerance at seedling stage in rice by genome-wide association study. BMC Genom 18:828

    Article  Google Scholar 

  • Zhao K, Aranzana M, Kim S, Lister C, Shindo C, Tang C, Toomajian C, Zheng H, Dean C, Marjoram P, Nordborg M (2007) An Arabidopsis example of association mapping in structured samples. PLoS Genet 3:e4

    Article  PubMed  PubMed Central  Google Scholar 

  • Zhao K, Tung CW, Eizenga GC, Wright MH, Ali ML, Price AH, Norton GJ, Islam MR, Reynolds A, Mezey J, McClung AM, Bustamante CD, McCouch SR (2011) Genome-wide association mapping reveals rich genetic architecture of complex traits in Oryza sativa. Nat Commun 2:1–10

    Google Scholar 

  • Zheng SJ (2010) Iron homeostasis and iron acquisition in plants: maintenance, functions and consequences. Ann Bot 105(6):799–800

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zheng SJ, Yang JL, He YF, Yu XH, Zhang L, You JF, Shen RF, Matsumoto H (2005) Immobilization of aluminum with phosphorus in roots is associated with high Al resistance in buck wheat. Plant Physiol 138:297–303

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zheng B, Yang L, Mao C, Huang Y, Wu P (2008) Comparison of QTLs for rice seedling morphology under different water supply conditions. J Genet Genom 35:473–484

    Article  Google Scholar 

  • Zhou S, Zhu M, Wang F, Huang J, Wang G (2013) Mapping of QTLs for yield and its componentsin a rice recombinant inbred line population. Pak J Bot 45:183–189

    CAS  Google Scholar 

  • Zhu B, Su J, Chang M, Verma DPS, Fan YL, Wu R (1998) Overexpression of a ∆1-pyrroline-5-carboxylate synthetase gene and analysis of tolerance to water-and salt-stress in transgenic rice. Plant Sci 139:41–48

    Article  CAS  Google Scholar 

  • Zong W, Tang N, Yang J, Peng L, Ma S, Xu Y, Li G, Xiong L (2016) Feedback regulation of ABA signalling and biosynthesis by a bZIP transcription factor targets drought-resistance-related genes. Plant Physiol 171(4):2810–2825

    Google Scholar 

  • Zou GH, Mei HW, Liu HY, Liu GL, Hu SP, Yu XQ, Li MS, Wu JH, Luo LJ (2005) Grain yield responses to moisture regimes in a rice population: association among traits and genetic markers. Theor Appl Genet 112:106–113

    Article  CAS  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Miftahudin .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2021 The Author(s), under exclusive license to Springer Nature Switzerland AG

About this chapter

Check for updates. Verify currency and authenticity via CrossMark

Cite this chapter

Miftahudin, Fendiyanto, M.H., Satrio, R.D., Turhadi, Chikmawati, T. (2021). Genomic Improvement of Rice for Drought, Aluminum, and Iron Toxicity Stress Tolerance. In: Kole, C. (eds) Genomic Designing for Abiotic Stress Resistant Cereal Crops. Springer, Cham. https://doi.org/10.1007/978-3-030-75875-2_1

Download citation

Publish with us

Policies and ethics