Abstract
Rice (Oryza sativa L.) belongs to Poaceae family and serves as food for more than half of the global population. Domesticated from O. preperennis about 10,000 years ago, it is cultivated in a wide range of ecosystems right from below the sea level to high mountain regions. Genetic improvement in India has helped in improving average productivity from 0.67 tons/ha in 1950–1951 to 2.74 t/ha during 2020–2021. Development of research infrastructure along with basic research helped in gaining understanding of the genetic nature of economically important traits. The major breakthrough in yield improvement was achieved through utilisation of sd1 in developing semi-dwarf high yielding varieties with sturdy stem, spurring the green revolution. Hybrid rice further enhanced rice productivity. Deciphering rice genome and advances in genomics helped in functional characterisation of ∼2800 economically important genes governing yield, resistance to major biotic and abiotic stresses, grain and nutritional quality, which enabled the integration of molecular markers in breeding. Thirty-six MAS-derived varieties with resistance to biotic and/or abiotic stress and 12 varieties with enhanced Zn and/or protein content have been released in India. Advances in genetics, breeding, genomics and phenomics, have enabled population improvement through genomic selection, while genome-editing has helped in creating novel alleles for useful genes. Aided by an evolving system for multi-location evaluation of elite genotypes under the All India Coordinated Rice Improvement Programme and a robust system of seed supply chain for dissemination of improved rice varieties, higher adoption by farmers has helped in improving and sustaining rice productivity. However, sustaining it in the face of climate change is a major challenge. Adoption of advanced tools and techniques can help rapid and precise breeding of improved rice varieties suited to changing human needs.
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References
Abe K, Araki E, Suzuki Y et al (2018) Production of high oleic/low linoleic rice by genome editing. Plant Physiol Biochem 131:58–62. https://doi.org/10.1016/j.plaphy.2018.04.033
Ali J (1993) Studies on temperature sensitive genic male sterility and chemical induced sterility towards development of two 122-line hybrids in rice (Oryza sativa L.). Ph.D. (Genetics) thesis. ICAR–Indian Agricultural Research Institute, New Delhi, p 138
Ali J, Siddiq EA, Zaman FU et al (1995) Identification and characterization of temperature sensitive genic male sterile sources in rice (Oryza sativa L.). Indian J Genet Plant Breed 55:243–259
Ali ML, Sanchez PL, Yu SB et al (2010) Chromosome segment substitution lines: a powerful tool for the introgression of valuable genes from Oryza wild species into cultivated rice (O. sativa). Rice 3:218–234. https://doi.org/10.1007/s12284-010-9058-3
Al-Tamimi N, Brien C, Oakey H et al (2016) Salinity tolerance loci revealed in rice using high-throughput non-invasive phenotyping. Nat Commun 7:13342. https://doi.org/10.1038/ncomms13342
Alvarez AM, Adachi T, Nakase M et al (1995) Classification of rice allergenic protein cDNAs belonging to the α-amylase/trypsin inhibitor gene family. Biochim Biophys Acta, Protein Struct 1251:201–204. https://doi.org/10.1016/0167-4838(95)00075-6
Andrade A, Tulmann-Neto A, Tcacenco FA et al (2018) Development of rice (Oryza sativa) lines resistant to aryloxyphenoxypropionate herbicides through induced mutation with gamma rays. Plant Breed 137:364–369. https://doi.org/10.1111/pbr.12592
Ashikari M, Sakakibara H, Lin S et al (2005) Cytokinin oxidase regulates rice grain production. Science 309(5735):741–745. https://doi.org/10.1126/science.1113373
Ashokkumar S, Jaganathan D, Ramanathan V et al (2020) Creation of novel alleles of fragrance gene OsBADH2 in rice through CRISPR/Cas9 mediated gene editing. PLoS One 15:e0237018. https://doi.org/10.1371/journal.pone.0237018
Babu VR, Padmavathi C, Neeraja CN et al (2016) 50 years of AICRIP—way forward. Technical bulletin No. 92/2016. ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad-500 030, Telangana State, India, p 292
Collard BCY, Beredo JC, Lenaerts B et al (2017) Revisiting rice breeding methods—evaluating the use of rapid generation advance (RGA) for routine rice breeding. Plant Prod Sci 20(4):337–352. https://doi.org/10.1080/1343943X.2017.1391705
Bradbury LM, Fitzgerald TL, Henry RJ et al (2005) The gene for fragrance in rice. Plant Biotechnol J 3(3):363–370. https://doi.org/10.1111/j.1467-7652.2005.00131.x
Bradbury LM, Gillies SA, Brushett DJ et al (2008) Inactivation of an aminoaldehyde dehydrogenase is responsible for fragrance in rice. Plant Mol Biol 68:439–449. https://doi.org/10.1007/s11103-008-9381-x
Cao YY, Duan H, Yang LN et al (2008) Effective heat stress during meio-sis on grain yield of rice cultivars differing in heat tolerance and its physiological mechanism. Acta Agron Sin 34:2134–2142. https://doi.org/10.3724/SP.J.1006.2008.02134
Chang JD, Huang S, Konishi N et al (2020) Overexpression of the manganese/cadmium transporter OsNRAMP5 reduces cadmium accumulation in rice grain. J Exp Bot 71:5705–5715. https://doi.org/10.1093/jxb/eraa287
Chang TT (1964) Present knowledge of rice genetics and cytogenetics. International Rice Research Institute, Los Baños, Philippines, p 95
Chang TT (1976) The origin, evolution, cultivation, dissemination and diversification of Asian and African rices. Euphytica 25:425–441. https://doi.org/10.1007/BF00041576
Chang TT, Bardenas EA (1965) The morphology and varietal characteristics of the rice plant. IRRI Technical Bulletin 4. The International Rice Research Institute, Los Baños, Philippines, p 40
Che R, Tong H, Shi B et al (2016) Control of grain size and rice yield by GL2-mediated brassinosteroid responses. Nat Plants 2(1):15195. https://doi.org/10.1038/nplants.2015.195
Chen S, Yang Y, Shi W et al (2008) Badh2, encoding betaine aldehyde dehydrogenase, inhibits the biosynthesis of 2-acetyl-1-pyrroline, a major component in rice fragrance. Plant Cell 20:1850–1861. https://doi.org/10.1105/tpc.108.058917
Cheng C, Motohashi R, Tsuchimoto S et al (2003) Polyphyletic origin of cultivated rice: based on the interspersion pattern of SINEs. Mol Biol Evol 20:67–75. https://doi.org/10.1093/molbev/msg004
Cheng S, Cao L, Zhuang J et al (2007) Super hybrid rice breeding in China: achievements and prospects. J Integr Plant Biol 49:805–810. https://doi.org/10.1111/j.1744-7909.2007.00514.x
Cheng S, Liao X, Min S (1998) China’s “super” rice research: background, goals and issues. China Rice 1:3–5. (in Chinese)
Cheng S, Sun Z, Si H et al (1995) Response to photoperiod and temperature in photo–thermo period sensitive genic male sterile line Xinguang S (Oryza sativa L. subsp. indica). Chin J Rice Sci 9:87–91
Choi HO, Bae SH, Chung GS et al (1974) A new short-statured rice variety Tongil. Res Rep ORO 16(Crop):1–12
Chung GS, Heu MH (1980) Status of japonica-indica hybridization in Korea. In: Selected papers from the 1979 international rice research. International Rice Research Institute, Los Baños, Philippines, pp 135–152
Chung GS, Heu MH (1991) Improvement of Tongil-Type rice cultivars from indica/japonica hybridization in Korea. Biotechnol Agric For:105–112. https://doi.org/10.1007/978-3-642-83986-3_9
Crossa J, Pérez-Rodríguez P, Cuevas J et al (2017) Genomic selection in plant breeding: methods, models, and perspectives. Trends Plant Sci 22:961–975. https://doi.org/10.1016/j.tplants.2017.08.011
Croughan TP (1998) Inventor. Herbicide resistant rice. Board of Supervisors of Louisiana State University. 5,773,704. US Patent. 1998 June 30
Cui Y, Li R, Li G et al (2020) Hybrid breeding of rice via genomic selection. Plant Biotechnol J 18:57–67. https://doi.org/10.1111/pbi.13170
Desai SV, Balasubramanian VN, Fukatsu T et al (2019) Automatic estimation of heading date of paddy rice using deep learning. Plant Methods 15:76. https://doi.org/10.1186/s13007-019-0457-1
Dimaano NGB, Ali J, Mahender A et al (2020) Identification of quantitative trait loci governing early germination and seedling vigor traits related to weed competitive ability in rice. Euphytica 216:159. https://doi.org/10.1007/s10681-020-02694-8
Ding JH, Lu Q, Yidan OY et al (2012) A long noncoding RNA regulates photoperiod-sensitive male sterility, an essential component of hybrid rice. Proc Natl Acad Sci U S A 109:2654–2659. https://doi.org/10.1073/pnas.1121374109
Dingkuhn M, Penning de Vries FWT, De Datta SK et al (1991) Concepts for a new plant type for direct seeded flooded tropical rice. In: Direct seeded flooded rice in the tropics. International Rice Research Institute, Los Banos, Philippines, pp 17–38
Dixit S, Grondin A, Lee CR et al (2015) Understanding rice adaptation to varying agro-ecosystems: trait interactions and quantitative trait loci. BMC Genet 516:86. https://doi.org/10.1186/s12863-015-0249-1
Dobermann A, Fairhurst T (2000) Rice: nutrient disorders and nutrient management, Handbook series. Potash & Phosphate Institute (PPI), Potash & Phosphate Institute of Canada (PPIC) and International Rice Research Institute, Los Baños, Philippine, p 191
Donald CM (1968) The breeding of crop ideotype. Euphytica 17:385–403. https://doi.org/10.1007/BF00056241
Dong NV, Subudhi PK, Luong PN et al (2000) Molecular mapping of a rice gene conditioning thermosensitive genic male sterility using AFLP, RFLP and SSR techniques. Theor Appl Genet 100:727–734. https://doi.org/10.1007/s001220051345
Duan L, Yang W, Huang C et al (2011) A novel machine-vision-based facility for the automatic evaluation of yield-related traits in rice. Plant Methods 7:44. https://doi.org/10.1186/1746-4811-7-44
Dwiyanti MS, Yamada T (2013) Molecular mapping and breeding for genes/qtls related to climate change. In: Kole C (ed) Genomics and breeding for climate-resilient crops. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-37045-8_4
Endo A, Saika H, Takemura M et al (2019) A novel approach to carotenoid accumulation in rice callus by mimicking the cauliflower Orange mutation via genome-editing. Rice 12(1):81. https://doi.org/10.1186/s12284-019-0345-3
Fan C, Xing Y, Mao H et al (2006) GS3, a major QTL for grain length and weight and minor QTL for grain width and thickness in rice, encodes a putative transmembrane protein. Theor Appl Genet 112(6):1164–1171. https://doi.org/10.1007/s00122-006-0218-1
Fehr WR (1987) Principles of cultivar development. Volume 1. Theory and technique. McGraw-Hill, Inc., New York, St. Louis, San Fansisco
Fitzgerald MA, McCouch SR, Hall RD (2009) Not just a grain of rice: the quest for quality. Trends Plant Sci 14:133–139. https://doi.org/10.1016/j.tplants.2008.12.004
Foster AJ, Martin-Urdiroz M, Yan X et al (2018) CRISPR-Cas9 ribonucleoprotein-mediated co-editing and counterselection in the rice blast fungus. Sci Rep 8(1):14355. https://doi.org/10.1038/s41598-018-32702-w
Freeman WH, Shastry SVS (1972) Rice improvement in India- the coordinated approach. In: Rice breeding. International Rice Research Institute, Los Baños, Philippines, pp 115–132
Fujii S, Toriyama K (2005) Molecular mapping of the fertility restorer gene for ms-CW-type cytoplasmic male sterility of rice. Theor Appl Genet 111:696–701. https://doi.org/10.1007/s00122-005-2054-0
Fujimaki H (1979) Recurrent selection by using genetic male sterility for rice improvement. Jpn Agric Res Q 13(3):153–156
Fukui K, Iijima K (1991) Somatic chromosome map of rice by imaging methods. Theor Appl Genet 81:589–596. https://doi.org/10.1007/BF00226723
Fukui K, Kakeda K, Hashimoto J et al (1987) In situ hybridization of 125I labelled rRNA to rice chromosomes. Rice Genet Newsl 4:114–115
Fukui K, Ohmido N, Khush GS (1994) Variability in rDNA loci in genus Oryza detected through fluorescence in situ hybridisation. Theor Appl Genet 87:893–899. https://doi.org/10.1007/BF00225782
Fukui K, Shishido R, Kinoshita T (1997) Identification of the rice D-genome chromosomes by genomic in situ hybridization. Theor Appl Genet 95:1239–1245. https://doi.org/10.1007/s001220050687
Fukuoka S, Saka N, Koga N et al (2009) Loss of function of a proline-containing protein confers durable disease resistance in rice. Science 325(5943):998–1001. https://doi.org/10.1126/science.1175550
Furukawa T, Maekawa M, Oki T et al (2006) The Rc and Rd genes are involved in proanthocyanidin synthesis in rice pericarp. Plant J 49:91–102. https://doi.org/10.1111/j.1365-313X.2006.02958.x
Gamboa C, Graterol E, de la Cruz R et al (2005) Advances in the Venezuelan recurrent selection program for population improvement in rice. In: Guimaraes EP (ed) Population improvement: a way of exploiting the rice genetic resources of Latin America. FAO, Rome, pp 187–201
Gao Q, Li G, Sun H et al (2020) Targeted mutagenesis of the rice FW 2.2-like gene family using the CRISPR/Cas9 system reveals OsFWL4 as a regulator of tiller number and plant yield in rice. Int J Mol Sci 21:809. https://doi.org/10.3390/ijms21030809
Gao ZY, Zheng DL, Cui X et al (2003) Map-based cloning of the ALK gene, which controls the gelatinization temperature of rice. Sci China C Life Sci 46:661–668. https://doi.org/10.1360/03yc0099
Ge S, Sang T, Lu BR et al (1999) Phylogeny of rice genomes with emphasis on origin of allotetraploid species. Proc Natl Acad Sci U S A 96:14400–14405. https://doi.org/10.1073/pnas.96.25.14400
Gilmore ECJ (1964) Suggested method of using reciprocal recurrent selection in some naturally self-pollinated species. Crop Sci 4:323–325. https://doi.org/10.2135/cropsci1964.0011183X000400030027x
Gopalakrishnan S, Sharma RK, Rajkumar A et al (2008) Integrating marker assisted background analysis with foreground selection for identification of superior bacterial blight resistant recombinants in Basmati rice. Plant Breed 127(2):131–139. https://doi.org/10.1111/j.1439-0523.2007.01458.x
Goulden CH (1939) Problems in plant selection. In: Burnett RC (ed) Proceeding of the seventh genetics congress. Cambridge University Press, Edinburgh, pp 132–133
Grover N, Kumar A, Yadav AK et al (2020) Marker assisted development and characterization of non-GM herbicide tolerant near Isogenic Lines of a mega Basmati rice variety, “Pusa Basmati 1121”. Rice 13:68. https://doi.org/10.1186/s12284-020-00423-2
Gu B, Zhou T, Luo J et al (2015) An-2 encodes a cytokinin synthesis enzyme that regulates awn length and grain production in rice. Mol Plant 8:1635–1650. https://doi.org/10.1016/j.molp.2015.08.001
Gu XY, Kianian SF, Hareland GA et al (2005) Genetic analysis of adaptive syndromes interrelated with seed dormancy in weedy rice (Oryza sativa). Theor Appl Genet 110:1108–1118. https://doi.org/10.1007/s00122-005-1939-2
Guo Z, Yang W, Chang Y et al (2018) Genome-wide association studies of image traits reveal genetic architecture of drought resistance in rice. Mol Plant 11:789–805. https://doi.org/10.1016/j.molp.2018.03.018
Guo T, Yu X, Li X et al (2019) Optimal designs for genomic selection in hybrid crops. Mol Plant 12(3):390–401. https://doi.org/10.1016/j.molp.2018.12.022
Hairmansis A, Berger B, Tester M et al (2014) Image-based phenotyping for non-destructive screening of different salinity tolerance traits in rice. Rice 7:16. https://doi.org/10.1186/s12284-014-0016-3
Hariprasad AS, Senguttuvel P, Revathi P et al (2011) Technical bulletin No. 56/2011. Directorate of Rice Research, (ICAR), Hyderabad, AP, India, p 57
He HA, Zhu CA, Huang WA et al (2005) Characterisation of an environmentally induced genic male sterile line of indica rice (Oryza sativa spp. indica). Aust J Agric Res 57:457–464. https://doi.org/10.1071/AR05102
Hector GP (1913) Notes on pollination and cross-fertilization in the common rice plant, Oryza sativa L. Mem Dept Agric Ind Bot Ser 6:1–10
Hernaiz LSI, Alvarado AJR, Châtel M et al (2000) Desarrollo de poblaciones japónica de arroz para Chile. In: Guimarães EP (ed) Avances en el mejoramiento poblacional en arroz. Embrapa Arroz e Feijão, Santo Antônio de Goiás, Brazil, pp 187–198
Heslop-Harrison J, Leitch A, Schwarzacher T et al (1990) Detection and characterization of 1B/1R translocations in hexaploid wheat. Heredity 65:385–392. https://doi.org/10.1038/hdy.1990.108
Heu MH, Chung GS, Kim DK et al (1982) Rapid generation advance in breeding rice for low temperature tolerance. In: International rice research conference. International Rice Research Institute, Los Baños, Philippines
Heu MH, Park SZ (1973) The segregation mode of plant height in the cross of rice varieties. Korean J Breed 5:112–118
Hideo P, Rangel N, de Morais OP et al (2002) Grain yield gains in three recurrent selection cycles in the CNAIRAT 4 irrigated rice population. Crop Breed Appl Biotechnol 2(3):369–374
Hirano HY, Sano Y (1991) Molecular characterization of the waxy locus of rice (Oryza sativa). Plant Cell Physiol 32:989–997
Hirano HY, Sano Y (1998) Enhancement of Wx gene expression and the accumulation of amylose in response to cool temperatures during seed development in rice. Plant Cell Physiol 39:807–812. https://doi.org/10.1093/oxfordjournals.pcp.a029438
Hodges RJ, Buzby JC, Bennett B (2011) Postharvest losses and waste in developed and less developed countries: opportunities to improve resource use. J Agric Sci 149:37–45. https://doi.org/10.1017/S0021859610000936
Hu CH (1961) Comparative karyological studies of wild and cultivated species of Oryza. Taiwan Provincial College of Agriculture, Taichung
Hu J, Wang Y, Fang Y et al (2015) A rare allele of GS2 enhances grain size and grain yield in rice. Mol Plant 8(10):1455–1465. https://doi.org/10.1016/j.molp.2015.07.002
Hu X, Wang C, Fu Y et al (2016) Expanding the range of CRISPR/Cas9 genome editing in rice. Mol Plant 9:943–945. https://doi.org/10.1016/j.molp.2016.03.003
Hua K, Jiang Y, Tao X et al (2020a) Precision genome engineering in rice using prime editing system. Plant Biotechnol J 18:2167–2169. https://doi.org/10.1111/pbi.13395
Hua K, Tao X, Liang W et al (2020b) Simplified adenine base editors improve adenine base editing efficiency in rice. Plant Biotechnol J 18(3):770–778. https://doi.org/10.1111/pbi.13244
Hua K, Tao X, Yuan F et al (2018) Precise A·T to G·C base editing in the rice genome. Mol Plant 11:627–630. https://doi.org/10.1016/j.molp.2018.02.007
Hua K, TaoX ZJK (2019) Expanding the base editing scope in rice by using Cas9 variants. Plant Biotechnol J 17:499–504. https://doi.org/10.1111/pbi.12993
Huang CH (1957) A study of cultivated varieties of Taiwan native rice [in Chinese, English summary]. J Agr Ass China 20(N.S):27–58
Huang CH, Chang WL, Chang TT (1972) Ponlai varieties and Tiachung Native 1. In: Rice breeding. International Rice Research Institute, Los Baños, Philippines, pp 31–46
Huang X, Qian Q, Liu Z et al (2009) Natural variation at the DEP1 locus enhances grain yield in rice. Nat Genet 41(4):494–497. https://doi.org/10.1038/ng.352
Huang JZ, ZG E, Zhang HL et al (2014) Workable male sterility systems for hybrid rice: genetics, biochemistry, molecular biology, and utilization. Rice 7:13. https://doi.org/10.1186/s12284-014-0013-6
Huang L, Li Q, Zhang C et al (2020) Creating novel Wx alleles with fine-tuned amylose levels and improved grain quality in rice by promoter editing using CRISPR/Cas9 system. Plant Biotechnol J 18:2164–2166. https://doi.org/10.1111/pbi.13391
Huang L, Zhang R, Huang G et al (2018) Developing superior alleles of yield genes in rice by artificial mutagenesis using the CRISPR/Cas9 system. Crop J 6:475–481. https://doi.org/10.1016/j.cj.2018.05.005
Huang TY, Wang Z, Hu YG et al (2008) Genetic analysis and primary mapping of pms4, a photoperiod-sensitive genic male sterility gene in rice (Oryza sativa). Rice Sci 15:153–156. https://doi.org/10.1016/S1672-6308(08)60035-9
Hull FH (1945) Agron J 37(2) 134-145. https://doi.org/https://doi.org/10.2134/agronj1945.00021962003700020006x
Igarashi K, Kazama T, Toriyama K (2016) A gene encoding pentatricopeptide repeat protein partially restores fertility in RT98-type cytoplasmic male-sterile rice. Plant Cell Physiol 57:2187–2193. https://doi.org/10.1093/pcp/pcw135
Iijima K, Kakeda K, Fukui K (1991) Identification and characterization of somatic rice chromosomes by imaging methods. Theor Appl Genet 81:597–605. https://doi.org/10.1007/BF00226724
Ikeda K, Nagasawa N, Nagato Y (2005) Aberrant panicle organization 1 temporally regulates meristem identity in rice. Dev Biol 282:349–360. https://doi.org/10.1016/j.ydbio.2005.03.016
Ikeda K, Sunohara H, Nagato Y (2004) Developmental course of inflorescence and spikelet in rice. Breed Sci 54:147–156. https://doi.org/10.1270/jsbbs.54.147
Ikehashi H (1977) New procedure for breeding photoperiod-sensitive deep-water rice with rapid generation advance. In: Proceedings of the workshop on deep-water rice. International Rice Research Institute, Los Baños, Philippines, pp 45–54
Ikehashi H, Fujimaki H (1980) Modified bulk population method for rice breeding. In: Innovative approaches to rice breeding. Selected papers from the 1979 international rice research conference. International Rice Research Institute, Los Baños, Philippines, pp 163–182
IRC (Int Rice Comm) (1950) Report of the first meeting of the rice breeders working party, 1–4 February. 1950. FAO (Food Agr Organ, UN), Rangoon/Rome, 9 p
Ishii T, Numaguchi K, Miura K et al (2013) OsLG1 regulates a closed panicle trait in domesticated rice. Nat Genet 45:462–465. https://doi.org/10.1038/ng.2567
Ishimaru Y, Suzuki M, Kobayashi T et al (2005) OsZIP4, a novel zinc-regulated zinc transporter in rice. J Exp Bot 56:3207–3214. https://doi.org/10.1093/jxb/eri317
Ishimaru K, Hirotsu N, Madoka M et al (2013) Loss of function of the IAA-glucose hydrolase gene TGW6 enhances rice grain weight and increases yield. Nat Genet 45(6):707–711. https://doi.org/10.1038/ng.2612
Itabashi E, Iwata N, Fujii S et al (2011) The fertility restorer gene, Rf2, for lead rice-type cytoplasmic male sterility of rice encodes a mitochondrial glycine-rich protein. Plant J 65:359–367. https://doi.org/10.1111/j.1365-313X.2010.04427.x
Itoh J, Nonomura K, Ikeda K et al (2005) Rice plant development: from zygote to spikelet. Plant Cell Physiol 46:23–47. https://doi.org/10.1093/pcp/pci501
Iwata N, Omura T (1975) Studies on the trisomics in rice plants (Oryza sativa L.) III. Relation between trisomics and genetic linkage groups. Jpn J Breed 25:363–368. https://doi.org/10.1270/jsbbs1951.25.363
Iyengar GAS, Sen SK (1978) Nuclear DNA content of the wild and cultivated Oryza species. Environ Exp Bot 18:219–224. https://doi.org/10.1016/0098-8472(78)90047-3
Jacob P, Avni A, Bendahmane A (2018) Translational research: exploring and creating genetic diversity. Trends Plant Sci 23:42–52. https://doi.org/10.1016/j.tplants.2017.10.002
Jacquemin J, Bhatia D, Singh K et al (2013) The international oryza map alignment project: development of a genus-wide comparative genomics platform to help solve the 9 billion-people question. Curr Opin Plant Biol 16:147–156. https://doi.org/10.1016/j.pbi.2013.02.014
Janaiah A (2002) Hybrid rice for Indian farmers: myths and realities. Econ Polit Wkly 37:4319–4328
Janoria MP (1989) A basic plant ideotype for rice. Intl Rice Res Newsl 14(3):12–13
Jensen NE (1970) Diallel selective mating system or cereal breeding. Crop Sci 10:629–635. https://doi.org/10.2135/cropsci1970.0011183X001000060006x
Jensen NF (1988) Plant breeding methodology. Wiley, New York, p 676
Jia JH, Li CY, Qu XP et al (2000) Constructing a genetic linkage map and mapping a new thermo–sensitive genic male–sterile gene (tms5) in rice. In: 1st national plant genome meet China. Dalian, China, p 37
Jia JH, Zhang DS, Li C et al (2001) Molecular mapping of the reverse thermo–sensitive genic male–sterile gene (rtms1) in rice. Theor Appl Genet 103:607–612. https://doi.org/10.1007/PL00002916
Jiang YM (1988) Studies on the effect of high temperature on fertility of the male sterile lines in Dian type hybrid rice (in China). J Juinnan Agric Univ 3:99–107
Jinek M, Chylinski K, Fonfara I et al (2012) A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 337:816–821. https://doi.org/10.1126/science.1225829a
Johannsen W (1903) Om arvelighed i samfund og i rene linier. Overs Kongel Danske Vidensk Selsk Forh 3:247–270
Jones JW (1926) Hybrid vigor in rice. J Am Soc Agron 18:424–428. https://doi.org/10.2134/agronj1926.00021962001800050010x
Jordon NE (1938) Experiments with artificial hybridization in rice. J Am Soc Agron 30:342–346. https://doi.org/10.2134/agronj1938.00021962003000040004x
Joseph CA, Chen Z, Ma D et al (2011) Analysis of short photoperiod-sensitive genic male sterility and molecular mapping of rpms3(t) gene in rice (Oryza sativa L.) using SSR markers. Genes Genomics 33:513–519. https://doi.org/10.1007/s13258-010-0074-x
Katara JL, Verma RL, Nayak D et al (2017) Frequency and fertility restoration efficiency of Rf3 and Rf4 genes in Indian rice. Plant Breed 136:74–82. https://doi.org/10.1111/pbr.12401
Kato S, Kosaka H, Hara S (1928) On the affinity of rice varieties as shown by fertility of hybrid plants (in Japanese). Bull Sci Fac Agric Kyushu Univ 3:132–147
Kawakami S, Ebana K, Nishikawa T, Sato YI, Vaughan DA, Kadowaki K (2007) Genetic variation in the chloroplast genome suggests multiple domestication of cultivated Asian rice (Oryza sativa L.). Genome 50:180–187. https://doi.org/10.1139/g06-139
Kawakatsu T, Takaiwa F (2010) Differences in transcriptional regulatory mechanisms functioning for free lysine content and seed storage protein accumulation in rice grain. Plant Cell Physiol 51:1964–1974. https://doi.org/10.1093/pcp/pcq164
Kawakatsu T, Yamamoto MP, Hirose S et al (2008) Characterization of a new rice glutelin gene GluD-1 expressed in the starchy endosperm. J Exp Bot 59:4233–4245. https://doi.org/10.1093/jxb/ern265
Khadr FH, Frey KJ (1965) Effectiveness of recurrent selection in oat breeding (Avena sativa L.). Crop Sci 5:349–354. https://doi.org/10.2135/cropsci1965.0011183X000500040020x
Khan MSS, Basnet R, Islam SA et al (2019) Mutational analysis of OsPLDα1 reveals its involvement in phytic acid biosynthesis in rice grains. J Agric Food Chem 67:11436–11443. https://doi.org/10.1021/acs.jafc.9b05052
Khanday I, Skinner D, Yang B et al (2019) A male-expressed rice embryogenic trigger redirected for asexual propagation through seeds. Nature 565:91–95. https://doi.org/10.1038/s41586-018-0785-8
Khush GS (1995) Modern varieties—their real contribution to food supply and equity. GeoJournal 35:275–284. https://doi.org/10.1007/BF00989135
Khush GS (1997) Origin, dispersal, cultivation and variation of rice. Plant Mol Biol 35:25–34. https://doi.org/10.1023/A:1005810616885
Khush GS (2007) Rice breeding for the 21st century. In: Aggarwal PK, Ladha JK, Singh RK, Devakumar C, Hardy B (eds) Science, technology, and trade for peace and prosperity. Proceedings of the 26th international rice research conference, 9–12 October 2006. International Rice Research Institute, Indian Council of Agricultural Research, and National Academy of Agricultural Sciences. Macmillan India Ltd., Los Baños (Philippines) and New Delhi (India), pp 63–76
Khush GS, Peng S (1996) Breaking the yield frontier of rice. In: Reynolds MP, Rajaram S, McNab A (eds) Increasing yield potential in wheat: breaking the barriers. International Maize and Wheat Improvement Center, Mexico, pp 36–51
Khush GS, Singh RJ, Sur SC et al (1984) Primary trisomics of rice: origin, morphology, cytology, and use in linkage mapping. Genetics 107:141–163. https://doi.org/10.1093/genetics/107.1.141
Khush GS, Virk PS (2005) IR varieties and their impacts. International Rice Research Institute, Los Baños, Philippines
Kim SI, Andaya CB, Newman JW et al (2008) Isolation and characterization of a low phytic acid rice mutant reveals a mutation in the rice orthologue of maize MIK. Theor Appl Genet 117:1291–1301. https://doi.org/10.1007/s00122-008-0863-7
Kim YA, Moon H, Park CJ (2019) CRISPR/Cas9-targeted mutagenesis of Os8N3 in rice to confer resistance to Xanthomonas oryzae pv. oryzae. Rice 12(1):67. https://doi.org/10.1186/s12284-019-0325-7
Kirk LE, Silow RA (1951) Report of the second meeting of the international rice commission's working party on rice breeding. 9–13 April. 1951, Bogor, Indonesia. FAO. (Food Agr. Organ. U.N.) Agri. Develop. Pap. 14, p 82
Koh HJ, Son YH, Heu MH et al (1999) Molecular mapping of a new genic male–sterility gene causing chalky endosperm in rice (Oryza sativa L.). Euphytica 106:57–62. https://doi.org/10.1023/a:1003575016035
Konishi S, Izawa T, Lin SY et al (2006) An SNP caused loss of seed shattering during rice domestication. Science 312:1392–1396. https://doi.org/10.1126/science.1126410
Korres NE, Norsworthy JK, Tehranchian P et al (2016) Cultivars to face climate change effects on crops and weeds: a review. Agron Sustain Dev 36:12. https://doi.org/10.1007/s13593-016-0350-5
Kuang Y, Li S, Ren B et al (2020) Base-Editing-mediated artificial evolution of OsALS1 in planta to develop novel herbicide-tolerant rice germplasms. Mol Plant 13:565–572. https://doi.org/10.1016/j.molp.2020.01.010
Kumar VVS, Verma RK, Yadav SK et al (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. https://doi.org/10.1007/s12298-020-00819-w
Kurata N (1985) Chromosome analysis of meiosis and mitosis in rice. In: Rice genetics I. International Rice Research Institute, Los Baños, Philippines, pp 143–152
Kurata N (2008) Chromosome and genome evolution in rice. In: Hirano HY, Sano Y, Hirai A, Sasaki T (eds) Rice biology in the genomics era. Biotechnology in agriculture and forestry, vol 62. Springer, Berlin. https://doi.org/10.1007/978-3-540-74250-0_18
Kurata N, Fukui K (2003) Chromosome research in genus Oryza. In: Nanda JS, Sharma SD (eds) Monograph on genus Oryza. Science Publishers, Enfield, pp 213–261
Kuwada (1910) A cytology of O. sativa L. Imp Inst Agric, New Delhi, pp 1936–1937
Ladha JK, Kirk GJD, Bennett J et al (1998) Opportunities for increased nitrogen-use efficiency from improved lowland rice germplasm. Field Crop Res 56:41–71. https://doi.org/10.1016/S0378-4290(97)00123-8
Lang NT, Subudhi PK, Virmani SS et al (1999) Development of PCR–based markers for thermosensitive genetic male sterility gene tms3(t) in rice (Oryza sativa L.). Hereditas 131:121–127. https://doi.org/10.1111/j.1601-5223.1999.00121.x
Lee DS, Chen LJ, Suh HS (2005) Genetic characterization and fine mapping of a novel thermo–sensitive genic male–sterile gene tms6 in rice (Oryza sativa L.). Theor Appl Genet 111:1271–1277. https://doi.org/10.1007/s00122-005-0044-x
Lee S, Kim SA, Lee J et al (2010) Zinc deficiency-inducible OsZIP8 encodes a plasma membrane-localized zinc transporter in rice. Mol Cell 29:551–558. https://doi.org/10.1007/s10059-010-0069-0
Li C, Zhou A, Sang T (2006) Rice domestication by reducing shattering. Science 311:1936–1939. https://doi.org/10.1126/science.1123604
Li D, Wang R, Xie C et al (2020) A recognition method for rice plant diseases and pests video detection based on deep convolutional neural network. Sensors 20:578. https://doi.org/10.3390/s20030578
Li J, Sun Y, Du J et al (2017) Generation of targeted point mutations in rice by a modified CRISPR/Cas9 system. Mol Plant 10:526–529. https://doi.org/10.1016/j.molp.2016.12.001
Li S, Yang D, Zhu Y (2007) Characterization and use of male sterility in hybrid rice breeding. J Integr Plant Biol 49:791–804. https://doi.org/10.1111/j.1744-7909.2007.00513.x
Li XY, Qian Q, Fu ZM et al (2003) Control of tillering in rice. Nature 422:618–621. https://doi.org/10.1038/nature01518
Li Y, Fan C, Xing Y et al (2014) Chalk5 encodes a vacuolar H+-translocating pyrophosphatase influencing grain chalkiness in rice. Nat Genet 46:398–404. https://doi.org/10.1038/ng.2923
Li S, Shen L, Hu P et al (2019) Developing disease-resistant thermosensitive male sterile rice by multiplex gene editing. J Integr Plant Biol 61(12):1201–1205. https://doi.org/10.1111/jipb.12774
Li YB, Fan CC, Xing YZ et al (2011) Natural variation in GS5 plays an important role in regulating grain size and yield in rice. Nat Genet 43:1266–1269. https://doi.org/10.1038/ng.977
Liang R, Qin R, Yang C et al (2019) Identification and characterization of a novel strigolactone-insensitive mutant, dwarfism with high tillering ability 34 (dhta-34) in rice (Oryza sativa L.). Biochem Genet 57:403–420. https://doi.org/10.1007/s10528-018-9896-z
Liao C, Yan W, Chen Z et al (2021) Innovation and development of the third-generation hybrid rice technology. Crop J 9:693–701. https://doi.org/10.1016/j.cj.2021.02.003
Liao S, Qin X, Luo L et al (2019) CRISPR/Cas9-induced mutagenesis of Semi-Rolled Leaf1,2 confers curled leaf phenotype and drought tolerance by influencing protein expression patterns and ROS scavenging in rice (Oryza sativa L.). Agronomy 9:728. https://doi.org/10.3390/agronomy9110728
Lin Q, Zong Y, Xue C et al (2020) Prime genome editing in rice and wheat. Nat Biotechnol 38:582–585. https://doi.org/10.1038/s41587-020-0455-x
Lin QB, Wang D, Dong H et al (2012) Rice APC/CTE controls tillering by mediating the degradation of MONOCULM 1. Nat Commun 3:752. https://doi.org/10.1038/ncomms1716
Lin SC, Yuan LP (1980) Hybrid rice breeding in China. In: IRRI (ed) Innovative approaches to rice breeding. International Rice Research Institute, Los Baños, Philippines, pp 35–51
Lin DG, Chou SY, Wang AZ et al (2014) A proteomic study of rice cultivar TNG67 and its high aroma mutant SA0420. Plant Sci 214:20–28. https://doi.org/10.1016/j.plantsci.2013.09.010
Liu E, Liu Y, Wu G et al (2016) Identification of a candidate gene for panicle length in rice (Oryza sativa L.) via association and linkage analysis. Front. Plant Sci 7(596). https://doi.org/10.3389/fpls.2016.00596
Liu Q, Han R, Wu K et al (2018) G-protein βγ subunits determine grain size through interaction with MADS-domain transcription factors in rice. Nat Commun 9(1):852. https://doi.org/10.1038/s41467-018-03047-9
Liu L, Kuang Y, Yan F et al (2021) Developing a novel artificial rice germplasm for dinitroaniline herbicide resistance by base editing of OsTubA2. Plant Biotechnol J 19:5–7. https://doi.org/10.1111/pbi.13430
Liu N, Shan Y, Wang FP et al (2001) Identification of an 85-kb DNA fragment containing pms1 a locus for photoperiod-sensitive genic male sterility in rice. Mol Gen Genomics 266:271–275. https://doi.org/10.1007/s004380100553
Liu X, Li X, Zhang X et al (2010) Genetic analysis and mapping of a thermosensitive genic male sterility gene, tms6(t), in rice (Oryza sativa L.). Genome 53:119–124. https://doi.org/10.1139/g09-092
Liu X, Qin R, Li J et al (2020) A CRISPR-Cas9-mediated domain-specific base-editing screen enables functional assessment of ACCase variants in rice. Plant Biotechnol J 18:1845–1847. https://doi.org/10.1111/pbi.13348
Liu XQ, Xu X, Tan YP et al (2004) Inheritance and molecular mapping of two fertility-restoring loci for Honglian gametophytic cytoplasmic male sterility in rice (Oryza sativa L.). Mol Gen Genomics 271:586–594. https://doi.org/10.1007/s00438-004-1005-9
Londo JP, Chiang YC, Hung KH et al (2006) Phylogeography of Asian wild rice, Oryza rufipogon, reveals multiple independent domestications of cultivated rice, Oryza sativa. Proc Natl Acad Sci U S A 20103:9578–9583. https://doi.org/10.1073/pnas.0603152103
Lopez M, Virmani S (2000) Development of TGMS lines for developing two-line rice hybrids for the tropics. Euphytica 114(3):211–215. https://doi.org/10.1023/A:1003947219699
Lu Q, Li XH, Guo D et al (2005) Localization of pms3, a gene for photoperiodsensitive genic male sterility, to a 28.4-kb DNA fragment. Mol Gen Genomics 273:507–511. https://doi.org/10.1007/s00438-005-1155-4
Lu XG, Zhang ZG, Maruyama K et al (1994) Current status of two–line method of hybrid rice breeding. In: Virmani SS (ed) Hybrid rice technology: new development and future prospects. International Rice Research Institute, Los Baños, Philippines, pp 37–49
Lu Y, Zhu JK (2017) Precise editing of a target base in the rice genome using a modified CRISPR/Cas9 system. Mol Plant 10:523–525. https://doi.org/10.1016/j.molp.2016.11.013
Lu L, Shao D, Qiu X et al (2013) Natural variation and artificial selection in four genes determine grain shape in rice. New Phytol 200(4):1269–1280. https://doi.org/10.1111/nph.12430
Luo D, Xu H, Liu Z et al (2013) A detrimental mitochondrial-nuclear interaction causes cytoplasmic male sterility in rice. Nat Genet 45:573–577. https://doi.org/10.1038/ng.2570
Lysak MA, Fransz PF, Ali HB et al (2001) Chromosome painting in Arabidopsis thaliana. Plant J 28:689–697. https://doi.org/10.1046/j.1365-313x.2001.01194.x
Ma X, Deng X, Qi L et al (2019) Fully convolutional network for rice seedling and weed image segmentation at the seedling stage in paddy fields. PLoS One 14:e0215676. https://doi.org/10.1371/journal.pone.0215676
Macovei A, Sevilla NR, Cantos C et al (2018) Novel alleles of rice eIF4G generated by CRISPR/Cas9-targeted mutagenesis confer resistance to Rice tungro spherical virus. Plant Biotechnol J 16(11):1918–1927. https://doi.org/10.1111/pbi.12927
Maeda H, Yamaguchi T, Omoteno M et al (2014) Genetic dissection of black grain rice by the development of a near isogenic line. Breed Sci 64:134–141. https://doi.org/10.1270/jsbbs.64.134
Maeda H, Murata K, Sakuma N et al (2019) A rice gene that confers broad-spectrum resistance to β-triketone herbicides. Science 365(6451):393–396. https://doi.org/10.1126/science.aax0379
Mao Y, Mao X, Zhao X et al (2003) Techniques for producing high F1 seed yield of Xieyou9308. Hybrid Rice 18:21–23. (in Chinese)
Martinez CP, Arumuganathan P, Kikuchi H et al (1994) Nuclear DNA content of ten rice species as determined by flow cytometry. Jpn J Genet 69(5):513–523. https://doi.org/10.1266/jjg.69.513
Martínez CP, Lentini Z, Châtel M et al (1997) Uso de selección recurrente en combinación con cultivos de anteras en el programa de arroz de riego del CIAT. In: Guimarães EP (ed) Selección recurrente en arroz. CIAT, Cali, Colombia, pp 139–149
Maruyama K, Araki H, Kato H (1990) Thermosensitive genetic male sterility induced by irradiation. In: Rice genetics II. International Rice Research Institute, Los Baños, Philippines, pp 227–235
Mei MH, Dai XK, Xu CG et al (1999) Mapping and genetic analysis of genes for photoperiod-sensitive genic male sterility in rice using the original mutant Nongken 58S. Crop Sci 39:1711–1715. https://doi.org/10.2135/CROPSCI1999.3961711X
Meuwissen THE, Hayes BJ, Goddard ME (2001) Prediction of total genetic value using genome-wide dense marker maps. Genetics 157:1819–1829. https://doi.org/10.1093/genetics/157.4.1819
Miao C, Xiao L, Hua K et al (2018) Mutations in a subfamily of abscisic acid receptor genes promote rice growth and productivity. Proc Natl Acad Sci U S A 115(23):6058–6063. https://doi.org/10.1073/pnas.1804774115
Min S, Cheng S, Zhu D (2002) China’s “super” rice breeding and demonstration in the rice production fields: an overview. China Rice 2:5–7. (in Chinese)
Miura K, Ikeda M, Matsubara A et al (2010) OsSPL14 promotes panicle branching and higher grain productivity in rice. Nat Genet 42:545–549. https://doi.org/10.1038/ng.592
Miyabayashi T, Nonomura KI, Kurata N (2007) Genome size determination of twenty wild Oryza species by flow cytometric and chromosome analyses. Breed Sci 57:73–78. https://doi.org/10.1270/jsbbs.57.73
Monroe JG, Arciniegas JP, Moreno JL et al (2020) The lowest hanging fruit: beneficial gene knockouts in past, present, and future crop evolution. Curr Plant Biol 24:100185. https://doi.org/10.1016/j.cpb.2020.100185
Morais Junior OP, Breseghello F, Duarte JB et al (2017) Effectiveness of recurrent selection in irrigated rice breeding. Crop Sci 57:3043–3058. https://doi.org/10.2135/cropsci2017.05.0276
Morinaga T, Fukushima E (1931) Preliminary report on the haploid plant of rice, Oryza sativa L. Proc Imp Acad 7:383–384
Mulimbayan M (1936) A comparative study of two methods of emasculating rice flowers for artificial hybridization. Philipp Agric 24:574–579
Müller D, Schopp P, Melchinger AE (2017) Persistency of prediction accuracy and genetic gain in synthetic populations under recurrent genomic selection. G3 (Bethesda) 7:801–811. https://doi.org/10.1534/g3.116.03658
Murray SS (2004) Searching for the origins of African rice domestication. Antiquity 78:1–3
NAAS (2018) Accelerating seed delivery systems for priming Indian farm productivity enhancement. A strategic view point. Strategy paper 9. National Academy of Agricultural Sciences, New Delhi, p 22
Nakamori E (1932) On the occurrence of the triploid plant of rice, Oryza sativa L. Proc Imp Acad 8:528–529
Nakamura Y, Francisco PB, Hosaka Y et al (2005) Essential amino acids of starch synthase IIa differentiate amylopectin structure and starch quality between japonica and indica rice varieties. Plant Mol Biol 58:213–227. https://doi.org/10.1007/s11103-005-6507-2
Nandi HK (1936) The chromosome morphology, secondary association and origin of cultivated rice. J Genet 33:315–336. https://doi.org/10.1007/BF02982539
Nas TMS, Sanchez DL, Diaz GQ et al (2005) Pyramiding of thermosensitive genetic male sterility (TGMS) genes and identification of a candidate tms5 gene in rice. Euphytica 145:67–75. https://doi.org/10.1007/s10681-005-0206-6
Nguchi Y (1929) Studies on the influence of external conditions on the flowering of rice plants. Jpn J Bot 4:237–276
Ohmido N, Akiyama Y, Fukui K (1998) Physical mapping of unique nucleotide sequences on identified rice chromosomes. Plant Mol Biol 38:1043–1052. https://doi.org/10.1023/a:1006062905742
Ohmido N, Fukui K (1997) Visual verification of close disposition between a rice A genome species DNA sequence (TrsA) and the telomere sequences. Plant Mol Biol 35:963–968. https://doi.org/10.1023/a:1005822504690
Ohmido N, Fukui K (2004) Recent advances in FISH analysis of plant chromosomes. Recent Res Devel Biochem 5:267–279
Ohmido N, Kijima K, Akiyama Y et al (2000) Quantification of total genomic DNA and selected repetitive sequences reveals concurrent changes in different DNA families in indica and japonica rice. Mol Gen Genet 263:388–394. https://doi.org/10.1007/s004380051182
Ohmido N, Fukui N, Kinoshita T (2010) Recent advances in rice genome and chromosome structure research by fluorescence in situ hybridization (FISH). Proc Jpn Acad Ser B 86(2):103–116. https://doi.org/10.2183/pjab.86.103
Ohtsubo H, Umeda M, Ohtsubo E (1991) Organization of DNA sequences highly repeated in tandem in rice genomes. Jpn J Genet 66:241–254. https://doi.org/10.1266/jjg.66.241
Oikawa T, Maeda H, Oguchi T et al (2015) The birth of a black rice gene and its local spread by introgression. Plant Cell 27:2401–2414. https://doi.org/10.1105/tpc.15.00310
Oka H (1957) Genic analysis for the sterility of hybrids between distantly related varieties of cultivated rice. J Genet 55(3) 397-409. https://doi.org/10.1007/BF02984059
Oka H, Wu HK (1988) Comparison of data on rice chromosomes presented by different authors. Rice Genet Newsl 5:34–41
Okazaki M, Kazama T, Murata H et al (2013) Whole mitochondrial genome sequencing and transcriptional analysis to uncover an RT102-type cytoplasmic male sterility-associated candidate gene derived from Oryza rufipogon. Plant Cell Physiol 54:1560–1568. https://doi.org/10.1093/pcp/pct102
Oliva R, Ji C, Atienza-Grande G et al (2019) Broad-spectrum resistance to bacterial blight in rice using genome editing. Nat Biotechnol 37(11):1344–1350. https://doi.org/10.1038/s41587-019-0267-z
Onogi A, Ideta O, Inoshita Y et al (2015) Exploring the areas of applicability of whole-genome prediction methods for Asian rice (Oryza sativa L.). Theor Appl Genet 128:41–53. https://doi.org/10.1007/s00122-014-2411-y
Ospina Y, Châtel M, Guimarães EP (2000) Mejoramiento poblacional del arroz de sabanas. In: Guimarães EP (ed) Avances en el mejoramiento poblacional en arroz. Embrapa Arroz e Feijão, Santo Antônio de Goiás, Brazil, pp 241–254
Ou SH (1985) Rice diseases, 2nd edn. Commonwealth Mycological Inst, Kew, pp 380
Pang Y, Chen K, Wang X et al (2017) Recurrent selection breeding by dominant male sterility for multiple abiotic stresses tolerant rice cultivars. Euphytica 213(12):268. https://doi.org/10.1007/s10681-017-2055-5
Parthasarathy N (1965) Progress report of the work of the International Rice Commission. Inter Rice Comm Newsl 14:26–34. FAO, Rome
Parthasarathy N (1972) Rice breeding in tropical Asia up to 1960. In: Rice breeding. International Rice Research Institute, Los Baños, Philippines, pp 5–29
Pathak H, Nayak AK, Jena M et al (2018) Rice research for enhancing productivity, profitability and climate resilience. ICAR National Rice Research Institute, Cuttack 753006, Odisha, India
Peng B, Kong H, Li Y et al (2014) OsAAP6 functions as an important regulator of grain protein content and nutritional quality in rice. Nat Commun 115:4847. https://doi.org/10.1038/ncomms5847
Peng HF, Chen XH, Lu YP et al (2010) Fine mapping of a gene for non–pollen type thermosensitive genic male sterility in rice (Oryza sativa L.). Theor Appl Genet 120:1013–1020. https://doi.org/10.1007/s00122-009-1229-5
Peng S, Khush GS, Cassman KG (1994) Evaluation of a new plant ideotype for increased yield potential. In: Cassman KG (ed) Breaking the yield barrier: proceedings of a workshop on rice yield potential in favourable environments. International Rice Research Institute, Los Baños, Philippines, pp 5–20
Peng S, Laza RC, Visperas RM et al (2004) Rice: progress in breaking the yield ceiling. In: New direction for a diverse planet. Proceedings of the 4th international crop science congress. September 26–October 1, 2004. Brisbane, Australia
Peng SB, Khush GS, Virk P et al (2008) Progress in ideotype breeding to increase rice yield potential. Field Crop Res 108:32–38. https://doi.org/10.1016/j.fcr.2008.04.001
Piao Z, Wang W, Wei Y et al (2018) Characterization of an acetohydroxy acid synthase mutant conferring tolerance to imidazolinone herbicides in rice (Oryza sativa). Planta 247:693–703. https://doi.org/10.1007/s00425-017-2817-2
Pinson SRM, Jia Y, Gibbons JW (2013) Three quantitative trait loci conferring resistance to kernel fissuring in rice identified by selective genotyping in two tropical japonica populations. Crop Sci 53:2434–2443. https://doi.org/10.2135/cropsci2013.03.0132
Qi P, Lin YS, Song XJ et al (2012) The novel quantitative trait locus GL3.1 controls rice grain size and yield by regulating cyclin-T13. Cell Res 22:1666–1680. https://doi.org/10.1038/cr.2012.151
Ramaiah K, Rao MBVN (1953) Rice breeding and genetics. ICAR science monograph 19. The Indian Council of Agricultural Research, New Delhi, p 360
Ramaiah K, Parthasarathy N (1938) X-ray mutation in rice. In: Proceedings of the 25th Indian science congress, vol 12, pp 212–213
Ramanujam S (1938) Cytogenetical studies in the Oryzeae. I. Chromosome studies in Oryzeae. Ann Bot 2:107–125. https://doi.org/10.1093/oxfordjournals.aob.a083989
Ramiah K (1927) Artificial hybridisation in rice. Agric J India 22:17–22
Ramiah K, Parthasarathy N, Ramanujam S (1933) Haploid plant in rice (Oryza sativa). Curr Sci 1:277–278
Ramiah K, Rao MBVN (1953) Rice breeding and genetics. ICAR science monograph 19. The Indian Council of Agricultural Research, New Delhi, p 360
Rangel PHN, Brondani C, de Morais OP et al (2007) Establishment of the irrigated rice cultivar SCSBRS Tio Taka by recurrent selection. Crop Breed Appl Biotechnol 7:103–110. https://doi.org/10.12702/1984-7033.v07n01a17
Rao AN, Chauhan BS (2015) Weeds and weed management in India—a review. In: Rao VS, Yaduraju NT, Chandrasena NR, Hassan G, Sharma AR (eds) Weed science in the Asian Pacific region. Asian Pacific Weed Science Society (APWSS) and Indian Society of Weed Science, Hyderabad, pp 87–118
Rao AN, Matsumoto H (2017) Weed management in rice in the Asian-Pacific region. Asian-Pacific Weed Science Society (APWSS); The Weed Science Society of Japan, Japan and Indian Society of Weed Science, India
Rao MJBK, Nagaraju M (1974) International Rice Commission newsletter 23. FAO, Rome, p 41
Reddy OUK, Siddiq EA, Sarma NP et al (2000) Genetic analysis of temperature–sensitive male sterility in rice. Theor Appl Genet 100:794–801
Reddy RC, Tonapi VA, Bezkorowajnyj PG et al (2007) Seeds system innovations in the semi-arid tropics of Andhra Pradesh. International Livestock Research Institute (ILRI), ICRISAT, Patancheru, Andhra Pradesh, India, p 224
Ren D, Rao Y, Huang L et al (2016) Fine mapping identifies a new QTL for brown rice rate in rice (Oryza Sativa L.). Rice 9:4. https://doi.org/10.1186/s12284-016-0076-7
Richharia RH (1962) Clonal propagation as a practical means of exploiting hybrid vigor in rice. Nature 194:598. https://doi.org/10.1038/194598a0
Rick CM (1948) Genetics and development of nine malesterile tomato mutants. Hilgardia 18:599–633. https://doi.org/10.3733/hilg.v18n17p599
Ryoo N, Yu C, Park CS et al (2007) Knockout of a starch synthase gene OsSSIIIa/Flo5 causes white-core floury endosperm in rice (Oryza sativa L.). Plant Cell Rep 26:1083–1095. https://doi.org/10.1007/s00299-007-0309-8
Sampath S, Mohanty HK (1954) Cytology of semi-sterile rice hybrid. Curr Sci 23:182–183
Sandhu N, Torres RO, Sta Cruz MT et al (2015) Traits and QTLs for development of dry direct-seeded rainfed rice varieties. J Exp Bot 66:225–244. https://doi.org/10.1093/jxb/eru413
Seetharaman R (1981) Rice improvement in India. Curr Sci 50(12):517–522
Sen SK (1963) Analysis of rice pachytene chromosomes. Nucleus 6(2):107–120
Sethi B (1937) Cytological studies in paddy varieties. Indian J Agric Sci 7:687–706
Sethi RL, Sethi BL, Mehta TR (1937) Inheritance of sheathed ear in rice. Indian J Agric Sci 7:134–148
Shan QW, Wang YP, Li J et al (2014) Genome editing in rice and wheat using the CRISPR/Cas system. Nat Protoc 9:2395–2410. https://doi.org/10.1038/nprot.2014.157
Sharma A, Satish D, Sharma S et al (2020) iRSVPred: a web server for artificial intelligence based prediction of major Basmati paddy seed varieties. Front Plant Sci 10:1791. https://doi.org/10.3389/fpls.2019.01791
Sharma SD (1982) Collection and evaluation of rice from NE India. PGR Newslett 50:62–69
Shastry SVS (1964) Is sterility genic in japonica-indica rice hybrid? In: Rice genetics and cytogenetics. Elsevier, Amsterdam, pp 154–157. https://doi.org/10.1142/9789812814302_0018
Shastry SVS, Ranga Rao DR, Misra RN (1960) Pachytene analysis in Oryza. I. Chromosome morphology in Oryza sativa. Indian J Genet 20:15–21
Shen C, Que Z, Xia Y et al (2017) Knock out of the annexin gene OsAnn3 via CRISPR/Cas9-mediated genome editing decreased cold tolerance in rice. J Plant Biol 60:539–547. https://doi.org/10.1007/s12374-016-0400-1
Shen YW, Kai QH, Gao M (1993) A new thermo sensitive radiation induced male sterile rice line. Rice Genet Newsl 10:97–98
Sheng Z, Tang L, Shao G et al (2015) The rice thermo-sensitive genic male sterility gene tms9: pollen abortion and gene isolation. Euphytica 203:145–152. https://doi.org/10.1007/s10681-014-1285-z
Shi MS (1981) Preliminary research report on breeding and utilization of the natural two-uses line in late japonica rice. Sci Agric 7:1–3
Shi MS, Deng JY (1986) The discovery, determination and utilization of the Hubei photosensitive genic male-sterile rice (Oryza sativa subsp. japonica). Acta Genet Sin 13:107–112
Shoba D, Raveendran M, Manonmani S et al (2017) Development and genetic characterization of a novel herbicide (imazethapyr) tolerant mutant in rice (Oryza sativa L.). Rice 10:10. https://doi.org/10.1186/s12284-017-0151-8
Shomura A, Izawa T, Ebana K et al (2008) Deletion in a gene associated with grain size increased yields during rice domestication. Nat Genet 40(8):1023–1028. https://doi.org/10.1038/ng.169
Si L, Chen J, Huang X et al (2016) OsSPL13 controls grain size in cultivated rice. Nat Genet 48(4):447–456. https://doi.org/10.1038/ng.3518
Siddiq EA, Ali J (1999) Innovative male sterility systems for exploitation of hybrid vigour in crop plants: I. Environment sensitive genic male sterility system. Proc Indian Natl Sci Acad B 65:331–350
Singh AK, Gopalakrishnan S, Singh VP et al (2011) Marker assisted selection: a paradigm shift in Basmati breeding. Indian J Genet Plant Breed 71(Special Issue):120–128
Singh AK, Krishnan SG (2016) Genetic improvement of basmati rice—the journey from conventional to molecular breeding. In: Rajpal V, Rao S, Raina S (eds) Molecular breeding for sustainable crop improvement. Sustainable development and biodiversity, vol 11. Springer, Cham. https://doi.org/10.1007/978-3-319-27090-6_10
Singh AK, Krishnan SG, Vinod KK et al (2019) Precision breeding with genomic tools: a decade long journey of molecular breeding in rice. Indian J Genet Plant Breed 79(1 Suppl):181–191. https://doi.org/10.31742/IJGPB.79S.1.7
Singh RJ, Ikehashi H (1981) Monogenic male-sterility in rice: introduction, identification and inheritance. Crop Sci 21:286–289. https://doi.org/10.2135/cropsci1981.0011183X002100020020x
Singh VP (1994) Quality breeding in rice. In: Singh HG, Mishra SN, Singh TB, Ram H, Singh DP (eds) Crop breeding in India. International Book Distributing Company, Lucknow, Uttar Pradesh, India, pp 117–126
Singh VP, Singh AK, Mohapatra T et al (2018) Pusa Basmati 1121—a rice variety with exceptional kernel elongation and volume expansion after cooking. Rice 11:19. https://doi.org/10.1186/s12284-018-0213-6
Song P, Wang JL, Guo XY et al (2021) High-throughput phenotyping: breaking through the bottleneck in future crop breeding. Crop J 9:633–645. https://doi.org/10.1016/j.cj.2021.03.015
Song XJ, Huang W, Shi M et al (2007) A QTL for rice grain width and weight encodes a previously unknown RING-type E3 ubiquitin ligase. Nat Genet 39:623–630. https://doi.org/10.1038/ng2014
Song XJ, Kuroha T, Ayano M et al (2015) Rare allele of a previously unidentified histone H4 acetyltransferase enhances grain weight, yield, and plant biomass in rice. Proc Natl Acad Sci U S A 112:76–81. https://doi.org/10.1073/pnas.1421127112
Sood BC, Siddiq EA (1978) A rapid technique for scent determination in rice. Indian J Genet Plant Breed 38:268–375
Sood BC, Siddiq EA, Zaman FU (1979) The mechanism of kernel elongation in rice. Indian J Genet Plant Breed 39:457–460
Spielman DJ, Kolady DE, Ward PS (2013) The prospects for hybrid rice in India. Food Sec 5:651–665. https://doi.org/10.1007/s12571-013-0291-7
Spindel J, Begum H, Akdemir D et al (2015) Genomic selection and association mapping in rice (Oryza sativa): effect of trait genetic architecture, training population composition, marker number and statistical model on accuracy of rice genomic selection in elite, tropical rice breeding lines. PLoS Genet 1711:e1004982. https://doi.org/10.1371/journal.pgen.1004982
Stein JC, Yu Y, Copetti D et al (2018) Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza. Nat Genet 50:285–296. https://doi.org/10.1038/s41588-018-0040-0
Stoskopf NC, Tomes DT, Christie BR (1993) Plant breeding: theory and practice. Westview Press, Boulder, p 550p
Sun JL, Nakagawa H, Karita S et al (1996) Rice embryo globulins: amino-terminal amino acid sequences, cDNA cloning and expression. Plant Cell Physiol 37:612–620. https://doi.org/10.1093/oxfordjournals.pcp.a028989
Sun L, Li X, Fu Y (2013) GS6, a member of the GRAS gene family, negatively regulates grain size in rice. J Integr Plant Biol 55(10):938–949. https://doi.org/10.1111/jipb.12062
Sun Y, Jiao G, Liu Z et al (2017) Generation of high-amylose rice through CRISPR/Cas9-mediated targeted mutagenesis of starch branching enzymes. Front Plant Sci 8:298. https://doi.org/10.3389/fpls.2017.00298
Sun ZX, Min SK, Xiong ZM (1989) A temperature-sensitive male-sterile line found in rice. Rice Genet Newsl 6:116–117
Suzuki Y, Nagamine T, Kobayashi A et al (1993) Detection of a new rice variety lacking lipoxygenase-3 by monoclonal antibodies. Jpn J Breed 43:405–409. https://doi.org/10.1270/jsbbs1951.43.405
Sweeney MT, Thomson MJ, Pfeil BE et al (2006) Caught red-handed: Rc encodes a basic helix-loop-helix protein conditioning red pericarp in rice. Plant Cell 18(2):283–294. https://doi.org/10.1105/tpc.105.038430
Taillebois J, Neves PCF (1989) CNA-IRAT 4, a new CMS indica rice population. Int Rice Res Notes 14:5–6
Takeda T, Suwa Y, Suzuki M et al (2003) The OsTB1 gene negatively regulates lateral branching in rice. Plant J 33:513–520. https://doi.org/10.1046/j.1365-313x.2003.01648.x
Tan L, Li X, Liu F et al (2008) Control of a key transition from prostrate to erect growth in rice domestication. Nat Genet 40:1360–1364. https://doi.org/10.1038/ng.197
Tan S, Evans RR, Dahmer ML et al (2005) Imidazolinone-tolerant crops: history, current status and future. Pest Manag Sci 61:246–257. https://doi.org/10.1002/ps.993
Tan XL, Tan YL, Zhao YH et al (2004) Identification of the Rf gene conferring fertility restoration of the CMS Dian-type 1 in rice by using simple sequence repeat markers and advanced inbred lines of restorer and maintainer. Plant Breed 123(4):338–341. https://doi.org/10.1111/j.1439-0523.2004.01004.x
Tan S, Evans R, Singh B (2006) Herbicidal inhibitors of amino acid biosynthesis and herbicide-tolerant crops. Amino Acids 30:195–204. https://doi.org/10.1007/s00726-005-0254-1
Tan ZC, Li Y, Chen B et al (1990) Studies on ecological and adaptability of dual purpose line Annong 1S. Hybrid Rice 3:35–38
Tang L, Mao B, Li Y et al (2017) Knockout of OsNramp5 using the CRISPR/Cas9 system produces low Cd-accumulating indica rice without compromising yield. Sci Rep 7:14438. https://doi.org/10.1038/s41598-017-14832-9
Tang X, Sretenovic S, Ren Q et al (2020) Plant prime editors enable precise gene editing in rice cells. Mol Plant 13:667–670. https://doi.org/10.1016/j.molp.2020.03.010
Tao C, Ming L, Zya Z et al (2013) Development and application of a functional marker associated with fertility restoring gene for BT-type cytoplasmic male sterility (CMS) in japonica rice. Chin J Rice Sci 27:259–264
Tian F, Fu Q, Zhu ZF et al (2006) Construction of introgression lines carrying wild rice (Oryza rufipogon Griff.) segments in cultivated rice (Oryza sativa L.) background and characterization of introgressed segments associated with yield-related traits. Theor Appl Genet 112:570–580. https://doi.org/10.1007/s00122-005-0165-2
Torrens JP (1930) Some experiences in rice hybridization. Philipp Agric Rev 20:261–264
Tsunoda S (1962) A developmental analysis of yielding ability in varieties of field crops. IV. Quantitative and spatial development of the stem-system. Jpn J Breed 12:49–55. https://doi.org/10.1270/jsbbs1951.12.49
Uozu S, Ohmido N, Ohtsubo H et al (1997) Repetitive sequences: cause for variation in genome size and chromosome morphology in the genus Oryza. Plant Mol Biol 35:791–799. https://doi.org/10.1023/a:1005823124989
Usman B, Nawaz G, Zhao N et al (2020) Precise editing of the OsPYL9 gene by RNA-guided Cas9 nuclease confers enhanced drought tolerance and grain yield in rice (Oryza sativa L.) by regulating circadian rhythm and abiotic stress responsive proteins. Int J Mol Sci 21:7854. https://doi.org/10.3390/ijms21217854
Usman B, Nawaz G, Zhao N et al (2021) Programmed editing of rice (Oryza sativa L.) OsSPL16 gene using CRISPR/Cas9 improves grain yield by modulating the expression of pyruvate enzymes and cell cycle proteins. Int J Mol Sci 22(1):249. https://doi.org/10.3390/ijms22010249
Vales M, Dossmann J, Borrero J (2000) Delivery of the first recurrent population with narrow genetic base. Collaborative CIAT-CIRAD sub-project. Enhancement of the genetic resources for the Latin America and the Caribbean. In: Annual report of the IP-4 rice project of CIAT. 2000. CIAT, Palmira, pp 31–36
Vales M, Dossmann J, Delgado D et al (2009) Parallel and interlaced recurrent selection (PAIRS): demonstration of the feasibility of implementing PAIRS to improve complete and partial resistance to blast (Magnaporthe grisea) and some other main traits in rice. Field Crop Res 111(1–2):173–178. https://doi.org/10.1016/j.fcr.2008.12.001
Vales MJ (2010) Some innovations in rice recurrent selection: the back recurrent selection (BCRS), the simplified and efficient rice breeding method (SERB), and the plant-parasite reciprocal recurrent selection (2P2RS). Crop Prot 29:311–317. https://doi.org/10.1016/j.cropro.2009.10.019
Vaughan DA (1994) The wild relatives of rice: a genetic resources handbook. International Rice Research Institute, Los Baños, Philippines, p 137
Vaughan DA, Lu BR, Tomooka N (2008) The evolving story of rice evolution. Plant Sci 174:394–408. https://doi.org/10.1016/j.plantsci.2008.01.016
Vinod KK, Krishnan SG, Babu NM et al (2013) Improving salt tolerance in rice: looking beyond the conventional. In: Ahmad P, Azooz MM, Prasad MNV (eds) Salt stress in plants: signalling, omics and adaptations. Springer Science+Business Media, New York. https://doi.org/10.1007/978-1-4614-6108-1_10
Vinod KK, Krishnan SG, Thribhuvan R et al (2019) Genetics of drought tolerance, mapping QTLs, candidate genes and their utilization in rice improvement. In: Rajpal V, Sehgal D, Kumar A, Raina S (eds) Genomics assisted breeding of crops for abiotic stress tolerance, vol II. Sustainable development and biodiversity, vol 21. Springer, Cham. https://doi.org/10.1007/978-3-319-99573-1_9
Virmani SS (1992) Transfer and induction of thrmo sensitive genic male sterile mutant. In: Proceedings of the second international symposium on hybrid rice, 21–25 April 1992. International Rice Research Institute, Los Baños, Philippines
Virmani SS, Sun ZX, Mou TM et al (2003) Two–line hybrid rice breeding manual. International Rice Research Institute, Los Baños, Philippines, p 88
Virmani SS, Voc PC (1991) Induction of photo– and thermosensitive genic male sterility in indica rice. Agron Abst 1991:119
Vitte C, Ishii T, Lamy F et al (2004) Genomic paleontology provides evidence for two distinct origins of Asian rice (Oryza sativa L.). Mol Gen Genomics 272:504–511. https://doi.org/10.1007/s00438-004-1069-6
Wang B, Xu WW, Wang JZ et al (1995) Tagging and mapping the thermo–sensitive genic male–sterile gene in rice (Oryza sativa L.) with molecular markers. Theor Appl Genet 91:1111–1114. https://doi.org/10.1007/BF00223928
Wang Y, Xiong G, Hu J et al (2015a) Copy number variation at the GL7 locus contributes to grain size diversity in rice. Nat Genet 47(8):944–948. https://doi.org/10.1038/ng.3346
Wang S, Li S, Liu Q et al (2015b) The OsSPL16-GW7 regulatory module determines grain shape and simultaneously improves rice yield and grain quality. Nat Genet 47(8):949–954. https://doi.org/10.1038/ng.3352
Wang F, Wang C, Liu P et al (2016) Enhanced rice blast resistance by CRISPR/Cas9-targeted mutagenesis of the ERF transcription factor gene OsERF922. PLoS One 11(4):e0154027. https://doi.org/10.1371/journal.pone.0154027
Wang C, Liu Q, Shen Y et al (2019) Clonal seeds from hybrid rice by simultaneous genome engineering of meiosis and fertilization genes. Nat Biotechnol 37:283–286. https://doi.org/10.1038/s41587-018-0003-0
Wang E, Wang J, Zhu X et al (2008) Control of rice grain-filling and yield by a gene with a potential signature of domestication. Nat Genet 40:1370–1374. https://doi.org/10.1038/ng.220
Wang S, Yang Y, Guo M et al (2020) Targeted mutagenesis of amino acid transporter genes for rice quality improvement using the CRISPR/Cas9 system. Crop J 8:457–464. https://doi.org/10.1016/j.cj.2020.02.005
Wang SK, Wu K, Yuan QB et al (2012) Control of grain size, shape and quality by OsSPL16 in rice. Nat Genet 44:950–954
Wang YG, Xing QH, Deng QY et al (2003) Fine mapping of the rice thermo–sensitive genic male–sterile gene tms5. Theor Appl Genet 107:917–921. https://doi.org/10.1007/s00122-003-1327-8
Weng J, Gu S, Wan X et al (2008) Isolation and initial characterization of GW5, a major QTL associated with rice grain width and weight. Cell Res 18:1199–1209. https://doi.org/10.1038/cr.2008.307
Woo M, Ham TH, Ji HS et al (2008) Inactivation of the UGPase1 gene causes genic male sterility and endosperm chalkiness in rice (Oryza sativa L.). Plant J 54(2):190–204. https://doi.org/10.1111/j.1365-313X.2008.03405.x
Wu Y, Zhao S, Li X et al (2018) Deletions linked to PROG1 gene participate in plant architecture domestication in Asian and African rice. Nat Commun 9(1):4157. https://doi.org/10.1038/s41467-018-06509-2
Wu W, Liu T, Zhou P et al (2019) Image analysis-based recognition and quantification of grain number per panicle in rice. Plant Methods 15:122. https://doi.org/10.1186/s13007-019-0510-0
Xing YZ, Zhang Q (2010) Genetic and molecular bases of rice yield. Annu Rev Plant Biol 61:421–442. https://doi.org/10.1146/annurev-arplant-042809-112209
Xiong X, Duan L, Liu L et al (2017) Panicle-SEG: a robust image segmentation method for rice panicles in the field based on deep learning and super pixel optimization. Plant Methods 2813:104. https://doi.org/10.1186/s13007-017-0254-7
Xu C, Wang YH, Yu YC et al (2012) Degradation of MONOCULM 1 by APC/CTAD1 regulates rice tillering. Nat Commun 3:750. https://doi.org/10.1038/ncomms1743
Xu JH, Messing J (2009) Amplification of prolamin storage protein genes in different subfamilies of the Poaceae. Theor Appl Genet 119:1397. https://doi.org/10.1007/s00122-009-1143-x
Xu R, Li J, Liu X et al (2020a) Development of plant prime-editing systems for precise genome editing. Plant Commun 1:100043. https://doi.org/10.1016/j.xplc.2020.100043
Xu R, Yang Y, Qin R et al (2016) Rapid improvement of grain weight via highly efficient CRISPR/Cas9-mediated multiplex genome editing in rice. J Genet Genomics 43:529–532. https://doi.org/10.1016/j.jgg.2016.07.003
Xu S, Zhu D, Zhang Q (2014) Predicting hybrid performance in rice using genomic best linear unbiased prediction. Proc Natl Acad Sci U S A 111:12456–12461. https://doi.org/10.1073/pnas.1413750111
Xu R, Yang Y, Qin R et al (2016) Rapid improvement of grain weight via highly efficient CRISPR/Cas9-mediated multiplex genome editing in rice. J Genet Genom 43(8):529–532. https://doi.org/10.1016/j.jgg.2016.07.003
Xu Z, Xu X, Gong Q et al (2019) Engineering broad-spectrum bacterial blight resistance by simultaneously disrupting variable TALE-binding elements of multiple susceptibility genes in rice. Mol Plant 12(11):1434–1446. https://doi.org/10.1016/j.molp.2019.08.006
Xu W, Zhang C, Yang Y et al (2020b) Versatile nucleotides substitution in plant using an improved prime editing system. Mol Plant 13:675–678. https://doi.org/10.1016/j.molp.2020.03.012
Xu Y, Lin Q, Li X et al (2021a) Fine-tuning the amylose content of rice by precise base editing of the Wx gene. Plant Biotechnol J 19(1):11–13. https://doi.org/10.1111/pbi.13433
Xu Y, Ma XM, Zhao Y et al (2021b) Genomic selection: a breakthrough technology in rice breeding. Crop J 9:669–677. https://doi.org/10.1016/j.cj.2021.03.008
Xu Y, Xu C, Xu S (2017) Prediction and association mapping of agronomic traits in maize using multiple omic data. Heredity 119:174–184. https://doi.org/10.1038/hdy.2017.27
Yamagishi T, Peng S, Cassman KG et al (1996) Studies on grain filling characteristics in “new plant type” rice lines developed in IRRI. Jpn J Crop Sci 65:169–170
Yamaguchi Y, Ikeda R, Hirasawa H et al (1997) Linkage analysis of thermosensitive genic male sterility gene, tms-2 in rice (Oryza sativa L.). Breed Sci 47:371–373. https://doi.org/10.1270/jsbbs1951.47.371
Yan WH, Liu HY, Zhou XC et al (2013) Natural variation in Ghd7.1 plays an important role in grain yield and adaptation in rice. Cell Res 23:969–971. https://doi.org/10.1038/cr.2013.43
Yan WH, Wang P, Chen HX et al (2011) A major QTL, Ghd8, plays pleiotropic roles in regulating grain productivity, plant height and heading date in rice. Mol Plant 4:319–330. https://doi.org/10.1093/mp/ssq070
Yang YC, Wang NY, Liang KJ et al (1990) Thermosensitive genic male sterile rice R59TS. Sci Agric Sin 23:90. (in Chinese)
Yang W, Peng S, Laza RC et al (2007) Grain yield and yield attributes of new plant type and hybrid rice. Crop Sci 47:1393–1400. https://doi.org/10.2135/cropsci2006.07.0457
Yang YQ, Wang L (1990) The breeding of thermosensitive male sterile rice R59TS. Sci Agric Sin 23:90
Yang Z, Gao S, Xiao F et al (2020) Leaf to panicle ratio (LPR): a new physiological trait indicative of source and sink relation in japonica rice based on deep learning. Plant Methods 16:117. https://doi.org/10.1186/s13007-020-00660-y
Ying JZ, Ma M, Bai C et al (2018) TGW3, a major QTL that negatively modulates grain length and weight in rice. Mol Plant 11(5):750–753. https://doi.org/10.1016/j.molp.2018.03.007
Yoshida S (1972) Physiological aspects of grain yield. Annu Rev Plant Physiol 23:437–464. https://doi.org/10.1146/annurev.pp.23.060172.002253
Yoshida S (1981) Fundamentals of rice crop science. The International Rice Reserves Institute, Los Baños, Philippines, p 269p
Yu J, Miao J, Zhang Z et al (2018) Alternative splicing of OsLG3b controls grain length and yield in japonica rice. Plant Biotechnol J 16(9):1667–1678. https://doi.org/10.1111/pbi.12903
Yuan H, Qin P, Hu L et al (2019) OsSPL18 controls grain weight and grain number in rice. J Genet Genomics 2046:41–51. https://doi.org/10.1016/j.jgg.2019.01.003
Yuan L (2001) Breeding of super hybrid rice. In: Peng S, Hardy B (eds) Rice research for food security and poverty alleviation. International Rice Research Institute, Los Baños, Philippines, pp 143–149
Yuan LP (1977) The execution and theory of developing hybrid rice. Chin Agric Sci 1:27–31. (In Chinese)
Yuan LP (1990) Progress of two-line system hybrid rice breeding. Sci Agric Sin 23:1–6
Yue E, Cao H, Liu B (2020) OsmiR535, a potential genetic editing target for drought and salinity stress tolerance in Oryza sativa. Plants 9:1337. https://doi.org/10.3390/plants9101337
Zeng Y, Wen J, Zhao W et al (2020) Rational improvement of rice yield and cold tolerance by editing the three genes OsPIN5b, GS3, and OsMYB30 with the CRISPR-Cas9 system. Front Plant Sci 10:1663. https://doi.org/10.3389/fpls.2019.01663
Zhang A, Liu Y, Wang F et al (2019) Enhanced rice salinity tolerance via CRISPR/Cas9-targeted mutagenesis of the OsRR22 gene. Mol Breed 39:47. https://doi.org/10.1007/s11032-019-0954-y
Zhang J, Zhang H, Botella JR et al (2018) Generation of new glutinous rice by CRISPR/Cas9-targeted mutagenesis of the Waxy gene in elite rice varieties. J Integr Plant Biol 60:369–375. https://doi.org/10.1111/jipb.12620
Zhang X, Wang J, Huang J et al (2012) Rare allele of OsPPKL1 associated with grain length causes extra-large grain and a significant yield increase in rice. Proc Natl Acad Sci U S A 109(52):21534–21539. https://doi.org/10.1073/pnas.1219776110
Zhang Z, Zeng H, Yang J et al (1994) Conditions inducing fertility alteration and ecological adaptation of photoperiod-sensitive genic male-sterile rice. Field Crop Res 38:111–120. https://doi.org/10.1016/0378-4290(94)90005-1
Zhang ZG, Yuan SC, Zen HL et al (1991) Preliminary observations of fertility changes in a new type temperature sensitive male sterile rice IVA. Hybrid Rice 1:31–34
Zhou H, Wang L, Liu G et al (2016) Critical roles of soluble starch synthase SSIIIa and granule-bound starch synthase Waxy in synthesizing resistant starch in rice. Proc Natl Acad Sci U S A 113(45):12844–12849. https://doi.org/10.1073/pnas.1615104113
Zhou C, Ye H, Hu J et al (2019) Automated counting of rice panicle by applying deep learning model to images from unmanned aerial vehicle platform. Sensors 19:3106. https://doi.org/10.3390/s19143106
Zhou H, Liu Q, Li J et al (2012) Photoperiod-and thermo-sensitive genic male sterility in rice are caused by a point mutation in a novel noncoding RNA that produces a small RNA. Cell Res 22:649–660. https://doi.org/10.1038/cr.2012.28
Zhou H, Xia D, Zhao D et al (2021) The origin of Wxla provides new insights into the improvement of grain quality in rice. J Integr Plant Biol 63:878–888. https://doi.org/10.1111/jipb.13011
Zhou H, Zhou M, Yang YZ et al (2014a) RNase ZS1 processes UbL40 mRNAs and controls thermosensitive genic male sterility in rice. Nat Commun 5:4884–4892. https://doi.org/10.1038/ncomms5884
Zhou LN, Yu HY, Zhang L et al (2014b) Rice blast prediction model based on analysis of chlorophyll fluorescence spectrum. Guang Pu Xue Yu Guang Pu Fen Xi 34:1003–1006
Zhou X, Zheng HB, Xu XQ et al (2017) Predicting grain yield in rice using multi-temporal vegetation indices from UAV-based multispectral and digital imagery. ISPRS J Photogramm Remote Sens 130:246–255. https://doi.org/10.1016/j.isprsjprs.2017.05.003
Zhou YF, Zhang XY, Xue QZ (2011) Fine mapping and candidate gene prediction of the photoperiod and thermo-sensitive genic male sterile gene pms1(t) in rice. J Zhejiang Univ Sci B 12(6):436–447. https://doi.org/10.1631/jzus.B1000306
Zhu Q, Zheng X, Luo J et al (2007) Multilocus analysis of nucleotide variation of Oryza sativa and its wild relatives: severe bottleneck during domestication of rice. Mol Biol Evol 24:875–888. https://doi.org/10.1093/molbev/msm005
Zhu BF, Si L, Wang Z et al (2011) Genetic control of a transition from black to straw-white seed hull in rice domestication. Plant Physiol 155:1301–1311. https://doi.org/10.1104/pp.110.168500
Zhu Q, Ge S (2005) Phylogenetic relationships among A-genome species of the genus Oryza revealed by intron sequences of four nuclear genes. New Phytol 167:249–267. https://doi.org/10.1111/j.1469-8137.2005.01406.x
Zou J, Chen Z, Zhang S et al (2005) Characterizations and fine mapping of a mutant gene for high tillering and dwarf in rice (Oryza sativa L.). Planta 2:604–612. https://doi.org/10.1007/s00425-005-0007-0
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Gopala Krishnan, S. et al. (2022). Rice Breeding. In: Yadava, D.K., Dikshit, H.K., Mishra, G.P., Tripathi, S. (eds) Fundamentals of Field Crop Breeding. Springer, Singapore. https://doi.org/10.1007/978-981-16-9257-4_3
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