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New quantitative trait loci for enhancing adaptation to salinity in rice from Hasawi, a Saudi landrace into three African cultivars at the reproductive stage

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Abstract

Salinity is a major constraint affecting rice productivity in rainfed and irrigated agro-ecosystems. Understanding salinity effects on rice production at the reproductive stage could improve adaptation for this trait. Identifying quantitative trait loci (QTLs) controlling adaptation to salinity may also accelerate breeding rice germplasm for environments prone to this stress. We used the salt tolerant landrace ‘Hasawi’ as a donor parent to generate three F2 offspring (consisting each of 500 individuals) with three African cultivars (‘NERICA-L-19’, ‘Sahel 108’ and ‘BG90-2’) used as recipient parents (RP). The F2s and F2:3s were evaluated for grain yield and other traits in saline fields. Salinity caused reduction in all measured traits across the F2-derived offspring, e.g. grain yield reduced between 65 and 73 %, but some offspring had twice the RP’s grain yield. QTL analysis revealed 75 QTLs for different traits in all 3 genetic backgrounds (GBs): 24 of them were common among all the 3 GBs while 31 were noted in 2 GBs, and 17 in one GB. ‘Hasawi’ contributed on average 49 % alleles to these QTLs. Two yield and yield related QTLs (qGY11 and qTN11) common in all 3 GBs were mapped on the same chromosomal segment suggesting these QTLs might be stable across different GBs. Four other QTLs were strongly associated with salinity tolerance with peak marker RM419, representing a potential candidate for MAS due to high LOD score and relatively large effect QTLs.

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Abbreviations

CIM:

Composite interval mapping

MAS:

Marker-aided selection

PCR:

Polymerase chain reaction

QTL:

Quantitative trait loci

SES:

Standard evaluation system

SMR:

Single-marker regression

SSR:

Simple sequence repeats

References

  • Al-Mssallem MQ, Hampton SM, Frost GS, Brown JE (2011) A study of Hasawi rice (Oryza sativa L.) in terms of its carbohydrate hydrolysis (in vitro) and glycaemic and insulinaemic indices (in vivo). Eur J Clin Nutr 65:627–634

    Article  PubMed  CAS  Google Scholar 

  • Ammar MHM, Pandit A, Singh RK et al (2009) Mapping of QTLs controlling Na+.K+ and CI- ion concentrations in salt tolerant indica rice variety CSR27. J Plant Biochem Biotechnol 18:139–150

    Article  CAS  Google Scholar 

  • Bimpong IK, Serraj R, Chin JH, Ramos J, Mendoza ETM, Hernandez J, Mendioro MS, Brar DS (2011) Identification of QTLs for drought-related traits in alien introgression lines derived from crosses of Rice (Oryza sativa cv IR64) × O. glaberrima under lowland drought stress. J Plant Bio 54:237–250

    Article  Google Scholar 

  • Chin JH, Kim JH, Kwon SW, Cho YI, Pia ZZ, Han LZ, Koh HJ (2003) Identification of subspecies specific RAPD markers in rice. Korean J Breed 35:102–108

    Google Scholar 

  • Claes B, Dekeyser R, Villarroel R, Vandenbulcke M, Bauw G, Van Montagu M, Caplan A (1990) Characterization of a rice gene showing organ-specific expression in response to salt stress and drought. Plant Cell 2:19–27

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  • Dellaporta SL, Wood J, Hicks JB (1983) A plant DNA minipreparation: version II. Plant Mol Bio Report 4:19–21

    Article  Google Scholar 

  • Evenson RE, Gollin D (1997) Genetic resources, international organization and improvement in rice varieties. Econ Dev Cult Change 45:471–500

    Article  Google Scholar 

  • Flowers TJ, Koyama ML, Flowers SA, Sudhakar C, Singh KP, Yeo AR (2000) QTL: their place in engineering tolerance of rice to salinity. J Exp Bot 51:99–106

    Article  PubMed  CAS  Google Scholar 

  • Hossain M, Gollin D, Cabanilla V, Cabrera E, Jonson N, Khush GS, McLaren G (2003) International research and genetic improvement and its effect on productivity: the impact of international agricultural research. In: Evenson RE, Gollin D (eds) Crop variety improvement and its effect on productivity: the impact of international agricultural research. CABI, Wallingford, pp 71–107

    Chapter  Google Scholar 

  • Islam MR, Salam MA, Hassan L, Collard BCY, Singh RK, Gregorio GB (2011) QTL mapping for salinity tolerance at seedling stage in rice. Emir J Food and Agric 23:137–146

    Google Scholar 

  • Ismail A, Tuong T (2009) Brackish water coastal zones of the monsoon tropics: challenges and opportunities. In: Haefele S, Ismail A (eds) Natural resource management for poverty reduction and environmental sustainability in rice-based systems. International Rice Research Institute, Los Banos, Philippines, pp 113–121

    Google Scholar 

  • Jones MP (1986) Genetic analysis of salt tolerance in mangrove swamp rice, in Rice genetics. In: Proceedings of the international rice genetics symposium, 27–31 May 1985, Manila, Philippines. International Rice Research Institute, Metro Manila, Philippines, pp 411–422

  • Khatun S, Rizzo CA, Flower TJ (1995) Genotypic variation in the effect of salinity on fertility in rice. Plant Soil 173:239–250

    Article  CAS  Google Scholar 

  • Lançon F, Erenstein O (2002) Potential and prospects for rice production in West Africa. In: Sub-regional workshop on harmonization of policies and coordination of programmes on rice in the ECOWAS sub-region, Accra, Ghana, 25–28 February 2002. Bouake, Côte d’Ivoire: West Africa Rice Development Association. http://www.hubrural.org/IMG/pdf/potential-and-prospects-for-rice-production-wa.pdf

  • Lang NT, Yanagihara SS, Buu BC (2001) QTL analysis of salt tolerance in rice (Oryza sativa L.) SABRAO. J. Breed Genet 33:11–20

    Google Scholar 

  • Lin HX, Zhu MZ, Yano M, Gao JP, Liang ZW, Su WA, Hu XH, Ren ZH, Chao DY (2004) QTLs for Na+ and K+ uptake of the shoots and roots controlling rice salt tolerance. Theor Appl Genet 108:253–260

    Article  PubMed  CAS  Google Scholar 

  • Lutts S, Kinet JM, Bouhamont J (1995) Changes in plant response to NaCI during development of rice (Oryza sativa L.) Varieties differing in salinity resistance. J Exp Bot 46:1843–1852

    Article  CAS  Google Scholar 

  • Maas EV, Hoffiman GJ (1997) Crop salt tolerance-current assessment. J Irrig Drain Div ASCE 103(IR2):115–134

    Google Scholar 

  • Mahmood IA, Quereshi RH, Aslam M (1999) Yield and quality of different rice (Oryza sativa L.) varieties as affected by soil salinity. Pak J Bot 31:475–479

    Google Scholar 

  • McCouch SR, Cho YG, Yano M et al (1997) Report on QTL nomenclature. Rice Genet Newsl 14:11

    Google Scholar 

  • McCouch S, Teytelman L, Xu Y et al (2002) Development of 2,240 new SSR markers for rice (Oryza sativa L.). DNA Res 9:199–207

    Article  PubMed  CAS  Google Scholar 

  • Moradi F, Ismail AM (2007) Responses of photosynthesis, chlorophyll fluorescence and ROS scavenging system to salt stress during seeding and reproductive stage in rice. Ann Bot 99:1161–1173

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  • Nakhoda B, Leung H, Mendioro MS, Mohammadi-nejad G, Ismail AM (2012) Isolation, characterization, and field evaluation of rice (Oryza sativa L., var. IR64) mutants with altered responses to salt stress. Field Crops Res 127:191–202

    Article  Google Scholar 

  • Negrao S, Courtois B, Ahmadi N, Abreu I, Saibo N, Oliveira MM (2011) Recent updates on salinity stress in rice: from physiological to molecular responses. Crit Rev Plant Sci 30:329–377

    Article  CAS  Google Scholar 

  • Nelson JC (1997) QGENE: software for marker-based genomic analysis and breeding. Mol Breed 3:239–245

    Article  CAS  Google Scholar 

  • Neraja CN, Maghirang-Rodriguez R, Pamplona A, Heuer S, Collard BCY, Septiningsih EM, Vergara G, Sanchez D, Xu K, Ismail AM et al (2007) A marker-assisted backcross approach for developing submergence-tolerant rice cultivars. Theor Appl Genet 115:767–776

    Article  Google Scholar 

  • Reddy MP, Sarla N, Laxminarayana SN, Reddy V, Siddiq EA (2005) Identification and mapping of yield and yield related QTLs from an Indian accession of Oryza rufipogon. BMC Genet 6:33

    PubMed  PubMed Central  Google Scholar 

  • Ren ZH, Gao JP, Li LG, Cai XL, Huang W, Chao DY, Zhu MZ, Wang ZY, Luan S, Lin HX (2005) A rice quantitative trait locus for salt tolerance encodes a sodium transporter. Nat Genet 37:1141–1146

    Article  PubMed  CAS  Google Scholar 

  • Sabouri H, Sabouri A (2009) New evidence of QTLs attributed to salinity tolerance in rice. Afr J Biotechnol 7:4376–4383

    Google Scholar 

  • Sabouri H, Reizai AM, Mouomeni A, Kavoussi M, Sabouri A (2009) QTLs mapping of physiological traits related to salt tolerance in young rice seedlings. Biol Plant 53:657–662

    Article  Google Scholar 

  • SAS Institute Inc (2004) SAS/STAT® 9.2 user’s guide. SAS Institute Inc, Cary, North Carolina

    Google Scholar 

  • Septiningsih EM, Pamplona AM, Sanchez DL, Neeraja CN, Vergara GV, Heuer S, Ismail AM, Mackill DJ (2009) Development of submergence tolerant rice cultivars: the Sub1 locus and beyond. Ann Bot 103:151–160

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  • Singh SP (1999) Developments in plant breeding: common bean improvement in the twenty-first century. Kluwer Academic Publishers, Dordrecht

    Google Scholar 

  • Singh RK, Flower TJ (2010) The physiology and molecular biology of the effects of salinity on rice. In: Pessarakli M (ed) Handbook of plant and crop stress, 3rd edn. Taylor and Francis, Boca Raton, Florida

    Google Scholar 

  • Takehisa H, Shimodate T, Fukuta Y, Ueda T, Yano M, Yamaya T, Kameya T, Sato T (2004) Identification of quantitative trait loci for plant growth of rice in paddy field flooded with salt water. Field Crops Res 89:85–95

    Article  Google Scholar 

  • Temnykh S, DeClerck G, Lukashova A, Lipovich L, Cartinhour S, McCouch S (2001) Computational and experimental analysis of microsatellites in rice (Oryza sativa L.): frequency, length variation, transposon associations and genetic marker potential. Genome Res 11:1441–1452

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  • Thomson M, de Ocampo M, Egdane J et al (2010) Characterizing the Saltol quantitative trait locus for salinity tolerance in rice. Rice 3:148–160

    Article  Google Scholar 

  • Xu YB, Crouch JH (2008) Maker-assisted selection in plant breeding from publications to practice. Crop Sci 48:391–407

    Article  Google Scholar 

  • Zang J, Sun Y, Wang Y et al (2008) Dissection of genetic overlap of salt tolerance QTLs at the seedling and tillering stages using backcross introgression lines in rice. Sci China Ser C Life Sci 51:583–591

    Article  Google Scholar 

  • Zeng L, Shannon MC, Grieve CM (2002) Evaluation of salt tolerance in rice genotypes by multiple agronomic parameters. Euphytica 127:235–245

    Article  CAS  Google Scholar 

Download references

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Authors and Affiliations

  1. Africa Rice Centre, Sahel Regional Station, B.P 96, Saint Louis, Senegal

    Isaac Kofi Bimpong, Baboucarr Manneh, Bathe Diop, Kanfany Ghislain, Abdulai Sow & Nana Kofi Abaka Amoah

  2. International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, Philippines

    Glenn Gregorio & Rakesh Kumar Singh

  3. Department of Plant Breeding, Swedish University of Agricultural Sciences (SLU), Box 101, 23053, Alnarp, Sweden

    Rodomiro Ortiz

  4. Africa Rice Centre, 01 BP 2031, Cotonou, Benin

    Marco Wopereis

Authors
  1. Isaac Kofi Bimpong
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  2. Baboucarr Manneh
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  3. Bathe Diop
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  4. Kanfany Ghislain
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  5. Abdulai Sow
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  6. Nana Kofi Abaka Amoah
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  7. Glenn Gregorio
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  8. Rakesh Kumar Singh
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  9. Rodomiro Ortiz
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  10. Marco Wopereis
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Correspondence to Isaac Kofi Bimpong.

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Bimpong, I.K., Manneh, B., Diop, B. et al. New quantitative trait loci for enhancing adaptation to salinity in rice from Hasawi, a Saudi landrace into three African cultivars at the reproductive stage. Euphytica 200, 45–60 (2014). https://doi.org/10.1007/s10681-014-1134-0

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  • DOI: https://doi.org/10.1007/s10681-014-1134-0

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