Validation of QTLs in Bangladeshi rice landrace Horkuch responsible for salt tolerance in seedling stage and maturation

• Autorzy: Noor A.U.Z. , Jewel G.M.N.A. , Haque T. , Elias S.M. , Biswas S. , Rahman M.S. , Seraj Z.I.
• Języki publikacji: EN

Abstrakty

EN

The upsurge in global temperatures and the increasing threat of salinity are adversely affecting rice productivity in the southern coastal lands of Bangladesh. A Bangladeshi rice landrace Horkuch, adapted to these saline conditions, has long been cultivated by farmers in this region. To understand the trend and heritability of its tolerance traits, a reciprocal population of Horkuch with the high-yielding sensitive rice IR29 was generated for mapping of quantitative trait loci (QTLs) at both seedling and reproductive stages in an F2:3 strategy using double-digest restriction associated DNA. We found 29 QTLs and some QTL clusters containing survival and yield-related QTLs showing pleiotropic effects over some phenotypes. We advanced the generation up to F₅ to obtain homozygosity and our current work is aimed at confirming these mapped QTLs at F₅ by salt stress physiological tests at both stages as well as DNA markers linked to these QTLs. We confirmed SES QTL (survival of seedling under stress) associated with SSR marker RM25789 and two QTL clusters at chromosome 10 and 11 associated with RM26964 and RM27027, respectively. One cluster harbored yield-related filled grain number, filled grain weight, total grain number, harvest index, ionic balance and transpiration-related total sodium, total potassium and stomatal conductance QTLs. The other cluster contained total grain weight, filled grain weight and seedling root relative water content QTLs. We identified some individuals based on their physiological performance under stress as well as the presence of QTLs associated with some SSR markers that can be used for breeding and production of highly salt-tolerant cultivars with high yield.

• Wydawca: -
• Czasopismo: Acta Physiologiae Plantarum
• Rocznik: 2019
• Tom: 41
• Numer: 10
• Opis fizyczny: Article 173 [15p.], fig.,ref.

Twórcy

autor

Noor A.U.Z.

• Plant Biotechnology Laboratory, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh

autor

Jewel G.M.N.A.

• Plant Biotechnology Laboratory, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
• Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet 3114, Bangladesh

autor

Haque T.

• Plant Biotechnology Laboratory, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh

autor

Elias S.M.

• Plant Biotechnology Laboratory, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh

autor

Biswas S.

• Plant Biotechnology Laboratory, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh

autor

Rahman M.S.

• Plant Physiology Division, Bangladesh Rice Research Institute, Gazipur, Bangladesh

autor

Seraj Z.I.

• Plant Biotechnology Laboratory, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh

Bibliografia

• Abdullah Z, Khan MA, Flowers T (2001) Causes of sterility in seed set of rice under salinity stress. J Agron Crop Sci 187:25–32
• Akinwale M, Gregorio G, Nwilene F, Akinyele B, Ogunbayo S, Odiyi A (2011) Heritability and correlation coefficient analysis for yield and its components in rice (Oryza sativa L.). Afr J Plant Sci 5:207–212
• Ashikari M, Ma JF (2015) Exploring the power of plants to overcome environmental stresses. Rice 8:10. https://doi.org/10.1186/s12284-014-0037-y
• Broman KW, Wu H, Sen Ś, Churchill GA (2003) R/qtl: QTL mapping in experimental crosses. Bioinformatics 19:889–890
• Chowdhury A, Haque M, Hoque M, Rokonuzzaman M (2012) Adoption of BRRI Dhan47 in the Coastal Saline areas of Bangladesh. Agric J 7:286–291
• Dasgupta S, Hossain MM, Huq M, Wheeler D (2014) Climate change, soil salinity, and the economics of high-yield rice production in coastal Bangladesh. The World Bank
• Elias SM, Rahman MS, Khan SF, Biswas S, Haque T, Razzaque S (2019) Combination of traits at two developmental stages under salt stress as a measure of tolerance in a reciprocally crossed rice (Oryza sativa L.) population. Crop and Pasture Science (under review)
• De Leon TB, Linscombe S, Gregorio G, Subudhi PK (2015) Genetic variation in Southern USA rice genotypes for seedling salinity tolerance. Front Plant Sci. https://doi.org/10.3389/fpls.2015.00374
• De Leon TB, Linscombe S, Subudhi PK (2016) Molecular dissection of seedling salinity tolerance in rice (Oryza sativa L.) using a high-density GBS-based SNP linkage map. Rice 9:52
• De Leon TB, Linscombe S, Subudhi PK (2017) Identification and validation of QTLs for seedling salinity tolerance in introgression lines of a salt tolerant rice landrace ‘Pokkali’. PLoS One 12:e0175361
• Dechaine JM, Brock MT, Weinig C (2014) QTL architecture of reproductive fitness characters in Brassica rapa. BMC Plant Biol 14:66
• Doyle JJ, Doyle JL (1990) Isolation of plant DNA from fresh tissue. Focus 12:13–15
• Frouin J et al (2018) Tolerance to mild salinity stress in japonica rice: a genome-wide association mapping study highlights calcium signaling and metabolism genes. PLoS One 13:e0190964
• Gomez KA (2001) Rice, the grain of culture. The Siam Society, Bangkok
• Gregorio GB, Senadhira D, Mendoza RD (1997) Screening rice for salinity tolerance. IRRI discussion paper series No. 22
• Haque SA (2006) Salinity problems and crop production in Coastal Regions of Bangladesh. Pak J Bot 38:1359–1365
• Hu SP et al (2009) Correlation and quantitative trait loci analyses of total chlorophyll content and photosynthetic rate of rice (Oryza sativa) under water stress and well-watered conditions. J Integr Plant Biol 51:879–888
• Ishimaru K et al (2001) Toward the mapping of physiological and agronomic characters on a rice function map: QTL analysis and comparison between QTLs and expressed sequence tags TAG. Theor Appl Genet 102:793–800
• Islam M, Sarker M, Sharma N, Rahman M, Collard B, Gregorio G, Ismail A (2016) Assessment of adaptability of recently released salt tolerant rice varieties in coastal regions of South Bangladesh. Field Crops Res 190:34–43
• Jiang G-H, He Y-Q, Xu C-G, Li X-H, Zhang Q (2004) The genetic basis of stay-green in rice analyzed in a population of doubled haploid lines derived from an indica by japonica cross. Theor Appl Genet 108:688–698
• Kawasaki S et al (2001) Gene expression profiles during the initial phase of salt stress in rice. Plant Cell 13:889–905
• Kearsey M, Farquhar A (1998) QTL analysis in plants; where are we now? Heredity 80:137–142
• Kumar V et al (2015) Genome-wide association mapping of salinity tolerance in rice (Oryza sativa). DNA Res 22:133–145
• Lisa LA et al (2004) Genetic variation in microsatellite DNA, physiology and morphology of coastal saline rice (Oryza sativa L.) landraces of Bangladesh. Plant and Soil 263:213–228
• Lisa LA et al (2011) Physiology and gene expression of the rice landrace Horkuch under salt stress. Funct Plant Biol 38:282–292
• Moradi F, Ismail AM (2007) Responses of photosynthesis, chlorophyll fluorescence and ROS-scavenging systems to salt stress during seedling and reproductive stages in rice. Ann Bot 99:1161–1173
• Moradi F, Ismail A, Gregorio G, Egdane J (2003) Salinity tolerance of rice during reproductive development and association with tolerance at the seedling stage. Indian J Plant Physiol 8:105–116
• Nutan KK, Kushwaha HR, Singla-Pareek SL, Pareek A (2017) Transcription dynamics of Saltol QTL localized genes encoding transcription factors, reveals their differential regulation in contrasting genotypes of rice. Funct Integr Genom 17:69–83
• Pang Y, Chen K, Wang X, Wang W, Xu J, Ali J, Li Z (2017) Simultaneous improvement and genetic dissection of salt tolerance of rice (Oryza sativa L.) by designed QTL pyramiding. Front Plant Sci 8:1275
• Parida AK, Das AB (2005) Salt tolerance and salinity effects on plants: a review. Ecotoxicol Environ Saf 60:324–349
• Peterson BK, Weber JN, Kay EH, Fisher HS, Hoekstra HE (2012) Double digest RADseq: an inexpensive method for de novo SNP discovery and genotyping in model and non-model species. PLoS One 7:e37135
• Pires IS, Negrão S, Oliveira MM, Purugganan MD (2015) Comprehensive phenotypic analysis of rice (Oryza sativa) response to salinity stress. Physiol Plant 155:43–54
• Rahman MA, Thomson MJ, Shah-E-Alam M, de Ocampo M, Egdane J, Ismail AM (2016) Exploring novel genetic sources of salinity tolerance in rice through molecular and physiological characterization. Ann Bot 117(6):1083–1097
• Razzaque S, Khan S, Jewel N, Haque T, Elias S, Rahman S, Seraj Z (2016) Genetic analysis of SSR markers in F₂ reciprocal populations of the rice genotypes, Horkuch and IR29 show high segregation distortion. Biores Commun 2:219–229
• Razzaque S et al (2017) Reproductive stage physiological and transcriptional responses to salinity stress in reciprocal populations derived from tolerant (Horkuch) and susceptible (IR29) rice. Sci Rep 7:46138
• Rieseberg LH, Archer MA, Wayne RK (1999) Transgressive segregation, adaptation and speciation. Heredity 83:363–372
• Seck PA, Diagne A, Mohanty S, Wopereis MCS (2012) Crops that feed the world 7: Rice. Food Secur 4:7–24. https://doi.org/10.1007/s12571-012-0168-1
• Singh R, Flowers TJ (2010) The physiology and molecular biology of the effects of salinity on rice. In: Handbook of plant and crop stress, pp 901–942
• Singh VK et al. (2018) Marker-Assisted Introgression of Saltol QTL Enhances Seedling Stage Salt Tolerance in the Rice Variety “Pusa Basmati 1” International journal of genomics 2018
• Waziri A, Kumar P, Purty R (2016) Saltol QTL and their role in salinity tolerance in rice. Austin J Biotechnol Bioeng 3:1067–1072
• Xie W, Wu L, Zhang Y, Wu T, Li X, Ouyang Z (2017) Effects of straw application on coastal saline topsoil salinity and wheat yield trend. Soil Tillage Res 169:1–6
• Yesmin N, Elias SM, Rahman MS, Haque T, Mahbub Hasan A, Seraj ZI (2014) Unique genotypic differences discovered among indigenous Bangladeshi rice landraces. Int J Genom. https://doi.org/10.1155/2014/210328
• Yoshida S, Forno D, Cock J, Gomez K (1976) Laboratory manual for physiological studies of rice. International Rice Research Institute, Manila
• Zhang Y-M, Xu S (2004) Mapping quantitative trait loci in F₂ incorporating phenotypes of F₃ progeny. Genetics 166:1981–1993

Identyfikatory

DOI

10.1007/s11738-019-2963-1