Revealing Genetic Relationship and Prospecting of Novel Donors Among Upland Rice Genotypes Using qDTY-Linked SSR Markers
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摘要
A total of 17 simple sequence repeat(SSR) markers linked to QTLs(qDTYs) governing grain yield under reproductive stage(RS) drought stress were used to assess the genetic relationship and prospecting new donors for q DTYs among 32 popular upland rice genotypes. These SSR markers generated a total of 36 alleles with an average allele count of 2.1 per locus. Polymorphic information content value of the markers ranged from 0.376 to 0.662 with an average value of 0.484. The expected heterozyogosity ranged from 0.381 to 0.632. STRUCTURE analysis divided the 32 genotypes into three sub-populations. Subsequent phenotyping revealed that all the tolerant genotypes were grouped into one sub-population, whereas the moderately tolerant and susceptible genotypes were grouped into separate sub-populations. Phylogenetic tree constructed by the unweighted neighbour-joining method also divided the genotypes into three clusters. The grouping pattern of genotypes into the clusters was similar to that into the STRUCTURE analysis, on the basis of drought tolerance level. The average value of genetic dissimilarity coefficient among the genotypes was observed to be 0.486. Furthermore, by combining genotyping data with phenotyping data, 16 new donors for 6 qDTYs were identified.
A total of 17 simple sequence repeat(SSR) markers linked to QTLs(qDTYs) governing grain yield under reproductive stage(RS) drought stress were used to assess the genetic relationship and prospecting new donors for q DTYs among 32 popular upland rice genotypes. These SSR markers generated a total of 36 alleles with an average allele count of 2.1 per locus. Polymorphic information content value of the markers ranged from 0.376 to 0.662 with an average value of 0.484. The expected heterozyogosity ranged from 0.381 to 0.632. STRUCTURE analysis divided the 32 genotypes into three sub-populations. Subsequent phenotyping revealed that all the tolerant genotypes were grouped into one sub-population, whereas the moderately tolerant and susceptible genotypes were grouped into separate sub-populations. Phylogenetic tree constructed by the unweighted neighbour-joining method also divided the genotypes into three clusters. The grouping pattern of genotypes into the clusters was similar to that into the STRUCTURE analysis, on the basis of drought tolerance level. The average value of genetic dissimilarity coefficient among the genotypes was observed to be 0.486. Furthermore, by combining genotyping data with phenotyping data, 16 new donors for 6 qDTYs were identified.
A total of 17 simple sequence repeat(SSR) markers linked to QTLs(qDTYs) governing grain yield under reproductive stage(RS) drought stress were used to assess the genetic relationship and prospecting new donors for q DTYs among 32 popular upland rice genotypes. These SSR markers generated a total of 36 alleles with an average allele count of 2.1 per locus. Polymorphic information content value of the markers ranged from 0.376 to 0.662 with an average value of 0.484. The expected heterozyogosity ranged from 0.381 to 0.632. STRUCTURE analysis divided the 32 genotypes into three sub-populations. Subsequent phenotyping revealed that all the tolerant genotypes were grouped into one sub-population, whereas the moderately tolerant and susceptible genotypes were grouped into separate sub-populations. Phylogenetic tree constructed by the unweighted neighbour-joining method also divided the genotypes into three clusters. The grouping pattern of genotypes into the clusters was similar to that into the STRUCTURE analysis, on the basis of drought tolerance level. The average value of genetic dissimilarity coefficient among the genotypes was observed to be 0.486. Furthermore, by combining genotyping data with phenotyping data, 16 new donors for 6 qDTYs were identified.
引文
Adhya T K,Singh O N,Swain P,Ghosh A.2008.Rice in Eastern India:Causes for low productivity and available options.J Rice Res,2:1-5.
Agricultural Statistics at a Glance.2014.Government of India Ministry of Agriculture Department of Agriculture&Cooperation Directorate of Economics&Statistics:63.
Ahmad R,Quadir S,Ahmad N,Shah K H.2003.Yield potential and stability of nine wheat varieties under water stress conditions.Int J Agric Biol,5(1):7-9.
Ali M L,McClung A M,Jia M H,Kimball J A,McCouch S R,Georgia C E.2011.A rice diversity panel evaluated for genetic and agro-morphological diversity between subpopulations and its geographic distribution.Crop Sci,51(5):2021-2035.
Anderson J A,Churchill G A,Autrique J E,Tanksley S D,Sorrels M E.1993.Optimizing parental selection for genetic maps.Genome,36(1):181-186.
Barik Madhusmita,Dash S K,Padhi S,Swain P.2017.Effect of drought on morpho-physiological,yield and yield traits of chromosome segment substitution lines(CSSLs)derived from wild species of rice.Oryza,54(1):65-72.
Bernier J,Kumar A,Ramaiah V,Spaner D,Atlin G.2007.Alarge-effect QTL forgrain yield under reproductive-stage drought stress in upland rice.Crop Sci,47(2):507-516.
Boonjung H,Fukai S.1996.Effects of soil water deficit at different growth stage on rice growth and yield under upland conditions:2.Phenology,biomass production and yield.Field Crops Res,48(1):47-55.
Botstein D,White R L,Skolnick M,Davis R W.1980.Construction of a genetic linkage map in man using restriction fragment length polymorphism.Am J Hum Genet,32(3):314-331.
Chakhonkaen S,Pitnjam K,Saisuk W,Ukoskit K,Muangprom A.2012.Genetic structure of Thai rice and rice accessions obtained from the international rice research institute.Rice,5:19.
Courtois B,Frouin J,Greco R,Bruschi G,Droc G,Hamelin C,Ruiz M,Clément G,Evrard J C,van Coppenole S,Katsantonis D,Oliveira M,Negrao S,Matos C,Cavigiolo S,Lupotto E,Piffanelli P,Ahmadi N.2012.Genetic diversity and population structure in a European collection of rice.Crop Sci,52(4):1663-1675.
Das B,Sengupta S,Parida S K,Roy B,Ghosh M,Prasad M,Ghose T K.2013.Genetic diversity and population structure of rice landraces from Eastern and North Eastern States of India.BMCGenet,14:71-84.
Dixit S,Swamy B P M,Vikram P,Ahmed H U,Sta Cruz M T,Amante M,Atri D,Leung H,Kumar A.2012a.Fine mapping of QTLs for rice grain yield under drought reveals sub-QTLs conferring a response to variable drought severities.Theor Appl Genet,125(1):155-169.
Dixit S,Swamy B P M,Vikram P,Bernier J,Sta Cruz M T,Amante M,Atri D,Kumar A.2012b.Increased drought tolerance and wider adaptability of qDTY12.1 conferred by its interaction with qDTY2.3 and qDTY3.2.Mol Breeding,30:1767-1779.
Evanno G,Regnaut S,Goudet J.2005.Detecting the number of clusters of individuals using the software STRUCTURE:Asimulation study.Mol Ecol,14(8):2611-2620.
Fischer R A,Maurer R.1978.Drought resistance in spring wheat cultivars:I.Grain yield responses in spring wheat.Aust J Agric Res,29(5):892-912.
Gao L Z.2005.Microsatellite diversity and population genetic structure of an endangered wild rice,Oryza officinalis(Poaceae)from China.Mol Ecol,14(14):4287-4297.
Ghimire K H,Quiatchon-Baeza L A,Vikram P,Swamy B P M,Dixit S,Ahmed H U,Hernandez J E,Borromeo T H,Kumar A.2012.Identification and mapping of QTL(q DTY1.1)with a consistent effect on grain yield under drought.Field Crops Res,131:88-96.
IRRI.2017.Trends in global rice consumption.http://irri.org/ricetoday/trends-in-global-rice-consumption.
Kumar A,Verulkar S B,Dixit S,Chauhan B,Bernier J,Venuprasad R,Zhao D,Shrivastava M N.2009.Yield and yield-attributing traits of rice(Oryza sativa L.)under lowland drought and suitability of early vigor as a selection criterion.Field Crops Res,114(1):99-107.
Mishra K K,Vikram P,Yadaw R B,Swamy B P M,Dixit S,Sta Cruz M T S,Maturan P,Marker S,Kumar A.2013.qDTY12.1:A locus with consistent effect on grain yield under drought in rice.BMC Genet,14:12-21.
Nagaraju J,Kathirvel M,Kumar R R,Siddiq E A,Hasnain S E.2002.Genetic analysis of traditional and evolved Basmati and nonBasmati rice varieties by using fluorescence-based ISSR-PCRand SSR markers.Proc Natl Acad Sci USA,99:5836-5841.
Nei M.1972.Genetic distance between populations.Am Nat,106:283-292.
Pachauri V,Taneja N,Vikram P,Singh N K,Singh S.2013.Molecular and morphological characterization of India farmers rice varieties.Aust J Crop Sci,7(7):923-932.
Peakall R,Smouse P E.2006.GENALEX 6:Genetic analysis in Excel:Population genetic software for teaching and research.Mol Ecol Notes,6:288-295.
Peakall R,Smouse P E.2012.GenAlEx 6.5:Genetic analysis in Excel:Population genetic software for teaching and research:An update.Bioinformatics,28:2537-2539.
Perrier X,Flori A,Bonnot F.2003.Data analysis methods.In:Hamon P,Seguin M,Perrier X,Glaszmann J C.Genetic diversity of cultivated tropical plants.Montpellier France:Enfield(Science Publishers):43-76.
Perrier X,Jacquemoud-Collet J P.2006.DARwin software http://darwin.cirad.fr/darwin[2017/10/15].
Pradhan S K,Barik S R,Sahoo A,Mohapatra S,Nayak D K,Mahender A,Meher J,Anandan A,Pandit E.2016.Population structure,genetic diversity and molecular marker-trait association analysis for high temperature stress tolerance in rice.PLoS One,11:e0160027.
Pritchard J K,Stephens M,Donnelly P.2000.Inference of population structure using multilocus genotype data.Genetics,155(2):945-959.
Rai M.2003.Genetic diversity in rice production:Past contribution and the potential of utilization for sustainable rice production.In:Tran D V,Duffy R.Sustainable Rice Production for Food Security:Proceedings of the 20th session of the International Rice Commission.Bangkok,United Nations:Food and Agricultural Organization.
Ramadan E A,Elmoghazy A M,El-Mowafi H F.2015.Molecular markers based genetic diversity analysis for drought tolerance in rice(Oryza sativa L.)using SSR markers.Int J Sci Res Agric Sci,2:137-146.
Ricepedia.2017.The online authority on rice:Rice productivity.http://ricepedia.org/rice-as-a-crop/rice-productivity.
Roy S,Bannerjee A,Mawkhlieng B,Misra A K,Pattanayak A,Harish G D,Singh S K,Ngachan S V,Bansal K C.2015.Genetic diversity and population structure in aromatic and quality rice(Oryza sativa L.)landraces from North Eastern India.PLoS One,10:e0129607.
Salem K F M,Sallam A.2016.Analysis of population structure and genetic diversity of Egyptian and exotic rice(Oryza sativa L.)genotypes.CR Biolog,339(1):1-9.
Shamsudin N A A,Swamy B P M,Ratnam W,Sta Cruz M T,Raman A,Kumar A.2016.Marker assisted pyramiding of drought QTLs into a popular Malaysian rice cultivar MR219.BMC Genet,17:30-43.
Shodhganga.2017.Abstract.http://shodhganga.inflibnet.ac.in/bitstream/10603/169176/9/09_abstract.pdf[2017/11/17].
Siddiq E A.2000.Bridging the rice yield gap in India.In:Papademetriou M K,Dent F J,Herath E M.Bridging the Rice Yield Gap in Asia and Pacific Regions.Bangkok,United Nations:Food and Agricultural Organization:84-111.
Sika K C,Kefela T,Sagbadja H A,Ahoton L,Saidou A,BabaMoussa L,Baptiste L J,Kotconi S O,Gachomo E W.2015.A simple and efficient genomic DNA extraction protocol for large scale genetic analyses of plant biological systems.Plant Gene,1:43-45.
Singh N,Choudhury D R,Singh A K,Kumar S,Srinivasan K,Tyagi R K,Singh N K,Singh R.2013.Comparison of SSR and SNP markers in estimation of genetic diversity and population structure of Indian rice varieties.PLoS One,8:e84136.
Singh N,Choudhury D R,Tiwari G,Singh A K,Kumar S,Srinivasan K,Tyagi R K,Sharma A D,Singh N K,Singh R.2016.Genetic diversity trend in Indian rice varieties:An analysis using SSR markers.BMC Genet,17:127-139.
Swamy B P M,Ahmed H U,Henry A,Mauleon R,Dixit S,Vikram P,Tilatto R,Verulkar S B,Perraju P,Mandal N P,Variar M,Robin S,Chandrababu R,Singh O N,Dwivedi J L,Das S P,Mishra KK,Yadaw R B,Aditya T L,Karmakar B,Satoh K,Moumeni A,Kikuchi S,Leung H,Kumar A.2013.Genetic,physiological,and gene expression analyses reveal that multiple QTL enhance yield of rice mega-variety IR64 under drought.PLoS One,8:e62795.
Swamy B P M,Shamsudin N A A,Rahman S N A,Mauleon R,RatnamW,Sta Cruz M T,Kumar A.2017.Association mapping of yield and yield-related traits under reproductive stage drought stress in rice(Oryza sativa L.).Rice,10:21-33.
Tarang A,Gashti A B.2016.The power of microsatellite markers and AFLPs in revealing the genetic diversity of Hashemi aromatic rice from Iran.J Int Agric,15(6):1186-1197.
Venuprasad R,Lafitte H R,Atlin G N.2007.Response to direct selection for grain yield under drought stress in rice.Crop Sci,47:285-293.
Venuprasad R,Sta Cruz M T,Amante M,Magbanua R,Kumar A,Atlin G A.2008.Response to two cycles of divergent selection for grain yield under drought stress in four rice breeding populations.Field Crops Res,107(3):232-244.
Verulkar S B,Mandal N P,Dwivedi J L,Singh B N,Sinha P K,Mahato R N,Dongre P,Singh O N,Bose L K,Swain P,Robin S,Chandrababu R,Senthil S,Jain A,Shashidhar H E,Hittalmani S,Vera Cruz C,Paris T,Raman A,Haefele S,Serraj R,Atlin G,Kumar A.2010.Breeding resilient and productive genotypes adapted to drought-prone rainfed ecosystem of India.Field Crops Res,117:197-208.
Vikram P,Swamy B P M,Dixit S,Singh R,Singh B P,Miro B,Kohli A,Henry A,Singh N K,Kumar A.2015.Drought susceptibility of modern rice varieties:An effect of linkage of drought tolerance with undesirable traits.Sci Rep,5:e14799.
Vikram P,Swamy B P M,Dixit S,Ahmed H U,Sta Cruz M T,Singh A K,Kumar A.2011.qDTY1.1,major QTL for rice GYunder reproductive-stage drought stress with a consistent effect in multiple elite genetic backgrounds.BMC Genet,12:89-104.
Yadav S,Singh A,Singh M R,Goel N,Vinod K K,Mohapatra T,Singh A K.2013.Assessment of genetic diversity in Indian rice germplasm(Oryza sativa L.):Use of random versus trait linked microsatellite markers.J Genet,92(3):545-557.
Yadaw R B,Dixit S,Raman A,Mishra K K,Vikram P,Swamy BP M,Sta Cruz M T,Maturan P T,Pandey M,Kumar A.2013.AQTL for high grain yield under lowland drought in the background of popular rice variety Sabitri from Nepal.Field Crops Res,144:281-287.
Yeh F C,Boyle T J B.1997.Population genetic analysis of co-dominant and dominant markers and quantitative traits.Belg J Bot,129:157-163.
Yu S B,Xu W J,Vijayakumar C H M,Ali J,Fu B Y,Xu J L,Jiang Y Z,Marghirang R,Domingo J,Aquino C,Virmani S S,Li Z K.2003.Molecular diversity and multilocus organization of the parental lines used in the International Rice Molecular Breeding Program.Theor Appl Genet,108(1):131-140.
Zhang T,Ni X L,Jiang K F,Deng H F,He Q,Yang Q H,Yang L,Wan X Q,Cao Y J,Zheng J K.2010.Relation between heterosis and parental genetic distance based on molecular markers for functional genes related to yield traits in rice.Rice Sci,17(4):288-295.
Agricultural Statistics at a Glance.2014.Government of India Ministry of Agriculture Department of Agriculture&Cooperation Directorate of Economics&Statistics:63.
Ahmad R,Quadir S,Ahmad N,Shah K H.2003.Yield potential and stability of nine wheat varieties under water stress conditions.Int J Agric Biol,5(1):7-9.
Ali M L,McClung A M,Jia M H,Kimball J A,McCouch S R,Georgia C E.2011.A rice diversity panel evaluated for genetic and agro-morphological diversity between subpopulations and its geographic distribution.Crop Sci,51(5):2021-2035.
Anderson J A,Churchill G A,Autrique J E,Tanksley S D,Sorrels M E.1993.Optimizing parental selection for genetic maps.Genome,36(1):181-186.
Barik Madhusmita,Dash S K,Padhi S,Swain P.2017.Effect of drought on morpho-physiological,yield and yield traits of chromosome segment substitution lines(CSSLs)derived from wild species of rice.Oryza,54(1):65-72.
Bernier J,Kumar A,Ramaiah V,Spaner D,Atlin G.2007.Alarge-effect QTL forgrain yield under reproductive-stage drought stress in upland rice.Crop Sci,47(2):507-516.
Boonjung H,Fukai S.1996.Effects of soil water deficit at different growth stage on rice growth and yield under upland conditions:2.Phenology,biomass production and yield.Field Crops Res,48(1):47-55.
Botstein D,White R L,Skolnick M,Davis R W.1980.Construction of a genetic linkage map in man using restriction fragment length polymorphism.Am J Hum Genet,32(3):314-331.
Chakhonkaen S,Pitnjam K,Saisuk W,Ukoskit K,Muangprom A.2012.Genetic structure of Thai rice and rice accessions obtained from the international rice research institute.Rice,5:19.
Courtois B,Frouin J,Greco R,Bruschi G,Droc G,Hamelin C,Ruiz M,Clément G,Evrard J C,van Coppenole S,Katsantonis D,Oliveira M,Negrao S,Matos C,Cavigiolo S,Lupotto E,Piffanelli P,Ahmadi N.2012.Genetic diversity and population structure in a European collection of rice.Crop Sci,52(4):1663-1675.
Das B,Sengupta S,Parida S K,Roy B,Ghosh M,Prasad M,Ghose T K.2013.Genetic diversity and population structure of rice landraces from Eastern and North Eastern States of India.BMCGenet,14:71-84.
Dixit S,Swamy B P M,Vikram P,Ahmed H U,Sta Cruz M T,Amante M,Atri D,Leung H,Kumar A.2012a.Fine mapping of QTLs for rice grain yield under drought reveals sub-QTLs conferring a response to variable drought severities.Theor Appl Genet,125(1):155-169.
Dixit S,Swamy B P M,Vikram P,Bernier J,Sta Cruz M T,Amante M,Atri D,Kumar A.2012b.Increased drought tolerance and wider adaptability of qDTY12.1 conferred by its interaction with qDTY2.3 and qDTY3.2.Mol Breeding,30:1767-1779.
Evanno G,Regnaut S,Goudet J.2005.Detecting the number of clusters of individuals using the software STRUCTURE:Asimulation study.Mol Ecol,14(8):2611-2620.
Fischer R A,Maurer R.1978.Drought resistance in spring wheat cultivars:I.Grain yield responses in spring wheat.Aust J Agric Res,29(5):892-912.
Gao L Z.2005.Microsatellite diversity and population genetic structure of an endangered wild rice,Oryza officinalis(Poaceae)from China.Mol Ecol,14(14):4287-4297.
Ghimire K H,Quiatchon-Baeza L A,Vikram P,Swamy B P M,Dixit S,Ahmed H U,Hernandez J E,Borromeo T H,Kumar A.2012.Identification and mapping of QTL(q DTY1.1)with a consistent effect on grain yield under drought.Field Crops Res,131:88-96.
IRRI.2017.Trends in global rice consumption.http://irri.org/ricetoday/trends-in-global-rice-consumption.
Kumar A,Verulkar S B,Dixit S,Chauhan B,Bernier J,Venuprasad R,Zhao D,Shrivastava M N.2009.Yield and yield-attributing traits of rice(Oryza sativa L.)under lowland drought and suitability of early vigor as a selection criterion.Field Crops Res,114(1):99-107.
Mishra K K,Vikram P,Yadaw R B,Swamy B P M,Dixit S,Sta Cruz M T S,Maturan P,Marker S,Kumar A.2013.qDTY12.1:A locus with consistent effect on grain yield under drought in rice.BMC Genet,14:12-21.
Nagaraju J,Kathirvel M,Kumar R R,Siddiq E A,Hasnain S E.2002.Genetic analysis of traditional and evolved Basmati and nonBasmati rice varieties by using fluorescence-based ISSR-PCRand SSR markers.Proc Natl Acad Sci USA,99:5836-5841.
Nei M.1972.Genetic distance between populations.Am Nat,106:283-292.
Pachauri V,Taneja N,Vikram P,Singh N K,Singh S.2013.Molecular and morphological characterization of India farmers rice varieties.Aust J Crop Sci,7(7):923-932.
Peakall R,Smouse P E.2006.GENALEX 6:Genetic analysis in Excel:Population genetic software for teaching and research.Mol Ecol Notes,6:288-295.
Peakall R,Smouse P E.2012.GenAlEx 6.5:Genetic analysis in Excel:Population genetic software for teaching and research:An update.Bioinformatics,28:2537-2539.
Perrier X,Flori A,Bonnot F.2003.Data analysis methods.In:Hamon P,Seguin M,Perrier X,Glaszmann J C.Genetic diversity of cultivated tropical plants.Montpellier France:Enfield(Science Publishers):43-76.
Perrier X,Jacquemoud-Collet J P.2006.DARwin software http://darwin.cirad.fr/darwin[2017/10/15].
Pradhan S K,Barik S R,Sahoo A,Mohapatra S,Nayak D K,Mahender A,Meher J,Anandan A,Pandit E.2016.Population structure,genetic diversity and molecular marker-trait association analysis for high temperature stress tolerance in rice.PLoS One,11:e0160027.
Pritchard J K,Stephens M,Donnelly P.2000.Inference of population structure using multilocus genotype data.Genetics,155(2):945-959.
Rai M.2003.Genetic diversity in rice production:Past contribution and the potential of utilization for sustainable rice production.In:Tran D V,Duffy R.Sustainable Rice Production for Food Security:Proceedings of the 20th session of the International Rice Commission.Bangkok,United Nations:Food and Agricultural Organization.
Ramadan E A,Elmoghazy A M,El-Mowafi H F.2015.Molecular markers based genetic diversity analysis for drought tolerance in rice(Oryza sativa L.)using SSR markers.Int J Sci Res Agric Sci,2:137-146.
Ricepedia.2017.The online authority on rice:Rice productivity.http://ricepedia.org/rice-as-a-crop/rice-productivity.
Roy S,Bannerjee A,Mawkhlieng B,Misra A K,Pattanayak A,Harish G D,Singh S K,Ngachan S V,Bansal K C.2015.Genetic diversity and population structure in aromatic and quality rice(Oryza sativa L.)landraces from North Eastern India.PLoS One,10:e0129607.
Salem K F M,Sallam A.2016.Analysis of population structure and genetic diversity of Egyptian and exotic rice(Oryza sativa L.)genotypes.CR Biolog,339(1):1-9.
Shamsudin N A A,Swamy B P M,Ratnam W,Sta Cruz M T,Raman A,Kumar A.2016.Marker assisted pyramiding of drought QTLs into a popular Malaysian rice cultivar MR219.BMC Genet,17:30-43.
Shodhganga.2017.Abstract.http://shodhganga.inflibnet.ac.in/bitstream/10603/169176/9/09_abstract.pdf[2017/11/17].
Siddiq E A.2000.Bridging the rice yield gap in India.In:Papademetriou M K,Dent F J,Herath E M.Bridging the Rice Yield Gap in Asia and Pacific Regions.Bangkok,United Nations:Food and Agricultural Organization:84-111.
Sika K C,Kefela T,Sagbadja H A,Ahoton L,Saidou A,BabaMoussa L,Baptiste L J,Kotconi S O,Gachomo E W.2015.A simple and efficient genomic DNA extraction protocol for large scale genetic analyses of plant biological systems.Plant Gene,1:43-45.
Singh N,Choudhury D R,Singh A K,Kumar S,Srinivasan K,Tyagi R K,Singh N K,Singh R.2013.Comparison of SSR and SNP markers in estimation of genetic diversity and population structure of Indian rice varieties.PLoS One,8:e84136.
Singh N,Choudhury D R,Tiwari G,Singh A K,Kumar S,Srinivasan K,Tyagi R K,Sharma A D,Singh N K,Singh R.2016.Genetic diversity trend in Indian rice varieties:An analysis using SSR markers.BMC Genet,17:127-139.
Swamy B P M,Ahmed H U,Henry A,Mauleon R,Dixit S,Vikram P,Tilatto R,Verulkar S B,Perraju P,Mandal N P,Variar M,Robin S,Chandrababu R,Singh O N,Dwivedi J L,Das S P,Mishra KK,Yadaw R B,Aditya T L,Karmakar B,Satoh K,Moumeni A,Kikuchi S,Leung H,Kumar A.2013.Genetic,physiological,and gene expression analyses reveal that multiple QTL enhance yield of rice mega-variety IR64 under drought.PLoS One,8:e62795.
Swamy B P M,Shamsudin N A A,Rahman S N A,Mauleon R,RatnamW,Sta Cruz M T,Kumar A.2017.Association mapping of yield and yield-related traits under reproductive stage drought stress in rice(Oryza sativa L.).Rice,10:21-33.
Tarang A,Gashti A B.2016.The power of microsatellite markers and AFLPs in revealing the genetic diversity of Hashemi aromatic rice from Iran.J Int Agric,15(6):1186-1197.
Venuprasad R,Lafitte H R,Atlin G N.2007.Response to direct selection for grain yield under drought stress in rice.Crop Sci,47:285-293.
Venuprasad R,Sta Cruz M T,Amante M,Magbanua R,Kumar A,Atlin G A.2008.Response to two cycles of divergent selection for grain yield under drought stress in four rice breeding populations.Field Crops Res,107(3):232-244.
Verulkar S B,Mandal N P,Dwivedi J L,Singh B N,Sinha P K,Mahato R N,Dongre P,Singh O N,Bose L K,Swain P,Robin S,Chandrababu R,Senthil S,Jain A,Shashidhar H E,Hittalmani S,Vera Cruz C,Paris T,Raman A,Haefele S,Serraj R,Atlin G,Kumar A.2010.Breeding resilient and productive genotypes adapted to drought-prone rainfed ecosystem of India.Field Crops Res,117:197-208.
Vikram P,Swamy B P M,Dixit S,Singh R,Singh B P,Miro B,Kohli A,Henry A,Singh N K,Kumar A.2015.Drought susceptibility of modern rice varieties:An effect of linkage of drought tolerance with undesirable traits.Sci Rep,5:e14799.
Vikram P,Swamy B P M,Dixit S,Ahmed H U,Sta Cruz M T,Singh A K,Kumar A.2011.qDTY1.1,major QTL for rice GYunder reproductive-stage drought stress with a consistent effect in multiple elite genetic backgrounds.BMC Genet,12:89-104.
Yadav S,Singh A,Singh M R,Goel N,Vinod K K,Mohapatra T,Singh A K.2013.Assessment of genetic diversity in Indian rice germplasm(Oryza sativa L.):Use of random versus trait linked microsatellite markers.J Genet,92(3):545-557.
Yadaw R B,Dixit S,Raman A,Mishra K K,Vikram P,Swamy BP M,Sta Cruz M T,Maturan P T,Pandey M,Kumar A.2013.AQTL for high grain yield under lowland drought in the background of popular rice variety Sabitri from Nepal.Field Crops Res,144:281-287.
Yeh F C,Boyle T J B.1997.Population genetic analysis of co-dominant and dominant markers and quantitative traits.Belg J Bot,129:157-163.
Yu S B,Xu W J,Vijayakumar C H M,Ali J,Fu B Y,Xu J L,Jiang Y Z,Marghirang R,Domingo J,Aquino C,Virmani S S,Li Z K.2003.Molecular diversity and multilocus organization of the parental lines used in the International Rice Molecular Breeding Program.Theor Appl Genet,108(1):131-140.
Zhang T,Ni X L,Jiang K F,Deng H F,He Q,Yang Q H,Yang L,Wan X Q,Cao Y J,Zheng J K.2010.Relation between heterosis and parental genetic distance based on molecular markers for functional genes related to yield traits in rice.Rice Sci,17(4):288-295.