Genotyping-by-sequencing and multilocation evaluation of two interspecific backcross populations identify QTLs for yield-related traits in pigeonpea
This study has identified single-nucleotide polymorphism (SNP) markers associated with nine yield-related traits in pigeonpea by using two backcross populations (BP) developed through interspecific crosses and evaluating them at two locations and 3 years. In both the populations, markers have shown...
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| Veröffentlicht in: | Theoretical and applied genetics 2020-03, Vol.133 (3), p.737-749 |
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| creator | Saxena, Rachit K. Kale, Sandip Mir, Reyazul Rouf Mallikarjuna, Nalini Yadav, Pooja Das, Roma Rani Molla, Johiruddin Sonnappa, Muniswamy Ghanta, Anuradha Narasimhan, Yamini Rathore, Abhishek Kumar, C. V. Sameer Varshney, Rajeev K. |
| description | This study has identified single-nucleotide polymorphism (SNP) markers associated with nine yield-related traits in pigeonpea by using two backcross populations (BP) developed through interspecific crosses and evaluating them at two locations and 3 years. In both the populations, markers have shown strong segregation distortion; therefore, a quantitative trait locus (QTL) mapping mixed model was used. A total of 86 QTLs explaining 12–21% phenotypic variation were detected in BP-1. On the other hand, 107 QTLs explaining 11–29% phenotypic variation were detected in BP-2. Although most QTLs were environment and trait specific, few stable and consistent QTLs were also detected. Interestingly, 11 QTLs in BP-2 were associated with more than one trait. Among these QTLs, eight QTLs associated with days to 50% flowering and days to 75% maturity were located on CcLG07. One SNP “S7_14185076” marker in BP-2 population has been found associated with four traits, namely days to 50% flowering, days to 75% maturity, primary branches per plant and secondary branches per plant with positive additive effect. Hence, the present study has not only identified QTLs for yield-related traits, but also discovered novel alleles from wild species, which can be used for improvement of traits through genomics-assisted breeding. |
| doi_str_mv | 10.1007/s00122-019-03504-z |
| format | Article |
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V. Sameer ; Varshney, Rajeev K.</creator><creatorcontrib>Saxena, Rachit K. ; Kale, Sandip ; Mir, Reyazul Rouf ; Mallikarjuna, Nalini ; Yadav, Pooja ; Das, Roma Rani ; Molla, Johiruddin ; Sonnappa, Muniswamy ; Ghanta, Anuradha ; Narasimhan, Yamini ; Rathore, Abhishek ; Kumar, C. V. Sameer ; Varshney, Rajeev K.</creatorcontrib><description>This study has identified single-nucleotide polymorphism (SNP) markers associated with nine yield-related traits in pigeonpea by using two backcross populations (BP) developed through interspecific crosses and evaluating them at two locations and 3 years. In both the populations, markers have shown strong segregation distortion; therefore, a quantitative trait locus (QTL) mapping mixed model was used. A total of 86 QTLs explaining 12–21% phenotypic variation were detected in BP-1. On the other hand, 107 QTLs explaining 11–29% phenotypic variation were detected in BP-2. Although most QTLs were environment and trait specific, few stable and consistent QTLs were also detected. Interestingly, 11 QTLs in BP-2 were associated with more than one trait. Among these QTLs, eight QTLs associated with days to 50% flowering and days to 75% maturity were located on CcLG07. One SNP “S7_14185076” marker in BP-2 population has been found associated with four traits, namely days to 50% flowering, days to 75% maturity, primary branches per plant and secondary branches per plant with positive additive effect. Hence, the present study has not only identified QTLs for yield-related traits, but also discovered novel alleles from wild species, which can be used for improvement of traits through genomics-assisted breeding.</description><identifier>ISSN: 0040-5752</identifier><identifier>EISSN: 1432-2242</identifier><identifier>DOI: 10.1007/s00122-019-03504-z</identifier><identifier>PMID: 31844966</identifier><language>eng</language><publisher>Berlin/Heidelberg: Springer Berlin Heidelberg</publisher><subject>Agricultural research ; Agriculture ; Alleles ; Biochemistry ; Biomedical and Life Sciences ; Biotechnology ; Cajanus - genetics ; Cajanus - growth & development ; Chromosome Mapping ; Chromosomes, Plant ; Crop yields ; Crosses, Genetic ; Flowering ; Gene mapping ; Genetic aspects ; Genetic Association Studies ; Genetic Linkage ; Genetic Markers ; Genetic transformation ; Genomics ; Genotype ; Genotyping ; Genotyping Techniques ; Interspecific ; Life Sciences ; Original Article ; Phenotype ; Phenotypic variations ; Pigeon pea ; Plant Biochemistry ; Plant Breeding/Biotechnology ; Plant Genetics and Genomics ; Polymorphism, Single Nucleotide ; Quantitative Trait Loci ; Sequence Analysis, DNA ; Single nucleotide polymorphisms ; Single-nucleotide polymorphism</subject><ispartof>Theoretical and applied genetics, 2020-03, Vol.133 (3), p.737-749</ispartof><rights>Springer-Verlag GmbH Germany, part of Springer Nature 2019</rights><rights>COPYRIGHT 2020 Springer</rights><rights>Theoretical and Applied Genetics is a copyright of Springer, (2019). All Rights Reserved.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c520t-6cd20935fc5b1aeebc49a42239625b6112b5d2accf84b09ff8a7efeab5506bc93</citedby><cites>FETCH-LOGICAL-c520t-6cd20935fc5b1aeebc49a42239625b6112b5d2accf84b09ff8a7efeab5506bc93</cites><orcidid>0000-0002-4562-9131</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://link.springer.com/content/pdf/10.1007/s00122-019-03504-z$$EPDF$$P50$$Gspringer$$H</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1007/s00122-019-03504-z$$EHTML$$P50$$Gspringer$$H</linktohtml><link.rule.ids>314,780,784,27923,27924,41487,42556,51318</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/31844966$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Saxena, Rachit K.</creatorcontrib><creatorcontrib>Kale, Sandip</creatorcontrib><creatorcontrib>Mir, Reyazul Rouf</creatorcontrib><creatorcontrib>Mallikarjuna, Nalini</creatorcontrib><creatorcontrib>Yadav, Pooja</creatorcontrib><creatorcontrib>Das, Roma Rani</creatorcontrib><creatorcontrib>Molla, Johiruddin</creatorcontrib><creatorcontrib>Sonnappa, Muniswamy</creatorcontrib><creatorcontrib>Ghanta, Anuradha</creatorcontrib><creatorcontrib>Narasimhan, Yamini</creatorcontrib><creatorcontrib>Rathore, Abhishek</creatorcontrib><creatorcontrib>Kumar, C. V. Sameer</creatorcontrib><creatorcontrib>Varshney, Rajeev K.</creatorcontrib><title>Genotyping-by-sequencing and multilocation evaluation of two interspecific backcross populations identify QTLs for yield-related traits in pigeonpea</title><title>Theoretical and applied genetics</title><addtitle>Theor Appl Genet</addtitle><addtitle>Theor Appl Genet</addtitle><description>This study has identified single-nucleotide polymorphism (SNP) markers associated with nine yield-related traits in pigeonpea by using two backcross populations (BP) developed through interspecific crosses and evaluating them at two locations and 3 years. In both the populations, markers have shown strong segregation distortion; therefore, a quantitative trait locus (QTL) mapping mixed model was used. A total of 86 QTLs explaining 12–21% phenotypic variation were detected in BP-1. On the other hand, 107 QTLs explaining 11–29% phenotypic variation were detected in BP-2. Although most QTLs were environment and trait specific, few stable and consistent QTLs were also detected. Interestingly, 11 QTLs in BP-2 were associated with more than one trait. Among these QTLs, eight QTLs associated with days to 50% flowering and days to 75% maturity were located on CcLG07. One SNP “S7_14185076” marker in BP-2 population has been found associated with four traits, namely days to 50% flowering, days to 75% maturity, primary branches per plant and secondary branches per plant with positive additive effect. Hence, the present study has not only identified QTLs for yield-related traits, but also discovered novel alleles from wild species, which can be used for improvement of traits through genomics-assisted breeding.</description><subject>Agricultural research</subject><subject>Agriculture</subject><subject>Alleles</subject><subject>Biochemistry</subject><subject>Biomedical and Life Sciences</subject><subject>Biotechnology</subject><subject>Cajanus - genetics</subject><subject>Cajanus - growth & development</subject><subject>Chromosome Mapping</subject><subject>Chromosomes, Plant</subject><subject>Crop yields</subject><subject>Crosses, Genetic</subject><subject>Flowering</subject><subject>Gene mapping</subject><subject>Genetic aspects</subject><subject>Genetic Association Studies</subject><subject>Genetic Linkage</subject><subject>Genetic Markers</subject><subject>Genetic transformation</subject><subject>Genomics</subject><subject>Genotype</subject><subject>Genotyping</subject><subject>Genotyping Techniques</subject><subject>Interspecific</subject><subject>Life Sciences</subject><subject>Original Article</subject><subject>Phenotype</subject><subject>Phenotypic variations</subject><subject>Pigeon pea</subject><subject>Plant Biochemistry</subject><subject>Plant Breeding/Biotechnology</subject><subject>Plant Genetics and Genomics</subject><subject>Polymorphism, Single Nucleotide</subject><subject>Quantitative Trait Loci</subject><subject>Sequence Analysis, DNA</subject><subject>Single nucleotide polymorphisms</subject><subject>Single-nucleotide polymorphism</subject><issn>0040-5752</issn><issn>1432-2242</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2020</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><recordid>eNp9kstu1DAYhSMEosPAC7BAltjAwsXXZLKsKiiVRkJAWVuO83vkkrGD7RTS5-CB8cwUqkEIeeFLvnPk45yqek7JKSWkeZMIoYxhQltMuCQC3z6oFlRwhhkT7GG1IEQQLBvJTqonKV0TQpgk_HF1wulKiLauF9XPC_Ahz6PzG9zNOMG3CbwpO6R9j7bTkN0QjM4ueAQ3epgOy2BR_h6Q8xliGsE46wzqtPlqYkgJjWGchj2ZkOvBZ2dn9PFqnZANEc0Ohh5HKAT0KEftcsE8Gt0Ggh9BP60eWT0keHY3L6sv795enb_H6w8Xl-dna2wkIxnXpmek5dIa2VEN0BnRasEYb2smu5pS1smeaWPsSnSktXalG7CgOylJ3ZmWL6tXB98xhpI7ZbV1ycAwaA9hSopx1rS85kwU9OVf6HWYoi-3K5QULWsKeU9t9ADKeRtKOrMzVWc1LW_f7AyX1ek_qDJ62DoTPFhXzo8Er48EhcnwI2_0lJK6_PzpmGUHdv8nIlg1RrfVcVaUqF1t1KE2qtRG7WujbovoxV26qdtC_0fyuycF4AcglU9-A_E-_n9sfwExF8-m</recordid><startdate>20200301</startdate><enddate>20200301</enddate><creator>Saxena, Rachit K.</creator><creator>Kale, Sandip</creator><creator>Mir, Reyazul Rouf</creator><creator>Mallikarjuna, Nalini</creator><creator>Yadav, Pooja</creator><creator>Das, Roma Rani</creator><creator>Molla, Johiruddin</creator><creator>Sonnappa, Muniswamy</creator><creator>Ghanta, Anuradha</creator><creator>Narasimhan, Yamini</creator><creator>Rathore, Abhishek</creator><creator>Kumar, C. 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V. Sameer</au><au>Varshney, Rajeev K.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Genotyping-by-sequencing and multilocation evaluation of two interspecific backcross populations identify QTLs for yield-related traits in pigeonpea</atitle><jtitle>Theoretical and applied genetics</jtitle><stitle>Theor Appl Genet</stitle><addtitle>Theor Appl Genet</addtitle><date>2020-03-01</date><risdate>2020</risdate><volume>133</volume><issue>3</issue><spage>737</spage><epage>749</epage><pages>737-749</pages><issn>0040-5752</issn><eissn>1432-2242</eissn><abstract>This study has identified single-nucleotide polymorphism (SNP) markers associated with nine yield-related traits in pigeonpea by using two backcross populations (BP) developed through interspecific crosses and evaluating them at two locations and 3 years. In both the populations, markers have shown strong segregation distortion; therefore, a quantitative trait locus (QTL) mapping mixed model was used. A total of 86 QTLs explaining 12–21% phenotypic variation were detected in BP-1. On the other hand, 107 QTLs explaining 11–29% phenotypic variation were detected in BP-2. Although most QTLs were environment and trait specific, few stable and consistent QTLs were also detected. Interestingly, 11 QTLs in BP-2 were associated with more than one trait. Among these QTLs, eight QTLs associated with days to 50% flowering and days to 75% maturity were located on CcLG07. One SNP “S7_14185076” marker in BP-2 population has been found associated with four traits, namely days to 50% flowering, days to 75% maturity, primary branches per plant and secondary branches per plant with positive additive effect. Hence, the present study has not only identified QTLs for yield-related traits, but also discovered novel alleles from wild species, which can be used for improvement of traits through genomics-assisted breeding.</abstract><cop>Berlin/Heidelberg</cop><pub>Springer Berlin Heidelberg</pub><pmid>31844966</pmid><doi>10.1007/s00122-019-03504-z</doi><tpages>13</tpages><orcidid>https://orcid.org/0000-0002-4562-9131</orcidid><oa>free_for_read</oa></addata></record> |
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| ispartof | Theoretical and applied genetics, 2020-03, Vol.133 (3), p.737-749 |
| issn | 0040-5752 1432-2242 |
| language | eng |
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| source | MEDLINE; SpringerLink Journals - AutoHoldings |
| subjects | Agricultural research Agriculture Alleles Biochemistry Biomedical and Life Sciences Biotechnology Cajanus - genetics Cajanus - growth & development Chromosome Mapping Chromosomes, Plant Crop yields Crosses, Genetic Flowering Gene mapping Genetic aspects Genetic Association Studies Genetic Linkage Genetic Markers Genetic transformation Genomics Genotype Genotyping Genotyping Techniques Interspecific Life Sciences Original Article Phenotype Phenotypic variations Pigeon pea Plant Biochemistry Plant Breeding/Biotechnology Plant Genetics and Genomics Polymorphism, Single Nucleotide Quantitative Trait Loci Sequence Analysis, DNA Single nucleotide polymorphisms Single-nucleotide polymorphism |
| title | Genotyping-by-sequencing and multilocation evaluation of two interspecific backcross populations identify QTLs for yield-related traits in pigeonpea |
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