Construction of genotyping-by-sequencing based high-density genetic maps and QTL mapping for fusarium wilt resistance in pigeonpea

Rachit K. Saxena; Vikas K. Singh; Sandip M. Kale; Revathi Tathineni; Swathi Parupalli; Vinay Kumar; Vanika Garg; Roma R. Das; Mamta Sharma; Kalinati Narasimhan Yamini; Sonnappa Muniswamy; Anuradha Ghanta; Abhishek Rathore; C. V.Sameer Kumar; K. B. Saxena; P. B.Kavi Kishor; Rajeev K. Varshney

doi:10.1038/s41598-017-01537-2

Construction of genotyping-by-sequencing based high-density genetic maps and QTL mapping for fusarium wilt resistance in pigeonpea

Rachit K. Saxena, Vikas K. Singh, Sandip M. Kale, Revathi Tathineni, Swathi Parupalli, Vinay Kumar, Vanika Garg, Roma R. Das, Mamta Sharma, Kalinati Narasimhan Yamini, Sonnappa Muniswamy, Anuradha Ghanta, Abhishek Rathore, C. V.Sameer Kumar, K. B. Saxena, P. B.Kavi Kishor, Rajeev K. Varshney

Institute of Agriculture

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47 Citations (Scopus)

Abstract

Fusarium wilt (FW) is one of the most important biotic stresses causing yield losses in pigeonpea. Genetic improvement of pigeonpea through genomics-assisted breeding (GAB) is an economically feasible option for the development of high yielding FW resistant genotypes. In this context, two recombinant inbred lines (RILs) (ICPB 2049 × ICPL 99050 designated as PRIL-A and ICPL 20096 × ICPL 332 designated as PRIL-B) and one F₂ (ICPL 85063 × ICPL 87119) populations were used for the development of high density genetic maps. Genotyping-by-sequencing (GBS) approach was used to identify and genotype SNPs in three mapping populations. As a result, three high density genetic maps with 964, 1101 and 557 SNPs with an average marker distance of 1.16, 0.84 and 2.60 cM were developed in PRIL-A, PRIL-B and F₂, respectively. Based on the multi-location and multi-year phenotypic data of FW resistance a total of 14 quantitative trait loci (QTLs) including six major QTLs explaining >10% phenotypic variance explained (PVE) were identified. Comparative analysis across the populations has revealed three important QTLs (qFW11.1, qFW11.2 and qFW11.3) with upto 56.45% PVE for FW resistance. This is the first report of QTL mapping for FW resistance in pigeonpea and identified genomic region could be utilized in GAB.

Original language	English
Article number	1911
Journal	Scientific Reports
Volume	7
Issue number	1
DOIs	https://doi.org/10.1038/s41598-017-01537-2
Publication status	Published - 1 Dec 2017

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Saxena, R. K., Singh, V. K., Kale, S. M., Tathineni, R., Parupalli, S., Kumar, V., Garg, V., Das, R. R., Sharma, M., Yamini, K. N., Muniswamy, S., Ghanta, A., Rathore, A., Kumar, C. V. S., Saxena, K. B., Kishor, P. B. K., & Varshney, R. K. (2017). Construction of genotyping-by-sequencing based high-density genetic maps and QTL mapping for fusarium wilt resistance in pigeonpea. Scientific Reports, 7(1), Article 1911. https://doi.org/10.1038/s41598-017-01537-2

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title = "Construction of genotyping-by-sequencing based high-density genetic maps and QTL mapping for fusarium wilt resistance in pigeonpea",

abstract = "Fusarium wilt (FW) is one of the most important biotic stresses causing yield losses in pigeonpea. Genetic improvement of pigeonpea through genomics-assisted breeding (GAB) is an economically feasible option for the development of high yielding FW resistant genotypes. In this context, two recombinant inbred lines (RILs) (ICPB 2049 × ICPL 99050 designated as PRIL-A and ICPL 20096 × ICPL 332 designated as PRIL-B) and one F2 (ICPL 85063 × ICPL 87119) populations were used for the development of high density genetic maps. Genotyping-by-sequencing (GBS) approach was used to identify and genotype SNPs in three mapping populations. As a result, three high density genetic maps with 964, 1101 and 557 SNPs with an average marker distance of 1.16, 0.84 and 2.60 cM were developed in PRIL-A, PRIL-B and F2, respectively. Based on the multi-location and multi-year phenotypic data of FW resistance a total of 14 quantitative trait loci (QTLs) including six major QTLs explaining >10% phenotypic variance explained (PVE) were identified. Comparative analysis across the populations has revealed three important QTLs (qFW11.1, qFW11.2 and qFW11.3) with upto 56.45% PVE for FW resistance. This is the first report of QTL mapping for FW resistance in pigeonpea and identified genomic region could be utilized in GAB.",

author = "Saxena, {Rachit K.} and Singh, {Vikas K.} and Kale, {Sandip M.} and Revathi Tathineni and Swathi Parupalli and Vinay Kumar and Vanika Garg and Das, {Roma R.} and Mamta Sharma and Yamini, {Kalinati Narasimhan} and Sonnappa Muniswamy and Anuradha Ghanta and Abhishek Rathore and Kumar, {C. V.Sameer} and Saxena, {K. B.} and Kishor, {P. B.Kavi} and Varshney, {Rajeev K.}",

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Saxena, RK, Singh, VK, Kale, SM, Tathineni, R, Parupalli, S, Kumar, V, Garg, V, Das, RR, Sharma, M, Yamini, KN, Muniswamy, S, Ghanta, A, Rathore, A, Kumar, CVS, Saxena, KB, Kishor, PBK & Varshney, RK 2017, 'Construction of genotyping-by-sequencing based high-density genetic maps and QTL mapping for fusarium wilt resistance in pigeonpea', Scientific Reports, vol. 7, no. 1, 1911. https://doi.org/10.1038/s41598-017-01537-2

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T1 - Construction of genotyping-by-sequencing based high-density genetic maps and QTL mapping for fusarium wilt resistance in pigeonpea

AU - Saxena, Rachit K.

AU - Singh, Vikas K.

AU - Kale, Sandip M.

AU - Tathineni, Revathi

AU - Parupalli, Swathi

AU - Kumar, Vinay

AU - Garg, Vanika

AU - Das, Roma R.

AU - Sharma, Mamta

AU - Yamini, Kalinati Narasimhan

AU - Muniswamy, Sonnappa

AU - Ghanta, Anuradha

AU - Rathore, Abhishek

AU - Kumar, C. V.Sameer

AU - Saxena, K. B.

AU - Kishor, P. B.Kavi

AU - Varshney, Rajeev K.

PY - 2017/12/1

Y1 - 2017/12/1

N2 - Fusarium wilt (FW) is one of the most important biotic stresses causing yield losses in pigeonpea. Genetic improvement of pigeonpea through genomics-assisted breeding (GAB) is an economically feasible option for the development of high yielding FW resistant genotypes. In this context, two recombinant inbred lines (RILs) (ICPB 2049 × ICPL 99050 designated as PRIL-A and ICPL 20096 × ICPL 332 designated as PRIL-B) and one F2 (ICPL 85063 × ICPL 87119) populations were used for the development of high density genetic maps. Genotyping-by-sequencing (GBS) approach was used to identify and genotype SNPs in three mapping populations. As a result, three high density genetic maps with 964, 1101 and 557 SNPs with an average marker distance of 1.16, 0.84 and 2.60 cM were developed in PRIL-A, PRIL-B and F2, respectively. Based on the multi-location and multi-year phenotypic data of FW resistance a total of 14 quantitative trait loci (QTLs) including six major QTLs explaining >10% phenotypic variance explained (PVE) were identified. Comparative analysis across the populations has revealed three important QTLs (qFW11.1, qFW11.2 and qFW11.3) with upto 56.45% PVE for FW resistance. This is the first report of QTL mapping for FW resistance in pigeonpea and identified genomic region could be utilized in GAB.

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Construction of genotyping-by-sequencing based high-density genetic maps and QTL mapping for fusarium wilt resistance in pigeonpea

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