Genotyping-by-sequencing of three mapping populations for identification of candidate genomic regions for resistance to sterility mosaic disease in pigeonpea

Rachit K. Saxena, Sandip M. Kale, Vinay Kumar, Swathi Parupali, Shourabh Joshi, Vikas K. Singh, Vanika Garg, Roma R. Das, Mamta Sharma, Kalinati Narasimhan Yamini, Anuradha Ghanta, Abhishek Rathore, C. V. Sameerkumar, K. B. Saxena, Rajeev K. Varshney

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Abstract

Sterility mosaic disease (SMD) is one of the serious production constraints that may lead to complete yield loss in pigeonpea. Three mapping populations including two recombinant inbred lines and one F2, were used for phenotyping for SMD resistance at two locations in three different years. Genotyping-by-sequencing approach was used for simultaneous identification and genotyping of SNPs on above mentioned populations. In total, 212,464, 89,699 and 64,798 SNPs were identified in ICPL 20096 × ICPL 332 (PRIL-B), ICPL 20097 × ICP 8863 (PRIL-C) and ICP 8863 × ICPL 87119 (F2) respectively. By using high-quality SNPs, genetic maps were developed for PRIL-B (1,101 SNPs; 921.21 cM), PRIL-C (484 SNPs; 798.25 cM) and F2 (996 SNPs; 1,597.30 cM) populations. The average inter marker distance on these maps varied from 0.84 cM to 1.65 cM, which was lowest in all genetic mapping studies in pigeonpea. Composite interval mapping based QTL analysis identified a total of 10 QTLs including three major QTLs across the three populations. The phenotypic variance of the identified QTLs ranged from 3.6 to 34.3%. One candidate genomic region identified on CcLG11 seems to be promising QTL for molecular breeding in developing superior lines with enhanced resistance to SMD.

LanguageEnglish
Article number1813
JournalScientific Reports
Volume7
Issue number1
DOIs
StatePublished - 1 Dec 2017

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Infertility
Single Nucleotide Polymorphism
Population
DNA Shuffling
Disease Resistance

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Saxena, Rachit K. ; Kale, Sandip M. ; Kumar, Vinay ; Parupali, Swathi ; Joshi, Shourabh ; Singh, Vikas K. ; Garg, Vanika ; Das, Roma R. ; Sharma, Mamta ; Yamini, Kalinati Narasimhan ; Ghanta, Anuradha ; Rathore, Abhishek ; Sameerkumar, C. V. ; Saxena, K. B. ; Varshney, Rajeev K./ Genotyping-by-sequencing of three mapping populations for identification of candidate genomic regions for resistance to sterility mosaic disease in pigeonpea. In: Scientific Reports. 2017 ; Vol. 7, No. 1.
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title = "Genotyping-by-sequencing of three mapping populations for identification of candidate genomic regions for resistance to sterility mosaic disease in pigeonpea",
abstract = "Sterility mosaic disease (SMD) is one of the serious production constraints that may lead to complete yield loss in pigeonpea. Three mapping populations including two recombinant inbred lines and one F2, were used for phenotyping for SMD resistance at two locations in three different years. Genotyping-by-sequencing approach was used for simultaneous identification and genotyping of SNPs on above mentioned populations. In total, 212,464, 89,699 and 64,798 SNPs were identified in ICPL 20096 × ICPL 332 (PRIL-B), ICPL 20097 × ICP 8863 (PRIL-C) and ICP 8863 × ICPL 87119 (F2) respectively. By using high-quality SNPs, genetic maps were developed for PRIL-B (1,101 SNPs; 921.21 cM), PRIL-C (484 SNPs; 798.25 cM) and F2 (996 SNPs; 1,597.30 cM) populations. The average inter marker distance on these maps varied from 0.84 cM to 1.65 cM, which was lowest in all genetic mapping studies in pigeonpea. Composite interval mapping based QTL analysis identified a total of 10 QTLs including three major QTLs across the three populations. The phenotypic variance of the identified QTLs ranged from 3.6 to 34.3{\%}. One candidate genomic region identified on CcLG11 seems to be promising QTL for molecular breeding in developing superior lines with enhanced resistance to SMD.",
author = "Saxena, {Rachit K.} and Kale, {Sandip M.} and Vinay Kumar and Swathi Parupali and Shourabh Joshi and Singh, {Vikas K.} and Vanika Garg and Das, {Roma R.} and Mamta Sharma and Yamini, {Kalinati Narasimhan} and Anuradha Ghanta and Abhishek Rathore and Sameerkumar, {C. V.} and Saxena, {K. B.} and Varshney, {Rajeev K.}",
year = "2017",
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Saxena, RK, Kale, SM, Kumar, V, Parupali, S, Joshi, S, Singh, VK, Garg, V, Das, RR, Sharma, M, Yamini, KN, Ghanta, A, Rathore, A, Sameerkumar, CV, Saxena, KB & Varshney, RK 2017, 'Genotyping-by-sequencing of three mapping populations for identification of candidate genomic regions for resistance to sterility mosaic disease in pigeonpea' Scientific Reports, vol 7, no. 1, 1813. DOI: 10.1038/s41598-017-01535-4

Genotyping-by-sequencing of three mapping populations for identification of candidate genomic regions for resistance to sterility mosaic disease in pigeonpea. / Saxena, Rachit K.; Kale, Sandip M.; Kumar, Vinay; Parupali, Swathi; Joshi, Shourabh; Singh, Vikas K.; Garg, Vanika; Das, Roma R.; Sharma, Mamta; Yamini, Kalinati Narasimhan; Ghanta, Anuradha; Rathore, Abhishek; Sameerkumar, C. V.; Saxena, K. B.; Varshney, Rajeev K.

In: Scientific Reports, Vol. 7, No. 1, 1813, 01.12.2017.

Research output: Contribution to journalArticle

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T1 - Genotyping-by-sequencing of three mapping populations for identification of candidate genomic regions for resistance to sterility mosaic disease in pigeonpea

AU - Saxena,Rachit K.

AU - Kale,Sandip M.

AU - Kumar,Vinay

AU - Parupali,Swathi

AU - Joshi,Shourabh

AU - Singh,Vikas K.

AU - Garg,Vanika

AU - Das,Roma R.

AU - Sharma,Mamta

AU - Yamini,Kalinati Narasimhan

AU - Ghanta,Anuradha

AU - Rathore,Abhishek

AU - Sameerkumar,C. V.

AU - Saxena,K. B.

AU - Varshney,Rajeev K.

PY - 2017/12/1

Y1 - 2017/12/1

N2 - Sterility mosaic disease (SMD) is one of the serious production constraints that may lead to complete yield loss in pigeonpea. Three mapping populations including two recombinant inbred lines and one F2, were used for phenotyping for SMD resistance at two locations in three different years. Genotyping-by-sequencing approach was used for simultaneous identification and genotyping of SNPs on above mentioned populations. In total, 212,464, 89,699 and 64,798 SNPs were identified in ICPL 20096 × ICPL 332 (PRIL-B), ICPL 20097 × ICP 8863 (PRIL-C) and ICP 8863 × ICPL 87119 (F2) respectively. By using high-quality SNPs, genetic maps were developed for PRIL-B (1,101 SNPs; 921.21 cM), PRIL-C (484 SNPs; 798.25 cM) and F2 (996 SNPs; 1,597.30 cM) populations. The average inter marker distance on these maps varied from 0.84 cM to 1.65 cM, which was lowest in all genetic mapping studies in pigeonpea. Composite interval mapping based QTL analysis identified a total of 10 QTLs including three major QTLs across the three populations. The phenotypic variance of the identified QTLs ranged from 3.6 to 34.3%. One candidate genomic region identified on CcLG11 seems to be promising QTL for molecular breeding in developing superior lines with enhanced resistance to SMD.

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