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Next‐generation sequencing for identification of candidate genes for Fusarium wilt and sterility mosaic disease in pigeonpea (Cajanus cajan)

To map resistance genes for Fusarium wilt (FW) and sterility mosaic disease (SMD) in pigeonpea, sequencing‐based bulked segregant analysis (Seq‐BSA) was used. Resistant (R) and susceptible (S) bulks from the extreme recombinant inbred lines of ICPL 20096 × ICPL 332 were sequenced. Subsequently, SNP...

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Autores principales: Singh, Vikas K., Khan, Aamir W., Saxena, Rachit K., Kumar, Vinay, Kale, Sandip M., Sinha, Pallavi, Chitikineni, Annapurna, Pazhamala, Lekha T., Garg, Vanika, Sharma, Mamta, Sameer Kumar, Chanda Venkata, Parupalli, Swathi, Vechalapu, Suryanarayana, Patil, Suyash, Muniswamy, Sonnappa, Ghanta, Anuradha, Yamini, Kalinati Narasimhan, Dharmaraj, Pallavi Subbanna, Varshney, Rajeev K.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: John Wiley and Sons Inc. 2015
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5054876/
https://www.ncbi.nlm.nih.gov/pubmed/26397045
http://dx.doi.org/10.1111/pbi.12470
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author Singh, Vikas K.
Khan, Aamir W.
Saxena, Rachit K.
Kumar, Vinay
Kale, Sandip M.
Sinha, Pallavi
Chitikineni, Annapurna
Pazhamala, Lekha T.
Garg, Vanika
Sharma, Mamta
Sameer Kumar, Chanda Venkata
Parupalli, Swathi
Vechalapu, Suryanarayana
Patil, Suyash
Muniswamy, Sonnappa
Ghanta, Anuradha
Yamini, Kalinati Narasimhan
Dharmaraj, Pallavi Subbanna
Varshney, Rajeev K.
author_facet Singh, Vikas K.
Khan, Aamir W.
Saxena, Rachit K.
Kumar, Vinay
Kale, Sandip M.
Sinha, Pallavi
Chitikineni, Annapurna
Pazhamala, Lekha T.
Garg, Vanika
Sharma, Mamta
Sameer Kumar, Chanda Venkata
Parupalli, Swathi
Vechalapu, Suryanarayana
Patil, Suyash
Muniswamy, Sonnappa
Ghanta, Anuradha
Yamini, Kalinati Narasimhan
Dharmaraj, Pallavi Subbanna
Varshney, Rajeev K.
author_sort Singh, Vikas K.
collection PubMed
description To map resistance genes for Fusarium wilt (FW) and sterility mosaic disease (SMD) in pigeonpea, sequencing‐based bulked segregant analysis (Seq‐BSA) was used. Resistant (R) and susceptible (S) bulks from the extreme recombinant inbred lines of ICPL 20096 × ICPL 332 were sequenced. Subsequently, SNP index was calculated between R‐ and S‐bulks with the help of draft genome sequence and reference‐guided assembly of ICPL 20096 (resistant parent). Seq‐BSA has provided seven candidate SNPs for FW and SMD resistance in pigeonpea. In parallel, four additional genotypes were re‐sequenced and their combined analysis with R‐ and S‐bulks has provided a total of 8362 nonsynonymous (ns) SNPs. Of 8362 nsSNPs, 60 were found within the 2‐Mb flanking regions of seven candidate SNPs identified through Seq‐BSA. Haplotype analysis narrowed down to eight nsSNPs in seven genes. These eight nsSNPs were further validated by re‐sequencing 11 genotypes that are resistant and susceptible to FW and SMD. This analysis revealed association of four candidate nsSNPs in four genes with FW resistance and four candidate nsSNPs in three genes with SMD resistance. Further, In silico protein analysis and expression profiling identified two most promising candidate genes namely C.cajan_01839 for SMD resistance and C.cajan_03203 for FW resistance. Identified candidate genomic regions/SNPs will be useful for genomics‐assisted breeding in pigeonpea.
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spelling pubmed-50548762016-10-19 Next‐generation sequencing for identification of candidate genes for Fusarium wilt and sterility mosaic disease in pigeonpea (Cajanus cajan) Singh, Vikas K. Khan, Aamir W. Saxena, Rachit K. Kumar, Vinay Kale, Sandip M. Sinha, Pallavi Chitikineni, Annapurna Pazhamala, Lekha T. Garg, Vanika Sharma, Mamta Sameer Kumar, Chanda Venkata Parupalli, Swathi Vechalapu, Suryanarayana Patil, Suyash Muniswamy, Sonnappa Ghanta, Anuradha Yamini, Kalinati Narasimhan Dharmaraj, Pallavi Subbanna Varshney, Rajeev K. Plant Biotechnol J Research Articles To map resistance genes for Fusarium wilt (FW) and sterility mosaic disease (SMD) in pigeonpea, sequencing‐based bulked segregant analysis (Seq‐BSA) was used. Resistant (R) and susceptible (S) bulks from the extreme recombinant inbred lines of ICPL 20096 × ICPL 332 were sequenced. Subsequently, SNP index was calculated between R‐ and S‐bulks with the help of draft genome sequence and reference‐guided assembly of ICPL 20096 (resistant parent). Seq‐BSA has provided seven candidate SNPs for FW and SMD resistance in pigeonpea. In parallel, four additional genotypes were re‐sequenced and their combined analysis with R‐ and S‐bulks has provided a total of 8362 nonsynonymous (ns) SNPs. Of 8362 nsSNPs, 60 were found within the 2‐Mb flanking regions of seven candidate SNPs identified through Seq‐BSA. Haplotype analysis narrowed down to eight nsSNPs in seven genes. These eight nsSNPs were further validated by re‐sequencing 11 genotypes that are resistant and susceptible to FW and SMD. This analysis revealed association of four candidate nsSNPs in four genes with FW resistance and four candidate nsSNPs in three genes with SMD resistance. Further, In silico protein analysis and expression profiling identified two most promising candidate genes namely C.cajan_01839 for SMD resistance and C.cajan_03203 for FW resistance. Identified candidate genomic regions/SNPs will be useful for genomics‐assisted breeding in pigeonpea. John Wiley and Sons Inc. 2015-09-23 2016-05 /pmc/articles/PMC5054876/ /pubmed/26397045 http://dx.doi.org/10.1111/pbi.12470 Text en © 2015 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd. This is an open access article under the terms of the Creative Commons Attribution‐NonCommercial‐NoDerivs (http://creativecommons.org/licenses/by-nc-nd/4.0/) License, which permits use and distribution in any medium, provided the original work is properly cited, the use is non‐commercial and no modifications or adaptations are made.
spellingShingle Research Articles
Singh, Vikas K.
Khan, Aamir W.
Saxena, Rachit K.
Kumar, Vinay
Kale, Sandip M.
Sinha, Pallavi
Chitikineni, Annapurna
Pazhamala, Lekha T.
Garg, Vanika
Sharma, Mamta
Sameer Kumar, Chanda Venkata
Parupalli, Swathi
Vechalapu, Suryanarayana
Patil, Suyash
Muniswamy, Sonnappa
Ghanta, Anuradha
Yamini, Kalinati Narasimhan
Dharmaraj, Pallavi Subbanna
Varshney, Rajeev K.
Next‐generation sequencing for identification of candidate genes for Fusarium wilt and sterility mosaic disease in pigeonpea (Cajanus cajan)
title Next‐generation sequencing for identification of candidate genes for Fusarium wilt and sterility mosaic disease in pigeonpea (Cajanus cajan)
title_full Next‐generation sequencing for identification of candidate genes for Fusarium wilt and sterility mosaic disease in pigeonpea (Cajanus cajan)
title_fullStr Next‐generation sequencing for identification of candidate genes for Fusarium wilt and sterility mosaic disease in pigeonpea (Cajanus cajan)
title_full_unstemmed Next‐generation sequencing for identification of candidate genes for Fusarium wilt and sterility mosaic disease in pigeonpea (Cajanus cajan)
title_short Next‐generation sequencing for identification of candidate genes for Fusarium wilt and sterility mosaic disease in pigeonpea (Cajanus cajan)
title_sort next‐generation sequencing for identification of candidate genes for fusarium wilt and sterility mosaic disease in pigeonpea (cajanus cajan)
topic Research Articles
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5054876/
https://www.ncbi.nlm.nih.gov/pubmed/26397045
http://dx.doi.org/10.1111/pbi.12470
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