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A Genome-wide Combinatorial Strategy Dissects Complex Genetic Architecture of Seed Coat Color in Chickpea
The study identified 9045 high-quality SNPs employing both genome-wide GBS- and candidate gene-based SNP genotyping assays in 172, including 93 cultivated (desi and kabuli) and 79 wild chickpea accessions. The GWAS in a structured population of 93 sequenced accessions detected 15 major genomic loci...
Autores principales: | , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Frontiers Media S.A.
2015
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4647070/ https://www.ncbi.nlm.nih.gov/pubmed/26635822 http://dx.doi.org/10.3389/fpls.2015.00979 |
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author | Bajaj, Deepak Das, Shouvik Upadhyaya, Hari D. Ranjan, Rajeev Badoni, Saurabh Kumar, Vinod Tripathi, Shailesh Gowda, C. L. Laxmipathi Sharma, Shivali Singh, Sube Tyagi, Akhilesh K. Parida, Swarup K. |
author_facet | Bajaj, Deepak Das, Shouvik Upadhyaya, Hari D. Ranjan, Rajeev Badoni, Saurabh Kumar, Vinod Tripathi, Shailesh Gowda, C. L. Laxmipathi Sharma, Shivali Singh, Sube Tyagi, Akhilesh K. Parida, Swarup K. |
author_sort | Bajaj, Deepak |
collection | PubMed |
description | The study identified 9045 high-quality SNPs employing both genome-wide GBS- and candidate gene-based SNP genotyping assays in 172, including 93 cultivated (desi and kabuli) and 79 wild chickpea accessions. The GWAS in a structured population of 93 sequenced accessions detected 15 major genomic loci exhibiting significant association with seed coat color. Five seed color-associated major genomic loci underlying robust QTLs mapped on a high-density intra-specific genetic linkage map were validated by QTL mapping. The integration of association and QTL mapping with gene haplotype-specific LD mapping and transcript profiling identified novel allelic variants (non-synonymous SNPs) and haplotypes in a MATE secondary transporter gene regulating light/yellow brown and beige seed coat color differentiation in chickpea. The down-regulation and decreased transcript expression of beige seed coat color-associated MATE gene haplotype was correlated with reduced proanthocyanidins accumulation in the mature seed coats of beige than light/yellow brown seed colored desi and kabuli accessions for their coloration/pigmentation. This seed color-regulating MATE gene revealed strong purifying selection pressure primarily in LB/YB seed colored desi and wild Cicer reticulatum accessions compared with the BE seed colored kabuli accessions. The functionally relevant molecular tags identified have potential to decipher the complex transcriptional regulatory gene function of seed coat coloration and for understanding the selective sweep-based seed color trait evolutionary pattern in cultivated and wild accessions during chickpea domestication. The genome-wide integrated approach employed will expedite marker-assisted genetic enhancement for developing cultivars with desirable seed coat color types in chickpea. |
format | Online Article Text |
id | pubmed-4647070 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2015 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
spelling | pubmed-46470702015-12-03 A Genome-wide Combinatorial Strategy Dissects Complex Genetic Architecture of Seed Coat Color in Chickpea Bajaj, Deepak Das, Shouvik Upadhyaya, Hari D. Ranjan, Rajeev Badoni, Saurabh Kumar, Vinod Tripathi, Shailesh Gowda, C. L. Laxmipathi Sharma, Shivali Singh, Sube Tyagi, Akhilesh K. Parida, Swarup K. Front Plant Sci Plant Science The study identified 9045 high-quality SNPs employing both genome-wide GBS- and candidate gene-based SNP genotyping assays in 172, including 93 cultivated (desi and kabuli) and 79 wild chickpea accessions. The GWAS in a structured population of 93 sequenced accessions detected 15 major genomic loci exhibiting significant association with seed coat color. Five seed color-associated major genomic loci underlying robust QTLs mapped on a high-density intra-specific genetic linkage map were validated by QTL mapping. The integration of association and QTL mapping with gene haplotype-specific LD mapping and transcript profiling identified novel allelic variants (non-synonymous SNPs) and haplotypes in a MATE secondary transporter gene regulating light/yellow brown and beige seed coat color differentiation in chickpea. The down-regulation and decreased transcript expression of beige seed coat color-associated MATE gene haplotype was correlated with reduced proanthocyanidins accumulation in the mature seed coats of beige than light/yellow brown seed colored desi and kabuli accessions for their coloration/pigmentation. This seed color-regulating MATE gene revealed strong purifying selection pressure primarily in LB/YB seed colored desi and wild Cicer reticulatum accessions compared with the BE seed colored kabuli accessions. The functionally relevant molecular tags identified have potential to decipher the complex transcriptional regulatory gene function of seed coat coloration and for understanding the selective sweep-based seed color trait evolutionary pattern in cultivated and wild accessions during chickpea domestication. The genome-wide integrated approach employed will expedite marker-assisted genetic enhancement for developing cultivars with desirable seed coat color types in chickpea. Frontiers Media S.A. 2015-11-17 /pmc/articles/PMC4647070/ /pubmed/26635822 http://dx.doi.org/10.3389/fpls.2015.00979 Text en Copyright © 2015 Bajaj, Das, Upadhyaya, Ranjan, Badoni, Kumar, Tripathi, Gowda, Sharma, Singh, Tyagi and Parida. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. |
spellingShingle | Plant Science Bajaj, Deepak Das, Shouvik Upadhyaya, Hari D. Ranjan, Rajeev Badoni, Saurabh Kumar, Vinod Tripathi, Shailesh Gowda, C. L. Laxmipathi Sharma, Shivali Singh, Sube Tyagi, Akhilesh K. Parida, Swarup K. A Genome-wide Combinatorial Strategy Dissects Complex Genetic Architecture of Seed Coat Color in Chickpea |
title | A Genome-wide Combinatorial Strategy Dissects Complex Genetic Architecture of Seed Coat Color in Chickpea |
title_full | A Genome-wide Combinatorial Strategy Dissects Complex Genetic Architecture of Seed Coat Color in Chickpea |
title_fullStr | A Genome-wide Combinatorial Strategy Dissects Complex Genetic Architecture of Seed Coat Color in Chickpea |
title_full_unstemmed | A Genome-wide Combinatorial Strategy Dissects Complex Genetic Architecture of Seed Coat Color in Chickpea |
title_short | A Genome-wide Combinatorial Strategy Dissects Complex Genetic Architecture of Seed Coat Color in Chickpea |
title_sort | genome-wide combinatorial strategy dissects complex genetic architecture of seed coat color in chickpea |
topic | Plant Science |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4647070/ https://www.ncbi.nlm.nih.gov/pubmed/26635822 http://dx.doi.org/10.3389/fpls.2015.00979 |
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