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Genome-wide generation and genotyping of informative SNPs to scan molecular signatures for seed yield in chickpea
We discovered 2150 desi and 2199 kabuli accessions-derived SNPs by cultivar-wise individual assembling of sequence-reads generated through genotyping-by-sequencing of 92 chickpea accessions. Subsequent large-scale validation and genotyping of these SNPs discovered 619 desi accessions-derived (DAD) S...
Autores principales: | , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group UK
2018
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6125345/ https://www.ncbi.nlm.nih.gov/pubmed/30185866 http://dx.doi.org/10.1038/s41598-018-29926-1 |
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author | Basu, Udita Srivastava, Rishi Bajaj, Deepak Thakro, Virevol Daware, Anurag Malik, Naveen Upadhyaya, Hari D. Parida, Swarup K. |
author_facet | Basu, Udita Srivastava, Rishi Bajaj, Deepak Thakro, Virevol Daware, Anurag Malik, Naveen Upadhyaya, Hari D. Parida, Swarup K. |
author_sort | Basu, Udita |
collection | PubMed |
description | We discovered 2150 desi and 2199 kabuli accessions-derived SNPs by cultivar-wise individual assembling of sequence-reads generated through genotyping-by-sequencing of 92 chickpea accessions. Subsequent large-scale validation and genotyping of these SNPs discovered 619 desi accessions-derived (DAD) SNPs, 531 kabuli accessions-derived (KAD) SNPs, 884 multiple accessions-derived (MAD) SNPs and 1083 two accessions (desi ICC 4958 and kabuli CDC Frontier)-derived (TAD) SNPs that were mapped on eight chromosomes. These informative SNPs were annotated in coding/non-coding regulatory sequence components of genes. The MAD-SNPs were efficient to detect high intra-specific polymorphic potential and wide natural allelic diversity level including high-resolution admixed-population genetic structure and precise phylogenetic relationship among 291 desi and kabuli accessions. This signifies their effectiveness in introgression breeding and varietal improvement studies targeting useful agronomic traits of chickpea. Six trait-associated genes with SNPs including quantitative trait nucleotides (QTNs) in combination explained 27.5% phenotypic variation for seed yield per plant (SYP). A pentatricopeptide repeat (PPR) gene with a synonymous-coding SNP/QTN significantly associated with SYP trait was found most-promising in chickpea. The essential information delineated can be of immense utility in genomics-assisted breeding applications to develop high-yielding chickpea cultivars. |
format | Online Article Text |
id | pubmed-6125345 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | Nature Publishing Group UK |
record_format | MEDLINE/PubMed |
spelling | pubmed-61253452018-09-10 Genome-wide generation and genotyping of informative SNPs to scan molecular signatures for seed yield in chickpea Basu, Udita Srivastava, Rishi Bajaj, Deepak Thakro, Virevol Daware, Anurag Malik, Naveen Upadhyaya, Hari D. Parida, Swarup K. Sci Rep Article We discovered 2150 desi and 2199 kabuli accessions-derived SNPs by cultivar-wise individual assembling of sequence-reads generated through genotyping-by-sequencing of 92 chickpea accessions. Subsequent large-scale validation and genotyping of these SNPs discovered 619 desi accessions-derived (DAD) SNPs, 531 kabuli accessions-derived (KAD) SNPs, 884 multiple accessions-derived (MAD) SNPs and 1083 two accessions (desi ICC 4958 and kabuli CDC Frontier)-derived (TAD) SNPs that were mapped on eight chromosomes. These informative SNPs were annotated in coding/non-coding regulatory sequence components of genes. The MAD-SNPs were efficient to detect high intra-specific polymorphic potential and wide natural allelic diversity level including high-resolution admixed-population genetic structure and precise phylogenetic relationship among 291 desi and kabuli accessions. This signifies their effectiveness in introgression breeding and varietal improvement studies targeting useful agronomic traits of chickpea. Six trait-associated genes with SNPs including quantitative trait nucleotides (QTNs) in combination explained 27.5% phenotypic variation for seed yield per plant (SYP). A pentatricopeptide repeat (PPR) gene with a synonymous-coding SNP/QTN significantly associated with SYP trait was found most-promising in chickpea. The essential information delineated can be of immense utility in genomics-assisted breeding applications to develop high-yielding chickpea cultivars. Nature Publishing Group UK 2018-09-05 /pmc/articles/PMC6125345/ /pubmed/30185866 http://dx.doi.org/10.1038/s41598-018-29926-1 Text en © The Author(s) 2018 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. |
spellingShingle | Article Basu, Udita Srivastava, Rishi Bajaj, Deepak Thakro, Virevol Daware, Anurag Malik, Naveen Upadhyaya, Hari D. Parida, Swarup K. Genome-wide generation and genotyping of informative SNPs to scan molecular signatures for seed yield in chickpea |
title | Genome-wide generation and genotyping of informative SNPs to scan molecular signatures for seed yield in chickpea |
title_full | Genome-wide generation and genotyping of informative SNPs to scan molecular signatures for seed yield in chickpea |
title_fullStr | Genome-wide generation and genotyping of informative SNPs to scan molecular signatures for seed yield in chickpea |
title_full_unstemmed | Genome-wide generation and genotyping of informative SNPs to scan molecular signatures for seed yield in chickpea |
title_short | Genome-wide generation and genotyping of informative SNPs to scan molecular signatures for seed yield in chickpea |
title_sort | genome-wide generation and genotyping of informative snps to scan molecular signatures for seed yield in chickpea |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6125345/ https://www.ncbi.nlm.nih.gov/pubmed/30185866 http://dx.doi.org/10.1038/s41598-018-29926-1 |
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