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SNPs in stress-responsive rice genes: validation, genotyping, functional relevance and population structure
BACKGROUND: Single nucleotide polymorphism (SNP) validation and large-scale genotyping are required to maximize the use of DNA sequence variation and determine the functional relevance of candidate genes for complex stress tolerance traits through genetic association in rice. We used the bead array...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2012
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3562522/ https://www.ncbi.nlm.nih.gov/pubmed/22921105 http://dx.doi.org/10.1186/1471-2164-13-426 |
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author | Parida, Swarup K Mukerji, Mitali Singh, Ashok K Singh, Nagendra K Mohapatra, Trilochan |
author_facet | Parida, Swarup K Mukerji, Mitali Singh, Ashok K Singh, Nagendra K Mohapatra, Trilochan |
author_sort | Parida, Swarup K |
collection | PubMed |
description | BACKGROUND: Single nucleotide polymorphism (SNP) validation and large-scale genotyping are required to maximize the use of DNA sequence variation and determine the functional relevance of candidate genes for complex stress tolerance traits through genetic association in rice. We used the bead array platform-based Illumina GoldenGate assay to validate and genotype SNPs in a select set of stress-responsive genes to understand their functional relevance and study the population structure in rice. RESULTS: Of the 384 putative SNPs assayed, we successfully validated and genotyped 362 (94.3%). Of these 325 (84.6%) showed polymorphism among the 91 rice genotypes examined. Physical distribution, degree of allele sharing, admixtures and introgression, and amino acid replacement of SNPs in 263 abiotic and 62 biotic stress-responsive genes provided clues for identification and targeted mapping of trait-associated genomic regions. We assessed the functional and adaptive significance of validated SNPs in a set of contrasting drought tolerant upland and sensitive lowland rice genotypes by correlating their allelic variation with amino acid sequence alterations in catalytic domains and three-dimensional secondary protein structure encoded by stress-responsive genes. We found a strong genetic association among SNPs in the nine stress-responsive genes with upland and lowland ecological adaptation. Higher nucleotide diversity was observed in indica accessions compared with other rice sub-populations based on different population genetic parameters. The inferred ancestry of 16% among rice genotypes was derived from admixed populations with the maximum between upland aus and wild Oryza species. CONCLUSIONS: SNPs validated in biotic and abiotic stress-responsive rice genes can be used in association analyses to identify candidate genes and develop functional markers for stress tolerance in rice. |
format | Online Article Text |
id | pubmed-3562522 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2012 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-35625222013-02-05 SNPs in stress-responsive rice genes: validation, genotyping, functional relevance and population structure Parida, Swarup K Mukerji, Mitali Singh, Ashok K Singh, Nagendra K Mohapatra, Trilochan BMC Genomics Research Article BACKGROUND: Single nucleotide polymorphism (SNP) validation and large-scale genotyping are required to maximize the use of DNA sequence variation and determine the functional relevance of candidate genes for complex stress tolerance traits through genetic association in rice. We used the bead array platform-based Illumina GoldenGate assay to validate and genotype SNPs in a select set of stress-responsive genes to understand their functional relevance and study the population structure in rice. RESULTS: Of the 384 putative SNPs assayed, we successfully validated and genotyped 362 (94.3%). Of these 325 (84.6%) showed polymorphism among the 91 rice genotypes examined. Physical distribution, degree of allele sharing, admixtures and introgression, and amino acid replacement of SNPs in 263 abiotic and 62 biotic stress-responsive genes provided clues for identification and targeted mapping of trait-associated genomic regions. We assessed the functional and adaptive significance of validated SNPs in a set of contrasting drought tolerant upland and sensitive lowland rice genotypes by correlating their allelic variation with amino acid sequence alterations in catalytic domains and three-dimensional secondary protein structure encoded by stress-responsive genes. We found a strong genetic association among SNPs in the nine stress-responsive genes with upland and lowland ecological adaptation. Higher nucleotide diversity was observed in indica accessions compared with other rice sub-populations based on different population genetic parameters. The inferred ancestry of 16% among rice genotypes was derived from admixed populations with the maximum between upland aus and wild Oryza species. CONCLUSIONS: SNPs validated in biotic and abiotic stress-responsive rice genes can be used in association analyses to identify candidate genes and develop functional markers for stress tolerance in rice. BioMed Central 2012-08-25 /pmc/articles/PMC3562522/ /pubmed/22921105 http://dx.doi.org/10.1186/1471-2164-13-426 Text en Copyright ©2012 Parida et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Research Article Parida, Swarup K Mukerji, Mitali Singh, Ashok K Singh, Nagendra K Mohapatra, Trilochan SNPs in stress-responsive rice genes: validation, genotyping, functional relevance and population structure |
title | SNPs in stress-responsive rice genes: validation, genotyping, functional relevance and population structure |
title_full | SNPs in stress-responsive rice genes: validation, genotyping, functional relevance and population structure |
title_fullStr | SNPs in stress-responsive rice genes: validation, genotyping, functional relevance and population structure |
title_full_unstemmed | SNPs in stress-responsive rice genes: validation, genotyping, functional relevance and population structure |
title_short | SNPs in stress-responsive rice genes: validation, genotyping, functional relevance and population structure |
title_sort | snps in stress-responsive rice genes: validation, genotyping, functional relevance and population structure |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3562522/ https://www.ncbi.nlm.nih.gov/pubmed/22921105 http://dx.doi.org/10.1186/1471-2164-13-426 |
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