ArticleBMC genomics2012
SNPs in stress-responsive rice genes: validation, genotyping, functional relevance and population structure.
Article in BMC genomics, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 47 papers, 1 of them a synthesis that pooled it.
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47 citing papers in PubMed, 1 synthesis or guideline pooled it, 73 citations in OpenAlex.
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- Genetic diversity and population structure analysis of Asian and African aromatic rice (Journal of genetics · 2019Article
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- Genotyping-by-Sequencing ofEvolutionary bioinformatics online · 2019Article
- Discovery of Functional SNPs via Genome-Wide Exploration of Malaysian Pigmented Rice Varieties.International journal of genomics · 2019Article
- A catalog of annotated high-confidence SNPs from exome capture and sequencing reveals highly polymorphic genes in Norway spruce (Picea abies).BMC genomics · 2018Article
- Genomics-Assisted Identification and Characterization of the Genetic Variants Underlying Differential Nitrogen Use Efficiencies in Allotetraploid Rapeseed Genotypes.G3 (Bethesda, Md.) · 2018Article
- Role of genomics in promoting the utilization of plant genetic resources in genebanks.Briefings in functional genomics · 2018Review
- Development and evaluation of high-density AxiomPlant biotechnology journal · 2018Article
- Genetic Diversity, Population Structure, and Linkage Disequilibrium of a Core Collection ofFrontiers in plant science · 2017Article
- In Silico identification of SNP diversity in cultivated and wild tomato species: insight from molecular simulations.Scientific reports · 2016Article
- Rice Improvement Through Genome-Based Functional Analysis and Molecular Breeding in India.Rice (New York, N.Y.) · 2016Article
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Authors and funding
5 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundSingle 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.
resultsOf 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.
conclusionsSNPs 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.
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