ArticlePloS one2018
Diversity analysis and genome-wide association studies of grain shape and eating quality traits in rice (Oryza sativa L.) using DArT markers.
Article in PloS one, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 23 papers.
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23 citing papers in PubMed.
- Amylose content in rice: integrating genetics, grain filling physiology, and breeding strategies.Frontiers in plant science · 2026Review
- Rice QTL hotspots related with seed grain size, shape, weight, and color based on genome wide association study and linkage mapping.Scientific reports · 2025Article
- Molecular dissection of the genetic architecture of phenology underlying Lupinus hispanicus early flowering and adaptation to winter- or spring sowing.Scientific reports · 2025Article
- QTN detection and candidate gene identification for improved eating and cooking quality in rice using GWAS and PLS regression analysis.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2025Article
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- Pearl millet a promising fodder crop for changing climate: a review.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2024Review
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- Genome-wide association studies of Striga resistance in extra-early maturing quality protein maize inbred lines.G3 (Bethesda, Md.) · 2023Article
- Genome-Wide Association Study Revealed SNP Alleles Associated with Seed Size Traits in African Yam Bean (Genes · 2022Article
- SNP markers identification by genome wide association study for chemical quality traits of coffee (Coffea spp.) Germplasm.Molecular biology reports · 2022Article
- Genetic Diversity and Population Structure of Myanmar Rice (Plants (Basel, Switzerland) · 2021Article
- Diversity, population structure, and linkage disequilibrium among cowpea accessions.The plant genome · 2021Article
- Development of anPlants (Basel, Switzerland) · 2021Article
- Superior haplotypes towards development of low glycemic index rice with preferred grain and cooking quality.Scientific reports · 2021Article
- Genetic diversity for starch quality and alkali spreading value in sorghum.The plant genome · 2021Article
- Haplotype Variations and Evolutionary Analysis of the Granule-Bound Starch Synthase I Gene in the Korean World Rice Collection.Frontiers in plant science · 2021Article
- Genome-Wide Association Study of Root Mealiness and Other Texture-Associated Traits in Cassava.Frontiers in plant science · 2021Article
- Genome-wide association study of Striga resistance in early maturing white tropical maize inbred lines.BMC plant biology · 2020Article
- Article
- Uncovering Phenotypic Diversity and DArTseq Marker Loci Associated with Antioxidant Activity in Common Bean.Genes · 2019Article
Corrections and comments
- Erratum issued
Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Microarray-based markers such as Diversity Arrays Technology (DArT) have become the genetic markers of choice for construction of high-density maps, quantitative trait loci (QTL) mapping and genetic diversity analysis based on their efficiency and low cost. More recently, the DArT technology was further developed in combination with high-throughput next-generation sequencing (NGS) technologies to generate the DArTseq platform representing a new sequencing tool of complexity-reduced representations. In this study, we used DArTseq markers to investigate genetic diversity and genome-wide association studies (GWAS) of grain quality traits in rice (Oryza sativa L.). The study was performed using 59 rice genotypes with 525 SNPs derived from DArTseq platform. Population structure analysis revealed only two distinct genetic clusters where genotypes were grouped based on environmental adaptation and pedigree information. Analysis of molecular variance indicated a low degree of differentiation among populations suggesting the need for broadening the genetic base of the current germplasm collection. GWAS revealed 22 significant associations between DArTseq-derived SNP markers and rice grain quality traits in the test genotypes. In general, 2 of the 22 significant associations were in chromosomal regions where the QTLs associated with the given traits had previously been reported, the other 20 significant SNP marker loci were indicative of the likelihood discovery of novel alleles associated with rice grain quality traits. DArTseq-derived SNP markers that include SNP12_100006178, SNP13_3052560 and SNP14_3057360 individually co-localised with two functional gene groups that were associated with QTLs for grain width and grain length to width ratio on chromosome 3, indicating trait dependency or pleiotropic-effect loci. This study demonstrated that DArTseq markers were useful genomic resources for genome-wide association studies of rice grain quality traits to accelerate varietal development and release.
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