ArticleBMC genomics2015
Genetic variation and association mapping for 12 agronomic traits in indica rice.
Article in BMC genomics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 44 papers.
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44 citing papers in PubMed, 80 citations in OpenAlex.
- Genome-wide association study uncovers the genetic loci for yield-related traits in waxy rice.Journal of applied genetics · 2026Article
- CWAGS: multi-trait genomic selection using channel weighted attention convolutional network.BMC genomics · 2026Article
- MoEGP: an efficient crop genomic prediction approach based on the mixture of experts network.Plant methods · 2026Article
- Genome-wide association study identifies elite alleles of FLA2 and FLA9 controlling flag leaf angle in rice.BMC genomics · 2025Article
- Integrative genomic and transcriptomic dissection of salt tolerance forFrontiers in plant science · 2025Article
- Deciphering the genetic basis of salinity tolerance in a diverse panel of cultivated and wild soybean accessions by genome-wide association mapping.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2024Article
- Genome wide association studies on seven yield-related traits of 183 rice varieties in Bangladesh.Plant direct · 2024Article
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- Analysis of Genetic Diversity in Adzuki Beans (Plants (Basel, Switzerland) · 2023Article
- A transformer-based genomic prediction method fused with knowledge-guided module.Briefings in bioinformatics · 2023Article
- Integrating genome-wide association study into genomic selection for the prediction of agronomic traits in rice (Molecular breeding : new strategies in plant improvement · 2023Article
- GWAS Combined with WGCNA of Transcriptome and Metabolome to Excavate Key Candidate Genes for Rice Anaerobic Germination.Rice (New York, N.Y.) · 2023Article
- Article
- Identification of a key locus, qNL3.1, associated with seed germination under salt stress via a genome-wide association study in rice.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2023Article
- HGD: an integrated homologous gene database across multiple species.Nucleic acids research · 2023Article
- Genome-wide association study of fiber yield-related traits uncovers the novel genomic regions and candidate genes in Indian upland cotton (Frontiers in plant science · 2023Article
- Leaf Count Aided Novel Framework for Rice (Plants (Basel, Switzerland) · 2022Article
- Genome-wide association analysis to delineate high-quality SNPs for seed micronutrient density in chickpea (Cicer arietinum L.).Scientific reports · 2022Article
- Genome-Wide Association Study Identifies a Rice Panicle Blast Resistance Gene,International journal of molecular sciences · 2022Article
- Identification of QTLs/ Candidate Genes for Seed Mineral Contents in Common Bean (Frontiers in genetics · 2022Article
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Authors and funding
12 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundIncreasing rice (Oryza sativa L.) yield is a crucial challenge for modern agriculture. The ideal plant architecture is considered to be critical to enhance rice yield. Elite plant morphological traits should include compact plant type, short stature, few unproductive tillers, thick and sturdy stems and erect leaves. To reveal the genetic variations of important morphological traits, 523 germplasm accessions were genotyped using the Illumina custom-designed array containing 5,291 single nucleotide polymorphisms (SNPs) and phenotyped in two independent environments. Genome-wide association studies were performed to uncover the genotypic and phenotypic variations using a mixed linear model.
resultsIn total, 126 and 172 significant loci were identified and these loci explained an average of 34.45% and 39.09% of the phenotypic variance in two environments, respectively, and 16 of 298 (~5.37%) loci were detected across the two environments. For the 16 loci, 423 candidate genes were predicted in a 200-kb region (±100 kb of the peak SNP). Expression-level analyses identified four candidate genes as the most promising regulators of tiller angle. Known (NAL1 and Rc) and new significant loci showed pleiotropy and gene linkage. In addition, a long genome region covering ~1.6 Mb on chromosome 11 was identified, which may be critical for rice leaf architecture because of a high association with flag leaf length and the ratio of flag leaf length and width. The pyramid effect of the elite alleles indicated that these significant loci could be beneficial for rice plant architecture improvements in the future. Finally, 37 elite varieties were chosen as breeding donors for further rice plant architectural modifications.
conclusionsThis study detected multiple novel loci and candidate genes related to rice morphological traits, and the work demonstrated that genome-wide association studies are powerful strategies for uncovering the genetic variations of complex traits and identifying candidate genes in rice, even though the linkage disequilibrium decayed slowly in self-pollinating species. Future research will focus on the biological validation of the candidate genes, and elite varieties will also be of interest in genome selection and breeding by design.
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