ArticleBMC genomics2021
Uncovering the genetic mechanisms regulating panicle architecture in rice with GPWAS and GWAS.
Article in BMC genomics, 2021. 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 29 papers.
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Who cites it
29 citing papers in PubMed.
- Genetic architecture and candidate loci associated with growth and yield-related traits in sweet fig banana (Musa acuminata cv Sotoumon, AA).BMC genomics · 2026Article
- Prediction of plant phase-separating proteins using positive-unlabeled learning.Genome biology · 2026Article
- Genome-wide Association Study Identifies SNPs and Candidate Genes Associated with Abdominal Meat Weight and Meat Yield of red Swamp Crayfish Procambarus clarkii.Marine biotechnology (New York, N.Y.) · 2026Article
- Mapping novel QTLs associated with grain number and primary branching in rice using new plant type derived RILs.BMC plant biology · 2026Article
- Genome-Wide Association Study Reveals Genetic Loci, Candidate Genes and Favorable Haplotypes for Important Agronomic Traits inJournal of fungi (Basel, Switzerland) · 2026Article
- Genome-wide association study identifies candidate genes associated with leaf morphological traits in grape (Frontiers in plant science · 2026Article
- The OsAP4-OsCATA/OsCATC Regulatory Module Orchestrates Drought Stress Adaptation in Rice Seedlings Through ROS Scavenging.Plants (Basel, Switzerland) · 2025Article
- Genomic Regions and Molecular Markers Associated with Deeper Rooting to Improve Grain Yield in Aerobic Rice (Oryza sativa L.) Production Systems.Rice (New York, N.Y.) · 2025Article
- Identification of quantitative trait nucleotides for grain quality in bread wheat under heat stress.Scientific reports · 2025Article
- Linkage Mapping and Identification of Candidate Genes for Cold Tolerance in Rice (Oryza Sativa L.) at the Bud Bursting Stage.Rice (New York, N.Y.) · 2025Article
- Genome-wide association study identifies candidate SNP markers and genes associated with low nitrogen tolerance inFrontiers in plant science · 2025Article
- Genomic regions associated with flag leaf and panicle architecture in rice (Oryza sativa L.).BMC genomics · 2024Article
- Characterization of quantitative trait loci from DJ123 (Molecular breeding : new strategies in plant improvement · 2024Article
- Genetic insights into agronomic and morphological traits of drug-type cannabis revealed by genome-wide association studies.Scientific reports · 2024Article
- Genomic introgressions from African rice (Oryza glaberrima) in Asian rice (O. sativa) lead to the identification of key QTLs for panicle architecture.BMC genomics · 2023Article
- Genome-wide association analysis identifies natural allelic variants associated with panicle architecture variation in African rice, Oryza glaberrima Steud.G3 (Bethesda, Md.) · 2023Article
- Article
- Identification of Newer Stable Genetic Sources for High Grain Number per Panicle and Understanding the Gene Action for Important Panicle Traits in Rice.Plants (Basel, Switzerland) · 2023Article
- Mining the candidate genes of rice panicle traits via a genome-wide association study.Frontiers in genetics · 2023Article
- Integrated multi-locus genome-wide association studies and transcriptome analysis for seed yield and yield-related traits inFrontiers in plant science · 2023Article
Corrections and comments
- Erratum issued
Authors and funding
8 authors.
Funding
Abstract
backgroundThe number of panicles per plant, number of grains per panicle, and 1000-grain weight are important factors contributing to the grain yield per plant in rice. The Rice Diversity Panel 1 (RDP1) contains a total of 421 purified, homozygous rice accessions representing diverse genetic variations within O. sativa. The release of High-Density Rice Array (HDRA, 700 k SNPs) dataset provides a new opportunity to discover the genetic variants of panicle architectures in rice.
resultsIn this report, a new method genome-phenome wide association study (GPWAS) was performed with 391 individuals and 27 traits derived from RDP1 to scan the relationship between the genes and multi-traits. A total of 1985 gene models were linked to phenomic variation with a p-value cutoff of 4.49E-18. Besides, 406 accessions derived from RDP1 with 411,066 SNPs were used to identify QTLs associated with the total spikelets number per panicle (TSNP), grain number per panicle (GNP), empty grain number per panicle (EGNP), primary branch number (PBN), panicle length (PL), and panicle number per plant (PN) by GLM, MLM, FarmCPU, and BLINK models for genome-wide association study (GWAS) analyses. A total of 18, 21, 18, 17, 15, and 17 QTLs were identified tightly linked with TSNP, GNP, EGNP, PBN, PL, and PN, respectively. Then, a total of 23 candidate genes were mapped simultaneously using both GWAS and GPWAS methods, composed of 6, 4, 5, 4, and 4 for TSNP, GNP, EGNP, PBN, and PL. Notably, one overlapped gene (Os01g0140100) were further investigated based on the haplotype and gene expression profile, indicating this gene might regulate the TSNP or panicle architecture in rice.
conclusionsNearly 30 % (30/106) QTLs co-located with the previous published genes or QTLs, indicating the power of GWAS. Besides, GPWAS is a new method to discover the relationship between genes and traits, especially the pleiotropy genes. Through comparing the results from GWAS and GPWAS, we identified 23 candidate genes related to panicle architectures in rice. This comprehensive study provides new insights into the genetic basis controlling panicle architectures in rice, which lays a foundation in rice improvement.
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