ArticleBMC genomics2016
Identification of favorable SNP alleles and candidate genes for traits related to early maturity via GWAS in upland cotton.
Article in BMC genomics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 62 papers.
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Who cites it
62 citing papers in PubMed, 135 citations in OpenAlex.
- Detection of QTLs and QTL-environment interactions for fruit branch number in Upland cotton (Gossypium hirsutum L.) using a restricted two-stage multi-locus genome-wide association study.BMC plant biology · 2026Article
- GhTPS11, underlying an early-maturity QTL cluster on Chr. D08, positively regulates flowering through the age pathway in cotton.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Review
- Cotton genetic mapping for plant biotechnology: from markers to graph pan-genomes and sustainable breeding.Frontiers in plant science · 2026Review
- Integrative genomic approaches to unravel genomic regions and candidate genes associated with flag leaf photosynthesis at the reproductive stage in rice.Frontiers in plant science · 2026Article
- Development of a Liquid-Phased Probe Array for Upland Cotton and Its Application in Cultivar Identification.Genes · 2025Article
- Establishment of a high-throughput field defoliation data survey strategy combined with genome-wide association studies to reveal the genetic basis of defoliation in cotton.Plant phenomics (Washington, D.C.) · 2025Article
- Comprehensive evolutionary, differential expression and VIGS analyses reveal the function of GhNST1 in regulating drought tolerance and early maturity in upland cotton.Functional & integrative genomics · 2025Article
- Genome-wide association study reveals novel SNP loci and candidate genes linked to flowering time in upland cotton.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2025Article
- Fine mapping and functional validation reveal two incomplete dominant genes controlling photoperiod-sensitive flowering in Gossypium hirsutum.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2025Article
- QTL Mapping and Candidate Gene Analysis for Cotton Fiber Quality and Early Maturity Using FPlants (Basel, Switzerland) · 2025Article
- Integrative GWAS and transcriptomics revealFrontiers in plant science · 2025Article
- Identification of QTLs for early maturity-related traits based on RIL population of two elite cotton cultivars.BMC plant biology · 2024Article
- A comprehensive overview of cotton genomics, biotechnology and molecular biological studies.Science China. Life sciences · 2023Review
- Alterations in Growth Habit to Channel End-of-Season Perennial Reserves towards Increased Yield and Reduced Regrowth after Defoliation in Upland Cotton (International journal of molecular sciences · 2023Article
- Mining the candidate genes of rice panicle traits via a genome-wide association study.Frontiers in genetics · 2023Article
- QTL mapping and BSA-seq map a major QTL for the node of the first fruiting branch in cotton.Frontiers in plant science · 2023Article
- Multi-omics analysis dissects the genetic architecture of seed coat content in Brassica napus.Genome biology · 2022Article
- Genome-wide association study for seedling biomass-related traits in Gossypium arboreum L.BMC plant biology · 2022Article
- Detection of Stable Elite Haplotypes and Potential Candidate Genes of Boll Weight Across Multiple Environments via GWAS in Upland Cotton.Frontiers in plant science · 2022Article
- QTL and candidate gene identification of the node of the first fruiting branch (NFFB) by QTL-seq in upland cotton (Gossypium hirsutum L.).BMC genomics · 2021Article
2 more citing papers are in PubMed but not listed here.
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Authors and funding
16 authors at 4 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundEarly maturity is one of the most important and complex agronomic traits in upland cotton (Gossypium hirsutum L). To dissect the genetic architecture of this agronomically important trait, a population consisting of 355 upland cotton germplasm accessions was genotyped using the specific-locus amplified fragment sequencing (SLAF-seq) approach, of which a subset of 185 lines representative of the diversity among the accessions was phenotypically characterized for six early maturity traits in four environments. A genome-wide association study (GWAS) was conducted using the generalized linear model (GLM) and mixed linear model (MLM).
resultsA total of 81,675 SNPs in 355 upland cotton accessions were discovered using SLAF-seq and were subsequently used in GWAS. Thirteen significant associations between eight SNP loci and five early maturity traits were successfully identified using the GLM and MLM; two of the 13 associations were common between the models. By computing phenotypic effect values for the associations detected at each locus, 11 highly favorable SNP alleles were identified for five early maturity traits. Moreover, dosage pyramiding effects of the highly favorable SNP alleles and significant linear correlations between the numbers of highly favorable alleles and the phenotypic values of the target traits were identified. Most importantly, a major locus (rs13562854) on chromosome Dt3 and a potential candidate gene (CotAD_01947) for early maturity were detected.
conclusionsThis study identified highly favorable SNP alleles and candidate genes associated with early maturity traits in upland cotton. The results demonstrate that GWAS is a powerful tool for dissecting complex traits and identifying candidate genes. The highly favorable SNP alleles and candidate genes for early maturity traits identified in this study should be show high potential for improvement of early maturity in future cotton breeding programs.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.