ArticleBMC genomics2016
Fine mapping and RNA-Seq unravels candidate genes for a major QTL controlling multiple fiber quality traits at the T1 region 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 23 papers.
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Who cites it
23 citing papers in PubMed.
- Independent component analysis deciphers the genetic basis of cotton fiber elongation through eQTLs and sQTLs.Journal of advanced research · 2026Article
- Cotton genetic mapping for plant biotechnology: from markers to graph pan-genomes and sustainable breeding.Frontiers in plant science · 2026Review
- QTL Mapping and Candidate Gene Screening for Enhancing Oil Content in Silage Maize.Plants (Basel, Switzerland) · 2025Article
- Molecular dissection of quantitative variation in fiber elongation betweenFrontiers in plant science · 2025Article
- An aldehyde dehydrogenase gene,Frontiers in plant science · 2024Article
- Integrated Bulk Segregant Analysis, Fine Mapping, and Transcriptome Revealed QTLs and Candidate Genes Associated with Drought Adaptation in Wild Watermelon.International journal of molecular sciences · 2023Article
- Genetic dissection of lint percentage in short-season cotton using combined QTL mapping and RNA-seq.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2023Article
- Design, execution, and interpretation of plant RNA-seq analyses.Frontiers in plant science · 2023Review
- Detection of Chromosomal Segments Introgressed from Wild Species of Carrot into Cultivars: Quantitative Trait Loci Mapping for Morphological Features in Backcross Inbred Lines.Plants (Basel, Switzerland) · 2022Article
- Cotton proteomics: Dissecting the stress response mechanisms in cotton.Frontiers in plant science · 2022Review
- Fine mapping of a kernel length-related gene with potential value for maize breeding.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2021Article
- Identification of Candidate Cotton Genes Associated With Fiber Length Through Quantitative Trait Loci Mapping and RNA-Sequencing Using a Chromosome Segment Substitution Line.Frontiers in plant science · 2021Article
- Genomic Insight into Differentiation and Selection Sweeps in the Improvement of Upland Cotton.Plants (Basel, Switzerland) · 2020Article
- Genome-wide quantitative trait loci reveal the genetic basis of cotton fibre quality and yield-related traits in a Gossypium hirsutum recombinant inbred line population.Plant biotechnology journal · 2020Article
- Identifying favorable alleles for improving key agronomic traits in upland cotton.BMC plant biology · 2019Article
- Fiber Quality Improvement in Upland Cotton (Frontiers in plant science · 2019Review
- Natural variation in a CENTRORADIALIS homolog contributed to cluster fruiting and early maturity in cotton.BMC plant biology · 2018Article
- Recent insights into cotton functional genomics: progress and future perspectives.Plant biotechnology journal · 2018Review
- A multiple near isogenic line (multi-NIL) RNA-seq approach to identify candidate genes underpinning QTL.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2018Article
- Fine mapping and candidate gene analysis of qFL-chr1, a fiber length QTL in cotton.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2017Article
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12 authors.
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Abstract
backgroundImproving fiber quality is a major challenge in cotton breeding, since the molecular basis of fiber quality traits is poorly understood. Fine mapping and candidate gene prediction of quantitative trait loci (QTL) controlling cotton fiber quality traits can help to elucidate the molecular basis of fiber quality. In our previous studies, one major QTL controlling multiple fiber quality traits was identified near the T1 locus on chromosome 6 in Upland cotton.
resultsTo finely map this major QTL, the F2 population with 6975 individuals was established from a cross between Yumian 1 and a recombinant inbred line (RIL118) selected from a recombinant inbred line population (T586 × Yumian 1). The QTL was mapped to a 0.28-cM interval between markers HAU2119 and SWU2302. The QTL explained 54.7 % (LOD = 222.3), 40.5 % (LOD = 145.0), 50.0 % (LOD = 194.3) and 30.1 % (LOD = 100.4) of phenotypic variation with additive effects of 2.78, -0.43, 2.92 and 1.90 units for fiber length, micronaire, strength and uniformity, respectively. The QTL region corresponded to a 2.7-Mb interval on chromosome 10 in the G. raimondii genome sequence and a 5.3-Mb interval on chromosome A06 in G. hirsutum. The fiber of Yumian 1 was much longer than that of RIL118 from 3 DPA to 7 DPA. RNA-Seq of ovules at 0 DPA and fibers at 5 DPA from Yumian 1 and RIL118 showed four genes in the QTL region of the G. raimondii genome to be extremely differentially expressed. RT-PCR analysis showed three genes in the QTL region of the G. hirsutum genome to behave similarly.
conclusionsThis study mapped a major QTL influencing four fiber quality traits to a 0.28-cM interval and identified three candidate genes by RNA-Seq and RT-PCR analysis. Integration of fine mapping and RNA-Seq is a powerful strategy to uncover candidates for QTL in large genomes.
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