ArticleBMC genomics2016
Genome-wide SSR-based association mapping for fiber quality in nation-wide upland cotton inbreed cultivars in China.
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 50 papers.
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50 citing papers in PubMed, 105 citations in OpenAlex.
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- Cotton under heat stress: a comprehensive review of molecular breeding, genomics, and multi-omics strategies.Frontiers in genetics · 2025Review
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- Genome-wide identification of the key kinesin genes during fiber and boll development in upland cotton (Gossypium hirsutum L.).Molecular genetics and genomics : MGG · 2024Article
- Genome-wide identification of the key Kinesin genes during fiber and boll development in upland cotton (Gossypium hirsutum L).Molecular genetics and genomics : MGG · 2024Article
- Genome-wide association study of the loci and candidate genes associated with agronomic traits in Amomum villosum Lour.PloS one · 2024Article
- Genomic and Cytogenetic Analysis of Synthetic Polyploids between Diploid and Tetraploid Cotton (Plants (Basel, Switzerland) · 2023Article
- Genome-Wide Association Study of Lint Percentage inInternational journal of molecular sciences · 2023Article
- CottonMD: a multi-omics database for cotton biological study.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
- Identification of superior parents with high fiber quality using molecular markers and phenotypes based on a core collection of upland cotton (Molecular breeding : new strategies in plant improvement · 2022Article
- Genetic diversity and population structure analysis for morphological traits in upland cotton (Gossypium hirsutum L.).Journal of applied genetics · 2022Article
- How financial development affects green energy finance? Relationship between environmental regulation and economic performance.Environmental science and pollution research international · 2022Article
- Genome-wide association mapping for agronomic traits in an 8-way Upland cotton MAGIC population by SLAF-seq.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2021Article
- The cellulose synthase (CesA) gene family in four Gossypium species: phylogenetics, sequence variation and gene expression in relation to fiber quality in Upland cotton.Molecular genetics and genomics : MGG · 2021Article
- Genome-wide association analysis reveals genetic variations and candidate genes associated with salt tolerance related traits in Gossypium hirsutum.BMC genomics · 2021Article
- Identification of Novel Marker-Trait Associations for Lint Yield Contributing Traits in Upland Cotton (Frontiers in plant science · 2021Article
- Genome-wide association study reveals the genetic basis of fiber quality traits in upland cotton (Gossypium hirsutum L.).BMC plant biology · 2020Article
- Non-canonical RNA-DNA differences and other human genomic features are enriched within very short tandem repeats.PLoS computational biology · 2020Article
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Authors and funding
13 authors at 3 institutions in 1 country.
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No grant is acknowledged in the PubMed record.
Abstract
backgroundSince upland cotton was introduced into China during the 1920s-1950s, hundreds of inbreed cultivars have been developed. To explore the molecular diversity, population structure and elite alleles, 503 inbred cultivars developed in China and some foreign cultivars from the United States and the Soviet Union were collected and analyzed by 494 genome-wide SSRs (Simple Sequence Repeats).
methodsFour hundred and ninety-four pairs of SSRs with high polymorphism and uniform distribution on 26 chromosomes were used to scan polymorphisms in 503 nation-wide upland cottons. The programming language R was used to make boxplots for the phenotypic traits in different environments. Molecular marker data and 6 fiber quality traits were analyzed by the method of MLM (mixed linear model) (P + G + Q + K) in the TASSEL software package on the basis of the population structure and linkage disequilibrium analysis. The loci of elite allelic variation and typical materials carrying elite alleles were identified based on phenotypic effect values.
resultsA total of 179 markers were polymorphic and generated 426 allele loci; the population based on molecular diversity was classified into seven subpopulations corresponding to pedigree origin, ecological and geographical distribution. The attenuation distance of linkage disequilibrium dropped significantly up to 0-5 cM. Association mapping for fiber quality showed that 216 marker loci were associated with fiber quality traits (P < 0.05) explaining 0.58 % ~ 5.12 % of the phenotypic variation, with an average of 2.70 %. Thirteen marker loci were coincident with other studies, and three were detected for the same trait. Seven quantitative trait loci were related to known genes in fiber development. Based on phenotypic effects, 48 typical materials that contained the elite allele loci related to fiber quality traits were identified and are widely used in practical breeding.
conclusionsThe molecular diversity and population structure of 503 nation-wide upland cottons in China were evaluated by 494 genome-wide SSRs, and association mapping for fiber quality revealed known and novel elite alleles. The molecular diversity provides a guide for parental mating in cotton breeding, and the association mapping results will aid in the fine-mapping genes related to fiber quality traits and facilitate further studies on candidate genes.
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