ArticleBMC plant biology2017
Diversity analysis of cotton (Gossypium hirsutum L.) germplasm using the CottonSNP63K Array.
Article in BMC plant biology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed, 75 citations in OpenAlex.
- Genetic diversity and population structure analysis of cotton (Gossypium hirsutum L.) genotypes using DArTseq technology.BMC genomics · 2026Article
- Population structure, genetic diversity analyses and genome-wide association study of photoperiod sensitivity in Pima cotton (Gossypium barbadense L.).BMC plant biology · 2026Article
- Speed breeding in upland cotton (Frontiers in plant science · 2026Review
- Development of a Liquid-Phased Probe Array for Upland Cotton and Its Application in Cultivar Identification.Genes · 2025Article
- The National Plant Germplasm System cotton collection-a review of germplasm resources, phenotypic characterization, and genomic variation.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2025Review
- Environmental pressures shape regional patterns of genetic diversity and ancestry in cotton landraces.Frontiers in plant science · 2025Article
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- Genome-Wide Association Analysis of Effective Tillers in Rice under Different Nitrogen Gradients.International journal of molecular sciences · 2024Article
- Limited genetic diversity found among genotypes of the Entada landrace (Frontiers in plant science · 2024Article
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- Effective identification of varieties by nucleotide polymorphisms and its application for essentially derived variety identification in rice.BMC bioinformatics · 2022Article
- Genetics, Breeding and Genetic Engineering to Improve Cottonseed Oil and Protein: A Review.Frontiers in plant science · 2022Review
- Genome-Wide Dissection of the Genetic Basis for Drought Tolerance inFrontiers in plant science · 2022Article
- Dissection of the Genetic Basis of Rice Panicle Architecture Using a Genome-wide Association Study.Rice (New York, N.Y.) · 2021Article
- Population structure and genetic diversity of the Pee Dee cotton breeding program.G3 (Bethesda, Md.) · 2021Article
- Finding Needles in a Haystack: Using Geo-References to Enhance the Selection and Utilization of Landraces in Breeding for Climate-Resilient Cultivars of Upland Cotton (Plants (Basel, Switzerland) · 2021Review
- Evaluation and genome-wide association study of resistance to bacterial blight race 18 in U.S. Upland cotton germplasm.Molecular genetics and genomics : MGG · 2021Article
- Reconstruction of the Largest Pedigree Network for Pear Cultivars and Evaluation of the Genetic Diversity of the USDA-ARS NationalG3 (Bethesda, Md.) · 2020Article
- Genomic diversifications of five Gossypium allopolyploid species and their impact on cotton improvement.Nature genetics · 2020Article
- A genome-wide comparative analysis of bZIP transcription factors inPhysiology and molecular biology of plants : an international journal of functional plant biology · 2020Article
Corrections and comments
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Authors and funding
23 authors at 12 institutions in 4 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundCotton germplasm resources contain beneficial alleles that can be exploited to develop germplasm adapted to emerging environmental and climate conditions. Accessions and lines have traditionally been characterized based on phenotypes, but phenotypic profiles are limited by the cost, time, and space required to make visual observations and measurements. With advances in molecular genetic methods, genotypic profiles are increasingly able to identify differences among accessions due to the larger number of genetic markers that can be measured. A combination of both methods would greatly enhance our ability to characterize germplasm resources. Recent efforts have culminated in the identification of sufficient SNP markers to establish high-throughput genotyping systems, such as the CottonSNP63K array, which enables a researcher to efficiently analyze large numbers of SNP markers and obtain highly repeatable results. In the current investigation, we have utilized the SNP array for analyzing genetic diversity primarily among cotton cultivars, making comparisons to SSR-based phylogenetic analyses, and identifying loci associated with seed nutritional traits.
resultsThe SNP markers distinctly separated G. hirsutum from other Gossypium species and distinguished the wild from cultivated types of G. hirsutum. The markers also efficiently discerned differences among cultivars, which was the primary goal when designing the CottonSNP63K array. Population structure within the genus compared favorably with previous results obtained using SSR markers, and an association study identified loci linked to factors that affect cottonseed protein content.
conclusionsOur results provide a large genome-wide variation data set for primarily cultivated cotton. Thousands of SNPs in representative cotton genotypes provide an opportunity to finely discriminate among cultivated cotton from around the world. The SNPs will be relevant as dense markers of genome variation for association mapping approaches aimed at correlating molecular polymorphisms with variation in phenotypic traits, as well as for molecular breeding approaches in cotton.
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