High-throughput genotyping arrays provide a standardized resource for plant breeding communities that are useful for a breadth of applications including high-density genetic mapping, genome-wide association studies (GWAS), genomic selection (GS), complex trait dissection, and studying patterns of genomic diversity among cultivars and wild accessions. We have developed the CottonSNP63K, an Illumina Infinium array containing assays for 45,104 putative intraspecific single nucleotide polymorphism (SNP) markers for use within the cultivated cotton species Gossypium hirsutum L. and 17,954 putative interspecific SNP markers for use with crosses of other cotton species with G. hirsutum. The SNPs on the array were developed from 13 different discovery sets that represent a diverse range of G. hirsutum germplasm and five other species: G. barbadense L., G. tomentosum Nuttal × Seemann, G. mustelinum Miers × Watt, G. armourianum Kearny, and G. longicalyx J.B. Hutchinson and Lee. The array was validated with 1,156 samples to generate cluster positions to facilitate automated analysis of 38,822 polymorphic markers. Two high-density genetic maps containing a total of 22,829 SNPs were generated for two F2 mapping populations, one intraspecific and one interspecific, and 3,533 SNP markers were co-occurring in both maps. The produced intraspecific genetic map is the first saturated map that associates into 26 linkage groups corresponding to the number of cotton chromosomes for a cross between two G. hirsutum lines. The linkage maps were shown to have high levels of collinearity to the JGI G. raimondii Ulbrich reference genome sequence. The CottonSNP63K array, cluster file and associated marker sequences constitute a major new resource for the global cotton research community.

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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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-017-0981-y) contains supplementary material, which is available to authorized users.

Eight extra‐long staple (ELS) upland cotton (Gossypium hirsutum L.) germplasm lines, TAM A106‐15 ELS (Reg. No. GP‐894, PI 654359), TAM A106‐16 ELS (Reg. No. GP‐895, PI 654360), TAM B147‐21 ELS (Reg. No. GP‐896, PI 654361), TAM B182‐33 ELS (Reg. No. GP‐897, PI 654362), TAM C66‐16 ELS (Reg. No. GP‐898, PI 654363), TAM C66‐26 ELS (Reg. No. GP‐899, PI 654364), TAM C147‐42 ELS (Reg. No. GP‐900, PI 654365), and TAM C155‐22 ELS (Reg. No. GP‐901, PI 654366), were developed by the Cotton Improvement Laboratory, Department of Soil and Crop Sciences, Texas AgriLife Research (Texas A&M University, College Station), and released in 2008 as part of an ongoing effort to create germplasm with combinations of improved fiber quality parameters, especially upper half mean (UHM) length and fiber bundle strength. All ELS lines exhibited high volume instrument (HVI) UHM fiber length greater than 32.0 mm, which is the minimum UHM to be classified as ELS upland according to Cotton Incorporated. Seven of the eight lines equaled or exceeded the minimum UHM length of 34.8 mm for pima (G. barbadense L.) in the USDA 2007 pima loan schedule in at least one performance trial. Fiber bundle strengths of the eight lines were equal to or higher than ‘Fibermax 832’.