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.

BackgroundCotton (Gossypium spp.) is the largest producer of natural fibers for textile and is an important crop worldwide. Crop production is comprised primarily of G. hirsutum L., an allotetraploid. However, elite cultivars express very small amounts of variation due to the species monophyletic origin, domestication and further bottlenecks due to selection. Conversely, wild cotton species harbor extensive genetic diversity of prospective utility to improve many beneficial agronomic traits, fiber characteristics, and resistance to disease and drought. Introgression of traits from wild species can provide a natural way to incorporate advantageous traits through breeding to generate higher-producing cotton cultivars and more sustainable production systems. Interspecific introgression efforts by conventional methods are very time-consuming and costly, but can be expedited using marker-assisted selection.ResultsUsing transcriptome sequencing we have developed the first gene-associated single nucleotide polymorphism (SNP) markers for wild cotton species G. tomentosum, G. mustelinum, G. armourianum and G. longicalyx. Markers were also developed for a secondary cultivated species G. barbadense cv. 3–79. A total of 62,832 non-redundant SNP markers were developed from the five wild species which can be utilized for interspecific germplasm introgression into cultivated G. hirsutum and are directly associated with genes. Over 500 of the G. barbadense markers have been validated by whole-genome radiation hybrid mapping. Overall 1,060 SNPs from the five different species have been screened and shown to produce acceptable genotyping assays.ConclusionsThis large set of 62,832 SNPs relative to cultivated G. hirsutum will allow for the first high-density mapping of genes from five wild species that affect traits of interest, including beneficial agronomic and fiber characteristics. Upon mapping, the markers can be utilized for marker-assisted introgression of new germplasm into cultivated cotton and in subsequent breeding of agronomically adapted types, including cultivar development.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-945) contains supplementary material, which is available to authorized users.

Cotton (Gossypium hirsutum L.) germplasm line BARBREN-713 (Reg. No. GP-987, PI 671965) was developed and released by the USDA-ARS, Mississippi Agricultural and Forestry Experiment Station, Texas A&M AgriLife Research, and Cotton Incorporated in 2012. The objective of the release was to provide public and private breeders with an agronomically desirable germplasm that is resistant to both the reniform nematode (Rotylenchulus reniformis Linford and Oliveira) and the root-knot nematode [Meloidogyne incognita (Kofoid and White) Chitwood]. The line also has excellent seedling vigor in ields infested with nematodes and fungal root rot pathogens, such as Thielaviopsis basicola, Rhizoctonia solani and Fusarium spp. Resistance to reniform nematode was transferred from G. barbadense GB713 (PI 608139) and is associated primarily with the Ren 2 GB713 gene on chromosome 21. Resistance to root-knot nematode was transferred from the germplasm line M-315 RNR (PI 592514), 'LA 887', or 'Acala Nem-X' and is associated primarily with the Mi-1 gene on chromosome 11. The codominant simple sequence repeat markers, BNL 3279_105 and CIR 316_202, respectively, were closely linked to the resistance genes. A single nucleotide polymorphism marker, Gl-187401, also was developed to detect the Ren 2 GB713 gene. In controlled environment assays, BARBREN-713 suppressed reproduction of both nematodes by 90% or more. It also reduced reniform nematode populations in the ield at eight locations in four states. The line has iber quality similar to M-315 RNR but yielded more than M-315 RNR in reniform nematode-infested ields. Abbreviations: QTL, quantitative trait locus; SNP, single nucleotide polymorphism.

A bacterial artificial chromosome library and BAC-end sequences for cultivated cotton (Gossypium hirsutum L.) have recently been developed. This report presents genome-wide single nucleotide polymorphism (SNP) mining utilizing resequencing data with BAC-end sequences as a reference by alignment of 12 G. hirsutum L. lines, one G. barbadense L. line, and one G. longicalyx Hutch and Lee line. A total of 132,262 intraspecific SNPs have been developed for G. hirsutum, whereas 223,138 and 470,631 interspecific SNPs have been developed for G. barbadense and G. longicalyx, respectively. Using a set of interspecific SNPs, 11 randomly selected and 77 SNPs that are putatively associated with the homeologous chromosome pair 12 and 26, we mapped 77 SNPs into two linkage groups representing these chromosomes, spanning a total of 236.2 cM in an interspecific F2 population (G. barbadense 3-79 × G. hirsutum TM-1). The mapping results validated the approach for reliably producing large numbers of both intraspecific and interspecific SNPs aligned to BAC-ends. This will allow for future construction of high-density integrated physical and genetic maps for cotton and other complex polyploid genomes. The methods developed will allow for future Gossypium resequencing data to be automatically genotyped for identified SNPs along the BAC-end sequence reference for anchoring sequence assemblies and comparative studies.

Cotton (Gossypium hirsutum L.) germplasm lines LONREN-1 (Reg. No. GP-977, PI 669509) and LONREN-2 (Reg. No. GP-978, PI 669510) were developed and released by the USDA-ARS, Texas Agricultural Experiment Station and Cotton Incorporated in 2007 to provide breeders with desirable germplasm resistant to the reniform nematode (Rotylenchulus reniformis Linford and Oliveira). The resistance was transferred from wild G. longicalyx via a triple-species hybrid. Crosses, backcrosses, and single plant selections were used to develop the F 2 progeny used for seed production. Resistance was followed with the codominant simple sequence repeat BNL 3279_114 marker, located 1.4 cM proximal and the phenotypic marker 'greenfuzz' (LTCOL_F) located 4.5 cM distal to the Ren lon resistance gene on chromosome 11. A single nucleotide polymorphism marker also was developed for rapid screening of large numbers of seed. The introgressed chromosome segment is smaller in LONREN-2 than in LONREN-1. Both lines reduced reniform populations by 95% in growth chamber bioassays and by 50 to 90% in ields. In the absence of nematodes in the ield, growth rate, yield, and iber quality of the lines were similar to that of the 'Fibermax 958' parent. In the presence of reniform nematodes in the ield, the lines often showed stunting and yield losses, probably due to enhanced severity of fungal seedling diseases, especially Thielaviopsis root rot. The seedling diseases in LONRENs were diminished by control measures such as fungicides, nematicides, and crop rotation with corn or sorghum, and were negligible in a second year of planting in the same ield.