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.
Microsatellite [simple-sequence repeat (SSR)] markers were developed and positioned on the genetic map of tetraploid cotton. Three hundred and ninety-two unique microsatellite sequences, all but two containing a (CA/GT) repeat, were isolated, and the deduced primers were used to screen for polymorphism between the Gossypium hirsutum and G. barbadense parents of the mapping population analyzed in our laboratory. The observed rate of polymorphism was 56%. The 204 polymorphic SSRs revealed 261 segregating bands, which ultimately gave rise to 233 mapped loci. The updated status of our genetic map is now of 1,160 loci and 5,519 cM, with an average distance between two loci of 4.8 cM. The presence of a total of 466 microsatellite loci, with an average distance of 12 cM between two SSR loci, now provides wide coverage of the genome of tetraploid cotton and thus represents a powerful means for the production of a consensus map and for the effective tracking of QTLs.
Cotton fiber properties are essential predictors of yarn performance. The suite of fiber quality traits that collectively affect the utility of the fiber for the textile industry include the length, the strength, the fineness and the color. These properties have been shown to be moderately to highly heritable. In an attempt to overcome the limitations of conventional breeding we undertook a marker‐assisted selection program aimed at introgressing fiber quality QTLs from Gossypium barbadense L. into G. hirsutum L. We describe the QTL analysis of 11 fiber properties measured on three phenotypic data sets. The three populations studied were the 1st (BC1) and 2nd (BC2 and BC2S1) backcross generations derived from the cross between ‘Guazuncho 2’, G. hirsutum, and ‘VH8’, G. barbadense Collectively we detected 80 QTLs, of which 50 surpassed the permutation‐based LOD thresholds (3.2–5.7). The most economically important traits, length (two correlated properties), strength, fineness (four properties), and color (two properties) were influenced by 15, 12, 21, and 16 QTLs, respectively, that could be detected in one or more populations. As expected, for the majority of QTLs, the favorable alleles came from the G. barbadense parent. Altogether one third (26) of the QTLs confirmed the map position and phenotypic effect of QTLs reported in the literature also detected in interspecific G. hirsutum × G. barbadense populations. Cases of colocalization of QTLs for different traits were more frequent than isolated positioning. Taking these QTL‐rich chromosomal regions into consideration, 19 regions on 15 different chromosomes, were identified as target regions for the marker‐assisted introgression strategy.
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