Abstract
BackgroundHigh-throughput genotyping platforms play important roles in plant genomic studies. Cotton (Gossypium spp.) is the world’s important natural textile fiber and oil crop. Upland cotton accounts for more than 90% of the world’s cotton production, however, modern upland cotton cultivars have narrow genetic diversity. The amounts of genomic sequencing and re-sequencing data released make it possible to develop a high-quality single nucleotide polymorphism (SNP) array for intraspecific genotyping detection in cotton.ResultsHere we report a high-throughput CottonSNP80K array and its utilization in genotyping detection in different cotton accessions. 82,259 SNP markers were selected from the re-sequencing data of 100 cotton cultivars and used to produce the array on the Illumina Infinium platform. 77,774 SNP loci (94.55%) were successfully synthesized on the array. Of them, 77,252 (99.33%) had call rates of >95% in 352 cotton accessions and 59,502 (76.51%) were polymorphic loci. Application tests using 22 cotton accessions with parent/F1 combinations or with similar genetic backgrounds showed that CottonSNP80K array had high genotyping accuracy, good repeatability, and wide applicability. Phylogenetic analysis of 312 cotton cultivars and landraces with wide geographical distribution showed that they could be classified into ten groups, irrelevant of their origins. We found that the different landraces were clustered in different subgroups, indicating that these landraces were major contributors to the development of different breeding populations of modern G. hirsutum cultivars in China. We integrated a total of 54,588 SNPs (MAFs >0.05) associated with 10 salt stress traits into 288 G. hirsutum accessions for genome-wide association studies (GWAS), and eight significant SNPs associated with three salt stress traits were detected.ConclusionsWe developed CottonSNP80K array with high polymorphism to distinguish upland cotton accessions. Diverse application tests indicated that the CottonSNP80K play important roles in germplasm genotyping, variety verification, functional genomics studies, and molecular breeding in cotton.
Highlights
High-throughput genotyping platforms play important roles in plant genomic studies
The population structure and genetic basis of the agronomic traits of upland cotton has been investigated in 503 G. hirsutum accessions using 11,975 quantified polymorphic single nucleotide polymorphism (SNP) in the CottonSNP63K SNP array [19]. These results indicate that the SNP array is a robust and highly efficient tool for use in cotton genetic studies and breeding improvement
In this study, based on the high quality reference sequence of the TM-1 genome [22] and re-sequencing data from different upland cotton cultivars [27], we focused on the development of a high-density upland cotton SNP array for intraspecific genotyping detection, with the advantages on addressable SNPs, genome-wide distribution, high-effective genotyping detection
Summary
High-throughput genotyping platforms play important roles in plant genomic studies. Cotton (Gossypium spp.) is the world’s important natural textile fiber and oil crop. Upland cotton accounts for more than 90% of the world’s cotton production, modern upland cotton cultivars have narrow genetic diversity. Cotton (Gossypium spp.) is the largest source of renewable fiber in the world and is a significant oil crop. Modern upland cotton cultivars have narrow genetic diversity, due to their development from the limited quantity of resources in the United States [1]. SSR markers have disadvantages; for example, they are low-throughput, labor-intensive and time-consuming as a genotyping platform. High-throughput molecular markers are imperative to saturate cotton genetic maps, and to significantly improve gene/quantitative trait loci (QTL) mapping for genomic studies and marker-assisted selection (MAS) breeding [4]
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