DOI: 10.3724/SP.J.1006.2019.84123

Acta Agronomica Sinica (作物学报) 2019/45:5 PP.647-655

Genome-wide screening and evaluation of SNP core loci for fingerprinting construction of cotton accessions (G. barbadense)

Sea-island cotton (G. barbadense), characterized by its extra-long staple (ELS), strong and fine fibers, and disease resistance, provides important natural fiber for textile industry, also key donor for improving agronomic traits of upland cotton. However, compared to G. hirsutum, there are few studies on genetic diversity and genotyping in G. barbadense. To obtain the SNP core loci for fingerprinting construction of sea-island cotton accessions, we performed SNP genotyping within 282 accessions using the CottonSNP80K array. A total of 2594 high-quality SNP loci were obtained based on the selective criteria of call frequency for each locus > 0.95, loci with polymorphism, minor allele frequency (MAF) > 0.01, heterozygosity rate < 0.05, and the removal of same genotype. Further, the number of optimized core loci was screened by gradients analysis. With the number of loci increasing, the discrimination ability of the sea-island cotton accessions increased gradually. When the loci were 200, the recognition rate was 89%, and when the number of the loci increased to 1500, the recognition rate was 99%. When the loci were further increased, no significantly improved recognition rate was detected. Based on the detection using the 1500 core loci combination, the average MAF value was 0.14, the average heterozygosity rate was 0.007, and the average polymorphism information content was 0.21. The polyacrylamide gel electrophoresis for the core SNP loci verified the consistency as high as 98.3% between SNP-PCR and chip genotyping. This study provides a set of core SNP loci suitable for constructing fingerprinting of sea-island cotton accessions, which can be used for genetic diversity analysis and fingerprinting identification of sea-island cotton.

Key words:gene array,DNA fingerprint,SNP,sea-island cotton

ReleaseDate:2019-11-05 15:29:58

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