利用CottonSNP63K芯片构建棉花品种的指纹图谱

doi:10.3864/j.issn.0578-1752.2017.24.003

Abstract

Abstract: 【Objective】 The objective of this study is to screen genomic-specific SNPs, considering the SNP with single loci and the reference genomic sequence information of upland cotton TM-1. 【Method】 Based on 719 natural germplasm resources with plentiful genetic backgrounds, using the CottonSNP63K array developed by Illumina, quality control of the original genotyping data obtained from chip scanning was performed by GenomeStudio software, the genotyping data of the SNP locus of the tested samples were obtained. According to the two published Gossypium hirsutum TM-1 genome versions, including the G. hirsutum (AD1) genome BGI v1.0 of Cotton Research Institute of Chinese Academy of Agricultural Sciences and the G. hirsutum (AD1) genome NBI v1.1 of Nanjing Agricultural University, the genome-wide BLAST analysis was performed on the flanking sequences of each SNP with CottonSNP63K (63 058 SNPs) array to screen specific SNP loci with single copy, and these SNPs were used for the construction of fingerprints. 【Result】 SNP genotyping of 719 materials using CottonSNP63K was classified into SNP locus without detectable signal, SNP locus without polymorphism and the polymorphism SNP loci. The polymorphism SNP loci could be divided into double-site SNP, multiple-site SNP and single-site SNP (genomic-specific SNP). The results of the Blast analysis with the two upland cotton TM-1 reference genome sequences showed that there were 5 474 specific SNP markers in the BGI v1.0 version, while NBI v1.1 TM-1 version only 1 850, and the common specific SNPs of both were 1 594. Further considering the three evaluation indexes including the genotyping effect, call rate and polymorphism, the SNPs with scores≥0.7, call frequency≥0.95 and MAF≥0.2 were screened, and 471 specific SNPs with high call rate and high polymorphism were obtained. Among these SNP loci, 430 were on chromosomes and 41 were on scaffolds. Taking into account of the degree of linkage between the markers, finally 393 core SNP loci were obtained after removing 37 linkage markers, and the DNA fingerprints of 719 resource materials were constructed by using 393 core SNPs. The results showed that 97% of the materials could be accurately and effectively identified except for some accessions with similar genetic background. 【Conclusion】 A total of 393 genomic-specific SNPs were screened out, and these core SNPs were used to construct the DNA fingerprints of 719 resource materials. This study will provide a reference for application of SNP molecular markers in genetic improvement of important cotton traits.

Key words: cotton, SNP marker, GenomeStudio, genotyping array, fingerprints

SUN ZhengWen, KUANG Meng, MA ZhiYing, WANG XingFen. Construction of Cotton Variety Fingerprints Using CottonSNP63K Array[J].Scientia Agricultura Sinica, 2017, 50(24): 4692-4704.

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Construction of Cotton Variety Fingerprints Using CottonSNP63K Array

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