The Development and Verification of SNP Lquid Chips for Common Bean Based on Targeted Sequencing Technology
A total of 61 950 high-quality SNP loci were identified based on published common bean genome and resequencing data using bioinformatic methods.By evaluating the target loci for probe design,40K,20K and 10K liquid chips containing 40 352,20 855 and 10 486 SNP loci were finally designed and developed,respectively.Using the 10K liquid chip,89 common bean varieties were genotyped by targeted sequencing.The results showed that the mean polymorphic information content and genetic diversity values of 89 common bean varieties were 0.35 and 0.29,respectively.The 89 common bean varieties were classified into two genetic subgroups by STRUCTURE and cluster analysis,which showed that the genetic background and fruit traits of common bean varieties in the same region were mostly similar.Based on selection signal analysis,a total of 103 regions subject to strong selective pressure were identified,and the loci in these regions will provide candidates for subsequent functional gene studies.
common beansingle nucleotide polymorphism(SNP)genotyping by target sequencing(GBTS)genetic diversity
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