基于多重PCR的SNP基因分型及其在辣椒种质遗传多样性及关联分析中的应用OA

In this study,a multiplex PCR-based SNP genotyping panel was developed using genotyping-by-sequencing(GBS)data,which includes 170 core SNP markers.Based on this SNP panel and 30 phenotypic traits,analysis was conducted on 202 pepper germplasms to resove their genetic diversity and explore the associated loci for excellent phenotypic traits of pepper.Research showed that a total of 170 core SNP markers distributed across 12 chromosomes,with the average Shannon's information index(Ⅰ),polymorphic information content(PIC)and Nei's gene diversity(H')being 0.616,0.334 and 0.428,respectively.This indicates high genetic diversity among the tested materials.Results from cluster analysis,population structure analysis,and principal component analysis were consistent:all divided the tested materials into five groups,and each group showed a certain correlation with geographical origin and fruit morphology.The coefficient of variation(CV)for the 30 phenotypic traits ranged from 7.00％to 87.88％,with an average of 34.85％.The Shannon-Wiener diversity index varied from 0.03 to 2.07,with an average of 1.19.Among these traits,single fruit weight showed the highest CV(87.88％),while fruit length had the highest Shannon-Wiener diversity index(2.07).Corolla color exhibited the lowest values of both CV(7.00％)and Shannon-Wiener diversity index(0.03).Most of the 30 phenotypic traits showed significant or highly significant correlations.Furthermore,association analysis was performed between phenotypic traits and SNP markers.The results showed that a total of 53 SNPs were detected by two methods(GLM and MLM),which were significantly associated with 12 phenotypic traits.GLM and MLM could explain 4.83％-48.41％and 10.86％-19.19％of the phenotypic variance,respectively.Marker 980-003 located on chromosome 4 explains the highest phenotypic variance for corolla color.Four of the 53 SNPs were simultaneously detected by both methods.The SNP genotyping panel developed in this study is a genotyping method with high throughput,good accuracy,and low cost,which can be applied to genetic structure analysis,molecular marker-assisted breeding,and variety identification of peppers.In addition,this study established a database of phenotypic traits and genotypes for 202 pepper germplasms,effectively establishing the correspondence between phenotypes and genotypes,and providing theoretical guidance and a material basis for the exploration of excellent pepper genes,germplasm innovation and the genetic improvement of varieties.