植物遗传资源学报2026，Vol.27Issue(1)：132-151,20.DOI:10.13430/j.cnki.jpgr.20250828002
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
SNP Genotyping Based on Multiplex PCR and Its Application in Genetic Diversity and Association Analysis of Pepper Germplasm
摘要
Abstract
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.关键词
辣椒/SNP基因分型/多重PCR/遗传多样性/关联分析Key words
pepper/SNP genotyping/multiplex PCR/genetic diversity/association analysis引用本文复制引用
黄月琴,陈学军,方荣,周坤华,雷刚,李歌歌,方钰,袁欣捷..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[J].植物遗传资源学报,2026,27(1):132-151,20.基金项目
江西省重点研发计划揭榜挂帅项目(20223BBF61003) （20223BBF61003）
国家自然科学基金(32160712) （32160712）
江西省主要学科学术和技术带头人培养计划(20225BCJ23010) （20225BCJ23010）
江西省农业科学院基础研究与人才培养专项(JXSNKYJCRC202341) （JXSNKYJCRC202341）
江西省重点研发计划青年科学家项目(20232BBF60002)Jiangxi Provincial Key R&D Program Tender and Lead Project(20223BBF61003) （20232BBF60002）
National Natural Science Foundation of China(32160712) （32160712）
Academic and Technical Leader Projects of Major Disciplines in Jiangxi Province(20225BCJ23010) （20225BCJ23010）
Project on Fundamental Research and Talent Cultivation at Jiangxi Academy of Agricultural Sciences(JXSNKYJCRC202341) （JXSNKYJCRC202341）
Jiangxi Provincial Key R&D Program for Young Scientists(20232BBF60002) （20232BBF60002）
