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桃花型(铃型/蔷薇型)性状相关SNP位点挖掘与候选基因分析
孟 歌,朱更瑞,方伟超,陈昌文,王新卫,王力荣,曹 珂
0
(中国农业科学院郑州果树研究所,郑州 450009)
摘要:
桃的花型分为铃型和蔷薇型,铃型花朵小且边缘卷曲,蔷薇型花朵大且完全展开,蔷薇型重瓣花是观赏桃育种时追求的主要性状之一。目前,与桃铃型/蔷薇型花型性状连锁的分子标记研究较少,限制了桃花型性状分子标记辅助育种进程。为了鉴定与桃花型关联的SNP(单核苷酸多态性位点)位点并挖掘候选基因,本研究通过对199份桃种质进行重测序,获得了1,042,687个SNP。采用一般线性模型对桃花型性状进行全基因组关联分析,获得7个与目标性状显著关联的位点,其中2个位于第2染色体,5个位于第8染色体。进而对第8染色体的3个SNP进行竞争性等位基因特异性PCR(kompetitive allele-specific PCR,KASP)分型,在5个F1群体进行了进一步的验证。χ2验证结果表明:Chr.8:14,484,624 bp与桃花型性状显著关联。5个F1群体基因型和表型的对应关系表明,Chr.8:14,484,624 bp准确率最高,为93.46%。组织特异表达结果显示,在上述定位区间内的6个注释基因中,Prupe.8G118100在花中特异表达,被认为是花型性状的候选基因。本研究鉴定了桃铃型/蔷薇型花型性状关联位点,并对候选基因进行了筛选,以上结果可进一步转化为分子标记,用于观赏桃分子标记辅助选择育种。
关键词:  观赏桃育种  重测序  单核苷酸多态性  候选基因
DOI:10.13430/j.cnki.jpgr.20210819003
投稿时间:2021-08-19修订日期:2021-09-15
基金项目:国家重点研发计划项目(2019YFD1000200);中国农科院创新工程项目(Grant CAAS-ASTIP-2017-ZFRI-01)
Genome-wide Association Study Identified SNP Alleles and Candidate Genes for Flower Shape (non-showy/showy) Trait in Peach (Prunus persica)
MENG Ge, ZHU Geng-rui, FANG Wei-chao, CHEN Chang-wen, WANG Xin-wei, WANG Li-rong, CAO Ke
(Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009)
Abstract:
The petals of blooming peach flowers can be large and showy, or small with curved edges (non-showy), while showy and double flower is desirable in terms of breeding ornamental peaches. Since few studies are conducted to detect the molecular markers linking with the non-showy/showy flower trait, that restricts the molecular breeding for this trait in peach. In the present study, by taking use of re-sequencing data generated from 199 peach accessions and 1,042,687 single-nucleotide polymorphisms (SNPs), we performed the genome-wide association scanning (GWAS) for the non-showy/showy flower trait. Using a general linear model (GLM), we thereby identified seven signals that were associated with the flower trait on chromosomes (Chr.) 2 and 8. Three SNPs on Chr. 8 were validated using kompetitive allele-specific PCR (KASP) genotyping in five F1 populations. The SNP on Chr. 8 at 14,484,624 bp was highly associated with the targeted trait based on the χ2 test. Based on the correlation of the genotyping and phenotypic results of five F1 populations, the highest accuracy was 93.46% at Chr. 8:14,484,624 bp. RNA-seq analysis of different tissues and gene annotation enabled identifying one gene (Prupe. 8G118100) that showed tissue-specific expression in flower. Collectively, this work identified one SNP which is highly associated with the non-showy/showy flower trait, and one candidate gene, which could facilitate marker-assisted selection for ornamental peaches.
Key words:  Ornamental peach breeding  re-sequencing  single nucleotide polymorphism  candidate gene