桃的花型性状相关 SNP 位点挖掘与候选基因分析
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中国农业科学院郑州果树研究所

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国家重点研发计划项目(2019YFD1000200);中国农业科学院创新工程项目(Grant CAAS-ASTIP-2017-ZFRI-01)


Genome-wide Association Study Identified SNP Alleles and Candidate Genes for Flower Shape Trait in Peach(Prunus persica)
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Zhengzhou Fruit Research Institute,Chinese Academy of Agricultural Sciences

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National Key R&D Program of China (2019YFD1000200), Agricultural Science and Technology Innovation Program (Grant CAAS-ASTIP-2017-ZFRI-01)

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    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 者追求的主要目标性状之一。目前,与桃铃型 / 蔷薇型花型性状连锁的分子标记研究较少,限制了桃的花型性状分子标 记辅助育种进程。为了鉴定与桃花型关联的单核苷酸多态性(SNP,single-nucleotide polymorphisms)位点并挖掘候选 基因,本研究通过对 199 份桃品种进行重测序,获得了 1042687 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(GWAS,genome wide association study),获得 7 个与目标性状显著关联的位点,其中 2 个位于 2 号染色体,5 个位于 8 号染色体。进而对 8 号染色体的 3 个 SNP 进行竞争性等位基因特异性 PCR(KASP,kompetitive allele-specific PCR)分型,在 5 个 F1 群体中进行进一步验证。χ2 验证结果表明:Chr.8:14484624 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.8:14484624 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,将其视为桃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。

    Abstract:

    The petals of blooming peach flowers can be large and showy,or small with curved edges(nonshowy),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 varieties and 1042687 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 Chr. 2 and Chr. 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 14484624 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: 14484624 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 markerassisted selection for ornamental peaches.

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孟 歌,朱更瑞,方伟超,等.桃的花型性状相关 SNP 位点挖掘与候选基因分析[J].植物遗传资源学报,2022,23(2):505-517.

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  • 收稿日期:2021-08-19
  • 最后修改日期:2021-09-15
  • 录用日期:2021-09-29
  • 在线发布日期: 2022-03-10
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