茶树新梢中香叶醇樱草糖苷含量的全基因组关联分析

Genome-wide association analysis of geraniol primrose glycoside abundance in tender tea shoots

香叶醇是茶树中含有的一种重要的挥发性单萜醇,在茶树与环境互作中起重要作用,也是茶叶中关键呈香成分之一,茶树新梢中的香叶醇主要以香叶醇樱草糖苷形式存在。发掘香叶醇樱草糖苷含量性状显著关联的SNP位点与候选基因,对香叶醇樱草糖苷含量的遗传调控机制研究与茶树遗传改良具有重要意义。以169个茶树种质为研究对象,连续3年对其新梢香叶醇樱草糖苷含量进行鉴定,基于SLAF简化基因组测序技术开发SNP标记,然后利用一般线性模型(GLM)对茶树新梢香叶醇樱草糖苷含量性状进行GWAS分析,发掘该性状显著关联的SNP位点与候选基因,最后对极端含量材料间的候选基因编码区碱基差异及其上游顺式作用元件进行分析。结果表明,参试群体在3个环境下香叶醇樱草糖苷含量变异系数范围为77.6%~81.8%,广义遗传力为62.6%。香叶醇樱草糖苷含量性状在基因型、环境间均呈现显著差异,变异受遗传影响为主。3个环境下共检测到340个SNP与香叶醇樱草糖苷含量显著相关,其中2个环境下重复检测到65个SNP。基于参考基因组与连锁不平衡衰减距离,获得重复检测到的SNP两侧各100 kb范围内的基因共88个,包含信号蛋白、激酶、磷酸酶、离子转运蛋白、转录因子、热激蛋白、激素相关蛋白、抗性蛋白、萜类代谢酶、糖基转移酶、糖苷酶,从中初筛出10个与香叶醇樱草糖苷含量相关的候选基因。极端含量材料之间的候选基因编码区序列均存在SNP非同义突变,多数候选基因上游2 kb区域存在不同数量的与环境胁迫和激素相关的顺式作用元件。本研究为阐明茶新梢中香叶醇樱草糖苷含量的遗传调控机制提供了新的视角,为分子标记辅助选择茶树新品种提供了标记与基因资源。

Geraniol is an important volatile monoterpene alcohol contained in tea plant,which plays an important role in the interaction between tea plant and environment and constitutes one of key aroma components in tea.Geraniol from tea plant tender shoots mainly exists in the form of geranylβ-primeveroside.Explore SNP loci and candidate genes significantly associated with geranylβ-primeveroside content is of great significance for the the genetic regulation mechanism of geranylβ-primeveroside content and tea plant genetic improvement.Regarding 169 tea germplasms as the research materials,the geranylβ-primeveroside content of tea plant tender shoots was identified for three consecutive years(three environments),and the SNP markers were developed based on SLAF-seq technology.Then,the geranylβ-primeveroside content of tea plant tender shoots was analyzed by genome-wide association analysis(GWAS)using general linear model(GLM).The candidate genes were further screened based on the SNP loci significantly with the geranylβ-primeveroside content.Ultimately,the base differences of candidate gene coding regions and their upstream cis acting elements among the extreme geranylβ-primeveroside content were analyzed.Results showed that the variation coefficient of geranylβ-primeveroside content in three environments ranged from 77.6%to 81.8%,and the broad heritability was 62.6%.The geranylβ-primeveroside content was significant differences among the genotypes and environments,and the variation was mainly affected by heredity.A total of 340 SNP markers significantly correlated with the geranylβ-primeveroside content were detected under three environments,in which 65 SNP markers were detected repeatedly under 2 environments.Based on the tea plant reference genome and linkage disequilibrium decay distance,a total of 88 genes within 100 kb on both sides of the repeated 65 SNP markers were obtained,including signal proteins,kinases,phosphatases,ion transporters,transcription factors,heat shock proteins,hormone related proteins,resistance proteins,terpene metabolic enzymes,glycosyltransferases,and glycosidases.10 candidate genes were preliminary screened out.SNP nonsynonymous mutations in the coding region sequences of 10 candidate genes between two extreme geranylβ-primeveroside content materials,and different numbers of cis acting elements related to environmental stress and hormones in the upstream 2 kb regions of most candidate genes were discovered.This study provides a new perspective for clarifying the genetic regulation mechanism of geranylβ-primeveroside content in tea plant tender shoots,and also provides the markers and gene resources for molecular marker assisted selection of new tea varieties.