SNP discovery of Camellia oleifera based on RNA-seq and its application for identification of genetic relationships and locus for oil content among different cultivars

Tea oil camellia (Camellia oleifera) is a perennial evergreen shrub or small tree. Enhancing oil content is an important breeding objective in this species. In this study, we (i) used the high-throughput RNA-seq to discovery SNP sites located in target genes involved in lipid biosynthesis, (ii) determined genetic relationship among 102 accessions based on SNP-seq data, and (iii) identify SNP loci associated with oil content. Results showed that 20 SNP markers of targeted genes were discovered based on RNA-seq data. The SNP-seq of 20 pairs of SNP primers across 102 accessions generated 644 SNPs. The phylogenetic tree was constructed based on these SNPs, which clearly presented genetic relationship among 102 accessions. The C. chekiangoleosa belonging to different sect. with other accessions is far from other accessions. Phylogenetic analysis showed the clustering of accessions into groups which was in good agreement with their taxonomic classification, and revealed the presence of different accessions with the same name and identical accessions but with a different name. Moreover, seven SNP locus associated with oil content were identified (p < 0.01). Our data discovered SNP sites of target genes involved in lipid biosynthesis, and provide scientific basic for germplasm collection and identification of tea oil camellia.

油茶（Camellia oleifera）为多年生常绿灌木或小乔木，提升含油率是该物种的重要育种目标。本研究开展了三项核心工作：（1）借助高通量RNA测序（RNA-seq）挖掘参与脂质生物合成的靶基因中的单核苷酸多态性（Single Nucleotide Polymorphism，SNP）位点；（2）基于SNP测序（SNP-seq）数据分析102份种质材料的遗传关系；（3）筛选与含油率相关的SNP位点。研究结果显示，基于RNA-seq数据共挖掘得到20个靶基因SNP标记。针对102份种质材料，使用20对SNP引物开展SNP-seq，共获得644个SNP位点。基于上述SNP位点构建的系统发育树可清晰展现102份种质材料的遗传关系。浙江红山茶（C. chekiangoleosa）隶属于与其他供试种质不同的组，与其余种质的遗传距离较远。系统发育分析表明，种质材料的聚类结果与其分类学地位高度吻合，同时揭示了同名异质与同物异名种质的存在。此外，本研究共鉴定得到7个与含油率显著相关的SNP位点（p < 0.01）。本研究挖掘得到参与脂质生物合成的靶基因SNP位点，可为油茶的种质资源收集与鉴定提供科学依据。