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

Abstract

ABSTRACT 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.