Genome-Wide Association Study to Identify Favorable SNP Allelic Variations and Candidate Genes That Control the Timing of Spring Bud Flush of Tea (Camellia sinensis) Using SLAF-seq

The timing of spring bud flush (TBF) is of economic importance for tea plant (Camellia sinensis) breeding. We employed a genome-wide association study (GWAS) to identify favorable single nucleotide polymorphism (SNP) allelic variations as well as candidate genes that control TBF of C. sinensis using specific-locus-amplified fragment sequencing (SLAF-seq) in a diversity panel comprising 151 tea plant germplasm resources. GWAS analysis revealed 26 SNPs associated with TBF in three years, and we eventually identified a final significant SNP for TBF. To identify candidate genes possibly related to TBF, we screened seven candidate genes within 100 kb regions surrounding the trait-related SNP loci. Furthermore, the favorable allelic variation, the “TT” genotype in the SNP loci, was discovered, and a derived cleaved amplified polymorphism (dCAPS) marker was designed that cosegregated with TBF, which could be used for marker-assisted selection (MAS) breeding in C. sinensis. The results obtained from this study can provide a theoretical and applied basis for the MAS of early breeding in tea plants in the future.春季芽萌动时间（Timing of Spring Bud Flush, TBF）对茶树（Camellia sinensis）育种具有重要经济价值。本研究以包含151份茶树种质资源的多样性群体为研究材料，采用特异性位点扩增片段测序（Specific-Locus Amplified Fragment Sequencing, SLAF-seq）技术开展全基因组关联分析（Genome-Wide Association Study, GWAS），以鉴定调控茶树春季芽萌动时间的有利单核苷酸多态性（Single Nucleotide Polymorphism, SNP）等位变异及候选基因。全基因组关联分析共在三年间鉴定出26个与春季芽萌动时间显著关联的单核苷酸多态性位点，最终筛选得到1个与该性状显著关联的核心单核苷酸多态性位点。为进一步挖掘与春季芽萌动时间相关的候选基因，本研究在与性状关联的单核苷酸多态性位点上下游100kb的基因组区域内筛选得到7个候选基因。此外，本研究还发现了该单核苷酸多态性位点上的有利等位变异——‘TT’基因型，并设计了1个与春季芽萌动时间共分离的衍生酶切扩增多态性（Derived Cleaved Amplified Polymorphism, dCAPS）标记，该标记可应用于茶树标记辅助选择（Marker-Assisted Selection, MAS）育种。本研究结果可为未来茶树早期育种的标记辅助选择提供理论与应用基础。