Genome-wide SNP discovery from Darjeeling tea cultivars - their functional impacts and application toward population structure and trait associations

Genotyping by sequencing and identification of functionally relevant nucleotide variations in crop accessions are the key steps to unravel genetic control of desirable traits. Elite cultivars of Darjeeling tea were undergone SNP genotyping by double-digest restriction-site associated DNA sequencing method. This study reports a set of 54,206 high-quality SNP markers discovered from ~10.4 GB sequence data, encompassing 15 chromosomes of the reference tea genome. Genetic relatedness among the accessions conforms to the analyses of Bayesian clustering, UPGMA, and PCoA methods. Genomic positions of the discovered SNPs and their putative effect on annotated genes designated a thoughtful understanding of their functional aspects in tea system biology. A group of 95 genes was identified to be affected by high impact variants. Genome-wide association analyses of 21 agronomic and biochemical phenotypes resulted in trait-linked polymorphic loci with strong confidence (p < 0.05 and 0.001).