Population Genomics and Genomics-Assisted Trait Improvement in Tea (Camellia sinensis (L.) O. Kuntze)

“Tea” is undoubtedly one of the most widely consumed beverage processed from young shoots of tea [Camellia sinensis (L.) O. Kuntze] plant. The popularity of tea is attributed to its taste, aroma, and multiple health benefits. Developing new tea cultivars with novel characteristics remains the ultimate goal for breeders. Several breeding approaches ranging from conventional techniques, including crossbreeding and mutational breeding, to a series of molecular breeding methods such as marker-assisted selection and genetic modification have been employed in tea. Additionally, advances in high-throughput sequencing technologies, mainly genomics, transcriptomics, metabolomics, and proteomics, have led to the generation of massive dataset, which can be integrated with phenotypic data to identify key genes and pathways controlling important traits in tea. The publication of tea genome has also led to the integration of genotyping-by-sequencing (GBS) approach in genome-wide association studies (GWAS), genomic selection (GS), genomic/genetic diversity, genetic linkage analysis, and ascertainment of trait-specific molecular markers. In spite of the advances made to expedite breeding in tea, success remains elusive due to bottlenecks including high heterozygosity, perennial nature, and self-incompatibility. The field of population genomics, which integrates advances in sequencing approaches, bioinformatics, and statistical analysis into research, has emerged as a novel tool for understanding new and long-standing queries on domestication, evolutionary history, genetic diversity, and population structure of tea plant. Moreover, with the availability of C. sinensis reference genome, population genomics allows for physical mapping of adaptive and molecular variants responsible for genotypic and phenotypic variations across the genome. In this chapter, we summarize achievements and future prospects of conventional, molecular breeding and population genomics in assessing/managing genetic diversity, unraveling the origin/evolution and domestication of tea plants, and identification of trait-specific genes in tea plants. Integration of population genomics with proteomics, metabolomics, lipidomics, and epigenomics is also highlighted in this chapter.