Revealing Distinctions in Genetic Diversity and Adaptive Evolution Between Two Varieties of Camellia sinensis by Whole-Genome Resequencing

Abstract

Camellia sinensis var. sinensis (CSS) and C. sinensis var. assamica (CSA) are the two most economically important tea varieties. They have different characteristics and geographical distribution. Their genetic diversity and differentiation are unclear. Here, we identified 18,903,625 single nucleotide polymorphisms (SNPs) and 7,314,133 insertion–deletion mutations (indels) by whole-genome resequencing of 30 cultivated and three wild related species. Population structure and phylogenetic tree analyses divided the cultivated accessions into CSS and CSA containing 6,440,419 and 6,176,510 unique variations, respectively. The CSS subgroup possessed higher genetic diversity and was enriched for rare alleles. The CSA subgroup had more non-synonymous mutations and might have experienced a greater degree of balancing selection. The evolution rate (dN/dS) and KEGG enrichment indicated that genes involved in the synthesis and metabolism of flavor substances were positively selected in both CSS and CSA subpopulations. However, there are extensive genome differentiation regions (2959 bins and approximately 148 M in size) between the two subgroups. Compared with CSA (141 selected regions containing 124 genes), the CSS subgroup (830 selected regions containing 687 genes) displayed more selection regions potentially related to environmental adaptability. Fifty-three pairs of polymorphic indel markers were developed. Some markers were located in hormone-related genes with distinct alleles in the two cultivated subgroups. These identified variations and selected regions provide clues for the differentiation and adaptive evolution of tea varieties. The newly developed indel markers will be valuable in further genetic research on tea plants.

QTL Mapping for Leaf Area of Tea Plants (Camellia sinensis) Based on a High-Quality Genetic Map Constructed by Whole Genome Resequencing

“…In this population, 30,925,005 variations, including 28,144,625 SNPs and 2,780,380 indels, were identified. The average SNP density was 9.6/Kb, which is much higher than that previously reported ( An et al, 2020 ). Similar to other crops ( Shen et al, 2017 ; Thakur and Randhawa, 2018 ; Muñoz-Espinoza et al, 2020 ), transitions had an absolute advantage in SNPs, and the ts/tv value was approximately 2.51, which was higher than Cucurbita ( Xanthopoulou et al, 2019 ) but lower than lotus ( Huang et al, 2018 ).…”

“…sinensis (CSS) and C. sinensis var. assamica (CSA) have significant differences in leaf area, plant type, cold resistance, secondary metabolic characteristics, and geographical distribution ( An et al, 2020 ). CSA is usually considered to be arborous or semi-arborous with a large leaf area, whereas CSS tea plants are mainly shrubs with small leaf areas.…”

Genetic Diversity and Genome Size Variability in the Russian Genebank Collection of Tea Plant [Camellia sinensis (L). O. Kuntze]

“…CSS have a broad geographic origin and therefore originate from complex natural environments. This may have led to the occurrence of more adaptive mutations, which is why these accessions have high genetic diversity (An et al, 2020). In contrast, cluster 3 probably contained mostly CSA × CSS hybrids.…”

“…Many cultivars in cluster 3, including the best national cultivar "Kolkhida, " show typical phenotypic characteristics of CSA, such as large, thin, soft, and wrinkled leaves of light green color. CSA were also introduced in the Caucasus, but most CSA accessions are distributed in tropical regions and have lower cold resistance (Hao et al, 2018;An et al, 2020). For this reason, most of these CSA accessions introduced to the Caucasus are thought to have likely died and only CSS × CSA hybrids have survived.…”

“…It is believed that only CSS and hybrid CSS × CSA genotypes were successfully domesticated in our region. The different morphological and biochemical characteristics of CSS and CSA are mainly due to their different geographical distribution and growing environment (Meegahakumbura et al, 2016;Hao et al, 2018;Li et al, 2019;An et al, 2020;Wang et al, 2020).…”