Abstract
Tea is an important global beverage crop and is largely clonally propagated. Despite previous studies on the species, its genetic and evolutionary history deserves further research. Here, we present a haplotype-resolved assembly of an Oolong tea cultivar, Tieguanyin. Analysis of allele-specific expression suggests a potential mechanism in response to mutation load during long-term clonal propagation. Population genomic analysis using 190 Camellia accessions uncovered independent evolutionary histories and parallel domestication in two widely cultivated varieties, var. sinensis and var. assamica. It also revealed extensive intra- and interspecific introgressions contributing to genetic diversity in modern cultivars. Strong signatures of selection were associated with biosynthetic and metabolic pathways that contribute to flavor characteristics as well as genes likely involved in the Green Revolution in the tea industry. Our results offer genetic and molecular insights into the evolutionary history of Camellia sinensis and provide genomic resources to further facilitate gene editing to enhance desirable traits in tea crops.
Highlights
Tea, produced from C. sinensis, is a widely consumed beverage that contains multiple polyphenolic compounds considered beneficial to human health[4]
A ~300-year clonal propagation has led to accumulation of substantial somatic mutations in the genome, allowing us to separate the two haplotypes using our newly developed algorithms (Khaper[15] and ALLHiC18) and identify allelic imbalance
ASEGs were classified into two major patterns: consistent ASEGs and inconsistent ASEGs
Summary
Tea, produced from C. sinensis, is a widely consumed beverage that contains multiple polyphenolic compounds considered beneficial to human health[4]. Assamica (CSA) with a number of distinct features, such as leaf size[8] Both varieties are flavorful, carry health-promoting bioactive compounds and have been domesticated for commercial tea production. Recent studies have provided reference genomes for the two varieties[9,10,11]; the mosaic assemblies likely missed allelic variations underlying important selected traits. Population structure and genetic diversity in tea plants have been extensively discussed recently[9,10,11], which substantially contributed to the study of tea genomics. Tea plants exhibit allogamy and self-incompatibility[13] This leads to a high level of heterozygosity in the genome, providing a model to investigate allelic variations that may play important roles during evolution. We resequenced several leading tea accessions and close relatives to explore genetic diversity among geographically distinct tea populations. Our results provide insight into the mechanism of heterosis and the evolutionary history of the tea plant and uncover important signatures of selection
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