Characterization of genome-wide genetic variations between two varieties of tea plant (Camellia sinensis) and development of InDel markers for genetic research

Abstract

Background: Single nucleotide polymorphisms (SNPs) and insertions/deletions (InDels) are the major genetic variations and are distributed extensively across the whole plant genome. However, few studies of these variations have been conducted in the long-lived perennial tea plant. Results: In this study, we investigated the genome-wide genetic variations between Camellia sinensis var. sinensis ‘Shuchazao’ and Camellia sinensis var. assamica ‘Yunkang 10’, identified 7,511,731 SNPs and 255,218 InDels based on their whole genome sequences, and we subsequently analyzed their distinct types and distribution patterns. A total of 48 InDel markers that yielded polymorphic and unambiguous fragments were developed when screening six tea cultivars. These markers were further deployed on forty-six tea cultivars for transferability and genetic diversity analysis, exhibiting information with an average 4.02 of the number of alleles (Na) and 0.457 of polymorphism information content (PIC). The dendrogram showed that the phylogenetic relationships among these tea cultivars are highly consistent with their genetic backgrounds or original places. Interestingly, we observed that the catechin/caffeine contents between ‘Shuchazao’ and ‘Yunkang 10’ were significantly different, and a large number of SNPs/InDels were identified within catechin/caffeine biosynthesis-related genes. Conclusion: The identified genome-wide genetic variations and newly-developed InDel markers will provide a valuable resource for tea plant genetic and genomic studies, especially the SNPs/InDels within catechin/caffeine biosynthesis-related genes, which may serve as pivotal candidates for elucidating the molecular mechanism governing catechin/caffeine biosynthesis.

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“…A higher ratio is an indicator of good quality SNPs, as sequencing errors and false positive variants have a ratio closer to one [ 33 ].We found the SNP transitions (A/G and C/T) are the most common substitution in the genome, which is consistent with other crop species like foxtail millet ( Setaria italica ) [ 34 ], tea ( Camellia sinensis ) [ 35 ], soybean [ 36 ], and rice [ 27 ]. We observed a Ts/Tv ratio of 1.71 is, however, less than the ratios reported in crops like rice [ 27 ], maize ( Zea mays ) [ 37 ] and tea [ 35 ]. The higher Ts/Tv could be because of more synonymous mutations resulting from from transitions other than transversions, which brings out the change in protein structure and function.…”