Abstract
BackgroundSingle 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.ResultsIn 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 46 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.ConclusionThe 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.
Highlights
Single nucleotide polymorphisms (SNPs) and insertions/deletions (InDels) are the major genetic variations and are distributed extensively across the whole plant genome
Mapping of clean reads to the reference genome ‘Shuchazao’ Camellia sinensis var. sinensis (CSS) ‘Shuchazao’ has been observed to have significant differences in bud, leaf and budding flower size compared with Camellia sinensis var. assamica (CSA) ‘Yunkang 10’ (Fig. 1)
We identified a number of SNPs and InDels in some crucial genes that are involved in the catechin biosynthesis pathway, including phenylalanine ammonia-lyase (PAL), cinnamic acid 4hydroxylase (C4H), 4-coumarate-CoA ligase (4CL), chalcone synthase (CHS), chalcone isomerase (CHI), flavanone 3-hydroxylase (F3H), flavonoid 3′-hydroxylase (F3’H), flavonoid 3′,5′-hydroxylase (F3’5’H), dihydroflavonol 4-reductase (DFR), leucoanthocyanidin reductase (LAR), anthocyanidin synthase (ANS), anthocyanidin reductase (ANR), and 1-O-galloyl-β-D-glucose Ogalloyltransferase (ECGT, which belongs to subclade 1A of serine carboxypeptidase-like (SCPL) acyltransferases) (Table 2)
Summary
Single nucleotide polymorphisms (SNPs) and insertions/deletions (InDels) are the major genetic variations and are distributed extensively across the whole plant genome. Liu et al BMC Genomics (2019) 20:935 incompatibility and long-term allogamy contributed considerably to the highly heterogeneous and abundant genetic variation of tea plant [11, 12]. Numerous molecular markers have been successfully developed and applied in genetic and genomic research in tea plant, such as restriction fragment length polymorphisms (RFLPs), amplified fragment length polymorphisms (AFLPs), random amplification of polymorphic DNAs (RAPDs), cleaved amplified polymorphic sequences (CAPS), inter-simple sequence repeats (ISSRs), and simple sequence repeats (SSRs) [12, 13]. With the rapid development of the high-throughput sequencing approaches, the thirdgeneration single nucleotide polymorphism (SNP) and insertion/deletion (InDel) markers are gradually becoming the most widely used molecular markers, demonstrating a promising future in plant genetic and breeding research
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
