High-density SNP linkage map construction and QTL mapping for flavonoid-related traits in a tea plant (Camellia sinensis) using 2b-RAD sequencing

Abstract

BackgroundFlavonoids are important components that confer upon tea plants a unique flavour and health functions. However, the traditional breeding method for selecting a cultivar with a high or unique flavonoid content is time consuming and labour intensive. High-density genetic map construction associated with quantitative trait locus (QTL) mapping provides an effective way to facilitate trait improvement in plant breeding. In this study, an F1 population (LJ43×BHZ) was genotyped using 2b-restriction site-associated DNA (2b-RAD) sequencing to obtain massive single nucleotide polymorphism (SNP) markers to construct a high-density genetic map for a tea plant. Furthermore, QTLs related to flavonoids were identified using our new genetic map.ResultsA total of 13,446 polymorphic SNP markers were developed using 2b-RAD sequencing, and 4,463 of these markers were available for constructing the genetic linkage map. A 1,678.52-cM high-density map at an average interval of 0.40 cM with 4,217 markers, including 427 frameset simple sequence repeats (SSRs) and 3,800 novel SNPs, mapped into 15 linkage groups was successfully constructed. After QTL analysis, a total of 27 QTLs related to flavonoids or caffeine content (CAF) were mapped to 8 different linkage groups, LG01, LG03, LG06, LG08, LG10, LG11, LG12, and LG13, with an LOD from 3.14 to 39.54, constituting 7.5% to 42.8% of the phenotypic variation.ConclusionsTo our knowledge, the highest density genetic map ever reported was constructed since the largest mapping population of tea plants was adopted in present study. Moreover, novel QTLs related to flavonoids and CAF were identified based on the new high-density genetic map. In addition, two markers were located in candidate genes that may be involved in flavonoid metabolism. The present study provides valuable information for gene discovery, marker-assisted selection breeding and map-based cloning for functional genes that are related to flavonoid content in tea plants.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-5291-8) contains supplementary material, which is available to authorized users.

Identification and distribution of a single nucleotide polymorphism responsible for the catechin content in tea plants

“…For example, large-scale SNPs combined with SSRs in an F1 population (YS × BD) were used for the construction of the first high-density genetic map of tea plant in 2015 32 . Then, a high-density SNP linkage map was constructed, and QTLs related to flavonoids that were dependent on the F1 population (LJ43 × BHZ) were identified in 2018 12 . Candidate QTLs and proteins were shown to be involved in flavonoid biosynthesis using DArTseq markers via two F1 populations (TRFK 303/577 × GW Ejulu and GW Ejulu × TRFK 303/577) in 2018 and 2019 33,34 .…”

“…As described by Lander in 1996 10 , SNPs exhibit a typical mutation rate of~10 −9 per nucleotide and have received increasing attention from researchers for their critical role in allele mining, genetic mapping and germplasm identification. Nevertheless, most of the SNPs identified in tea plant are putative 11,12 and have not been functionally assessed. Specifically, only a few SNPs have been validated and developed into markers for screening tea genetic resources to date.…”

Characterization and Development of Genomic SSRs in Pecan (Carya illinoinensis)

“…However, MAS study in pecan is less often carried out. Thereby, MAS in pecan has lagged behind other fruit trees and forestry species [24][25][26][27].…”

A high-density SNP-based genetic map in Pelteobagrus vachelli and mapping of growth, sex determination and hypoxia tolerance related loci

“…It is universally acknowledged that high-resolution linkage maps have become more and more significant for a large number of genetic studies, such as fine-scale quantitative trait locus (QTL) mapping, comparative genomic analysis (CGA), genome scaffolding and assembly (GSA) and mapping molecular marker-assisted selection (MAS) [ 1,2]. For the construction of high-density genetic linkage maps, single-nucleotide polymorphism (SNP) markers representing the most abundant sources of variation in the genome are increasingly utilized [ 3].…”

“…-Authors' Information 1 College of Marine Science and Engineering, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China. 2 Key laboratory for physiology biochemistry and application, School of agriculture and bioengineering, Heze University, Heze, Shandong 274015, China.…”