Genome-wide association study of leaf-related traits in tea plant in Guizhou based on genotyping-by-sequencing

Abstract

Background Studying the genetic characteristics of tea plant (Camellia spp.) leaf traits is essential for improving yield and quality through breeding and selection. Guizhou Plateau, an important part of the original center of tea plants, has rich genetic resources. However, few studies have explored the associations between tea plant leaf traits and single nucleotide polymorphism (SNP) markers in Guizhou. Results In this study, we used the genotyping-by-sequencing (GBS) method to identify 100,829 SNP markers from 338 accessions of tea germplasm in Guizhou Plateau, a region with rich genetic resources. We assessed population structure based on high-quality SNPs, constructed phylogenetic relationships, and performed genome-wide association studies (GWASs). Four inferred pure groups (G-I, G-II, G-III, and G-IV) and one inferred admixture group (G-V), were identified by a population structure analysis, and verified by principal component analyses and phylogenetic analyses. Through GWAS, we identified six candidate genes associated with four leaf traits, including mature leaf size, texture, color and shape. Specifically, two candidate genes, located on chromosomes 1 and 9, were significantly associated with mature leaf size, while two genes, located on chromosomes 8 and 11, were significantly associated with mature leaf texture. Additionally, two candidate genes, located on chromosomes 1 and 2 were identified as being associated with mature leaf color and mature leaf shape, respectively. We verified the expression level of two candidate genes was verified using reverse transcription quantitative polymerase chain reaction (RT-qPCR) and designed a derived cleaved amplified polymorphism (dCAPS) marker that co-segregated with mature leaf size, which could be used for marker-assisted selection (MAS) breeding in Camellia sinensis. Conclusions In the present study, by using GWAS approaches with the 338 tea accessions population in Guizhou, we revealed a list of SNPs markers and candidate genes that were significantly associated with four leaf traits. This work provides theoretical and practical basis for the genetic breeding of related traits in tea plant leaves.

Pigment Diversity in Leaves of Caladium × hortulanum Birdsey and Transcriptomic and Metabolic Comparisons between Red and White Leaves

“…Previous studies have successfully identified loci significantly associated with chlorophyll or anthocyanin in the leaves or petals of various plants, such as tea plant ( Camellia spp. Kamel) [ 23 ], peanut ( Arachis hypogaea L.) [ 24 ], rose ( Rosa rugosa Thunb.) [ 25 ], Gerbera hybrida [ 20 ], rice ( Oryza sativa L.) [ 26 , 27 , 28 ], and Perilla frutescens (L.) Britt.…”

Genome-Wide Association Study (GWAS) Identifies Key Candidate Genes Associated with Leaf Size in Alfalfa (Medicago sativa L.)

“…GWAS and QTL mapping are powerful approaches to elucidate the genetic architecture of complex quantitative traits in plants. For example, Chen et al [39] performed a GWAS on tea plants and identified six candidate genes associated with leaf size and other morphological traits. The expression of the two-leaf size-related candidates was validated using RT-qPCR, which confirmed their functional roles.…”

“…Here, we conducted the first GWAS for leaf morphology in alfalfa using a diverse panel evaluated over three years in Hebei Province, China. The GLM selected in this study is a model with a wide detection range that can detect many SNPs associated with target traits [39]. We identified 26 significant SNPs and six candidates influencing LL and LW.…”

Application of Multi-Perspectives in Tea Breeding and the Main Directions

“…Furthermore, key genes related to characteristic metabolites such as theanine were identified in SNP markers generated from the population consisting of 191 germplasms, while 17 SNP markers related to specific metabolites were determined in another 98 germplasms, providing reliable marker information for the research of tea metabolites [ 20 ]. Six key genes associated with leaf traits were obtained after GWAS of 338 tea germplasm mined for SNP loci verified by linkage disequilibrium, which provided the essential reference for subsequent breeding of leaf traits [ 119 ].…”