Konwar Tashmi, Sarma Ramendra Nath, Sarmah Bidyut Kumar
Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, 785013, India.
Department of Plant Breeding and Genetics, Assam Agricultural University, Jorhat, Assam, 785013, India.
BMC Plant Biol. 2025 Jul 14;25(1):911. doi: 10.1186/s12870-025-06889-w.
Tea [Camellia sinensis (L.) Kuntze] is a type of evergreen shrub that belongs to the family Theaceae. The widespread consumption of this crop is attributed to its refreshing taste, pleasant aroma, stimulating properties, numerous health benefits and therapeutic uses because it is the richest source of secondary metabolites, especially catechin derivatives, caffeine, polyphenols, theanine, tannins, etc. As such, the present study aimed to evaluate the genome-wide associated significant loci to identify potential candidate genes for flavour-related traits of indigenous tea germplasm maintained at Assam Agricultural University, Jorhat, India.
A total of 401,865 filtered SNPs were used for the genotyping of 160 tea germplasms. Chromosome 1 had the highest number of detected SNPs, with 40,154, whereas chromosome 14 had the lowest number, with 15,646 SNPs. Significant variation was observed between the metabolites, and among them, the EGCG content was notably the highest. A total of 162 loci were commonly identified as significant QTNs for all 13 traits via the MLM and FarmCPU models through the GAPIT and rMVP approaches. However, certain loci are commonly associated with multiple traits. From these significant QTNs, more than 100 candidate genes associated with flavour-related traits were identified at different marker positions and the expression analysis of gene viz. CsbHLH, chalcone flavonone, serine carboxylase etc. showed higher expression.
This GWAS identified several genes that could be linked to flavour-related traits in tea plants. While some of these genes are not directly involved in biosynthetic pathways, their influence on metabolism under stress highlights their importance in the broader metabolic network and plant adaptability. The identified SNPs and candidate genes can be leveraged for marker-assisted selection, accelerating the breeding of tea plants with desirable traits. This information offers key insights into the genetic mechanisms behind flavour profiles and stress response, opening new avenues for future genetic enhancement and breeding approaches in tea cultivation.
茶树[Camellia sinensis (L.) Kuntze]是一种属于山茶科的常绿灌木。这种作物广泛消费归因于其清新的口感、宜人的香气、刺激特性、众多健康益处和治疗用途，因为它是次生代谢产物的最丰富来源，尤其是儿茶素衍生物、咖啡因、多酚、茶氨酸、单宁等。因此，本研究旨在评估全基因组关联的显著位点，以鉴定印度乔哈特阿萨姆邦农业大学保存的本土茶种质风味相关性状的潜在候选基因。
共401,865个过滤后的单核苷酸多态性（SNP）用于160份茶种质的基因分型。1号染色体检测到的SNP数量最多，为40,154个，而14号染色体数量最少，为15,646个SNP。代谢物之间观察到显著差异，其中表没食子儿茶素没食子酸酯（EGCG）含量显著最高。通过GAPIT和rMVP方法，利用混合线性模型（MLM）和固定和随机模型循环概率统一法（FarmCPU）模型，共鉴定出162个位点为所有13个性状的显著数量性状核苷酸（QTN）。然而，某些位点通常与多个性状相关。从这些显著的QTN中，在不同标记位置鉴定出100多个与风味相关性状的候选基因，基因即CsbHLH、查尔酮黄酮、丝氨酸羧化酶等的表达分析显示表达较高。
这项全基因组关联研究（GWAS）鉴定出几个可能与茶树风味相关性状有关的基因。虽然其中一些基因不直接参与生物合成途径，但它们在胁迫下对代谢的影响突出了它们在更广泛的代谢网络和植物适应性中的重要性。鉴定出的SNP和候选基因可用于标记辅助选择，加速具有理想性状的茶树育种。这些信息为风味特征和胁迫反应背后的遗传机制提供了关键见解，为未来茶树栽培的遗传改良和育种方法开辟了新途径。
