Genome-wide SNP discovery from Darjeeling tea cultivars - their functional impacts and application toward population structure and trait associations

Abstract

Genotyping by sequencing and identification of functionally relevant nucleotide variations in crop accessions are the key steps to unravel genetic control of desirable traits. In the scope of present work, elite cultivars of Darjeeling tea were undergone SNP genotyping by doubledigest restriction site associated DNA sequencing method. This study reports a set of 54,206 high-quality SNP markers discovered from ~10.4 GB sequence data, encompassing 15 chromosomes of reference tea genome. Genetic relatedness among the accessions conforms to the analyses of Bayesian clustering, UPGMA, and PCoA methods. High percent of heterozygous loci in the majority of the cultivars reflect their 'hybrid' ancestry as reported earlier. Genomic positions of the discovered SNPs and their putative effect on annotated genes designated a thoughtful understanding of their functional aspects in tea system biology.A group of 95 genes was identified to be affected by high impact variants, most of them are involved in signal transduction, biosynthesis of secondary metabolite, transcriptional and translational regulation. Genome-wide association analyses of 21 agronomic and biochemical phenotypes resulted in trait-linked polymorphic loci with strong confidence (p < 0.05 and 0.001). The selection of significant marker-trait associations with the Bonferroni correction threshold retained a set of 57 SNPs distributed across 14 chromosomes to be linked with eight phenotypic traits. High impact and trait-associated nucleotide polymorphisms perceived in this study can be exploited in worldwide germplasm of contrasting origin to depict their heritability and to unlock their potentiality in marker-assisted breeding.

Pan-transcriptome assembly combined with multiple association analysis provides new insights into the regulatory network of specialized metabolites in the tea plant Camellia sinensis

“…Several recent studies have used a GWAS approach to explore major genes associated with several important specialized metabolites. Hazra et al (2020) conducted a GWAS analysis of 23 Darjeeling tea cultivars and identified 12 SNPs related to epigallocatechin gallate (EGCG), 8 SNPs related to flavonoids, 8 SNPs related to flavor, and 3 SNPs related to phenolics [ 16 ]. Zhang et al (2020) conducted a GWAS on the catechin trait of 176 ancient tea plant accessions and revealed that the CsANR , CsF3′5′H , and CsMYB5 genes may affect tea plant catechin content [ 17 ].…”

Depicting the genetic and metabolic panorama of chemical diversity in the tea plant

“…With the development of mass spectrometry (MS) platforms and sequencing technology, metabolome-based genome-wide association studies (mGWAS) has been successfully applied to exploit natural genotypic variation and identify metabolic quantitative trait loci (mQTL) responsible for metabolomic variation in humans (Hagenbeek et al, 2020;Qin et al, 2012;Zhang et al, 2015), animals (Hartiala et al, 2016) This is an open access article under the terms of the Creative Commons Attribution-NonCommercial-NoDerivs License, which permits use and distribution in any medium, provided the original work is properly cited, the use is non-commercial and no modifications or adaptations are made. (Alseekh et al, 2018;Francisco et al, 2016;Slaten et al, 2020;Wang et al, 2021b;Wen et al, 2014;Zhu et al, 2018).…”

“…The diverse tea genetic resources, coupled with metabolite detection methodologies, enable the identification of mQTL which would further lead to better understanding of the natural variation of metabolites in tea plant. However, previous studies using tea germplasm to map mQTL have merely been pursued on a handful of metabolites or inadequate genotypic data (Fang et al ., 2021 ; Hazra et al ., 2021 ; Huang et al ., 2022 ; Yamashita et al ., 2020 ; Yu et al ., 2020 ; Zhang et al ., 2020b , 2021 ). As such a large‐scale combined metabolomics and population genetics study in tea research can yield significant insights into the genetic and metabolic landscape of tea chemical diversity.…”

Ecophysiological traits differentially modulate secondary metabolite accumulation and antioxidant properties of tea plant [Camellia sinensis (L.) O. Kuntze]

“…Genotypic variation is one of the key factors by which the plant can differentially respond to a particular environmental stimuli 11 . In tea, challenges remained viable to explore the genetic diversity underlying varying physiological response to environment 12,13 . This study aimed to explore natural variations in the ecophysiological traits within seasons and the corresponding multifaceted biochemical responses given by the gene pool of 22 tea cultivars.…”