Anthocyanin-rich purple tea: Integrative multi-locus GWAS and SNP effect analysis reveal the genetic basis for development of “speciality tea”

Title : Anthocyanin-rich purple tea: Integrative multi-locus GWAS and SNP effect analysis reveal the genetic basis for development of “speciality tea”

Abstract:

Tea (Camellia sinensis) is worldwide known to be most popular non-alcoholic beverage however the quality of tea is compromised in global market due to environment extremities. The development of “speciality tea” offering high nutritional quality decided by microclimates can seize the problem. Speciality tea is like feeding two birds with a single scone via dealing with consumer preference, tackling nutrition associated diseases at the same time capitalizing onto the niche market. Kangra region, an important part of the Indian tea plants, has rich genetic resources for the collection purple leaf containing high anthocyanin content (AC). Less study have explored the associations between tea plant anthocyanin accumulation and single nucleotide polymorphism (SNP) markers. Whole genome association study to identify causal genes linked with AC biosynthesis is major goal of this objectives. Genotyping-by-Sequencing (GBS) method is used to identify ~157K SNPs in >200 tea accessions grown and maintained at CSIR-IHBT tea garden. Biochemical assay of TAC and metabolites profiling of cyanidin-3glucoside was done using UV spectrophotometry and HPLC respectively. Population stratification of high quality ~57K SNP clustered into 3 major groups via phylogenetic analysis and kinship. Three association frameworks with MLM, BLINK and FarmCPU models identified 62 QTNs on seven tea chromosome further GxE identified 22 environment specific allelic across two years. BLINK and MLM identified a higher number of significant associations with sharper signal resolution, whereas FarmCPU detected fewer but highly stable QTNs. Identified prominent SNPs markers linked with total AC and cyanidin-3-glucoside on chr1 and chr13 are reliable and would be effective translational breeding for the development of Indian purple tea will offer healthy beverage for the consumers.

Biography:

Shimran Yadav is a molecular genomics and genetics researcher working at the interface of phenotypic plasticity, regulatory genomics, and tea (Camellia sinensis) quality improvement, with a primary focus on anthocyanin-rich tea germplasm. Her research explores how genetic and epigenetic variation influence adaptive trait stability, pigment retention, and stress-associated metabolic responses in tea for the development of specialty teas that reflect the unique characteristics of specific geographic regions. Using integrative approaches combining genome-wide association studies (GWAS), transcriptomics, metabolite profiling, and epigenomic analyses, she investigates the regulatory architecture underlying anthocyanin accumulation and degradation dynamics across genetically diverse tea populations in the northern Himalayas (Himachal Pradesh). Her ongoing research has identified candidate loci linked to pigment degradation dynamics, including coding-region variation associated with contrasting purple phenotypes, alongside transcriptional signatures of enhanced degradation activity in low-pigment genotypes. Current whole-genome bisulfite sequencing analyses further aim to resolve the epigenetic mechanisms regulating anthocyanin retention and adaptive metabolic responses that ultimately determine tea quality.