Genome wide association analysis of flavour related metabolites in tea germplasm [Camellia sinensis (L.) Kuntze] from Assam using a genotyping by sequencing strategy
Abstract Background 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...
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2025-07-01
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| Online Access: | https://doi.org/10.1186/s12870-025-06889-w |
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| author | Tashmi Konwar Ramendra Nath Sarma Bidyut Kumar Sarmah |
| author_facet | Tashmi Konwar Ramendra Nath Sarma Bidyut Kumar Sarmah |
| author_sort | Tashmi Konwar |
| collection | DOAJ |
| description | Abstract Background 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. Results 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. Conclusion 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. |
| format | Article |
| id | doaj-art-7d1aa0f9281a4c41bc9e72b6067d203f |
| institution | Kabale University |
| issn | 1471-2229 |
| language | English |
| publishDate | 2025-07-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Plant Biology |
| spelling | doaj-art-7d1aa0f9281a4c41bc9e72b6067d203f2025-08-20T04:01:53ZengBMCBMC Plant Biology1471-22292025-07-0125111910.1186/s12870-025-06889-wGenome wide association analysis of flavour related metabolites in tea germplasm [Camellia sinensis (L.) Kuntze] from Assam using a genotyping by sequencing strategyTashmi Konwar0Ramendra Nath Sarma1Bidyut Kumar Sarmah2Department of Agricultural Biotechnology, Assam Agricultural UniversityDepartment of Plant Breeding and Genetics, Assam Agricultural UniversityDepartment of Agricultural Biotechnology, Assam Agricultural UniversityAbstract Background 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. Results 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. Conclusion 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.https://doi.org/10.1186/s12870-025-06889-wFlavourLinkageMarker–trait associationCandidate gene |
| spellingShingle | Tashmi Konwar Ramendra Nath Sarma Bidyut Kumar Sarmah Genome wide association analysis of flavour related metabolites in tea germplasm [Camellia sinensis (L.) Kuntze] from Assam using a genotyping by sequencing strategy BMC Plant Biology Flavour Linkage Marker–trait association Candidate gene |
| title | Genome wide association analysis of flavour related metabolites in tea germplasm [Camellia sinensis (L.) Kuntze] from Assam using a genotyping by sequencing strategy |
| title_full | Genome wide association analysis of flavour related metabolites in tea germplasm [Camellia sinensis (L.) Kuntze] from Assam using a genotyping by sequencing strategy |
| title_fullStr | Genome wide association analysis of flavour related metabolites in tea germplasm [Camellia sinensis (L.) Kuntze] from Assam using a genotyping by sequencing strategy |
| title_full_unstemmed | Genome wide association analysis of flavour related metabolites in tea germplasm [Camellia sinensis (L.) Kuntze] from Assam using a genotyping by sequencing strategy |
| title_short | Genome wide association analysis of flavour related metabolites in tea germplasm [Camellia sinensis (L.) Kuntze] from Assam using a genotyping by sequencing strategy |
| title_sort | genome wide association analysis of flavour related metabolites in tea germplasm camellia sinensis l kuntze from assam using a genotyping by sequencing strategy |
| topic | Flavour Linkage Marker–trait association Candidate gene |
| url | https://doi.org/10.1186/s12870-025-06889-w |
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