Abstract
Effectively using genomic information greatly accelerates conventional breeding and applying it to long-lived crops promotes the conversion to genomic breeding. Because tea plants are bred using conventional methods, we evaluated the potential of genomic predictions (GPs) and genome-wide association studies (GWASs) for the genetic breeding of tea quality-related metabolites using genome-wide single nucleotide polymorphisms (SNPs) detected from restriction site-associated DNA sequencing of 150 tea accessions. The present GP, based on genome-wide SNPs, and six models produced moderate prediction accuracy values (r) for the levels of most catechins, represented by ( −)-epigallocatechin gallate (r = 0.32–0.41) and caffeine (r = 0.44–0.51), but low r values for free amino acids and chlorophylls. Integrated analysis of GWAS and GP detected potential candidate genes for each metabolite using 80–160 top-ranked SNPs that resulted in the maximum cumulative prediction value. Applying GPs and GWASs to tea accession traits will contribute to genomics-assisted tea breeding.
Highlights
Using genomic information greatly accelerates conventional breeding and applying it to long-lived crops promotes the conversion to genomic breeding
We evaluated the potential of performing integrated analysis by genomic predictions (GPs) and genomewide association studies (GWASs) for genetic improvement of tea quality-related metabolites using genome-wide single nucleotide polymorphisms (SNPs) from restriction site-associated DNA sequencing (RAD-seq) data
Genomics-based approaches may be especially useful in crop breeding and reduce the required breeding time compared with conventional breeding[18]
Summary
Using genomic information greatly accelerates conventional breeding and applying it to long-lived crops promotes the conversion to genomic breeding. Because tea plants are bred using conventional methods, we evaluated the potential of genomic predictions (GPs) and genomewide association studies (GWASs) for the genetic breeding of tea quality-related metabolites using genome-wide single nucleotide polymorphisms (SNPs) detected from restriction site-associated DNA sequencing of 150 tea accessions. The emergence of restriction site-associated DNA sequencing (RAD-seq) and genotype-by-sequencing resulted from the implementation of SNPs suitable for GP in both model and non-model crops[17,18,21] These high-throughput genome-wide SNP genotyping platforms have enabled the use of genome-wide association studies (GWASs) and GPs in many important c rops[22,23,24,25,26]. GWASs enable detection of QTLs or genes that control phenotypic variations in a population of cultivars or germplasm accessions without preparing a bi-parental segregating p opulation[27]
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