Identification and analysis of alleles in the aroma biosynthesis pathways based on Camellia sinensis ‘Jinguanyin’ haplotype-resolved genomes

Key message The specifically expressed alleles of CsMCT , CsGGPPS2 , CsHMGS2 , CsHMGR3 , CsTPS10 , CsADH4 , CsDAHPS , CsCM3 , and CsAS2 may play critical roles in the aroma formation of Camellia sinensis 'Jinguanyin' cultivar. CsMVD , CsDXS2 , CsTPS3 , CsTPS9 , CsTPS10 , CsTPS13 and CsTPS14 play an essential role in the formation of the characteristic floral and fruit aromas of oolong tea. Abstract To explore the role of alleles in the aroma biosynthesis pathways of the tea plant, this study was conducted to identify and analyze the alleles of structural genes in the MVA, MEP, LOX and shikimate pathways based on Camellia sinensis ‘Jinguanyin’ haplotype-resolved genomes. The results showed that 69 pairs of alleles were identified in the four pathways, of which 24 genes showed allele-specific expression (ASE) in at least one tissue. TGY-allele and HD-allele correlations of buds, young leaves, and stems were higher in the six tissues of JGY. KEGG analysis revealed that 24 ASEGs were significantly enriched in GPI-anchor biosynthesis and monoterpenoid biosynthesis pathways. The results suggest that the specifically expressed alleles of CsMCT, CsGGPPS2 , CsHMGS2 , CsHMGR3 , CsTPS10 , CsADH4 , CsDAHPS , CsCM3 , and CsAS2 may play critical roles in the aroma formation of JGY cultivars. The qRT‒PCR results showed that the bias of CsTPS1 , CsMVD , CsDHQS , and CsAS2 alleles was basically consistent with the expression of the parents (TGY and HD) of JGY in young leaves. In addition, qRT‒PCR was used to detect the expression of aroma-related genes during the manufacturing process of JGY and parents (TGY and HD) oolong tea. It showed that CsMVD , CsDXS2 , CsTPS3 , CsTPS9 , CsTPS10 , CsTPS13 and CsTPS14 play an essential role in the formation of the characteristic floral and fruit aromas of oolong tea.