eQTL Analysis of Key Monoterpene Biosynthesis Genes in Table Grape

The eQTL mapping for monoterpene biosynthesis related gene expression traits were performed and the candidate genes were mined to deeply understand the regulation mechanism of monoterpene synthesis, so as to lay a foundation for the cultivation of new Muscat grape varieties and germplasm improvement.

The F₁ population generated by crossing Moldova and Ruiduxiangyu were used as materials in this study, and the grape berry samples were collected at verasion and ripening stage respectively. The phenotypic data of expression traits were obtained by detecting the expression levels of seven monoterpene synthesis pathway genes (VvDXS1, VvDXS3, VvDXR, VvHDR, VvLiner, VvTerp, and VvGermD) by using real-time quantitative qPCR technique. eQTL mapping of monoterpene gene expression traits were performed with the mapQTL6.0 software based on the interval mapping method. The associated markers of eQTL were mapped to the genomic region, and the genes within eQTLs were annotated and analyzed via the databases of Ensembl Plants and NCBI. The expression profiles of candidate genes in the samples of parents at different developmental stages were detected by grape whole genome microarray.

The expression levels of seven monoterpene biosynthesis related genes in F₁ population showed a continuous quantitative genetic distribution. A significant correlation between the expression of monoterpene genes was observed. At verasion, 13 eQTLs for the seven expression traits were mapped on chromosome 1, 6, 14, 16, 17, 10 and 12, respectively, and the phenotypic explanation value ranged from 12.2% to 23.5%. Among them, eQTLs (qDXS1-v14, qHDR-v14-1 and qTerp-v14) on chromosome 14 covered the same genetic interval of 57.582-76.979 cM, and qLiner-v10, qTerp-v10 and qGermD-v10 were co-located on chromosome 10. At the mature stage, 16 eQTLs were detected, mainly located on chromosome 1, 6, 12, 8, 13 and 19. qDXS1-m6-2, qDXR-m6-2, qLiner-m6 and qGermD-m6 were co-located in the genetic interval 139.212-143.161 cM of chromosome 6. In addition, a total of 18 eQTLs on chromosomes 1, 3, 7, 10, 12, 15 and 19 were detected for the change ratio of each gene expression between maturity and verasion, respectively. qDXS1-r12-1, qDXR-r12-1, qHDR-r12, qLiner-r12 and qGermD-r12 covered the same genetic interval of 6.330-6.967cM on chromosome 12. The eQTL region for multiple expression traits co-located were further annotated, 90 transcription factor genes were screened, and 11 candidate genes were finally identified by expression profile and correlation analysis. Among them, four candidate genes of VIT_06s0009g01380, VIT_14s0006g02290, VIT_12s0028g01170 and VIT_15s0046g00290 were predicted to participate in the regulation of hormone signaling pathway, one candidate gene VIT_12s0028g01110 encodes a phytochrome interacting factor related to light response, and some other genes encode Myb, WRKY transcription factors or unknown functional proteins.

A total of 37 eQTLs linked to monoterpene synthesis gene expression traits were detected at two different development stages, which mainly located on chromosome 6, 12 and 14. Based on the results of gene annotation and expression profile analysis, 11 candidate genes including VIT_14s0006g02290 and VIT_06s0009g01380 were identified, and these candidate genes were highly correlated with the expression of multiple monoterpene genes.