QTL mapping for berry shape based on a high-density genetic map constructed by whole-genome resequencing in grape

Abstract

Grape berry shape is an important agricultural trait. Clarifying its genetic basis is significant for cultivating grape varieties that meet market demands. However, the current study by forward genetics has not achieved in-depth results. Here, a high-density map was constructed to identify quantitative trait loci (QTLs) for berry shape. A total of 358 709 polymorphic SNPs were obtained using whole-genome resequencing (WGS) based on 208 F2 individuals derived from round grape ‘E42-6’ and oblong grape ‘Rizamat’. The 1 635.65 cM high-density map was divided into 19 linkage groups with an average distance of 0.37 cM. Using this map, three significant QTLs for fruit shape index (ShI: ratio of berry length to berry width) identified over three years were mapped onto LG4 and LG5, including one stable QTL on Chr5 with the genomic region of 0.47–1.94 Mb. Combining with gene annotation and expression patterns based on RNA-seq data from two contrasting F2 individuals with round and oblong berry (their average ShI was 1.89 and 1.10, respectively) at four developmental stages, four candidate genes were selected from the above QTLs. They were mainly involved in DNA replication, cell wall modification, and phytohormone biosynthesis. Further analysis of RNA-seq data revealed that several important phytohormone synthesis and metabolic pathways were enriched based on differentially expressed genes (DEGs), which was consistent with the results of QTL mapping for genes related to plant hormone biosynthesis in the F2 population. Furthermore, a comparison of plant hormone content showed that there were significant differences in IAA and tZ content between the two contrasting F2 individuals at different developmental stages. Our findings provide molecular insights into the genetic variation in grape berry shape. Stable QTLs and their tightly linked markers offer the possibility of marker-assisted selection to accelerate berry shape breeding.