QTL mapping combined RNA-seq technology identified potential genes involved in regulation of apple size

Abstract

Fruit size is an important external indicator of apple quality. However, fruit-size breeding is complicated because multiple factors, including cultivar management, plant hormones and genetic factors, influence the final fruit size. Genetic factors are the most fundamental determinants of fruit size, mainly through cell division and expansion. Hence, the genes involved in regulation of cell development and plant hormone signalling are important regulators of fruit size. This work presents a dense genetic linkage map constructed using a 'Golden Delicious' × 'Fuji' population. Two algorithms: Kruskal-Wallis (KW) and Interval Mapping (IM) was used to identify the quantitative trait loci (QTL) for fruit size. Several size QTLs were detected, generating three genomic regions for fruit size and analysing the biological functions revealed 339 genes from the three regions as possible candidate genes controlling apple fruit size. Meanwhile, the transcriptome profiles of fruit flesh between large (LF) and small fruits (SF) at 30 and 60 days after full bloom (DAFB) revealed 2635 and 3922 DEGs at 30 DAFB and 60 DAFB, respectively. The 339 genes identified by QTL-Mapping revealed 41 DEGs, with 23 genes at both 30 and 60 DAFB (five genes in common), as the final candidate genes controlling fruit size. These results maybe reveal the molecular regulation mechanism of fruit size and provide basic evidence for developing gene markers for apple breeding.