Mining of candidate genes for grape berry cracking using a genome-wide association study

Abstract

Fruit cracking is a common phenomenon during the growth and development of horticultural crops that seriously affects fruit yield and quality. However, there are few studies on the mining of candidate genes related to berry cracking. To better understand the genetic basis of grape berry cracking, we conducted a genome-wide association study (GWAS) of grape varieties. Based on the mixed linear model (MLM), we detected five single nucleotide polymorphism (SNP) loci associated with berry-cracking index and two SNP loci associated with berry-cracking type in two years. These loci were mainly distributed on four chromosomes, namely 1, 2, 3, and 18, and were associated with ten unique candidate berry-cracking genes. The gene expression patterns indicated that the candidate genes in the susceptible berry-cracking variety were more abundant than in the resistant berry-cracking variety. Grape berry-cracking is a complex trait controlled by multiple genes, mainly including genes involved in polygalacturonase, copper transporter, and receptor-like proteins. The high expression of the candidate berry-cracking genes may promote the occurrence of berry cracking, so the present study helps to further elucidate the genetic mechanism of berry cracking.