QTL mapping and candidate gene analysis of berry and cluster traits in table grapevine bred for warm climates

Abstract

Table grapes are a valuable fruit crop worldwide. Warm climates are emerging as important global production suppliers. Traditional grapevine cultivars are poorly adapted to higher temperatures and other abiotic factors of warm zones, conditions increasingly common in temperate areas due to climate change. Understanding the genetic architecture of production traits in breeding families developed for warm climates is crucial to advance cultivar development. The current work mapped and investigated genomic regions controlling cluster and berry traits in two table grape biparental populations developed for warm climates. Progenies were phenotyped over at least three seasons for three cluster and nine berry traits. Individuals were genotyped with 1904 single nucleotide polymorphism (SNP) markers using the EMBRAPA Multi65K multi-species Illumina Infinium chip. Linkage maps for the families were built, aligned to the most recent chromosome-scale Vitis genome and used for multivariate Bayesian QTL mapping to identify 10 QTLs in family 1630 and nine in family 1637. QTL reliability was assessed by its reproducibility in analyses using different repetitions and models. QTLs were found on chromosomes 8, 11, 15 and 17 in line with reliable QTLs mapped in previous studies, providing additional evidence for stable effect loci for berry and cluster architecture traits. Functional gene enrichment analyses of the mapped QTLs identified viable candidate genes for the investigated traits, including specialized metabolism genes for astringency and cytoskeleton components for berry length. Flanking SNPs to the mapped QTLs could allow accelerated breeding by increasing selection intensity within-family on yet to be phenotyped seedlings.