GWAS and QTLanalysis for 124 individual traits

Investigating the genetic architecture of important agronomic traits in
grapevine, like grape quality and resilience to abiotic stress, has been
hampered by bottlenecks in genotyping and phenotyping. Here, we developed
a high-density 200K single nucleotide polymorphism array and validated its
effectiveness by genotyping 471 accessions from three F1 breeding
populations. We developed a high-throughput grape phenotyping tool that
accurately captures berry color, shape and size. By integrating data from
the two platforms, associated loci were identified over three growing
seasons. Association mapping, and haplotype analysis identified novel loci
and candidate genes for berry shape (bHLH017), soluble sugars (ACT) and
organic acids (ALTM1 and FUSC2), as well as vine cold tolerance (NAC08),
and fine mapped the flower sex determination locus. Furthermore, we
validated the functional role of NAC08, demonstrating that it activated
the expression of RFS6 to increase raffinose levels and confer cold
tolerance. Together, these augmented tools, the integrated data, and novel
loci establish a better foundation for trait aggregation that will enhance
breeding efficiency and boost the development of high-quality grape
varieties.