Quantitative trait locus (QTL) identification in perennial fruit crops is impeded largely by their lengthy generation time, resulting in costly and labor-intensive maintenance of breeding programs. In a grapevine (genus Vitis) breeding program, although experimental families are typically unreplicated, the genetic backgrounds may contain similar progenitors previously selected due to their contribution of favorable alleles. In this study, we investigated the utility of joint QTL identification provided by analyzing half-sib families. The genetic control of powdery mildew was studied using two half-sib F1 families, namely GE0711/1009 (MN1264 × MN1214; N = 147) and GE1025 (MN1264 × MN1246; N = 125) with multiple species in their ancestry. Maternal genetic maps consisting of 1077 and 1641 single nucleotide polymorphism (SNP) markers, respectively, were constructed using a pseudo-testcross strategy. Ratings of field resistance to powdery mildew were obtained based on whole-plant evaluation of disease severity. This 2-year analysis uncovered two QTLs that were validated on a consensus map in these half-sib families with improved precision relative to the parental maps. Examination of haplotype combinations based on the two QTL regions identified strong association of haplotypes inherited from ‘Seyval blanc’, through MN1264, with powdery mildew resistance. This investigation also encompassed the use of microsatellite markers to establish a correlation between 206-bp (UDV-015b) and 357-bp (VViv67) fragment sizes with resistance-carrying haplotypes. Our work is one of the first reports in grapevine demonstrating the use of SNP-based maps and haplotypes for QTL identification and tagging of powdery mildew resistance in half-sib families.
Bibliographical noteFunding Information:
We thank Peter R. Hemstad (2014 phenotypic data), Steven J. McKay (internal review), and the USDA-NIFA Specialty Crops Research Initiative (Award No. 2011-51181-30635) for funding the Vitis Gen project (http://www.vitisgen.org/ ), which supports JFR. We also acknowledge Jason Londo and members of the Cornell University Biotechnology Resource Center, in particular Peter Schweitzer, Linda Cote, and the Genomic Diversity Facility, for their roles in generating SSR and GBS data, and for helpful discussions related to the project. In addition, we are grateful to John Thull and Jennifer Thull for vineyard management.
- Half-sib progeny
- Powdery mildew