Genetic Dissection of Powdery Mildew Resistance in Interspecific Half-Sib Grapevine Families Using SNP-Based Maps

Soon Li Teh , University of Minnesota, Saint Paul, MN
Matthew D. Clark , University of Minnesota, St. Paul, MN
Jonathan Fresnedo Ramirez , Institute of Biotechnology, Cornell University, Ithaca, NY
Qi Sun , Institute for Genomic Diversity, Cornell University, Ithaca, NY
Lance Cadle-Davidson , USDA-ARS Grape Genetics Research Unit, Geneva, NY
James J. Luby , University of Minnesota, St. Paul, MN
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 1,077 and 1,641 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 two-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 MN 1264, with powdery mildew resistance. This investigation also encompassed the use of SSR 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.