Date of Graduation

Spring 2019


Master of Science in Biology



Committee Chair

Laszlo Kovacs


Linkage maps and quantitative trait loci (QTL) analysis have become essential tools for the positional cloning of agronomically important genes and for marker-assisted breeding. In this study, two North American grape species, Vitis rupestris and Vitis riparia, and their 294 F1 progeny were used to construct parental linkage maps and to perform QTL analysis for downy mildew resistance. Single nucleotide polymorphism (SNP) discovery was accomplished using genotyping-by-sequencing (GBS) and resulted in 348,888 SNPs. Of these, 11,063 informative SNP markers (3.17% of the original SNP dataset) were derived after filtering for various quality parameters and missing data. A two-way pseudo-testcross strategy was followed for map construction using JOINMAP®5.0. The 1,115 and 1,177 significant markers (threshold LOD ≥ 14) for V. riparia and V. rupestris were grouped into 19 linkage groups covering 1657.4 and 1401.3 centimorgan (cM) of genetic distances with an average marker interval of 1.49 and 1.19 cM, respectively. Maps were validated by pinpointing a single significant QTL which determined maleness on chromosome 2 in the genetic background of the V. riparia male parent. Phenotype data for leaf downy mildew resistance were collected with both in vitro and naturally inoculated leaves of 86 and 136 F1 progeny, respectively. With both methods, QTL analysis for reduced leaf area coverage by mildew lead to a significant peak on chromosome 10 in V. rupestris explaining 15-45% of the phenotypic variance. For in vitro inoculation, a significant QTL was detected for reduced sporangiophore density on chromosome 8 of V. riparia, explaining 15% of the variance. These are the first SNP-based linkage maps of these native North American grape species. The maps are expected to serve as a resource for breeding modern varieties for environment-friendly grape cultivation.


linkage map, genotyping-by-sequencing, single nucleotide polymorphism, marker-assisted selection, QTL, downy mildew, resistance

Subject Categories

Biology | Genetics | Genomics | Plant Breeding and Genetics | Plant Pathology


© Gaurab Bhattarai

Open Access