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Research Project: Management of Temperate-Adapted Fruit, Nut, and Specialty Crop Genetic Resources and Associated Information

Location: National Clonal Germplasm Repository

Title: The development of a dense SNP-based consensus map and QTL detection for black spot resistance in five diploid rose populations [abstract]

item YAN, MUQING - Texas A&M University
item BYRNE, DAVID - Texas A&M University
item Zurn, Jason
item DONG, QIANNI - Texas A&M University
item KLEIN, PATRICIA - Texas A&M University

Submitted to: Plant and Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: 10/30/2016
Publication Date: 1/14/2017
Citation: Yan, M., Byrne, D., Zurn, J.D., Dong, Q., Klein, P. 2017. The development of a dense SNP-based consensus map and QTL detection for black spot resistance in five diploid rose populations [abstract]. Plant and Animal Genome Conference. January 13-18, 2017, San Diego, California.

Interpretive Summary: Rose black spot is one of the most important disseases of cultivated roses for both the home and commercial market in warm areas. The use of genetic resistance is the most economic and environmentally friendly management strategy for controling the disease. Currently, little is known about resistance found in roses and only three resistance genes have been mapped and characterized. In addition to these genes, broad non-isolate specific resistance has been observed. To caracterize this broad reistance in three diploid rose populations, genetic mapping was conducted. A genotype-by-sequencing approach was used to generate 3,500 SNP markers and construct a consensus map. Moreover, multiple genetic regions of interest associated with black spot reistance were identified in the subsiqent analysis. Future work will focus on developing new tools to use this resistance in future varieties.

Technical Abstract: Black spot (BS) disease (Diplocarpon rosae (Lib.) Wolf) of rose is the most important leaf disease of garden roses in warm humid areas. Although the partial (horizontal) resistance to black spot has been shown to be moderately heritable, the responsible quantitative trait loci (QTL) remain unidentified. Because of the interspecific nature and high heterozygosity in commercial roses the genetic information available on rose is limited. We utilized genotyping by sequencing (GBS) technology to create abundant SNP markers. This was done with the use of a methylation sensitive restriction enzyme NgoMIV (G'CCGCC) to construct the DNA template for three diploid rose populations segregating for resistance (derived from Rosa wichuriana) to the black spot fungus. The DNA fragments were sequenced using the Illumina Hiseq2500 platform and then aligned to the strawberry genome sequence to identify SNPs. Filtering the potential SNPs for informative polymorphism resulted in about 3500 SNPs to use in the consensus map construction. The consensus map was created by first developing individual maps for three populations, each with about 1,500 markers. Then the 677 SNPs and 14 SSRs bridge markers were used to link three individual populations. The anchor SSRs were used to determine the pseudo-chromosomes as defined in the current consensus map. In this diploid consensus map, the seven linkage groups (LGs) were covered with 3,527 markers resulting in a total length of 892.2cM for the diploid rose genome. The average distance between markers was 0.25cM. This is the first report of a high-density integrated consensus map for diploid roses (ICD). The high level of synteny between strawberry and diploid rose genome was revealed in this study. The analysis of the partial (horizontal) resistance to black spot as measured in a detached leaf assay among five diploid populations identified important QTLs for black spot resistance on various chromosomes.