Linkage mapping in segmental allopolyploids: a case study in rose

Authors: Zurn, Jason; ZLESAK, DAVID - University Of Wisconsin; HOLEN, MATTHEW - University Of Minnesota; BRADEEN, JAMES - University Of Minnesota; HOKANSON, STAN - University Of Minnesota; Bassil, Nahla

Submitted to: American Society of Horticulture Science Meeting
Publication Type: Abstract Only
Publication Acceptance Date: 3/1/2019
Publication Date: 7/21/2019
Citation: Zurn, J.D., Zlesak, D.C., Holen, M., Bradeen, J.M., Hokanson, S.C., Bassil, N.V. 2019. Linkage mapping in segmental allopolyploids: a case study in rose. American Society of Horticulture Science Meeting. American Society of Horticulture Science Meeting.

Interpretive Summary: Rose black spot is one of the most devastating diseases of cultivated roses for both the home and commercial market. The use of genetic resistance is the most economic and environmentally friendly management strategy for controlling the disease. Currently, little is known about resistance found in roses and only four resistance genes have been characterized. One of these genes, Rdr3, was identified by never mapped to a genetic location due to the complex genetics displayed in roses. Because of this we do not know if Rdr3 is a unique gene or a varient of one of the other known genes. New tools have recently been developed that has allowed us to finally map the position of Rdr3. The work presented is an overview of how to map genes in organisms with complex genetics, like roses, and answers the questions surrounding the genetic mapping Rdr3.

Technical Abstract: Genetic mapping in polyploid organisms that undergo random pairing during meiosis can be a complex process. Early genetic maps were constructed using single dose allele markers that segregate 1:1. These markers are incapable of being used to identify homoeologous or ohnologous chromosomes. Recently, software capable of identifying allelic dosage for SNP markers and mapping software that allows for the use of higher-dose markers has become available. This has allowed for great advancements in the mapping of segmental allopolyploids, like hybrid roses. The black spot resistance gene Rdr3 was previously identified in the tetraploid rose ‘George Vancouver’ but has not been mapped. As such, a mapping population was developed by crossing ‘George Vancouver’ with the susceptible tetraploid rose ‘Morden Blush’. Phenotyping was conducted via a detached leaf assay with the Diplocaron rosae race 8 isolate ACT. The population was genotyped with the WagRhSNP 68K rose Axiom array and allelic dosages were called using the R package ‘fitPoly’. Genetic mapping was conducted using the R package ‘polymapR’, that allows for the use of single and higher-dose markers for triploid, tetraploid, and hexaploid populations. Rdr3 was mapped to a chromosome 6 homoeolog. To date, three additional black spot resistance genes have been mapped (Rdr1, Rdr2, and Rdr4). Both Rdr1 and Rdr2 map to a chromosome 1 homoeolog and Rdr4 maps to a chromosome 5 homoeolog. Because Rdr3 maps to a different region than any of the previously mapped genes, it is a unique gene and not an allele of the other genes. The mapping of Rdr3 demonstrates how new analysis tools can be used to create maps with much greater marker density for polyploids and begin answering some of the complex genetic questions surrounding them.