High density SNP and SSR linkage map and QTL analysis for resistance to black spot in segregating rose population

D.C. Lopez Arias, A. Chastellier, T. Thouroude, M. Leduc, F. Foucher, L. Hibrand-Saint Oyant, V. Soufflet-Freslon
Black spot disease (BSD), caused by the fungus Diplocarpon rosae Wolf, is one of the most important and widespread disease of roses in outdoor landscaping. Up to now, an efficient control of black spot disease still requires intensive use of fungicides. However, new laws to decrease agrochemical use (Labbé, 2014) have encouraged breeders and researchers to study this disease and to develop varieties with higher levels of resistance. A better understanding of disease resistance in rose cultivars and the use of resistant rose cultivars would help to reduce the application of chemicals but most of the cultivars with the highest economic impact are susceptible to black spot disease. Qualitative resistance conferred by major genes (Rdr genes) have been widely described (Hattendorf et al., 2004; Kaufmann et al., 2010; Malek and Debener, 1998; Malek et al., 2000; Menz et al., 2018; Terefe-Ayana et al., 2011; Whitaker and Hokanson, 2009; Whitaker et al., 2010a; Yokoya et al., 2000) whereas the genetic basis of quantitative resistance has not yet been elucidated. The objective of our project is to study the genetic resistance to BSD and to identify genes involved in quantitative resistance to it. A progeny referred as OW (151 hybrids), from the cross between 'Old blush' (susceptible parent) and Rosa × wichurana (resistant parent) was developed. This progeny was scored for BSD resistance after natural infections in field over four years (from 2014 to 2017) at INRA in Angers, France. This cross has been considered as a pseudo-test cross and two high density consensus individual maps (male and female maps) with SSR and SNP markers were developed. Quantitative trait locus (QTL) analysis using SIM (simple interval mapping), CIM (composite interval mapping) and MQM (multiple QTL mapping) methods have been performed. For the male map, three QTL were identified: one QTL was localized on linkage group 3 for all the years of evaluation, a second QTL was identified on linkage group 5 for 2016 and 2017 and another one on linkage group 4 but only for 2017. The stability of these QTL in different genetic backgrounds will be evaluated which should help to get a better precision of genomic localizations and to validate efficiency of detected QTL. Candidate genes underlying these QTL will be explore thanks to rose genome sequence.
Lopez Arias, D.C., Chastellier, A., Thouroude, T., Leduc, M., Foucher, F., Hibrand-Saint Oyant, L. and Soufflet-Freslon, V. (2020). High density SNP and SSR linkage map and QTL analysis for resistance to black spot in segregating rose population. Acta Hortic. 1283, 191-198
DOI: 10.17660/ActaHortic.2020.1283.26
diploid rose, quantitative resistance, natural infection, Diplocarpon rosae, interval mapping, genetic map

Acta Horticulturae