QTL mapping and characterization of black spot disease resistance using two multi-parental diploid rose populations

Abstract

Black spot disease (BSD) (Diplocarpon rosae) is the most common and damaging fungal disease in garden roses (Rosa sp.). Although qualitative resistance to BSD has been extensively investigated, the research on quantitative resistance lags behind. The goal of this research was to study the genetic basis of BSD resistance in two multi-parental populations (TX2WOB and TX2WSE) through a pedigree-based analysis approach (PBA). Both populations were genotyped and evaluated for BSD incidence over five years in three locations in Texas. A total of 28 QTLs, distributed over all linkage groups (LGs), were detected across both populations. Consistent minor effect QTLs included two on LG1 and LG3 (TX2WOB and TX2WSE), two on LG4 and LG5 (TX2WSE), and one QTL on LG7 (TX2WOB). In addition, one major QTL detected in both populations was consistently mapped on LG3. This QTL was localized to an interval ranging from 18.9 to 27.8 Mbp on the Rosa chinensis genome and explained 20 and 33% of the phenotypic variation. Furthermore, haplotype analysis showed that this QTL had three distinct functional alleles. The parent PP-J14–3 was the common source of the LG3 BSD resistance in both populations. Taken together, this research presents the characterization of new SNP-tagged genetic determinants of BSD resistance, the discovery of marker-trait associations to enable parental choice based on their BSD resistance QTL haplotypes, and substrates for the development of trait-predictive DNA tests for routine use in marker-assisted breeding for BSD resistance.

Pedigree-based analysis in multi-parental diploid rose populations reveals QTLs for cercospora leaf spot disease resistance

“…The position of CLS QTLs coincided with the positions of BSD QTLs previously reported in similar and different germplasm (Lopez Arias et al, 2020a;Lopez Arias et al, 2020b;Rawandoozi et al, 2022). Thus, these results indicate that there is a relationship between some loci that affect resistance to these two fungal diseases.…”

“…This multi-parental population was evaluated in three years, 2018, 2020, and 2021. More details on populations and field conditions are described by Rawandoozi et al (2022).…”

“…As for TX2WSE linkage map construction, the same steps mentioned above were followed, except markers were filtered in PLINK v. 1.9 to zero Mendelian-inconsistent errors per population. For more details on the linkage map development, see Young et al (2022) and Rawandoozi et al (2022).…”

“…After further data curation was conducted through FlexQTL to fix/remove problematic markers and double-recombinant singletons, a total of 1,115 SNP markers for the TX2WOB population and 866 SNP markers for the TX2WSE population were utilized for QTL mapping. A detailed description can be found in Young et al (2022) and Rawandoozi et al (2022).…”

“…facilitated the detection of numerous QTLs with major and minor effects associated with CLS resistance. PBA has been used successfully for quantitative and complex traits on highly heterozygous, clonally propagated crops, including rose (Mangandi et al, 2017;Cai et al, 2018;Rawandoozi et al, 2020;Rawandoozi et al, 2022;Young et al, 2022).…”