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

Zena J Rawandoozi; Ellen L Young; Stella Kang; Muqing Yan; Seza Noyan; Qiuyi Fu; Tessa Hochhaus; Maad Y Rawandoozi; Patricia E Klein; David H Byrne; Oscar Riera-Lizarazu

doi:10.3389/fpls.2022.1082461

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

Front Plant Sci. 2023 Jan 6:13:1082461. doi: 10.3389/fpls.2022.1082461. eCollection 2022.

Authors

Affiliations

¹ Department of Horticultural Sciences, Texas A&M University, College Station, TX, United States.
² Norman Borlaug Institute for International Agriculture and Development, Texas A&M AgriLife Research, Texas A&M System, College Station, TX, United States.

Abstract

Cercospora leaf spot (CLS) (Cercospora rosicola) is a major fungal disease of roses (Rosa sp.) in the southeastern U.S. Developing CLS-resistant cultivars offers a potential solution to reduce pesticide use. Yet, no work has been performed on CLS resistance. This study aimed to identify QTLs and to characterize alleles for resistance to CLS. The study used pedigree-based QTL analysis to dissect the genetic basis of CLS resistance using two multi-parental diploid rose populations (TX2WOB and TX2WSE) evaluated across five years in two Texas locations. A total 38 QTLs were identified across both populations and distributed over all linkage groups. Three QTLs on LG3, LG4, and LG6 were consistently mapped over multiple environments. The LG3 QTL was mapped in a region between 18.9 and 27.8 Mbp on the Rosa chinensis genome assembly. This QTL explained 13 to 25% of phenotypic variance. The LG4 QTL detected in the TX2WOB population spanned a 35.2 to 39.7 Mbp region with phenotypic variance explained (PVE) up to 48%. The LG6 QTL detected in the TX2WSE population was localized to 17.9 to 33.6 Mbp interval with PVE up to 36%. Also, this study found multiple degrees of favorable allele effects (q-allele) associated with decreasing CLS at major loci. Ancestors 'OB', 'Violette', and PP-M4-4 were sources of resistance q-alleles. These results will aid breeders in parental selection to develop CLS-resistant rose cultivars. Ultimately, high throughput DNA tests that target major loci for CLS could be developed for routine use in a DNA-informed breeding program.

Keywords: Cercospora rosicola; flexQTL; haplotype; pedigree-based analysis; rosa.

Grants and funding

This work was supported by the Robert E. Basye Endowment in Rose Genetics and the US Department of Agriculture Specialty Crop Research Initiative projects “Combating rose rosette disease: short term and long-term approaches” (2014-51181-22644); “RosBREED: combining disease resistance with horticultural quality in new rosaceous cultivars” (2014-51181-22378); and “Tools for genomics-assisted breeding polyploids: development of a community resource” (2020-51181-32156). We also acknowledge the Turkish Ministry of National Education’s funding provided to SN.