ABSTRACT
Rose (Rosa spp.) is one of the most economically important ornamental species worldwide. Flower diameter, flower weight, and the number of petals and petaloids are key flower-size parameters and attractive targets for DNA-informed breeding. Pedigree-based analysis (PBA) using FlexQTL software was conducted using two sets of multi-parental diploid rose populations. Phenotypic data for flower diameter (Diam), flower weight (fresh (FWT)/dry (DWT)), number of petals (NP), and number of petaloids (PD) were collected over six environments (seasons) at two locations in Texas. The objectives of this study were to 1) identify new and/or validate previously reported QTL(s); 2) identify SNP haplotypes associated with QTL alleles (Q-/q-) of a trait and their sources; and 3) determine QTL genotypes for important rose breeding parents. Several new and previously reported QTLs for NP and Diam traits were identified. In addition, QTLs associated with flower weight and PD were identified for the first time. Two major QTLs with large effects were mapped for all traits. The first QTL was at the distal end of LG1 (60.44-60.95 Mbp) and was associated with Diam and DWT in the TX2WOB populations. The second QTL was consistently mapped in the middle region on LG3 (30.15-39.34 Mbp) and associated with NP, PD, and flower weight across two multi-parent populations (TX2WOB and TX2WSE). Haplotype results revealed a series of QTL alleles with differing effects at important loci for most traits. This work is distinct from previous studies by conducting co-factor analysis to account for the DOUBLE FLOWER locus while mapping QTL for NP. Sources of high-value (Q) alleles were identified, namely, 'Old Blush' and Rosa wichuraiana from J14-3 for Diam, while 'Violette' and PP-J14-3 were sources for other traits. In addition, the source of the low-value (q) alleles for Diam was 'Little Chief', and Rosa wichuraiana through J14-3 was the source for the remaining traits. Hence, our results can potentially inform parental/seedling selections as means to improve ornamental quality in roses and a step towards implementing DNA-informed techniques for use in rose breeding programs.
ABSTRACT
Rose rosette disease (RRD), caused by the rose rosette emaravirus (RRV), is a major viral disease in roses (Rosa sp.) that threatens the rose industry. Recent studies have revealed quantitative trait loci (QTL) for reduced susceptibility to RRD in the linkage groups (LGs) 1, 5, 6, and 7 in tetraploid populations and the LGs 1, 3, 5, and 6 in diploid populations. In this study, we seek to better localize and understand the relationship between QTL identified in both diploid and tetraploid populations. We do so by remapping the populations found in these studies and performing a meta-analysis. This analysis reveals that the peaks and intervals for QTL using diploid and tetraploid populations co-localized on LG 1, suggesting that these are the same QTL. The same was seen on LG 3. Three meta-QTL were identified on LG 5, and two were discovered on LG 6. The meta-QTL on LG 1, MetaRRD1.1, had a confidence interval (CI) of 10.53 cM. On LG 3, MetaRRD3.1 had a CI of 5.94 cM. MetaRRD5.1 had a CI of 17.37 cM, MetaRRD5.2 had a CI of 4.33 cM, and MetaRRD5.3 had a CI of 21.95 cM. For LG 6, MetaRRD6.1 and MetaRRD6.2 had CIs of 9.81 and 8.81 cM, respectively. The analysis also led to the identification of potential disease resistance genes, with a primary interest in genes localized in meta-QTL intervals on LG 5 as this LG was found to explain the greatest proportion of phenotypic variance for RRD resistance. The results from this study may be used in the design of more robust marker-based selection tools to track and use a given QTL in a plant breeding context.
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.
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.
