Main and epistatic QTL analyses for Sclerotinia Head Rot resistance in sunflower

Abstract

Sclerotinia Head Rot (SHR), a disease caused by Sclerotinia sclerotiorum, is one of the most limiting factors in sunflower production. In this study, we identified genomic loci associated with resistance to SHR to support the development of assisted breeding strategies. We genotyped 114 Recombinant Inbred Lines (RILs) along with their parental lines (PAC2 –partially resistant–and RHA266 –susceptible–) by using a 384 single nucleotide polymorphism (SNP) Illumina Oligo Pool Assay to saturate a sunflower genetic map. Subsequently, we tested these lines for SHR resistance using assisted inoculations with S. sclerotiorum ascospores. We also conducted a randomized complete-block assays with three replicates to visually score disease incidence (DI), disease severity (DS), disease intensity (DInt) and incubation period (IP) through four field trials (2010–2014). We finally assessed main effect quantitative trait loci (M-QTLs) and epistatic QTLs (E-QTLs) by composite interval mapping (CIM) and mixed-model-based composite interval mapping (MCIM), respectively. As a result of this study, the improved map incorporates 61 new SNPs over candidate genes. We detected a broad range of narrow sense heritability (h2) values (1.86–59.9%) as well as 36 M-QTLs and 13 E-QTLs along 14 linkage groups (LGs). On LG1, LG10, and LG15, we repeatedly detected QTLs across field trials; which emphasizes their putative effectiveness against SHR. In all selected variables, most of the identified QTLs showed high determination coefficients, associated with moderate to high heritability values. Using markers shared with previous Sclerotinia resistance studies, we compared the QTL locations in LG1, LG2, LG8, LG10, LG11, LG15 and LG16. This study constitutes the largest report of QTLs for SHR resistance in sunflower. Further studies focusing on the regions in LG1, LG10, and LG15 harboring the detected QTLs are necessary to identify causal alleles and contribute to unraveling the complex genetic basis governing the resistance.

SNP Discovery and QTL Mapping of Sclerotinia Basal Stalk Rot Resistance in Sunflower using Genotyping‐by‐Sequencing

“…The DS QTL were located on LGs 2, 4, 8, 9, 10, 12, and 13, explaining between 8.4 and 34.5% of phenotypic variance. Zubrzycki et al (2012) identified a total of 20 head rot QTL for DI, DS, and the area under the disease progress curve on LGs 10, 13, and 14.…”

Analysis of genetic determination of partial resistance to white rot in sunflower

“…A good example of this is the hybrid DM220AO, which showed the most favorable BLUP for RIPt (0.14) and the worst (0.18) for RDGLt (Table 3). Filippi et al (2017) and Zubrzycki et al (2017) estimated highly significant phenotypic correlations between several of the WR variables they evaluated. Besides, these authors suggested that these associated WR variables could be used as components of WR partial resistance.…”

Validated markers for sunflower (Helianthus annuusL.) breeding

“…However, breeding lines such as HA-BSR1 have been registered, which have high tolerance to Sclerotinia basal stalk mold originating from parents HA 441/RHA 439 (Talukder et al, 2017). Narrow sense heritability ranged between 2-60% for Sclerotinia resistance (Zubrzycki and Maringolo, 2017), indicating the possibility for good gain from selection, and the possibility of identifying genes of major effect on resistance. Gene identification studies using different methods have been successful in this effort.…”

“…Association mapping showed that candidate gene HaRIC_B caused a 20% reduction in the head rot incidence. Several mapping studies were carried out to identify QTLs linked to Sclerotinia resistance (Davar et al, 2010;Zubrzycki and Maringolo, 2017). However, markers proposed by transcript profiling, association, or linkage mapping have not been validated in independent populations.…”