Characterization and mapping of a downy mildew resistance gene, Pl36, in sunflower (Helianthus annuus L.)

Whole-genome sequencing enables molecular dissection and candidate gene identification of the rust resistance gene R12 in sunflower (Helianthus annuus L.)

KEY MESSAGE

We finely mapped the rust resistance gene R₁₂ to a 0.1248-cM region, identified a potential R₁₂ candidate gene in the XRQ reference genome, and developed three diagnostic SNP markers for R₁₂. Rust is a devastating disease in sunflower that is damaging to the sunflower production globally. Identification and utilization of host-plant resistance are proven to be preferable means for disease control. The rust resistance gene R₁₂ with broad-spectrum specificity to rust was previously localized to a 2.4 Mb region on sunflower chromosome 11. To understand the molecular mechanism of resistance, we conducted whole-genome sequencing of RHA 464 (R₁₂ donor line) and reference genome-based fine mapping of the gene R₁₂. Overall, the 213 markers including 186 SNPs and 27 SSRs' were identified from RHA 464 sequences and used to survey polymorphisms between the parents HA 89 and RHA 464. Saturation mapping identified 26 new markers positioned in the R₁₂ region, and fine mapping with a large population of 2004 individuals positioned R₁₂ at a genetic distance of 0.1248 cM flanked by SNP markers C11_150451336 and S11_189205190. One gene, HanXRQChr11g0348661, with a defense-related NB-ARC-LRR domain, was identified in the XRQr1.0 genome assembly in the R₁₂ region; it is predicted to be a potential R₁₂ candidate gene. Comparative analysis clearly distinguished R₁₂ from the rust R₁₄ gene located in the vicinity of the R₁₂ gene on chromosome 11. Three diagnostic SNP markers, C11_147181749, C11_147312085, and C11_149085167, specific for R₁₂ were developed in the current study, facilitating more accurate and efficient selection in sunflower rust resistance breeding. The current study provides a new genetic resource and starting point for cloning R₁₂ in the future.

Introgression and targeting of the Pl37 and Pl38 genes for downy mildew resistance from wild Helianthus annuus and H. praecox into cultivated sunflower (Helianthus annuus L.)

Two new downy mildew resistance genes, Pl₃₇ and Pl₃₈, were introgressed from wild sunflower species into cultivated sunflower and mapped to sunflower chromosomes 4 and 2, respectively Downy mildew (DM), caused by the oomycete pathogen Plasmopara halstedii (Farl.) Berl. & de Toni, is known as the most prevalent disease occurring in global sunflower production areas, especially in North America and Europe. In this study, we report the introgression and molecular mapping of two new DM resistance genes from wild sunflower species, Helianthus annuus and H. praecox, into cultivated sunflower. Two mapping populations were developed from the crosses of HA 89/H. annuus PI 435417 (Pop1) and CMS HA 89/H. praecox PRA-417 (Pop2). The phenotypic evaluation of DM resistance/susceptibility was conducted in the BC₁F₂-derived BC₁F₃ populations using P. halstedii race 734. The BC₁F₂ segregating Pop1 was genotyped using an Optimal GBS AgriSeq™ Panel consisting of 768 mapped SNP markers, while the BC₁F₂ segregating Pop2 was genotyped using a genotyping-by-sequencing approach. Linkage analysis and subsequent saturation mapping placed the DM resistance gene, designated Pl₃₇, derived from H. annuus PI 435417 in a 1.6 cM genetic interval on sunflower chromosome 4. Pl₃₇ co-segregated with SNP markers SPB0003 and C4_5738736. Similarly, linkage analysis and subsequent saturation mapping placed the DM resistance gene, designated Pl₃₈, derived from H. praecox PRA-417 in a 0.8 cM genetic interval on sunflower chromosome 2. Pl₃₈ co-segregated with seven SNP markers. Multi-pathotype tests revealed that lines with Pl₃₇ or Pl₃₈ are immune to the most prevalent and virulent P. halstedii races tested. Two germplasm lines, HA-DM15 with Pl₃₇ and HA-DM16 with Pl₃₈, were developed for use in sunflower DM-resistance breeding.

Spatial Genetic Structure and Pathogenic Race Composition at the Field Scale in the Sunflower Downy Mildew Pathogen, Plasmopara halstedii

Yield losses in sunflower crops caused by Plasmopara halstedii can be up to 100%, depending on the cultivar susceptibility, environmental conditions, and virulence of the pathogen population. The aim of this study was to investigate the genetic and phenotypic structure of a sunflower downy mildew agent at the field scale. The genetic diversity of 250 P. halstedii isolates collected from one field in southern France was assessed using single-nucleotide polymorphisms (SNPs) and single sequence repeats (SSR). A total of 109 multilocus genotypes (MLG) were identified among the 250 isolates collected in the field. Four genotypes were repeated more than 20 times and spatially spread over the field. Estimates of genetic relationships among P. halstedii isolates using principal component analysis and a Bayesian clustering approach demonstrated that the isolates are grouped into two main genetic clusters. A high level of genetic differentiation among clusters was detected (F_ST = 0.35), indicating overall limited exchange between them, but our results also suggest that recombination between individuals of these groups is not rare. Genetic clusters were highly related to pathotypes, as previously described for this pathogen species. Eight different races were identified (100, 300, 304, 307, 703, 704, 707, and 714), with race 304 being predominant and present at most of the sites. The co-existence of multiple races at the field level is a new finding that could have important implications for the management of sunflower downy mildew. These data provide the first population-wide picture of the genetic structure of P. halstedii at a fine spatial scale.

Genetic Insight into Disease Resistance Gene Clusters by Using Sequencing-Based Fine Mapping in Sunflower (Helianthus annuus L.)

Rust and downy mildew (DM) are two important sunflower diseases that lead to significant yield losses globally. The use of resistant hybrids to control rust and DM in sunflower has a long history. The rust resistance genes, R13a and R16, were previously mapped to a 3.4 Mb region at the lower end of sunflower chromosome 13, while the DM resistance gene, Pl33, was previously mapped to a 4.2 Mb region located at the upper end of chromosome 4. High-resolution fine mapping was conducted using whole genome sequencing of HA-R6 (R13a) and TX16R (R16 and Pl33) and large segregated populations. R13a and R16 were fine mapped to a 0.48 cM region in chromosome 13 corresponding to a 790 kb physical interval on the XRQr1.0 genome assembly. Four disease defense-related genes with nucleotide-binding leucine-rich repeat (NLR) motifs were found in this region from XRQr1.0 gene annotation as candidate genes for R13a and R16. Pl33 was fine mapped to a 0.04 cM region in chromosome 4 corresponding to a 63 kb physical interval. One NLR gene, HanXRQChr04g0095641, was predicted as the candidate gene for Pl33. The diagnostic SNP markers developed for each gene in the current study will facilitate marker-assisted selections of resistance genes in sunflower breeding programs.