Map and sequence-based chromosome walking towards cloning of the male fertility restoration gene Rf5 linked to R11 in sunflower

Origin of CMS-PET1 cytotype in cultivated sunflower: A new insight

The vast majority of commercial sunflower hybrids worldwide are produced using cytoplasmic male sterility (CMS) of the PET1 type, resulting from the interspecific hybridization of Helianthus petiolaris with Helianthus annuus. Due to the fact that CMS-PET1 was not previously detected in wild sunflower, it was believed that this cytotype could arise during interspecific hybridization and is specific solely for cultivated sunflower. In this study, the open reading frame, orfH522, associated with the CMS-PET1 phenotype, was revealed for the first time in the 3'-flanking region of the mitochondrial atpA gene in wild H. annuus. An analysis of whole genome data from 1089 accessions showed that the frequency of occurrence of CMS-orfH522 in wild H. annuus populations is 3.58%, while in wild H. petiolaris populations, it is 1.26%. In general, the analysis demonstrated that PET1-CMS is a natural cytotype of H. annuus, and the appearance of the CMS phenotype in cultivated sunflowers is associated with the loss of stabilizing nuclear genes of fertility restorers, which occurred during interspecific hybridization. These data can explain the patterns of differential cytoplasmic and nuclear introgression occurring in wild sunflower and are useful for further evolutionary studies.

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.

Mutation and sequencing-based cloning and functional studies of a rust resistance gene in sunflower (Helianthus annuus)

Rust, caused by the fungus Puccinia helianthi Schwein., is one of the most devastating diseases of sunflower (Helianthus annuus L.), affecting global production. The rust R gene R₁₁ in sunflower line HA-R9 shows broad-spectrum resistance to P. helianthi virulent races and was previously mapped to an interval on sunflower chromosome 13 encompassing three candidate genes annotated in the XRQr1.0 reference genome assembly. In the current study, we combined ethyl methane sulfonate (EMS) mutagenesis with targeted region capture and PacBio long-read sequencing to clone the R₁₁ gene. Sequencing of a 60-kb region spanning the R₁₁ locus from the R₁₁ -HA-R9 rust-resistant line and three EMS-induced susceptible mutants facilitated the identification of R₁₁ and definition of induced mutations. The R₁₁ gene is predicted to have a single 3996-bp open reading frame and encodes a protein of 1331 amino acids with CC-NBS-LRR domains typical of genes conferring plant resistance to biotrophic pathogens. Point mutations identified in the R₁₁ rust-susceptible mutants resulted in premature stop codons, consistent with loss of function leading to rust susceptibility. Additional functional studies using comparative RNA sequencing of the resistant line R₁₁ -HA-R9 and R₁₁ -susceptible mutants revealed substantial differences in gene expression patterns associated with R₁₁ -mediated resistance at 7 days post-inoculation with rust, and uncovered the potential roles of terpenoid biosynthesis and metabolism in sunflower rust resistance.

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.

Discovery and mapping of two new rust resistance genes, R17 and R18, in sunflower using genotyping by sequencing

Discovery of two rust resistance genes, R₁₇ and R₁₈, from the sunflower lines introduced from South Africa and genetic mapping of them to sunflower chromosome 13. Rust, caused by the fungus Puccinia helianthi Schw., is one of the most serious diseases of sunflower in the world. The rapid changes that occur in the virulence characteristics of pathogen populations present a continuous threat to the effectiveness of existing rust-resistant hybrids. Thus, there is a continued need for the characterization of genetically diverse sources of rust resistance. In this study, we report to identify two new rust resistance genes, R₁₇ and R₁₈, from the sunflower lines, KP193 and KP199, introduced from South Africa. The inheritance of rust resistance was investigated in both lines using two mapping populations developed by crossing the resistant plants selected from KP193 and KP199 with a common susceptible parent HA 89. The F₂ populations were first genotyped using genotyping by sequencing for mapping of the rust genes and further saturated with markers in the target region. Molecular mapping positioned the two genes at the lower end of sunflower chromosome 13 within a large gene cluster. Two co-segregating SNP markers, SFW01497 and SFW08875, were distal to R₁₇ at a 1.9 cM genetic distance, and a cluster of five co-segregating SNPs was proximal to R₁₇ at 0.7 cM. R₁₈ co-segregated with the SNP marker SFW04317 and was proximal to two cosegregating SNPs, SFW01497 and SFW05453, at 1.9 cM. These maps provide markers for stacking R₁₇ or R₁₈ with other broadly effective rust resistance genes to extend the durability of rust resistance. The relationship of the six rust resistance genes in the cluster was discussed.