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Ma GJ, Talukder ZI, Song QJ, Li XH, Qi LL. Whole-genome sequencing enables molecular dissection and candidate gene identification of the rust resistance gene R 12 in sunflower (Helianthus annuus L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:143. [PMID: 37247164 DOI: 10.1007/s00122-023-04389-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 05/16/2023] [Indexed: 05/30/2023]
Abstract
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.
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Affiliation(s)
- G J Ma
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA
- Ball Horticultural Company, 622 Town Road, West Chicago, IL, 60185, USA
| | - Z I Talukder
- USDA-Agricultural Research Service, Edward T. Schafer Agricultural Research Center, Fargo, ND, 58102-2765, USA
| | - Q J Song
- Soybean Genomics and Improvement Laboratory, USDA-Agricultural Research Service, Beltsville, MD, 20705-2350, USA
| | - X H Li
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA
| | - L L Qi
- USDA-Agricultural Research Service, Edward T. Schafer Agricultural Research Center, Fargo, ND, 58102-2765, USA.
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Qi LL, Talukder ZI, Ma GJ, Seiler GJ. Introgression and targeting of the Pl 37 and Pl 38 genes for downy mildew resistance from wild Helianthus annuus and H. praecox into cultivated sunflower (Helianthus annuus L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:82. [PMID: 36952051 DOI: 10.1007/s00122-023-04316-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 01/31/2023] [Indexed: 06/18/2023]
Abstract
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.
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Affiliation(s)
- L L Qi
- USDA-Agricultural Research Service, Edward T. Schafer Agricultural Research Center, 1616 Albrecht Blvd. N, Fargo, ND, 58102-2765, USA.
| | - Z I Talukder
- USDA-Agricultural Research Service, Edward T. Schafer Agricultural Research Center, 1616 Albrecht Blvd. N, Fargo, ND, 58102-2765, USA
| | - G J Ma
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA
- Ball Horticultural Company, 622 Town Road, West Chicago, IL, 60185, USA
| | - G J Seiler
- USDA-Agricultural Research Service, Edward T. Schafer Agricultural Research Center, 1616 Albrecht Blvd. N, Fargo, ND, 58102-2765, USA
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Spatial Genetic Structure and Pathogenic Race Composition at the Field Scale in the Sunflower Downy Mildew Pathogen, Plasmopara halstedii. J Fungi (Basel) 2022; 8:jof8101084. [PMID: 36294648 PMCID: PMC9605284 DOI: 10.3390/jof8101084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 09/27/2022] [Accepted: 10/11/2022] [Indexed: 11/22/2022] Open
Abstract
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 (FST = 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.
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Ma G, Song Q, Li X, Qi L. Genetic Insight into Disease Resistance Gene Clusters by Using Sequencing-Based Fine Mapping in Sunflower (Helianthus annuus L.). Int J Mol Sci 2022; 23:ijms23179516. [PMID: 36076914 PMCID: PMC9455867 DOI: 10.3390/ijms23179516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 08/04/2022] [Accepted: 08/19/2022] [Indexed: 11/16/2022] Open
Abstract
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.
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Affiliation(s)
- Guojia Ma
- Department of Plant Sciences, North Dakota State University, Fargo, ND 58102-6050, USA
| | - Qijian Song
- Soybean Genomics and Improvement Laboratory, USDA-Agricultural Research Service, Beltsville, MD 20705-2350, USA
| | - Xuehui Li
- Department of Plant Sciences, North Dakota State University, Fargo, ND 58102-6050, USA
| | - Lili Qi
- USDA-Agricultural Research Service, Edward T. Schafer Agricultural Research Center, Fargo, ND 58102-2765, USA
- Correspondence:
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Qi LL, Cai XW. Characterization and mapping of a downy mildew resistance gene, Pl36, in sunflower ( Helianthus annuus L.). MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2022; 42:8. [PMID: 37309323 PMCID: PMC10248693 DOI: 10.1007/s11032-022-01280-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 01/23/2022] [Indexed: 06/14/2023]
Abstract
Downy mildew (DM) is one of the most serious diseases in sunflower-growing regions worldwide, often significantly reducing sunflower yields. The causal agent of sunflower DM, the oomycete pathogen Plasmopara halstedii, is highly virulent and aggressive. Studying regional disease spread and virulence evolution in the DM pathogen population is important for the development of new sunflower inbred lines with resistance to the existing DM pathogen. The sunflower line 803-1, as one of nine international differential hosts, has been used in the identification of P. halstedii virulent pathotypes in sunflower since 2000. The DM resistance gene in 803-1 was temporally designated Pl5 + based on allelic analysis but has not been molecularly characterized. In the present study, bulked segregant analysis and genetic mapping confirmed the presence of the Pl gene within a large gene cluster on sunflower chromosome 13 in 803-1, as previously reported. Subsequent saturation mapping in the gene target region with single nucleotide polymorphism (SNP) markers placed this gene at an interval of 3.4 Mb in the XRQ reference genome assembly, a location different from that of Pl5. Therefore, the Pl gene in 803-1 was re-designated Pl36 because it is not allelic with Pl5. Four SNP markers co-segregated with Pl36, and SNP SFW05743 was 1.1 cM proximal to Pl36. The relationship of eight Pl genes in the cluster is discussed based on their origin, map position, and specificity of resistance/susceptibility to DM infection. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-022-01280-1.
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Affiliation(s)
- L. L. Qi
- USDA-Agricultural Research Service, Edward T. Schafer Agricultural Research Center, 1616 Albrecht Blvd. N, Fargo, ND 58102-2765 USA
| | - X. W. Cai
- USDA-Agricultural Research Service, Wheat, Sorghum and Forage Research Unit, 251 Filley Hall/Food Ind. Complex, Lincoln, NE 68583 USA
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Yu L, Nie Y, Jiao J, Jian L, Zhao J. The Sequencing-Based Mapping Method for Effectively Cloning Plant Mutated Genes. Int J Mol Sci 2021; 22:ijms22126224. [PMID: 34207582 PMCID: PMC8226582 DOI: 10.3390/ijms22126224] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 06/03/2021] [Accepted: 06/05/2021] [Indexed: 11/23/2022] Open
Abstract
A forward genetic approach is a powerful tool for identifying the genes underlying the phenotypes of interest. However, the conventional map-based cloning method is lengthy, requires a large mapping population and confirmation of many candidate genes in a broad genetic region to clone the causal variant. The whole-genome sequencing method clones the variants with a certain failure probability for multiple reasons, especially for heterozygotes, and could not be used to clone the mutation of epigenetic modifications. Here, we applied the highly complementary characteristics of these two methods and developed a sequencing-based mapping method (SBM) for identifying the location of plant variants effectively with a small population and low cost, which is very user-friendly for most popular laboratories. This method used the whole-genome sequencing data of two pooled populations to screen out enough markers. These markers were used to identify and narrow the candidate region by analyzing the marker-indexes and recombinants. Finally, the possible mutational sites were identified using the whole-genome sequencing data and verified in individual mutants. To elaborate the new method, we displayed the cloned processes in one Arabidopsis heterozygous mutant and two rice homozygous mutants. Thus, the sequencing-based mapping method could clone effectively different types of plant mutations and was a powerful tool for studying the functions of plant genes in the species with known genomic sequences.
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