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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: 1] [Impact Index Per Article: 1.0] [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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Molinero-Ruiz L. Sustainable and efficient control of sunflower downy mildew by means of genetic resistance: a review. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:3757-3771. [PMID: 35084515 DOI: 10.1007/s00122-022-04038-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 01/12/2022] [Indexed: 06/14/2023]
Abstract
The breeding of sunflower (Helianthus annuus L.) for resistance to downy mildew (caused by the oomycete Plasmopara halstedii Farl. Berl. & de Toni) is reviewed in this work under the scope of its sustainability and efficiency. When sunflower turned into an oilseed crop, resistance to the disease was included in its initial breeding strategies. Subsequent development of genomic tools allowed a significant expansion of the knowledge on the diversity of its genetic resistance and its application to the genetic control of the disease. Simultaneously to genetic improvements, and as a consequence of the close interaction between the pathogen and its host plant, an enormous variety of pathotypes has been described in all the sunflower-growing areas worldwide. Thus, the genetic control of sunflower downy mildew is an active research field subjected to continuous evolution and challenge. In practice, genetic resistance constitutes the base tier of Integrated Pest Management against sunflower downy mildew. The second tier is composed of elements related to crop management: rotation, removal of volunteer plants, sowing date, tillage. Biological control alternatives and resistance inducers could also provide additional restraint. Finally, the top tier includes chemical treatments that should only be used when necessary and if the more basal Integrated Pest Management elements fail to keep pathogen populations under the economic threshold.
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Affiliation(s)
- L Molinero-Ruiz
- Institute for Sustainable Agriculture (IAS), Spanish National Research Council (CSIC), Alameda del Obispo s/n, 14004, Córdoba, Spain.
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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; 23:9516. [PMID: 36076914 PMCID: PMC9455867 DOI: 10.3390/ijms23179516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [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
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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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Ma G, Song Q, Li X, Qi L. High-Density Mapping and Candidate Gene Analysis of Pl18 and Pl20 in Sunflower by Whole-Genome Resequencing. Int J Mol Sci 2020; 21:E9571. [PMID: 33339111 PMCID: PMC7765508 DOI: 10.3390/ijms21249571] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 12/09/2020] [Accepted: 12/11/2020] [Indexed: 12/17/2022] Open
Abstract
Downy mildew (DM) is one of the severe biotic threats to sunflower production worldwide. The inciting pathogen, Plasmopara halstedii, could overwinter in the field for years, creating a persistent threat to sunflower. The dominant genes Pl18 and Pl20 conferring resistance to known DM races have been previously mapped to 1.5 and 1.8 cM intervals on sunflower chromosomes 2 and 8, respectively. Utilizing a whole-genome resequencing strategy combined with reference sequence-based chromosome walking and high-density mapping in the present study, Pl18 was placed in a 0.7 cM interval on chromosome 2. A candidate gene HanXRQChr02g0048181 for Pl18 was identified from the XRQ reference genome and predicted to encode a protein with typical NLR domains for disease resistance. The Pl20 gene was placed in a 0.2 cM interval on chromosome 8. The putative gene with the NLR domain for Pl20, HanXRQChr08g0210051, was identified within the Pl20 interval. SNP markers closely linked to Pl18 and Pl20 were evaluated with 96 diverse sunflower lines, and a total of 13 diagnostic markers for Pl18 and four for Pl20 were identified. These markers will facilitate to transfer these new genes to elite sunflower lines and to pyramid these genes with broad-spectrum DM resistance in sunflower breeding.
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Affiliation(s)
- Guojia Ma
- Department of Plant Sciences, North Dakota State University, Fargo, ND 58108, USA; (G.M.); (X.L.)
| | - Qijian Song
- USDA-Agricultural Research Service, Soybean Genomics and Improvement Laboratory, Beltsville, MD 20705-2350, USA;
| | - Xuehui Li
- Department of Plant Sciences, North Dakota State University, Fargo, ND 58108, USA; (G.M.); (X.L.)
| | - Lili Qi
- USDA-Agricultural Research Service, Edward T. Schafer Agricultural Research Center, Fargo, ND 58102-2765, USA
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Gilley MA, Gulya TJ, Seiler GJ, Underwood W, Hulke BS, Misar CG, Markell SG. Determination of Virulence Phenotypes of Plasmopara halstedii in the United States. PLANT DISEASE 2020; 104:2823-2831. [PMID: 32955406 DOI: 10.1094/pdis-10-19-2063-re] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Downy mildew, caused by Plasmopara halstedii (Farl.) Berl. and de Toni, is an economically important disease in cultivated sunflowers, Helianthus annuus L. Resistance genes incorporated into commercial hybrids are used as an effective disease management tool, but the duration of effectiveness is limited as virulence evolves in the pathogen population. A comprehensive assessment of pathogen virulence was conducted in 2014 and 2015 in the U.S. Great Plains states of North Dakota and South Dakota, where approximately 75% of the U.S. sunflower is produced annually. The virulence phenotypes (and races) of 185 isolates were determined using the U.S. standard set of nine differentials. Additionally, the virulence phenotypes of 61 to 185 isolates were determined on 13 additional lines that have been used to evaluate pathogen virulence in North America and/or internationally. Although widespread virulence was identified on several genes, new virulence was identified on the Pl8 resistance gene, and no virulence was observed on the PlArg, Pl15, Pl17 and Pl18 genes. Results of this study suggest that three additional lines should be used as differentials and agree with previous studies that six lines proposed as differentials should be used in two internationally accepted differential sets. For effective disease management using genetic resistance, it is critical that virulence data be relevant and timely. This is best accomplished when pathogen virulence is determined frequently and by using genetic lines containing resistance genes actively incorporated into commercial cultivars.
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Affiliation(s)
- Michelle A Gilley
- Department of Plant Pathology, North Dakota State University, Fargo, ND 58102
| | | | | | | | | | | | - Samuel G Markell
- Department of Plant Pathology, North Dakota State University, Fargo, ND 58102
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Liu Z, Gu W, Seiler GJ, Jan CC. A Unique Cytoplasmic-Nuclear Interaction in Sunflower ( Helianthus annuus L.) Causing Reduced-Vigor Plants and the Genetics of Vigor Restoration. FRONTIERS IN PLANT SCIENCE 2020; 11:1010. [PMID: 32754176 PMCID: PMC7367100 DOI: 10.3389/fpls.2020.01010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 06/19/2020] [Indexed: 06/11/2023]
Abstract
Wild Helianthus species are an important genetic resource for sunflower improvement, but sometimes there are adverse interactions between the wild and cultivated sunflowers. This study reports the inheritance of reduced vigor and its restoration resulting from an interaction of perennial Helianthus cytoplasms with nuclear genes of cultivated sunflower lines. The large number of vigor restoration (V) genes identified in cultivated lines are all located at the same locus, designated V1 , suggesting a common origin of these genes. Additional V genes derived from the wild perennial species H. giganteus L. and H. hirsutus Raf. are located at a different locus than V1 , designated V2 . A major difference between the wild annual Helianthus cytoplasms and perennial cytoplasms is the lack of the vigor-reducing cytoplasms, but surprisingly V genes were observed in wild annual H. annuus L. and H. petiolaris Nutt. which were at the same locus as V1 . A common vigor-reducing cytoplasmic effect of the perennial Helianthus species and the existence of a common vigor restoration V gene in most perennial Helianthus species could be explained as a result of vigor selection during Helianthus speciation. V1 was mapped on linkage group (LG) 7 of the sunflower genome, using an F2 population derived from MOL-RV/HA 821. V1 co-segregated with an InDel marker ZVG31, with three single-nucleotide polymorphism (SNP) markers, SFW01024, SFW07230, and SFW00604, located above it on the map at a genetic distance of 0.8 cM, and another SNP marker, SFW08671, below it at a distance of 0.4 cM. The physical distance between the two closest flanking SNP markers corresponds to 0.56 and 1.37 Mb on the HA 412-HO and XRQ assemblies, respectively. The tightly linked markers will help select normal vigor progenies when using perennial Helianthus cytoplasms in a breeding program, which will also provide a basis for studying the mechanism of the cytonuclear interaction, and the speciation of annual and perennial Helianthus species.
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Affiliation(s)
- Zhao Liu
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States
| | - Wei Gu
- Institute of Plant Protection, Postdoctoral Program, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Gerald J. Seiler
- USDA-ARS, Edward T. Schafer Agricultural Research Center, Fargo, ND, United States
| | - Chao-Chien Jan
- USDA-ARS, Edward T. Schafer Agricultural Research Center, Fargo, ND, United States
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Qi LL, Ma GJ, Li XH, Seiler GJ. Diversification of the downy mildew resistance gene pool by introgression of a new gene, Pl 35, from wild Helianthus argophyllus into oilseed and confection sunflowers (Helianthus annuus L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:2553-2565. [PMID: 31214741 DOI: 10.1007/s00122-019-03370-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 06/03/2019] [Indexed: 05/22/2023]
Abstract
We have mapped a new downy mildew resistance gene, Pl35, derived from wild Helianthus argophyllus to sunflower linkage group 1. New germplasms incorporating the Pl35 gene were developed for both oilseed and confection sunflower Sunflower downy mildew (DM), caused by the oomycete pathogen Plasmopara halstedii, is an economically important and widespread sunflower disease worldwide. Non-race-specific resistance is not available in sunflower, and breeding for DM resistance relies on race-specific resistance to control this disease. The discovery of the novel DM resistance genes is a long-term task due to the highly virulent and aggressive nature of the P. halstedii pathogen, which reduces the effectiveness of resistance genes. The objectives of this study were to: (1) transfer DM resistance from a wild sunflower species Helianthus argophyllus (PI 494576) into cultivated sunflowers; (2) map the resistance gene; and (3) develop diagnostic single-nucleotide polymorphism (SNP) markers for efficient targeting of the gene in breeding programs. The H. argophyllus accession PI 494576 previously identified with resistance to the most virulent P. halstedii race 777 was crossed with oilseed and confection sunflower in 2012. Molecular mapping using the BC2F2 and BC2F3 populations derived from the cross CONFSCLB1/PI 494576 located a new resistance gene Pl35 on linkage group 1 of the sunflower genome. The new gene Pl35 was successfully transferred from PI 494576 into cultivated sunflowers. SNP markers flanking Pl35 were surveyed in a validation panel of 548 diversified sunflower lines collected globally. Eleven SNP markers were found to be diagnostic for Pl35 SNP alleles, with four co-segregating with Pl35. The developed oilseed and confection germplasms with diagnostic SNP markers for Pl35 will be very useful resources for breeding of DM resistance in sunflower.
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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.
| | - G J Ma
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA
| | - X H Li
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, 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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Şahin EÇ, Kalenderoğlu A, Aydın Y, Evci G, Uncuoğlu AA. SSR Markers Suitable for Marker Assisted Selection in Sunflower for Downy Mildew Resistance. Open Life Sci 2018; 13:319-326. [PMID: 33817099 PMCID: PMC7874726 DOI: 10.1515/biol-2018-0039] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2018] [Accepted: 06/10/2018] [Indexed: 11/15/2022] Open
Abstract
The effectiveness of Pl genes is known to be resistant to downy mildew (DM) disease affected by fungus Plasmopara halstedii in sunflower. In this study phenotypic analysis was performed using inoculation tests and genotypic analysis were carried out with three DM resistance genes Plarg, Pl13 and Pl8. A total of 69 simple sequence repeat markers and 241 F2 individuals derived from a cross of RHA-419 (R) x P6LC (S), RHA-419 (R) x CL (S), RHA-419 (R) x OL (S), RHA419 (R) x 9758R (S), HA-R5 (R) x P6LC (S) and HA89 (R) x P6LC (S) parental lines were used to identify resistant hybrids in sunflower. Results of SSR analysis using markers linked with downy mildew resistance genes (Plarg, Pl8 and Pl13) and downy mildew inoculation tests were evaluated together and ORS716 (for Plarg and Pl13), HA4011 (for Pl8) markers showed positive correlation with their phenotypic results. These results suggest that these markers are associated with DM resistance and they can be used successfully in marker-assisted selection for sunflower breeding programs specific for downy mildew resistance.
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Affiliation(s)
- Ezgi Çabuk Şahin
- Department of Biology, Faculty of Science and Letters, Marmara University, Istanbul, 34722, Turkey
| | - Aral Kalenderoğlu
- Department of Bioengineering, Faculty of Engineering, Marmara University, Istanbul, 34722, Turkey
| | - Yıldız Aydın
- Department of Biology, Faculty of Science and Letters, Marmara University, Istanbul, 34722, Turkey
| | - Göksel Evci
- Republic of Turkey Ministry of Food, Agriculture and Livestock Directorate of Trakya Agricultural, Research Institute, Edirne, 22100, Turkey
| | - Ahu Altınkut Uncuoğlu
- Department of Bioengineering, Faculty of Engineering, Marmara University, Istanbul, 34722, Turkey
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Dimitrijevic A, Horn R. Sunflower Hybrid Breeding: From Markers to Genomic Selection. FRONTIERS IN PLANT SCIENCE 2018; 8:2238. [PMID: 29387071 PMCID: PMC5776114 DOI: 10.3389/fpls.2017.02238] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2017] [Accepted: 12/20/2017] [Indexed: 05/03/2023]
Abstract
In sunflower, molecular markers for simple traits as, e.g., fertility restoration, high oleic acid content, herbicide tolerance or resistances to Plasmopara halstedii, Puccinia helianthi, or Orobanche cumana have been successfully used in marker-assisted breeding programs for years. However, agronomically important complex quantitative traits like yield, heterosis, drought tolerance, oil content or selection for disease resistance, e.g., against Sclerotinia sclerotiorum have been challenging and will require genome-wide approaches. Plant genetic resources for sunflower are being collected and conserved worldwide that represent valuable resources to study complex traits. Sunflower association panels provide the basis for genome-wide association studies, overcoming disadvantages of biparental populations. Advances in technologies and the availability of the sunflower genome sequence made novel approaches on the whole genome level possible. Genotype-by-sequencing, and whole genome sequencing based on next generation sequencing technologies facilitated the production of large amounts of SNP markers for high density maps as well as SNP arrays and allowed genome-wide association studies and genomic selection in sunflower. Genome wide or candidate gene based association studies have been performed for traits like branching, flowering time, resistance to Sclerotinia head and stalk rot. First steps in genomic selection with regard to hybrid performance and hybrid oil content have shown that genomic selection can successfully address complex quantitative traits in sunflower and will help to speed up sunflower breeding programs in the future. To make sunflower more competitive toward other oil crops higher levels of resistance against pathogens and better yield performance are required. In addition, optimizing plant architecture toward a more complex growth type for higher plant densities has the potential to considerably increase yields per hectare. Integrative approaches combining omic technologies (genomics, transcriptomics, proteomics, metabolomics and phenomics) using bioinformatic tools will facilitate the identification of target genes and markers for complex traits and will give a better insight into the mechanisms behind the traits.
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Affiliation(s)
| | - Renate Horn
- Institut für Biowissenschaften, Abteilung Pflanzengenetik, Universität Rostock, Rostock, Germany
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Pecrix Y, Penouilh-Suzette C, Muños S, Vear F, Godiard L. Ten Broad Spectrum Resistances to Downy Mildew Physically Mapped on the Sunflower Genome. FRONTIERS IN PLANT SCIENCE 2018; 9:1780. [PMID: 30564260 PMCID: PMC6288771 DOI: 10.3389/fpls.2018.01780] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 11/15/2018] [Indexed: 05/12/2023]
Abstract
Resistance to downy mildew (Plasmopara halstedii) in sunflower (Helianthus annuus L.) is conferred by major resistance genes, denoted Pl. Twenty-two Pl genes have been identified and genetically mapped so far. However, over the past 50 years, wide-scale presence of only a few of them in sunflower crops led to the appearance of new, more virulent pathotypes (races) so it is important for sunflower varieties to carry as wide a range of resistance genes as possible. We analyzed phenotypically 12 novel resistant sources discovered in breeding pools derived from two wild Helianthus species and in eight wild H. annuus ecotypes. All were effective against at least 16 downy mildew pathotypes. We mapped their resistance genes on the sunflower reference genome of 3,600 Mb, in intervals that varied from 75 Kb to 32 Mb using an AXIOM® genotyping array of 49,449 SNP. Ten probably new genes were identified according to resistance spectrum, map position, hypersensitive response to the transient expression of a P. halstedii RXLR effector, or the ecotype/species from which they originated. The resistance source HAS6 was found to carry the first downy mildew resistance gene mapped on chromosome 11, whereas the other resistances were positioned on chromosomes 1, 2, 4, and 13 carrying already published Pl genes that we also mapped physically on the same reference genome. The new genes were designated Pl23-Pl32 according to the current nomenclature. However, since sunflower downy mildew resistance genes have not yet been sequenced, rules for designation are discussed. This is the first large scale physical mapping of both 10 new and 10 already reported downy mildew resistance genes in sunflower.
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Affiliation(s)
- Yann Pecrix
- Laboratoire des Interactions Plantes Microorganismes, INRA, CNRS, Université de Toulouse, Castanet-Tolosan, France
| | - Charlotte Penouilh-Suzette
- Laboratoire des Interactions Plantes Microorganismes, INRA, CNRS, Université de Toulouse, Castanet-Tolosan, France
| | - Stéphane Muños
- Laboratoire des Interactions Plantes Microorganismes, INRA, CNRS, Université de Toulouse, Castanet-Tolosan, France
| | - Felicity Vear
- INRA, Génétique, Diversité, Ecophysiologie des Céréales, UMR 1095, Clermont-Ferrand, France
- *Correspondence: Felicity Vear, Laurence Godiard,
| | - Laurence Godiard
- Laboratoire des Interactions Plantes Microorganismes, INRA, CNRS, Université de Toulouse, Castanet-Tolosan, France
- *Correspondence: Felicity Vear, Laurence Godiard,
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Ma GJ, Markell SG, Song QJ, Qi LL. Genotyping-by-sequencing targeting of a novel downy mildew resistance gene Pl 20 from wild Helianthus argophyllus for sunflower (Helianthus annuus L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2017; 130:1519-1529. [PMID: 28432412 DOI: 10.1007/s00122-017-2906-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 04/07/2017] [Indexed: 05/20/2023]
Abstract
Genotyping-by-sequencing revealed a new downy mildew resistance gene, Pl 20 , from wild Helianthus argophyllus located on linkage group 8 of the sunflower genome and closely linked to SNP markers that facilitate the marker-assisted selection of resistance genes. Downy mildew (DM), caused by Plasmopara halstedii, is one of the most devastating and yield-limiting diseases of sunflower. Downy mildew resistance identified in wild Helianthus argophyllus accession PI 494578 was determined to be effective against the predominant and virulent races of P. halstedii occurring in the United States. The evaluation of 114 BC1F2:3 families derived from the cross between HA 89 and PI 494578 against P. halstedii race 734 revealed that single dominant gene controls downy mildew resistance in the population. Genotyping-by-sequencing analysis conducted in the BC1F2 population indicated that the DM resistance gene derived from wild H. argophyllus PI 494578 is located on the upper end of the linkage group (LG) 8 of the sunflower genome, as was determined single nucleotide polymorphism (SNP) markers associated with DM resistance. Analysis of 11 additional SNP markers previously mapped to this region revealed that the resistance gene, named Pl 20 , co-segregated with four markers, SFW02745, SFW09076, S8_11272025, and S8_11272046, and is flanked by SFW04358 and S8_100385559 at an interval of 1.8 cM. The newly discovered P. halstedii resistance gene has been introgressed from wild species into cultivated sunflower to provide a novel gene with DM resistance. The homozygous resistant individuals were selected from BC2F2 progenies with the use of markers linked to the Pl 20 gene, and these lines should benefit the sunflower community for Helianthus improvement.
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Affiliation(s)
- G J Ma
- Department of Plant Pathology, North Dakota State University, Fargo, ND, 58108, USA
| | - S G Markell
- Department of Plant Pathology, North Dakota State University, Fargo, ND, 58108, USA
| | - Q J Song
- Soybean Genomics and Improvement Lab, USDA-Agricultural Research Service, Beltsville, MD, 20705-2350, USA
| | - L L Qi
- Red River Valley Agricultural Research Center, USDA-Agricultural Research Service, 1605 Albrecht Blvd N, Fargo, ND, 58102-2765, USA.
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Qi LL, Talukder ZI, Hulke BS, Foley ME. Development and dissection of diagnostic SNP markers for the downy mildew resistance genes Pl Arg and Pl 8 and maker-assisted gene pyramiding in sunflower (Helianthus annuus L.). Mol Genet Genomics 2017; 292:551-563. [PMID: 28160079 DOI: 10.1007/s00438-017-1290-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 01/09/2017] [Indexed: 12/17/2022]
Abstract
Diagnostic DNA markers are an invaluable resource in breeding programs for successful introgression and pyramiding of disease resistance genes. Resistance to downy mildew (DM) disease in sunflower is mediated by Pl genes which are known to be effective against the causal fungus, Plasmopara halstedii. Two DM resistance genes, Pl Arg and Pl 8 , are highly effective against P. halstedii races in the USA, and have been previously mapped to the sunflower linkage groups (LGs) 1 and 13, respectively, using simple sequence repeat (SSR) markers. In this study, we developed high-density single nucleotide polymorphism (SNP) maps encompassing the Pl arg and Pl 8 genes and identified diagnostic SNP markers closely linked to these genes. The specificity of the diagnostic markers was validated in a highly diverse panel of 548 sunflower lines. Dissection of a large marker cluster co-segregated with Pl Arg revealed that the closest SNP markers NSA_007595 and NSA_001835 delimited Pl Arg to an interval of 2.83 Mb on the LG1 physical map. The SNP markers SFW01497 and SFW06597 delimited Pl 8 to an interval of 2.85 Mb on the LG13 physical map. We also developed sunflower lines with homozygous, three gene pyramids carrying Pl Arg , Pl 8 , and the sunflower rust resistance gene R 12 using the linked SNP markers from a segregating F2 population of RHA 340 (carrying Pl 8 )/RHA 464 (carrying Pl Arg and R 12 ). The high-throughput diagnostic SNP markers developed in this study will facilitate marker-assisted selection breeding, and the pyramided sunflower lines will provide durable resistance to downy mildew and rust diseases.
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Affiliation(s)
- L L Qi
- Northern Crop Science Laboratory, USDA-Agricultural Research Service, 1605 Albrecht Blvd N, Fargo, ND, 58102-2765, USA.
| | - Z I Talukder
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA
| | - B S Hulke
- Northern Crop Science Laboratory, USDA-Agricultural Research Service, 1605 Albrecht Blvd N, Fargo, ND, 58102-2765, USA
| | - M E Foley
- Northern Crop Science Laboratory, USDA-Agricultural Research Service, 1605 Albrecht Blvd N, Fargo, ND, 58102-2765, USA
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Zhang ZW, Ma GJ, Zhao J, Markell SG, Qi LL. Discovery and introgression of the wild sunflower-derived novel downy mildew resistance gene Pl 19 in confection sunflower (Helianthus annuus L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2017; 130:29-39. [PMID: 27677630 DOI: 10.1007/s00122-016-2786-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 09/03/2016] [Indexed: 05/20/2023]
Abstract
A new downy mildew resistance gene, Pl 19 , was identified from wild Helianthus annuus accession PI 435414, introduced to confection sunflower, and genetically mapped to linkage group 4 of the sunflower genome. Wild Helianthus annuus accession PI 435414 exhibited resistance to downy mildew, which is one of the most destructive diseases to sunflower production globally. Evaluation of the 140 BC1F2:3 families derived from the cross of CMS CONFSCLB1 and PI 435414 against Plasmopara halstedii race 734 revealed that a single dominant gene controls downy mildew resistance in the population. Bulked segregant analysis conducted in the BC1F2 population with 860 simple sequence repeat (SSR) markers indicated that the resistance derived from wild H. annuus was associated with SSR markers located on linkage group (LG) 4 of the sunflower genome. To map and tag this resistance locus, designated Pl 19 , 140 BC1F2 individuals were used to construct a linkage map of the gene region. Two SSR markers, ORS963 and HT298, were linked to Pl 19 within a distance of 4.7 cM. After screening 27 additional single nucleotide polymorphism (SNP) markers previously mapped to this region, two flanking SNP markers, NSA_003564 and NSA_006089, were identified as surrounding the Pl 19 gene at a distance of 0.6 cM from each side. Genetic analysis indicated that Pl 19 is different from Pl 17 , which had previously been mapped to LG4, but is closely linked to Pl 17 . This new gene is highly effective against the most predominant and virulent races of P. halstedii currently identified in North America and is the first downy mildew resistance gene that has been transferred to confection sunflower. The selected resistant germplasm derived from homozygous BC2F3 progeny provides a novel gene for use in confection sunflower breeding programs.
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Affiliation(s)
- Z W Zhang
- Department of Agronomy, Inner Mongolia Agricultural University, Huhhot, 010019, Inner Mongolia, China
| | - G J Ma
- Department of Plant Pathology, North Dakota State University, Fargo, ND, 58108, USA
| | - J Zhao
- Department of Agronomy, Inner Mongolia Agricultural University, Huhhot, 010019, Inner Mongolia, China
| | - S G Markell
- Department of Plant Pathology, North Dakota State University, Fargo, ND, 58108, USA
| | - L L Qi
- Northern Crop Science Laboratory, USDA-Agricultural Research Service, 1605 Albrecht Blvd. N, Fargo, ND, 58102-2765, USA.
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Qi LL, Foley ME, Cai XW, Gulya TJ. Genetics and mapping of a novel downy mildew resistance gene, Pl(18), introgressed from wild Helianthus argophyllus into cultivated sunflower (Helianthus annuus L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2016; 129:741-752. [PMID: 26747047 DOI: 10.1007/s00122-015-2662-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Accepted: 12/14/2015] [Indexed: 05/20/2023]
Abstract
A novel downy mildew resistance gene, Pl(18), was introgressed from wild Helianthus argophyllus into cultivated sunflower and genetically mapped to linkage group 2 of the sunflower genome. The new germplasm, HA-DM1, carrying Pl(18) has been released to the public. Sunflower downy mildew (DM) is considered to be the most destructive foliar disease that has spread to every major sunflower-growing country of the world, except Australia. A new dominant downy mildew resistance gene (Pl 18) transferred from wild Helianthus argophyllus (PI 494573) into cultivated sunflower was mapped to linkage group (LG) 2 of the sunflower genome using bulked segregant analysis with 869 simple sequence repeat (SSR) markers. Phenotyping 142 BC1F2:3 families derived from the cross of HA 89 and H. argophyllus confirmed the single gene inheritance of resistance. Since no other Pl gene has been mapped to LG2, this gene was novel and designated as Pl (18). SSR markers CRT214 and ORS203 flanked Pl(18) at a genetic distance of 1.1 and 0.4 cM, respectively. Forty-six single nucleotide polymorphism (SNP) markers that cover the Pl(18) region were surveyed for saturation mapping of the region. Six co-segregating SNP markers were 1.2 cM distal to Pl(18), and another four co-segregating SNP markers were 0.9 cM proximal to Pl(18). The new BC2F4-derived germplasm, HA-DM1, carrying Pl(18) has been released to the public. This new line is highly resistant to all Plasmopara halstedii races identified in the USA providing breeders with an effective new source of resistance against downy mildew in sunflower. The molecular markers that were developed will be especially useful in marker-assisted selection and pyramiding of Pl resistance genes because of their close proximity to the gene and the availability of high-throughput SNP detection assays.
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Affiliation(s)
- L L Qi
- USDA-Agricultural Research Service, Northern Crop Science Laboratory, 1605 Albrecht Blvd. N, Fargo, ND, 58102-2765, USA.
| | - M E Foley
- USDA-Agricultural Research Service, Northern Crop Science Laboratory, 1605 Albrecht Blvd. N, Fargo, ND, 58102-2765, USA
| | - X W Cai
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA
| | - T J Gulya
- USDA-Agricultural Research Service, Northern Crop Science Laboratory, 1605 Albrecht Blvd. N, Fargo, ND, 58102-2765, USA
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Qi LL, Long YM, Jan CC, Ma GJ, Gulya TJ. Pl(17) is a novel gene independent of known downy mildew resistance genes in the cultivated sunflower (Helianthus annuus L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2015; 128:757-67. [PMID: 25673143 DOI: 10.1007/s00122-015-2470-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Accepted: 01/26/2015] [Indexed: 05/02/2023]
Abstract
Pl 17, a novel downy mildew resistance gene independent of known downy mildew resistance genes in sunflowers, was genetically mapped to linkage group 4 of the sunflower genome. Downy mildew (DM), caused by Plasmopara halstedii (Farl.). Berl. et de Toni, is one of the serious sunflower diseases in the world due to its high virulence and the variability of the pathogen. DM resistance in the USDA inbred line, HA 458, has been shown to be effective against all virulent races of P. halstedii currently identified in the USA. To determine the chromosomal location of this resistance, 186 F 2:3 families derived from a cross of HA 458 with HA 234 were phenotyped for their resistance to race 734 of P. halstedii. The segregation ratio of the population supported that the resistance was controlled by a single dominant gene, Pl 17. Simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) primers were used to identify molecular markers linked to Pl 17. Bulked segregant analysis using 849 SSR markers located Pl 17 to linkage group (LG) 4, which is the first DM gene discovered in this linkage group. An F2 population of 186 individuals was screened with polymorphic SSR and SNP primers from LG4. Two flanking markers, SNP SFW04052 and SSR ORS963, delineated Pl 17 in an interval of 3.0 cM. The markers linked to Pl 17 were validated in a BC3 population. A search for the physical location of flanking markers in sunflower genome sequences revealed that the Pl 17 region had a recombination frequency of 0.59 Mb/cM, which was a fourfold higher recombination rate relative to the genomic average. This region can be considered amenable to molecular manipulation for further map-based cloning of Pl 17.
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Affiliation(s)
- L L Qi
- USDA-Agricultural Research Service, Northern Crop Science Laboratory, 1605 Albrecht Blvd N, Fargo, ND, 58102-2765, USA,
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Gascuel Q, Martinez Y, Boniface MC, Vear F, Pichon M, Godiard L. The sunflower downy mildew pathogen Plasmopara halstedii. MOLECULAR PLANT PATHOLOGY 2015; 16:109-22. [PMID: 25476405 PMCID: PMC6638465 DOI: 10.1111/mpp.12164] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
UNLABELLED Downy mildew of sunflower is caused by Plasmopara halstedii (Farlow) Berlese & de Toni. Plasmopara halstedii is an obligate biotrophic oomycete pathogen that attacks annual Helianthus species and cultivated sunflower, Helianthus annuus. Depending on the sunflower developmental stage at which infection occurs, the characteristic symptoms range from young seedling death, plant dwarfing, leaf bleaching and sporulation to the production of infertile flowers. Downy mildew attacks can have a great economic impact on sunflower crops, and several Pl resistance genes are present in cultivars to protect them against the disease. Nevertheless, some of these resistances have been overcome by the occurrence of novel isolates of the pathogen showing increased virulence. A better characterization of P. halstedii infection and dissemination mechanisms, and the identification of the molecular basis of the interaction with sunflower, is a prerequisite to efficiently fight this pathogen. This review summarizes what is currently known about P. halstedii, provides new insights into its infection cycle on resistant and susceptible sunflower lines using scanning electron and light microscopy imaging, and sheds light on the pathogenicity factors of P. halstedii obtained from recent molecular data. TAXONOMY Kingdom Stramenopila; Phylum Oomycota; Class Oomycetes; Order Peronosporales; Family Peronosporaceae; Genus Plasmopara; Species Plasmopara halstedii. DISEASE SYMPTOMS Sunflower seedling damping off, dwarfing of the plant, bleaching of leaves, starting from veins, and visible white sporulation, initially on the lower side of cotyledons and leaves. Plasmopara halstedii infection may severely impact sunflower seed yield. INFECTION PROCESS In spring, germination of overwintered sexual oospores leads to sunflower root infection. Intercellular hyphae are responsible for systemic plant colonization and the induction of disease symptoms. Under humid and fresh conditions, dissemination structures are produced by the pathogen on all plant organs to release asexual zoosporangia. These zoosporangia play an important role in pathogen dissemination, as they release motile zoospores that are responsible for leaf infections on neighbouring plants. DISEASE CONTROL Disease control is obtained by both chemical seed treatment (mefenoxam) and the deployment of dominant major resistance genes, denoted Pl. However, the pathogen has developed fungicide resistance and has overcome some plant resistance genes. Research for more sustainable strategies based on the identification of the molecular basis of the interaction are in progress. USEFUL WEBSITES http://www.heliagene.org/HP, http://lipm-helianthus.toulouse.inra.fr/dokuwiki/doku.php?id=start, https://www.heliagene.org/PlasmoparaSpecies (soon available).
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Affiliation(s)
- Quentin Gascuel
- INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR441, F-31326, Castanet-Tolosan, France; CNRS, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR2594, F-31326, Castanet-Tolosan, France
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Talukder ZI, Gong L, Hulke BS, Pegadaraju V, Song Q, Schultz Q, Qi L. A high-density SNP Map of sunflower derived from RAD-sequencing facilitating fine-mapping of the rust resistance gene R12. PLoS One 2014; 9:e98628. [PMID: 25014030 PMCID: PMC4094432 DOI: 10.1371/journal.pone.0098628] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Accepted: 05/06/2014] [Indexed: 11/19/2022] Open
Abstract
A high-resolution genetic map of sunflower was constructed by integrating SNP data from three F2 mapping populations (HA 89/RHA 464, B-line/RHA 464, and CR 29/RHA 468). The consensus map spanned a total length of 1443.84 cM, and consisted of 5,019 SNP markers derived from RAD tag sequencing and 118 publicly available SSR markers distributed in 17 linkage groups, corresponding to the haploid chromosome number of sunflower. The maximum interval between markers in the consensus map is 12.37 cM and the average distance is 0.28 cM between adjacent markers. Despite a few short-distance inversions in marker order, the consensus map showed high levels of collinearity among individual maps with an average Spearman's rank correlation coefficient of 0.972 across the genome. The order of the SSR markers on the consensus map was also in agreement with the order of the individual map and with previously published sunflower maps. Three individual and one consensus maps revealed the uneven distribution of markers across the genome. Additionally, we performed fine mapping and marker validation of the rust resistance gene R12, providing closely linked SNP markers for marker-assisted selection of this gene in sunflower breeding programs. This high resolution consensus map will serve as a valuable tool to the sunflower community for studying marker-trait association of important agronomic traits, marker assisted breeding, map-based gene cloning, and comparative mapping.
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Affiliation(s)
- Zahirul I. Talukder
- Department of Plant Sciences, North Dakota State University, Fargo, North Dakota, United States of America
| | - Li Gong
- Department of Plant Pathology, North Dakota State University, Fargo, North Dakota, United States of America
| | - Brent S. Hulke
- Northern Crop Science Laboratory, USDA- Agricultural Research Service, Fargo, North Dakota, United States of America
| | | | - Qijian Song
- Soybean Genomics and Improvement Lab, USDA- Agricultural Research Service, Beltsville, Maryland, United States of America
| | - Quentin Schultz
- BioDiagnostics Inc., River Falls, Wisconsin, United States of America
| | - Lili Qi
- Northern Crop Science Laboratory, USDA- Agricultural Research Service, Fargo, North Dakota, United States of America
- * E-mail:
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