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Zhang C, Huang CH, Liu M, Hu Y, Panero JL, Luebert F, Gao T, Ma H. Phylotranscriptomic insights into Asteraceae diversity, polyploidy, and morphological innovation. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2021; 63:1273-1293. [PMID: 33559953 DOI: 10.1111/jipb.13078] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 02/08/2021] [Indexed: 05/29/2023]
Abstract
Biodiversity is not evenly distributed among related groups, raising questions about the factors contributing to such disparities. The sunflower family (Asteraceae, >26,000 species) is among the largest and most diverse plant families, but its species diversity is concentrated in a few subfamilies, providing an opportunity to study the factors affecting biodiversity. Phylotranscriptomic analyses here of 244 transcriptomes and genomes produced a phylogeny with strong support for the monophyly of Asteraceae and the monophyly of most subfamilies and tribes. This phylogeny provides a reference for detecting changes in diversification rates and possible factors affecting Asteraceae diversity, which include global climate shifts, whole-genome duplications (WGDs), and morphological evolution. The origin of Asteraceae was estimated at ~83 Mya, with most subfamilies having diverged before the Cretaceous-Paleocene boundary. Phylotranscriptomic analyses supported the existence of 41 WGDs in Asteraceae. Changes to herbaceousness and capitulescence with multiple flower-like capitula, often with distinct florets and scaly pappus/receptacular bracts, are associated with multiple upshifts in diversification rate. WGDs might have contributed to the survival of early Asteraceae by providing new genetic materials to support morphological transitions. The resulting competitive advantage for adapting to different niches would have increased biodiversity in Asteraceae.
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Affiliation(s)
- Caifei Zhang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Biodiversity Sciences, Institute of Plant Biology, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Chien-Hsun Huang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Biodiversity Sciences, Institute of Plant Biology, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
- Department of Biology, the Huck Institutes of the Life Sciences, the Pennsylvania State University, University Park, Pennslyvania, 16802, USA
| | - Mian Liu
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Biodiversity Sciences, Institute of Plant Biology, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Yi Hu
- Department of Biology, the Huck Institutes of the Life Sciences, the Pennsylvania State University, University Park, Pennslyvania, 16802, USA
| | - Jose L Panero
- Department of Integrative Biology, The University of Texas, University Station C0930, Austin, Texas, 78712, USA
| | - Federico Luebert
- Institut für Bodiversität der Pflanzen, Universität Bonn, Bonn, D - 53115, Germany
- Department of Silviculture and Nature Conservation, University of Chile, Santiago, 9206, Chile
| | - Tiangang Gao
- State Key Laboratory of Evolutionary and Systematic Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
| | - Hong Ma
- Department of Biology, the Huck Institutes of the Life Sciences, the Pennsylvania State University, University Park, Pennslyvania, 16802, USA
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Map and sequence-based chromosome walking towards cloning of the male fertility restoration gene Rf5 linked to R 11 in sunflower. Sci Rep 2021; 11:777. [PMID: 33437028 PMCID: PMC7804242 DOI: 10.1038/s41598-020-80659-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 12/11/2020] [Indexed: 11/28/2022] Open
Abstract
The nuclear fertility restorer gene Rf5 in HA-R9, originating from the wild sunflower species Helianthus annuus, is able to restore the widely used PET1 cytoplasmic male sterility in sunflowers. Previous mapping placed Rf5 at an interval of 5.8 cM on sunflower chromosome 13, distal to a rust resistance gene R11 at a 1.6 cM genetic distance in an SSR map. In the present study, publicly available SNP markers were further mapped around Rf5 and R11 using 192 F2 individuals, reducing the Rf5 interval from 5.8 to 0.8 cM. Additional SNP markers were developed in the target region of the two genes from the whole-genome resequencing of HA-R9, a donor line carrying Rf5 and R11. Fine mapping using 3517 F3 individuals placed Rf5 at a 0.00071 cM interval and the gene co-segregated with SNP marker S13_216392091. Similarly, fine mapping performed using 8795 F3 individuals mapped R11 at an interval of 0.00210 cM, co-segregating with two SNP markers, S13_225290789 and C13_181790141. Sequence analysis identified Rf5 as a pentatricopeptide repeat-encoding gene. The high-density map and diagnostic SNP markers developed in this study will accelerate the use of Rf5 and R11 in sunflower breeding.
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Mapping of the New Fertility Restorer Gene Rf-PET2 Close to Rf1 on Linkage Group 13 in Sunflower ( Helianthus annuus L.). Genes (Basel) 2020; 11:genes11030269. [PMID: 32121545 PMCID: PMC7140827 DOI: 10.3390/genes11030269] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 02/23/2020] [Accepted: 02/27/2020] [Indexed: 01/25/2023] Open
Abstract
The PET2-cytoplasm represents a well characterized new source of cytoplasmic male sterility (CMS) in sunflower. It is distinct from the PET1-cytoplasm, used worldwide for commercial hybrid breeding, although it was, as PET1, derived from an interspecific cross between Helianthus. petiolaris and H. annuus. Fertility restoration is essential for the use of CMS PET2 in sunflower hybrid breeding. Markers closely linked to the fertility restorer gene are needed to build up a pool of restorer lines. Fertility-restored F1-hybrids RHA 265(PET2) × IH-51 showed pollen viability of 98.2% ± 1.2, indicating a sporophytic mode of fertility restoration. Segregation analyses in the F2-population of the cross RHA 265(PET2) × IH-51 revealed that this cross segregated for one major restorer gene Rf-PET2. Bulked-segregant analyses investigating 256 amplified fragment length polymorphism (AFLP) primer combinations revealed a high degree of polymorphism in this cross. Using a subset of 24 AFLP markers, three sequence-tagged site (STS) markers and three microsatellite markers, Rf-PET2 could be mapped to the distal region of linkage group 13 between ORS1030 and ORS630. Three AFLP markers linked to Rf-PET2 were cloned and sequenced. Homology search against the sunflower genome sequence of HanXRQ v1r1 confirmed the physical location of Rf-PET2 close to the restorer gene Rf1 for CMS PET1. STS markers were mapped that can now be used for marker-assisted selection.
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Talukder ZI, Ma G, Hulke BS, Jan CC, Qi L. Linkage Mapping and Genome-Wide Association Studies of the Rf Gene Cluster in Sunflower ( Helianthus annuus L.) and Their Distribution in World Sunflower Collections. Front Genet 2019; 10:216. [PMID: 30923538 PMCID: PMC6426773 DOI: 10.3389/fgene.2019.00216] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 02/27/2019] [Indexed: 01/20/2023] Open
Abstract
Commercial hybrid seed production in sunflower currently relies on a single cytoplasmic male sterility (CMS) source, PET1 and the major fertility restoration gene, Rf1, leaving the crop highly vulnerable to issues with genetic bottlenecks. Therefore, having multiple CMS/Rf systems is important for sustainable sunflower production. Here, we report the identification of a new fertility restoration gene, Rf7, which is tightly linked to a new downy mildew (DM) resistance gene, Pl34 , in the USDA sunflower inbred line, RHA 428. The Rf7 gene was genetically mapped to an interval of 0.6 cM on the lower end of linkage group (LG) 13, while Pl34 was mapped 2.1 cM proximal to the Rf7. Both the genes are located in a cluster of Rf and Pl genes. To gain further insights into the distribution of Rf genes in the sunflower breeding lines, we used a genome-wide association study (GWAS) approach to identify markers associated with the fertility restoration trait in a panel of 333 sunflower lines genotyped with 8,723 single nucleotide polymorphism (SNP) markers. Twenty-four SNP markers on the lower end of LG13 spanning a genomic region of 2.47 cM were significantly associated with the trait. The significant markers were surveyed in a world collection panel of 548 sunflower lines and validated to be associated with the Rf1 gene. The SNP haplotypes for the Rf1 gene are different from Rf5 and the Rf7gene located in the Rf gene cluster on LG13. The SNP and SSR markers tightly flanking the Rf7 gene and the Pl34 gene would benefit the sunflower breeders in facilitating marker assisted selection (MAS) of Rf and Pl genes.
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Affiliation(s)
- Zahirul I Talukder
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States
| | - Guojia Ma
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States
| | - Brent S Hulke
- Edward T. Schafer Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Fargo, ND, United States
| | - Chao-Chien Jan
- Edward T. Schafer Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Fargo, ND, United States
| | - Lili Qi
- Edward T. Schafer Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Fargo, ND, United States
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5
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Talukder ZI, Ma G, Hulke BS, Jan CC, Qi L. Linkage Mapping and Genome-Wide Association Studies of the Rf Gene Cluster in Sunflower ( Helianthus annuus L.) and Their Distribution in World Sunflower Collections. Front Genet 2019. [PMID: 30923538 DOI: 10.3389/fgene] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/24/2023] Open
Abstract
Commercial hybrid seed production in sunflower currently relies on a single cytoplasmic male sterility (CMS) source, PET1 and the major fertility restoration gene, Rf1, leaving the crop highly vulnerable to issues with genetic bottlenecks. Therefore, having multiple CMS/Rf systems is important for sustainable sunflower production. Here, we report the identification of a new fertility restoration gene, Rf7, which is tightly linked to a new downy mildew (DM) resistance gene, Pl34 , in the USDA sunflower inbred line, RHA 428. The Rf7 gene was genetically mapped to an interval of 0.6 cM on the lower end of linkage group (LG) 13, while Pl34 was mapped 2.1 cM proximal to the Rf7. Both the genes are located in a cluster of Rf and Pl genes. To gain further insights into the distribution of Rf genes in the sunflower breeding lines, we used a genome-wide association study (GWAS) approach to identify markers associated with the fertility restoration trait in a panel of 333 sunflower lines genotyped with 8,723 single nucleotide polymorphism (SNP) markers. Twenty-four SNP markers on the lower end of LG13 spanning a genomic region of 2.47 cM were significantly associated with the trait. The significant markers were surveyed in a world collection panel of 548 sunflower lines and validated to be associated with the Rf1 gene. The SNP haplotypes for the Rf1 gene are different from Rf5 and the Rf7gene located in the Rf gene cluster on LG13. The SNP and SSR markers tightly flanking the Rf7 gene and the Pl34 gene would benefit the sunflower breeders in facilitating marker assisted selection (MAS) of Rf and Pl genes.
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Affiliation(s)
- Zahirul I Talukder
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States
| | - Guojia Ma
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States
| | - Brent S Hulke
- Edward T. Schafer Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Fargo, ND, United States
| | - Chao-Chien Jan
- Edward T. Schafer Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Fargo, ND, United States
| | - Lili Qi
- Edward T. Schafer Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Fargo, ND, United States
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Zhou F, Liu Y, Liang C, Wang W, Li C, Guo Y, Ma J, Yu Y, Fan L, Yao Y, Zhao D, Liu X, Huang X. Construction of a high-density genetic linkage map and QTL mapping of oleic acid content and three agronomic traits in sunflower ( Helianthus annuus L.) using specific-locus amplified fragment sequencing (SLAF-seq). BREEDING SCIENCE 2018; 68:596-605. [PMID: 30697121 PMCID: PMC6345229 DOI: 10.1270/jsbbs.18051] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 09/18/2018] [Indexed: 05/19/2023]
Abstract
High-density genetic linkage maps are particularly important for quantitative trait loci (QTL) mapping, genome assembly, and marker-assisted selection (MAS) in plants. In this study, a high-density genetic linkage map of sunflower (Helianthus annuus L.) was constructed using an F2 population generated from a cross between Helianthus annuus L. '86-1' and 'L-1-OL-1' via specific-locus amplified fragment sequencing (SLAF-seq). After sequence preprocessing, 530.50 M reads (105.60 Gb) were obtained that contained a total of 343,197 SLAFs, of which 39,589 were polymorphic. Of the polymorphic SLAFs, 6,136 were organized into a linkage map consisting of 17 linkage groups (LGs) spanning 2,221.86 cM, with an average genetic distance of 0.36 cM between SLAFs. Based on this high-density genetic map, QTL analysis was performed that focused on four sunflower phenotypic traits: oleic acid content (OAC), plant height (PH), head diameter (HD), and stem diameter (SD). Subsequently, for these four traits eight QTLs were detected that will likely be useful for increasing our understanding of genetic factors underlying these traits and for use in marker-assisted selection (MAS) for future sunflower breeding.
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Affiliation(s)
- Fei Zhou
- College of Life Science, Northeast Forestry University,
Harbin, 150040,
China
- Institute of Industrial Crops, Heilongjiang Academy of Agricultural Sciences,
Harbin, 150086,
China
| | - Yan Liu
- College of Life Science, Northeast Forestry University,
Harbin, 150040,
China
- Institute of Industrial Crops, Heilongjiang Academy of Agricultural Sciences,
Harbin, 150086,
China
| | - Chunbo Liang
- Institute of Industrial Crops, Heilongjiang Academy of Agricultural Sciences,
Harbin, 150086,
China
| | - Wenjun Wang
- Institute of Industrial Crops, Heilongjiang Academy of Agricultural Sciences,
Harbin, 150086,
China
| | - Cen Li
- Institute of Industrial Crops, Heilongjiang Academy of Agricultural Sciences,
Harbin, 150086,
China
| | - Yongli Guo
- Institute of Industrial Crops, Heilongjiang Academy of Agricultural Sciences,
Harbin, 150086,
China
| | - Jun Ma
- Institute of Industrial Crops, Heilongjiang Academy of Agricultural Sciences,
Harbin, 150086,
China
| | - Ying Yu
- Institute of Industrial Crops, Heilongjiang Academy of Agricultural Sciences,
Harbin, 150086,
China
| | - Lijuan Fan
- Institute of Industrial Crops, Heilongjiang Academy of Agricultural Sciences,
Harbin, 150086,
China
| | - Yubo Yao
- Institute of Industrial Crops, Heilongjiang Academy of Agricultural Sciences,
Harbin, 150086,
China
| | - Dongsheng Zhao
- Institute of Industrial Crops, Heilongjiang Academy of Agricultural Sciences,
Harbin, 150086,
China
| | - Xuemei Liu
- College of Life Science, Northeast Forestry University,
Harbin, 150040,
China
| | - Xutang Huang
- Institute of Industrial Crops, Heilongjiang Academy of Agricultural Sciences,
Harbin, 150086,
China
- Corresponding author (e-mail: )
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7
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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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Ma GJ, Song QJ, Markell SG, Qi LL. High-throughput genotyping-by-sequencing facilitates molecular tagging of a novel rust resistance gene, R 15 , in sunflower (Helianthus annuus L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2018; 131:1423-1432. [PMID: 29564500 DOI: 10.1007/s00122-018-3087-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 03/12/2018] [Indexed: 06/08/2023]
Abstract
A novel rust resistance gene, R 15 , derived from the cultivated sunflower HA-R8 was assigned to linkage group 8 of the sunflower genome using a genotyping-by-sequencing approach. SNP markers closely linked to R 15 were identified, facilitating marker-assisted selection of resistance genes. The rust virulence gene is co-evolving with the resistance gene in sunflower, leading to the emergence of new physiologic pathotypes. This presents a continuous threat to the sunflower crop necessitating the development of resistant sunflower hybrids providing a more efficient, durable, and environmentally friendly host plant resistance. The inbred line HA-R8 carries a gene conferring resistance to all known races of the rust pathogen in North America and can be used as a broad-spectrum resistance resource. Based on phenotypic assessments of 140 F2 individuals derived from a cross of HA 89 with HA-R8, rust resistance in the population was found to be conferred by a single dominant gene (R 15 ) originating from HA-R8. Genotypic analysis with the currently available SSR markers failed to find any association between rust resistance and any markers. Therefore, we used genotyping-by-sequencing (GBS) analysis to achieve better genomic coverage. The GBS data showed that R 15 was located at the top end of linkage group (LG) 8. Saturation with 71 previously mapped SNP markers selected within this region further showed that it was located in a resistance gene cluster on LG8, and mapped to a 1.0-cM region between three co-segregating SNP makers SFW01920, SFW00128, and SFW05824 as well as the NSA_008457 SNP marker. These closely linked markers will facilitate marker-assisted selection and breeding in sunflower.
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Affiliation(s)
- G J Ma
- Department of Plant Pathology, North Dakota State University, Fargo, ND, 58108, USA
| | - Q J Song
- Soybean Genomics and Improvement Laboratory, USDA-Agricultural Research Service, Beltsville, MD, 20705-2350, USA
| | - S G Markell
- Department of Plant Pathology, North Dakota State University, Fargo, ND, 58108, USA
| | - L L Qi
- Red River Valley Agricultural Research Center, USDA-Agricultural Research Service, Fargo, ND, 58102-2765, USA.
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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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Zubrzycki JE, Maringolo CA, Filippi CV, Quiróz FJ, Nishinakamasu V, Puebla AF, Di Rienzo JA, Escande A, Lia VV, Heinz RA, Hopp HE, Cervigni GDL, Paniego NB. Main and epistatic QTL analyses for Sclerotinia Head Rot resistance in sunflower. PLoS One 2017; 12:e0189859. [PMID: 29261806 PMCID: PMC5738076 DOI: 10.1371/journal.pone.0189859] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2017] [Accepted: 12/04/2017] [Indexed: 02/04/2023] Open
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.
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Affiliation(s)
- Jeremías Enrique Zubrzycki
- Instituto de Biotecnología, Centro de Investigaciones en Ciencias Agronómicas y Veterinarias, Instituto Nacional de Tecnología Agropecuaria, Hurlingham, Buenos Aires, Argentina
| | - Carla Andrea Maringolo
- Laboratorio de Patología Vegetal, Unidad Integrada Universidad Nacional de Mar del Plata, Estación Experimental Agropecuaria INTA Balcarce, Balcarce, Buenos Aires, Argentina
| | - Carla Valeria Filippi
- Instituto de Biotecnología, Centro de Investigaciones en Ciencias Agronómicas y Veterinarias, Instituto Nacional de Tecnología Agropecuaria, Hurlingham, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires, Argentina
| | - Facundo José Quiróz
- Laboratorio de Patología Vegetal, Unidad Integrada Universidad Nacional de Mar del Plata, Estación Experimental Agropecuaria INTA Balcarce, Balcarce, Buenos Aires, Argentina
| | - Verónica Nishinakamasu
- Instituto de Biotecnología, Centro de Investigaciones en Ciencias Agronómicas y Veterinarias, Instituto Nacional de Tecnología Agropecuaria, Hurlingham, Buenos Aires, Argentina
| | - Andrea Fabiana Puebla
- Instituto de Biotecnología, Centro de Investigaciones en Ciencias Agronómicas y Veterinarias, Instituto Nacional de Tecnología Agropecuaria, Hurlingham, Buenos Aires, Argentina
| | - Julio A. Di Rienzo
- Cátedra de Estadística y Biometría, Facultad de Ciencias Agropecuarias, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Alberto Escande
- Laboratorio de Patología Vegetal, Unidad Integrada Universidad Nacional de Mar del Plata, Estación Experimental Agropecuaria INTA Balcarce, Balcarce, Buenos Aires, Argentina
| | - Verónica Viviana Lia
- Instituto de Biotecnología, Centro de Investigaciones en Ciencias Agronómicas y Veterinarias, Instituto Nacional de Tecnología Agropecuaria, Hurlingham, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires, Argentina
- Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
| | - Ruth Amalia Heinz
- Instituto de Biotecnología, Centro de Investigaciones en Ciencias Agronómicas y Veterinarias, Instituto Nacional de Tecnología Agropecuaria, Hurlingham, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires, Argentina
- Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
| | - Horacio Esteban Hopp
- Instituto de Biotecnología, Centro de Investigaciones en Ciencias Agronómicas y Veterinarias, Instituto Nacional de Tecnología Agropecuaria, Hurlingham, Buenos Aires, Argentina
- Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
| | - Gerardo D. L. Cervigni
- Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires, Argentina
- Centro de Estudios Fotosintéticos y Bioquímicos, Rosario, Santa Fe, Argentina
| | - Norma Beatriz Paniego
- Instituto de Biotecnología, Centro de Investigaciones en Ciencias Agronómicas y Veterinarias, Instituto Nacional de Tecnología Agropecuaria, Hurlingham, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires, Argentina
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Bordat A, Marchand G, Langlade NB, Pouilly N, Muños S, Dechamp-Guillaume G, Vincourt P, Bret-Mestries E. Different genetic architectures underlie crop responses to the same pathogen: the {Helianthus annuus * Phoma macdonaldii} interaction case for black stem disease and premature ripening. BMC PLANT BIOLOGY 2017; 17:167. [PMID: 29052528 PMCID: PMC5649070 DOI: 10.1186/s12870-017-1116-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 10/09/2017] [Indexed: 05/31/2023]
Abstract
BACKGROUND Phoma macdonaldii has been reported as the causal agent of black stem disease (BS) and premature ripening (PR) on sunflower. PR is considered as the most widespread and detrimental disease on sunflower in France. While genetic variability and QTL mapping for partial resistance of sunflower to stem, collar and roots attacks have been reported on plantlets in controlled conditions, this work aims to describe the genetic variability in a subset of a sunflower lines, and for the first time to map QTL involved in PR resistance evaluated in field conditions using controlled inoculation. RESULTS An efficient and reliable method for inoculation used in field experiments induced stem base necrosis on up to 98% of all plants. A significant genetic variability for PR resistance in the field was detected among the 20 inbred lines of the core collection tested across the two years. For QTL mapping, the PR resistance evaluation was performed on two recombinant inbred lines (RIL) populations derived from the crosses XRQxPSC8 and FUxPAZ2 in two different years. QTL analyses were based on a newly developed consensus genetic map comprising 1007 non-redundant molecular markers. In each of the two RIL populations, different QTL involved in PR partial sunflower resistance were detected. The most significant QTL were detected 49 days post infection (DPI) on LG10 (LOD 7.7) and on LG7 (LOD 12.1) in the XRQxPSC8 and FUxPAZ2 RIL population, respectively. In addition, different QTL were detected on both populations for PR resistance measured between 14 and 35 DPI. In parallel, the incidence of natural attack of P. macdonaldii resulting in BS disease was recorded, showing that in these populations, the genetic of resistance to both diseases is not governed by the same factors. CONCLUSION This work provides the first insights on the genetic architecture of sunflower PR resistance in the field. Moreover, the separate studies of symptoms on different organs and in time series allowed the identification of a succession of genetic components involved in the sunflower resistance to PR and BS diseases caused by Phoma macdonaldii along the development of the {plant * pathogen} interaction.
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Affiliation(s)
- Amandine Bordat
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
- Present address: INRA, Université de Bordeaux, UMR 1332 de Biologie du Fruit et Pathologie, CS 20032, 33882 Villenave d’Ornon, France
| | - Gwenaëlle Marchand
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
- Present address: EURALIS Semences, Domaine de Sandreau, 6 Chemin de Panedautes, 31700 Mondonville, France
| | | | - Nicolas Pouilly
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | - Stéphane Muños
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | - Grégory Dechamp-Guillaume
- ENSAT, UMR 1248 AGIR, BP52627, F-31326 Castanet-Tolosan, France
- AGIR, Université de Toulouse, INRA, INPT, INP-EI PURPAN, Castanet-Tolosan, France
| | - Patrick Vincourt
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
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Huang CH, Zhang C, Liu M, Hu Y, Gao T, Qi J, Ma H. Multiple Polyploidization Events across Asteraceae with Two Nested Events in the Early History Revealed by Nuclear Phylogenomics. Mol Biol Evol 2016; 33:2820-2835. [PMID: 27604225 PMCID: PMC5062320 DOI: 10.1093/molbev/msw157] [Citation(s) in RCA: 105] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Biodiversity results from multiple evolutionary mechanisms, including genetic variation and natural selection. Whole-genome duplications (WGDs), or polyploidizations, provide opportunities for large-scale genetic modifications. Many evolutionarily successful lineages, including angiosperms and vertebrates, are ancient polyploids, suggesting that WGDs are a driving force in evolution. However, this hypothesis is challenged by the observed lower speciation and higher extinction rates of recently formed polyploids than diploids. Asteraceae includes about 10% of angiosperm species, is thus undoubtedly one of the most successful lineages and paleopolyploidization was suggested early in this family using a small number of datasets. Here, we used genes from 64 new transcriptome datasets and others to reconstruct a robust Asteraceae phylogeny, covering 73 species from 18 tribes in six subfamilies. We estimated their divergence times and further identified multiple potential ancient WGDs within several tribes and shared by the Heliantheae alliance, core Asteraceae (Asteroideae-Mutisioideae), and also with the sister family Calyceraceae. For two of the WGD events, there were subsequent great increases in biodiversity; the older one proceeded the divergence of at least 10 subfamilies within 10 My, with great variation in morphology and physiology, whereas the other was followed by extremely high species richness in the Heliantheae alliance clade. Our results provide different evidence for several WGDs in Asteraceae and reveal distinct association among WGD events, dramatic changes in environment and species radiations, providing a possible scenario for polyploids to overcome the disadvantages of WGDs and to evolve into lineages with high biodiversity.
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Affiliation(s)
- Chien-Hsun Huang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, Institute of Biodiversity Sciences, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Caifei Zhang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, Institute of Biodiversity Sciences, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Mian Liu
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, Institute of Biodiversity Sciences, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Yi Hu
- Department of Biology, Huck Institutes of the Life Sciences, Pennsylvania State University, State College, PA
| | - Tiangang Gao
- State Key Laboratory of Evolutionary and Systematic Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, China
| | - Ji Qi
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, Institute of Biodiversity Sciences, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Hong Ma
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, Institute of Biodiversity Sciences, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, China
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Bohra A, Jha UC, Adhimoolam P, Bisht D, Singh NP. Cytoplasmic male sterility (CMS) in hybrid breeding in field crops. PLANT CELL REPORTS 2016; 35:967-93. [PMID: 26905724 DOI: 10.1007/s00299-016-1949-3] [Citation(s) in RCA: 123] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Accepted: 02/02/2016] [Indexed: 05/20/2023]
Abstract
A comprehensive understanding of CMS/Rf system enabled by modern omics tools and technologies considerably improves our ability to harness hybrid technology for enhancing the productivity of field crops. Harnessing hybrid vigor or heterosis is a promising approach to tackle the current challenge of sustaining enhanced yield gains of field crops. In the context, cytoplasmic male sterility (CMS) owing to its heritable nature to manifest non-functional male gametophyte remains a cost-effective system to promote efficient hybrid seed production. The phenomenon of CMS stems from a complex interplay between maternally-inherited (mitochondrion) and bi-parental (nucleus) genomic elements. In recent years, attempts aimed to comprehend the sterility-inducing factors (orfs) and corresponding fertility determinants (Rf) in plants have greatly increased our access to candidate genomic segments and the cloned genes. To this end, novel insights obtained by applying state-of-the-art omics platforms have substantially enriched our understanding of cytoplasmic-nuclear communication. Concomitantly, molecular tools including DNA markers have been implicated in crop hybrid breeding in order to greatly expedite the progress. Here, we review the status of diverse sterility-inducing cytoplasms and associated Rf factors reported across different field crops along with exploring opportunities for integrating modern omics tools with CMS-based hybrid breeding.
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Affiliation(s)
- Abhishek Bohra
- Indian Institute of Pulses Research (IIPR), Kanpur, India.
| | - Uday C Jha
- Indian Institute of Pulses Research (IIPR), Kanpur, India
| | | | - Deepak Bisht
- National Research Centre on Plant Biotechnology (NRCPB), New Delhi, India
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14
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Seiler GJ, Rieseberg LH. Systematics, Origin, and Germplasm Resources of the Wild and Domesticated Sunflower. ACTA ACUST UNITED AC 2015. [DOI: 10.2134/agronmonogr35.c2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
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15
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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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16
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Owart BR, Corbi J, Burke JM, Dechaine JM. Selection on crop-derived traits and QTL in sunflower (Helianthus annuus) crop-wild hybrids under water stress. PLoS One 2014; 9:e102717. [PMID: 25048600 PMCID: PMC4105569 DOI: 10.1371/journal.pone.0102717] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Accepted: 06/21/2014] [Indexed: 12/02/2022] Open
Abstract
Locally relevant conditions, such as water stress in irrigated agricultural regions, should be considered when assessing the risk of crop allele introgression into wild populations following hybridization. Although research in cultivars has suggested that domestication traits may reduce fecundity under water stress as compared to wild-like phenotypes, this has not been investigated in crop-wild hybrids. In this study, we examine phenotypic selection acting on, as well as the genetic architecture of vegetative, reproductive, and physiological characteristics in an experimental population of sunflower crop-wild hybrids grown under wild-like low water conditions. Crop-derived petiole length and head diameter were favored in low and control water environments. The direction of selection differed between environments for leaf size and leaf pressure potential. Interestingly, the additive effect of the crop-derived allele was in the direction favored by selection for approximately half the QTL detected in the low water environment. Selection favoring crop-derived traits and alleles in the low water environment suggests that a subset of these alleles would be likely to spread into wild populations under water stress. Furthermore, differences in selection between environments support the view that risk assessments should be conducted under multiple locally relevant conditions.
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Affiliation(s)
- Birkin R. Owart
- Department of Biological Sciences, Central Washington University, Ellensburg, Washington, United States of America
| | - Jonathan Corbi
- Department of Plant Biology, University of Georgia, Athens, Georgia, United States of America
| | - John M. Burke
- Department of Plant Biology, University of Georgia, Athens, Georgia, United States of America
| | - Jennifer M. Dechaine
- Department of Biological Sciences, Central Washington University, Ellensburg, Washington, United States of America
- * E-mail:
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17
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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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18
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Toward Marker Assisted Selection for Fungal Disease Resistance in Sunflower. Utilization ofH. Bolanderias a Source of Resistance to Downy Mildew. BIOTECHNOL BIOTEC EQ 2014. [DOI: 10.2478/v10133-009-0007-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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19
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Wang X, Wang H, Long Y, Li D, Yin Y, Tian J, Chen L, Liu L, Zhao W, Zhao Y, Yu L, Li M. Identification of QTLs associated with oil content in a high-oil Brassica napus cultivar and construction of a high-density consensus map for QTLs comparison in B. napus. PLoS One 2013; 8:e80569. [PMID: 24312482 PMCID: PMC3846612 DOI: 10.1371/journal.pone.0080569] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Accepted: 10/04/2013] [Indexed: 01/15/2023] Open
Abstract
Increasing seed oil content is one of the most important goals in breeding of rapeseed (B. napus L.). To dissect the genetic basis of oil content in B. napus, a large and new double haploid (DH) population containing 348 lines was obtained from a cross between 'KenC-8' and 'N53-2', two varieties with >10% difference in seed oil content, and this population was named the KN DH population. A genetic linkage map consisting of 403 markers was constructed, which covered a total length of 1783.9 cM with an average marker interval of 4.4 cM. The KN DH population was phenotyped in eight natural environments and subjected to quantitative trait loci (QTL) analysis for oil content. A total of 63 identified QTLs explaining 2.64-17.88% of the phenotypic variation were identified, and these QTLs were further integrated into 24 consensus QTLs located on 11 chromosomes using meta-analysis. A high-density consensus map with 1335 marker loci was constructed by combining the KN DH map with seven other published maps based on the common markers. Of the 24 consensus QTLs in the KN DH population, 14 were new QTLs including five new QTLs in A genome and nine in C genome. The analysis revealed that a larger population with significant differences in oil content gave a higher power detecting new QTLs for oil content, and the construction of the consensus map provided a new clue for comparing the QTLs detected in different populations. These findings enriched our knowledge of QTLs for oil content and should be a potential in marker-assisted breeding of B. napus.
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Affiliation(s)
- Xiaodong Wang
- Institute of Resource Biology and Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Hao Wang
- Hybrid Rapeseed Research Center of Shaanxi Province, Shaanxi Rapeseed Branch of National Centre for Oil Crops Genetic Improvement, Dali, China
| | - Yan Long
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Dianrong Li
- Hybrid Rapeseed Research Center of Shaanxi Province, Shaanxi Rapeseed Branch of National Centre for Oil Crops Genetic Improvement, Dali, China
| | - Yongtai Yin
- Institute of Resource Biology and Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Jianhua Tian
- Hybrid Rapeseed Research Center of Shaanxi Province, Shaanxi Rapeseed Branch of National Centre for Oil Crops Genetic Improvement, Dali, China
| | - Li Chen
- Institute of Resource Biology and Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Liezhao Liu
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Weiguo Zhao
- Hybrid Rapeseed Research Center of Shaanxi Province, Shaanxi Rapeseed Branch of National Centre for Oil Crops Genetic Improvement, Dali, China
| | - Yajun Zhao
- Hybrid Rapeseed Research Center of Shaanxi Province, Shaanxi Rapeseed Branch of National Centre for Oil Crops Genetic Improvement, Dali, China
| | - Longjiang Yu
- Institute of Resource Biology and Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Maoteng Li
- Institute of Resource Biology and Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
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Pegadaraju V, Nipper R, Hulke B, Qi L, Schultz Q. De novo sequencing of sunflower genome for SNP discovery using RAD (Restriction site Associated DNA) approach. BMC Genomics 2013; 14:556. [PMID: 23947483 PMCID: PMC3765701 DOI: 10.1186/1471-2164-14-556] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2013] [Accepted: 08/09/2013] [Indexed: 12/31/2022] Open
Abstract
Background Application of Single Nucleotide Polymorphism (SNP) marker technology as a tool in sunflower breeding programs offers enormous potential to improve sunflower genetics, and facilitate faster release of sunflower hybrids to the market place. Through a National Sunflower Association (NSA) funded initiative, we report on the process of SNP discovery through reductive genome sequencing and local assembly of six diverse sunflower inbred lines that represent oil as well as confection types. Results A combination of Restriction site Associated DNA Sequencing (RAD-Seq) protocols and Illumina paired-end sequencing chemistry generated high quality 89.4 M paired end reads from the six lines which represent 5.3 GB of the sequencing data. Raw reads from the sunflower line, RHA 464 were assembled de novo to serve as a framework reference genome. About 15.2 Mb of sunflower genome distributed over 42,267 contigs were obtained upon assembly of RHA 464 sequencing data, the contig lengths ranged from 200 to 950 bp with an N50 length of 393 bp. SNP calling was performed by aligning sequencing data from the six sunflower lines to the assembled reference RHA 464. On average, 1 SNP was located every 143 bp of the sunflower genome sequence. Based on several filtering criteria, a final set of 16,467 putative sequence variants with characteristics favorable for Illumina Infinium Genotyping Technology (IGT) were mined from the sequence data generated across six diverse sunflower lines. Conclusion Here we report the molecular and computational methodology involved in SNP development for a complex genome like sunflower lacking reference assembly, offering an attractive tool for molecular breeding purposes in sunflower.
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Gong L, Gulya TJ, Markell SG, Hulke BS, Qi LL. Genetic mapping of rust resistance genes in confection sunflower line HA-R6 and oilseed line RHA 397. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2013; 126:2039-49. [PMID: 23719761 DOI: 10.1007/s00122-013-2116-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2012] [Accepted: 05/08/2013] [Indexed: 05/20/2023]
Abstract
Few widely effective resistance sources to sunflower rust, incited by Puccinia helianthi Schwein., have been identified in confection sunflower (Helianthus annuus L.). The USDA inbred line HA-R6 is one of the few confection sunflower lines resistant to rust. A previous allelism test indicated that rust resistance genes in HA-R6 and RHA 397, an oilseed-type restorer line, are either allelic or closely linked; however, neither have been characterized nor molecularly mapped. The objectives of this study are (1) to locate the rust resistance genes in HA-R6 and RHA 397 on a molecular map, (2) to develop closely linked molecular markers for rust resistance diagnostics, and (3) to determine the resistance spectrum of two lines when compared with other rust-resistant lines. Two populations of 140 F2:3 families each from the crosses of HA 89, as susceptible parent, with HA-R6 and RHA 397 were inoculated with race 336 of P. helianthi in the greenhouse. The resistance genes (R-genes) in HA-R6 and RHA 397 were molecularly mapped to the lower end of linkage group 13, which encompasses a large R-gene cluster, and were designated as R 13a and R 13b, respectively. In the initial maps, SSR (simple sequence repeat) and InDel (insertion and deletion) markers revealed 2.8 and 8.2 cM flanking regions for R 13a and R 13b, respectively, linked with a common marker set of four co-segregating markers, ORS191, ORS316, ORS581, and ZVG61, in the distal side and one marker ORS464 in the proximal side. To identify new markers closer to the genes, sunflower RGC (resistance gene candidate) markers linked to the downy mildew R-gene Pl 8 and located at the same region as R 13a and R 13b were selected to screen the two F2 populations. The RGC markers RGC15/16 and a newly developed marker SUN14 designed from a BAC contig anchored by RGC251 further narrowed down the region flanking R 13a and R 13b to 1.1 and 0.1 cM, respectively. Both R 13a and R 13b are highly effective against all rust races tested so far. Our newly developed molecular markers will facilitate breeding efforts to pyramid the R 13 genes with other rust R-genes and accelerate the development of rust-resistant sunflower hybrids in both confection and oilseed sunflowers.
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Affiliation(s)
- L Gong
- Department of Plant Pathology, North Dakota State University, Fargo, ND 58102, USA
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Diversifying sunflower germplasm by integration and mapping of a novel male fertility restoration gene. Genetics 2013; 193:727-37. [PMID: 23307903 DOI: 10.1534/genetics.112.146092] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
The combination of a single cytoplasmic male-sterile (CMS) PET-1 and the corresponding fertility restoration (Rf) gene Rf1 is used for commercial hybrid sunflower (Helianthus annuus L., 2n = 34) seed production worldwide. A new CMS line 514A was recently developed with H. tuberosus cytoplasm. However, 33 maintainers and restorers for CMS PET-1 and 20 additional tester lines failed to restore the fertility of CMS 514A. Here, we report the discovery, characterization, and molecular mapping of a novel Rf gene for CMS 514A derived from an amphiploid (Amp H. angustifolius/P 21, 2n = 68). Progeny analysis of the male-fertile (MF) plants (2n = 35) suggested that this gene, designated Rf6, was located on a single alien chromosome. Genomic in situ hybridization (GISH) indicated that Rf6 was on a chromosome with a small segment translocation on the long arm in the MF progenies (2n = 34). Rf6 was mapped to linkage group (LG) 3 of the sunflower SSR map. Eight markers were identified to be linked to this gene, covering a distance of 10.8 cM. Two markers, ORS13 and ORS1114, were only 1.6 cM away from the gene. Severe segregation distortions were observed for both the fertility trait and the linked marker loci, suggesting the possibility of a low frequency of recombination or gamete selection in this region. This study discovered a new CMS/Rf gene system derived from wild species and provided significant insight into the genetic basis of this system. This will diversify the germplasm for sunflower breeding and facilitate understanding of the interaction between the cytoplasm and nuclear genes.
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Toward a molecular cytogenetic map for cultivated sunflower (Helianthus annuus L.) by landed BAC/BIBAC clones. G3-GENES GENOMES GENETICS 2013; 3:31-40. [PMID: 23316437 PMCID: PMC3538341 DOI: 10.1534/g3.112.004846] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2012] [Accepted: 11/01/2012] [Indexed: 11/18/2022]
Abstract
Conventional karyotypes and various genetic linkage maps have been established in sunflower (Helianthus annuus L., 2n = 34). However, the relationship between linkage groups and individual chromosomes of sunflower remains unknown and has considerable relevance for the sunflower research community. Recently, a set of linkage group-specific bacterial /binary bacterial artificial chromosome (BAC/BIBAC) clones was identified from two complementary BAC and BIBAC libraries constructed for cultivated sunflower cv. HA89. In the present study, we used these linkage group-specific clones (∼100 kb in size) as probes to in situ hybridize to HA89 mitotic chromosomes at metaphase using the BAC- fluorescence in situ hybridization (FISH) technique. Because a characteristic of the sunflower genome is the abundance of repetitive DNA sequences, a high ratio of blocking DNA to probe DNA was applied to hybridization reactions to minimize the background noise. As a result, all sunflower chromosomes were anchored by one or two BAC/BIBAC clones with specific FISH signals. FISH analysis based on tandem repetitive sequences, such as rRNA genes, has been previously reported; however, the BAC-FISH technique developed here using restriction fragment length polymorphism (RFLP)−derived BAC/BIBAC clones as probes to apply genome-wide analysis is new for sunflower. As chromosome-specific cytogenetic markers, the selected BAC/BIBAC clones that encompass the 17 linkage groups provide a valuable tool for identifying sunflower cytogenetic stocks (such as trisomics) and tracking alien chromosomes in interspecific crosses. This work also demonstrates the potential of using a large-insert DNA library for the development of molecular cytogenetic resources.
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Development of an ultra-dense genetic map of the sunflower genome based on single-feature polymorphisms. PLoS One 2012; 7:e51360. [PMID: 23284684 PMCID: PMC3526535 DOI: 10.1371/journal.pone.0051360] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2012] [Accepted: 11/06/2012] [Indexed: 11/19/2022] Open
Abstract
The development of ultra-dense genetic maps has the potential to facilitate detailed comparative genomic analyses and whole genome sequence assemblies. Here we describe the use of a custom Affymetrix GeneChip containing nearly 2.4 million features (25 bp sequences) targeting 86,023 unigenes from sunflower (Helianthus annuus L.) and related species to test for single-feature polymorphisms (SFPs) in a recombinant inbred line (RIL) mapping population derived from a cross between confectionery and oilseed sunflower lines (RHA280×RHA801). We then employed an existing genetic map derived from this same population to rigorously filter out low quality data and place 67,486 features corresponding to 22,481 unigenes on the sunflower genetic map. The resulting map contains a substantial fraction of all sunflower genes and will thus facilitate a number of downstream applications, including genome assembly and the identification of candidate genes underlying QTL or traits of interest.
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Kane NC, Burke JM, Marek L, Seiler G, Vear F, Baute G, Knapp SJ, Vincourt P, Rieseberg LH. Sunflower genetic, genomic and ecological resources. Mol Ecol Resour 2012; 13:10-20. [PMID: 23039950 DOI: 10.1111/1755-0998.12023] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2011] [Revised: 08/22/2012] [Accepted: 08/24/2012] [Indexed: 11/29/2022]
Abstract
Long a major focus of genetic research and breeding, sunflowers (Helianthus) are emerging as an increasingly important experimental system for ecological and evolutionary studies. Here, we review the various attributes of wild and domesticated sunflowers that make them valuable for ecological experimentation and describe the numerous publicly available resources that have enabled rapid advances in ecological and evolutionary genetics. Resources include seed collections available from germplasm centres at the USDA and INRA, genomic and EST sequences, mapping populations, genetic markers, genetic and physical maps and other forward- and reverse-genetic tools. We also discuss some of the key evolutionary, genetic and ecological questions being addressed in sunflowers, as well as gaps in our knowledge and promising areas for future research.
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Affiliation(s)
- Nolan C Kane
- Department of Ecology and Evolutionary Biology, University of Colorado at Boulder, Boulder, CO 80309, USA.
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Qi LL, Seiler GJ, Vick BA, Gulya TJ. Genetics and mapping of the R₁₁ gene conferring resistance to recently emerged rust races, tightly linked to male fertility restoration, in sunflower (Helianthus annuus L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2012; 125:921-32. [PMID: 22610307 DOI: 10.1007/s00122-012-1883-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2011] [Accepted: 04/04/2012] [Indexed: 05/20/2023]
Abstract
Sunflower oil is one of the major sources of edible oil. As the second largest hybrid crop in the world, hybrid sunflowers are developed by using the PET1 cytoplasmic male sterility system that contributes to a 20 % yield advantage over the open-pollinated varieties. However, sunflower production in North America has recently been threatened by the evolution of new virulent pathotypes of sunflower rust caused by the fungus Puccinia helianthi Schwein. Rf ANN-1742, an 'HA 89' backcross restorer line derived from wild annual sunflower (Helianthus annuus L.), was identified as resistant to the newly emerged rust races. The aim of this study was to elucidate the inheritance of rust resistance and male fertility restoration and identify the chromosome location of the underlying genes in Rf ANN-1742. Chi-squared analysis of the segregation of rust response and male fertility in F(2) and F(3) populations revealed that both traits are controlled by single dominant genes, and that the rust resistance gene is closely linked to the restorer gene in the coupling phase. The two genes were designated as R ( 11 ) and Rf5, respectively. A set of 723 mapped SSR markers of sunflower was used to screen the polymorphism between HA 89 and the resistant plant. Bulked segregant analysis subsequently located R ( 11 ) on linkage group (LG) 13 of sunflower. Based on the SSR analyses of 192 F(2) individuals, R ( 11 ) and Rf5 both mapped to the lower end of LG13 at a genetic distance of 1.6 cM, and shared a common marker, ORS728, which was mapped 1.3 cM proximal to Rf5 and 0.3 cM distal to R ( 11 ) (Rf5/ORS728/R ( 11 )). Two additional SSRs were linked to Rf5 and R ( 11 ): ORS995 was 4.5 cM distal to Rf5 and ORS45 was 1.0 cM proximal to R ( 11 ). The advantage of such an introduced alien segment harboring two genes is its large phenotypic effect and simple inheritance, thereby facilitating their rapid deployment in sunflower breeding programs. Suppressed recombination was observed in LGs 2, 9, and 11 as it was evident that no recombination occurred in the introgressed regions of LGs 2, 9, and 11 detected by 5, 9, and 22 SSR markers, respectively. R ( 11 ) is genetically independent from the rust R-genes R ( 1 ), R ( 2 ), and R ( 5 ), but may be closely linked to the rust R-gene R ( adv ) derived from wild Helianthus argophyllus, forming a large rust R-gene cluster of R ( adv )/R ( 11 )/R ( 4 ) in the lower end of LG13. The relationship of Rf5 with Rf1 is discussed based on the marker association analysis.
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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.
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Gautami B, Foncéka D, Pandey MK, Moretzsohn MC, Sujay V, Qin H, Hong Y, Faye I, Chen X, BhanuPrakash A, Shah TM, Gowda MVC, Nigam SN, Liang X, Hoisington DA, Guo B, Bertioli DJ, Rami JF, Varshney RK. An international reference consensus genetic map with 897 marker loci based on 11 mapping populations for tetraploid groundnut (Arachis hypogaea L.). PLoS One 2012; 7:e41213. [PMID: 22815973 PMCID: PMC3399818 DOI: 10.1371/journal.pone.0041213] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2012] [Accepted: 06/18/2012] [Indexed: 01/21/2023] Open
Abstract
Only a few genetic maps based on recombinant inbred line (RIL) and backcross (BC) populations have been developed for tetraploid groundnut. The marker density, however, is not very satisfactory especially in the context of large genome size (2800 Mb/1C) and 20 linkage groups (LGs). Therefore, using marker segregation data for 10 RILs and one BC population from the international groundnut community, with the help of common markers across different populations, a reference consensus genetic map has been developed. This map is comprised of 897 marker loci including 895 simple sequence repeat (SSR) and 2 cleaved amplified polymorphic sequence (CAPS) loci distributed on 20 LGs (a01-a10 and b01-b10) spanning a map distance of 3, 863.6 cM with an average map density of 4.4 cM. The highest numbers of markers (70) were integrated on a01 and the least number of markers (21) on b09. The marker density, however, was lowest (6.4 cM) on a08 and highest (2.5 cM) on a01. The reference consensus map has been divided into 20 cM long 203 BINs. These BINs carry 1 (a10_02, a10_08 and a10_09) to 20 (a10_04) loci with an average of 4 marker loci per BIN. Although the polymorphism information content (PIC) value was available for 526 markers in 190 BINs, 36 and 111 BINs have at least one marker with >0.70 and >0.50 PIC values, respectively. This information will be useful for selecting highly informative and uniformly distributed markers for developing new genetic maps, background selection and diversity analysis. Most importantly, this reference consensus map will serve as a reliable reference for aligning new genetic and physical maps, performing QTL analysis in a multi-populations design, evaluating the genetic background effect on QTL expression, and serving other genetic and molecular breeding activities in groundnut.
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Affiliation(s)
- Bhimana Gautami
- Center of Excellence in Genomics, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | - Daniel Foncéka
- UMR Développement et Amélioration des plantes, Centre de coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), Montpellier, France
| | - Manish K. Pandey
- Center of Excellence in Genomics, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
- Department of Plant Pathology, University of Georgia (UGA), Tifton, Georgia, United States of America
- Crop Protection and Management Research Unit, USDA-Agricultural Research Service, Tifton, Georgia, United States of America
| | - Márcio C. Moretzsohn
- Plant Genetics Lab, EMBRAPA Genetic Resources and Biotechnology, Brasilia, Brazil
| | - Venkataswamy Sujay
- Center of Excellence in Genomics, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
- Department of Genetics and Plant Breeding, University of Agricultural Sciences (UAS-D), Dharwad, India
| | - Hongde Qin
- Department of Plant Pathology, University of Georgia (UGA), Tifton, Georgia, United States of America
- Cash Crop Research Institute, Hubei Academy of Agricultural Sciences (HAAS), Wuhan, Hubei, China
| | - Yanbin Hong
- Crops Research Institute, Guangdong Academy of Agricultural Sciences (GAAS), Guangzhou, Guangdong, China
| | - Issa Faye
- Centre National de Recherche Agronomique (CNRA), Institut Sénégalais de Recherches Agricoles (ISRA), Bambey, Sénégal
| | - Xiaoping Chen
- Crops Research Institute, Guangdong Academy of Agricultural Sciences (GAAS), Guangzhou, Guangdong, China
| | - Amindala BhanuPrakash
- Center of Excellence in Genomics, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | - Trushar M. Shah
- Center of Excellence in Genomics, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | - Makanahally V. C. Gowda
- Department of Genetics and Plant Breeding, University of Agricultural Sciences (UAS-D), Dharwad, India
| | - Shyam N. Nigam
- Center of Excellence in Genomics, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | - Xuanqiang Liang
- Crops Research Institute, Guangdong Academy of Agricultural Sciences (GAAS), Guangzhou, Guangdong, China
| | - Dave A. Hoisington
- Center of Excellence in Genomics, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | - Baozhu Guo
- Crop Protection and Management Research Unit, USDA-Agricultural Research Service, Tifton, Georgia, United States of America
| | | | - Jean-Francois Rami
- UMR Développement et Amélioration des plantes, Centre de coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), Montpellier, France
| | - Rajeev K. Varshney
- Center of Excellence in Genomics, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
- Crops Research Institute, Guangdong Academy of Agricultural Sciences (GAAS), Guangzhou, Guangdong, China
- Theme- Comparative and Applied Genomics, CGIAR Generation Challenge Programme (GCP), CIMMYT, Mexico, Mexico
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Development of a 10,000 locus genetic map of the sunflower genome based on multiple crosses. G3-GENES GENOMES GENETICS 2012; 2:721-9. [PMID: 22870395 PMCID: PMC3385978 DOI: 10.1534/g3.112.002659] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2012] [Accepted: 04/23/2012] [Indexed: 12/03/2022]
Abstract
Genetic linkage maps have the potential to facilitate the genetic dissection of complex traits and comparative analyses of genome structure, as well as molecular breeding efforts in species of agronomic importance. Until recently, the majority of such maps was based on relatively low-throughput marker technologies, which limited marker density across the genome. The availability of high-throughput genotyping technologies has, however, made possible the efficient development of high-density genetic maps. Here, we describe the analysis and integration of genotypic data from four sunflower (Helianthus annuus L.) mapping populations to produce a consensus linkage map of the sunflower genome. Although the individual maps (which contained 3500–5500 loci each) were highly colinear, we observed localized variation in recombination rates in several genomic regions. We also observed several gaps up to 26 cM in length that completely lacked mappable markers in individual crosses, presumably due to regions of identity by descent in the mapping parents. Because these regions differed by cross, the consensus map of 10,080 loci contained no such gaps, clearly illustrating the value of simultaneously analyzing multiple mapping populations.
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Wieckhorst S, Bachlava E, Dußle CM, Tang S, Gao W, Saski C, Knapp SJ, Schön CC, Hahn V, Bauer E. Fine mapping of the sunflower resistance locus Pl(ARG) introduced from the wild species Helianthus argophyllus. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2010; 121:1633-44. [PMID: 20700574 PMCID: PMC2963734 DOI: 10.1007/s00122-010-1416-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2010] [Accepted: 07/08/2010] [Indexed: 05/04/2023]
Abstract
Downy mildew, caused by Plasmopara halstedii, is one of the most destructive diseases in cultivated sunflower (Helianthus annuus L.). The dominant resistance locus Pl(ARG) originates from silverleaf sunflower (H. argophyllus Torrey and Gray) and confers resistance to all known races of P. halstedii. We mapped Pl(ARG) on linkage group (LG) 1 of (cms)HA342 × ARG1575-2, a population consisting of 2,145 F(2) individuals. Further, we identified resistance gene candidates (RGCs) that cosegregated with Pl(ARG) as well as closely linked flanking markers. Markers from the target region were mapped with higher resolution in NDBLOS(sel) × KWS04, a population consisting of 2,780 F(2) individuals that does not segregate for Pl(ARG). A large-insert sunflower bacterial artificial chromosome (BAC) library was screened with overgo probes designed for markers RGC52 and RGC151, which cosegregated with Pl(ARG). Two RGC-containing BAC contigs were anchored to the Pl(ARG) region on LG 1.
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Affiliation(s)
- S. Wieckhorst
- Plant Breeding, Center of Life and Food Sciences Weihenstephan, Technische Universität München, 85354 Freising, Germany
| | - E. Bachlava
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA 30602 USA
| | - C. M. Dußle
- State Plant Breeding Institute, Universität Hohenheim, 70599 Stuttgart, Germany
| | - S. Tang
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA 30602 USA
| | - W. Gao
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA 30602 USA
| | - C. Saski
- Clemson University Genomics Institute, Clemson, SC 29634 USA
| | - S. J. Knapp
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA 30602 USA
- Present Address: Monsanto Vegetables, Inc., 37437 State Highway 16, Woodland, CA 95695 USA
| | - C.-C. Schön
- Plant Breeding, Center of Life and Food Sciences Weihenstephan, Technische Universität München, 85354 Freising, Germany
| | - V. Hahn
- State Plant Breeding Institute, Universität Hohenheim, 70599 Stuttgart, Germany
| | - E. Bauer
- Plant Breeding, Center of Life and Food Sciences Weihenstephan, Technische Universität München, 85354 Freising, Germany
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Talia P, Greizerstein E, Quijano CD, Peluffo L, Fernández L, Fernández P, Hopp HE, Paniego N, Heinz RA, Poggio L. Cytological characterization of sunflower by in situ hybridization using homologous rDNA sequences and a BAC clone containing highly represented repetitive retrotransposon-like sequences. Genome 2010; 53:172-9. [PMID: 20237595 DOI: 10.1139/g09-097] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In the present work we report new tools for the characterization of the complete chromosome complement of sunflower (Helianthus annuus L.), using a bacterial artificial chromosome (BAC) clone containing repetitive sequences with similarity to retrotransposons and a homologous rDNA sequence isolated from the sunflower genome as probes for FISH. The rDNA signal was found in 3 pairs of chromosomes, coinciding with the location of satellites. The BAC clone containing highly represented retroelements hybridized with all the chromosome complement in FISH, and used together with the rDNA probe allowed the discrimination of all chromosome pairs of sunflower. Their distinctive distribution pattern suggests that these probes could be useful for karyotype characterization and for chromosome identification. The karyotype could be subdivided into 3 clear-cut groups of 12 metacentric pairs, 1 submetacentric pair, and 4 subtelocentric pairs, thus resolving previously described karyotype controversies. The use of BAC clones containing single sequences of specific markers and (or) genes associated with important agricultural traits represents an important tool for future locus-specific identification and physical mapping.
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Affiliation(s)
- P Talia
- Instituto de Biotecnología, CICVyA, Instituto Nacional de Tecnología Agropecuaria (INTA) Castelar, Dr. N. Repetto y Los Reseros s/n, (1686) Hurlingham, Provincia de Buenos Aires, Argentina.
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Mulpuri S, Liu Z, Feng J, Gulya TJ, Jan CC. Inheritance and molecular mapping of a downy mildew resistance gene, Pl (13) in cultivated sunflower (Helianthus annuus L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2009; 119:795-803. [PMID: 19557383 DOI: 10.1007/s00122-009-1089-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2008] [Accepted: 05/30/2009] [Indexed: 05/20/2023]
Abstract
The inheritance of resistance to sunflower downy mildew (SDM) derived from HA-R5 conferring resistance to nine races of the pathogen has been determined and the new source has been designated as Pl ( 13 ) . The F(2) individuals and F(3) families of the cross HA-R5 (resistant) x HA 821 (susceptible) were screened against the four predominant SDM races 300, 700, 730, and 770 in separate tests which indicated dominant control by a single locus or a cluster of tightly linked genes. Bulked segregant analysis (BSA) was carried out on 116 F(2) individuals with 500 SSR primer pairs that resulted in the identification of 10 SSR markers of linkage groups 1 (9 markers) and 10 (1 marker) of the genetic map (Tang et al. in Theor Appl Genet 105:1124-1136, 2002) that distinguished the bulks. Of these, the SSR marker ORS 1008 of linkage group 10 was tightly linked (0.9 cM) to the Pl (13) gene. Genotyping the F(2) population and linkage analysis with 20 polymorphic primer pairs located on linkage group 10 failed to show linkage of the markers with downy mildew resistance and the ORS 1008 marker. Nevertheless, validation of polymorphic SSR markers of linkage group 1 along with six RFLP-based STS markers of linkage group 12 of the RFLP map of Jan et al. (Theor Appl Genet 96:15-22, 1998) corresponding to linkage group 1 of the SSR map, mapped seven SSR markers (ORS 965-1, ORS 965-2, ORS 959, ORS 371, ORS 716, and ORS 605) including ORS 1008 and one STS marker (STS10D6) to linkage group 1 covering a genetic distance of 65.0 cM. The Pl (13) gene, as a different source with its location on linkage group 1, was flanked by ORS 1008 on one side at a distance of 0.9 cM and ORS 965-1 on another side at a distance of 5.8 cM. These closely linked markers to the Pl (13) gene provide a valuable basis for marker-assisted selection in sunflower breeding programs.
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Affiliation(s)
- Sujatha Mulpuri
- Directorate of Oilseeds Research, Rajendranagar, Hyderabad 500030, India
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Yue B, Cai X, Vick B, Hu J. Genetic characterization and molecular mapping of a chlorophyll deficiency gene in sunflower (Helianthus annuus). JOURNAL OF PLANT PHYSIOLOGY 2009; 166:644-51. [PMID: 18947900 DOI: 10.1016/j.jplph.2008.09.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2008] [Revised: 09/02/2008] [Accepted: 09/02/2008] [Indexed: 05/04/2023]
Abstract
A major gene controlling chlorophyll deficiency (phenotyped by yellow leaf color, yl) in sunflower was identified and mapped in an F(2) population derived from a cross between two breeding lines. Greenness degree was scored by a hand-held chlorophyll meter in the F(2) population. Leaf tissue from the parents, F(1) hybrids, and some F(2) progenies were also sampled to determine the chlorophyll content. All F(1) plants had normal green leaf color and the segregation of the plants in the F(2) population fits the monogenic ratio (chi((3:1))(2)=0.03, p>0.9), indicating that leaf color is a monogenic trait with normal green dominant over yellow leaf color in this population. The contents of chlorophyll a, chlorophyll b, and total chlorophyll in the yellow-leafed lines were reduced by 41.6%, 53.5%, and 44.3%, respectively, in comparison with those in the green-leafed lines. Genetic mapping with molecular markers positioned the gene, yl, to linkage group 10 of sunflower. An SSR marker, ORS 595, cosegregated with yl, and a TRAP marker, B26P17ga5-300, was linked to yl with a genetic distance of 4.2cM. The molecular marker tightly linked to the chlorophyll deficiency gene will provide insight into the process of chlorophyll metabolism in sunflower.
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Affiliation(s)
- Bing Yue
- Department of Plant Sciences, North Dakota State University, Fargo, ND 58105, USA
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Lacombe S, Souyris I, Bervillé AJ. An insertion of oleate desaturase homologous sequence silences via siRNA the functional gene leading to high oleic acid content in sunflower seed oil. Mol Genet Genomics 2008; 281:43-54. [PMID: 18956214 DOI: 10.1007/s00438-008-0391-9] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2008] [Accepted: 10/10/2008] [Indexed: 11/29/2022]
Abstract
Classical sunflower varieties display a high linoleic acid content in their seeds [low oleic (LO) varieties] whereas genotypes carrying the Pervenets mutation display an increased oleic acid content of above 83% [high oleic (HO) varieties]. Despite the advantage in health terms of oleic acid, the nature of the mutation was still unknown. Previous work reported that HO genotypes carried a specific oleate desaturase (OD) allele. This enzyme catalyses the desaturation of oleic acid into linoleic acid. The present work demonstrates that this allele is organised in two parts: the first section present in both HO and LO genotypes carries a normal OD gene, the second section is specific to HO genotypes and carries OD duplications. The study of mRNA accumulation in LO and HO seeds revealed that the mutation is dominant and induces an OD mRNA down-regulation. Furthermore, OD small interfering RNA, characteristic of gene silencing, accumulated specifically in HO seeds. Considered together, these observations show that the mutation is associated with OD duplications leading to gene silencing of the OD gene and consequently, to oleic acid accumulation. This finding allowed the development of molecular markers characterising the mutation that can be used in breeding programmes to facilitate the selection of HO genotypes.
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Affiliation(s)
- Séverine Lacombe
- Monsanto SAS, Croix de Pardies, BP 21, 40305, Peyrehorade Cedex, France
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Barker MS, Kane NC, Matvienko M, Kozik A, Michelmore RW, Knapp SJ, Rieseberg LH. Multiple paleopolyploidizations during the evolution of the Compositae reveal parallel patterns of duplicate gene retention after millions of years. Mol Biol Evol 2008; 25:2445-55. [PMID: 18728074 DOI: 10.1093/molbev/msn187] [Citation(s) in RCA: 226] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Of the approximately 250,000 species of flowering plants, nearly one in ten are members of the Compositae (Asteraceae), a diverse family found in almost every habitat on all continents except Antarctica. With an origin in the mid Eocene, the Compositae is also a relatively young family with remarkable diversifications during the last 40 My. Previous cytologic and systematic investigations suggested that paleopolyploidy may have occurred in at least one Compositae lineage, but a recent analysis of genomic data was equivocal. We tested for evidence of paleopolyploidy in the evolutionary history of the family using recently available expressed sequence tag (EST) data from the Compositae Genome Project. Combined with data available on GenBank, we analyzed nearly 1 million ESTs from 18 species representing seven genera and four tribes. Our analyses revealed at least three ancient whole-genome duplications in the Compositae-a paleopolyploidization shared by all analyzed taxa and placed near the origin of the family just prior to the rapid radiation of its tribes and independent genome duplications near the base of the tribes Mutisieae and Heliantheae. These results are consistent with previous research implicating paleopolyploidy in the evolution and diversification of the Heliantheae. Further, we observed parallel retention of duplicate genes from the basal Compositae genome duplication across all tribes, despite divergence times of 33-38 My among these lineages. This pattern of retention was also repeated for the paleologs from the Heliantheae duplication. Intriguingly, the categories of genes retained in duplicate were substantially different from those in Arabidopsis. In particular, we found that genes annotated to structural components or cellular organization Gene Ontology categories were significantly enriched among paleologs, whereas genes associated with transcription and other regulatory functions were significantly underrepresented. Our results suggest that paleopolyploidy can yield strikingly consistent signatures of gene retention in plant genomes despite extensive lineage radiations and recurrent genome duplications but that these patterns vary substantially among higher taxonomic categories.
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Affiliation(s)
- Michael S Barker
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada.
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Feng J, Jan CC. Introgression and molecular tagging of Rf (4), a new male fertility restoration gene from wild sunflower Helianthus maximiliani L. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2008; 117:241-9. [PMID: 18437344 DOI: 10.1007/s00122-008-0769-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2007] [Accepted: 04/03/2008] [Indexed: 05/20/2023]
Abstract
Cytoplasmic male sterility (CMS) and its fertility restoration (Rf) genes are critical tools for hybrid seed production to utilize heterosis. In sunflower, CMS PET1 and the associated Rf gene Rf (1) is the only source extensively used in commercial hybrid production. The objective of this research was to develop new sources of CMS and fertility restorers to broaden the genetic diversity of hybrid seed production. We identified a new type of CMS, named as CMS GIG2, from an interspecific cross between Helianthus giganteus accession1934 and H. annuus cv. HA 89. Based on reactions to a set of standard Rf testers, CMS GIG2 is different from all previously reported CMS types, including the CMS GIG1 from another H. giganteus accession. We also identified an Rf gene for CMS GIG2 from wild species H. maximiliani accession 1631. The CMS GIG2 and its restoration gene were introduced into HA 89 background through recurrent backcross and single plant selection techniques. Genetic analysis revealed that the CMS GIG2-Rf system is controlled by a completely dominant gene, named as Rf (4), and the gene additive and dominance effects were estimated as 39.9 and 42.2%, respectively, in the HA 89 background. The gene Rf (4) was mapped onto linkage group 3 with simple sequence repeat (SSR) markers and RFLP-derived STS-marker, and is about 0.9 cM away from the SSR marker ORS1114 based on a segregation population of 933 individuals. The CMS GIG2-Rf (4) system tagged by molecular markers provides an alternative genetic source for hybrid breeding in the sunflower crop.
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Affiliation(s)
- Jiuhuan Feng
- Department of Plant Sciences, North Dakota State University, Fargo, ND 58105, USA
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Rojas-Barros P, Hu J, Jan CC. Molecular mapping of an apical branching gene of cultivated sunflower (Helianthus annuus L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2008; 117:19-28. [PMID: 18389209 DOI: 10.1007/s00122-008-0748-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2007] [Accepted: 03/10/2008] [Indexed: 05/04/2023]
Abstract
Commercial hybrids of cultivated sunflower (Helianthus annuus L.) are obtained by crossing a cytoplasmic male sterile line (A-line) with a restorer pollinator (R-line). The incorporation of a recessive branching trait to extend the pollination period of R-lines during hybrid seed production is laborious and time-consuming. By using target region polymorphism (TRAP) and bulked segregant analysis (BSA), we identified 15 TRAP markers linked to the b(1) (branching) locus in a population of 229 F(2) plants derived from a cross between nonbranched (HA 234) and branched (RHA 271) lines. TBr4-720 and TBr8-555 markers were linked to the b(1) gene in the coupling phase at 0.5 cM (0.004 recombination frequency). The Tbr20-297 and Tbr20-494 markers flanked the b(1) locus in the repulsion phase at genetic distances of 7.5 and 2.5 cM, respectively. Tbr19-395, also in the repulsion phase, mapped at 3.8 cM from the b(1) locus and on the opposite side of the marker Tbr20-297. The 8A1 and 15B3 restriction fragment length polymorphic (RFLP) markers of linkage group (LG) 16 of the RHA 271 x HA 234 cultivated sunflower map anchored the b(1) LG onto the RFLP map. Polymerase chain reaction (PCR)-based markers tightly linked to the recessive b(1) gene have been developed. Their identification and the incorporation of the LG containing the b(1) locus onto an RFLP map will be useful for marker-assisted selection (MAS) in breeding programs and provide the bases for map-based cloning of this gene.
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Affiliation(s)
- Pilar Rojas-Barros
- Department of Plant Sciences, North Dakota State University, Fargo, ND 58105, USA
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Yue B, Vick BA, Yuan W, Hu J. Mapping one of the 2 genes controlling lemon ray flower color in sunflower (Helianthus annuus L.). J Hered 2008; 99:564-7. [PMID: 18477587 DOI: 10.1093/jhered/esn033] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
In an F2 population of 120 plants derived from a cross between 2 breeding lines with yellow ray flowers, we observed 111 plants with yellow-colored and 9 plants with lemon-colored ray flowers. The segregation pattern fits a 15:1 (chi2(15:1) = 0.32, P > 0.5) ratio, suggesting that the lemon ray flower color is conditioned by 2 independent recessive genes that had been contributed individually by each of the parents. We sampled 111 plants from the 3 F(2:3) families displaying a 3 to 1 segregating ratio for genotyping with molecular markers. One of the genes, Yf(1), was mapped onto linkage group 11 of the public sunflower map. A targeted region amplified polymorphism marker (B26P17Trap13-68) had a genetic distance of 1.5 cM to Yf(1), and one simple sequence repeat marker (ORS733) and one expressed sequence tag (EST)-based marker (HT167) previously mapped to linkage group 11 were linked to Yf(1) with distances of 9.9 and 2.3 cM, respectively.
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Affiliation(s)
- Bing Yue
- Department of Plant Sciences, North Dakota State University, Fargo, ND 58105, USA
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Fusari CM, Lia VV, Hopp HE, Heinz RA, Paniego NB. Identification of single nucleotide polymorphisms and analysis of linkage disequilibrium in sunflower elite inbred lines using the candidate gene approach. BMC PLANT BIOLOGY 2008; 8:7. [PMID: 18215288 PMCID: PMC2266750 DOI: 10.1186/1471-2229-8-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2007] [Accepted: 01/23/2008] [Indexed: 05/04/2023]
Abstract
BACKGROUND Association analysis is a powerful tool to identify gene loci that may contribute to phenotypic variation. This includes the estimation of nucleotide diversity, the assessment of linkage disequilibrium structure (LD) and the evaluation of selection processes. Trait mapping by allele association requires a high-density map, which could be obtained by the addition of Single Nucleotide Polymorphisms (SNPs) and short insertion and/or deletions (indels) to SSR and AFLP genetic maps. Nucleotide diversity analysis of randomly selected candidate regions is a promising approach for the success of association analysis and fine mapping in the sunflower genome. Moreover, knowledge of the distance over which LD persists, in agronomically meaningful sunflower accessions, is important to establish the density of markers and the experimental design for association analysis. RESULTS A set of 28 candidate genes related to biotic and abiotic stresses were studied in 19 sunflower inbred lines. A total of 14,348 bp of sequence alignment was analyzed per individual. In average, 1 SNP was found per 69 nucleotides and 38 indels were identified in the complete data set. The mean nucleotide polymorphism was moderate (theta = 0.0056), as expected for inbred materials. The number of haplotypes per region ranged from 1 to 9 (mean = 3.54 +/- 1.88). Model-based population structure analysis allowed detection of admixed individuals within the set of accessions examined. Two putative gene pools were identified (G1 and G2), with a large proportion of the inbred lines being assigned to one of them (G1). Consistent with the absence of population sub-structuring, LD for G1 decayed more rapidly (r2 = 0.48 at 643 bp; trend line, pooled data) than the LD trend line for the entire set of 19 individuals (r2 = 0.64 for the same distance). CONCLUSION Knowledge about the patterns of diversity and the genetic relationships between breeding materials could be an invaluable aid in crop improvement strategies. The relatively high frequency of SNPs within the elite inbred lines studied here, along with the predicted extent of LD over distances of 100 kbp (r2 approximately 0.1) suggest that high resolution association mapping in sunflower could be achieved with marker densities lower than those usually reported in the literature.
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Affiliation(s)
- Corina M Fusari
- Instituto Nacional de Tecnología Agropecuaria (INTA), Instituto de Biotecnología (CNIA), CC 25, Castelar (B1712WAA), Buenos Aires, Argentina
| | - Verónica V Lia
- Instituto Nacional de Tecnología Agropecuaria (INTA), Instituto de Biotecnología (CNIA), CC 25, Castelar (B1712WAA), Buenos Aires, Argentina
- Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - H Esteban Hopp
- Instituto Nacional de Tecnología Agropecuaria (INTA), Instituto de Biotecnología (CNIA), CC 25, Castelar (B1712WAA), Buenos Aires, Argentina
- Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Ruth A Heinz
- Instituto Nacional de Tecnología Agropecuaria (INTA), Instituto de Biotecnología (CNIA), CC 25, Castelar (B1712WAA), Buenos Aires, Argentina
- Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Norma B Paniego
- Instituto Nacional de Tecnología Agropecuaria (INTA), Instituto de Biotecnología (CNIA), CC 25, Castelar (B1712WAA), Buenos Aires, Argentina
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Fusari CM, Lia VV, Hopp HE, Heinz RA, Paniego NB. Identification of single nucleotide polymorphisms and analysis of linkage disequilibrium in sunflower elite inbred lines using the candidate gene approach. BMC PLANT BIOLOGY 2008; 8:7. [PMID: 18215288 DOI: 10.1186/147-2229.8-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Received: 10/22/2007] [Accepted: 01/23/2008] [Indexed: 05/20/2023]
Abstract
BACKGROUND Association analysis is a powerful tool to identify gene loci that may contribute to phenotypic variation. This includes the estimation of nucleotide diversity, the assessment of linkage disequilibrium structure (LD) and the evaluation of selection processes. Trait mapping by allele association requires a high-density map, which could be obtained by the addition of Single Nucleotide Polymorphisms (SNPs) and short insertion and/or deletions (indels) to SSR and AFLP genetic maps. Nucleotide diversity analysis of randomly selected candidate regions is a promising approach for the success of association analysis and fine mapping in the sunflower genome. Moreover, knowledge of the distance over which LD persists, in agronomically meaningful sunflower accessions, is important to establish the density of markers and the experimental design for association analysis. RESULTS A set of 28 candidate genes related to biotic and abiotic stresses were studied in 19 sunflower inbred lines. A total of 14,348 bp of sequence alignment was analyzed per individual. In average, 1 SNP was found per 69 nucleotides and 38 indels were identified in the complete data set. The mean nucleotide polymorphism was moderate (theta = 0.0056), as expected for inbred materials. The number of haplotypes per region ranged from 1 to 9 (mean = 3.54 +/- 1.88). Model-based population structure analysis allowed detection of admixed individuals within the set of accessions examined. Two putative gene pools were identified (G1 and G2), with a large proportion of the inbred lines being assigned to one of them (G1). Consistent with the absence of population sub-structuring, LD for G1 decayed more rapidly (r2 = 0.48 at 643 bp; trend line, pooled data) than the LD trend line for the entire set of 19 individuals (r2 = 0.64 for the same distance). CONCLUSION Knowledge about the patterns of diversity and the genetic relationships between breeding materials could be an invaluable aid in crop improvement strategies. The relatively high frequency of SNPs within the elite inbred lines studied here, along with the predicted extent of LD over distances of 100 kbp (r2 approximately 0.1) suggest that high resolution association mapping in sunflower could be achieved with marker densities lower than those usually reported in the literature.
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Affiliation(s)
- Corina M Fusari
- Instituto Nacional de Tecnología Agropecuaria, Instituto de Biotecnología (CNIA), CC 25, Castelar (B1712WAA), Buenos Aires, Argentina.
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Ceccarelli M, Sarri V, Natali L, Giordani T, Cavallini A, Zuccolo A, Jurman I, Morgante M, Cionini PG. Characterization of the chromosome complement of Helianthus annuus by in situ hybridization of a tandemly repeated DNA sequence. Genome 2007; 50:429-34. [PMID: 17612611 DOI: 10.1139/g07-019] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A tandemly repeated sequence isolated from a clone (HAG004N15) of a nebulized genomic DNA library of sunflower (Helianthus annuus L., 2n = 34) was characterized and used to study the chromosome complement of sunflower. HAG004N15 repeat units (368 bp in length) were found to be highly methylated, and their copy number per haploid (1C) genome was estimated to be 7800. After in situ hybridization of HAG004N15 repeats onto chromosome spreads, signals were observed at the end of both chromosome arms in 4 pairs and at the end of only one arm in 8 other pairs. Signals were also observed at the intercalary (mostly subtelomeric) regions in all pairs, in both arms in 8 pairs, and in only one arm in the other 9 pairs. The short arm of 1 pair was labelled entirely. The chromosomal location of ribosomal DNA was also studied by hybridizing the wheat ribosomal probe pTa71. Four chromosome pairs contained ribosomal cistrons at the end of their shorter arm, but a satellite was seen in only 3 pairs. These hybridization patterns were the same in the 3 sunflower lines studied (HA89, RA20031, and HOR). The chromosomal localization of HAG004N15-related sequences allowed all of the chromosome pairs to be distinguished from each other, in spite of small size and similar morphology.
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Affiliation(s)
- M Ceccarelli
- Dipartimento di Biologia Cellulare e Ambientale, Sezione di Biologia Cellulare e Molecolare, Universitá di Perugia, Via Elce di Sotto, Perugia, Italy
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41
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Jan CC, Seiler G. Sunflower. GENETIC RESOURCES, CHROMOSOME ENGINEERING, AND CROP IMPROVEMENT 2006. [DOI: 10.1201/9781420005363.ch5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
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Hu J. Defining the sunflower (Helianthus annuus L.) linkage group ends with the Arabidopsis-type telomere sequence repeat-derived markers. Chromosome Res 2006; 14:535-48. [PMID: 16823616 DOI: 10.1007/s10577-006-1051-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2006] [Revised: 03/10/2006] [Accepted: 03/10/2006] [Indexed: 10/24/2022]
Abstract
The target region amplification polymorphism (TRAP) marker technique was employed to define sunflower (Helianthus annuus L.) linkage group ends. In combination with eight arbitrary primers, nine fixed primers containing the Arabidopsis-type telomere repeat sequences worked successfully in generating polymorphic markers in the mapping population of 92 F(7) recombinant inbred lines (RIL) derived from the cross RHA 280 x RHA 801. This population was used in the construction of the densest sunflower linkage map of 577 simple sequence repeat (SSR) markers. With 18 sets of PCR reactions, 226 polymorphic TRAP markers were amplified from the two parental lines and 92 RIL. The computer program, Mapmaker, placed 183 markers into the established 17 linkage groups of the SSR map. Although most of the added markers spread across the genome, 32 markers were mapped to the outermost positions of the linkage groups, defining 21 of the 34 linkage group ends of the sunflower linkage map. The telomeric origin of a few of these markers was confirmed by sequence analyses. These telomere-associated markers will provide an accurate assessment of the completeness of a linkage group and a better estimate of the actual genetic lengths. The potential application of the telomere mapping to sunflower improvement is discussed.
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Affiliation(s)
- Jinguo Hu
- U.S. Department of Agriculture, Agricultural Research Service, Northern Crop Science Laboratory, Fargo, ND 58105, USA.
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Nakazato T, Jung MK, Housworth EA, Rieseberg LH, Gastony GJ. Genetic map-based analysis of genome structure in the homosporous fern Ceratopteris richardii. Genetics 2006; 173:1585-97. [PMID: 16648591 PMCID: PMC1526675 DOI: 10.1534/genetics.106.055624] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2006] [Accepted: 04/18/2006] [Indexed: 11/18/2022] Open
Abstract
Homosporous ferns have extremely high chromosome numbers relative to flowering plants, but the species with the lowest chromosome numbers show gene expression patterns typical of diploid organisms, suggesting that they may be diploidized ancient polyploids. To investigate the role of polyploidy in fern genome evolution, and to provide permanent genetic resources for this neglected group, we constructed a high-resolution genetic linkage map of the homosporous fern model species, Ceratopteris richardii (n = 39). Linkage map construction employed 488 doubled haploid lines (DHLs) that were genotyped for 368 RFLP, 358 AFLP, and 3 isozyme markers. Forty-one linkage groups were recovered, with average spacing between markers of 3.18 cM. Most loci (approximately 76%) are duplicated and most duplicates occur on different linkage groups, indicating that as in other eukaryotic genomes, gene duplication plays a prominent role in shaping the architecture of fern genomes. Although past polyploidization is a potential mechanism for the observed abundance of gene duplicates, a wide range in the number of gene duplicates as well as the absence of large syntenic regions consisting of duplicated gene copies implies that small-scale duplications may be the primary mode of gene duplication in C. richardii. Alternatively, evidence of past polyploidization(s) may be masked by extensive chromosomal rearrangements as well as smaller-scale duplications and deletions following polyploidization(s).
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Affiliation(s)
- Takuya Nakazato
- Department of Biology, Indiana University, Bloomington, Indiana 47405-7005, USA.
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Feng J, Vick BA, Lee MK, Zhang HB, Jan CC. Construction of BAC and BIBAC libraries from sunflower and identification of linkage group-specific clones by overgo hybridization. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2006; 113:23-32. [PMID: 16612648 DOI: 10.1007/s00122-006-0265-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2005] [Accepted: 03/09/2006] [Indexed: 05/04/2023]
Abstract
Complementary BAC and BIBAC libraries were constructed from nuclear DNA of sunflower cultivar HA 89. The BAC library, constructed with BamHI in the pECBAC1 vector, contains 107,136 clones and has an average insert size of 140 kb. The BIBAC library was constructed with HindIII in the plant-transformation-competent binary vector pCLD04541 and contains 84,864 clones, with an average insert size of 137 kb. The two libraries combined contain 192,000 clones and are equivalent to approximately 8.9 haploid genomes of sunflower (3,000 Mb/1C), and provide a greater than 99% probability of obtaining a clone of interest. The frequencies of BAC and BIBAC clones carrying chloroplast or mitochondrial DNA sequences were estimated to be 2.35 and 0.04%, respectively, and insert-empty clones were less than 0.5%. To facilitate chromosome engineering and anchor the sunflower genetic map to its chromosomes, one to three single- or low-copy RFLP markers from each linkage group of sunflower were used to design pairs of overlapping oligonucleotides (overgos). Thirty-six overgos were designed and pooled as probes to screen a subset (5.1x) of the BAC and BIBAC libraries. Of the 36 overgos, 33 (92%) gave at least one positive clone and 3 (8%) failed to hit any clone. As a result, 195 BAC and BIBAC clones representing 19 linkage groups were identified, including 76 BAC clones and 119 BIBAC clones, further verifying the genome coverage and utility of the libraries. These BAC and BIBAC libraries and linkage group-specific clones provide resources essential for comprehensive research of the sunflower genome.
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Affiliation(s)
- Jiuhuan Feng
- Department of Plant Sciences, North Dakota State University, Fargo, ND 58105, USA
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Bouzidi MF, Franchel J, Tao Q, Stormo K, Mraz A, Nicolas P, Mouzeyar S. A sunflower BAC library suitable for PCR screening and physical mapping of targeted genomic regions. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2006; 113:81-9. [PMID: 16783592 DOI: 10.1007/s00122-006-0274-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2005] [Accepted: 03/17/2006] [Indexed: 05/10/2023]
Abstract
A sunflower BAC library consisting of 147,456 clones with an average size of 118 kb has been constructed and characterized. It represents approximately 5x sunflower haploid genome equivalents. The BAC library has been arranged in pools and superpools of DNA allowing screening with various PCR-based markers. Each of the 32 superpools contains 4,608 clones and corresponds to a 36 matrix pools. Thus, the screening of the entire library could be accomplished in less than 80 PCR reactions including positive and negative controls. As a demonstration of the feasibility of the concept, a set of 24 SSR markers covering about 36 cM in the sunflower SSR map (Tang et al. in Theor Appl Genet 105:1124-1136, 2002) have been used to screen the BAC library. About 125 BAC clones have been identified and then organized in 23 contigs by HindIII digestion. The contigs are anchored on the SSR map and thus constitutes a first-generation physical map of this region. The utility of this BAC library as a genomic resource for physical mapping and map-based cloning in sunflower is discussed.
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Affiliation(s)
- Mohamed Fouad Bouzidi
- UMR 1095 INRA-UBP Amélioration et Santé des Plantes, Université Blaise Pascal, 24 avenue des Landais, 63177, Aubière Cedex, France
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46
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Pelgas B, Bousquet J, Beauseigle S, Isabel N. A composite linkage map from two crosses for the species complex Picea mariana x Picea rubens and analysis of synteny with other Pinaceae. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2005; 111:1466-88. [PMID: 16215729 DOI: 10.1007/s00122-005-0068-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2005] [Accepted: 07/04/2005] [Indexed: 05/04/2023]
Abstract
Four individual linkage maps were constructed from two crosses for the species complex Picea mariana (Mill.) B.S.P. x Picea rubens Sarg in order to integrate their information into a composite map and to compare with other Pinaceae. For all individual linkage maps, 12 major linkage groups were recovered with 306 markers per map on average. Before building the composite linkage map, the common male parent between the two crosses made it possible to construct a reference linkage map to validate the relative position of homologous markers. The final composite map had a length of 2,319 cM (Haldane) and contained a total of 1,124 positioned markers, including 1,014 AFLPs, 3 RAPDs, 53 SSRs, and 54 ESTPs, assembled into 12 major linkage groups. Marker density of the composite map was statistically homogenous and was much higher (one marker every 2.1 cM) than that of the individual linkage maps (one marker every 5.7 to 7.1 cM). Synteny was well conserved between individual, reference, and composite linkage maps and 94% of homologous markers were colinear between the reference and composite maps. The combined information from the two crosses increased by about 24% the number of anchor markers compared to the information from any single cross. With a total number of 107 anchor markers (SSRs and ESTPs), the composite linkage map is a useful starting point for large-scale genome comparisons at the intergeneric level in the Pinaceae. Comparisons of this map with those in Pinus and Pseudotsuga allowed the identification of one breakdown in synteny where one linkage group homologous to both Picea and Pinus corresponded to two linkage groups in Pseudotsuga. Implications for the evolution of the Pinaceae genome are discussed.
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Affiliation(s)
- Betty Pelgas
- Chaire de recherche du Canada en génomique forestière et environnementale, Centre de recherche en biologie forestière, Pavillon Charles-Eugène-Marchand, Université Laval, Sainte-Foy, QC, G1K 7P4, Canada
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Lai Z, Livingstone K, Zou Y, Church SA, Knapp SJ, Andrews J, Rieseberg LH. Identification and mapping of SNPs from ESTs in sunflower. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2005; 111:1532-44. [PMID: 16205907 PMCID: PMC2442914 DOI: 10.1007/s00122-005-0082-4] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2005] [Accepted: 08/12/2005] [Indexed: 05/04/2023]
Abstract
More than 67,000 expressed sequence tags (ESTs) have recently been generated for sunflower (Helianthus), including 44,000 from cultivated confectionery (RHA280) and oilseed (RHA801) lines of Helianthus annuus and 23,000 from drought- and salt-tolerant wild sunflowers, H. argophyllus and H. paradoxus, respectively. To create a transcript map for sunflower, we identified 605 ESTs that displayed small insertion-deletion polymorphism (SNP) variation in silico, had apparent tissue-specific expression patterns, and/or were ESTs with candidate functions in traits such as development, cell transport, metabolism, plant defense, and tolerance to abiotic stress. Primer pairs for 535 of the loci were designed from the ESTs and screened for polymorphism in recombinant inbred lines derived from a cross between the same cultivars (RHA280 x RHA801) employed for sequencing. In total, 273 of the loci amplified polymorphic products, of which 243 mapped to the 17 linkage groups previously identified for sunflower. Comparisons with previously mapped QTL revealed some cases where ESTs with putatively related functions mapped near QTLs identified in other crosses for salt tolerance and for domestication traits such as stem diameter, shattering, flowering time, and achene size.
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Affiliation(s)
- Z Lai
- Department of Biology and Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN 47405, USA.
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Micic Z, Hahn V, Bauer E, Schön CC, Knapp SJ, Tang S, Melchinger AE. QTL mapping of Sclerotinia midstalk-rot resistance in sunflower. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2004; 109:1474-84. [PMID: 15480534 DOI: 10.1007/s00122-004-1764-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2004] [Accepted: 07/04/2004] [Indexed: 05/04/2023]
Abstract
In many sunflower-growing regions of the world, Sclerotinia sclerotiorum (Lib.) de Bary is the major disease of sunflower (Helianthus annuus L.). In this study, we mapped and characterized quantitative trait loci (QTL) involved in resistance to S. sclerotiorum midstalk rot and two morphological traits. A total of 351 F3 families developed from a cross between a resistant inbred line from the germplasm pool NDBLOS and the susceptible line CM625 were assayed for their parental F2 genotype at 117 codominant simple sequence repeat markers. Disease resistance of the F3 families was screened under artificial infection in field experiments across two sowing times in 1999. For the three resistance traits (leaf lesion, stem lesion, and speed of fungal growth) and the two morphological traits, genotypic variances were highly significant. Heritabilities were moderate to high (h2=0.55-0.89). Genotypic correlations between resistance traits were highly significant (P<0.01) but moderate. QTL were detected for all three resistance traits, but estimated effects at most QTL were small. Simultaneously, they explained between 24.4% and 33.7% of the genotypic variance for resistance against S. sclerotiorum. Five of the 15 genomic regions carrying a QTL for either of the three resistance traits also carried a QTL for one of the two morphological traits. The prospects of marker-assisted selection (MAS) for resistance to S. sclerotiorum are limited due to the complex genetic architecture of the trait. MAS can be superior to classical phenotypic selection only with low marker costs and fast selection cycles.
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Affiliation(s)
- Z Micic
- State Plant Breeding Institute (720), University of Hohenheim, 70593 Stuttgart, Germany
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Al-Chaarani GR, Gentzbittel L, Huang XQ, Sarrafi A. Genotypic variation and identification of QTLs for agronomic traits, using AFLP and SSR markers in RILs of sunflower (Helianthus annuus L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2004; 109:1353-60. [PMID: 15365625 DOI: 10.1007/s00122-004-1770-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2003] [Accepted: 06/30/2004] [Indexed: 05/04/2023]
Abstract
A population of 77 recombinant inbred lines (RILs) were developed through single-seed descent from a cross between 'PAC-2' and 'RHA-266'. Seeds of the above-mentioned RILs and their parents were planted in the field in a randomised complete block design with two replications. Genetic control for some agronomical traits-sowing-to-flowering date, plant height, stem diameter (SD), head diameter (HD), grain weight per plant, 1,000-grain weight (TGW) and the percentage of oil in grains-were measured for RILs and their parents. Genetic variability was observed among 77 RILs for all traits studied. Transgressive segregation occurred for some traits, and the comparison between 10% of selected RILs with the best parent showed significant difference for SD and HD as well as for TGW. A set of 123 RILs from the same cross, including the 77 above-mentioned RILs and their two parents, were screened with 409 AFLP and SSR markers, and a linkage map was constructed based on 367 markers. Several QTLs associated with the studied traits were identified. The effects of each QTL are moderate, ranging from 7% to 37%, but a high percentage of phenotypic variance is explained when considering all the covariants (TR2 mean around 80% in each trait). Although the detected regions need to be more precisely mapped, the information obtained should help in marker-assisted selection.
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Affiliation(s)
- G Rachid Al-Chaarani
- Department of Biotechnology and Plant Breeding BAP, INP-ENSAT, 18 Chemin de Borde Rouge, BP 107, 31326 Castanet, France
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Dussle CM, Hahn V, Knapp SJ, Bauer E. PlArg from Helianthus argophyllus is unlinked to other known downy mildew resistance genes in sunflower. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2004; 109:1083-6. [PMID: 15221147 DOI: 10.1007/s00122-004-1722-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2003] [Accepted: 05/06/2004] [Indexed: 05/04/2023]
Abstract
The PlArg locus in the sunflower (Helianthus annuus L.) inbred line Arg1575-2 conferring resistance to at least four tested races (300, 700, 730, 770) of downy mildew (Plasmopara halstedii) was localized by the use of simple sequence repeat (SSR) markers. Bulked segregant analysis (BSA) was conducted on 126 individuals of an F2 progeny from a cross between a downy mildew susceptible line, CmsHA342, and Arg1575-2. Twelve SSR markers linked to the PlArg locus were identified. All markers were located proximal to PlArg on linkage group LG1 based on the map of Yu et al. (2003) in a window of 9.3 cM. Since PlArg was mapped to a linkage group different from all other Pl genes previously mapped with SSRs, it can be concluded that PlArg provides a new source of resistance against P. halstedii in sunflower.
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Affiliation(s)
- C M Dussle
- State Plant Breeding Institute (720), University of Hohenheim, 70593, Stuttgart, Germany
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