251
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Lin JZ, Ritland K. Construction of a genetic linkage map in the wild plant Mimulus using RAPD and isozyme markers. Genome 2012; 39:63-70. [PMID: 18469878 DOI: 10.1139/g96-009] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
As a first step to mapping quantitative trait loci for mating system differences, a genetic linkage map was generated from an interspecific backcross between Mimulus guttatus and Mimulus platycalyx. The linkage map consists of 99 RAPD and two isozyme markers. Eighty-one of these markers were mapped to 15 linkage groups, spanning 1437 contiguous centiMorgans, and covering 58% of the estimated genome. The genome length of Mimulus is estimated at 2474 +/- 35 cM; bootstrapping indicates that only ca. 40 markers are needed to give an accurate estimate of genome length. Further statistical analyses indicate that many RAPD markers cannot be ordered with certainty and that uncertain linkage groups tend to map nonlinearly even under commonly used mapping functions. Strategies for speeding up the mapping process for a wild species and possible applications of a partial linkage map in evolutionary studies are discussed. Key words : linkage map, mating system, Mimulus, RAPD.
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252
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Jiang C, Lewis ME, Sink KC. Combined RAPD and RFLP molecular linkage map of asparagus. Genome 2012; 40:69-76. [PMID: 18464808 DOI: 10.1139/g97-009] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Two linkage maps of asparagus (Asparagus officinalis L.) were constructed using a double pseudotestcross mapping strategy with restriction fragment length polymorphisms (RFLPs), random amplified polymorphic DNAs (RAPDs), and allozymes as markers in a population generated from crossing MW25 x A19, two heterozygous parents. All data were inverted and combined with the natural data to detect linkages in repulsion phase. Two sets of data, one for each parent, were formed according to the inheritance patterns of the markers. The maternal MW25 map has a total of 163 marker loci placed in 13 linkage groups covering 1281 cM, with an average and a maximum distance between adjacent loci of 7.9 and 29 cM, respectively. The paternal A19 map has 183 marker loci covering 1324 cM in 9 linkage groups, with an average and a maximum distance between two adjacent loci of 7.7 and 29 cM, respectively. Six multiallelic RFLPs segregating in the pattern a/c x b/c and eight heterozygous loci (four RAPDs, and four RFLPs segregating in the pattern a/b x a/b (HZ loci)) were common to both maps. These 14 loci were used as bridges to align homologous groups between the two maps. In this case, RFLPs were more frequent and informative than RAPDs. Nine linkage groups in the MW25 map were homologous to six groups in the A19 map. In two cases, two or more bridge loci were common to a group; thus, the orientation of homologous linkage groups was also determined. In four other cases, only one locus was common to the two homologous groups and the orientation was unknown. Mdh, four RFLPs, and 14 RAPDs were assigned to chromosome L5, which also has the sex locus M.
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253
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Gomez R, Angel F, Bonierbale MW, Rodriguez F, Tohme J, Roca WM. Inheritance of random amplified polymorphic DNA markers in cassava (Manihot esculenta Crantz). Genome 2012; 39:1039-43. [PMID: 18469953 DOI: 10.1139/g96-130] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The informativeness and inheritance of randomly amplified polymorphic DNA (RAPD) markers were investigated in an intraspecific F1 progeny derived from two heterozygous parents. The analysis confirmed the utility of RAPD markers for comparing candidate parents for the development of a molecular genetic map, and provided numerous markers for linkage analysis in a crop with a very limited history of classical or molecular genetic studies. Six potential parental lines (themselves F1 hybrid clones) showed between 1.82 and 0.62 segregating bands per primer in three hybrid families. Forty-three percent (309) of 722 primers produced polymorphic products in the most informative of these three crosses, revealing 328 single-dose (SD) markers segregating 1:1 for presence/absence in a progeny of 90 individuals. A second class of informative markers were those present in both parents but segregating in the progeny. Fifty-seven or 67% of the monomorphic but segregating markers exhibited the 3:1 ratio expected for SD dominant markers in a cross between heterozygotes. Linkage groups were constructed from the segregation of SD RAPD markers originating in the female (TMS 30572) and the male (CM2177-2) parent. Key words : RAPDs, molecular markers, genetic segregation, Manihot, single-dose markers.
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254
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Monclus R, Leplé JC, Bastien C, Bert PF, Villar M, Marron N, Brignolas F, Jorge V. Integrating genome annotation and QTL position to identify candidate genes for productivity, architecture and water-use efficiency in Populus spp. BMC PLANT BIOLOGY 2012. [PMID: 23013168 DOI: 10.15454/easuqv] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
BACKGROUND Hybrid poplars species are candidates for biomass production but breeding efforts are needed to combine productivity and water use efficiency in improved cultivars. The understanding of the genetic architecture of growth in poplar by a Quantitative Trait Loci (QTL) approach can help us to elucidate the molecular basis of such integrative traits but identifying candidate genes underlying these QTLs remains difficult. Nevertheless, the increase of genomic information together with the accessibility to a reference genome sequence (Populus trichocarpa Nisqually-1) allow to bridge QTL information on genetic maps and physical location of candidate genes on the genome. The objective of the study is to identify QTLs controlling productivity, architecture and leaf traits in a P. deltoides x P. trichocarpa F1 progeny and to identify candidate genes underlying QTLs based on the anchoring of genetic maps on the genome and the gene ontology information linked to genome annotation. The strategy to explore genome annotation was to use Gene Ontology enrichment tools to test if some functional categories are statistically over-represented in QTL regions. RESULTS Four leaf traits and 7 growth traits were measured on 330 F1 P. deltoides x P. trichocarpa progeny. A total of 77 QTLs controlling 11 traits were identified explaining from 1.8 to 17.2% of the variation of traits. For 58 QTLs, confidence intervals could be projected on the genome. An extended functional annotation was built based on data retrieved from the plant genome database Phytozome and from an inference of function using homology between Populus and the model plant Arabidopsis. Genes located within QTL confidence intervals were retrieved and enrichments in gene ontology (GO) terms were determined using different methods. Significant enrichments were found for all traits. Particularly relevant biological processes GO terms were identified for QTLs controlling number of sylleptic branches: intervals were enriched in GO terms of biological process like 'ripening' and 'adventitious roots development'. CONCLUSION Beyond the simple identification of QTLs, this study is the first to use a global approach of GO terms enrichment analysis to fully explore gene function under QTLs confidence intervals in plants. This global approach may lead to identification of new candidate genes for traits of interest.
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Affiliation(s)
- Romain Monclus
- UFR-Faculté des Sciences, UPRES EA 1207 Laboratoire de Biologie des Ligneux et des Grandes Cultures, Université d'Orléans, F-45067, Orléans, France
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255
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Monclus R, Leplé JC, Bastien C, Bert PF, Villar M, Marron N, Brignolas F, Jorge V. Integrating genome annotation and QTL position to identify candidate genes for productivity, architecture and water-use efficiency in Populus spp. BMC PLANT BIOLOGY 2012; 12:173. [PMID: 23013168 PMCID: PMC3520807 DOI: 10.1186/1471-2229-12-173] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2012] [Accepted: 09/22/2012] [Indexed: 05/20/2023]
Abstract
BACKGROUND Hybrid poplars species are candidates for biomass production but breeding efforts are needed to combine productivity and water use efficiency in improved cultivars. The understanding of the genetic architecture of growth in poplar by a Quantitative Trait Loci (QTL) approach can help us to elucidate the molecular basis of such integrative traits but identifying candidate genes underlying these QTLs remains difficult. Nevertheless, the increase of genomic information together with the accessibility to a reference genome sequence (Populus trichocarpa Nisqually-1) allow to bridge QTL information on genetic maps and physical location of candidate genes on the genome. The objective of the study is to identify QTLs controlling productivity, architecture and leaf traits in a P. deltoides x P. trichocarpa F1 progeny and to identify candidate genes underlying QTLs based on the anchoring of genetic maps on the genome and the gene ontology information linked to genome annotation. The strategy to explore genome annotation was to use Gene Ontology enrichment tools to test if some functional categories are statistically over-represented in QTL regions. RESULTS Four leaf traits and 7 growth traits were measured on 330 F1 P. deltoides x P. trichocarpa progeny. A total of 77 QTLs controlling 11 traits were identified explaining from 1.8 to 17.2% of the variation of traits. For 58 QTLs, confidence intervals could be projected on the genome. An extended functional annotation was built based on data retrieved from the plant genome database Phytozome and from an inference of function using homology between Populus and the model plant Arabidopsis. Genes located within QTL confidence intervals were retrieved and enrichments in gene ontology (GO) terms were determined using different methods. Significant enrichments were found for all traits. Particularly relevant biological processes GO terms were identified for QTLs controlling number of sylleptic branches: intervals were enriched in GO terms of biological process like 'ripening' and 'adventitious roots development'. CONCLUSION Beyond the simple identification of QTLs, this study is the first to use a global approach of GO terms enrichment analysis to fully explore gene function under QTLs confidence intervals in plants. This global approach may lead to identification of new candidate genes for traits of interest.
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Affiliation(s)
- Romain Monclus
- UFR-Faculté des Sciences, UPRES EA 1207 Laboratoire de Biologie des Ligneux et des Grandes Cultures (LBLGC), Université d'Orléans, F-45067, Orléans, France
| | - Jean-Charles Leplé
- INRA, UR0588 Amélioration Génétique et Physiologie Forestières (AGPF), F-45075, Orléans, France
| | - Catherine Bastien
- INRA, UR0588 Amélioration Génétique et Physiologie Forestières (AGPF), F-45075, Orléans, France
| | - Pierre-François Bert
- INRA, UR0588 Amélioration Génétique et Physiologie Forestières (AGPF), F-45075, Orléans, France
- Present address: INRA, UMR1287 Ecophysiologie et Génomique Fonctionnelle de la Vigne, F-33882, Villenave d'Ornon, France
| | - Marc Villar
- INRA, UR0588 Amélioration Génétique et Physiologie Forestières (AGPF), F-45075, Orléans, France
| | - Nicolas Marron
- INRA, UMR1137 Écologie et Écophysiologie Forestières (EEF), F-54280, Champenoux, France
- Université de Lorraine, UMR 1137, Ecologie et Ecophysiologie Forestières (EEF), Faculté des Sciences, F-54500, Vandœuvre-lès-Nancy, France
| | - Franck Brignolas
- UFR-Faculté des Sciences, UPRES EA 1207 Laboratoire de Biologie des Ligneux et des Grandes Cultures (LBLGC), Université d'Orléans, F-45067, Orléans, France
- INRA, USC1328 Arbres et Réponses aux Contraintes Hydriques et Environnementales (ARCHE), F-45067, Orléans, France
| | - Véronique Jorge
- INRA, UR0588 Amélioration Génétique et Physiologie Forestières (AGPF), F-45075, Orléans, France
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256
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Deschamps S, Llaca V, May GD. Genotyping-by-Sequencing in Plants. BIOLOGY 2012; 1:460-83. [PMID: 24832503 PMCID: PMC4009820 DOI: 10.3390/biology1030460] [Citation(s) in RCA: 152] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/06/2012] [Revised: 08/07/2012] [Accepted: 09/13/2012] [Indexed: 12/12/2022]
Abstract
The advent of next-generation DNA sequencing (NGS) technologies has led to the development of rapid genome-wide Single Nucleotide Polymorphism (SNP) detection applications in various plant species. Recent improvements in sequencing throughput combined with an overall decrease in costs per gigabase of sequence is allowing NGS to be applied to not only the evaluation of small subsets of parental inbred lines, but also the mapping and characterization of traits of interest in much larger populations. Such an approach, where sequences are used simultaneously to detect and score SNPs, therefore bypassing the entire marker assay development stage, is known as genotyping-by-sequencing (GBS). This review will summarize the current state of GBS in plants and the promises it holds as a genome-wide genotyping application.
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Affiliation(s)
- Stéphane Deschamps
- DuPont Agricultural Biotechnology, Experimental Station, PO Box 80353, 200 Powder Mill Road, Wilmington, DE 19880-0353, USA.
| | - Victor Llaca
- DuPont Agricultural Biotechnology, Experimental Station, PO Box 80353, 200 Powder Mill Road, Wilmington, DE 19880-0353, USA.
| | - Gregory D May
- DuPont Pioneer, 7300 NW 62nd Ave., P.O. Box 1004, Johnston, IA 50131-1004, USA.
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257
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Genomic characterization of DArT markers based on high-density linkage analysis and physical mapping to the Eucalyptus genome. PLoS One 2012; 7:e44684. [PMID: 22984541 PMCID: PMC3439404 DOI: 10.1371/journal.pone.0044684] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2012] [Accepted: 08/06/2012] [Indexed: 01/07/2023] Open
Abstract
Diversity Arrays Technology (DArT) provides a robust, high throughput, cost-effective method to query thousands of sequence polymorphisms in a single assay. Despite the extensive use of this genotyping platform for numerous plant species, little is known regarding the sequence attributes and genome-wide distribution of DArT markers. We investigated the genomic properties of the 7,680 DArT marker probes of a Eucalyptus array, by sequencing them, constructing a high density linkage map and carrying out detailed physical mapping analyses to the Eucalyptus grandis reference genome. A consensus linkage map with 2,274 DArT markers anchored to 210 microsatellites and a framework map, with improved support for ordering, displayed extensive collinearity with the genome sequence. Only 1.4 Mbp of the 75 Mbp of still unplaced scaffold sequence was captured by 45 linkage mapped but physically unaligned markers to the 11 main Eucalyptus pseudochromosomes, providing compelling evidence for the quality and completeness of the current Eucalyptus genome assembly. A highly significant correspondence was found between the locations of DArT markers and predicted gene models, while most of the 89 DArT probes unaligned to the genome correspond to sequences likely absent in E. grandis, consistent with the pan-genomic feature of this multi-Eucalyptus species DArT array. These comprehensive linkage-to-physical mapping analyses provide novel data regarding the genomic attributes of DArT markers in plant genomes in general and for Eucalyptus in particular. DArT markers preferentially target the gene space and display a largely homogeneous distribution across the genome, thereby providing superb coverage for mapping and genome-wide applications in breeding and diversity studies. Data reported on these ubiquitous properties of DArT markers will be particularly valuable to researchers working on less-studied crop species who already count on DArT genotyping arrays but for which no reference genome is yet available to allow such detailed characterization.
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258
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Taniguchi F, Furukawa K, Ota-Metoku S, Yamaguchi N, Ujihara T, Kono I, Fukuoka H, Tanaka J. Construction of a high-density reference linkage map of tea (Camellia sinensis). BREEDING SCIENCE 2012; 62:263-73. [PMID: 23226087 PMCID: PMC3501944 DOI: 10.1270/jsbbs.62.263] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2011] [Accepted: 05/14/2012] [Indexed: 05/19/2023]
Abstract
A few linkage maps of tea have been constructed using pseudo-testcross theory based on dominant marker systems. However, dominant markers are not suitable as landmark markers across a wide range of materials. Therefore, we developed co-dominant SSR markers from genomic DNA and ESTs and constructed a reference map using these co-dominant markers as landmarks. A population of 54 F(1) clones derived from reciprocal crosses between 'Sayamakaori' and 'Kana-Ck17' was used for the linkage analysis. Maps of both parents were constructed from the F(1) population that was taken for BC(1) population. The order of most of the dominant markers in the parental maps was consistent. We constructed a core map by merging the linkage data for markers that detected polymorphisms in both parents. The core map contains 15 linkage groups, which corresponds to the basic chromosome number of tea. The total length of the core map is 1218 cM. Here, we present the reference map as a central core map sandwiched between the parental maps for each linkage group; the combined maps contain 441 SSRs, 7 CAPS, 2 STS and 674 RAPDs. This newly constructed linkage map can be used as a basic reference linkage map of tea.
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Affiliation(s)
- Fumiya Taniguchi
- Makurazaki Tea Research Station, NARO Institute of Vegetable and Tea Science, 87 Seto, Makurazaki, Kagoshima 898-0032, Japan
- Graduate School of Life and Environmental Science, University of Tsukuba, 2-1-18 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Kazumi Furukawa
- Makurazaki Tea Research Station, NARO Institute of Vegetable and Tea Science, 87 Seto, Makurazaki, Kagoshima 898-0032, Japan
- Present address: Numazu National College of Technology, 3600 Ooka, Numazu, Shizuoka 410-8501, Japan
| | - Sakura Ota-Metoku
- Makurazaki Tea Research Station, NARO Institute of Vegetable and Tea Science, 87 Seto, Makurazaki, Kagoshima 898-0032, Japan
| | - Nobuo Yamaguchi
- Makurazaki Tea Research Station, NARO Institute of Vegetable and Tea Science, 87 Seto, Makurazaki, Kagoshima 898-0032, Japan
- Present address: Marine Biological Laboratory, Graduate School of Science, Hiroshima University, 2445 Mukaishima, Onomichi, Hiroshima 722-0073, Japan
| | - Tomomi Ujihara
- Kanaya Tea Research Station, NARO Institute of Vegetable and Tea Science, 2769 Kanaya, Shimada, Shizuoka 428-8501, Japan
| | - Izumi Kono
- STAFF-Institute, 446-1 Ippaizuka, Kamiyokoba, Tsukuba, Ibaraki 305-0854, Japan
- Present address: Laboratory of Synaptic Plasticity and Connectivity, RIKEN Brain Science Institute, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Hiroyuki Fukuoka
- NARO Institute of Vegetable and Tea Science, 360 Kusawa, Ano, Tsu, Mie 514-2392, Japan
| | - Junichi Tanaka
- Makurazaki Tea Research Station, NARO Institute of Vegetable and Tea Science, 87 Seto, Makurazaki, Kagoshima 898-0032, Japan
- Graduate School of Life and Environmental Science, University of Tsukuba, 2-1-18 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
- Present address: NARO Institute of Crop Science, 2-1-18 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
- Corresponding author (e-mail: )
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259
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Bodénès C, Chancerel E, Gailing O, Vendramin GG, Bagnoli F, Durand J, Goicoechea PG, Soliani C, Villani F, Mattioni C, Koelewijn HP, Murat F, Salse J, Roussel G, Boury C, Alberto F, Kremer A, Plomion C. Comparative mapping in the Fagaceae and beyond with EST-SSRs. BMC PLANT BIOLOGY 2012; 12:153. [PMID: 22931513 PMCID: PMC3493355 DOI: 10.1186/1471-2229-12-153] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2012] [Accepted: 08/22/2012] [Indexed: 05/02/2023]
Abstract
BACKGROUND Genetic markers and linkage mapping are basic prerequisites for comparative genetic analyses, QTL detection and map-based cloning. A large number of mapping populations have been developed for oak, but few gene-based markers are available for constructing integrated genetic linkage maps and comparing gene order and QTL location across related species. RESULTS We developed a set of 573 expressed sequence tag-derived simple sequence repeats (EST-SSRs) and located 397 markers (EST-SSRs and genomic SSRs) on the 12 oak chromosomes (2n = 2x = 24) on the basis of Mendelian segregation patterns in 5 full-sib mapping pedigrees of two species: Quercus robur (pedunculate oak) and Quercus petraea (sessile oak). Consensus maps for the two species were constructed and aligned. They showed a high degree of macrosynteny between these two sympatric European oaks. We assessed the transferability of EST-SSRs to other Fagaceae genera and a subset of these markers was mapped in Castanea sativa, the European chestnut. Reasonably high levels of macrosynteny were observed between oak and chestnut. We also obtained diversity statistics for a subset of EST-SSRs, to support further population genetic analyses with gene-based markers. Finally, based on the orthologous relationships between the oak, Arabidopsis, grape, poplar, Medicago, and soybean genomes and the paralogous relationships between the 12 oak chromosomes, we propose an evolutionary scenario of the 12 oak chromosomes from the eudicot ancestral karyotype. CONCLUSIONS This study provides map locations for a large set of EST-SSRs in two oak species of recognized biological importance in natural ecosystems. This first step toward the construction of a gene-based linkage map will facilitate the assignment of future genome scaffolds to pseudo-chromosomes. This study also provides an indication of the potential utility of new gene-based markers for population genetics and comparative mapping within and beyond the Fagaceae.
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Affiliation(s)
- Catherine Bodénès
- INRA, UMR1202 BIOGECO, Cestas, F-33610, France
- Université de Bordeaux, UMR1202 BIOGECO, Cestas, F-33610, France
| | - Emilie Chancerel
- INRA, UMR1202 BIOGECO, Cestas, F-33610, France
- Université de Bordeaux, UMR1202 BIOGECO, Cestas, F-33610, France
| | - Oliver Gailing
- Forest Genetics and Forest Tree Breeding Büsgen Institute Faculty of Forest Sciences and Forest Ecology Göttingen University, Büsgenweg 2, 37077, Göttingen, Germany
- New address: School of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI, 49931, USA
| | - Giovanni G Vendramin
- Plant Genetics Institute, National Research Council, Via Madonna del Piano 10, Sesto Fiorentino, FI, 50019, Italy
| | - Francesca Bagnoli
- Plant Protection Institute, National Research Council, Via Madonna del Piano 10, Sesto Fiorentino, FI, 50019, Italy
| | - Jerome Durand
- INRA, UMR1202 BIOGECO, Cestas, F-33610, France
- Université de Bordeaux, UMR1202 BIOGECO, Cestas, F-33610, France
| | - Pablo G Goicoechea
- NEIKER-Tecnalia, Dpto Biotecnologia, PO Box 46, Vitoria-Gasteiz, 01080, Spain
| | - Carolina Soliani
- Unidad de Genética Ecológica y Mejoramiento Forestal, INTA EEA Bariloche, Bariloche, CC277 8400, Argentina
| | - Fiorella Villani
- CNR Istituto di Biologia Agroambientale e Forestale, Porano, TR, 05010, Italy
| | - Claudia Mattioni
- CNR Istituto di Biologia Agroambientale e Forestale, Porano, TR, 05010, Italy
| | | | - Florent Murat
- INRA, UMR1095 GDEC, Clermont-Ferrand, F-63100, France
| | - Jerome Salse
- INRA, UMR1095 GDEC, Clermont-Ferrand, F-63100, France
| | - Guy Roussel
- INRA, UMR1202 BIOGECO, Cestas, F-33610, France
- Université de Bordeaux, UMR1202 BIOGECO, Cestas, F-33610, France
| | - Christophe Boury
- INRA, UMR1202 BIOGECO, Cestas, F-33610, France
- Université de Bordeaux, UMR1202 BIOGECO, Cestas, F-33610, France
| | - Florian Alberto
- INRA, UMR1202 BIOGECO, Cestas, F-33610, France
- Université de Bordeaux, UMR1202 BIOGECO, Cestas, F-33610, France
| | - Antoine Kremer
- INRA, UMR1202 BIOGECO, Cestas, F-33610, France
- Université de Bordeaux, UMR1202 BIOGECO, Cestas, F-33610, France
| | - Christophe Plomion
- INRA, UMR1202 BIOGECO, Cestas, F-33610, France
- Université de Bordeaux, UMR1202 BIOGECO, Cestas, F-33610, France
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260
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Wang N, Fang L, Xin H, Wang L, Li S. Construction of a high-density genetic map for grape using next generation restriction-site associated DNA sequencing. BMC PLANT BIOLOGY 2012; 12:148. [PMID: 22908993 PMCID: PMC3528476 DOI: 10.1186/1471-2229-12-148] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2012] [Accepted: 07/18/2012] [Indexed: 05/18/2023]
Abstract
BACKGROUND Genetic mapping and QTL detection are powerful methodologies in plant improvement and breeding. Construction of a high-density and high-quality genetic map would be of great benefit in the production of superior grapes to meet human demand. High throughput and low cost of the recently developed next generation sequencing (NGS) technology have resulted in its wide application in genome research. Sequencing restriction-site associated DNA (RAD) might be an efficient strategy to simplify genotyping. Combining NGS with RAD has proven to be powerful for single nucleotide polymorphism (SNP) marker development. RESULTS An F1 population of 100 individual plants was developed. In-silico digestion-site prediction was used to select an appropriate restriction enzyme for construction of a RAD sequencing library. Next generation RAD sequencing was applied to genotype the F1 population and its parents. Applying a cluster strategy for SNP modulation, a total of 1,814 high-quality SNP markers were developed: 1,121 of these were mapped to the female genetic map, 759 to the male map, and 1,646 to the integrated map. A comparison of the genetic maps to the published Vitis vinifera genome revealed both conservation and variations. CONCLUSIONS The applicability of next generation RAD sequencing for genotyping a grape F1 population was demonstrated, leading to the successful development of a genetic map with high density and quality using our designed SNP markers. Detailed analysis revealed that this newly developed genetic map can be used for a variety of genome investigations, such as QTL detection, sequence assembly and genome comparison.
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Affiliation(s)
- Nian Wang
- Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Linchuan Fang
- Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- Graduate School of Chinese Academy of Sciences, Beijing, 100049, China
| | - Haiping Xin
- Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Lijun Wang
- Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Shaohua Li
- Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
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261
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Wang N, Fang L, Xin H, Wang L, Li S. Construction of a high-density genetic map for grape using next generation restriction-site associated DNA sequencing. BMC PLANT BIOLOGY 2012. [PMID: 22908993 DOI: 10.1186/1471-2229-12148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
BACKGROUND Genetic mapping and QTL detection are powerful methodologies in plant improvement and breeding. Construction of a high-density and high-quality genetic map would be of great benefit in the production of superior grapes to meet human demand. High throughput and low cost of the recently developed next generation sequencing (NGS) technology have resulted in its wide application in genome research. Sequencing restriction-site associated DNA (RAD) might be an efficient strategy to simplify genotyping. Combining NGS with RAD has proven to be powerful for single nucleotide polymorphism (SNP) marker development. RESULTS An F1 population of 100 individual plants was developed. In-silico digestion-site prediction was used to select an appropriate restriction enzyme for construction of a RAD sequencing library. Next generation RAD sequencing was applied to genotype the F1 population and its parents. Applying a cluster strategy for SNP modulation, a total of 1,814 high-quality SNP markers were developed: 1,121 of these were mapped to the female genetic map, 759 to the male map, and 1,646 to the integrated map. A comparison of the genetic maps to the published Vitis vinifera genome revealed both conservation and variations. CONCLUSIONS The applicability of next generation RAD sequencing for genotyping a grape F1 population was demonstrated, leading to the successful development of a genetic map with high density and quality using our designed SNP markers. Detailed analysis revealed that this newly developed genetic map can be used for a variety of genome investigations, such as QTL detection, sequence assembly and genome comparison.
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Affiliation(s)
- Nian Wang
- Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
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Comparison of the genetic determinism of two key phenological traits, flowering and maturity dates, in three Prunus species: peach, apricot and sweet cherry. Heredity (Edinb) 2012; 109:280-92. [PMID: 22828898 DOI: 10.1038/hdy.2012.38] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
The present study investigates the genetic determinism of flowering and maturity dates, two traits highly affected by global climate change. Flowering and maturity dates were evaluated on five progenies from three Prunus species, peach, apricot and sweet cherry, during 3-8 years. Quantitative trait locus (QTL) detection was performed separately for each year and also by integrating data from all years together. High heritability estimates were obtained for flowering and maturity dates. Several QTLs for flowering and maturity dates were highly stable, detected each year of evaluation, suggesting that they were not affected by climatic variations. For flowering date, major QTLs were detected on linkage groups (LG) 4 for apricot and sweet cherry and on LG6 for peach. QTLs were identified on LG2, LG3, LG4 and LG7 for the three species. For maturity date, a major QTL was detected on LG4 in the three species. Using the peach genome sequence data, candidate genes underlying the major QTLs on LG4 and LG6 were investigated and key genes were identified. Our results provide a basis for the identification of genes involved in flowering and maturity dates that could be used to develop cultivar ideotypes adapted to future climatic conditions.
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263
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Kullan ARK, van Dyk MM, Hefer CA, Jones N, Kanzler A, Myburg AA. Genetic dissection of growth, wood basic density and gene expression in interspecific backcrosses of Eucalyptus grandis and E. urophylla. BMC Genet 2012; 13:60. [PMID: 22817272 PMCID: PMC3416674 DOI: 10.1186/1471-2156-13-60] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2012] [Accepted: 07/20/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND F1 hybrid clones of Eucalyptus grandis and E. urophylla are widely grown for pulp and paper production in tropical and subtropical regions. Volume growth and wood quality are priority objectives in Eucalyptus tree improvement. The molecular basis of quantitative variation and trait expression in eucalypt hybrids, however, remains largely unknown. The recent availability of a draft genome sequence (http://www.phytozome.net) and genome-wide genotyping platforms, combined with high levels of genetic variation and high linkage disequilibrium in hybrid crosses, greatly facilitate the detection of quantitative trait loci (QTLs) as well as underlying candidate genes for growth and wood property traits. In this study, we used Diversity Arrays Technology markers to assess the genetic architecture of volume growth (diameter at breast height, DBH) and wood basic density in four-year-old progeny of an interspecific backcross pedigree of E. grandis and E. urophylla. In addition, we used Illumina RNA-Seq expression profiling in the E. urophylla backcross family to identify cis- and trans-acting polymorphisms (eQTLs) affecting transcript abundance of genes underlying QTLs for wood basic density. RESULTS A total of five QTLs for DBH and 12 for wood basic density were identified in the two backcross families. Individual QTLs for DBH and wood basic density explained 3.1 to 12.2% of phenotypic variation. Candidate genes underlying QTLs for wood basic density on linkage groups 8 and 9 were found to share trans-acting eQTLs located on linkage groups 4 and 10, which in turn coincided with QTLs for wood basic density suggesting that these QTLs represent segregating components of an underlying transcriptional network. CONCLUSION This is the first demonstration of the use of next-generation expression profiling to quantify transcript abundance in a segregating tree population and identify candidate genes potentially affecting wood property variation. The QTLs identified in this study provide a resource for identifying candidate genes and developing molecular markers for marker-assisted breeding of volume growth and wood basic density. Our results suggest that integrated analysis of transcript and trait variation in eucalypt hybrids can be used to dissect the molecular basis of quantitative variation in wood property traits.
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Affiliation(s)
- Anand Raj Kumar Kullan
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0002, South Africa
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Tong C, Zhang B, Li H, Shi J. Model selection for quantitative trait loci mapping in a full-sib family. Genet Mol Biol 2012; 35:622-31. [PMID: 23055802 PMCID: PMC3459413 DOI: 10.1590/s1415-47572012005000044] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2011] [Accepted: 04/21/2012] [Indexed: 11/25/2022] Open
Abstract
Statistical methods for mapping quantitative trait loci (QTLs) in full-sib forest trees, in which the number of alleles and linkage phase can vary from locus to locus, are still not well established. Previous studies assumed that the QTL segregation pattern was fixed throughout the genome in a full-sib family, despite the fact that this pattern can vary among regions of the genome. In this paper, we propose a method for selecting the appropriate model for QTL mapping based on the segregation of different types of markers and QTLs in a full-sib family. The QTL segregation patterns were classified into three types: test cross (1:1 segregation), F2 cross (1:2:1 segregation) and full cross (1:1:1:1 segregation). Akaike’s information criterion (AIC), the Bayesian information criterion (BIC) and the Laplace-empirical criterion (LEC) were used to select the most likely QTL segregation pattern. Simulations were used to evaluate the power of these criteria and the precision of parameter estimates. A Windows-based software was developed to run the selected QTL mapping method. A real example is presented to illustrate QTL mapping in forest trees based on an integrated linkage map with various segregation markers. The implications of this method for accurate QTL mapping in outbred species are discussed.
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Affiliation(s)
- Chunfa Tong
- Key Laboratory of Forest Genetics and Biotechnology of the Ministry of Education, Nanjing Forestry University, Nanjing, China
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265
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Bushakra JM, Stephens MJ, Atmadjaja AN, Lewers KS, Symonds VV, Udall JA, Chagné D, Buck EJ, Gardiner SE. Construction of black (Rubus occidentalis) and red (R. idaeus) raspberry linkage maps and their comparison to the genomes of strawberry, apple, and peach. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2012; 125:311-27. [PMID: 22398438 DOI: 10.1007/s00122-012-1835-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2011] [Accepted: 02/17/2012] [Indexed: 05/23/2023]
Abstract
The genus Rubus belongs to the Rosaceae and is comprised of 600-800 species distributed world-wide. To date, genetic maps of the genus consist largely of non-transferable markers such as amplified fragment length polymorphisms. An F(1) population developed from a cross between an advanced breeding selection of Rubus occidentalis (96395S1) and R. idaeus 'Latham' was used to construct a new genetic map consisting of DNA sequence-based markers. The genetic linkage maps presented here are constructed of 131 markers on at least one of the two parental maps. The majority of the markers are orthologous, including 14 Rosaceae conserved orthologous set markers, and 60 new gene-based markers developed for raspberry. Thirty-four published raspberry simple sequence repeat markers were used to align the new maps to published raspberry maps. The 96395S1 genetic map consists of six linkage groups (LG) and covers 309 cM with an average of 10 cM between markers; the 'Latham' genetic map consists of seven LG and covers 561 cM with an average of 5 cM between markers. We used BLAST analysis to align the orthologous sequences used to design primer pairs for Rubus genetic mapping with the genome sequences of Fragaria vesca 'Hawaii 4', Malus × domestica 'Golden Delicious', and Prunus 'Lovell'. The alignment of the orthologous markers designed here suggests that the genomes of Rubus and Fragaria have a high degree of synteny and that synteny decreases with phylogenetic distance. Our results give unprecedented insights into the genome evolution of raspberry from the putative ancestral genome of the single ancestor common to Rosaceae.
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Affiliation(s)
- J M Bushakra
- The New Zealand Institute for Plant & Food Research Limited, Batchelar Road, Private Bag 11600, Palmerston North 4442, New Zealand.
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Palhares AC, Rodrigues-Morais TB, Van Sluys MA, Domingues DS, Maccheroni W, Jordão H, Souza AP, Marconi TG, Mollinari M, Gazaffi R, Garcia AAF, Vieira MLC. A novel linkage map of sugarcane with evidence for clustering of retrotransposon-based markers. BMC Genet 2012; 13:51. [PMID: 22742069 PMCID: PMC3443450 DOI: 10.1186/1471-2156-13-51] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2012] [Accepted: 06/13/2012] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND The development of sugarcane as a sustainable crop has unlimited applications. The crop is one of the most economically viable for renewable energy production, and CO2 balance. Linkage maps are valuable tools for understanding genetic and genomic organization, particularly in sugarcane due to its complex polyploid genome of multispecific origins. The overall objective of our study was to construct a novel sugarcane linkage map, compiling AFLP and EST-SSR markers, and to generate data on the distribution of markers anchored to sequences of scIvana_1, a complete sugarcane transposable element, and member of the Copia superfamily. RESULTS The mapping population parents ('IAC66-6' and 'TUC71-7') contributed equally to polymorphisms, independent of marker type, and generated markers that were distributed into nearly the same number of co-segregation groups (or CGs). Bi-parentally inherited alleles provided the integration of 19 CGs. The marker number per CG ranged from two to 39. The total map length was 4,843.19 cM, with a marker density of 8.87 cM. Markers were assembled into 92 CGs that ranged in length from 1.14 to 404.72 cM, with an estimated average length of 52.64 cM. The greatest distance between two adjacent markers was 48.25 cM. The scIvana_1-based markers (56) were positioned on 21 CGs, but were not regularly distributed. Interestingly, the distance between adjacent scIvana_1-based markers was less than 5 cM, and was observed on five CGs, suggesting a clustered organization. CONCLUSIONS Results indicated the use of a NBS-profiling technique was efficient to develop retrotransposon-based markers in sugarcane. The simultaneous maximum-likelihood estimates of linkage and linkage phase based strategies confirmed the suitability of its approach to estimate linkage, and construct the linkage map. Interestingly, using our genetic data it was possible to calculate the number of retrotransposon scIvana_1 (~60) copies in the sugarcane genome, confirming previously reported molecular results. In addition, this research possibly will have indirect implications in crop economics e.g., productivity enhancement via QTL studies, as the mapping population parents differ in response to an important fungal disease.
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Affiliation(s)
- Alessandra C Palhares
- Departamento de Genética, Escola Superior de Agricultura “Luiz de Queiroz”, Universidade de São Paulo, 13418-900, Piracicaba, Brazil
| | - Taislene B Rodrigues-Morais
- Departamento de Genética, Escola Superior de Agricultura “Luiz de Queiroz”, Universidade de São Paulo, 13418-900, Piracicaba, Brazil
| | - Marie-Anne Van Sluys
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, 05508-090, São Paulo, Brazil
| | - Douglas S Domingues
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, 05508-090, São Paulo, Brazil
- Present address: Laboratório de Biotecnologia Vegetal, Instituto Agronômico do Paraná, 86047-902, Londrina, Brazil
| | - Walter Maccheroni
- CanaVialis/Monsanto Co, Condomínio Techno Park, 13069-380, Campinas, Brazil
- Present address: Companhia Vale do Rio Doce, 20020-900, Rio de Janeiro, Brazil
| | - Hamilton Jordão
- CanaVialis/Monsanto Co, Condomínio Techno Park, 13069-380, Campinas, Brazil
- Present address: Companhia Vale do Rio Doce, 20020-900, Rio de Janeiro, Brazil
| | - Anete P Souza
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, 13083-875, Campinas, Brazil
| | - Thiago G Marconi
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, 13083-875, Campinas, Brazil
| | - Marcelo Mollinari
- Departamento de Genética, Escola Superior de Agricultura “Luiz de Queiroz”, Universidade de São Paulo, 13418-900, Piracicaba, Brazil
| | - Rodrigo Gazaffi
- Departamento de Genética, Escola Superior de Agricultura “Luiz de Queiroz”, Universidade de São Paulo, 13418-900, Piracicaba, Brazil
| | - Antonio Augusto F Garcia
- Departamento de Genética, Escola Superior de Agricultura “Luiz de Queiroz”, Universidade de São Paulo, 13418-900, Piracicaba, Brazil
| | - Maria Lucia Carneiro Vieira
- Departamento de Genética, Escola Superior de Agricultura “Luiz de Queiroz”, Universidade de São Paulo, 13418-900, Piracicaba, Brazil
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Hudson CJ, Freeman JS, Kullan ARK, Petroli CD, Sansaloni CP, Kilian A, Detering F, Grattapaglia D, Potts BM, Myburg AA, Vaillancourt RE. A reference linkage map for Eucalyptus. BMC Genomics 2012; 13:240. [PMID: 22702473 PMCID: PMC3436727 DOI: 10.1186/1471-2164-13-240] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2012] [Accepted: 06/04/2012] [Indexed: 01/26/2023] Open
Abstract
Background Genetic linkage maps are invaluable resources in plant research. They provide a key tool for many genetic applications including: mapping quantitative trait loci (QTL); comparative mapping; identifying unlinked (i.e. independent) DNA markers for fingerprinting, population genetics and phylogenetics; assisting genome sequence assembly; relating physical and recombination distances along the genome and map-based cloning of genes. Eucalypts are the dominant tree species in most Australian ecosystems and of economic importance globally as plantation trees. The genome sequence of E. grandis has recently been released providing unprecedented opportunities for genetic and genomic research in the genus. A robust reference linkage map containing sequence-based molecular markers is needed to capitalise on this resource. Several high density linkage maps have recently been constructed for the main commercial forestry species in the genus (E. grandis, E. urophylla and E. globulus) using sequenced Diversity Arrays Technology (DArT) and microsatellite markers. To provide a single reference linkage map for eucalypts a composite map was produced through the integration of data from seven independent mapping experiments (1950 individuals) using a marker-merging method. Results The composite map totalled 1107 cM and contained 4101 markers; comprising 3880 DArT, 213 microsatellite and eight candidate genes. Eighty-one DArT markers were mapped to two or more linkage groups, resulting in the 4101 markers being mapped to 4191 map positions. Approximately 13% of DArT markers mapped to identical map positions, thus the composite map contained 3634 unique loci at an average interval of 0.31 cM. Conclusion The composite map represents the most saturated linkage map yet produced in Eucalyptus. As the majority of DArT markers contained on the map have been sequenced, the map provides a direct link to the E. grandis genome sequence and will serve as an important reference for progressing eucalypt research.
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Affiliation(s)
- Corey J Hudson
- School of Plant Science and CRC for Forestry, University of Tasmania, Private Bag 55 Hobart, Tasmania, 7001, Australia.
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268
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Zuriaga E, Molina L, Badenes ML, Romero C. Physical mapping of a pollen modifier locus controlling self-incompatibility in apricot and synteny analysis within the Rosaceae. PLANT MOLECULAR BIOLOGY 2012; 79:229-242. [PMID: 22481163 DOI: 10.1007/s11103-012-9908-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2011] [Accepted: 03/23/2012] [Indexed: 05/31/2023]
Abstract
S-locus products (S-RNase and F-box proteins) are essential for the gametophytic self-incompatibility (GSI) specific recognition in Prunus. However, accumulated genetic evidence suggests that other S-locus unlinked factors are also required for GSI. For instance, GSI breakdown was associated with a pollen-part mutation unlinked to the S-locus in the apricot (Prunus armeniaca L.) cv. 'Canino'. Fine-mapping of this mutated modifier gene (M-locus) and the synteny analysis of the M-locus within the Rosaceae are here reported. A segregation distortion loci mapping strategy, based on a selectively genotyped population, was used to map the M-locus. In addition, a bacterial artificial chromosome (BAC) contig was constructed for this region using overlapping oligonucleotides probes, and BAC-end sequences (BES) were blasted against Rosaceae genomes to perform micro-synteny analysis. The M-locus was mapped to the distal part of chr.3 flanked by two SSR markers within an interval of 1.8 cM corresponding to ~364 Kb in the peach (Prunus persica L. Batsch) genome. In the integrated genetic-physical map of this region, BES were mapped against the peach scaffold_3 and BACs were anchored to the apricot map. Micro-syntenic blocks were detected in apple (Malus × domestica Borkh.) LG17/9 and strawberry (Fragaria vesca L.) FG6 chromosomes. The M-locus fine-scale mapping provides a solid basis for self-compatibility marker-assisted selection and for positional cloning of the underlying gene, a necessary goal to elucidate the pollen rejection mechanism in Prunus. In a wider context, the syntenic regions identified in peach, apple and strawberry might be useful to interpret GSI evolution in Rosaceae.
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Affiliation(s)
- Elena Zuriaga
- Instituto Valenciano de Investigaciones Agrarias-IVIA, Apartado Oficial, 46113 Moncada, Valencia, Spain.
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Zorrilla-Fontanesi Y, Rambla JL, Cabeza A, Medina JJ, Sánchez-Sevilla JF, Valpuesta V, Botella MA, Granell A, Amaya I. Genetic analysis of strawberry fruit aroma and identification of O-methyltransferase FaOMT as the locus controlling natural variation in mesifurane content. PLANT PHYSIOLOGY 2012; 159:851-70. [PMID: 22474217 PMCID: PMC3375946 DOI: 10.1104/pp.111.188318] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2011] [Accepted: 04/02/2012] [Indexed: 05/18/2023]
Abstract
Improvement of strawberry (Fragaria × ananassa) fruit flavor is an important goal in breeding programs. To investigate genetic factors controlling this complex trait, a strawberry mapping population derived from genotype '1392', selected for its superior flavor, and '232' was profiled for volatile compounds over 4 years by headspace solid phase microextraction coupled to gas chromatography and mass spectrometry. More than 300 volatile compounds were detected, of which 87 were identified by comparison of mass spectrum and retention time to those of pure standards. Parental line '1392' displayed higher volatile levels than '232', and these and many other compounds with similar levels in both parents segregated in the progeny. Cluster analysis grouped the volatiles into distinct chemically related families and revealed a complex metabolic network underlying volatile production in strawberry fruit. Quantitative trait loci (QTL) detection was carried out over 3 years based on a double pseudo-testcross strategy. Seventy QTLs covering 48 different volatiles were detected, with several of them being stable over time and mapped as major QTLs. Loci controlling γ-decalactone and mesifurane content were mapped as qualitative traits. Using a candidate gene approach we have assigned genes that are likely responsible for several of the QTLs. As a proof of concept we show that one homoeolog of the O-methyltransferase gene (FaOMT) is the locus responsible for the natural variation of mesifurane content. Sequence analysis identified 30 bp in the promoter of this FaOMT homoeolog containing putative binding sites for basic/helix-loop-helix, MYB, and BZIP transcription factors. This polymorphism fully cosegregates with both the presence of mesifurane and the high expression of FaOMT during ripening.
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Affiliation(s)
- Yasmín Zorrilla-Fontanesi
- Instituto Andaluz de Investigación y Formación Agraria y Pesquera, Centro de Churriana, 29140 Málaga, Spain (Y.Z.-F., A.C., J.S.-S., I.A); Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia 46022 Valencia, Spain (J.L.R., A.G.); Instituto Andaluz de Investigación y Formación Agraria y Pesquera, Centro las Torres, Alcalá del Río, Sevilla, Spain (J.-J.M.); and Departmento de Biología Molecular y Bioquímica, Instituto de Hortofruticultura Subtropical y Mediterránea, Consejo Superior de Investigaciones Científicas-Universidad de Málaga 29071 Málaga, Spain (V.V., M.A.B.)
| | - José-Luis Rambla
- Instituto Andaluz de Investigación y Formación Agraria y Pesquera, Centro de Churriana, 29140 Málaga, Spain (Y.Z.-F., A.C., J.S.-S., I.A); Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia 46022 Valencia, Spain (J.L.R., A.G.); Instituto Andaluz de Investigación y Formación Agraria y Pesquera, Centro las Torres, Alcalá del Río, Sevilla, Spain (J.-J.M.); and Departmento de Biología Molecular y Bioquímica, Instituto de Hortofruticultura Subtropical y Mediterránea, Consejo Superior de Investigaciones Científicas-Universidad de Málaga 29071 Málaga, Spain (V.V., M.A.B.)
| | - Amalia Cabeza
- Instituto Andaluz de Investigación y Formación Agraria y Pesquera, Centro de Churriana, 29140 Málaga, Spain (Y.Z.-F., A.C., J.S.-S., I.A); Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia 46022 Valencia, Spain (J.L.R., A.G.); Instituto Andaluz de Investigación y Formación Agraria y Pesquera, Centro las Torres, Alcalá del Río, Sevilla, Spain (J.-J.M.); and Departmento de Biología Molecular y Bioquímica, Instituto de Hortofruticultura Subtropical y Mediterránea, Consejo Superior de Investigaciones Científicas-Universidad de Málaga 29071 Málaga, Spain (V.V., M.A.B.)
| | - Juan J. Medina
- Instituto Andaluz de Investigación y Formación Agraria y Pesquera, Centro de Churriana, 29140 Málaga, Spain (Y.Z.-F., A.C., J.S.-S., I.A); Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia 46022 Valencia, Spain (J.L.R., A.G.); Instituto Andaluz de Investigación y Formación Agraria y Pesquera, Centro las Torres, Alcalá del Río, Sevilla, Spain (J.-J.M.); and Departmento de Biología Molecular y Bioquímica, Instituto de Hortofruticultura Subtropical y Mediterránea, Consejo Superior de Investigaciones Científicas-Universidad de Málaga 29071 Málaga, Spain (V.V., M.A.B.)
| | - José F. Sánchez-Sevilla
- Instituto Andaluz de Investigación y Formación Agraria y Pesquera, Centro de Churriana, 29140 Málaga, Spain (Y.Z.-F., A.C., J.S.-S., I.A); Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia 46022 Valencia, Spain (J.L.R., A.G.); Instituto Andaluz de Investigación y Formación Agraria y Pesquera, Centro las Torres, Alcalá del Río, Sevilla, Spain (J.-J.M.); and Departmento de Biología Molecular y Bioquímica, Instituto de Hortofruticultura Subtropical y Mediterránea, Consejo Superior de Investigaciones Científicas-Universidad de Málaga 29071 Málaga, Spain (V.V., M.A.B.)
| | - Victoriano Valpuesta
- Instituto Andaluz de Investigación y Formación Agraria y Pesquera, Centro de Churriana, 29140 Málaga, Spain (Y.Z.-F., A.C., J.S.-S., I.A); Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia 46022 Valencia, Spain (J.L.R., A.G.); Instituto Andaluz de Investigación y Formación Agraria y Pesquera, Centro las Torres, Alcalá del Río, Sevilla, Spain (J.-J.M.); and Departmento de Biología Molecular y Bioquímica, Instituto de Hortofruticultura Subtropical y Mediterránea, Consejo Superior de Investigaciones Científicas-Universidad de Málaga 29071 Málaga, Spain (V.V., M.A.B.)
| | - Miguel A. Botella
- Instituto Andaluz de Investigación y Formación Agraria y Pesquera, Centro de Churriana, 29140 Málaga, Spain (Y.Z.-F., A.C., J.S.-S., I.A); Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia 46022 Valencia, Spain (J.L.R., A.G.); Instituto Andaluz de Investigación y Formación Agraria y Pesquera, Centro las Torres, Alcalá del Río, Sevilla, Spain (J.-J.M.); and Departmento de Biología Molecular y Bioquímica, Instituto de Hortofruticultura Subtropical y Mediterránea, Consejo Superior de Investigaciones Científicas-Universidad de Málaga 29071 Málaga, Spain (V.V., M.A.B.)
| | - Antonio Granell
- Instituto Andaluz de Investigación y Formación Agraria y Pesquera, Centro de Churriana, 29140 Málaga, Spain (Y.Z.-F., A.C., J.S.-S., I.A); Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia 46022 Valencia, Spain (J.L.R., A.G.); Instituto Andaluz de Investigación y Formación Agraria y Pesquera, Centro las Torres, Alcalá del Río, Sevilla, Spain (J.-J.M.); and Departmento de Biología Molecular y Bioquímica, Instituto de Hortofruticultura Subtropical y Mediterránea, Consejo Superior de Investigaciones Científicas-Universidad de Málaga 29071 Málaga, Spain (V.V., M.A.B.)
| | - Iraida Amaya
- Instituto Andaluz de Investigación y Formación Agraria y Pesquera, Centro de Churriana, 29140 Málaga, Spain (Y.Z.-F., A.C., J.S.-S., I.A); Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia 46022 Valencia, Spain (J.L.R., A.G.); Instituto Andaluz de Investigación y Formación Agraria y Pesquera, Centro las Torres, Alcalá del Río, Sevilla, Spain (J.-J.M.); and Departmento de Biología Molecular y Bioquímica, Instituto de Hortofruticultura Subtropical y Mediterránea, Consejo Superior de Investigaciones Científicas-Universidad de Málaga 29071 Málaga, Spain (V.V., M.A.B.)
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Kim C, Zhang D, Auckland SA, Rainville LK, Jakob K, Kronmiller B, Sacks EJ, Deuter M, Paterson AH. SSR-based genetic maps of Miscanthus sinensis and M. sacchariflorus, and their comparison to sorghum. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2012; 124:1325-38. [PMID: 22274765 DOI: 10.1007/s00122-012-1790-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2011] [Accepted: 01/11/2012] [Indexed: 05/07/2023]
Abstract
We present SSR-based genetic maps from a cross between Miscanthus sacchariflorus Robustus and M. sinensis, the progenitors of the promising cellulosic biofuel feedstock Miscanthus × giganteus. cDNA-derived SSR markers were mapped by the two-way pseudo-testcross model due to the high heterozygosity of each parental species. A total of 261 loci were mapped in M. sacchariflorus, spanning 40 linkage groups and 1,998.8 cM, covering an estimated 72.7% of the genome. For M. sinensis, a total of 303 loci were mapped, forming 23 linkage groups and 2,238.3 cM, covering 84.9% of the genome. The use of cDNA-derived SSR loci permitted alignment of the Miscanthus linkage groups to the sorghum chromosomes, revealing a whole genome duplication affecting the Miscanthus lineage after the divergence of subtribes Sorghinae and Saccharinae, as well as traces of the pan-cereal whole genome duplication. While the present maps provide for many early research needs in this emerging crop, additional markers are also needed to improve map density and to further characterize the structural changes of the Miscanthus genome since its divergence from sorghum and Saccharum.
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Affiliation(s)
- Changsoo Kim
- Plant Genome Mapping Laboratory, University of Georgia, 111 Riverbend Road, Rm 228, Athens, GA 30602, USA
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271
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Li J, Lindqvist-Kreuze H, Tian Z, Liu J, Song B, Landeo J, Portal L, Gastelo M, Frisancho J, Sanchez L, Meijer D, Xie C, Bonierbale M. Conditional QTL underlying resistance to late blight in a diploid potato population. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2012; 124:1339-1350. [PMID: 22274766 DOI: 10.1007/s00122-012-1791-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2011] [Accepted: 01/11/2012] [Indexed: 05/31/2023]
Abstract
A large number of quantitative trait loci (QTL) for resistance to late blight of potato have been reported with a "conventional" method in which each phenotypic trait reflects the cumulative genetic effects for the duration of the disease process. However, as genes controlling response to disease may have unique contributions with specific temporal features, it is important to consider the phenotype as dynamic. Here, using the net genetic effects evidenced at consecutive time points during disease development, we report the first conditional mapping of QTL underlying late blight resistance in potato under five environments in Peru. Six conditional QTL were mapped, one each on chromosome 2, 7 and 12 and three on chromosome 9. These QTL represent distinct contributions to the phenotypic variation at different stages of disease development. By comparison, when conventional mapping was conducted, only one QTL was detected on chromosome 9. This QTL was the same as one of the conditional QTL. The results imply that conditional QTL reflect genes that function at particular stages during the host-pathogen interaction. The dynamics revealed by conditional QTL mapping could contribute to the understanding of the molecular mechanism of late blight resistance and these QTL could be used to target genes for marker development or manipulation to improve resistance.
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Affiliation(s)
- Jingcai Li
- Key Laboratory of Horticultural Plant Biology, Huazhong Agricultural University, Ministry of Education, National Center for Vegetable Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, People's Republic of China
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272
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Wang W, Tian Y, Kong J, Li X, Liu X, Yang C. Integration genetic linkage map construction and several potential QTLs mapping of Chinese shrimp (Fenneropenaeus chinensis) based on three types of molecular markers. RUSS J GENET+ 2012. [DOI: 10.1134/s102279541204014x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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273
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Yang X, Lv Y, Pang X, Tong C, Wang Z, Li X, Feng S, Tobias CM, Wu R. A unifying framework for bivalent multilocus linkage analysis of allotetraploids. Brief Bioinform 2012; 14:96-108. [DOI: 10.1093/bib/bbs011] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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274
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Pauly L, Flajoulot S, Garon J, Julier B, Béguier V, Barre P. Detection of favorable alleles for plant height and crown rust tolerance in three connected populations of perennial ryegrass (Lolium perenne L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2012; 124:1139-1153. [PMID: 22234605 DOI: 10.1007/s00122-011-1775-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2011] [Accepted: 12/15/2011] [Indexed: 05/31/2023]
Abstract
Plant height, which is an estimator of vegetative yield, and crown rust tolerance are major criteria for perennial ryegrass breeding. Genetic improvement has been achieved through phenotypic selection but it should be speeded up using marker-assisted selection, especially in this heterozygous species suffering from inbreeding depression. Using connected multiparental populations should increase the diversity studied and could substantially increase the power of quantitative trait loci (QTL) detection. The objective of this study was to detect the best alleles for plant height and rust tolerance among three connected populations derived from elite material by comparing an analysis per parent and a multipopulation connected analysis. For the studied traits, 17 QTL were detected with the analysis per parent while the additive and dominance models of the multipopulation connected analysis made it possible to detect 33 and 21 QTL, respectively. Favorable alleles have been detected in all parents. Only a few dominance effects were detected and they generally had lower values than the additive effects. The additive model of the multipopulation connected analysis was the most powerful as it made it possible to detect most of the QTL identified in the other analyses and 11 additional QTL. Using this model, plant growth QTL and rust tolerance QTL explained up to 19 and 38.6% of phenotypic variance, respectively. This example involving three connected populations is promising for an application on polycross progenies, traditionally used in breeding programs. Indeed, polycross progenies actually are a set of several connected populations.
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Affiliation(s)
- Laurence Pauly
- Jouffray-Drillaud, Station expérimentale La Litière, 86 600, Saint Sauvant, France.
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275
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Ma XF, Jensen E, Alexandrov N, Troukhan M, Zhang L, Thomas-Jones S, Farrar K, Clifton-Brown J, Donnison I, Swaller T, Flavell R. High resolution genetic mapping by genome sequencing reveals genome duplication and tetraploid genetic structure of the diploid Miscanthus sinensis. PLoS One 2012; 7:e33821. [PMID: 22439001 PMCID: PMC3306302 DOI: 10.1371/journal.pone.0033821] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2011] [Accepted: 02/17/2012] [Indexed: 11/19/2022] Open
Abstract
We have created a high-resolution linkage map of Miscanthus sinensis, using genotyping-by-sequencing (GBS), identifying all 19 linkage groups for the first time. The result is technically significant since Miscanthus has a very large and highly heterozygous genome, but has no or limited genomics information to date. The composite linkage map containing markers from both parental linkage maps is composed of 3,745 SNP markers spanning 2,396 cM on 19 linkage groups with a 0.64 cM average resolution. Comparative genomics analyses of the M. sinensis composite linkage map to the genomes of sorghum, maize, rice, and Brachypodium distachyon indicate that sorghum has the closest syntenic relationship to Miscanthus compared to other species. The comparative results revealed that each pair of the 19 M. sinensis linkages aligned to one sorghum chromosome, except for LG8, which mapped to two sorghum chromosomes (4 and 7), presumably due to a chromosome fusion event after genome duplication. The data also revealed several other chromosome rearrangements relative to sorghum, including two telomere-centromere inversions of the sorghum syntenic chromosome 7 in LG8 of M. sinensis and two paracentric inversions of sorghum syntenic chromosome 4 in LG7 and LG8 of M. sinensis. The results clearly demonstrate, for the first time, that the diploid M. sinensis is tetraploid origin consisting of two sub-genomes. This complete and high resolution composite linkage map will not only serve as a useful resource for novel QTL discoveries, but also enable informed deployment of the wealth of existing genomics resources of other species to the improvement of Miscanthus as a high biomass energy crop. In addition, it has utility as a reference for genome sequence assembly for the forthcoming whole genome sequencing of the Miscanthus genus.
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Affiliation(s)
- Xue-Feng Ma
- Ceres, Inc., Thousand Oaks, California, United States of America
| | - Elaine Jensen
- Institute of Biological, Environmental & Rural Sciences (IBERS), Aberystwyth University, Gogerddan, United Kingdom
| | | | - Maxim Troukhan
- Ceres, Inc., Thousand Oaks, California, United States of America
| | - Liping Zhang
- Ceres, Inc., Thousand Oaks, California, United States of America
| | - Sian Thomas-Jones
- Institute of Biological, Environmental & Rural Sciences (IBERS), Aberystwyth University, Gogerddan, United Kingdom
| | - Kerrie Farrar
- Institute of Biological, Environmental & Rural Sciences (IBERS), Aberystwyth University, Gogerddan, United Kingdom
| | - John Clifton-Brown
- Institute of Biological, Environmental & Rural Sciences (IBERS), Aberystwyth University, Gogerddan, United Kingdom
| | - Iain Donnison
- Institute of Biological, Environmental & Rural Sciences (IBERS), Aberystwyth University, Gogerddan, United Kingdom
| | - Timothy Swaller
- Ceres, Inc., Thousand Oaks, California, United States of America
- * E-mail:
| | - Richard Flavell
- Ceres, Inc., Thousand Oaks, California, United States of America
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276
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Pastina MM, Malosetti M, Gazaffi R, Mollinari M, Margarido GRA, Oliveira KM, Pinto LR, Souza AP, van Eeuwijk FA, Garcia AAF. A mixed model QTL analysis for sugarcane multiple-harvest-location trial data. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2012; 124:835-49. [PMID: 22159754 PMCID: PMC3284670 DOI: 10.1007/s00122-011-1748-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2010] [Accepted: 10/28/2011] [Indexed: 05/05/2023]
Abstract
Sugarcane-breeding programs take at least 12 years to develop new commercial cultivars. Molecular markers offer a possibility to study the genetic architecture of quantitative traits in sugarcane, and they may be used in marker-assisted selection to speed up artificial selection. Although the performance of sugarcane progenies in breeding programs are commonly evaluated across a range of locations and harvest years, many of the QTL detection methods ignore two- and three-way interactions between QTL, harvest, and location. In this work, a strategy for QTL detection in multi-harvest-location trial data, based on interval mapping and mixed models, is proposed and applied to map QTL effects on a segregating progeny from a biparental cross of pre-commercial Brazilian cultivars, evaluated at two locations and three consecutive harvest years for cane yield (tonnes per hectare), sugar yield (tonnes per hectare), fiber percent, and sucrose content. In the mixed model, we have included appropriate (co)variance structures for modeling heterogeneity and correlation of genetic effects and non-genetic residual effects. Forty-six QTLs were found: 13 QTLs for cane yield, 14 for sugar yield, 11 for fiber percent, and 8 for sucrose content. In addition, QTL by harvest, QTL by location, and QTL by harvest by location interaction effects were significant for all evaluated traits (30 QTLs showed some interaction, and 16 none). Our results contribute to a better understanding of the genetic architecture of complex traits related to biomass production and sucrose content in sugarcane.
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Affiliation(s)
- M. M. Pastina
- Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz (ESALQ), Universidade de São Paulo (USP), CP 83, 13400-970 Piracicaba, SP Brazil
| | - M. Malosetti
- Biometris, Wageningen University, P.O. Box 100, 6700 AC Wageningen, The Netherlands
| | - R. Gazaffi
- Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz (ESALQ), Universidade de São Paulo (USP), CP 83, 13400-970 Piracicaba, SP Brazil
| | - M. Mollinari
- Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz (ESALQ), Universidade de São Paulo (USP), CP 83, 13400-970 Piracicaba, SP Brazil
| | - G. R. A. Margarido
- Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz (ESALQ), Universidade de São Paulo (USP), CP 83, 13400-970 Piracicaba, SP Brazil
| | - K. M. Oliveira
- Centro de Tecnologia Canavieira (CTC), CP 162, 13400-970 Piracicaba-SP, Brazil
| | - L. R. Pinto
- Centro Avançado da Pesquisa Tecnológica do Agronegócio de Cana, IAC/Apta, CP 206, 14001-970 Ribeirão Preto, SP Brazil
| | - A. P. Souza
- Centro de Biologia Molecular e Engenharia Genética (CBMEG), Departamento de Genética e Evolução, Universidade Estadual de Campinas (UNICAMP), Cidade Universitária Zeferino Vaz, CP 6010, 13083-875 Campinas, SP Brazil
| | - F. A. van Eeuwijk
- Biometris, Wageningen University, P.O. Box 100, 6700 AC Wageningen, The Netherlands
| | - A. A. F. Garcia
- Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz (ESALQ), Universidade de São Paulo (USP), CP 83, 13400-970 Piracicaba, SP Brazil
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277
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Macedo SE, Moretzsohn MC, M Leal-Bertioli SC, Alves DM, Gouvea EG, Azevedo VC, Bertioli DJ. Development and characterization of highly polymorphic long TC repeat microsatellite markers for genetic analysis of peanut. BMC Res Notes 2012; 5:86. [PMID: 22305491 PMCID: PMC3296580 DOI: 10.1186/1756-0500-5-86] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2011] [Accepted: 02/03/2012] [Indexed: 11/12/2022] Open
Abstract
Background Peanut (Arachis hypogaea L.) is a crop of economic and social importance, mainly in tropical areas, and developing countries. Its molecular breeding has been hindered by a shortage of polymorphic genetic markers due to a very narrow genetic base. Microsatellites (SSRs) are markers of choice in peanut because they are co-dominant, highly transferrable between species and easily applicable in the allotetraploid genome. In spite of substantial effort over the last few years by a number of research groups, the number of SSRs that are polymorphic for A. hypogaea is still limiting for routine application, creating the demand for the discovery of more markers polymorphic within cultivated germplasm. Findings A plasmid genomic library enriched for TC/AG repeats was constructed and 1401 clones sequenced. From the sequences obtained 146 primer pairs flanking mostly TC microsatellites were developed. The average number of repeat motifs amplified was 23. These 146 markers were characterized on 22 genotypes of cultivated peanut. In total 78 of the markers were polymorphic within cultivated germplasm. Most of those 78 markers were highly informative with an average of 5.4 alleles per locus being amplified. Average gene diversity index (GD) was 0.6, and 66 markers showed a GD of more than 0.5. Genetic relationship analysis was performed and corroborated the current taxonomical classification of A. hypogaea subspecies and varieties. Conclusions The microsatellite markers described here are a useful resource for genetics and genomics in Arachis. In particular, the 66 markers that are highly polymorphic in cultivated peanut are a significant step towards routine genetic mapping and marker-assisted selection for the crop.
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Affiliation(s)
- Selma E Macedo
- Institute of Biological Sciences, Campus Darcy Ribeiro, University of Brasilia, CEP 70,910-900 Brasília, DF, Brazil.
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278
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Kim C, Zhang D, Auckland SA, Rainville LK, Jakob K, Kronmiller B, Sacks EJ, Deuter M, Paterson AH. SSR-based genetic maps of Miscanthus sinensis and M. sacchariflorus, and their comparison to sorghum. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2012. [PMID: 22274765 DOI: 10.1007/s00122‐012‐1790‐1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We present SSR-based genetic maps from a cross between Miscanthus sacchariflorus Robustus and M. sinensis, the progenitors of the promising cellulosic biofuel feedstock Miscanthus × giganteus. cDNA-derived SSR markers were mapped by the two-way pseudo-testcross model due to the high heterozygosity of each parental species. A total of 261 loci were mapped in M. sacchariflorus, spanning 40 linkage groups and 1,998.8 cM, covering an estimated 72.7% of the genome. For M. sinensis, a total of 303 loci were mapped, forming 23 linkage groups and 2,238.3 cM, covering 84.9% of the genome. The use of cDNA-derived SSR loci permitted alignment of the Miscanthus linkage groups to the sorghum chromosomes, revealing a whole genome duplication affecting the Miscanthus lineage after the divergence of subtribes Sorghinae and Saccharinae, as well as traces of the pan-cereal whole genome duplication. While the present maps provide for many early research needs in this emerging crop, additional markers are also needed to improve map density and to further characterize the structural changes of the Miscanthus genome since its divergence from sorghum and Saccharum.
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Affiliation(s)
- Changsoo Kim
- Plant Genome Mapping Laboratory, University of Georgia, 111 Riverbend Road, Rm 228, Athens, GA 30602, USA
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279
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Chagné D, Krieger C, Rassam M, Sullivan M, Fraser J, André C, Pindo M, Troggio M, Gardiner SE, Henry RA, Allan AC, McGhie TK, Laing WA. QTL and candidate gene mapping for polyphenolic composition in apple fruit. BMC PLANT BIOLOGY 2012; 12:12. [PMID: 22269060 PMCID: PMC3285079 DOI: 10.1186/1471-2229-12-12] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2011] [Accepted: 01/23/2012] [Indexed: 05/03/2023]
Abstract
BACKGROUND The polyphenolic products of the phenylpropanoid pathway, including proanthocyanidins, anthocyanins and flavonols, possess antioxidant properties that may provide health benefits. To investigate the genetic architecture of control of their biosynthesis in apple fruit, various polyphenolic compounds were quantified in progeny from a 'Royal Gala' × 'Braeburn' apple population segregating for antioxidant content, using ultra high performance liquid chromatography of extracts derived from fruit cortex and skin. RESULTS Construction of genetic maps for 'Royal Gala' and 'Braeburn' enabled detection of 79 quantitative trait loci (QTL) for content of 17 fruit polyphenolic compounds. Seven QTL clusters were stable across two years of harvest and included QTLs for content of flavanols, flavonols, anthocyanins and hydroxycinnamic acids. Alignment of the parental genetic maps with the apple whole genome sequence in silico enabled screening for co-segregation with the QTLs of a range of candidate genes coding for enzymes in the polyphenolic biosynthetic pathway. This co-location was confirmed by genetic mapping of markers derived from the gene sequences. Leucoanthocyanidin reductase (LAR1) co-located with a QTL cluster for the fruit flavanols catechin, epicatechin, procyanidin dimer and five unknown procyanidin oligomers identified near the top of linkage group (LG) 16, while hydroxy cinnamate/quinate transferase (HCT/HQT) co-located with a QTL for chlorogenic acid concentration mapping near the bottom of LG 17. CONCLUSION We conclude that LAR1 and HCT/HQT are likely to influence the concentration of these compounds in apple fruit and provide useful allele-specific markers for marker assisted selection of trees bearing fruit with healthy attributes.
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Affiliation(s)
- David Chagné
- The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research), Palmerston North Research Centre, Palmerston North 4442, New Zealand
| | - Célia Krieger
- The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research), Palmerston North Research Centre, Palmerston North 4442, New Zealand
- UMR 1121 Nancy Université-Institut National de la Recherche Agronomique Agronomie Environnement Nancy-Colmar, 2 Avenue de la Forêt de Haye, 54505 Vandoeuvre-lès-Nancy, France
| | - Maysoon Rassam
- Plant & Food Research, Mount Albert Research Centre, Auckland, New Zealand
| | - Mike Sullivan
- Plant & Food Research, Mount Albert Research Centre, Auckland, New Zealand
| | - Jenny Fraser
- Plant & Food Research, Central Otago Research Centre, Clyde, New Zealand
| | - Christelle André
- Plant & Food Research, Mount Albert Research Centre, Auckland, New Zealand
| | - Massimo Pindo
- IASMA Research and Innovation Centre, Foundation Edmund Mach, San Michele all'Adige, Trento, Italy
| | - Michela Troggio
- IASMA Research and Innovation Centre, Foundation Edmund Mach, San Michele all'Adige, Trento, Italy
| | - Susan E Gardiner
- The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research), Palmerston North Research Centre, Palmerston North 4442, New Zealand
| | - Rebecca A Henry
- Plant & Food Research, Mount Albert Research Centre, Auckland, New Zealand
| | - Andrew C Allan
- Plant & Food Research, Mount Albert Research Centre, Auckland, New Zealand
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand
| | - Tony K McGhie
- The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research), Palmerston North Research Centre, Palmerston North 4442, New Zealand
| | - William A Laing
- Plant & Food Research, Mount Albert Research Centre, Auckland, New Zealand
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280
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Lu J, Wang S, Zhao H, Liu J, Wang H. Genetic linkage map of EST-SSR and SRAP markers in the endangered Chinese endemic herb Dendrobium (Orchidaceae). GENETICS AND MOLECULAR RESEARCH 2012; 11:4654-67. [DOI: 10.4238/2012.december.21.1] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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281
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Genome evolution and meiotic maps by massively parallel DNA sequencing: spotted gar, an outgroup for the teleost genome duplication. Genetics 2011; 188:799-808. [PMID: 21828280 PMCID: PMC3176089 DOI: 10.1534/genetics.111.127324] [Citation(s) in RCA: 271] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Genomic resources for hundreds of species of evolutionary, agricultural, economic, and medical importance are unavailable due to the expense of well-assembled genome sequences and difficulties with multigenerational studies. Teleost fish provide many models for human disease but possess anciently duplicated genomes that sometimes obfuscate connectivity. Genomic information representing a fish lineage that diverged before the teleost genome duplication (TGD) would provide an outgroup for exploring the mechanisms of evolution after whole-genome duplication. We exploited massively parallel DNA sequencing to develop meiotic maps with thrift and speed by genotyping F(1) offspring of a single female and a single male spotted gar (Lepisosteus oculatus) collected directly from nature utilizing only polymorphisms existing in these two wild individuals. Using Stacks, software that automates the calling of genotypes from polymorphisms assayed by Illumina sequencing, we constructed a map containing 8406 markers. RNA-seq on two map-cross larvae provided a reference transcriptome that identified nearly 1000 mapped protein-coding markers and allowed genome-wide analysis of conserved synteny. Results showed that the gar lineage diverged from teleosts before the TGD and its genome is organized more similarly to that of humans than teleosts. Thus, spotted gar provides a critical link between medical models in teleost fish, to which gar is biologically similar, and humans, to which gar is genomically similar. Application of our F(1) dense mapping strategy to species with no prior genome information promises to facilitate comparative genomics and provide a scaffold for ordering the numerous contigs arising from next generation genome sequencing.
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282
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Al-Niemi T, Weeden NF, McCown BH, Hoch WA. Genetic analysis of an interspecific cross in ornamental Viburnum (Viburnum). J Hered 2011; 103:2-12. [PMID: 22147754 DOI: 10.1093/jhered/esr133] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
A genetic analysis was performed on a population derived from crosses between Viburnum lantana and Viburnum carlesii. Linkage maps were developed for each species using AFLP, random amplified polymorphic DNA (RAPD), and sequence-tagged site markers and a half-sib approach that took advantage of both the polymorphism between the species and the heterozygosity within each parent. The map for V. lantana consisted of 153 DNA markers and spanned approximately 750 cM, whereas that for V. carlesii contained 133 markers and covered 700 cM. These maps were used to determine the location of several major genes influencing leaf spot resistance, Verticillium wilt resistance, bud color, and flower scent. Both species contained moderate levels of heterozygosity. Flow cytometric analysis revealed that the genome of V. lantana was 40% larger than that of V. carlesii, and this difference was paralleled by a proportionally greater number of intercross markers (markers segregating 3:1) from V. lantana than from V. carlesii. In addition, V. lantana (n = 9) displayed a 10th linkage group for which no homolog in V. carlesii (n = 9) could be found and which contained only markers present in the former species and absent in the latter. These results suggest that Viburnum could be an interesting genetic model for Caprifoliaceae sensu lato.
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Affiliation(s)
- Thamir Al-Niemi
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT 59717, USA
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283
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Matita, a new retroelement from peanut: characterization and evolutionary context in the light of the Arachis A-B genome divergence. Mol Genet Genomics 2011; 287:21-38. [PMID: 22120641 DOI: 10.1007/s00438-011-0656-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2011] [Accepted: 10/20/2011] [Indexed: 12/16/2022]
Abstract
Cultivated peanut is an allotetraploid with an AB-genome. In order to learn more of the genomic structure of peanut, we characterized and studied the evolution of a retrotransposon originally isolated from a resistance gene analog (RGA)-containing bacterial artificial chromosome (BAC) clone. It is a moderate copy number Ty1-copia retrotransposon from the Bianca lineage and we named it Matita. Fluorescent in situ hybridization (FISH) experiments showed that Matita is mainly located on the distal regions of chromosome arms and is of approximately equal frequency on both A- and B-chromosomes. Its chromosome-specific hybridization pattern facilitates the identification of individual chromosomes, a useful cytogenetic tool considering that chromosomes in peanut are mostly metacentric and of similar size. Phylogenetic analysis of Matita elements, molecular dating of transposition events, and an estimation of the evolutionary divergence of the most probable A- and B-donor species suggest that Matita underwent its last major burst of transposition activity at around the same time of the A- and B-genome divergence about 3.5 million years ago. By probing BAC libraries with overgos probes for Matita, resistance gene analogues, and single- or low-copy genes, it was demonstrated that Matita is not randomly distributed in the genome but exhibits a significant tendency of being more abundant near resistance gene homologues than near single-copy genes. The described work is a further step towards broadening the knowledge on genomic and chromosomal structure of peanut and on its evolution.
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Cabezas JA, Ibáñez J, Lijavetzky D, Vélez D, Bravo G, Rodríguez V, Carreño I, Jermakow AM, Carreño J, Ruiz-García L, Thomas MR, Martinez-Zapater JM. A 48 SNP set for grapevine cultivar identification. BMC PLANT BIOLOGY 2011; 11:153. [PMID: 22060012 PMCID: PMC3221639 DOI: 10.1186/1471-2229-11-153] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2011] [Accepted: 11/08/2011] [Indexed: 05/20/2023]
Abstract
BACKGROUND Rapid and consistent genotyping is an important requirement for cultivar identification in many crop species. Among them grapevine cultivars have been the subject of multiple studies given the large number of synonyms and homonyms generated during many centuries of vegetative multiplication and exchange. Simple sequence repeat (SSR) markers have been preferred until now because of their high level of polymorphism, their codominant nature and their high profile repeatability. However, the rapid application of partial or complete genome sequencing approaches is identifying thousands of single nucleotide polymorphisms (SNP) that can be very useful for such purposes. Although SNP markers are bi-allelic, and therefore not as polymorphic as microsatellites, the high number of loci that can be multiplexed and the possibilities of automation as well as their highly repeatable results under any analytical procedure make them the future markers of choice for any type of genetic identification. RESULTS We analyzed over 300 SNP in the genome of grapevine using a re-sequencing strategy in a selection of 11 genotypes. Among the identified polymorphisms, we selected 48 SNP spread across all grapevine chromosomes with allele frequencies balanced enough as to provide sufficient information content for genetic identification in grapevine allowing for good genotyping success rate. Marker stability was tested in repeated analyses of a selected group of cultivars obtained worldwide to demonstrate their usefulness in genetic identification. CONCLUSIONS We have selected a set of 48 stable SNP markers with a high discrimination power and a uniform genome distribution (2-3 markers/chromosome), which is proposed as a standard set for grapevine (Vitis vinifera L.) genotyping. Any previous problems derived from microsatellite allele confusion between labs or the need to run reference cultivars to identify allele sizes disappear using this type of marker. Furthermore, because SNP markers are bi-allelic, allele identification and genotype naming are extremely simple and genotypes obtained with different equipments and by different laboratories are always fully comparable.
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Affiliation(s)
- José A Cabezas
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología, CSIC, C/Darwin 3, 28049 Madrid, Spain
- Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria. Ctra de A Coruña, Km 7. 28040. Madrid. Spain
| | - Javier Ibáñez
- Instituto de Ciencias de la Vid y del Vino (CSIC-Universidad de La Rioja-Gobierno de La Rioja). Complejo Científico Tecnológico. C/Madre de Dios 51. 26006 Logroño. Spain
| | - Diego Lijavetzky
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología, CSIC, C/Darwin 3, 28049 Madrid, Spain
- Instituto de Biología Agrícola de Mendoza, Facultad de Ciencias Agrarias, CONYCET-Universidad Nacional de Cuyo, Almirante Brown 500, M5528AHB Chacras de Coria, Argentina
| | - Dolores Vélez
- Instituto Madrileño de Investigación y Desarrollo Rural, Agrario y Alimentario (IMIDRA). Finca "El Encín". Ctra A2, Km 38.200. 28800 Alcalá de Henares. Madrid. Spain
| | - Gema Bravo
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología, CSIC, C/Darwin 3, 28049 Madrid, Spain
| | - Virginia Rodríguez
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología, CSIC, C/Darwin 3, 28049 Madrid, Spain
| | - Iván Carreño
- Instituto Murciano de Investigación y Desarrollo Agrario y Alimentario (IMIDA). Estación Sericícola. C/Mayor, s/n. 30150 La Alberca. Murcia. Spain
| | | | - Juan Carreño
- Instituto Murciano de Investigación y Desarrollo Agrario y Alimentario (IMIDA). Estación Sericícola. C/Mayor, s/n. 30150 La Alberca. Murcia. Spain
| | - Leonor Ruiz-García
- Instituto Murciano de Investigación y Desarrollo Agrario y Alimentario (IMIDA). Estación Sericícola. C/Mayor, s/n. 30150 La Alberca. Murcia. Spain
| | - Mark R Thomas
- CSIRO Plant Industry, PO Box 350, Glen Osmond, SA 5064, Australia
| | - José M Martinez-Zapater
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología, CSIC, C/Darwin 3, 28049 Madrid, Spain
- Instituto de Ciencias de la Vid y del Vino (CSIC-Universidad de La Rioja-Gobierno de La Rioja). Complejo Científico Tecnológico. C/Madre de Dios 51. 26006 Logroño. Spain
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285
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Sonnante G, Gatto A, Morgese A, Montemurro F, Sarli G, Blanco E, Pignone D. Genetic map of artichoke × wild cardoon: toward a consensus map for Cynara cardunculus. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2011; 123:1215-29. [PMID: 21800142 DOI: 10.1007/s00122-011-1661-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2011] [Accepted: 07/09/2011] [Indexed: 05/07/2023]
Abstract
An integrated consensus linkage map is proposed for globe artichoke. Maternal and paternal genetic maps were constructed on the basis of an F(1) progeny derived from crossing an artichoke genotype (Mola) with its progenitor, the wild cardoon (Tolfa), using EST-derived SSRs, genomic SSRs, AFLPs, ten genes, and two morphological traits. For most genes, mainly belonging to the chlorogenic acid pathway, new markers were developed. Five of these were SNP markers analyzed through high-resolution melt technology. From the maternal (Mola) and paternal (Tolfa) maps, an integrated map was obtained, containing 337 molecular and one morphological markers ordered in 17 linkage groups (LGs), linked between Mola and Tolfa. The integrated map covers 1,488.8 cM, with an average distance of 4.4 cM between markers. The map was aligned with already existing maps for artichoke, and 12 LGs were linked via 31 bridge markers. LG numbering has been proposed. A total of 124 EST-SSRs and two genes were mapped here for the first time, providing a framework for the construction of a functional map in artichoke. The establishment of a consensus map represents a necessary condition to plan a complete sequencing of the globe artichoke genome.
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Affiliation(s)
- Gabriella Sonnante
- Institute of Plant Genetics, National Research Council, Via Amendola, 165/A, 70126, Bari, Italy.
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286
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Tong C, Zhang B, Wang Z, Xu M, Pang X, Si J, Huang M, Wu R. Multiallelic epistatic model for an out-bred cross and mapping algorithm of interactive quantitative trait loci. BMC PLANT BIOLOGY 2011; 11:148. [PMID: 22039993 PMCID: PMC3377927 DOI: 10.1186/1471-2229-11-148] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2011] [Accepted: 10/31/2011] [Indexed: 05/03/2023]
Abstract
BACKGROUND Genetic mapping has proven to be powerful for studying the genetic architecture of complex traits by characterizing a network of the underlying interacting quantitative trait loci (QTLs). Current statistical models for genetic mapping were mostly founded on the biallelic epistasis of QTLs, incapable of analyzing multiallelic QTLs and their interactions that are widespread in an outcrossing population. RESULTS Here we have formulated a general framework to model and define the epistasis between multiallelic QTLs. Based on this framework, we have derived a statistical algorithm for the estimation and test of multiallelic epistasis between different QTLs in a full-sib family of outcrossing species. We used this algorithm to genomewide scan for the distribution of multiallelic epistasis for a rooting ability trait in an outbred cross derived from two heterozygous poplar trees. The results from simulation studies indicate that the positions and effects of multiallelic QTLs can well be estimated with a modest sample and heritability. CONCLUSIONS The model and algorithm developed provide a useful tool for better characterizing the genetic control of complex traits in a heterozygous family derived from outcrossing species, such as forest trees, and thus fill a gap that occurs in genetic mapping of this group of important but underrepresented species.
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Affiliation(s)
- Chunfa Tong
- The Key Laboratory of Forest Genetics and Gene Engineering, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
- Center for Statistical Genetics, The Pennsylvania State University, Hershey, PA 17033, USA
| | - Bo Zhang
- The Key Laboratory of Forest Genetics and Gene Engineering, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
| | - Zhong Wang
- Center for Statistical Genetics, The Pennsylvania State University, Hershey, PA 17033, USA
- Center for Computational Biology, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Beijing Forestry University, Beijing 100083, China
| | - Meng Xu
- The Key Laboratory of Forest Genetics and Gene Engineering, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
| | - Xiaoming Pang
- Center for Computational Biology, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Beijing Forestry University, Beijing 100083, China
| | - Jingna Si
- Center for Computational Biology, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Beijing Forestry University, Beijing 100083, China
| | - Minren Huang
- The Key Laboratory of Forest Genetics and Gene Engineering, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
| | - Rongling Wu
- Center for Statistical Genetics, The Pennsylvania State University, Hershey, PA 17033, USA
- Center for Computational Biology, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Beijing Forestry University, Beijing 100083, China
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287
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Russell JR, Bayer M, Booth C, Cardle L, Hackett CA, Hedley PE, Jorgensen L, Morris JA, Brennan RM. Identification, utilisation and mapping of novel transcriptome-based markers from blackcurrant (Ribes nigrum). BMC PLANT BIOLOGY 2011; 11:147. [PMID: 22035129 PMCID: PMC3217869 DOI: 10.1186/1471-2229-11-147] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2011] [Accepted: 10/28/2011] [Indexed: 05/27/2023]
Abstract
BACKGROUND Deep-level second generation sequencing (2GS) technologies are now being applied to non-model species as a viable and favourable alternative to Sanger sequencing. Large-scale SNP discovery was undertaken in blackcurrant (Ribes nigrum L.) using transcriptome-based 2GS 454 sequencing on the parental genotypes of a reference mapping population, to generate large numbers of novel markers for the construction of a high-density linkage map. RESULTS Over 700,000 reads were produced, from which a total of 7,000 SNPs were found. A subset of polymorphic SNPs was selected to develop a 384-SNP OPA assay using the Illumina BeadXpress platform. Additionally, the data enabled identification of 3,000 novel EST-SSRs. The selected SNPs and SSRs were validated across diverse Ribes germplasm, including mapping populations and other selected Ribes species.SNP-based maps were developed from two blackcurrant mapping populations, incorporating 48% and 27% of assayed SNPs respectively. A relatively high proportion of visually monomorphic SNPs were investigated further by quantitative trait mapping of theta score outputs from BeadStudio analysis, and this enabled additional SNPs to be placed on the two maps. CONCLUSIONS The use of 2GS technology for the development of markers is superior to previously described methods, in both numbers of markers and biological informativeness of those markers. Whilst the numbers of reads and assembled contigs were comparable to similar sized studies of other non-model species, here a high proportion of novel genes were discovered across a wide range of putative function and localisation. The potential utility of markers developed using the 2GS approach in downstream breeding applications is discussed.
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Affiliation(s)
- Joanne R Russell
- Cell & Molecular Sciences, James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Micha Bayer
- Cell & Molecular Sciences, James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Clare Booth
- Cell & Molecular Sciences, James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Linda Cardle
- Cell & Molecular Sciences, James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Christine A Hackett
- Biomathematics and Statistics Scotland, James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Pete E Hedley
- Cell & Molecular Sciences, James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Linzi Jorgensen
- Cell & Molecular Sciences, James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Jenny A Morris
- Cell & Molecular Sciences, James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Rex M Brennan
- Cell & Molecular Sciences, James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
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288
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Zorrilla-Fontanesi Y, Cabeza A, Domínguez P, Medina JJ, Valpuesta V, Denoyes-Rothan B, Sánchez-Sevilla JF, Amaya I. Quantitative trait loci and underlying candidate genes controlling agronomical and fruit quality traits in octoploid strawberry (Fragaria × ananassa). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2011. [PMID: 21667037 DOI: 10.1007/s00122-011-1624-1626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Breeding for fruit quality traits in strawberry (Fragaria × ananassa, 2n = 8x = 56) is complex due to the polygenic nature of these traits and the octoploid constitution of this species. In order to improve the efficiency of genotype selection, the identification of quantitative trait loci (QTL) and associated molecular markers will constitute a valuable tool for breeding programs. However, the implementation of these markers in breeding programs depends upon the complexity and stability of QTLs across different environments. In this work, the genetic control of 17 agronomical and fruit quality traits was investigated in strawberry using a F(1) population derived from an intraspecific cross between two contrasting selection lines, '232' and '1392'. QTL analyses were performed over three successive years based on the separate parental linkage maps and a pseudo-testcross strategy. The integrated strawberry genetic map consists of 338 molecular markers covering 37 linkage groups, thus exceeding the 28 chromosomes. 33 QTLs were identified for 14 of the 17 studied traits and approximately 37% of them were stable over time. For each trait, 1-5 QTLs were identified with individual effects ranging between 9.2 and 30.5% of the phenotypic variation, indicating that all analysed traits are complex and quantitatively inherited. Many QTLs controlling correlated traits were co-located in homoeology group V, indicating linkage or pleiotropic effects of loci. Candidate genes for several QTLs controlling yield, anthocyanins, firmness and L-ascorbic acid are proposed based on both their co-localization and predicted function. We also report conserved QTLs among strawberry and other Rosaceae based on their syntenic location.
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289
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Zorrilla-Fontanesi Y, Cabeza A, Domínguez P, Medina JJ, Valpuesta V, Denoyes-Rothan B, Sánchez-Sevilla JF, Amaya I. Quantitative trait loci and underlying candidate genes controlling agronomical and fruit quality traits in octoploid strawberry (Fragaria × ananassa). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2011; 123:755-78. [PMID: 21667037 DOI: 10.1007/s00122-011-1624-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2011] [Accepted: 05/14/2011] [Indexed: 05/04/2023]
Abstract
Breeding for fruit quality traits in strawberry (Fragaria × ananassa, 2n = 8x = 56) is complex due to the polygenic nature of these traits and the octoploid constitution of this species. In order to improve the efficiency of genotype selection, the identification of quantitative trait loci (QTL) and associated molecular markers will constitute a valuable tool for breeding programs. However, the implementation of these markers in breeding programs depends upon the complexity and stability of QTLs across different environments. In this work, the genetic control of 17 agronomical and fruit quality traits was investigated in strawberry using a F(1) population derived from an intraspecific cross between two contrasting selection lines, '232' and '1392'. QTL analyses were performed over three successive years based on the separate parental linkage maps and a pseudo-testcross strategy. The integrated strawberry genetic map consists of 338 molecular markers covering 37 linkage groups, thus exceeding the 28 chromosomes. 33 QTLs were identified for 14 of the 17 studied traits and approximately 37% of them were stable over time. For each trait, 1-5 QTLs were identified with individual effects ranging between 9.2 and 30.5% of the phenotypic variation, indicating that all analysed traits are complex and quantitatively inherited. Many QTLs controlling correlated traits were co-located in homoeology group V, indicating linkage or pleiotropic effects of loci. Candidate genes for several QTLs controlling yield, anthocyanins, firmness and L-ascorbic acid are proposed based on both their co-localization and predicted function. We also report conserved QTLs among strawberry and other Rosaceae based on their syntenic location.
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290
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Hou W, Lin S, Li Y, Pang X, Zeng Y, Wu R. A model for linkage analysis with apomixis. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2011; 123:681-691. [PMID: 21625991 DOI: 10.1007/s00122-011-1618-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2011] [Accepted: 05/09/2011] [Indexed: 05/30/2023]
Abstract
Apomixis, or asexual reproduction through seeds, occurs in over 400 species of angiosperms. Although apomixis can favorably perpetuate desired genotypes through successive seed generation, it may also bring about some difficulty for linkage analysis and quantitative trait locus mapping. In this article, we explore the issue of how apomixis affects the precision and power of linkage analysis with molecular markers. We derive a statistical model for estimating the linkage between different markers when some progeny are derived from apomixis. The model was constructed within the maximum likelihood framework and implemented with the EM algorithm. A series of procedures are formulated to test the linkage of markers, the rate of apomixis, and the degree of genetic interference during meiosis. The model was examined and validated through simulation studies. The model will provide a tool for linkage mapping and evolutionary studies for plant species that undergo apomixis.
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Affiliation(s)
- Wei Hou
- Department of Biostatistics, University of Florida, Gainesville, FL 32611, USA
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291
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Multipoint maximum likelihood mapping in a full-sib family of an outbreeding species. Genet Res (Camb) 2011; 93:343-9. [PMID: 21878144 DOI: 10.1017/s0016672311000279] [Citation(s) in RCA: 287] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The fast multipoint maximum likelihood mapping algorithm for crosses between inbred lines, introduced by Jansen et al. (2001), is extended for mapping in a full-sib family of an outbreeding species. The method accommodates different segregation types of markers and differences in recombination between parents. The two separate parental multipoint maximum likelihood maps are joined into an integrated map by averaging lengths over anchored segments and by interpolating or extrapolating for markers segregating in one parent only. The method is illustrated with simulated data. The method will enable a more accurate estimation of maps in outbreeding species than current methods.
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292
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Li X, Wang X, Wei Y, Brummer EC. Prevalence of segregation distortion in diploid alfalfa and its implications for genetics and breeding applications. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2011; 123:667-79. [PMID: 21625992 DOI: 10.1007/s00122-011-1617-5] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2011] [Accepted: 05/09/2011] [Indexed: 05/22/2023]
Abstract
Segregation distortion (SD) is often observed in plant populations; its presence can affect mapping and breeding applications. To investigate the prevalence of SD in diploid alfalfa (Medicago sativa L.), we developed two unrelated segregating F(1) populations and one F(2) population. We genotyped all populations with SSR markers and assessed SD at each locus in each population. The three maps were syntenic and largely colinear with the Medicago truncatula genome sequence. We found genotypic SD for 24 and 34% of markers in the F(1) populations and 68% of markers in the F(2) population; distorted markers were identified on every linkage group. The smaller percentage of genotypic SD in the F(1) populations could be because they were non-inbred and/or due to non-fully informative markers. For the F(2) population, 60 of 90 mapped markers were distorted, and they clustered into eight segregation distortion regions (SDR). Most SDR identified in the F(1) populations were also identified in the F(2) population. Genotypic SD was primarily due to zygotic rather than allelic distortion, suggesting zygotic not gametic selection is the main cause of SD. On the F(2) linkage map, distorted markers in all SDR except two showed heterozygote excess. The severe SD in the F(2) population likely biased genetic distances among markers and possibly also marker ordering and could affect QTL mapping of agronomic traits. To reduce the effects of SD and non-fully informative markers, we suggest constructing linkage maps and conducting QTL mapping in advanced generation populations.
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Affiliation(s)
- Xuehui Li
- Forage Improvement Division, The Samuel Roberts Noble Foundation, Ardmore, OK 73401, USA
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293
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Vera Ruiz EM, Soriano JM, Romero C, Zhebentyayeva T, Terol J, Zuriaga E, Llácer G, Abbott AG, Badenes ML. Narrowing down the apricot Plum pox virus resistance locus and comparative analysis with the peach genome syntenic region. MOLECULAR PLANT PATHOLOGY 2011; 12:535-47. [PMID: 21722293 PMCID: PMC6640391 DOI: 10.1111/j.1364-3703.2010.00691.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Sharka disease, caused by the Plum pox virus (PPV), is one of the main limiting factors for stone fruit crops worldwide. Only a few resistance sources have been found in apricot (Prunus armeniaca L.), and most studies have located a major PPV resistance locus (PPVres) on linkage group 1 (LG1). However, the mapping accuracy was not sufficiently reliable and PPVres was predicted within a low confidence interval. In this study, we have constructed two high-density simple sequence repeat (SSR) improved maps with 0.70 and 0.68 markers/cm, corresponding to LG1 of 'Lito' and 'Goldrich' PPV-resistant cultivars, respectively. Using these maps, and excluding genotype-phenotype incongruent individuals, a new binary trait locus (BTL) analysis for PPV resistance was performed, narrowing down the PPVres support intervals to 7.3 and 5.9 cm in 'Lito' and 'Goldrich', respectively. Subsequently, 71 overlapping oligonucleotides (overgo) probes were hybridized against an apricot bacterial artificial chromosome (BAC) library, identifying 870 single BACs from which 340 were anchored onto a map region of approximately 30-40 cm encompassing PPVres. Partial BAC contigs assigned to the two allelic haplotypes (resistant/susceptible) of the PPVres locus were built by high-information content fingerprinting (HICF). In addition, a total of 300 BAC-derived sequences were obtained, and 257 showed significant homology with the peach genome scaffold_1 corresponding to LG1. According to the peach syntenic genome sequence, PPVres was predicted within a region of 2.16 Mb in which a few candidate resistance genes were identified.
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Affiliation(s)
- Elsa María Vera Ruiz
- Instituto Valenciano de Investigaciones Agrarias (IVIA), Apartado Oficial, Moncada, Valencia, Spain
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294
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Development and implementation of a highly-multiplexed SNP array for genetic mapping in maritime pine and comparative mapping with loblolly pine. BMC Genomics 2011; 12:368. [PMID: 21767361 PMCID: PMC3146957 DOI: 10.1186/1471-2164-12-368] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2011] [Accepted: 07/18/2011] [Indexed: 01/15/2023] Open
Abstract
Background Single nucleotide polymorphisms (SNPs) are the most abundant source of genetic variation among individuals of a species. New genotyping technologies allow examining hundreds to thousands of SNPs in a single reaction for a wide range of applications such as genetic diversity analysis, linkage mapping, fine QTL mapping, association studies, marker-assisted or genome-wide selection. In this paper, we evaluated the potential of highly-multiplexed SNP genotyping for genetic mapping in maritime pine (Pinus pinaster Ait.), the main conifer used for commercial plantation in southwestern Europe. Results We designed a custom GoldenGate assay for 1,536 SNPs detected through the resequencing of gene fragments (707 in vitro SNPs/Indels) and from Sanger-derived Expressed Sequenced Tags assembled into a unigene set (829 in silico SNPs/Indels). Offspring from three-generation outbred (G2) and inbred (F2) pedigrees were genotyped. The success rate of the assay was 63.6% and 74.8% for in silico and in vitro SNPs, respectively. A genotyping error rate of 0.4% was further estimated from segregating data of SNPs belonging to the same gene. Overall, 394 SNPs were available for mapping. A total of 287 SNPs were integrated with previously mapped markers in the G2 parental maps, while 179 SNPs were localized on the map generated from the analysis of the F2 progeny. Based on 98 markers segregating in both pedigrees, we were able to generate a consensus map comprising 357 SNPs from 292 different loci. Finally, the analysis of sequence homology between mapped markers and their orthologs in a Pinus taeda linkage map, made it possible to align the 12 linkage groups of both species. Conclusions Our results show that the GoldenGate assay can be used successfully for high-throughput SNP genotyping in maritime pine, a conifer species that has a genome seven times the size of the human genome. This SNP-array will be extended thanks to recent sequencing effort using new generation sequencing technologies and will include SNPs from comparative orthologous sequences that were identified in the present study, providing a wider collection of anchor points for comparative genomics among the conifers.
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295
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Moury B, Caromel B, Johansen E, Simon V, Chauvin L, Jacquot E, Kerlan C, Lefebvre V. The helper component proteinase cistron of Potato virus Y induces hypersensitivity and resistance in Potato genotypes carrying dominant resistance genes on chromosome IV. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2011; 24:787-797. [PMID: 21405985 DOI: 10.1094/mpmi-10-10-0246] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
The Nc(tbr) and Ny(tbr) genes in Solanum tuberosum determine hypersensitive reactions, characterized by necrotic reactions and restriction of the virus systemic movement, toward isolates belonging to clade C and clade O of Potato virus Y (PVY), respectively. We describe a new resistance from S. sparsipilum which possesses the same phenotype and specificity as Nc(tbr) and is controlled by a dominant gene designated Nc(spl). Nc(spl) maps on potato chromosome IV close or allelic to Ny(tbr). The helper component proteinase (HC-Pro) cistron of PVY was shown to control necrotic reactions and resistance elicitation in plants carrying Nc(spl), Nc(tbr), and Ny(tbr). However, inductions of necrosis and of resistance to the systemic virus movement in plants carrying Nc(spl) reside in different regions of the HC-Pro cistron. Also, genomic determinants outside the HC-Pro cistron are involved in the systemic movement of PVY after induction of necroses on inoculated leaves of plants carrying Ny(tbr). These results suggest that the Ny(tbr) resistance may have been involved in the recent emergence of PVY isolates with a recombination breakpoint near the junction of HC-Pro and P3 cistrons in potato crops. Therefore, this emergence could constitute one of the rare examples of resistance breakdown by a virus which was caused by recombination instead of by successive accumulation of nucleotide substitutions.
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Affiliation(s)
- Benoît Moury
- INRA, UR407 Pathologie Vegetale, Montfavet, France.
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296
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Kang BY, Major JE, Rajora OP. A high-density genetic linkage map of a black spruce (Picea mariana) × red spruce (Picea rubens) interspecific hybrid. Genome 2011; 54:128-43. [PMID: 21326369 DOI: 10.1139/g10-099] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Genetic maps provide an important genomic resource of basic and applied significance. Spruce (Picea) has a very large genome size (between 0.85 × 1010 and 2.4 × 1010 bp; 8.5-24.0 pg/1C, a mean of 17.7 pg/1C ). We have constructed a near-saturated genetic linkage map for an interspecific backcross (BC1) hybrid of black spruce (BS; Picea mariana (Mill.) B.S.P.) and red spruce (RS; Picea rubens Sarg.), using selectively amplified microsatellite polymorphic loci (SAMPL) markers. A total of 2284 SAMPL markers were resolved using 31 SAMPL-MseI selective nucleotide primer combinations. Of these, 1216 SAMPL markers showing Mendelian segregation were mapped, whereas 1068 (46.8%) SAMPL fragments showed segregation distortion at α = 0.05. Maternal, paternal, and consensus maps consistently coalesced into 12 linkage groups, corresponding to the haploid chromosome number (1n = 1x = 12) of 12 in the genus Picea. The maternal BS map consisted of 814 markers distributed over 12 linkage groups, covering 1670 cM, with a mean map distance of 2.1 cM between adjacent markers. The paternal BS × RS map consisted of 773 markers distributed over 12 linkage groups, covering 1563 cM, with a mean map distance of 2.0 cM between adjacent markers. The consensus interspecific hybrid BC1 map consisted of 1216 markers distributed over 12 linkage groups, covering 1865 cM (98% genome coverage), with a mean map distance of 1.5 cM between adjacent markers. The genetic map reported here provides an important genomic resource in Picea, Pinaceae, and conifers.
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Affiliation(s)
- Bum-Yong Kang
- Forest Genetics and Biotechnology Group, Department of Biology, Life Sciences Centre, Dalhousie University, Halifax, NS B3H 4J1, Canada
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297
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Gion JM, Carouché A, Deweer S, Bedon F, Pichavant F, Charpentier JP, Baillères H, Rozenberg P, Carocha V, Ognouabi N, Verhaegen D, Grima-Pettenati J, Vigneron P, Plomion C. Comprehensive genetic dissection of wood properties in a widely-grown tropical tree: Eucalyptus. BMC Genomics 2011; 12:301. [PMID: 21651758 PMCID: PMC3130712 DOI: 10.1186/1471-2164-12-301] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2011] [Accepted: 06/08/2011] [Indexed: 11/16/2022] Open
Abstract
Background Eucalyptus is an important genus in industrial plantations throughout the world and is grown for use as timber, pulp, paper and charcoal. Several breeding programmes have been launched worldwide to concomitantly improve growth performance and wood properties (WPs). In this study, an interspecific cross between Eucalyptus urophylla and E. grandis was used to identify major genomic regions (Quantitative Trait Loci, QTL) controlling the variability of WPs. Results Linkage maps were generated for both parent species. A total of 117 QTLs were detected for a series of wood and end-use related traits, including chemical, technological, physical, mechanical and anatomical properties. The QTLs were mainly clustered into five linkage groups. In terms of distribution of QTL effects, our result agrees with the typical L-shape reported in most QTL studies, i.e. most WP QTLs had limited effects and only a few (13) had major effects (phenotypic variance explained > 15%). The co-locations of QTLs for different WPs as well as QTLs and candidate genes are discussed in terms of phenotypic correlations between traits, and of the function of the candidate genes. The major wood property QTL harbours a gene encoding a Cinnamoyl CoA reductase (CCR), a structural enzyme of the monolignol-specific biosynthesis pathway. Conclusions Given the number of traits analysed, this study provides a comprehensive understanding of the genetic architecture of wood properties in this Eucalyptus full-sib pedigree. At the dawn of Eucalyptus genome sequence, it will provide a framework to identify the nature of genes underlying these important quantitative traits.
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Affiliation(s)
- Jean-Marc Gion
- CIRAD, Department of Biological System, Research Unit "Genetic improvement and adaptation of mediterranean and tropical plants" TA A-108/C, Campus International de Baillarguet, 34398 Montpellier Cedex, France.
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298
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Gar O, Sargent DJ, Tsai CJ, Pleban T, Shalev G, Byrne DH, Zamir D. An autotetraploid linkage map of rose (Rosa hybrida) validated using the strawberry (Fragaria vesca) genome sequence. PLoS One 2011; 6:e20463. [PMID: 21647382 PMCID: PMC3103584 DOI: 10.1371/journal.pone.0020463] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2011] [Accepted: 04/24/2011] [Indexed: 01/21/2023] Open
Abstract
Polyploidy is a pivotal process in plant evolution as it increase gene redundancy and morphological intricacy but due to the complexity of polysomic inheritance we have only few genetic maps of autopolyploid organisms. A robust mapping framework is particularly important in polyploid crop species, rose included (2n = 4x = 28), where the objective is to study multiallelic interactions that control traits of value for plant breeding. From a cross between the garden, peach red and fragrant cultivar Fragrant Cloud (FC) and a cut-rose yellow cultivar Golden Gate (GG), we generated an autotetraploid GGFC mapping population consisting of 132 individuals. For the map we used 128 sequence-based markers, 141 AFLP, 86 SSR and three morphological markers. Seven linkage groups were resolved for FC (Total 632 cM) and GG (616 cM) which were validated by markers that segregated in both parents as well as the diploid integrated consensus map.The release of the Fragaria vesca genome, which also belongs to the Rosoideae, allowed us to place 70 rose sequenced markers on the seven strawberry pseudo-chromosomes. Synteny between Rosa and Fragaria was high with an estimated four major translocations and six inversions required to place the 17 non-collinear markers in the same order. Based on a verified linear order of the rose markers, we could further partition each of the parents into its four homologous groups, thus providing an essential framework to aid the sequencing of an autotetraploid genome.
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Affiliation(s)
- Oron Gar
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| | | | - Ching-Jung Tsai
- Department of Horticultural Sciences, Texas A&M University, College Station, Texas, United States of America
| | - Tzili Pleban
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Gil Shalev
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| | - David H. Byrne
- Department of Horticultural Sciences, Texas A&M University, College Station, Texas, United States of America
| | - Dani Zamir
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
- * E-mail:
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299
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Garcia RAV, Rangel PN, Brondani C, Martins WS, Melo LC, Carneiro MS, Borba TCO, Brondani RPV. The characterization of a new set of EST-derived simple sequence repeat (SSR) markers as a resource for the genetic analysis of Phaseolus vulgaris. BMC Genet 2011; 12:41. [PMID: 21554695 PMCID: PMC3102039 DOI: 10.1186/1471-2156-12-41] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2010] [Accepted: 05/09/2011] [Indexed: 11/10/2022] Open
Abstract
Background Over recent years, a growing effort has been made to develop microsatellite markers for the genomic analysis of the common bean (Phaseolus vulgaris) to broaden the knowledge of the molecular genetic basis of this species. The availability of large sets of expressed sequence tags (ESTs) in public databases has given rise to an expedient approach for the identification of SSRs (Simple Sequence Repeats), specifically EST-derived SSRs. In the present work, a battery of new microsatellite markers was obtained from a search of the Phaseolus vulgaris EST database. The diversity, degree of transferability and polymorphism of these markers were tested. Results From 9,583 valid ESTs, 4,764 had microsatellite motifs, from which 377 were used to design primers, and 302 (80.11%) showed good amplification quality. To analyze transferability, a group of 167 SSRs were tested, and the results showed that they were 82% transferable across at least one species. The highest amplification rates were observed between the species from the Phaseolus (63.7%), Vigna (25.9%), Glycine (19.8%), Medicago (10.2%), Dipterix (6%) and Arachis (1.8%) genera. The average PIC (Polymorphism Information Content) varied from 0.53 for genomic SSRs to 0.47 for EST-SSRs, and the average number of alleles per locus was 4 and 3, respectively. Among the 315 newly tested SSRs in the BJ (BAT93 X Jalo EEP558) population, 24% (76) were polymorphic. The integration of these segregant loci into a framework map composed of 123 previously obtained SSR markers yielded a total of 199 segregant loci, of which 182 (91.5%) were mapped to 14 linkage groups, resulting in a map length of 1,157 cM. Conclusions A total of 302 newly developed EST-SSR markers, showing good amplification quality, are available for the genetic analysis of Phaseolus vulgaris. These markers showed satisfactory rates of transferability, especially between species that have great economic and genomic values. Their diversity was comparable to genomic SSRs, and they were incorporated in the common bean reference genetic map, which constitutes an important contribution to and advance in Phaseolus vulgaris genomic research.
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Affiliation(s)
- Robertha A V Garcia
- Embrapa Arroz e Feijão, Rodovia GO-462, km 12 Zona Rural, CEP 75375-000, Santo Antônio de Goiás, GO, Brazil
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300
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Pfender WF, Saha MC, Johnson EA, Slabaugh MB. Mapping with RAD (restriction-site associated DNA) markers to rapidly identify QTL for stem rust resistance in Lolium perenne. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2011; 122:1467-80. [PMID: 21344184 DOI: 10.1007/s00122-011-1546-3] [Citation(s) in RCA: 113] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2010] [Accepted: 01/31/2011] [Indexed: 05/21/2023]
Abstract
A mapping population was created to detect quantitative trait loci (QTL) for resistance to stem rust caused by Puccinia graminis subsp. graminicola in Lolium perenne. A susceptible and a resistant plant were crossed to produce a pseudo-testcross population of 193 F(1) individuals. Markers were produced by the restriction-site associated DNA (RAD) process, which uses massively parallel and multiplexed sequencing of reduced-representation libraries. Additional simple sequence repeat (SSR) and sequence-tagged site (STS) markers were combined with the RAD markers to produce maps for the female (738 cM) and male (721 cM) parents. Stem rust phenotypes (number of pustules per plant) were determined in replicated greenhouse trials by inoculation with a field-collected, genetically heterogeneous population of urediniospores. The F(1) progeny displayed continuous distribution of phenotypes and transgressive segregation. We detected three resistance QTL. The most prominent QTL (qLpPg1) is located near 41 cM on linkage group (LG) 7 with a 2-LOD interval of 8 cM, and accounts for 30-38% of the stem rust phenotypic variance. QTL were detected also on LG1 (qLpPg2) and LG6 (qLpPg3), each accounting for approximately 10% of phenotypic variance. Alleles of loci closely linked to these QTL originated from the resistant parent for qLpPg1 and from both parents for qLpPg2 and qLpPg3. Observed quantitative nature of the resistance may be due to partial-resistance effects against all pathogen genotypes, or qualitative effects completely preventing infection by only some genotypes in the genetically mixed inoculum. RAD markers facilitated rapid construction of new genetic maps in this outcrossing species and will enable development of sequence-based markers linked to stem rust resistance in L. perenne.
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Affiliation(s)
- W F Pfender
- Department of Botany and Plant Pathology, USDA-ARS Forage Seed and Cereal Research Unit, Oregon State University, 3450 SW Campus Way, Corvallis, OR 97331, USA.
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