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He L, Braz GT, Torres GA, Jiang J. Chromosome painting in meiosis reveals pairing of specific chromosomes in polyploid Solanum species. Chromosoma 2018; 127:505-513. [PMID: 30242479 DOI: 10.1007/s00412-018-0682-9] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 09/13/2018] [Accepted: 09/14/2018] [Indexed: 10/28/2022]
Abstract
Analysis of chromosome pairing has been an important tool to assess the genetic similarity of homologous and homoeologous chromosomes in polyploids. However, it is technically challenging to monitor the pairing of specific chromosomes in polyploid species, especially for plant species with a large number of small chromosomes. We developed oligonucleotide-based painting probes for four different potato chromosomes. We demonstrate that these probes are robust enough to monitor a single chromosome throughout the prophase I of meiosis in polyploid Solanum species. Cultivated potato (Solanum tuberosum, 2n = 4x = 48) is an autotetraploid. We demonstrate that the four copies of each potato chromosome pair as a quadrivalent in 66-78% of the meiotic cells at the pachytene stage. Solanum demissum (2n = 6x = 72) is a hexaploid and has been controversial regarding its nature as an autopolyploid or allopolyploid. Interestingly, no hexavalent pairing was observed in meiosis. Instead, we observed three independent bivalents in 83-98% of the meiotic cells at late diakinesis and early metaphase I for the four chromosomes. These results suggest that S. demissum has evolved into a cytologically stable state with predominantly bivalent pairing in meiosis.
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Affiliation(s)
- Li He
- Horticulture Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, Sichuan, China.,Department of Horticulture, University of Wisconsin-Madison, Madison, WI, 53706, USA.,Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA.,Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
| | - Guilherme T Braz
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI, 53706, USA.,Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA.,Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA.,Departmento de Biologia, Universidade Federal de Lavras, Lavras, MG, 37200, Brazil
| | - Giovana A Torres
- Departmento de Biologia, Universidade Federal de Lavras, Lavras, MG, 37200, Brazil
| | - Jiming Jiang
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI, 53706, USA. .,Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA. .,Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA.
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Skrzypek E, Warzecha T, Noga A, Warchoł M, Czyczyło-Mysza I, Dziurka K, Marcińska I, Kapłoniak K, Sutkowska A, Nita Z, Werwińska K, Idziak-Helmcke D, Rojek M, Hosiawa-Barańska M. Complex characterization of oat ( Avena sativa L.) lines obtained by wide crossing with maize ( Zea mays L.). PeerJ 2018; 6:e5107. [PMID: 29967749 PMCID: PMC6022724 DOI: 10.7717/peerj.5107] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2018] [Accepted: 06/06/2018] [Indexed: 01/13/2023] Open
Abstract
Background The oat × maize addition (OMA) lines are used for mapping of the maize genome, the studies of centromere-specific histone (CENH3), gene expression, meiotic chromosome behavior and also for introducing maize C4 photosynthetic system to oat. The aim of our study was the identification and molecular-cytogenetic characterization of oat × maize hybrids. Methods Oat DH lines and oat × maize hybrids were obtained using the wide crossing of Avena sativa L. with Zea mays L. The plants identified as having a Grande-1 retrotransposon fragment, which produced seeds, were used for genomic in situ hybridization (GISH). Results A total of 138 oat lines obtained by crossing of 2,314 oat plants from 80 genotypes with maize cv. Waza were tested for the presence of maize chromosomes. The presence of maize chromatin was indicated in 66 lines by amplification of the PCR product (500 bp) generated using primers specific for the maize retrotransposon Grande-1. Genomic in situ hybridization (GISH) detected whole maize chromosomes in eight lines (40%). All of the analyzed plants possessed full complement of oat chromosomes. The number of maize chromosomes differed between the OMA lines. Four OMA lines possessed two maize chromosomes similar in size, three OMA—one maize chromosome, and one OMA—four maize chromosomes. In most of the lines, the detected chromosomes were labeled uniformly. The presence of six 45S rDNA loci was detected in oat chromosomes, but none of the added maize chromosomes in any of the lines carried 45S rDNA locus. Twenty of the analyzed lines did not possess whole maize chromosomes, but the introgression of maize chromatin in the oat chromosomes. Five of 66 hybrids were shorter in height, grassy type without panicles. Twenty-seven OMA lines were fertile and produced seeds ranging in number from 1–102 (in total 613). Sixty-three fertile DH lines, out of 72 which did not have an addition of maize chromosomes or chromatin, produced seeds in the range of 1–343 (in total 3,758). Obtained DH and OMA lines were fertile and produced seeds. Discussion In wide hybridization of oat with maize, the complete or incomplete chromosomes elimination of maize occur. Hybrids of oat and maize had a complete set of oat chromosomes without maize chromosomes, and a complete set of oat chromosomes with one to four retained maize chromosomes.
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Affiliation(s)
- Edyta Skrzypek
- Department of Biotechnology, Polish Academy of Sciences, The Franciszek Górski Institute of Plant Physiology, Kraków, Poland
| | - Tomasz Warzecha
- Department of Plant Breeding and Seed Science, University of Agriculture, Kraków, Polska
| | - Angelika Noga
- Department of Biotechnology, Polish Academy of Sciences, The Franciszek Górski Institute of Plant Physiology, Kraków, Poland
| | - Marzena Warchoł
- Department of Biotechnology, Polish Academy of Sciences, The Franciszek Górski Institute of Plant Physiology, Kraków, Poland
| | - Ilona Czyczyło-Mysza
- Department of Biotechnology, Polish Academy of Sciences, The Franciszek Górski Institute of Plant Physiology, Kraków, Poland
| | - Kinga Dziurka
- Department of Biotechnology, Polish Academy of Sciences, The Franciszek Górski Institute of Plant Physiology, Kraków, Poland
| | - Izabela Marcińska
- Department of Biotechnology, Polish Academy of Sciences, The Franciszek Górski Institute of Plant Physiology, Kraków, Poland
| | - Kamila Kapłoniak
- Department of Biotechnology, Polish Academy of Sciences, The Franciszek Górski Institute of Plant Physiology, Kraków, Poland
| | - Agnieszka Sutkowska
- Department of Plant Breeding and Seed Science, University of Agriculture, Kraków, Polska
| | - Zygmunt Nita
- Plant Breeding Strzelce Ltd., PBAI Group, Strzelce, Polska
| | | | - Dominika Idziak-Helmcke
- Department of Plant Anatomy and Cytology, University of Silesia in Katowice, Katowice, Polska
| | - Magdalena Rojek
- Department of Plant Anatomy and Cytology, University of Silesia in Katowice, Katowice, Polska
| | - Marta Hosiawa-Barańska
- Department of Plant Anatomy and Cytology, University of Silesia in Katowice, Katowice, Polska
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Baek YS, Royer SM, Broz AK, Covey PA, López-Casado G, Nuñez R, Kear PJ, Bonierbale M, Orillo M, van der Knaap E, Stack SM, McClure B, Chetelat RT, Bedinger PA. Interspecific reproductive barriers between sympatric populations of wild tomato species (Solanum section Lycopersicon). AMERICAN JOURNAL OF BOTANY 2016; 103:1964-1978. [PMID: 27864262 DOI: 10.3732/ajb.1600356] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 10/21/2016] [Indexed: 05/09/2023]
Abstract
PREMISE OF THE STUDY Interspecific reproductive barriers (IRBs) often prevent hybridization between closely related species in sympatry. In the tomato clade (Solanum section Lycopersicon), interspecific interactions between natural sympatric populations have not been evaluated previously. In this study, we assessed IRBs between members of the tomato clade from nine sympatric sites in Peru. METHODS Coflowering was assessed at sympatric sites in Peru. Using previously collected seeds from sympatric sites in Peru, we evaluated premating prezygotic (floral morphology), postmating prezygotic (pollen-tube growth), and postzygotic barriers (fruit and seed development) between sympatric species in common gardens. Pollen-tube growth and seed development were examined in reciprocal crosses between sympatric species. KEY RESULTS We confirmed coflowering of sympatric species at five sites in Peru. We found three types of postmating prezygotic IRBs during pollen-pistil interactions: (1) unilateral pollen-tube rejection between pistils of self-incompatible species and pollen of self-compatible species; (2) potential conspecific pollen precedence in a cross between two self-incompatible species; and (3) failure of pollen tubes to target ovules. In addition, we found strong postzygotic IRBs that prevented normal seed development in 11 interspecific crosses, resulting in seed-like structures containing globular embryos and aborted endosperm and, in some cases, overgrown endothelium. Viable seed and F1 hybrid plants were recovered from three of 19 interspecific crosses. CONCLUSIONS We have identified diverse prezygotic and postzygotic IRBs that would prevent hybridization between sympatric wild tomato species, but interspecific hybridization is possible in a few cases.
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Affiliation(s)
- You Soon Baek
- Department of Biology, Colorado State University, Fort Collins, Colorado 80523-1878, USA
| | - Suzanne M Royer
- Department of Biology, Colorado State University, Fort Collins, Colorado 80523-1878, USA
| | - Amanda K Broz
- Department of Biology, Colorado State University, Fort Collins, Colorado 80523-1878, USA
| | - Paul A Covey
- Department of Biology, Colorado State University, Fort Collins, Colorado 80523-1878, USA
| | - Gloria López-Casado
- Department of Plant Biology, Cornell University, Ithaca, New York 14853, USA
| | - Reynaldo Nuñez
- Department of Horticulture and Crop Science, Ohio State University, Wooster, Ohio 44691, USA
| | - Philip J Kear
- Quality and Nutrition Laboratory, Centro Internacional de la Papa, Perú Postal 1558, Lima, Peru
| | - Merideth Bonierbale
- Quality and Nutrition Laboratory, Centro Internacional de la Papa, Perú Postal 1558, Lima, Peru
| | - Matilde Orillo
- Quality and Nutrition Laboratory, Centro Internacional de la Papa, Perú Postal 1558, Lima, Peru
| | - Esther van der Knaap
- Department of Horticulture and Crop Science, Ohio State University, Wooster, Ohio 44691, USA
- Department of Horticulture, University of Georgia, Athens, Georgia 30602, USA
| | - Stephen M Stack
- Department of Biology, Colorado State University, Fort Collins, Colorado 80523-1878, USA
| | - Bruce McClure
- Department of Biochemistry, University of Missouri-Columbia, Columbia, Missouri 65211, USA
| | - Roger T Chetelat
- Department of Plant Sciences, University of California Davis, Davis, California 95616, USA
| | - Patricia A Bedinger
- Department of Biology, Colorado State University, Fort Collins, Colorado 80523-1878, USA
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Shi G, Zhang Z, Friesen TL, Bansal U, Cloutier S, Wicker T, Rasmussen JB, Faris JD. Marker development, saturation mapping, and high-resolution mapping of the Septoria nodorum blotch susceptibility gene Snn3-B1 in wheat. Mol Genet Genomics 2015; 291:107-19. [PMID: 26187026 DOI: 10.1007/s00438-015-1091-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Accepted: 07/01/2015] [Indexed: 12/29/2022]
Abstract
Septoria nodorum blotch (SNB), caused by Parastagonospora nodorum, is a severe foliar and glume disease on durum and common wheat. Pathogen-produced necrotrophic effectors (NEs) are the major determinants for SNB on leaves. One such NE is SnTox3, which evokes programmed cell death and leads to disease when recognized by the wheat Snn3-B1 gene. Here, we developed saturated genetic linkage maps of the Snn3-B1 region using two F2 populations derived from the SnTox3-sensitive line Sumai 3 crossed with different SnTox3-insensitive lines. Markers were identified and/or developed from various resources including previously mapped simple sequence repeats, bin-mapped expressed sequence tags, single nucleotide polymorphisms, and whole genome survey sequences. Subsequent high-resolution mapping of the Snn3-B1 locus in 5600 gametes delineated the gene to a 1.5 cM interval. Analysis of micro-colinearity of the Snn3-B1 region indicated that it was highly disrupted compared to rice and Brachypodium distachyon. The screening of a collection of durum and common wheat cultivars with tightly linked markers indicated they are not diagnostic for the presence of Snn3-B1, but can be useful for marker-assisted selection if the SnTox3 reactions of lines are first determined. Finally, we developed an ethyl methanesulfonate-induced mutant population of Sumai 3 where the screening of 408 M2 families led to the identification of 17 SnTox3-insensitive mutants. These mutants along with the markers and high-resolution map developed in this research provide a strong foundation for the map-based cloning of Snn3-B1, which will broaden our understanding of the wheat-P. nodorum system and plant-necrotrophic pathogen interactions in general.
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Affiliation(s)
- Gongjun Shi
- Department of Plant Pathology, North Dakota State University, Fargo, ND, 58102, USA
| | - Zengcui Zhang
- USDA-ARS Cereal Crops Research Unit, USDA-ARS NPA NCSL, Red River Valley Agricultural Research Center, 1605 Albrecht BLVD, Fargo, ND, 58102-2765, USA
| | - Timothy L Friesen
- USDA-ARS Cereal Crops Research Unit, USDA-ARS NPA NCSL, Red River Valley Agricultural Research Center, 1605 Albrecht BLVD, Fargo, ND, 58102-2765, USA
| | - Urmil Bansal
- The University of Sydney PBI-Cobbity, Private Bag 4011, Narellan, NSW, 2567, Australia
| | - Sylvie Cloutier
- Eastern Cereal and Oil Research Centre, Agriculture and Agri-Food Canada, K.W. Neatby Building, 960 Carling Avenue, Ottawa, ON, K1A 0C6, Canada
| | - Thomas Wicker
- Institute of Plant Biology, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland
| | - Jack B Rasmussen
- Department of Plant Pathology, North Dakota State University, Fargo, ND, 58102, USA
| | - Justin D Faris
- USDA-ARS Cereal Crops Research Unit, USDA-ARS NPA NCSL, Red River Valley Agricultural Research Center, 1605 Albrecht BLVD, Fargo, ND, 58102-2765, USA.
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Thapa SP, Miyao EM, Michael Davis R, Coaker G. Identification of QTLs controlling resistance to Pseudomonas syringae pv. tomato race 1 strains from the wild tomato, Solanum habrochaites LA1777. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2015; 128:681-692. [PMID: 25634105 DOI: 10.1007/s00122-015-2463-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Accepted: 01/10/2015] [Indexed: 06/04/2023]
Abstract
Screening of wild tomato accessions revealed a source of resistance to Pseudomonas syringe pv. tomato race 1 from Solanum habrochaites and facilitated mapping of QTLs controlling disease resistance. Pseudomonas syringae pv. tomato (Pst) causes bacterial speck of tomato, which is one of the most persistent bacterial diseases in tomato worldwide. Existing Pst populations have overcome genetic resistance mediated by the tomato genes Pto and Prf. The objective of this study was to identify sources of resistance to race 1 strains and map quantitative trait loci (QTLs) controlling resistance in the wild tomato Solanum habrochaites LA1777. Pst strains A9 and 407 are closely related to current field strains and genome sequencing revealed the lack of the avrPto effector as well as select mutations in the avrPtoB effector, which are recognized by Pto and Prf. Strains A9 and 407 were used to screen 278 tomato accessions, identifying five exhibiting resistance: S. peruvianum LA3799, S. peruvianum var. dentatum PI128655, S. chilense LA2765, S. habrochaites LA2869, and S. habrochaites LA1777. An existing set of 93 introgression lines developed from S. habrochaites LA1777 was screened for resistance to strain A9 in a replicated greenhouse trial. Four QTLs were identified using composite interval mapping and mapped to different chromosomes. bsRr1-1 was located on chromosome 1, bsRr1-2 on chromosome 2, and bsRr1-12a and bsRr1-12b on chromosome 12. The QTLs detected explained 10.5-12.5% of the phenotypic variation. Promising lines were also subjected to bacterial growth curves to verify resistance and were analyzed for general horticultural attributes under greenhouse conditions. These findings will provide useful information for future high-resolution mapping of each QTL and integration into marker-assisted breeding programs.
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Affiliation(s)
- Shree Prasad Thapa
- Department of Plant Pathology, University of California, Davis, CA, 95616, USA
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Tellier A, Fischer I, Merino C, Xia H, Camus-Kulandaivelu L, Städler T, Stephan W. Fitness effects of derived deleterious mutations in four closely related wild tomato species with spatial structure. Heredity (Edinb) 2011; 107:189-99. [PMID: 21245893 DOI: 10.1038/hdy.2010.175] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
A key issue in evolutionary biology is an improved understanding of the genetic mechanisms by which species adapt to various environments. Using DNA sequence data, it is possible to quantify the number of adaptive and deleterious mutations, and the distribution of fitness effects of new mutations (its mean and variance) by simultaneously taking into account the demography of a given species. We investigated how selection functions at eight housekeeping genes of four closely related, outcrossing species of wild tomatoes that are native to diverse environments in western South America (Solanum arcanum, S. chilense, S. habrochaites and S. peruvianum). We found little evidence for adaptive mutations but pervasive evidence for strong purifying selection in coding regions of the four species. In contrast, the strength of purifying selection seems to vary among the four species in non-coding (NC) regions (introns). Using F(ST)-based measures of fixation in subdivided populations, we suggest that weak purifying selection has affected the NC regions of S. habrochaites, S. chilense and S. peruvianum. In contrast, NC regions in S. arcanum show a distribution of fitness effects with mutations being either nearly neutral or very strongly deleterious. These results suggest that closely related species with similar genetic backgrounds but experiencing contrasting environments differ in the variance of deleterious fitness effects.
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Affiliation(s)
- A Tellier
- Section of Evolutionary Biology, Department Biology II, University of Munich (LMU), Planegg-Martinsried, Germany.
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Chester M, Leitch AR, Soltis PS, Soltis DE. Review of the Application of Modern Cytogenetic Methods (FISH/GISH) to the Study of Reticulation (Polyploidy/Hybridisation). Genes (Basel) 2010; 1. [PMID: 24710040 PMCID: PMC3954085 DOI: 10.3390/genes1010166] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
The convergence of distinct lineages upon interspecific hybridisation, including when accompanied by increases in ploidy (allopolyploidy), is a driving force in the origin of many plant species. In plant breeding too, both interspecific hybridisation and allopolyploidy are important because they facilitate introgression of alien DNA into breeding lines enabling the introduction of novel characters. Here we review how fluorescence in situ hybridisation (FISH) and genomic in situ hybridisation (GISH) have been applied to: 1) studies of interspecific hybridisation and polyploidy in nature, 2) analyses of phylogenetic relationships between species, 3) genetic mapping and 4) analysis of plant breeding materials. We also review how FISH is poised to take advantage of nextgeneration sequencing (NGS) technologies, helping the rapid characterisation of the repetitive fractions of a genome in natural populations and agricultural plants.
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Affiliation(s)
- Michael Chester
- Department of Biology, University of Florida, Gainesville, Florida 32611, USA.
| | - Andrew R Leitch
- School of Biological and Chemical Sciences, Queen Mary, University of London, UK.
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611, USA.
| | - Douglas E Soltis
- Department of Biology, University of Florida, Gainesville, Florida 32611, USA.
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Chester M, Leitch AR, Soltis PS, Soltis DE. Review of the Application of Modern Cytogenetic Methods (FISH/GISH) to the Study of Reticulation (Polyploidy/Hybridisation). Genes (Basel) 2010; 1:166-92. [PMID: 24710040 PMCID: PMC3954085 DOI: 10.3390/genes1020166] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2010] [Revised: 06/30/2010] [Accepted: 06/30/2010] [Indexed: 11/16/2022] Open
Abstract
The convergence of distinct lineages upon interspecific hybridisation, including when accompanied by increases in ploidy (allopolyploidy), is a driving force in the origin of many plant species. In plant breeding too, both interspecific hybridisation and allopolyploidy are important because they facilitate introgression of alien DNA into breeding lines enabling the introduction of novel characters. Here we review how fluorescence in situ hybridisation (FISH) and genomic in situ hybridisation (GISH) have been applied to: 1) studies of interspecific hybridisation and polyploidy in nature, 2) analyses of phylogenetic relationships between species, 3) genetic mapping and 4) analysis of plant breeding materials. We also review how FISH is poised to take advantage of nextgeneration sequencing (NGS) technologies, helping the rapid characterisation of the repetitive fractions of a genome in natural populations and agricultural plants.
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Affiliation(s)
- Michael Chester
- Department of Biology, University of Florida, Gainesville, Florida 32611, USA.
| | - Andrew R Leitch
- School of Biological and Chemical Sciences, Queen Mary, University of London, UK.
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611, USA.
| | - Douglas E Soltis
- Department of Biology, University of Florida, Gainesville, Florida 32611, USA.
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Detailed recombination studies along chromosome 3B provide new insights on crossover distribution in wheat (Triticum aestivum L.). Genetics 2008; 181:393-403. [PMID: 19064706 DOI: 10.1534/genetics.108.097469] [Citation(s) in RCA: 110] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In wheat (Triticum aestivum L.), the crossover (CO) frequency increases gradually from the centromeres to the telomeres. However, little is known about the factors affecting both the distribution and the intensity of recombination along this gradient. To investigate this, we studied in detail the pattern of CO along chromosome 3B of bread wheat. A dense reference genetic map comprising 102 markers homogeneously distributed along the chromosome was compared to a physical deletion map. Most of the COs (90%) occurred in the distal subtelomeric regions that represent 40% of the chromosome. About 27% of the proximal regions surrounding the centromere showed a very weak CO frequency with only three COs found in the 752 gametes studied. Moreover, we observed a clear decrease of CO frequency on the distal region of the short arm. Finally, the intensity of interference was assessed for the first time in wheat using a Gamma model. The results showed m values of 1.2 for male recombination and 3.5 for female recombination, suggesting positive interference along wheat chromosome 3B.
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