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Kajla A, Schoen A, Paulson C, Yadav IS, Neelam K, Riera-Lizarazu O, Leonard J, Gill BS, Venglat P, Datla R, Poland J, Coleman G, Rawat N, Tiwari V. Physical mapping of the wheat genes in low-recombination regions: radiation hybrid mapping of the C-locus. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:159. [PMID: 37344686 DOI: 10.1007/s00122-023-04403-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 06/09/2023] [Indexed: 06/23/2023]
Abstract
KEY MESSAGE This work reports the physical mapping of an important gene affecting spike compactness located in a low-recombination region of hexaploid wheat. This work paves the way for the eventual isolation and characterization of the factor involved but also opens up possibilities to use this approach to precisely map other wheat genes located on proximal parts of wheat chromosomes that show highly reduced recombination. Mapping wheat genes, in the centromeric and pericentromeric regions (~ 2/3rd of a given chromosome), poses a formidable challenge due to highly suppressed recombination. Using an example of compact spike locus (C-locus), this study provides an approach to precisely map wheat genes in the pericentromeric and centromeric regions that house ~ 30% of wheat genes. In club-wheat, spike compactness is controlled by the dominant C-locus, but previous efforts have failed to localize it, on a particular arm of chromosome 2D. We integrated radiation hybrid (RH) and high-resolution genetic mapping to locate C-locus on the short arm of chromosome 2D. Flanking markers of the C-locus span a physical distance of 11.0 Mb (231.0-242 Mb interval) and contain only 11 high-confidence annotated genes. This work demonstrates the value of this integrated strategy in mapping dominant genes in the low-recombination regions of the wheat genome. A comparison of the mapping resolutions of the RH and genetic maps using common anchored markers indicated that the RH map provides ~ 9 times better resolution that the genetic map even with much smaller population size. This study provides a broadly applicable approach to fine map wheat genes in regions of suppressed recombination.
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Affiliation(s)
- Anmol Kajla
- Department of Plant Sciences and Landscape Architecture, University of Maryland College Park, College Park, USA
| | - Adam Schoen
- Department of Plant Sciences and Landscape Architecture, University of Maryland College Park, College Park, USA
| | - Carl Paulson
- Department of Plant Sciences and Landscape Architecture, University of Maryland College Park, College Park, USA
| | - Inderjit Singh Yadav
- Department of Plant Sciences and Landscape Architecture, University of Maryland College Park, College Park, USA
| | | | | | - Jeff Leonard
- Department of Crop and Soil Sciences, Oregon State University, Corvallis, OR, USA
| | - Bikram S Gill
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
| | | | - Raju Datla
- Global Institute of Food Security, Saskatoon, SK, Canada
| | - Jesse Poland
- Center for Desert Agriculture, KAUST, Thuwal, Saudi Arabia
| | - Gary Coleman
- Department of Plant Sciences and Landscape Architecture, University of Maryland College Park, College Park, USA
| | - Nidhi Rawat
- Department of Plant Sciences and Landscape Architecture, University of Maryland College Park, College Park, USA
| | - Vijay Tiwari
- Department of Plant Sciences and Landscape Architecture, University of Maryland College Park, College Park, USA.
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Mahlandt A, Rawat N, Leonard J, Venglat P, Datla R, Meier N, Gill BS, Riera-Lizarazu O, Coleman G, Murphy AS, Tiwari VK. High-resolution mapping of the Mov-1 locus in wheat by combining radiation hybrid (RH) and recombination-based mapping approaches. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:2303-2314. [PMID: 33830295 DOI: 10.1007/s00122-021-03827-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 03/29/2021] [Indexed: 06/12/2023]
Abstract
This work reports a quick method that integrates RH mapping and genetic mapping to map the dominant Mov-1 locus to a 1.1-Mb physical interval with a small number of candidate genes. Bread wheat is an important crop for global human population. Identification of genes and alleles controlling agronomic traits is essential toward sustainably increasing crop production. The unique multi-ovary (MOV) trait in wheat holds potential for improving yields and is characterized by the formation of 2-3 grains per spikelet. The genetic basis of the multi-ovary trait is known to be monogenic and dominant in nature. Its precise mapping and functional characterization is critical to utilizing this trait in a feasible manner. Previous mapping efforts of the locus controlling multiple ovary/pistil formation in the hexaploid wheat have failed to produce a consensus for a particular chromosome. We describe a mapping strategy integrating radiation hybrid mapping and high-resolution genetic mapping to locate the chromosomal position of the Mov-1 locus in hexaploid wheat. We used RH mapping approach using a panel of 188 lines to map the Mov-1 locus in the terminal part of long arm of wheat chromosome 2D with a map resolution of 1.67 Mb/cR1500. Then using a genetic population of MOV × Synthetic wheat of F2 lines, we delineated the Mov-1 locus to a 1.1-Mb physical region with a small number of candidate genes. This demonstrates the value of this integrated strategy to mapping dominant genes in wheat.
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Affiliation(s)
- Alexander Mahlandt
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, USA
| | - Nidhi Rawat
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, USA
| | - Jeff Leonard
- Department of Crop and Soil Sciences, Oregon State University, Corvallis, OR, USA
| | - Prakash Venglat
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, Canada
| | - Raju Datla
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, Canada
| | - Nathan Meier
- Department of Plant Biology, University of California, Davis, CA, USA
| | - Bikram S Gill
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
| | | | - Gary Coleman
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, USA
| | - Angus S Murphy
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, USA
| | - Vijay K Tiwari
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, USA.
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Buerstmayr M, Steiner B, Wagner C, Schwarz P, Brugger K, Barabaschi D, Volante A, Valè G, Cattivelli L, Buerstmayr H. High-resolution mapping of the pericentromeric region on wheat chromosome arm 5AS harbouring the Fusarium head blight resistance QTL Qfhs.ifa-5A. PLANT BIOTECHNOLOGY JOURNAL 2018; 16:1046-1056. [PMID: 29024288 PMCID: PMC5902775 DOI: 10.1111/pbi.12850] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 09/17/2017] [Accepted: 10/08/2017] [Indexed: 05/24/2023]
Abstract
The Qfhs.ifa-5A allele, contributing to enhanced Fusarium head blight resistance in wheat, resides in a low-recombinogenic region of chromosome 5A close to the centromere. A near-isogenic RIL population segregating for the Qfhs.ifa-5A resistance allele was developed and among 3650 lines as few as four recombined within the pericentromeric C-5AS1-0.40 bin, yielding only a single recombination point. Genetic mapping of the pericentromeric region using a recombination-dependent approach was thus not successful. To facilitate fine-mapping the physically large Qfhs.ifa-5A interval, two gamma-irradiated deletion panels were generated: (i) seeds of line NIL3 carrying the Qfhs.ifa-5A resistance allele in an otherwise susceptible background were irradiated and plants thereof were selfed to obtain deletions in homozygous state and (ii) a radiation hybrid panel was produced using irradiated pollen of the wheat line Chinese Spring (CS) for pollinating the CS-nullisomic5Atetrasomic5B. In total, 5157 radiation selfing and 276 radiation hybrid plants were screened for deletions on 5AS and plants containing deletions were analysed using 102 5AS-specific markers. Combining genotypic information of both panels yielded an 817-fold map improvement (cR/cM) for the centromeric bin and was 389-fold increased across the Qfhs.ifa-5A interval compared to the genetic map, with an average map resolution of 0.77 Mb/cR. We successfully proved that the RH mapping technique can effectively resolve marker order in low-recombining regions, including pericentromeric intervals, and simultaneously allow developing an in vivo panel of sister lines differing for induced deletions across the Qfhs.ifa-5A interval that can be used for phenotyping.
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Affiliation(s)
- Maria Buerstmayr
- Department of Agrobiotechnology TullnBOKU ‐ University of Natural Resources and Life Sciences, ViennaTullnAustria
| | - Barbara Steiner
- Department of Agrobiotechnology TullnBOKU ‐ University of Natural Resources and Life Sciences, ViennaTullnAustria
| | - Christian Wagner
- Department of Agrobiotechnology TullnBOKU ‐ University of Natural Resources and Life Sciences, ViennaTullnAustria
| | - Petra Schwarz
- Department of Agrobiotechnology TullnBOKU ‐ University of Natural Resources and Life Sciences, ViennaTullnAustria
| | - Klaus Brugger
- Department of Agrobiotechnology TullnBOKU ‐ University of Natural Resources and Life Sciences, ViennaTullnAustria
| | - Delfina Barabaschi
- Council for Agricultural Research and Economics (CREA)Genomics Research CentreFiorenzuola d'ArdaItaly
| | - Andrea Volante
- Council for Agricultural Research and Economics (CREA)Research Centre for Cereal and Industrial CropsVercelliItaly
| | - Giampiero Valè
- Council for Agricultural Research and Economics (CREA)Research Centre for Cereal and Industrial CropsVercelliItaly
| | - Luigi Cattivelli
- Council for Agricultural Research and Economics (CREA)Genomics Research CentreFiorenzuola d'ArdaItaly
| | - Hermann Buerstmayr
- Department of Agrobiotechnology TullnBOKU ‐ University of Natural Resources and Life Sciences, ViennaTullnAustria
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Balcárková B, Frenkel Z, Škopová M, Abrouk M, Kumar A, Chao S, Kianian SF, Akhunov E, Korol AB, Doležel J, Valárik M. A High Resolution Radiation Hybrid Map of Wheat Chromosome 4A. FRONTIERS IN PLANT SCIENCE 2017; 7:2063. [PMID: 28119729 PMCID: PMC5222868 DOI: 10.3389/fpls.2016.02063] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 12/26/2016] [Indexed: 05/18/2023]
Abstract
Bread wheat has a large and complex allohexaploid genome with low recombination level at chromosome centromeric and peri-centromeric regions. This significantly hampers ordering of markers, contigs of physical maps and sequence scaffolds and impedes obtaining of high-quality reference genome sequence. Here we report on the construction of high-density and high-resolution radiation hybrid (RH) map of chromosome 4A supported by high-density chromosome deletion map. A total of 119 endosperm-based RH lines of two RH panels and 15 chromosome deletion bin lines were genotyped with 90K iSelect single nucleotide polymorphism (SNP) array. A total of 2316 and 2695 markers were successfully mapped to the 4A RH and deletion maps, respectively. The chromosome deletion map was ordered in 19 bins and allowed precise identification of centromeric region and verification of the RH panel reliability. The 4A-specific RH map comprises 1080 mapping bins and spans 6550.9 cR with a resolution of 0.13 Mb/cR. Significantly higher mapping resolution in the centromeric region was observed as compared to recombination maps. Relatively even distribution of deletion frequency along the chromosome in the RH panel was observed and putative functional centromere was delimited within a region characterized by two SNP markers.
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Affiliation(s)
- Barbora Balcárková
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural ResearchOlomouc, Czechia
| | - Zeev Frenkel
- Institute of Evolution, University of HaifaHaifa, Israel
| | - Monika Škopová
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural ResearchOlomouc, Czechia
| | - Michael Abrouk
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural ResearchOlomouc, Czechia
| | - Ajay Kumar
- Department of Plant Sciences, North Dakota State University, FargoND, USA
| | - Shiaoman Chao
- Biosciences Research Laboratory, United States Department of Agriculture-Agricultural Research Service, FargoND, USA
| | - Shahryar F. Kianian
- Cereal Disease Laboratory, United States Department of Agriculture-Agricultural Research Service, University of Minnesota, St. PaulMN, USA
| | - Eduard Akhunov
- Department of Plant Pathology, Kansas State University, ManhattanKS, USA
| | | | - Jaroslav Doležel
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural ResearchOlomouc, Czechia
| | - Miroslav Valárik
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural ResearchOlomouc, Czechia
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5
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Staňková H, Hastie AR, Chan S, Vrána J, Tulpová Z, Kubaláková M, Visendi P, Hayashi S, Luo M, Batley J, Edwards D, Doležel J, Šimková H. BioNano genome mapping of individual chromosomes supports physical mapping and sequence assembly in complex plant genomes. PLANT BIOTECHNOLOGY JOURNAL 2016; 14:1523-31. [PMID: 26801360 PMCID: PMC5066648 DOI: 10.1111/pbi.12513] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Revised: 11/12/2015] [Accepted: 11/13/2015] [Indexed: 05/09/2023]
Abstract
The assembly of a reference genome sequence of bread wheat is challenging due to its specific features such as the genome size of 17 Gbp, polyploid nature and prevalence of repetitive sequences. BAC-by-BAC sequencing based on chromosomal physical maps, adopted by the International Wheat Genome Sequencing Consortium as the key strategy, reduces problems caused by the genome complexity and polyploidy, but the repeat content still hampers the sequence assembly. Availability of a high-resolution genomic map to guide sequence scaffolding and validate physical map and sequence assemblies would be highly beneficial to obtaining an accurate and complete genome sequence. Here, we chose the short arm of chromosome 7D (7DS) as a model to demonstrate for the first time that it is possible to couple chromosome flow sorting with genome mapping in nanochannel arrays and create a de novo genome map of a wheat chromosome. We constructed a high-resolution chromosome map composed of 371 contigs with an N50 of 1.3 Mb. Long DNA molecules achieved by our approach facilitated chromosome-scale analysis of repetitive sequences and revealed a ~800-kb array of tandem repeats intractable to current DNA sequencing technologies. Anchoring 7DS sequence assemblies obtained by clone-by-clone sequencing to the 7DS genome map provided a valuable tool to improve the BAC-contig physical map and validate sequence assembly on a chromosome-arm scale. Our results indicate that creating genome maps for the whole wheat genome in a chromosome-by-chromosome manner is feasible and that they will be an affordable tool to support the production of improved pseudomolecules.
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Affiliation(s)
- Helena Staňková
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | | | - Saki Chan
- BioNano Genomics, San Diego, CA, USA
| | - Jan Vrána
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Zuzana Tulpová
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Marie Kubaláková
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Paul Visendi
- Australian Centre for Plant Functional Genomics, University of Queensland, Brisbane, QLD, Australia
| | - Satomi Hayashi
- School of Agriculture and Food Sciences, University of Queensland, Brisbane, QLD, Australia
| | - Mingcheng Luo
- Department of Plant Sciences, University of California, Davis, CA, USA
| | - Jacqueline Batley
- School of Agriculture and Food Sciences, University of Queensland, Brisbane, QLD, Australia
- School of Plant Biology, University of Western Australia, Crawley, WA, Australia
| | - David Edwards
- School of Plant Biology, University of Western Australia, Crawley, WA, Australia
| | - Jaroslav Doležel
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Hana Šimková
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
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Tiwari VK, Heesacker A, Riera-Lizarazu O, Gunn H, Wang S, Wang Y, Gu YQ, Paux E, Koo DH, Kumar A, Luo MC, Lazo G, Zemetra R, Akhunov E, Friebe B, Poland J, Gill BS, Kianian S, Leonard JM. A whole-genome, radiation hybrid mapping resource of hexaploid wheat. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 86:195-207. [PMID: 26945524 DOI: 10.1111/tpj.13153] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Revised: 02/04/2016] [Accepted: 02/22/2016] [Indexed: 06/05/2023]
Abstract
Generating a contiguous, ordered reference sequence of a complex genome such as hexaploid wheat (2n = 6x = 42; approximately 17 GB) is a challenging task due to its large, highly repetitive, and allopolyploid genome. In wheat, ordering of whole-genome or hierarchical shotgun sequencing contigs is primarily based on recombination and comparative genomics-based approaches. However, comparative genomics approaches are limited to syntenic inference and recombination is suppressed within the pericentromeric regions of wheat chromosomes, thus, precise ordering of physical maps and sequenced contigs across the whole-genome using these approaches is nearly impossible. We developed a whole-genome radiation hybrid (WGRH) resource and tested it by genotyping a set of 115 randomly selected lines on a high-density single nucleotide polymorphism (SNP) array. At the whole-genome level, 26 299 SNP markers were mapped on the RH panel and provided an average mapping resolution of approximately 248 Kb/cR1500 with a total map length of 6866 cR1500 . The 7296 unique mapping bins provided a five- to eight-fold higher resolution than genetic maps used in similar studies. Most strikingly, the RH map had uniform bin resolution across the entire chromosome(s), including pericentromeric regions. Our research provides a valuable and low-cost resource for anchoring and ordering sequenced BAC and next generation sequencing (NGS) contigs. The WGRH developed for reference wheat line Chinese Spring (CS-WGRH), will be useful for anchoring and ordering sequenced BAC and NGS based contigs for assembling a high-quality, reference sequence of hexaploid wheat. Additionally, this study provides an excellent model for developing similar resources for other polyploid species.
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Affiliation(s)
- Vijay K Tiwari
- Department of Plant Pathology, Wheat Genetics Resource Center, Kansas State University, Manhattan, KS, USA
| | - Adam Heesacker
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR, USA
| | | | - Hilary Gunn
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR, USA
| | - Shichen Wang
- Department of Plant Pathology, Wheat Genetics Resource Center, Kansas State University, Manhattan, KS, USA
| | - Yi Wang
- Crop Improvement and Genetics Research Unit, USDA-ARS, Albany, NY, USA
| | - Young Q Gu
- Crop Improvement and Genetics Research Unit, USDA-ARS, Albany, NY, USA
| | - Etienne Paux
- Diversité et Ecophysiologie des Céréales, INRA, UMR 1095 Génétique, 5 chemin de Beaulieu, F-63039, Clermont-Ferrand, France
- Diversité et Ecophysiologie des Céréales, UMR 1095 Génétique, Université Blaise Pascal, F-63177, Aubière Cedex, France
| | - Dal-Hoe Koo
- Department of Plant Pathology, Wheat Genetics Resource Center, Kansas State University, Manhattan, KS, USA
| | - Ajay Kumar
- Department of Plant Sciences, North Dakota State University, Fargo, ND, USA
| | - Ming-Cheng Luo
- Department of Plant Sciences, University of California, Davis, CA, USA
| | - Gerard Lazo
- Crop Improvement and Genetics Research Unit, USDA-ARS, Albany, NY, USA
| | - Robert Zemetra
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR, USA
| | - Eduard Akhunov
- Department of Plant Pathology, Wheat Genetics Resource Center, Kansas State University, Manhattan, KS, USA
| | - Bernd Friebe
- Department of Plant Pathology, Wheat Genetics Resource Center, Kansas State University, Manhattan, KS, USA
| | - Jesse Poland
- Department of Plant Pathology, Wheat Genetics Resource Center, Kansas State University, Manhattan, KS, USA
| | - Bikram S Gill
- Department of Plant Pathology, Wheat Genetics Resource Center, Kansas State University, Manhattan, KS, USA
| | - Shahryar Kianian
- Cereal Disease Laboratory, University of Minnesota, Saint Paul, MN, USA
| | - Jeffrey M Leonard
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR, USA
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7
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Verma SK, Kumar S, Sheikh I, Malik S, Mathpal P, Chugh V, Kumar S, Prasad R, Dhaliwal HS. Transfer of useful variability of high grain iron and zinc from Aegilops kotschyi into wheat through seed irradiation approach. Int J Radiat Biol 2016; 92:132-9. [PMID: 26883304 DOI: 10.3109/09553002.2016.1135263] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
PURPOSE To transfer the 2S chromosomal fragment(s) of Aegilops kotschyi (2S(k)) into the bread wheat genome which could lead to the biofortification of wheat with high grain iron and zinc content. MATERIALS AND METHODS Wheat-Ae. kotschyi 2A/2S(k) substitution lines with high grain iron and zinc content were used to transfer the gene/loci for high grain Fe and Zn content into wheat using seed irradiation approach. RESULTS Bread wheat plants derived from 40 krad-irradiated seeds showed the presence of univalents and multivalents during meiotic metaphase-I. Genomic in situ hybridization analysis of seed irradiation hybrid F2 seedlings showed several terminal and interstitial signals indicated the introgression of Ae. kotschyi chromosome segments. This proves the efficacy of seed radiation hybrid approach in gene transfer experiments. All the radiation-treated hybrid plants with high grain Fe and Zn content were analyzed with wheat group 2 chromosome-specific polymorphic simple sequence repeat markers to identify the introgression of small alien chromosome fragment(s). CONCLUSION Radiation-induced hybrids showed more than 65% increase in grain iron and 54% increase in Zn contents with better harvest index than the elite wheat cultivar WL711 indicating effective and compensating translocations of 2S(k) fragments into wheat genome.
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Affiliation(s)
- Shailender Kumar Verma
- a School of Life Sciences , Central University of Himachal Pradesh , Dharamshala, Kangra , Himachal Pradesh ;,b Department of Biotechnology , Indian Institute of Technology Roorkee , Roorkee , Uttarakhand
| | - Satish Kumar
- b Department of Biotechnology , Indian Institute of Technology Roorkee , Roorkee , Uttarakhand
| | - Imran Sheikh
- c Akal College of Agriculture , Eternal University , Baru-Sahib , Sirmour , Himachal Pradesh
| | - Sachin Malik
- d Department of Molecular Biology and Genetic Engineering, College of Basic Sciences and Humanities , G. B. Pant University of Agriculture and Technology , Pantnagar , Uttarakhand , India
| | - Priyanka Mathpal
- d Department of Molecular Biology and Genetic Engineering, College of Basic Sciences and Humanities , G. B. Pant University of Agriculture and Technology , Pantnagar , Uttarakhand , India
| | - Vishal Chugh
- c Akal College of Agriculture , Eternal University , Baru-Sahib , Sirmour , Himachal Pradesh
| | - Sundip Kumar
- d Department of Molecular Biology and Genetic Engineering, College of Basic Sciences and Humanities , G. B. Pant University of Agriculture and Technology , Pantnagar , Uttarakhand , India
| | - Ramasare Prasad
- b Department of Biotechnology , Indian Institute of Technology Roorkee , Roorkee , Uttarakhand
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8
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Kumar A, Seetan R, Mergoum M, Tiwari VK, Iqbal MJ, Wang Y, Al-Azzam O, Šimková H, Luo MC, Dvorak J, Gu YQ, Denton A, Kilian A, Lazo GR, Kianian SF. Radiation hybrid maps of the D-genome of Aegilops tauschii and their application in sequence assembly of large and complex plant genomes. BMC Genomics 2015; 16:800. [PMID: 26475137 PMCID: PMC4609151 DOI: 10.1186/s12864-015-2030-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Accepted: 10/09/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The large and complex genome of bread wheat (Triticum aestivum L., ~17 Gb) requires high resolution genome maps with saturated marker scaffolds to anchor and orient BAC contigs/ sequence scaffolds for whole genome assembly. Radiation hybrid (RH) mapping has proven to be an excellent tool for the development of such maps for it offers much higher and more uniform marker resolution across the length of the chromosome compared to genetic mapping and does not require marker polymorphism per se, as it is based on presence (retention) vs. absence (deletion) marker assay. METHODS In this study, a 178 line RH panel was genotyped with SSRs and DArT markers to develop the first high resolution RH maps of the entire D-genome of Ae. tauschii accession AL8/78. To confirm map order accuracy, the AL8/78-RH maps were compared with:1) a DArT consensus genetic map constructed using more than 100 bi-parental populations, 2) a RH map of the D-genome of reference hexaploid wheat 'Chinese Spring', and 3) two SNP-based genetic maps, one with anchored D-genome BAC contigs and another with anchored D-genome sequence scaffolds. Using marker sequences, the RH maps were also anchored with a BAC contig based physical map and draft sequence of the D-genome of Ae. tauschii. RESULTS A total of 609 markers were mapped to 503 unique positions on the seven D-genome chromosomes, with a total map length of 14,706.7 cR. The average distance between any two marker loci was 29.2 cR which corresponds to 2.1 cM or 9.8 Mb. The average mapping resolution across the D-genome was estimated to be 0.34 Mb (Mb/cR) or 0.07 cM (cM/cR). The RH maps showed almost perfect agreement with several published maps with regard to chromosome assignments of markers. The mean rank correlations between the position of markers on AL8/78 maps and the four published maps, ranged from 0.75 to 0.92, suggesting a good agreement in marker order. With 609 mapped markers, a total of 2481 deletions for the whole D-genome were detected with an average deletion size of 42.0 Mb. A total of 520 markers were anchored to 216 Ae. tauschii sequence scaffolds, 116 of which were not anchored earlier to the D-genome. CONCLUSION This study reports the development of first high resolution RH maps for the D-genome of Ae. tauschii accession AL8/78, which were then used for the anchoring of unassigned sequence scaffolds. This study demonstrates how RH mapping, which offered high and uniform resolution across the length of the chromosome, can facilitate the complete sequence assembly of the large and complex plant genomes.
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Affiliation(s)
- Ajay Kumar
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58102, USA
| | - Raed Seetan
- Department of Computer Sciences, North Dakota State University, Fargo, ND, 58102, USA
- Department of Computer Science, Slippery Rock University, Slippery Rock, PA, 16057, USA
| | - Mohamed Mergoum
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58102, USA
| | - Vijay K Tiwari
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506-5502, USA
| | - Muhammad J Iqbal
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58102, USA
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Yi Wang
- USDA-ARS, Western Regional Research Center, Albany, CA, 94710, USA
| | - Omar Al-Azzam
- Department of Computer Sciences, North Dakota State University, Fargo, ND, 58102, USA
- Department of Computer Science and Information Technology, St. Cloud State University, St. Cloud, MN, 56301, USA
| | - Hana Šimková
- Faculty of Science, Palacký University, 783 71, Olomouc, Czech Republic
- Institute of Experimental Botany, Šlechtitelů 31, 783-71, Olomouc, Czech Republic
| | - Ming-Cheng Luo
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Jan Dvorak
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Yong Q Gu
- USDA-ARS, Western Regional Research Center, Albany, CA, 94710, USA
| | - Anne Denton
- Department of Computer Sciences, North Dakota State University, Fargo, ND, 58102, USA
| | - Andrzej Kilian
- Diversity Arrays Technology Pty Limited, 1 Wilf Crane Crescent, Yarralumla, ACT2600, Australia
| | - Gerard R Lazo
- USDA-ARS, Western Regional Research Center, Albany, CA, 94710, USA
| | - Shahryar F Kianian
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58102, USA.
- USDA-ARS, Cereal Disease Laboratory, University of Minnesota, St. Paul, MN, 55108, USA.
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9
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Wang Y, Drader T, Tiwari VK, Dong L, Kumar A, Huo N, Ghavami F, Iqbal MJ, Lazo GR, Leonard J, Gill BS, Kianian SF, Luo MC, Gu YQ. Development of a D genome specific marker resource for diploid and hexaploid wheat. BMC Genomics 2015; 16:646. [PMID: 26315263 PMCID: PMC4552153 DOI: 10.1186/s12864-015-1852-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Accepted: 08/17/2015] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Mapping and map-based cloning of genes that control agriculturally and economically important traits remain great challenges for plants with complex highly repetitive genomes such as those within the grass tribe, Triticeae. Mapping limitations in the Triticeae are primarily due to low frequencies of polymorphic gene markers and poor genetic recombination in certain genetic regions. Although the abundance of repetitive sequence may pose common problems in genome analysis and sequence assembly of large and complex genomes, they provide repeat junction markers with random and unbiased distribution throughout chromosomes. Hence, development of a high-throughput mapping technology that combine both gene-based and repeat junction-based markers is needed to generate maps that have better coverage of the entire genome. RESULTS In this study, the available genomics resource of the diploid Aegilop tauschii, the D genome donor of bread wheat, were used to develop genome specific markers that can be applied for mapping in modern hexaploid wheat. A NimbleGen array containing both gene-based and repeat junction probe sequences derived from Ae. tauschii was developed and used to map the Chinese Spring nullisomic-tetrasomic lines and deletion bin lines of the D genome chromosomes. Based on these mapping data, we have now anchored 5,171 repeat junction probes and 10,892 gene probes, corresponding to 5,070 gene markers, to the delineated deletion bins of the D genome. The order of the gene-based markers within the deletion bins of the Chinese Spring can be inferred based on their positions on the Ae. tauschii genetic map. Analysis of the probe sequences against the Chinese Spring chromosome sequence assembly database facilitated mapping of the NimbleGen probes to the sequence contigs and allowed assignment or ordering of these sequence contigs within the deletion bins. The accumulated length of anchored sequence contigs is about 155 Mb, representing ~ 3.2 % of the D genome. A specific database was developed to allow user to search or BLAST against the probe sequence information and to directly download PCR primers for mapping specific genetic loci. CONCLUSIONS In bread wheat, aneuploid stocks have been extensively used to assign markers linked with genes/traits to chromosomes, chromosome arms, and their specific bins. Through this study, we added thousands of markers to the existing wheat chromosome bin map, representing a significant step forward in providing a resource to navigate the wheat genome. The database website ( http://probes.pw.usda.gov/ATRJM/ ) provides easy access and efficient utilization of the data. The resources developed herein can aid map-based cloning of traits of interest and the sequencing of the D genome of hexaploid wheat.
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Affiliation(s)
- Yi Wang
- Western Regional Research Center, USDA-ARS, Albany, CA, 94710, USA. .,Department of Plant Sciences, University of California, Davis, CA, 95616, USA.
| | - Thomas Drader
- Western Regional Research Center, USDA-ARS, Albany, CA, 94710, USA.
| | - Vijay K Tiwari
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR, 97331, USA. .,Wheat Genetic Resource Center, Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA.
| | - Lingli Dong
- Western Regional Research Center, USDA-ARS, Albany, CA, 94710, USA. .,Department of Plant Sciences, University of California, Davis, CA, 95616, USA.
| | - Ajay Kumar
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA. ajay.kumar.2.@ndsu.edu
| | - Naxin Huo
- Western Regional Research Center, USDA-ARS, Albany, CA, 94710, USA.,Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Farhad Ghavami
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA.,Molecular Breeding and Genomics Technology Laboratory, BioDiagnostics Inc., River Falls, WI, 54022, USA
| | - M Javed Iqbal
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA
| | - Gerard R Lazo
- Western Regional Research Center, USDA-ARS, Albany, CA, 94710, USA.
| | - Jeff Leonard
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR, 97331, USA.
| | - Bikram S Gill
- Wheat Genetic Resource Center, Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA.
| | | | - Ming-Cheng Luo
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA.
| | - Yong Q Gu
- Western Regional Research Center, USDA-ARS, Albany, CA, 94710, USA.
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10
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Kobayashi F, Wu J, Kanamori H, Tanaka T, Katagiri S, Karasawa W, Kaneko S, Watanabe S, Sakaguchi T, Hanawa Y, Fujisawa H, Kurita K, Abe C, Iehisa JCM, Ohno R, Šafář J, Šimková H, Mukai Y, Hamada M, Saito M, Ishikawa G, Katayose Y, Endo TR, Takumi S, Nakamura T, Sato K, Ogihara Y, Hayakawa K, Doležel J, Nasuda S, Matsumoto T, Handa H. A high-resolution physical map integrating an anchored chromosome with the BAC physical maps of wheat chromosome 6B. BMC Genomics 2015; 16:595. [PMID: 26265254 PMCID: PMC4534020 DOI: 10.1186/s12864-015-1803-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Accepted: 07/31/2015] [Indexed: 11/10/2022] Open
Abstract
Background A complete genome sequence is an essential tool for the genetic improvement of wheat. Because the wheat genome is large, highly repetitive and complex due to its allohexaploid nature, the International Wheat Genome Sequencing Consortium (IWGSC) chose a strategy that involves constructing bacterial artificial chromosome (BAC)-based physical maps of individual chromosomes and performing BAC-by-BAC sequencing. Here, we report the construction of a physical map of chromosome 6B with the goal of revealing the structural features of the third largest chromosome in wheat. Results We assembled 689 informative BAC contigs (hereafter reffered to as contigs) representing 91 % of the entire physical length of wheat chromosome 6B. The contigs were integrated into a radiation hybrid (RH) map of chromosome 6B, with one linkage group consisting of 448 loci with 653 markers. The order and direction of 480 contigs, corresponding to 87 % of the total length of 6B, were determined. We also characterized the contigs that contained a part of the nucleolus organizer region or centromere based on their positions on the RH map and the assembled BAC clone sequences. Analysis of the virtual gene order along 6B using the information collected for the integrated map revealed the presence of several chromosomal rearrangements, indicating evolutionary events that occurred on chromosome 6B. Conclusions We constructed a reliable physical map of chromosome 6B, enabling us to analyze its genomic structure and evolutionary progression. More importantly, the physical map should provide a high-quality and map-based reference sequence that will serve as a resource for wheat chromosome 6B. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1803-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Fuminori Kobayashi
- Plant Genome Research Unit, National Institute of Agrobiological Sciences, Tsukuba, 305-8602, Japan.
| | - Jianzhong Wu
- Plant Genome Research Unit, National Institute of Agrobiological Sciences, Tsukuba, 305-8602, Japan. .,Advanced Genomics Laboratory, National Institute of Agrobiological Sciences, Tsukuba, 305-8602, Japan.
| | - Hiroyuki Kanamori
- Plant Genome Research Unit, National Institute of Agrobiological Sciences, Tsukuba, 305-8602, Japan.
| | - Tsuyoshi Tanaka
- Bioinformatics Research Unit, National Institute of Agrobiological Sciences, Tsukuba, 305-8602, Japan.
| | - Satoshi Katagiri
- Advanced Genomics Laboratory, National Institute of Agrobiological Sciences, Tsukuba, 305-8602, Japan.
| | - Wataru Karasawa
- Advanced Genomics Laboratory, National Institute of Agrobiological Sciences, Tsukuba, 305-8602, Japan.
| | - Satoko Kaneko
- Laboratory of Plant Genetics, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan.
| | - Shota Watanabe
- Laboratory of Plant Genetics, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan.
| | - Toyotaka Sakaguchi
- Laboratory of Plant Genetics, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan.
| | - Yumiko Hanawa
- Advanced Genomics Laboratory, National Institute of Agrobiological Sciences, Tsukuba, 305-8602, Japan.
| | - Hiroko Fujisawa
- Advanced Genomics Laboratory, National Institute of Agrobiological Sciences, Tsukuba, 305-8602, Japan.
| | - Kanako Kurita
- Plant Genome Research Unit, National Institute of Agrobiological Sciences, Tsukuba, 305-8602, Japan.
| | - Chikako Abe
- Cereal Science Research Center of Tsukuba, Nisshin Flour Milling Inc., Tsukuba, 300-2611, Japan.
| | - Julio C M Iehisa
- Laboratory of Plant Genetics, Graduate School of Agricultural Science, Kobe University, Kobe, 657-8501, Japan.
| | - Ryoko Ohno
- Core Research Division, Organization of Advanced Science and Technology, Kobe University, Kobe, 657-8501, Japan.
| | - Jan Šafář
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, CZ-78371, Olomouc, Czech Republic.
| | - Hana Šimková
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, CZ-78371, Olomouc, Czech Republic.
| | - Yoshiyuki Mukai
- Advanced Genomics Laboratory, National Institute of Agrobiological Sciences, Tsukuba, 305-8602, Japan.
| | - Masao Hamada
- Advanced Genomics Laboratory, National Institute of Agrobiological Sciences, Tsukuba, 305-8602, Japan.
| | - Mika Saito
- Wheat Breeding Group, NARO Tohoku Agricultural Research Center, Morioka, 020-0198, Japan.
| | - Goro Ishikawa
- Wheat Breeding Group, NARO Tohoku Agricultural Research Center, Morioka, 020-0198, Japan.
| | - Yuichi Katayose
- Advanced Genomics Laboratory, National Institute of Agrobiological Sciences, Tsukuba, 305-8602, Japan.
| | - Takashi R Endo
- Laboratory of Plant Genetics, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan.
| | - Shigeo Takumi
- Laboratory of Plant Genetics, Graduate School of Agricultural Science, Kobe University, Kobe, 657-8501, Japan.
| | - Toshiki Nakamura
- Wheat Breeding Group, NARO Tohoku Agricultural Research Center, Morioka, 020-0198, Japan.
| | - Kazuhiro Sato
- Institute of Plant Science and Resources, Okayama University, Kurashiki, 710-0046, Japan.
| | - Yasunari Ogihara
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, 244-0813, Japan.
| | - Katsuyuki Hayakawa
- Cereal Science Research Center of Tsukuba, Nisshin Flour Milling Inc., Tsukuba, 300-2611, Japan.
| | - Jaroslav Doležel
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, CZ-78371, Olomouc, Czech Republic.
| | - Shuhei Nasuda
- Laboratory of Plant Genetics, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan.
| | - Takashi Matsumoto
- Plant Genome Research Unit, National Institute of Agrobiological Sciences, Tsukuba, 305-8602, Japan.
| | - Hirokazu Handa
- Plant Genome Research Unit, National Institute of Agrobiological Sciences, Tsukuba, 305-8602, Japan.
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11
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Pu J, Wang Q, Shen Y, Zhuang L, Li C, Tan M, Bie T, Chu C, Qi Z. Physical mapping of chromosome 4J of Thinopyrum bessarabicum using gamma radiation-induced aberrations. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2015; 128:1319-28. [PMID: 25851001 DOI: 10.1007/s00122-015-2508-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Accepted: 03/20/2015] [Indexed: 05/23/2023]
Abstract
Gamma radiation induced a series of structural aberrations involving Thinopyrum bessarabicum chromosome 4J. The aberrations allowed for deletion mapping of 101 4J-specific markers and fine mapping of blue-grained gene BaThb. Irradiation can induce translocations and deletions to assist physically locating genes and markers on chromosomes. In this study, a 12-Gy dosage of (60)Co-γ was applied to pollen and eggs of a wheat (Triticum aestivum) landrace Chinese Spring (CS)-Thinopyrum bessarabicum chromosome 4J disomic addition line (DA4J), and the gametes from irradiated plants were fertilized with normal CS eggs or pollen to produce M1 seeds. Based on genomic in situ hybridization analysis of 261 M1 plants, we identified 74 lines carrying structural aberrations involving chromosome 4J with the higher aberration rate in treated pollen (31.2 %) than in the treated eggs (21.3 %). We further identified 43 (53.8 %) lines with structural aberrations on chromosome 4J by analyzing another 80 M1 plants with 74 4J-specific markers, indicating that combining molecular and cytological methods was more efficient for detecting chromosome aberrations. Marker analysis thus was performed prior to cytogenetic identification on M2-M4 seeds to detect chromosome structural aberrations. Sixty-eight M3 lines with structural aberrations on chromosome 4J and six previously obtained chromosome 4J alien lines were then analyzed using 101 chromosome 4J-specific markers. After combining marker results with chromosome aberrations in each line, chromosome 4J was physically divided into 24 segmental blocks with 7 in the short arm and 17 in the long arm. The blue-grained gene BaThb was further mapped into the region corresponding to block 4JL-11. The chromosome aberrations and the physical map developed in this research provide useful stocks and tools for introgression of genes on chromosome 4J into wheat.
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Affiliation(s)
- Jing Pu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095, China
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12
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Wang JS, Sui JM, Xie YD, Guo HJ, Qiao LX, Zhao LL, Yu SL, Liu LX. Generation of peanut mutants by fast neutron irradiation combined with in vitro culture. JOURNAL OF RADIATION RESEARCH 2015; 56:437-445. [PMID: 25653418 PMCID: PMC4426915 DOI: 10.1093/jrr/rru121] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Revised: 11/17/2014] [Accepted: 11/24/2014] [Indexed: 06/01/2023]
Abstract
Induced mutations have played an important role in the development of new plant varieties. In this study, we investigated the effects of fast neutron irradiation on somatic embryogenesis combined with plant regeneration in embryonic leaflet culture to develop new peanut (Arachis hypogaea L.) germplasm for breeding. The dry seeds of the elite cultivar Luhua 11 were irradiated with fast neutrons at dosages of 9.7, 14.0 and 18.0 Gy. The embryonic leaflets were separated and incubated in a medium with 10.0-mg/l 2,4-D to induce somatic embryogenesis. Next, they were incubated in a medium with 4.0-mg/l BAP for plant regeneration. As the irradiation dosage increased, the frequency of both somatic embryo formation and plantlet regeneration decreased. The regenerated plantlets were grafted onto rootstocks and were transplanted into the field. Later, the mature seeds of the regenerated plants were harvested. The M2 generation plants from most of the regenerated cultivars exhibited variations and segregation in vigor, plant height, branch and pod number, pod size, and pod shape. To determine whether the phenotypes were associated with genomic modification, we compared the DNA polymorphisms between the wild-type plants and 19 M3-generation individuals from different regenerated plants. We used 20 pairs of simple sequence repeat (SSR) primers and detected polymorphisms between most of the mutants and the wild-type plants (Luhua 11). Our results indicate that using a combination of fast neutron irradiation and tissue culture is an effective approach for creating new peanut germplasm.
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Affiliation(s)
- Jing-Shan Wang
- College of Life Sciences, Qingdao Agricultural University/Key Lab of Plant Biotechnology in Universities of Shandong Province, Qingdao 266109, China
| | - Jiong-Ming Sui
- College of Life Sciences, Qingdao Agricultural University/Key Lab of Plant Biotechnology in Universities of Shandong Province, Qingdao 266109, China
| | - Yong-Dun Xie
- Institute of Crop Science, Chinese Academy of Agricultural Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, National Center of Space Mutagenesis for Crop Improvement, Beijing 100081, China
| | - Hui-Jun Guo
- Institute of Crop Science, Chinese Academy of Agricultural Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, National Center of Space Mutagenesis for Crop Improvement, Beijing 100081, China
| | - Li-Xian Qiao
- College of Life Sciences, Qingdao Agricultural University/Key Lab of Plant Biotechnology in Universities of Shandong Province, Qingdao 266109, China
| | - Li-Lan Zhao
- Shandong Agricultural Broadcasting and Television School, Penglai 265600, China
| | - Shan-Lin Yu
- Peanut Research Institute, Shandong Academy of Agricultural Sciences, Qingdao 266100, China
| | - Lu-Xiang Liu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, National Center of Space Mutagenesis for Crop Improvement, Beijing 100081, China
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13
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Bassi FM, Kumar A, Zhang Q, Paux E, Huttner E, Kilian A, Dizon R, Feuillet C, Xu SS, Kianian SF. Radiation hybrid QTL mapping of Tdes2 involved in the first meiotic division of wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2013; 126:1977-1990. [PMID: 23715938 DOI: 10.1007/s00122-013-2111-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2013] [Accepted: 04/20/2013] [Indexed: 06/02/2023]
Abstract
Since the dawn of wheat cytogenetics, chromosome 3B has been known to harbor a gene(s) that, when removed, causes chromosome desynapsis and gametic sterility. The lack of natural genetic diversity for this gene(s) has prevented any attempt to fine map and further characterize it. Here, gamma radiation treatment was used to create artificial diversity for this locus. A total of 696 radiation hybrid lines were genotyped with a custom mini array of 140 DArT markers, selected to evenly span the whole 3B chromosome. The resulting map spanned 2,852 centi Ray with a calculated resolution of 0.384 Mb. Phenotyping for the occurrence of meiotic desynapsis was conducted by measuring the level of gametic sterility as seeds produced per spikelet and pollen viability at booting. Composite interval mapping revealed a single QTL with LOD of 16.2 and r (2) of 25.6 % between markers wmc326 and wPt-8983 on the long arm of chromosome 3B. By independent analysis, the location of the QTL was confirmed to be within the deletion bin 3BL7-0.63-1.00 and to correspond to a single gene located ~1.4 Mb away from wPt-8983. The meiotic behavior of lines lacking this gene was characterized cytogenetically to reveal striking similarities with mutants for the dy locus, located on the syntenic chromosome 3 of maize. This represents the first example to date of employing radiation hybrids for QTL analysis. The success achieved by this approach provides an ideal starting point for the final cloning of this interesting gene involved in meiosis of cereals.
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Affiliation(s)
- F M Bassi
- Department of Plant Sciences, North Dakota State University, Fargo, ND 58102, USA.
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