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Jia Z, Gao P, Yin F, Quilichini TD, Sheng H, Song J, Yang H, Gao J, Chen T, Yang B, Kochian LV, Zou J, Patterson N, Yang Q, Gillmor CS, Datla R, Li Q, Xiang D. Asymmetric gene expression in grain development of reciprocal crosses between tetraploid and hexaploid wheats. Commun Biol 2022; 5:1412. [PMID: 36564439 PMCID: PMC9789062 DOI: 10.1038/s42003-022-04374-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Accepted: 12/13/2022] [Indexed: 12/24/2022] Open
Abstract
Production of viable progeny from interploid crosses requires precise regulation of gene expression from maternal and paternal chromosomes, yet the transcripts contributed to hybrid seeds from polyploid parent species have rarely been explored. To investigate the genome-wide maternal and paternal contributions to polyploid grain development, we analyzed the transcriptomes of developing embryos, from zygote to maturity, alongside endosperm in two stages of development, using reciprocal crosses between tetraploid and hexaploid wheats. Reciprocal crosses between species with varied levels of ploidy displayed broad impacts on gene expression, including shifts in alternative splicing events in select crosses, as illustrated by active splicing events, enhanced protein synthesis and chromatin remodeling. Homoeologous gene expression was repressed on the univalent D genome in pentaploids, but this suppression was attenuated in crosses with a higher ploidy maternal parent. Imprinted genes were identified in endosperm and early embryo tissues, supporting predominant maternal effects on early embryogenesis. By systematically investigating the complex transcriptional networks in reciprocal-cross hybrids, this study presents a framework for understanding the genomic incompatibility and transcriptome shock that results from interspecific hybridization and uncovers the transcriptional impacts on hybrid seeds created from agriculturally-relevant polyploid species.
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Affiliation(s)
- Zhen Jia
- grid.35155.370000 0004 1790 4137National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070 Wuhan, China
| | - Peng Gao
- grid.25152.310000 0001 2154 235XGlobal Institute for Food Security, University of Saskatchewan, Saskatoon, SK S7N 4J8 Canada
| | - Feifan Yin
- grid.35155.370000 0004 1790 4137National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070 Wuhan, China ,grid.35155.370000 0004 1790 4137Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, 430070 Wuhan, China
| | - Teagen D. Quilichini
- grid.24433.320000 0004 0449 7958Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0W9 Canada
| | - Huajin Sheng
- grid.25152.310000 0001 2154 235XGlobal Institute for Food Security, University of Saskatchewan, Saskatoon, SK S7N 4J8 Canada
| | - Jingpu Song
- grid.24433.320000 0004 0449 7958Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0W9 Canada
| | - Hui Yang
- grid.24433.320000 0004 0449 7958Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0W9 Canada
| | - Jie Gao
- grid.35155.370000 0004 1790 4137National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070 Wuhan, China
| | - Ting Chen
- grid.35155.370000 0004 1790 4137National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070 Wuhan, China
| | - Bo Yang
- grid.35155.370000 0004 1790 4137National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070 Wuhan, China
| | - Leon V. Kochian
- grid.25152.310000 0001 2154 235XGlobal Institute for Food Security, University of Saskatchewan, Saskatoon, SK S7N 4J8 Canada
| | - Jitao Zou
- grid.24433.320000 0004 0449 7958Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0W9 Canada
| | - Nii Patterson
- grid.24433.320000 0004 0449 7958Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0W9 Canada
| | - Qingyong Yang
- grid.35155.370000 0004 1790 4137National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070 Wuhan, China ,grid.35155.370000 0004 1790 4137Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, 430070 Wuhan, China
| | - C. Stewart Gillmor
- grid.512574.0Langebio, Unidad de Genómica Avanzada, Centro de Investigación y Estudios Avanzados del IPN (CINVESTAV-IPN), Irapuato, Guanajuato, 36821 México
| | - Raju Datla
- grid.25152.310000 0001 2154 235XGlobal Institute for Food Security, University of Saskatchewan, Saskatoon, SK S7N 4J8 Canada
| | - Qiang Li
- grid.35155.370000 0004 1790 4137National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070 Wuhan, China
| | - Daoquan Xiang
- grid.24433.320000 0004 0449 7958Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0W9 Canada
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Bogdanova VS. Genetic and Molecular Genetic Basis of Nuclear-Plastid Incompatibilities. PLANTS (BASEL, SWITZERLAND) 2019; 9:E23. [PMID: 31878042 PMCID: PMC7020172 DOI: 10.3390/plants9010023] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 12/18/2019] [Accepted: 12/20/2019] [Indexed: 01/21/2023]
Abstract
Genetic analysis of nuclear-cytoplasm incompatibilities is not straightforward and requires an elaborated experimental design. A number of species have been genetically studied, but notable advances in genetic mapping of nuclear loci involved in nuclear-plastid incompatibility have been achieved only in wheat and pea. This review focuses on the study of the genetic background underlying nuclear-plastid incompatibilities, including cases where the molecular genetic basis of such incompatibility has been unveiled, such as in tobacco, Oenothera, pea, and wheat.
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Affiliation(s)
- Vera S Bogdanova
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
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3
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Padmanaban S, Zhang P, Hare RA, Sutherland MW, Martin A. Pentaploid Wheat Hybrids: Applications, Characterisation, and Challenges. FRONTIERS IN PLANT SCIENCE 2017; 8:358. [PMID: 28367153 PMCID: PMC5355473 DOI: 10.3389/fpls.2017.00358] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 03/01/2017] [Indexed: 05/09/2023]
Abstract
Interspecific hybridisation between hexaploid and tetraploid wheat species leads to the development of F1 pentaploid hybrids with unique chromosomal constitutions. Pentaploid hybrids derived from bread wheat (Triticum aestivum L.) and durum wheat (Triticum turgidum spp. durum Desf.) crosses can improve the genetic background of either parent by transferring traits of interest. The genetic variability derived from bread and durum wheat and transferred into pentaploid hybrids has the potential to improve disease resistance, abiotic tolerance, and grain quality, and to enhance agronomic characters. Nonetheless, pentaploid wheat hybrids have not been fully exploited in breeding programs aimed at improving crops. There are several potential barriers for efficient pentaploid wheat production, such as low pollen compatibility, poor seed set, failed seedling establishment, and frequent sterility in F1 hybrids. However, most of the barriers can be overcome by careful selection of the parental genotypes and by employing the higher ploidy level genotype as the maternal parent. In this review, we summarize the current research on pentaploid wheat hybrids and analyze the advantages and pitfalls of current methods used to assess pentaploid-derived lines. Furthermore, we discuss current and potential applications in commercial breeding programs and future directions for research into pentaploid wheat.
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Affiliation(s)
- Sriram Padmanaban
- Centre for Crop Health, University of Southern Queensland, ToowoombaQLD, Australia
| | - Peng Zhang
- Plant Breeding Institute, The University of Sydney, SydneyNSW, Australia
| | - Ray A. Hare
- Centre for Crop Health, University of Southern Queensland, ToowoombaQLD, Australia
| | - Mark W. Sutherland
- Centre for Crop Health, University of Southern Queensland, ToowoombaQLD, Australia
| | - Anke Martin
- Centre for Crop Health, University of Southern Queensland, ToowoombaQLD, Australia
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4
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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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Bassi FM, Ghavami F, Hayden MJ, Wang Y, Forrest KL, Kong S, Dizon R, Michalak de Jimenez MK, Meinhardt SW, Mergoum M, Gu YQ, Kianian SF. Fast-forward genetics by radiation hybrids to saturate the locus regulating nuclear-cytoplasmic compatibility in Triticum. PLANT BIOTECHNOLOGY JOURNAL 2016; 14:1716-1726. [PMID: 26915753 PMCID: PMC5067624 DOI: 10.1111/pbi.12532] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Revised: 11/24/2015] [Accepted: 12/24/2015] [Indexed: 05/29/2023]
Abstract
The nuclear-encoded species cytoplasm specific (scs) genes control nuclear-cytoplasmic compatibility in wheat (genus Triticum). Alloplasmic cells, which have nucleus and cytoplasm derived from different species, produce vigorous and vital organisms only when the correct version of scs is present in their nucleus. In this study, bulks of in vivo radiation hybrids segregating for the scs phenotype have been genotyped by sequencing with over 1.9 million markers. The high marker saturation obtained for a critical region of chromosome 1D allowed identification of 3318 reads that mapped in close proximity of the scs. A novel in silico approach was deployed to extend these short reads to sequences of up to 70 Kb in length and identify candidate open reading frames (ORFs). Markers were developed to anchor the short contigs containing ORFs to a radiation hybrid map of 650 individuals with resolution of 288 Kb. The region containing the scs locus was narrowed to a single Bacterial Artificial Chromosome (BAC) contig of Aegilops tauschii. Its sequencing and assembly by nano-mapping allowed rapid identification of a rhomboid gene as the only ORF existing within the refined scs locus. Resequencing of this gene from multiple germplasm sources identified a single nucleotide mutation, which gives rise to a functional amino acid change. Gene expression characterization revealed that an active copy of this rhomboid exists on all homoeologous chromosomes of wheat, and depending on the specific cytoplasm each copy is preferentially expressed. Therefore, a new methodology was applied to unique genetic stocks to rapidly identify a strong candidate gene for the control of nuclear-cytoplasmic compatibility in wheat.
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Affiliation(s)
- Filippo M Bassi
- Department of Plant Sciences, North Dakota State University, Fargo, ND, USA
- International Center for the Agricultural Research in the Dry Areas (ICARDA), Rabat, Morocco
| | - Farhad Ghavami
- Department of Plant Sciences, North Dakota State University, Fargo, ND, USA
- Eurofins BioDiagnostics, Inc., River Falls, WI, USA
| | - Matthew J Hayden
- Department of Environment and Primary Industries, AgriBiosciences Center, Bundoora, Vic, Australia
| | - Yi Wang
- USDA-ARS, Western Regional Research Center, Albany, CA, USA
| | - Kerrie L Forrest
- Department of Environment and Primary Industries, AgriBiosciences Center, Bundoora, Vic, Australia
| | - Stephan Kong
- Department of Environment and Primary Industries, AgriBiosciences Center, Bundoora, Vic, Australia
| | - Rhoderissa Dizon
- Department of Plant Sciences, North Dakota State University, Fargo, ND, USA
| | | | - Steven W Meinhardt
- Department of Plant Pathology, North Dakota State University, Fargo, ND, USA
| | - Mohamed Mergoum
- Department of Plant Sciences, North Dakota State University, Fargo, ND, USA
| | - Yong Q Gu
- USDA-ARS, Western Regional Research Center, Albany, CA, USA
| | - Shahryar F Kianian
- Department of Plant Sciences, North Dakota State University, Fargo, ND, USA
- USDA-ARS Cereal Disease Laboratory, University of Minnesota, Saint Paul, MN, USA
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6
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Kianian PMA, Liberatore KL, Miller ME, Hegstad JB, Kianian SF. Dissecting Plant Chromosomes by the Use of Ionizing Radiation. Methods Mol Biol 2016; 1429:91-101. [PMID: 27511169 DOI: 10.1007/978-1-4939-3622-9_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Radiation treatment of genomes is used to generate chromosome breaks for numerous applications. This protocol describes the preparation of seeds and the determination of the optimal level of irradiation dosage for the creation of a radiation hybrid (RH) population. These RH lines can be used to generate high-resolution physical maps for the assembly of sequenced genomes as well as the fine mapping of genes. This procedure can also be used for mutation breeding and forward/reverse genetics.
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Affiliation(s)
- Penny M A Kianian
- Department of Horticultural Science, University of Minnesota, 1970 Folwell Ave., St. Paul, MN, 55108, USA.
| | - Katie L Liberatore
- USDA-ARS, Cereal Disease Laboratory, Department of Plant Pathology, University of Minnesota, 1551 Lindig Ave., St. Paul, MN, 55108, USA
| | - Marisa E Miller
- Department of Horticultural Science, University of Minnesota, 1970 Folwell Ave., St. Paul, MN, 55108, USA
| | - Justin B Hegstad
- Department of Plant Sciences, North Dakota State University, Fargo, ND, USA
| | - Shahryar F Kianian
- USDA-ARS, Cereal Disease Laboratory, Department of Plant Pathology, University of Minnesota, 1551 Lindig Ave., St. Paul, MN, 55108, USA.
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7
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Rastas P, Calboli FCF, Guo B, Shikano T, Merilä J. Construction of Ultradense Linkage Maps with Lep-MAP2: Stickleback F2 Recombinant Crosses as an Example. Genome Biol Evol 2015; 8:78-93. [PMID: 26668116 PMCID: PMC4758246 DOI: 10.1093/gbe/evv250] [Citation(s) in RCA: 94] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
High-density linkage maps are important tools for genome biology and evolutionary genetics by quantifying the extent of recombination, linkage disequilibrium, and chromosomal rearrangements across chromosomes, sexes, and populations. They provide one of the best ways to validate and refine de novo genome assemblies, with the power to identify errors in assemblies increasing with marker density. However, assembly of high-density linkage maps is still challenging due to software limitations. We describe Lep-MAP2, a software for ultradense genome-wide linkage map construction. Lep-MAP2 can handle various family structures and can account for achiasmatic meiosis to gain linkage map accuracy. Simulations show that Lep-MAP2 outperforms other available mapping software both in computational efficiency and accuracy. When applied to two large F2-generation recombinant crosses between two nine-spined stickleback (Pungitius pungitius) populations, it produced two high-density (∼6 markers/cM) linkage maps containing 18,691 and 20,054 single nucleotide polymorphisms. The two maps showed a high degree of synteny, but female maps were 1.5–2 times longer than male maps in all linkage groups, suggesting genome-wide recombination suppression in males. Comparison with the genome sequence of the three-spined stickleback (Gasterosteus aculeatus) revealed a high degree of interspecific synteny with a low frequency (<5%) of interchromosomal rearrangements. However, a fairly large (ca. 10 Mb) translocation from autosome to sex chromosome was detected in both maps. These results illustrate the utility and novel features of Lep-MAP2 in assembling high-density linkage maps, and their usefulness in revealing evolutionarily interesting properties of genomes, such as strong genome-wide sex bias in recombination rates.
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Affiliation(s)
- Pasi Rastas
- Metapopulation Research Group, Department of Biosciences, University of Helsinki, Helsinki, Finland Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - Federico C F Calboli
- Ecological Genetics Research Unit, Department of Biosciences, University of Helsinki, Helsinki, Finland
| | - Baocheng Guo
- Ecological Genetics Research Unit, Department of Biosciences, University of Helsinki, Helsinki, Finland
| | - Takahito Shikano
- Ecological Genetics Research Unit, Department of Biosciences, University of Helsinki, Helsinki, Finland
| | - Juha Merilä
- Ecological Genetics Research Unit, Department of Biosciences, University of Helsinki, Helsinki, Finland
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8
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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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9
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Staňková H, Valárik M, Lapitan NLV, Berkman PJ, Batley J, Edwards D, Luo MC, Tulpová Z, Kubaláková M, Stein N, Doležel J, Šimková H. Chromosomal genomics facilitates fine mapping of a Russian wheat aphid resistance gene. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2015; 128:1373-1383. [PMID: 25862680 DOI: 10.1007/s00122-015-2512-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Accepted: 03/27/2015] [Indexed: 06/04/2023]
Abstract
Making use of wheat chromosomal resources, we developed 11 gene-associated markers for the region of interest, which allowed reducing gene interval and spanning it by four BAC clones. Positional gene cloning and targeted marker development in bread wheat are hampered by high complexity and polyploidy of its nuclear genome. Aiming to clone a Russian wheat aphid resistance gene Dn2401 located on wheat chromosome arm 7DS, we have developed a strategy overcoming problems due to polyploidy and enabling efficient development of gene-associated markers from the region of interest. We employed information gathered by GenomeZipper, a synteny-based tool combining sequence data of rice, Brachypodium, sorghum and barley, and took advantage of a high-density linkage map of Aegilops tauschii. To ensure genome- and locus-specificity of markers, we made use of survey sequence assemblies of isolated wheat chromosomes 7A, 7B and 7D. Despite the low level of polymorphism of the wheat D subgenome, our approach allowed us to add in an efficient and cost-effective manner 11 new gene-associated markers in the Dn2401 region and narrow down the target interval to 0.83 cM. Screening 7DS-specific BAC library with the flanking markers revealed a contig of four BAC clones that span the Dn2401 region in wheat cultivar 'Chinese Spring'. With the availability of sequence assemblies and GenomeZippers for each of the wheat chromosome arms, the proposed strategy can be applied for focused marker development in any region of the wheat genome.
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Affiliation(s)
- Helena Staňková
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Šlechtitelů 31, 783 71, Olomouc, Czech Republic
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10
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Doležel J, Vrána J, Cápal P, Kubaláková M, Burešová V, Šimková H. Advances in plant chromosome genomics. Biotechnol Adv 2014; 32:122-36. [DOI: 10.1016/j.biotechadv.2013.12.011] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Revised: 12/20/2013] [Accepted: 12/21/2013] [Indexed: 01/09/2023]
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11
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Karafiátová M, Bartoš J, Kopecký D, Ma L, Sato K, Houben A, Stein N, Doležel J. Mapping nonrecombining regions in barley using multicolor FISH. Chromosome Res 2013; 21:739-51. [DOI: 10.1007/s10577-013-9380-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2013] [Revised: 08/26/2013] [Accepted: 08/30/2013] [Indexed: 12/22/2022]
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12
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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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13
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Alnemer LM, Seetan RI, Bassi FM, Chitraranjan C, Helsene A, Loree P, Goshn SB, Gu YQ, Luo MC, Iqbal MJ, Lazo GR, Denton AM, Kianian SF. Wheat Zapper: a flexible online tool for colinearity studies in grass genomes. Funct Integr Genomics 2013; 13:11-7. [PMID: 23474942 DOI: 10.1007/s10142-013-0317-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2012] [Revised: 02/08/2013] [Accepted: 02/12/2013] [Indexed: 10/27/2022]
Abstract
In the course of evolution, the genomes of grasses have maintained an observable degree of gene order conservation. The information available for already sequenced genomes can be used to predict the gene order of nonsequenced species by means of comparative colinearity studies. The "Wheat Zapper" application presented here performs on-demand colinearity analysis between wheat, rice, Sorghum, and Brachypodium in a simple, time efficient, and flexible manner. This application was specifically designed to provide plant scientists with a set of tools, comprising not only synteny inference, but also automated primer design, intron/exon boundaries prediction, visual representation using the graphic tool Circos 0.53, and the possibility of downloading FASTA sequences for downstream applications. Quality of the "Wheat Zapper" prediction was confirmed against the genome of maize, with good correlation (r > 0.83) observed between the gene order predicted on the basis of synteny and their actual position on the genome. Further, the accuracy of "Wheat Zapper" was calculated at 0.65 considering the "Genome Zipper" application as the "gold" standard. The differences between these two tools are amply discussed, making the point that "Wheat Zapper" is an accurate and reliable on-demand tool that is sure to benefit the cereal scientific community. The Wheat Zapper is available at http://wge.ndsu.nodak.edu/wheatzapper/ .
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Affiliation(s)
- Loai M Alnemer
- Computer Information Systems Department, The University of Jordan, Amman, 11942, Jordan
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