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Sun H, Hu J, Song W, Qiu D, Cui L, Wu P, Zhang H, Liu H, Yang L, Qu Y, Li Y, Li T, Cheng W, Zhou Y, Liu Z, Li J, Li H. Pm61: a recessive gene for resistance to powdery mildew in wheat landrace Xuxusanyuehuang identified by comparative genomics analysis. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2018; 131:2085-2097. [PMID: 29967989 DOI: 10.1007/s00122-018-3135-1] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 06/21/2018] [Indexed: 05/23/2023]
Abstract
A single recessive powdery mildew resistance gene Pm61 from wheat landrace Xuxusanyuehuang was mapped within a 0.46-cM genetic interval spanning a 1.3-Mb interval of the genomic region of chromosome arm 4AL. Epidemics of powdery mildew incited by the biotrophic fungus Blumeria graminis f. sp. tritici (Bgt) have caused significant yield reductions in many wheat (Triticum aestivum)-producing regions. Identification of powdery mildew resistance genes is required for sustainable improvement of wheat for disease resistance. Chinese wheat landrace Xuxusanyuehuang was resistant to several Bgt isolates at the seedling stage. Genetic analysis based on the inoculation of Bgt isolate E09 on the F1, F2, and F2:3 populations produced by crossing Xuxusanyuehuang to susceptible cultivar Mingxian 169 revealed that the resistance of Xuxusanyuehuang was controlled by a single recessive gene. Bulked segregant analysis and simple sequence repeat (SSR) mapping placed the gene on chromosome bin 4AL-4-0.80-1.00. Comparative genomics analysis was performed to detect the collinear genomic regions of Brachypodium distachyon, rice, sorghum, Aegilops tauschii, T. urartu, and T. turgidum ssp. dicoccoides. Based on the use of 454 contig sequences and the International Wheat Genome Sequence Consortium survey sequence of Chinese Spring wheat, four EST-SSR and seven SSR markers were linked to the gene. An F5 recombinant inbred line population derived from Xuxusanyuehuang × Mingxian 169 cross was used to develop the genetic linkage map. The gene was localized in a 0.46-cM genetic interval between Xgwm160 and Xicsx79 corresponding to 1.3-Mb interval of the genomic region in wheat genome. This is a new locus for powdery mildew resistance on chromosome arm 4AL and is designated Pm61.
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Affiliation(s)
- Huigai Sun
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- College of Life and Environmental Science, Minzu University of China, Beijing, 100081, China
| | - Jinghuang Hu
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Wei Song
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- College of Biology, Hunan University, Changsha, 410082, China
| | - Dan Qiu
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Lei Cui
- Institute of Crop Science, Shanxi Academy of Agricultural Sciences, Taiyuan, 030031, China
| | - Peipei Wu
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Hongjun Zhang
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Hongwei Liu
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Li Yang
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yunfeng Qu
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- College of Life Science and Technology, Harbin Normal University, Harbin, 150080, China
| | - Yahui Li
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Teng Li
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Wei Cheng
- College of Chemistry and Environment Engineering, Pingdingshan University, Pingdingshan, 467000, China
| | - Yang Zhou
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Zhiyong Liu
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Jingting Li
- College of Chemistry and Environment Engineering, Pingdingshan University, Pingdingshan, 467000, China.
| | - Hongjie Li
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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Mutti JS, Bhullar RK, Gill KS. Evolution of Gene Expression Balance Among Homeologs of Natural Polyploids. G3 (BETHESDA, MD.) 2017; 7:1225-1237. [PMID: 28193629 PMCID: PMC5386871 DOI: 10.1534/g3.116.038711] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/24/2016] [Accepted: 02/11/2017] [Indexed: 11/18/2022]
Abstract
Polyploidy is a major evolutionary process in eukaryotes, yet the expression balance of homeologs in natural polyploids is largely unknown. To study this expression balance, the expression patterns of 2180 structurally well-characterized genes of wheat were studied, of which 813 had the expected three copies and 375 had less than three. Copy numbers of the remaining 992 ranged from 4 to 14, including homeologs, orthologs, and paralogs. Of the genes with three structural copies corresponding to homeologs, 55% expressed from all three, 38% from two, and the remaining 7% expressed from only one of the three copies. Homeologs of 76-87% of the genes showed differential expression patterns in different tissues, thus have evolved different gene expression controls, possibly resulting in novel functions. Homeologs of 55% of the genes showed tissue-specific expression, with the largest percentage (14%) in the anthers and the smallest (7%) in the pistils. The highest number (1.72/3) of homeologs/gene expression was in the roots and the lowest (1.03/3) in the anthers. As the expression of homeologs changed with changes in structural copy number, about 30% of the genes showed dosage dependence. Chromosomal location also impacted expression pattern as a significantly higher proportion of genes in the proximal regions showed expression from all three copies compared to that present in the distal regions.
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Affiliation(s)
- Jasdeep S Mutti
- Department of Crop and Soil Sciences, Washington State University, Pullman, Washington 99164-6420
| | - Ramanjot K Bhullar
- Department of Crop and Soil Sciences, Washington State University, Pullman, Washington 99164-6420
| | - Kulvinder S Gill
- Department of Crop and Soil Sciences, Washington State University, Pullman, Washington 99164-6420
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Makhloufi E, Yousfi FE, Marande W, Mila I, Hanana M, Bergès H, Mzid R, Bouzayen M. Isolation and molecular characterization of ERF1, an ethylene response factor gene from durum wheat (Triticum turgidum L. subsp. durum), potentially involved in salt-stress responses. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:6359-71. [PMID: 25205575 DOI: 10.1093/jxb/eru352] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
As food crop, wheat is of prime importance for human society. Nevertheless, our understanding of the genetic and molecular mechanisms controlling wheat productivity conditions has been, so far, hampered by the lack of sufficient genomic resources. The present work describes the isolation and characterization of TdERF1, an ERF gene from durum wheat (Triticum turgidum L. subsp. durum). The structural features of TdERF1 supported the hypothesis that it is a novel member of the ERF family in durum wheat and, considering its close similarity to TaERF1 of Triticum aestivum, it probably plays a similar role in mediating responses to environmental stresses. TdERF1 displayed an expression pattern that discriminated between two durum wheat genotypes contrasted with regard to salt-stress tolerance. The high number of cis-regulatory elements related to stress responses present in the TdERF1 promoter and the ability of TdERF1 to regulate the transcription of ethylene and drought-responsive promoters clearly indicated its potential role in mediating plant responses to a wide variety of environmental constrains. TdERF1 was also regulated by abscisic acid, ethylene, auxin, and salicylic acid, suggesting that it may be at the crossroads of multiple hormone signalling pathways. Four TdERF1 allelic variants have been identified in durum wheat genome, all shown to be transcriptionally active. Interestingly, the expression of one allelic form is specific to the tolerant genotype, further supporting the hypothesis that this gene is probably associated with the susceptibility/tolerance mechanism to salt stress. In this regard, the TdERF1 gene may provide a discriminating marker between tolerant and sensitive wheat varieties.
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MESH Headings
- Alleles
- Amino Acid Sequence
- Cell Nucleus/drug effects
- Cell Nucleus/metabolism
- Chromosomes, Artificial, Bacterial/metabolism
- DNA, Complementary/genetics
- Droughts
- Ethylenes/metabolism
- Ethylenes/pharmacology
- Gene Expression Regulation, Plant/drug effects
- Genes, Plant
- Genotype
- Molecular Sequence Annotation
- Molecular Sequence Data
- Phylogeny
- Plant Proteins/chemistry
- Plant Proteins/genetics
- Plant Proteins/metabolism
- Polymerase Chain Reaction
- Promoter Regions, Genetic/genetics
- Protein Transport/drug effects
- Salt Tolerance
- Sequence Alignment
- Sequence Analysis, DNA
- Sodium Chloride/pharmacology
- Stress, Physiological/drug effects
- Stress, Physiological/genetics
- Transcription, Genetic/drug effects
- Triticum/drug effects
- Triticum/genetics
- Triticum/physiology
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Affiliation(s)
- Emna Makhloufi
- University of Toulouse, INPT, Laboratoire de Génomique et Biotechnologie des Fruits, Avenue de l'Agrobiopole BP 32607, Castanet-Tolosan F-31326, France INRA, UMR990 Génomique et Biotechnologie des Fruits, Castanet-Tolosan, F-31326, France Center of Biotechnology of Borj Cedria (CBBC). Lab. Plant Molecular Physiology. Borj Cedria Science and Technology Park - B.P.901, Hammam-lif 2050, Tunisia
| | - Fatma-Ezzahra Yousfi
- University of Toulouse, INPT, Laboratoire de Génomique et Biotechnologie des Fruits, Avenue de l'Agrobiopole BP 32607, Castanet-Tolosan F-31326, France INRA, UMR990 Génomique et Biotechnologie des Fruits, Castanet-Tolosan, F-31326, France Center of Biotechnology of Borj Cedria (CBBC). Lab. Plant Molecular Physiology. Borj Cedria Science and Technology Park - B.P.901, Hammam-lif 2050, Tunisia
| | - William Marande
- Centre National de Ressources Génomiques Végétales, INRA-CNRGV, 24 Chemin de Borde Rouge, CS 52627, 31326 Castanet-Tolosan, France
| | - Isabelle Mila
- University of Toulouse, INPT, Laboratoire de Génomique et Biotechnologie des Fruits, Avenue de l'Agrobiopole BP 32607, Castanet-Tolosan F-31326, France INRA, UMR990 Génomique et Biotechnologie des Fruits, Castanet-Tolosan, F-31326, France
| | - Mohsen Hanana
- Center of Biotechnology of Borj Cedria (CBBC). Lab. Plant Molecular Physiology. Borj Cedria Science and Technology Park - B.P.901, Hammam-lif 2050, Tunisia
| | - Hélène Bergès
- Centre National de Ressources Génomiques Végétales, INRA-CNRGV, 24 Chemin de Borde Rouge, CS 52627, 31326 Castanet-Tolosan, France
| | - Rim Mzid
- Center of Biotechnology of Borj Cedria (CBBC). Lab. Plant Molecular Physiology. Borj Cedria Science and Technology Park - B.P.901, Hammam-lif 2050, Tunisia
| | - Mondher Bouzayen
- University of Toulouse, INPT, Laboratoire de Génomique et Biotechnologie des Fruits, Avenue de l'Agrobiopole BP 32607, Castanet-Tolosan F-31326, France INRA, UMR990 Génomique et Biotechnologie des Fruits, Castanet-Tolosan, F-31326, France
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Belova T, Grønvold L, Kumar A, Kianian S, He X, Lillemo M, Springer NM, Lien S, Olsen OA, Sandve SR. Utilization of deletion bins to anchor and order sequences along the wheat 7B chromosome. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2014; 127:2029-2040. [PMID: 25134516 DOI: 10.1007/s00122-014-2358-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2014] [Accepted: 07/13/2014] [Indexed: 06/03/2023]
Abstract
A total of 3,671 sequence contigs and scaffolds were mapped to deletion bins on wheat chromosome 7B providing a foundation for developing high-resolution integrated physical map for this chromosome. Bread wheat (Triticum aestivum L.) has a large, complex and highly repetitive genome which is challenging to assemble into high quality pseudo-chromosomes. As part of the international effort to sequence the hexaploid bread wheat genome by the international wheat genome sequencing consortium (IWGSC) we are focused on assembling a reference sequence for chromosome 7B. The successful completion of the reference chromosome sequence is highly dependent on the integration of genetic and physical maps. To aid the integration of these two types of maps, we have constructed a high-density deletion bin map of chromosome 7B. Using the 270 K Nimblegen comparative genomic hybridization (CGH) array on a set of cv. Chinese spring deletion lines, a total of 3,671 sequence contigs and scaffolds (~7.8 % of chromosome 7B physical length) were mapped into nine deletion bins. Our method of genotyping deletions on chromosome 7B relied on a model-based clustering algorithm (Mclust) to accurately predict the presence or absence of a given genomic sequence in a deletion line. The bin mapping results were validated using three different approaches, viz. (a) PCR-based amplification of randomly selected bin mapped sequences (b) comparison with previously mapped ESTs and (c) comparison with a 7B genetic map developed in the present study. Validation of the bin mapping results suggested a high accuracy of the assignment of 7B sequence contigs and scaffolds to the 7B deletion bins.
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Affiliation(s)
- Tatiana Belova
- Department of Plant Sciences, Norwegian University of Life Sciences, Ås, Norway,
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Ouyang S, Zhang D, Han J, Zhao X, Cui Y, Song W, Huo N, Liang Y, Xie J, Wang Z, Wu Q, Chen YX, Lu P, Zhang DY, Wang L, Sun H, Yang T, Keeble-Gagnere G, Appels R, Doležel J, Ling HQ, Luo M, Gu Y, Sun Q, Liu Z. Fine physical and genetic mapping of powdery mildew resistance gene MlIW172 originating from wild emmer (Triticum dicoccoides). PLoS One 2014; 9:e100160. [PMID: 24955773 PMCID: PMC4067302 DOI: 10.1371/journal.pone.0100160] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Accepted: 05/22/2014] [Indexed: 11/18/2022] Open
Abstract
Powdery mildew, caused by Blumeria graminis f. sp. tritici, is one of the most important wheat diseases in the world. In this study, a single dominant powdery mildew resistance gene MlIW172 was identified in the IW172 wild emmer accession and mapped to the distal region of chromosome arm 7AL (bin7AL-16-0.86-0.90) via molecular marker analysis. MlIW172 was closely linked with the RFLP probe Xpsr680-derived STS marker Xmag2185 and the EST markers BE405531 and BE637476. This suggested that MlIW172 might be allelic to the Pm1 locus or a new locus closely linked to Pm1. By screening genomic BAC library of durum wheat cv. Langdon and 7AL-specific BAC library of hexaploid wheat cv. Chinese Spring, and after analyzing genome scaffolds of Triticum urartu containing the marker sequences, additional markers were developed to construct a fine genetic linkage map on the MlIW172 locus region and to delineate the resistance gene within a 0.48 cM interval. Comparative genetics analyses using ESTs and RFLP probe sequences flanking the MlIW172 region against other grass species revealed a general co-linearity in this region with the orthologous genomic regions of rice chromosome 6, Brachypodium chromosome 1, and sorghum chromosome 10. However, orthologous resistance gene-like RGA sequences were only present in wheat and Brachypodium. The BAC contigs and sequence scaffolds that we have developed provide a framework for the physical mapping and map-based cloning of MlIW172.
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Affiliation(s)
- Shuhong Ouyang
- State Key Laboratory for Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement/Key Laboratory of Crop Heterosis Research & Utilization, Ministry of Education, China Agricultural University, Beijing, China
| | - Dong Zhang
- State Key Laboratory for Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement/Key Laboratory of Crop Heterosis Research & Utilization, Ministry of Education, China Agricultural University, Beijing, China
| | - Jun Han
- State Key Laboratory for Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement/Key Laboratory of Crop Heterosis Research & Utilization, Ministry of Education, China Agricultural University, Beijing, China
- Agriculture University of Beijing, Beijing, China
| | - Xiaojie Zhao
- State Key Laboratory for Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement/Key Laboratory of Crop Heterosis Research & Utilization, Ministry of Education, China Agricultural University, Beijing, China
| | - Yu Cui
- State Key Laboratory for Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement/Key Laboratory of Crop Heterosis Research & Utilization, Ministry of Education, China Agricultural University, Beijing, China
| | - Wei Song
- State Key Laboratory for Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement/Key Laboratory of Crop Heterosis Research & Utilization, Ministry of Education, China Agricultural University, Beijing, China
- Maize Research Center, Beijing Academy of Agricultural and Forestry Sciences, Beijing, China
| | - Naxin Huo
- USDA-ARS West Regional Research Center, Albany, California, United States of America
| | - Yong Liang
- State Key Laboratory for Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement/Key Laboratory of Crop Heterosis Research & Utilization, Ministry of Education, China Agricultural University, Beijing, China
| | - Jingzhong Xie
- State Key Laboratory for Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement/Key Laboratory of Crop Heterosis Research & Utilization, Ministry of Education, China Agricultural University, Beijing, China
| | - Zhenzhong Wang
- State Key Laboratory for Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement/Key Laboratory of Crop Heterosis Research & Utilization, Ministry of Education, China Agricultural University, Beijing, China
| | - Qiuhong Wu
- State Key Laboratory for Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement/Key Laboratory of Crop Heterosis Research & Utilization, Ministry of Education, China Agricultural University, Beijing, China
| | - Yong-Xing Chen
- State Key Laboratory for Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement/Key Laboratory of Crop Heterosis Research & Utilization, Ministry of Education, China Agricultural University, Beijing, China
| | - Ping Lu
- State Key Laboratory for Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement/Key Laboratory of Crop Heterosis Research & Utilization, Ministry of Education, China Agricultural University, Beijing, China
| | - De-Yun Zhang
- State Key Laboratory for Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement/Key Laboratory of Crop Heterosis Research & Utilization, Ministry of Education, China Agricultural University, Beijing, China
| | - Lili Wang
- State Key Laboratory for Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement/Key Laboratory of Crop Heterosis Research & Utilization, Ministry of Education, China Agricultural University, Beijing, China
| | - Hua Sun
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institutes of Genetics & Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Tsomin Yang
- State Key Laboratory for Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement/Key Laboratory of Crop Heterosis Research & Utilization, Ministry of Education, China Agricultural University, Beijing, China
| | | | - Rudi Appels
- Murdoch University, Perth, Western Australia, Australia
| | - Jaroslav Doležel
- Institute of Experimental Botany, Centre of Plant Structural and Functional Genomics, Olomouc, Czech Republic
| | - Hong-Qing Ling
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institutes of Genetics & Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Mingcheng Luo
- Department of Plant Sciences, University of California, Davis, Davis, California, United States of America
| | - Yongqiang Gu
- USDA-ARS West Regional Research Center, Albany, California, United States of America
| | - Qixin Sun
- State Key Laboratory for Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement/Key Laboratory of Crop Heterosis Research & Utilization, Ministry of Education, China Agricultural University, Beijing, China
| | - Zhiyong Liu
- State Key Laboratory for Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement/Key Laboratory of Crop Heterosis Research & Utilization, Ministry of Education, China Agricultural University, Beijing, China
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Berkman PJ, Visendi P, Lee HC, Stiller J, Manoli S, Lorenc MT, Lai K, Batley J, Fleury D, Simková H, Kubaláková M, Weining S, Doležel J, Edwards D. Dispersion and domestication shaped the genome of bread wheat. PLANT BIOTECHNOLOGY JOURNAL 2013; 11:564-71. [PMID: 23346876 DOI: 10.1111/pbi.12044] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2012] [Revised: 12/10/2012] [Accepted: 12/11/2012] [Indexed: 05/20/2023]
Abstract
Despite the international significance of wheat, its large and complex genome hinders genome sequencing efforts. To assess the impact of selection on this genome, we have assembled genomic regions representing genes for chromosomes 7A, 7B and 7D. We demonstrate that the dispersion of wheat to new environments has shaped the modern wheat genome. Most genes are conserved between the three homoeologous chromosomes. We found differential gene loss that supports current theories on the evolution of wheat, with greater loss observed in the A and B genomes compared with the D. Analysis of intervarietal polymorphisms identified fewer polymorphisms in the D genome, supporting the hypothesis of early gene flow between the tetraploid and hexaploid. The enrichment for genes on the D genome that confer environmental adaptation may be associated with dispersion following wheat domestication. Our results demonstrate the value of applying next-generation sequencing technologies to assemble gene-rich regions of complex genomes and investigate polyploid genome evolution. We anticipate the genome-wide application of this reduced-complexity syntenic assembly approach will accelerate crop improvement efforts not only in wheat, but also in other polyploid crops of significance.
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Affiliation(s)
- Paul J Berkman
- School of Agriculture and Food Sciences, University of Queensland, Brisbane, QLD, Australia
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Huynh BL, Mather DE, Schreiber AW, Toubia J, Baumann U, Shoaei Z, Stein N, Ariyadasa R, Stangoulis JCR, Edwards J, Shirley N, Langridge P, Fleury D. Clusters of genes encoding fructan biosynthesizing enzymes in wheat and barley. PLANT MOLECULAR BIOLOGY 2012; 80:299-314. [PMID: 22864927 DOI: 10.1007/s11103-012-9949-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2012] [Accepted: 07/23/2012] [Indexed: 05/21/2023]
Abstract
Fructans are soluble carbohydrates with health benefits and possible roles in plant adaptation. Fructan biosynthetic genes were isolated using comparative genomics and physical mapping followed by BAC sequencing in barley. Genes encoding sucrose:sucrose 1-fructosyltransferase (1-SST), fructan:fructan 1-fructosyltransferase (1-FFT) and sucrose:fructan 6-fructosyltransferase (6-SFT) were clustered together with multiple copies of vacuolar invertase genes and a transposable element on two barley BAC. Intron-exon structures of the genes were similar. Phylogenetic analysis of the fructosyltransferases and invertases in the Poaceae showed that the fructan biosynthetic genes may have evolved from vacuolar invertases. Quantitative real-time PCR was performed using leaf RNA extracted from three wheat cultivars grown under different conditions. The 1-SST, 1-FFT and 6-SFT genes had correlated expression patterns in our wheat experiment and in existing barley transcriptome database. Single nucleotide polymorphism (SNP) markers were developed and successfully mapped to a major QTL region affecting wheat grain fructan accumulation in two independent wheat populations. The alleles controlling high- and low- fructan in parental lines were also found to be associated in fructan production in a diverse set of 128 wheat lines. To the authors' knowledge, this is the first report on the mapping and sequencing of a fructan biosynthetic gene cluster and in particular, the isolation of a novel 1-FFT gene from barley.
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Affiliation(s)
- Bao-Lam Huynh
- Australian Centre for Plant Functional Genomics and School of Agriculture, Food and Wine, Waite Research Institute, The University of Adelaide, PMB 1, Glen Osmond 5064, South Australia,
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Ren RS, Wang MN, Chen XM, Zhang ZJ. Characterization and molecular mapping of Yr52 for high-temperature adult-plant resistance to stripe rust in spring wheat germplasm PI 183527. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2012; 125:847-57. [PMID: 22562146 DOI: 10.1007/s00122-012-1877-8] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2012] [Accepted: 04/19/2012] [Indexed: 05/20/2023]
Abstract
Stripe rust, caused by Puccinia striiformis f. sp. tritici, is one of the most destructive diseases of wheat worldwide. Resistance is the best approach to control the disease. High-temperature adult-plant (HTAP) stripe rust resistance has proven to be race non-specific and durable. However, genes conferring high-levels of HTAP resistance are limited in number and new genes are urgently needed for breeding programs to develop cultivars with durable high-level resistance to stripe rust. Spring wheat germplasm PI 183527 showed a high-level of HTAP resistance against stripe rust in our germplasm evaluations over several years. To elucidate the genetic basis of resistance, we crossed PI 183527 and susceptible wheat line Avocet S. Adult plants of parents, F(1), F(2) and F(2:3) progeny were tested with selected races under the controlled greenhouse conditions and in fields under natural infection. PI 183527 has a single dominant gene conferring HTAP resistance. Resistance gene analog polymorphism (RGAP) and simple sequence repeat (SSR) markers in combination with bulked segregant analysis (BSA) were used to identify markers linked to the resistance gene. A linkage map consisting of 4 RGAP and 7 SSR markers was constructed for the resistance gene using data from 175 F(2) plants and their derived F(2:3) lines. Amplification of nulli-tetrasomic, ditelosomic and deletion lines of Chinese Spring with three RGAP markers mapped the gene to the distal region (0.86-1.0) of chromosome 7BL. The molecular map spanned a genetic distance of 27.3 cM, and the resistance gene was narrowed to a 2.3-cM interval flanked by markers Xbarc182 and Xwgp5258. The polymorphism rates of the flanking markers in 74 wheat lines were 74 and 30 %, respectively; and the two markers in combination could distinguish the alleles at the resistance locus in 82 % of tested genotypes. To determine the genetic relationship between this resistance gene and Yr39, a gene also on 7BL conferring HTAP resistance in Alpowa, a cross was made between PI 183527 and Alpowa. F(2) segregation indicated that the genes were 36.5 ± 6.75 cM apart. The gene in PI 183527 was therefore designed as Yr52. This new gene and flanking markers should be useful in developing wheat cultivars with high-level and possible durable resistance to stripe rust.
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Affiliation(s)
- R S Ren
- Department of Plant Pathology, China Agricultural University, Beijing 100193, People's Republic of China
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9
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Jakobson I, Reis D, Tiidema A, Peusha H, Timofejeva L, Valárik M, Kladivová M, Simková H, Doležel J, Järve K. Fine mapping, phenotypic characterization and validation of non-race-specific resistance to powdery mildew in a wheat-Triticum militinae introgression line. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2012; 125:609-623. [PMID: 22534789 DOI: 10.1007/s00122-012-1856-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2011] [Accepted: 03/21/2012] [Indexed: 05/31/2023]
Abstract
Introgression of several genomic loci from tetraploid Triticum militinae into bread wheat cv. Tähti has increased resistance of introgression line 8.1 to powdery mildew in seedlings and adult plants. In our previous work, only a major quantitative trait locus (QTL) on chromosome 4AL of the line 8.1 contributed significantly to resistance, whereas QTL on chromosomes 1A, 1B, 2A, 5A and 5B were detected merely on a suggestive level. To verify and characterize all QTLs in the line 8.1, a mapping population of double haploid lines was established. Testing for seedling resistance to 16 different races/mixtures of Blumeria graminis f. sp. tritici revealed four highly significant non-race-specific resistance QTL including the main QTL on chromosome 4AL, and a race-specific QTL on chromosome 5B. The major QTL on chromosome 4AL (QPm.tut-4A) as well as QTL on chromosome 5AL and a newly detected QTL on 7AL were highly effective at the adult stage. The QPm.tut-4A QTL accounts on average for 33-49 % of the variation in resistance in the double haploid population. Interactions between the main QTL QPm.tut-4A and the minor QTL were evaluated and discussed. A population of 98 F(2) plants from a cross of susceptible cv. Chinese Spring and the line 8.1 was created that allowed mapping the QPm.tut-4A locus to the proximal 2.5-cM region of the introgressed segment on chromosome 4AL. The results obtained in this work make it feasible to use QPm.tut-4A in resistance breeding and provide a solid basis for positional cloning of the major QTL.
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Affiliation(s)
- Irena Jakobson
- Department of Gene Technology, Tallinn University of Technology, Akadeemia tee 15, 12618, Tallinn, Estonia.
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10
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Construction of whole genome radiation hybrid panels and map of chromosome 5A of wheat using asymmetric somatic hybridization. PLoS One 2012; 7:e40214. [PMID: 22815731 PMCID: PMC3398029 DOI: 10.1371/journal.pone.0040214] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2011] [Accepted: 06/06/2012] [Indexed: 11/23/2022] Open
Abstract
To explore the feasibility of constructing a whole genome radiation hybrid (WGRH) map in plant species with large genomes, asymmetric somatic hybridization between wheat (Triticum aestivum L.) and Bupleurum scorzonerifolium Willd. was performed. The protoplasts of wheat were irradiated with ultraviolet light (UV) and gamma-ray and rescued by protoplast fusion using B. scorzonerifolium as the recipient. Assessment of SSR markers showed that the radiation hybrids have the average marker retention frequency of 15.5%. Two RH panels (RHPWI and RHPWII) that contained 92 and 184 radiation hybrids, respectively, were developed and used for mapping of 68 SSR markers in chromosome 5A of wheat. A total of 1557 and 2034 breaks were detected in each panel. The RH map of chromosome 5A based on RHPWII was constructed. The distance of the comprehensive map was 2103 cR and the approximate resolution was estimated to be ∼501.6 kb/break. The RH panels evaluated in this study enabled us to order the ESTs in a single deletion bin or in the multiple bins cross the chromosome. These results demonstrated that RH mapping via protoplast fusion is feasible at the whole genome level for mapping purposes in wheat and the potential value of this mapping approach for the plant species with large genomes.
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11
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Azhaguvel P, Rudd JC, Ma Y, Luo MC, Weng Y. Fine genetic mapping of greenbug aphid-resistance gene Gb3 in Aegilops tauschii. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2012; 124:555-64. [PMID: 22038487 DOI: 10.1007/s00122-011-1728-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2011] [Accepted: 10/07/2011] [Indexed: 05/11/2023]
Abstract
The greenbug, Schizaphis graminum (Rondani), is an important aphid pest of small grain crops especially wheat (Triticum aestivum L., 2n = 6x = 42, genomes AABBDD) in many parts of the world. The greenbug-resistance gene Gb3 originated from Aegilops tauschii Coss. (2n = 2x = 14, genome D(t)D(t)) has shown consistent and durable resistance against prevailing greenbug biotypes in wheat fields. We previously mapped Gb3 in a recombination-rich, telomeric bin of wheat chromosome arm 7DL. In this study, high-resolution genetic mapping was carried out using an F(2:3) segregating population derived from two Ae. tauschii accessions, the resistant PI 268210 (original donor of Gb3 in the hexaploid wheat germplasm line 'Largo') and susceptible AL8/78. Molecular markers were developed by exploring bin-mapped wheat RFLPs, SSRs, ESTs and the Ae. tauschii physical map (BAC contigs). Wheat EST and Ae. tauschii BAC end sequences located in the deletion bin 7DL3-0.82-1.00 were used to design STS (sequence tagged site) or CAPS (Cleaved Amplified Polymorphic Sequence) markers. Forty-five PCR-based markers were developed and mapped to the chromosomal region spanning the Gb3 locus. The greenbug-resistance gene Gb3 now was delimited in an interval of 1.1 cM by two molecular markers (HI067J6-R and HI009B3-R). This localized high-resolution genetic map with markers closely linked to Gb3 lays a solid foundation for map based cloning of Gb3 and marker-assisted selection of this gene in wheat breeding.
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Affiliation(s)
- Perumal Azhaguvel
- Texas AgriLife Research, 6500 Amarillo Blvd W, Amarillo, TX 79106, USA.
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12
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Berkman PJ, Skarshewski A, Manoli S, Lorenc MT, Stiller J, Smits L, Lai K, Campbell E, Kubaláková M, Simková H, Batley J, Doležel J, Hernandez P, Edwards D. Sequencing wheat chromosome arm 7BS delimits the 7BS/4AL translocation and reveals homoeologous gene conservation. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2012; 124:423-432. [PMID: 22001910 DOI: 10.1007/s00122-011-1717-2] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2011] [Accepted: 09/27/2011] [Indexed: 05/29/2023]
Abstract
Complex Triticeae genomes pose a challenge to genome sequencing efforts due to their size and repetitive nature. Genome sequencing can reveal details of conservation and rearrangements between related genomes. We have applied Illumina second generation sequencing technology to sequence and assemble the low copy and unique regions of Triticum aestivum chromosome arm 7BS, followed by the construction of a syntenic build based on gene order in Brachypodium. We have delimited the position of a previously reported translocation between 7BS and 4AL with a resolution of one or a few genes and report approximately 13% genes from 7BS having been translocated to 4AL. An additional 13 genes are found on 7BS which appear to have originated from 4AL. The gene content of the 7DS and 7BS syntenic builds indicate a total of ~77,000 genes in wheat. Within wheat syntenic regions, 7BS and 7DS share 740 genes and a common gene conservation rate of ~39% of the genes from the corresponding regions in Brachypodium, as well as a common rate of colinearity with Brachypodium of ~60%. Comparison of wheat homoeologues revealed ~84% of genes previously identified in 7DS have a homoeologue on 7BS or 4AL. The conservation rates we have identified among wheat homoeologues and with Brachypodium provide a benchmark of homoeologous gene conservation levels for future comparative genomic analysis. The syntenic build of 7BS is publicly available at http://www.wheatgenome.info.
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Affiliation(s)
- Paul J Berkman
- School of Agriculture and Food Sciences and Australian Centre for Plant Functional Genomics, University of Queensland, Brisbane, QLD, 4072, Australia
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13
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Dobrovolskaya O, Boeuf C, Salse J, Pont C, Sourdille P, Bernard M, Salina E. Microsatellite mapping of Ae. speltoides and map-based comparative analysis of the S, G, and B genomes of Triticeae species. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2011; 123:1145-1157. [PMID: 21792632 DOI: 10.1007/s00122-011-1655-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2008] [Accepted: 07/09/2011] [Indexed: 05/31/2023]
Abstract
The first microsatellite linkage map of Ae. speltoides Tausch (2n = 2x = 14, SS), which is a wild species with a genome closely related to the B and G genomes of polyploid wheats, was developed based on two F(2) mapping populations using microsatellite (SSR) markers from Ae. speltoides, wheat genomic SSRs (g-SSRs) and EST-derived SSRs. A total of 144 different microsatellite loci were mapped in the Ae. speltoides genome. The transferability of the SSRs markers between the related S, B, and G genomes allowed possible integration of new markers into the T. timopheevii G genome chromosomal maps and map-based comparisons. Thirty-one new microsatellite loci assigned to the genetic framework of the T. timopheevii G genome maps were composed of wheat g-SSR (genomic SSR) markers. Most of the used Ae. speltoides SSRs were mapped onto chromosomes of the G genome supporting a close relationship between the G and S genomes. Comparative microsatellite mapping of the S, B, and G genomes demonstrated colinearity between the chromosomes within homoeologous groups, except for intergenomic T6A(t)S.1G, T4AL.5AL.7BS translocations. A translocation between chromosomes 2 and 6 that is present in the T. aestivum B genome was found in neither Ae. speltoides nor in T. timopheevii. Although the marker order was generally conserved among the B, S, and G genomes, the total length of the Ae. speltoides chromosomal maps and the genetic distances between homoeologous loci located in the proximal regions of the S genome chromosomes were reduced compared with the B, and G genome chromosomes.
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Affiliation(s)
- O Dobrovolskaya
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Lavrentieva Ave. 10, Novosibirsk, 630090, Russia.
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14
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Berkman PJ, Skarshewski A, Lorenc MT, Lai K, Duran C, Ling EYS, Stiller J, Smits L, Imelfort M, Manoli S, McKenzie M, Kubaláková M, Šimková H, Batley J, Fleury D, Doležel J, Edwards D. Sequencing and assembly of low copy and genic regions of isolated Triticum aestivum chromosome arm 7DS. PLANT BIOTECHNOLOGY JOURNAL 2011; 9:768-75. [PMID: 21356002 DOI: 10.1111/j.1467-7652.2010.00587.x] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The genome of bread wheat (Triticum aestivum) is predicted to be greater than 16 Gbp in size and consist predominantly of repetitive elements, making the sequencing and assembly of this genome a major challenge. We have reduced genome sequence complexity by isolating chromosome arm 7DS and applied second-generation technology and appropriate algorithmic analysis to sequence and assemble low copy and genic regions of this chromosome arm. The assembly represents approximately 40% of the chromosome arm and all known 7DS genes. Comparison of the 7DS assembly with the sequenced genomes of rice (Oryza sativa) and Brachypodium distachyon identified large regions of conservation. The syntenic relationship between wheat, B. distachyon and O. sativa, along with available genetic mapping data, has been used to produce an annotated draft 7DS syntenic build, which is publicly available at http://www.wheatgenome.info. Our results suggest that the sequencing of isolated chromosome arms can provide valuable information of the gene content of wheat and is a step towards whole-genome sequencing and variation discovery in this important crop.
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Affiliation(s)
- Paul J Berkman
- School of Land, Crop and Food Sciences and Australian Centre for Plant Functional Genomics, University of Queensland, Brisbane, QLD, Australia
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15
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Wang GF, Wei X, Fan R, Zhou H, Wang X, Yu C, Dong L, Dong Z, Wang X, Kang Z, Ling H, Shen QH, Wang D, Zhang X. Molecular analysis of common wheat genes encoding three types of cytosolic heat shock protein 90 (Hsp90): functional involvement of cytosolic Hsp90s in the control of wheat seedling growth and disease resistance. THE NEW PHYTOLOGIST 2011; 191:418-431. [PMID: 21488877 DOI: 10.1111/j.1469-8137.2011.03715.x] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Heat shock protein 90 (Hsp90) molecular chaperones play important roles in plant growth and responses to environmental stimuli. However, little is known about the genes encoding Hsp90s in common wheat. Here, we report genetic and functional analysis of the genes specifying cytosolic Hsp90s in this species. Three groups of homoeologous genes (TaHsp90.1, TaHsp90.2 and TaHsp90.3), encoding three types of cytosolic Hsp90, were isolated. The loci containing TaHsp90.1, TaHsp90.2 and TaHsp90.3 genes were assigned to groups 2, 7 and 5 chromosomes, respectively. TaHsp90.1 genes exhibited higher transcript levels in the stamen than in the leaf, root and culm. TaHsp90.2 and TaHsp90.3 genes were more ubiquitously transcribed in the vegetative and reproductive organs examined. Decreasing the expression of TaHsp90.1 genes through virus-induced gene silencing (VIGS) caused pronounced inhibition of wheat seedling growth, whereas the suppression of TaHsp90.2 or TaHsp90.3 genes via VIGS compromised the hypersensitive resistance response of the wheat variety Suwon 11 to stripe rust fungus. Our work represents the first systematic determination of wheat genes encoding cytosolic Hsp90s, and provides useful evidence for the functional involvement of cytosolic Hsp90s in the control of seedling growth and disease resistance in common wheat.
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Affiliation(s)
- Guan-Feng Wang
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- Graduate School of Chinese Academy of Sciences, Yuquan Road, Beijing 100039, China
| | - Xuening Wei
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- Graduate School of Chinese Academy of Sciences, Yuquan Road, Beijing 100039, China
| | - Renchun Fan
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Huanbin Zhou
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- Graduate School of Chinese Academy of Sciences, Yuquan Road, Beijing 100039, China
| | - Xianping Wang
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Chunmei Yu
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- Graduate School of Chinese Academy of Sciences, Yuquan Road, Beijing 100039, China
| | - Lingli Dong
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- Graduate School of Chinese Academy of Sciences, Yuquan Road, Beijing 100039, China
| | - Zhenying Dong
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiaojie Wang
- College of Plant Protection and Shaanxi Key Laboratory of Molecular Biology for Agriculture, Northwest A & F University, Yangling 712100, China
| | - Zhensheng Kang
- College of Plant Protection and Shaanxi Key Laboratory of Molecular Biology for Agriculture, Northwest A & F University, Yangling 712100, China
| | - Hongqing Ling
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Qian-Hua Shen
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Daowen Wang
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiangqi Zhang
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
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16
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Barrero RA, Bellgard M, Zhang X. Diverse approaches to achieving grain yield in wheat. Funct Integr Genomics 2011; 11:37-48. [PMID: 21221697 DOI: 10.1007/s10142-010-0208-x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2010] [Accepted: 12/19/2010] [Indexed: 11/28/2022]
Abstract
Artificial selection (domestication and breeding) leaves a strong footprint in plant genomes. Second generation high throughput DNA sequencing technologies make it possible to sequence the gene complement of a plant genome within 3 to 5 months, and the costs of doing so are declining very quickly. This makes it practical to identify genomic regions that have undergone very strong selection. Available reference sequences of important crops such as rice, maize, and sorghum will promote the wide use of re-sequencing strategies in these crops. Marker/trait associations, especially haplotype (or haplotype block) association analyses, will help the precise mapping of important genomic regions and location of favored alleles or haplotypes for breeding. This mini-review examines a genomics approach to defining yield traits in wheat.
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Affiliation(s)
- Roberto A Barrero
- Centre for Comparative Genomics, Murdoch University, Murdoch, WA, 6150, Australia
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17
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Akhunov ED, Akhunova AR, Anderson OD, Anderson JA, Blake N, Clegg MT, Coleman-Derr D, Conley EJ, Crossman CC, Deal KR, Dubcovsky J, Gill BS, Gu YQ, Hadam J, Heo H, Huo N, Lazo GR, Luo MC, Ma YQ, Matthews DE, McGuire PE, Morrell PL, Qualset CO, Renfro J, Tabanao D, Talbert LE, Tian C, Toleno DM, Warburton ML, You FM, Zhang W, Dvorak J. Nucleotide diversity maps reveal variation in diversity among wheat genomes and chromosomes. BMC Genomics 2010; 11:702. [PMID: 21156062 PMCID: PMC3022916 DOI: 10.1186/1471-2164-11-702] [Citation(s) in RCA: 138] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2010] [Accepted: 12/14/2010] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND A genome-wide assessment of nucleotide diversity in a polyploid species must minimize the inclusion of homoeologous sequences into diversity estimates and reliably allocate individual haplotypes into their respective genomes. The same requirements complicate the development and deployment of single nucleotide polymorphism (SNP) markers in polyploid species. We report here a strategy that satisfies these requirements and deploy it in the sequencing of genes in cultivated hexaploid wheat (Triticum aestivum, genomes AABBDD) and wild tetraploid wheat (Triticum turgidum ssp. dicoccoides, genomes AABB) from the putative site of wheat domestication in Turkey. Data are used to assess the distribution of diversity among and within wheat genomes and to develop a panel of SNP markers for polyploid wheat. RESULTS Nucleotide diversity was estimated in 2114 wheat genes and was similar between the A and B genomes and reduced in the D genome. Within a genome, diversity was diminished on some chromosomes. Low diversity was always accompanied by an excess of rare alleles. A total of 5,471 SNPs was discovered in 1791 wheat genes. Totals of 1,271, 1,218, and 2,203 SNPs were discovered in 488, 463, and 641 genes of wheat putative diploid ancestors, T. urartu, Aegilops speltoides, and Ae. tauschii, respectively. A public database containing genome-specific primers, SNPs, and other information was constructed. A total of 987 genes with nucleotide diversity estimated in one or more of the wheat genomes was placed on an Ae. tauschii genetic map, and the map was superimposed on wheat deletion-bin maps. The agreement between the maps was assessed. CONCLUSIONS In a young polyploid, exemplified by T. aestivum, ancestral species are the primary source of genetic diversity. Low effective recombination due to self-pollination and a genetic mechanism precluding homoeologous chromosome pairing during polyploid meiosis can lead to the loss of diversity from large chromosomal regions. The net effect of these factors in T. aestivum is large variation in diversity among genomes and chromosomes, which impacts the development of SNP markers and their practical utility. Accumulation of new mutations in older polyploid species, such as wild emmer, results in increased diversity and its more uniform distribution across the genome.
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Affiliation(s)
- Eduard D Akhunov
- Department of Plant Sciences, University of California, Davis, CA 95616, USA
- Department of Plant Pathology, KSU, Manhattan, KS 66506, USA
| | - Alina R Akhunova
- Department of Plant Sciences, University of California, Davis, CA 95616, USA
- Department of Plant Pathology, KSU, Manhattan, KS 66506, USA
| | - Olin D Anderson
- Genomics and Gene Discovery Unit, USDA/ARS Western Regional Research Center, Albany, CA 94710, USA
| | - James A Anderson
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, USA
| | - Nancy Blake
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT 59717, USA
| | - Michael T Clegg
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697, USA
| | - Devin Coleman-Derr
- Genomics and Gene Discovery Unit, USDA/ARS Western Regional Research Center, Albany, CA 94710, USA
| | - Emily J Conley
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, USA
| | - Curt C Crossman
- Genomics and Gene Discovery Unit, USDA/ARS Western Regional Research Center, Albany, CA 94710, USA
| | - Karin R Deal
- Department of Plant Sciences, University of California, Davis, CA 95616, USA
| | - Jorge Dubcovsky
- Department of Plant Sciences, University of California, Davis, CA 95616, USA
| | - Bikram S Gill
- Department of Plant Pathology, Kansas State University, Manhattan KS 66506, USA
| | - Yong Q Gu
- Genomics and Gene Discovery Unit, USDA/ARS Western Regional Research Center, Albany, CA 94710, USA
| | - Jakub Hadam
- Department of Plant Pathology, Kansas State University, Manhattan KS 66506, USA
| | - Hwayoung Heo
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT 59717, USA
| | - Naxin Huo
- Genomics and Gene Discovery Unit, USDA/ARS Western Regional Research Center, Albany, CA 94710, USA
| | - Gerard R Lazo
- Genomics and Gene Discovery Unit, USDA/ARS Western Regional Research Center, Albany, CA 94710, USA
| | - Ming-Cheng Luo
- Department of Plant Sciences, University of California, Davis, CA 95616, USA
| | - Yaqin Q Ma
- Department of Plant Sciences, University of California, Davis, CA 95616, USA
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
| | | | - Patrick E McGuire
- Department of Plant Sciences, University of California, Davis, CA 95616, USA
| | - Peter L Morrell
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, USA
| | - Calvin O Qualset
- Department of Plant Sciences, University of California, Davis, CA 95616, USA
| | - James Renfro
- Genomics and Gene Discovery Unit, USDA/ARS Western Regional Research Center, Albany, CA 94710, USA
| | - Dindo Tabanao
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, USA
- Philippine Rice Research Institute, Maligaya, Nueva Ecija, Philippines
| | - Luther E Talbert
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT 59717, USA
| | - Chao Tian
- Department of Plant Sciences, University of California, Davis, CA 95616, USA
| | - Donna M Toleno
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697, USA
| | - Marilyn L Warburton
- The International Maize and Wheat Improvement Center (CIMMYT), 06600 Mexico, D.F., Mexico
- Corn Host Plant Research Resistance Unit, USDA/ARS MSU MS 39762, USA
| | - Frank M You
- Department of Plant Sciences, University of California, Davis, CA 95616, USA
| | - Wenjun Zhang
- Department of Plant Sciences, University of California, Davis, CA 95616, USA
| | - Jan Dvorak
- Department of Plant Sciences, University of California, Davis, CA 95616, USA
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18
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Akhunov ED, Akhunova AR, Anderson OD, Anderson JA, Blake N, Clegg MT, Coleman-Derr D, Conley EJ, Crossman CC, Deal KR, Dubcovsky J, Gill BS, Gu YQ, Hadam J, Heo H, Huo N, Lazo GR, Luo MC, Ma YQ, Matthews DE, McGuire PE, Morrell PL, Qualset CO, Renfro J, Tabanao D, Talbert LE, Tian C, Toleno DM, Warburton ML, You FM, Zhang W, Dvorak J. Nucleotide diversity maps reveal variation in diversity among wheat genomes and chromosomes. BMC Genomics 2010. [PMID: 21156062 DOI: 10.1186/1471‐2164‐11‐702] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND A genome-wide assessment of nucleotide diversity in a polyploid species must minimize the inclusion of homoeologous sequences into diversity estimates and reliably allocate individual haplotypes into their respective genomes. The same requirements complicate the development and deployment of single nucleotide polymorphism (SNP) markers in polyploid species. We report here a strategy that satisfies these requirements and deploy it in the sequencing of genes in cultivated hexaploid wheat (Triticum aestivum, genomes AABBDD) and wild tetraploid wheat (Triticum turgidum ssp. dicoccoides, genomes AABB) from the putative site of wheat domestication in Turkey. Data are used to assess the distribution of diversity among and within wheat genomes and to develop a panel of SNP markers for polyploid wheat. RESULTS Nucleotide diversity was estimated in 2114 wheat genes and was similar between the A and B genomes and reduced in the D genome. Within a genome, diversity was diminished on some chromosomes. Low diversity was always accompanied by an excess of rare alleles. A total of 5,471 SNPs was discovered in 1791 wheat genes. Totals of 1,271, 1,218, and 2,203 SNPs were discovered in 488, 463, and 641 genes of wheat putative diploid ancestors, T. urartu, Aegilops speltoides, and Ae. tauschii, respectively. A public database containing genome-specific primers, SNPs, and other information was constructed. A total of 987 genes with nucleotide diversity estimated in one or more of the wheat genomes was placed on an Ae. tauschii genetic map, and the map was superimposed on wheat deletion-bin maps. The agreement between the maps was assessed. CONCLUSIONS In a young polyploid, exemplified by T. aestivum, ancestral species are the primary source of genetic diversity. Low effective recombination due to self-pollination and a genetic mechanism precluding homoeologous chromosome pairing during polyploid meiosis can lead to the loss of diversity from large chromosomal regions. The net effect of these factors in T. aestivum is large variation in diversity among genomes and chromosomes, which impacts the development of SNP markers and their practical utility. Accumulation of new mutations in older polyploid species, such as wild emmer, results in increased diversity and its more uniform distribution across the genome.
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Affiliation(s)
- Eduard D Akhunov
- Department of Plant Sciences, University of California, Davis, CA 95616, USA
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19
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Luo S, Peng J, Li K, Wang M, Kuang H. Contrasting Evolutionary Patterns of the Rp1 Resistance Gene Family in Different Species of Poaceae. Mol Biol Evol 2010; 28:313-25. [DOI: 10.1093/molbev/msq216] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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20
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Ben-David R, Xie W, Peleg Z, Saranga Y, Dinoor A, Fahima T. Identification and mapping of PmG16, a powdery mildew resistance gene derived from wild emmer wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2010; 121:499-510. [PMID: 20407741 DOI: 10.1007/s00122-010-1326-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2009] [Accepted: 03/12/2010] [Indexed: 05/04/2023]
Abstract
The gene-pool of wild emmer wheat, Triticum turgidum ssp. dicoccoides, harbors a rich allelic repertoire for disease resistance. In the current study, we made use of tetraploid wheat mapping populations derived from a cross between durum wheat (cv. Langdon) and wild emmer (accession G18-16) to identify and map a new powdery mildew resistance gene derived from wild emmer wheat. Initially, the two parental lines were screened with a collection of 42 isolates of Blumeria graminis f. sp. tritici (Bgt) from Israel and 5 isolates from Switzerland. While G18-16 was resistant to 34 isolates, Langdon was resistant only to 5 isolates and susceptible to 42 isolates. Isolate Bgt#15 was selected to differentiate between the disease reactions of the two genotypes. Segregation ratio of F(2-3) and recombinant inbreed line (F(7)) populations to inoculation with isolate Bgt#15 indicated the role of a single dominant gene in conferring resistance to Bgt#15. This gene, temporarily designated PmG16, was located on the distal region of chromosome arm 7AL. Genetic map of PmG16 region was assembled with 32 simple sequence repeat (SSR), sequence tag site (STS), Diversity array technology (DArT) and cleaved amplified polymorphic sequence (CAPS) markers and assigned to the 7AL physical bin map (7AL-16). Using four DNA markers we established colinearity between the genomic region spanning the PmG16 locus within the distal region of chromosome arm 7AL and the genomic regions on rice chromosome 6 and Brachypodium Bd1. A comparative analysis was carried out between PmG16 and other known Pm genes located on chromosome arm 7AL. The identified PmG16 may facilitate the use of wild alleles for improvement of powdery mildew resistance in elite wheat cultivars via marker-assisted selection.
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Affiliation(s)
- Roi Ben-David
- Department of Evolutionary and Environmental Biology, The Institute of Evolution, Faculty of Science and Science Education, University of Haifa, Mt. Carmel, 31905, Haifa, Israel
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Shavrukov Y, Gupta NK, Miyazaki J, Baho MN, Chalmers KJ, Tester M, Langridge P, Collins NC. HvNax3—a locus controlling shoot sodium exclusion derived from wild barley (Hordeum vulgare ssp. spontaneum). Funct Integr Genomics 2010; 10:277-91. [DOI: 10.1007/s10142-009-0153-8] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2009] [Revised: 12/03/2009] [Accepted: 12/13/2009] [Indexed: 01/17/2023]
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Kuraparthy V, Sood S, Gill BS. Molecular genetic description of the cryptic wheat-Aegilops geniculata introgression carrying rust resistance genes Lr57 and Yr40 using wheat ESTs and synteny with rice. Genome 2009; 52:1025-36. [PMID: 19953130 DOI: 10.1139/g09-076] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
The cryptic wheat-alien translocation T5DL.5DS-5MgS(0.95), with leaf rust and stripe rust resistance genes Lr57 and Yr40 transferred from Aegilops geniculata (UgMg) into common wheat, was further analyzed. Molecular genetic analysis using physically mapped ESTs showed that the alien segment in T5DL.5DS-5MgS(0.95) represented only a fraction of the wheat deletion bin 5DS2-0.78-1.00 and was less than 3.3 cM in length in the diploid wheat genetic map. Comparative genomic analysis indicated a high level of colinearity between the distal region of the long arm of chromosome 12 of rice and the genomic region spanning the Lr57 and Yr40 genes in wheat. The alien segment with genes Lr57 and Yr40 corresponds to fewer than four overlapping BAC or PAC clones of the syntenic rice chromosome arm 12L. The wheat-alien translocation breakpoint in T5DL.5DS-5MgS(0.95) was further localized to a single BAC clone of the syntenic rice genomic sequence. The small size of the terminal wheat-alien translocation, as established precisely with respect to Chinese Spring deletion bins and the syntenic rice genomic sequence, further confirmed the escaping nature of cryptic wheat-alien translocations in introgressive breeding. The molecular genetic resources and information developed in the present study will facilitate further fine-scale physical mapping and map-based cloning of the Lr57 and Yr40 genes.
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Affiliation(s)
- Vasu Kuraparthy
- Crop Science Department, North Carolina State University, Raleigh, NC 27695, USA
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A molecular-cytogenetic method for locating genes to pericentromeric regions facilitates a genomewide comparison of synteny between the centromeric regions of wheat and rice. Genetics 2009; 183:1235-47. [PMID: 19797045 DOI: 10.1534/genetics.109.107409] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Centromeres, because of their repeat structure and lack of sequence conservation, are difficult to assemble and compare across organisms. It was recently discovered that rice centromeres often contain genes. This suggested a method for studying centromere homologies between wheat and rice chromosomes by mapping rice centromeric genes onto wheat aneuploid stocks. Three of the seven cDNA clones of centromeric genes from rice centromere 8 (Cen8), 6729.t09, 6729.t10, and 6730.t11 which lie in the Cen8 kinetochore region, and three wheat ESTs, BJ301191, BJ305475, and BJ280500, with similarity to sequences of rice centromeric genes, were mapped to the centromeric regions of the wheat group-7 (W7) chromosomes. A possible pericentric inversion in chromosome 7D was detected. Genomewide comparison of wheat ESTs that mapped to centromeric regions against rice genome sequences revealed high conservation and a one-to-one correspondence of centromeric regions between wheat and rice chromosome pairs W1-R5, W2-R7, W3-R1, W5-R12, W6-R2, and W7-R8. The W4 centromere may share homology with R3 only or with R3 + R11. Wheat ESTs that mapped to the pericentromeric region of the group-5 long arm anchored to the rice BACs located in the recently duplicated region at the distal ends of the short arms of rice chromosomes 11 and 12. A pericentric inversion specific to the rice lineage was detected. The depicted framework provides a working model for further studies on the structure and evolution of cereal chromosome centromeres.
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Ishikawa G, Nakamura T, Ashida T, Saito M, Nasuda S, Endo TR, Wu J, Matsumoto T. Localization of anchor loci representing five hundred annotated rice genes to wheat chromosomes using PLUG markers. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2009; 118:499-514. [PMID: 19057889 DOI: 10.1007/s00122-008-0916-y] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2008] [Accepted: 10/09/2008] [Indexed: 05/02/2023]
Abstract
PCR-based Landmark Unique Gene (PLUG) markers are EST-PCR markers developed based on the orthologous gene conservation between rice and wheat, and on the intron polymorphisms among the three orthologous genes derived from the A, B and D genomes of wheat. We designed a total of 960 primer sets from wheat ESTs that showed high similarity with 951 single-copy rice genes. When genomic DNA of Chinese Spring wheat was used as a template, 872 primer sets amplified one to five distinct products. Out of these 872 PLUG markers, 531 were assigned to one or more chromosomes by nullisomic-tetrasomic analysis. For each wheat chromosome, the number of loci detected ranged from 32 for chromosome 6A to 73 for chromosome 7D, with an average of 48 loci per chromosome. Several novel synteny perturbations were identified using deletion bin-mapping of markers. Furthermore, we demonstrated that PLUG markers can be used as probes to simultaneously identify BAC clones that contain homoeologous regions from all three genomes.
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Affiliation(s)
- Goro Ishikawa
- Tohoku National Agriculture Research Center, Morioka, Iwate, 020-0198, Japan
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25
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Maccaferri M, Mantovani P, Tuberosa R, Deambrogio E, Giuliani S, Demontis A, Massi A, Sanguineti MC. A major QTL for durable leaf rust resistance widely exploited in durum wheat breeding programs maps on the distal region of chromosome arm 7BL. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2008; 117:1225-40. [PMID: 18712342 DOI: 10.1007/s00122-008-0857-5] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2008] [Accepted: 07/28/2008] [Indexed: 05/02/2023]
Abstract
A recombinant inbred line (RIL) population and a set of advanced lines from multiple crosses were used to investigate the leaf rust (Puccinia triticina Eriks.) resistance carried by the durum wheat cultivar Creso and its derivatives (Colosseo and Plinio). One hundred seventy-six RILs from the cross Colosseo x Lloyd were tested under artificial rust inoculation in the field. The response at the seedling stage was also investigated. A major QTL (QLr.ubo-7B.2) for leaf rust resistance controlling both the seedling and the adult open field based-response was mapped on 7BL, with the favourable allele inherited from Colosseo. QLr.ubo-7B.2 showed R2 and LOD peak values for the area under disease progress curve (AUDPC) equal to 72.9% and 44.5, respectively. The presence and location of QLr.ubo-7B.2 was validated by a linkage disequilibrium-based test using two-year field data of 62 advanced lines from 21 crosses with Creso, Colosseo or Plinio as resistance donors. QLr.ubo-7B.2 maps in a gene-dense region (7BL10-0.78-1.00) carrying several genes/QTLs in wheat and barley for resistance to rusts and other fungal diseases.
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Affiliation(s)
- M Maccaferri
- Department of Agroenvironmental Science and Technology, University of Bologna, Viale G. Fanin 44, 40127, Bologna, Italy
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Jenkins G, Phillips D, Mikhailova EI, Timofejeva L, Jones RN. Meiotic genes and proteins in cereals. Cytogenet Genome Res 2008; 120:291-301. [PMID: 18504358 DOI: 10.1159/000121078] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/23/2007] [Indexed: 12/20/2022] Open
Abstract
We review the current status of our understanding and knowledge of the genes and proteins controlling meiosis in five major cereals, rye, wheat, barley, rice and maize. For each crop, we describe the genetic and genomic infrastructure available to investigators, before considering the inventory of genes and proteins that have roles to play in this process. Emphasis is given throughout as to how translational genomic and proteomic approaches have enabled us to circumvent some of the intractable features of this important group of plants.
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Affiliation(s)
- G Jenkins
- Institute of Biological Sciences, University of Wales, Aberystwyth, UK.
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Zhou RN, Shi R, Jiang SM, Yin WB, Wang HH, Chen YH, Hu J, Wang RRC, Zhang XQ, Hu ZM. Rapid EST isolation from chromosome 1R of rye. BMC PLANT BIOLOGY 2008; 8:28. [PMID: 18366673 PMCID: PMC2322994 DOI: 10.1186/1471-2229-8-28] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2007] [Accepted: 03/18/2008] [Indexed: 05/26/2023]
Abstract
BACKGROUND To obtain important expressed sequence tags (ESTs) located on specific chromosomes is currently difficult. Construction of single-chromosome EST library could be an efficient strategy to isolate important ESTs located on specific chromosomes. In this research we developed a method to rapidly isolate ESTs from chromosome 1R of rye by combining the techniques of chromosome microdissection with hybrid specific amplification (HSA). RESULTS Chromosome 1R was isolated by a glass needle and digested with proteinase K (PK). The DNA of chromosome 1R was amplified by two rounds of PCR using a degenerated oligonucleotide 6-MW sequence with a Sau3AI digestion site as the primer. The PCR product was digested with Sau3AI and linked with adaptor HSA1, then hybridized with the Sau3AI digested cDNA with adaptor HSA2 of rye leaves with and without salicylic acid (SA) treatment, respectively. The hybridized DNA fragments were recovered by the HSA method and cloned into pMD18-T vector. The cloned inserts were released by PCR using the partial sequences in HSA1 and HSA2 as the primers and then sequenced. Of the 94 ESTs obtained and analyzed, 6 were known sequences located on rye chromosome 1R or on homologous group 1 chromosomes of wheat; all of them were highly homologous with ESTs of wheat, barley and/or other plants in Gramineae, some of which were induced by abiotic or biotic stresses. Isolated in this research were 22 ESTs with unknown functions, probably representing some new genes on rye chromosome 1R. CONCLUSION We developed a new method to rapidly clone chromosome-specific ESTs from chromosome 1R of rye. The information reported here should be useful for cloning and investigating the new genes found on chromosome 1R.
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Affiliation(s)
- Ruo-Nan Zhou
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, P. R. China
- Graduate University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Rui Shi
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, P. R. China
- Forest Biotechnology Group, N.C. State University, Campus Box 7247, Raleigh, NC 27695-7247, USA
| | - Shu-Mei Jiang
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, P. R. China
- South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, P. R. China
| | - Wei-Bo Yin
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, P. R. China
| | - Huang-Huang Wang
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, P. R. China
| | - Yu-Hong Chen
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, P. R. China
| | - Jun Hu
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, P. R. China
| | - Richard RC Wang
- USDA-ARS, FRRL, Utah State University, Logan, UT 84322-6300, USA
| | - Xiang-Qi Zhang
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, P. R. China
| | - Zan-Min Hu
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, P. R. China
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Perugini LD, Murphy JP, Marshall D, Brown-Guedira G. Pm37, a new broadly effective powdery mildew resistance gene from Triticum timopheevii. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2008; 116:417-25. [PMID: 18092148 DOI: 10.1007/s00122-007-0679-x] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2007] [Accepted: 11/10/2007] [Indexed: 05/18/2023]
Abstract
Powdery mildew is an important foliar disease in wheat, especially in areas with a cool or maritime climate. A dominant powdery mildew resistance gene transferred to the hexaploid germplasm line NC99BGTAG11 from T. timopheevii subsp. armeniacum was mapped distally on the long arm of chromosome 7A. Differential reactions were observed between the resistance gene in NC99BGTAG11 and the alleles of the Pm1 locus that is also located on chromosome arm 7AL. Observed segregation in F2:3 lines from the cross NC99BGTAG11xAxminster (Pm1a) demonstrate that germplasm line NC99BGTAG11 carries a novel powdery mildew resistance gene, which is now designated as Pm37. This new gene is highly effective against all powdery mildew isolates tested so far. Analyses of the population with molecular markers indicate that Pm37 is located 16 cM proximal to the Pm1 complex. Simple sequence repeat (SSR) markers Xgwm332 and Xwmc790 were located 0.5 cM proximal and distal, respectively, to Pm37. In order to identify new markers in the region, wheat expressed sequence tags (ESTs) located in the distal 10% of 7AL that were orthologous to sequences from chromosome 6 of rice were targeted. The two new EST-derived STS markers were located distal to Pm37 and one marker was closely linked to the Pm1a region. These new markers can be used in marker-assisted selection schemes to develop wheat cultivars with pyramids of powdery mildew resistance genes, including combinations of Pm37 in coupling linkage with alleles of the Pm1 locus.
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Affiliation(s)
- L D Perugini
- Department of Crop Science, North Carolina State University, Raleigh, NC 27695, USA.
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29
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Leonard JM, Watson CJW, Carter AH, Hansen JL, Zemetra RS, Santra DK, Campbell KG, Riera-Lizarazu O. Identification of a candidate gene for the wheat endopeptidase Ep-D1 locus and two other STS markers linked to the eyespot resistance gene Pch1. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2008; 116:261-70. [PMID: 17952400 DOI: 10.1007/s00122-007-0664-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2007] [Accepted: 10/07/2007] [Indexed: 05/11/2023]
Abstract
Wheat is prone to strawbreaker foot rot (eyespot), a fungal disease caused by Oculimacula yallundae and O. acuformis. The most effective source of genetic resistance is Pch1, a gene derived from Aegilops ventricosa. The endopeptidase isozyme marker allele Ep-D1b, linked to Pch1, has been shown to be more effective for tracking resistance than DNA-based markers developed to date. Therefore, we sought to identify a candidate gene for Ep-D1 as a basis for a DNA-based marker. Comparative mapping suggested that the endopeptidase loci Ep-D1 (wheat), enp1 (maize), and Enp (rice) were orthologous. Since the product of the maize endopeptidase locus enp1 has been shown to exhibit biochemical properties similar to oligopeptidase B purified from E. coli, we reasoned that Ep-D1 may also encode an oligopeptidase B. Consistent with this hypothesis, a sequence-tagged-site (STS) marker, Xorw1, derived from an oligopeptidase B-encoding wheat expressed-sequence-tag (EST) showed complete linkage with Ep-D1 and Pch1 in a population of 254 recombinant inbred lines (RILs) derived from a cross between wheat cultivars Coda and Brundage. Two other STS markers, Xorw5 and Xorw6, and three microsatellite markers (Xwmc14, Xbarc97, and Xcfd175) were also completely linked to Pch1. On the other hand, Xwmc14, Xbarc97, and Xcfd175 showed recombination in the W7984 x Opata85 RIL population suggesting that recombination near Pch1 is reduced in the Coda/Brundage population. In a panel of 44 wheat varieties with known eyespot reactions, Xorw1, Xorw5, and Xorw6 were 100% accurate in predicting the presence or absence of Pch1 whereas Xwmc14, Xbarc97, and Xcfd175 were less effective. Thus, linkage mapping and a germplasm survey suggest that the STS markers identified here should be useful for indirect selection of Pch1.
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Affiliation(s)
- Jeffrey M Leonard
- Department of Crop and Soil Science, Oregon State University, 107 Crop Science Bldg, Corvallis, OR 97331, USA
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30
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Xu ZS, Xia LQ, Chen M, Cheng XG, Zhang RY, Li LC, Zhao YX, Lu Y, Ni ZY, Liu L, Qiu ZG, Ma YZ. Isolation and molecular characterization of the Triticum aestivum L. ethylene-responsive factor 1 (TaERF1) that increases multiple stress tolerance. PLANT MOLECULAR BIOLOGY 2007; 65:719-32. [PMID: 17874224 DOI: 10.1007/s11103-007-9237-9] [Citation(s) in RCA: 196] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2007] [Accepted: 08/29/2007] [Indexed: 05/02/2023]
Abstract
ERF transcription factors play important roles in regulating gene expression under abiotic and biotic stresses. The first member of the ERF gene family in wheat (Triticum aestivum L.) was isolated by screening a drought-induced cDNA library and designated as T. aestivum ethylene-responsive factor 1 (TaERF1), which encoded a putative protein of 355 amino acids with a conserved DNA-binding domain and a conserved N-terminal motif (MCGGAIL). The TaERF1 gene was located on chromosome 7A. Protein interaction assays indicated that TaERF1, with a putative phosphorylation site (TPDITS) in the C-terminal region, was a potential phosphorylation substrate for TaMAPK1 protein kinase. Deletion of the N-terminal motif enhanced the interaction of TaERF1 with TaMAPK1. The predicted TaERF1 protein contained three putative nuclear localization signals (NLSs), and three NLSs modulated synergistically the activity of subcellular localization. As a trans-acting factor, TaERF1 was capable of binding to the GCC-box and CRT/DRE elements in vitro, and of trans-activating reporter gene expression in tobacco (Nicotiana tabacum L.) leaves. Transcription of the TaERF1 gene was induced not only by drought, salinity and low-temperature stresses and exogenous ABA, ethylene and salicylic acid, but also by infection with Blumeria graminis f. sp. tritici. Furthermore, overexpression of TaERF1 activated stress-related genes, including PR and COR/RD genes, under normal growth conditions, and improved pathogen and abiotic stress tolerance in transgenic plants. These results suggested that the TaERF1 gene encodes a GCC-box and CRT/DRE element binding factor that might be involved in multiple stress signal transduction pathways.
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Affiliation(s)
- Zhao-Shi Xu
- National Key Facility of Crop Gene Resources and Genetic Improvement, Key Laboratory of Crop Genetics and Breeding, Ministry of Agriculture, Institute of Crop Science, Chinese Academy of Agriculture Sciences, Beijing 100081, PR China
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Ayala-Navarrete L, Bariana HS, Singh RP, Gibson JM, Mechanicos AA, Larkin PJ. Trigenomic chromosomes by recombination of Thinopyrum intermedium and Th. ponticum translocations in wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2007; 116:63-75. [PMID: 17906848 DOI: 10.1007/s00122-007-0647-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2007] [Accepted: 09/09/2007] [Indexed: 05/17/2023]
Abstract
Rusts and barley yellow dwarf virus (BYDV) are among the main diseases affecting wheat production world wide for which wild relatives have been the source of a number of translocations carrying resistance genes. Nevertheless, along with desirable traits, alien translocations often carry deleterious genes. We have generated recombinants in a bread wheat background between two alien translocations: TC5, ex-Thinopyrum (Th) intermedium, carrying BYDV resistance gene Bdv2; and T4m, ex-Th. ponticum, carrying rust resistance genes Lr19 and Sr25. Because both these translocations are on the wheat chromosome arm 7DL, homoeologous recombination was attempted in the double hemizygote (TC5/T4m) in a background homozygous for the ph1b mutation. The identification of recombinants was facilitated by the use of newly developed molecular markers for each of the alien genomes represented in the two translocations and by studying derived F(2), F(3) and doubled haploid populations. The occurrence of recombination was confirmed with molecular markers and bioassays on families of testcrosses between putative recombinants and bread wheat, and in F(2) populations derived from the testcrosses. As a consequence it has been possible to derive a genetic map of markers and resistance genes on these previously fixed alien linkage blocks. We have obtained fertile progeny carrying new tri-genomic recombinant chromosomes. Furthermore we have demonstrated that some of the recombinants carried resistance genes Lr19 and Bdv2 yet lacked the self-elimination trait associated with shortened T4 segments. We have also shown that the recombinant translocations are fixed and stable once removed from the influence of the ph1b. The molecular markers developed in this study will facilitate selection of individuals carrying recombinant Th. intermedium-Th. ponticum translocations (Pontin series) in breeding programs.
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Schnurbusch T, Collins NC, Eastwood RF, Sutton T, Jefferies SP, Langridge P. Fine mapping and targeted SNP survey using rice-wheat gene colinearity in the region of the Bo1 boron toxicity tolerance locus of bread wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2007; 115:451-61. [PMID: 17571251 DOI: 10.1007/s00122-007-0579-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2007] [Accepted: 05/21/2007] [Indexed: 05/11/2023]
Abstract
Toxicity due to high levels of soil boron (B) represents a significant limitation to cereal production in some regions, and the Bo1 gene provides a major source of B toxicity tolerance in bread wheat (Triticum aestivum L.). A novel approach was used to develop primers to amplify and sequence gene fragments specifically from the Bo1 region of the hexaploid wheat genome. Single-nucleotide polymorphisms (SNPs) identified were then used to generate markers close to Bo1 on the distal end of chromosome 7BL. In the 16 gene fragments totaling 19.6 kb, SNPs were observed between the two cultivars Cranbrook and Halberd at a low frequency (one every 613 bp). Furthermore, SNPs were distributed unevenly, being limited to only two genes. In contrast, RFLP provided a much greater number of genetic markers, with every tested gene identifying polymorphism. Bo1 previously known only as a QTL was located as a discrete Mendelian locus. In total, 28 new RFLP, PCR and SSR markers were added to the existing map. The 1.8 cM Bo1 interval of wheat corresponds to a 227 kb section of rice chromosome 6L encoding 21 predicted proteins with no homology to any known B transporters. The co-dominant PCR marker AWW5L7 co-segregated with Bo1 and was highly predictive of B tolerance status within a set of 94 Australian bread wheat cultivars and breeding lines. The markers and rice colinearity described here represent tools that will assist B tolerance breeding and the positional cloning of Bo1.
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Affiliation(s)
- Thorsten Schnurbusch
- Australian Centre for Plant Functional Genomics, University of Adelaide, Waite Campus, PMB1, Glen Osmond, SA, 5064, Australia.
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33
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Röder MS, Huang XQ, Börner A. Fine mapping of the region on wheat chromosome 7D controlling grain weight. Funct Integr Genomics 2007; 8:79-86. [PMID: 17554574 DOI: 10.1007/s10142-007-0053-8] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2007] [Revised: 05/10/2007] [Accepted: 05/14/2007] [Indexed: 10/23/2022]
Abstract
We report the fine mapping of the previously described quantitative trait loci (QTL) for grain weight QTgw.ipk-7D associated with microsatellite marker Xgwm1002-7D by using introgression lines (ILs) carrying introgressions of the synthetic wheat W-7984 in the genetic background of the German winter wheat variety 'Prinz'. The BC(4)F(3) ILs had a 10% increased thousand grain weight compared to the control group and the recurrent parent 'Prinz', and 84.7% of the phenotypic variance could be explained by the segregation of marker Xgwm1002-7D, suggesting the presence of a gene modulating grain weight, which was preliminarily designated gw1. It was possible to delimit the QTL QTgw.ipk-7D to the interval Xgwm295-Xgwm1002, which is located in the most telomeric bin 7DS4-0.61-1.00 in the physical map of wheat chromosome arm 7DS. Furthermore, our data suggest the presence of a novel plant height-reducing locus Rht on chromosome arm 7DS of 'Prinz'. Larger grain and increased plant height may reflect the pleiotropic action of one gene or may be caused by two linked genes. In general, our data support the concept of using nearly isogenic ILs for validating and dissecting QTLs into single Mendelian genes and open the gateway for map-based cloning of a grain-weight QTL in wheat.
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Affiliation(s)
- Marion S Röder
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Gatersleben, Germany.
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Yao G, Zhang J, Yang L, Xu H, Jiang Y, Xiong L, Zhang C, Zhang Z, Ma Z, Sorrells ME. Genetic mapping of two powdery mildew resistance genes in einkorn (Triticum monococcum L.) accessions. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2007; 114:351-8. [PMID: 17091263 DOI: 10.1007/s00122-006-0438-4] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2006] [Accepted: 10/17/2006] [Indexed: 05/12/2023]
Abstract
Powdery mildew is a severe foliar disease for wheat and could cause great yield loss in epidemic years. To explore new powdery mildew resistance genes, two einkorn accessions including TA2033 and M80, both resistant to this disease, were studied for the inheritance of resistance. Each accession possessed a single but different dominant resistance gene that was designated as Mlm2033 and Mlm80, respectively. Marker mapping indicated that they are both linked to Xgwm344 on the long arm of chromosome 7A. To establish their genetic relationship with Pm1 on 7AL, five RFLP markers previously reported to co-segregate with Pm1a were converted to STS markers. Three of them detected polymorphism between the mapping parents and were mapped close to Mlm2033 or Mlm80 or both. Xmag2185, the locus determined by the STS marker derived from PSR680, one of the RFLP markers, was placed less than 2 cM away from them. The allelism test indicated that Mlm2033 and Mlm80 are likely allelic to each other. In addition, through comparative and EST mapping, more markers linked to these two genes were identified. The high density mapping of Mlm2033 and Mlm80 will contribute to map-based cloning of the Pm1 locus. The markers for both genes will also facilitate their transfer to wheat.
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Affiliation(s)
- Guoqi Yao
- The Applied Plant Genomics Lab and National Key Lab for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 210095, Jiangsu, People's Republic of China
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Janni M, Di Giovanni M, Roberti S, Capodicasa C, D'Ovidio R. Characterization of expressed Pgip genes in rice and wheat reveals similar extent of sequence variation to dicot PGIPs and identifies an active PGIP lacking an entire LRR repeat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2006; 113:1233-45. [PMID: 16906405 DOI: 10.1007/s00122-006-0378-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2006] [Accepted: 07/20/2006] [Indexed: 05/11/2023]
Abstract
Polygalacturonase-inhibiting proteins (PGIPs) are leucine-rich repeat (LRR) proteins involved in plant defence. A number of PGIPs have been characterized from dicot species, whereas only a few data are available from monocots. Database searches and genome-specific cloning strategies allowed the identification of four rice (Oryza sativa L.) and two wheat (Triticum aestivum L.) Pgip genes. The rice Pgip genes (Ospgip1, Ospgip2, Ospgip3 and Ospgip4) are distributed over a 30 kbp region of the short arm of chromosome 5, whereas the wheat Pgip genes, Tapgip1 and Tapgip2, are localized on the short arm of chromosome 7B and 7D, respectively. Deduced amino acid sequences show the typical LRR modular organization and a conserved distribution of the eight cysteines at the N- and C-terminal regions. Sequence comparison suggests that monocot and dicot PGIPs form two separate clusters sharing about 40% identity and shows that this value is close to the extent of variability observed within each cluster. Gene-specific RT-PCR and biochemical analyses demonstrate that both Ospgips and Tapgips are expressed in the whole plant or in a tissue-specific manner, and that OsPGIP1, lacking an entire LRR repeat, is an active inhibitor of fungal polygalacturonases. This last finding can contribute to define the molecular features of PG-PGIP interactions and highlights that the genetic events that can generate variability at the Pgip locus are not only limited to substitutions or small insertions/deletions, as so far reported, but can also involve variation in the number of LRRs.
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Affiliation(s)
- Michela Janni
- Dipartimento di Agrobiologia e Agrochimica, Università della Tuscia, Via San Camillo de Lellis, s.n.c., 01100 Viterbo, Italy
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Ramalingam J, Pathan MS, Feril O, Ross K, Ma XF, Mahmoud AA, Layton J, Rodriguez-Milla MA, Chikmawati T, Valliyodan B, Skinner R, Matthews DE, Gustafson JP, Nguyen HT. Structural and functional analyses of the wheat genomes based on expressed sequence tags (ESTs) related to abiotic stresses. Genome 2006; 49:1324-40. [PMID: 17218960 DOI: 10.1139/g06-094] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
To gain insights into the structure and function of the wheat (Triticum aestivum L.) genomes, we identified 278 ESTs related to abiotic stress (cold, heat, drought, salinity, and aluminum) from 7671 ESTs previously mapped to wheat chromosomes. Of the 278 abiotic stress related ESTs, 259 (811 loci) were assigned to chromosome deletion bins and analyzed for their distribution pattern among the 7 homoeologous chromosome groups. Distribution of abiotic stress related EST loci were not uniform throughout the different regions of the chromosomes of the 3 wheat genomes. Both the short and long arms of group 4 chromosomes showed a higher number of loci in their distal regions compared with proximal regions. Of the 811 loci, the number of mapped loci on the A, B, and D genomes were 258, 281, and 272, respectively. The highest number of abiotic stress related loci were found in homoeologous chromosome group 2 (142 loci) and the lowest number were found in group 6 (94 loci). When considering the genome-specific ESTs, the B genome showed the highest number of unique ESTs (7 loci), while none were found in the D genome. Similarly, considering homoeologous group-specific ESTs, group 2 showed the highest number with 16 unique ESTs (58 loci), followed by group 4 with 9 unique ESTs (33 loci). Many of the classified proteins fell into the biological process categories associated with metabolism, cell growth, and cell maintenance. Most of the mapped ESTs fell into the category of enzyme activity (28%), followed by binding activity (27%). Enzymes related to abiotic stress such as β-galactosidase, peroxidase, glutathione reductase, and trehalose-6-phosphate synthase were identified. The comparison of stress-responsive ESTs with genomic sequences of rice (Oryza sativa L.) chromosomes revealed the complexities of colinearity. This bin map provides insight into the structural and functional details of wheat genomic regions in relation to abiotic stress.
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Affiliation(s)
- J Ramalingam
- Division of Plant Sciences, University of Missouri, Columbia, MO 65211, USA
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37
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Singh NK, Dalal V, Batra K, Singh BK, Chitra G, Singh A, Ghazi IA, Yadav M, Pandit A, Dixit R, Singh PK, Singh H, Koundal KR, Gaikwad K, Mohapatra T, Sharma TR. Single-copy genes define a conserved order between rice and wheat for understanding differences caused by duplication, deletion, and transposition of genes. Funct Integr Genomics 2006; 7:17-35. [PMID: 16865332 DOI: 10.1007/s10142-006-0033-4] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2005] [Revised: 04/15/2006] [Accepted: 04/23/2006] [Indexed: 01/10/2023]
Abstract
The high-quality rice genome sequence is serving as a reference for comparative genome analysis in crop plants, especially cereals. However, early comparisons with bread wheat showed complex patterns of conserved synteny (gene content) and colinearity (gene order). Here, we show the presence of ancient duplicated segments in the progenitor of wheat, which were first identified in the rice genome. We also show that single-copy (SC) rice genes, those representing unique matches with wheat expressed sequence tag (EST) unigene contigs in the whole rice genome, show more than twice the proportion of genes mapping to syntenic wheat chromosome as compared to the multicopy (MC) or duplicated rice genes. While 58.7% of the 1,244 mapped SC rice genes were located in single syntenic wheat chromosome groups, the remaining 41.3% were distributed randomly to the other six non-syntenic wheat groups. This could only be explained by a background dispersal of genes in the genome through transposition or other unknown mechanism. The breakdown of rice-wheat synteny due to such transpositions was much greater near the wheat centromeres. Furthermore, the SC rice genes revealed a conserved primordial gene order that gives clues to the origin of rice and wheat chromosomes from a common ancestor through polyploidy, aneuploidy, centromeric fusions, and translocations. Apart from the bin-mapped wheat EST contigs, we also compared 56,298 predicted rice genes with 39,813 wheat EST contigs assembled from 409,765 EST sequences and identified 7,241 SC rice gene homologs of wheat. Based on the conserved colinearity of 1,063 mapped SC rice genes across the bins of individual wheat chromosomes, we predicted the wheat bin location of 6,178 unmapped SC rice gene homologs and validated the location of 213 of these in the telomeric bins of 21 wheat chromosomes with 35.4% initial success. This opens up the possibility of directed mapping of a large number of conserved SC rice gene homologs in wheat. Overall, only 46.4% of these SC genes code for proteins with known functional domains; the remaining 53.6% have unknown function, and hence, represent an important, but yet, under explored category of genes.
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Affiliation(s)
- Nagendra K Singh
- Rice Genome Laboratory, National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi, 110012, India.
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38
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Kalavacharla V, Hossain K, Gu Y, Riera-Lizarazu O, Vales MI, Bhamidimarri S, Gonzalez-Hernandez JL, Maan SS, Kianian SF. High-resolution radiation hybrid map of wheat chromosome 1D. Genetics 2006; 173:1089-99. [PMID: 16624903 PMCID: PMC1526521 DOI: 10.1534/genetics.106.056481] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2006] [Accepted: 04/05/2006] [Indexed: 11/18/2022] Open
Abstract
Physical mapping methods that do not rely on meiotic recombination are necessary for complex polyploid genomes such as wheat (Triticum aestivum L.). This need is due to the uneven distribution of recombination and significant variation in genetic to physical distance ratios. One method that has proven valuable in a number of nonplant and plant systems is radiation hybrid (RH) mapping. This work presents, for the first time, a high-resolution radiation hybrid map of wheat chromosome 1D (D genome) in a tetraploid durum wheat (T. turgidum L., AB genomes) background. An RH panel of 87 lines was used to map 378 molecular markers, which detected 2312 chromosome breaks. The total map distance ranged from approximately 3,341 cR(35,000) for five major linkage groups to 11,773 cR(35,000) for a comprehensive map. The mapping resolution was estimated to be approximately 199 kb/break and provided the starting point for BAC contig alignment. To date, this is the highest resolution that has been obtained by plant RH mapping and serves as a first step for the development of RH resources in wheat.
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Affiliation(s)
- Venu Kalavacharla
- Department of Bioscience & Biotechnology, Drexel University, Philadelphia, Pennsylvania 19141, USA
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39
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Abstract
Pairing between wheat (Triticum turgidum and T. aestivum) homeologous chromosomes is prevented by the expression of the Ph1 locus on the long arm of chromosome 5B. The genome of Aegilops speltoides suppresses Ph1 expression in wheat x Ae. speltoides hybrids. Suppressors with major effects were mapped as Mendelian loci on the long arms of Ae. speltoides chromosomes 3S and 7S. The chromosome 3S locus was designated Su1-Ph1 and the chromosome 7S locus was designated Su2-Ph1. A QTL with a minor effect was mapped on the short arm of chromosome 5S and was designated QPh.ucd-5S. The expression of Su1-Ph1 and Su2-Ph1 increased homeologous chromosome pairing in T. aestivum x Ae. speltoides hybrids by 8.4 and 5.8 chiasmata/cell, respectively. Su1-Ph1 was completely epistatic to Su2-Ph1, and the two genes acting together increased homeologous chromosome pairing in T. aestivum x Ae. speltoides hybrids to the same level as Su1-Ph1 acting alone. QPh.ucd-5S expression increased homeologous chromosome pairing by 1.6 chiasmata/cell in T. aestivum x Ae. speltoides hybrids and was additive to the expression of Su2-Ph1. It is hypothesized that the products of Su1-Ph1 and Su2-Ph1 affect pairing between homeologous chromosomes by regulating the expression of Ph1 but the product of QPh.ucd-5S may primarily regulate recombination between homologous chromosomes.
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Affiliation(s)
- J Dvorak
- Department of Plant Sciences, University of California, Davis, California 95616, USA.
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40
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Rossini L, Vecchietti A, Nicoloso L, Stein N, Franzago S, Salamini F, Pozzi C. Candidate genes for barley mutants involved in plant architecture: an in silico approach. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2006; 112:1073-85. [PMID: 16501940 DOI: 10.1007/s00122-006-0209-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2005] [Accepted: 12/28/2005] [Indexed: 05/06/2023]
Abstract
To individuate candidate genes (CGs) for a set of barley developmental mutants, a synteny approach comparing the genomes of barley and rice has been introduced. Based on map positions of mutants, sequenced RFLP markers linked to the target loci were selected. The markers were mapped in silico by BLAST searches against the rice genome sequence and chromosomal regions syntenous to barley target intervals were identified. Rice syntenous regions were defined for 15 barley chromosomal intervals hosting 23 mutant loci affecting plant height (brh1; brh2; sld4), shoot and inflorescence branching (als; brc1; cul-2, -3, -5, -15, -16; dub1; mnd6; vrs1), development of leaves (lig) and leaf-like organs (cal-b19, -C15, -d4; lks5; suKD-25; suKE-74; suKF-76; trd; trp). Annotation of 110 Mb of rice genomic sequence made it possible to screen for putative CGs which are listed together with the reasons supporting mutant-gene associations. For two loci, CGs were identified with a clear probability to represent the locus considered. These include FRIZZY PANICLE, a candidate for the brc1 barley mutant, and the rice ortholog of maize Liguleless1 (Lg1), a candidate for the barley lig locus on chromosome 2H. For this locus, the validity of the approach was supported by the PCR-amplification of a genomic fragment of the orthologous barley sequence. SNP mapping located this fragment on chromosome 2H in the region hosting the lig genetic locus.
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Affiliation(s)
- Laura Rossini
- Dipartimento di Produzione Vegetale, Università degli Studi di Milano, Via Celoria 2, 20133 Milan, Italy
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41
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Lu H, Faris JD. Macro- and microcolinearity between the genomic region of wheat chromosome 5B containing the Tsn1 gene and the rice genome. Funct Integr Genomics 2005; 6:90-103. [PMID: 16372189 DOI: 10.1007/s10142-005-0020-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2005] [Revised: 11/21/2005] [Accepted: 11/22/2005] [Indexed: 12/18/2022]
Abstract
The Tsn1 gene in wheat confers sensitivity to a proteinaceous host-selective toxin (Ptr ToxA) produced by the tan spot fungus (Pyrenophora tritici-repentis) and lies within a gene-rich region of chromosome 5B. To use the rice genome sequence information for the map-based cloning of Tsn1, colinearity between the wheat genomic region containing Tsn1 and the rice genome was determined at the macro- and microlevels. Macrocolinearity was determined by testing 28 expressed sequence markers (ESMs) spanning a 25.5-cM segment and encompassing Tsn1 for similarity to rice sequences. Twelve ESMs had no similarity to rice sequences, and 16 had similarity to sequences on seven different rice chromosomes. Segments of colinearity with rice chromosomes 3 and 9 were identified, but frequent rearrangements and disruptions occurred. Microcolinearity was determined by testing the sequences of 26 putative genes identified from BAC contigs of 205 and 548 kb in length and flanking Tsn1 for similarity to rice genomic sequences. Fourteen of the predicted genes detected orthologous sequences on six different rice chromosomes, whereas the remaining 12 had no similarity with rice sequences. Four genes were colinear on rice chromosome 9, but multiple disruptions, rearrangements, and duplications were observed in wheat relative to rice. The data reported provide a detailed analysis of a region of wheat chromosome 5B that is highly rearranged relative to rice.
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Affiliation(s)
- Huangjun Lu
- Department of Plant Sciences, North Dakota State University, Fargo, ND 58105, USA
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42
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Miller AK, Galiba G, Dubcovsky J. A cluster of 11 CBF transcription factors is located at the frost tolerance locus Fr-Am2 in Triticum monococcum. Mol Genet Genomics 2005; 275:193-203. [PMID: 16362370 DOI: 10.1007/s00438-005-0076-6] [Citation(s) in RCA: 114] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2005] [Accepted: 11/04/2005] [Indexed: 10/25/2022]
Abstract
Due to the adverse effects of cold temperatures on winter wheat, frost tolerance is an important trait for breeding programs in regions with severe winters. Frost tolerance locus Fr-A(m)2 was recently discovered in diploid wheat (Triticum monococcum L.). This locus was mapped as a QTL on chromosome 5A(m) in the same region as a QTL for the level of transcription of the cold-regulated gene COR14b at 15 degrees C. A CBF transcription factor was mapped in the center of these two overlapping QTLs. However, since the CBF gene family in wheat has numerous members, it was possible that multiple CBF genes were present at Fr-A(m)2. To investigate this possibility we initiated a systematic characterization of the CBF family in T. monococcum. Here we report the molecular characterization of thirteen TmCBF genes. Nine of them were numbered according to the closest barley HvCBF gene, and the other four that have no clear barley orthologues were assigned numbers TmCBF15 to TmCBF18. TmCBF5 and TmCBF18 were mapped on T. monococcum chromosomes 7A(m) and 6A(m), respectively, and are thus not candidates for the Fr-A(m)2 gene. The remaining eleven TmCBF genes are clustered at the Fr-A(m)2 locus within five different Bacterial Artificial Chromosome (BAC) clones. These BACs were mapped using a high-density map and recombination events were found between most BACs. Lines carrying these recombination events will be useful to identify which of the CBF genes is responsible for the differences in frost tolerance between the T. monococcum parental lines at the Fr-A(m)2 locus.
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Affiliation(s)
- Andrea K Miller
- Department of Plant Sciences, University of California, Davis, 95616, USA
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43
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Cho S, Garvin DF, Muehlbauer GJ. Transcriptome analysis and physical mapping of barley genes in wheat-barley chromosome addition lines. Genetics 2005; 172:1277-85. [PMID: 16322516 PMCID: PMC1456225 DOI: 10.1534/genetics.105.049908] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Wheat-barley chromosome addition lines are useful genetic resources for a variety of studies. In this study, transcript accumulation patterns in Betzes barley, Chinese Spring wheat, and Chinese Spring-Betzes chromosome addition lines were examined with the Barley1 Affymetrix GeneChip probe array. Of the 4014 transcripts detected in Betzes but not in Chinese Spring, 365, 271, 265, 323, 194, and 369 were detected in wheat-barley disomic chromosome addition lines 2(2H), 3(3H), 4(4H), 7(5H), 6(6H), and 1(7H), respectively. Thus, 1787 barley transcripts were detected in a wheat genetic background and, by virtue of the addition line in which they were detected, were physically mapped to barley chromosomes. We validated and extended our approach to physically map barley genes to the long and short arms of chromosome 6(6H). Our physical map data exhibited a high level of synteny with homologous sequences on the wheat and/or rice syntenous chromosomes, indicating that our barley physical maps are robust. Our results show that barley transcript detection in wheat-barley chromosome addition lines is an efficient approach for large-scale physical mapping of genes.
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Affiliation(s)
- Seungho Cho
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108, USA
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44
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Salina EA, Leonova IN, Efremova TT, Röder MS. Wheat genome structure: translocations during the course of polyploidization. Funct Integr Genomics 2005; 6:71-80. [PMID: 15983785 DOI: 10.1007/s10142-005-0001-4] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2004] [Revised: 04/20/2005] [Accepted: 04/21/2005] [Indexed: 12/19/2022]
Abstract
The genomic organization of Triticum timopheevii (2n=28, AtAtGG) was compared with hexaploid wheat T. aestivum (2n=42, AABBDD) by comparative mapping using microsatellites derived from bread wheat. Genetic maps for the two crosses T. timopheevii var. timopheevii x T. timopheevii var. typica and T. timopheevii K-38555xT. militinae were constructed. On the first population, 121 loci were mapped, and on the second population 103 loci. The transferability of the wheat markers to T. timopheevii was generally better for the A genome-specific markers (76-78% produced amplification products; 26 and 29% were polymorphic) than for B genome-specific markers (54% produced amplification products; 14 and 16% were polymorphic). Of the D genome-specific markers, one third produced amplification products in T. timopheevii, but only 5 and 2% were polymorphic in the corresponding mapping populations. The maps constructed confirmed the previously described translocation between chromosome arms 6AtS and 1GS and revealed at least two yet unknown rearrangements on chromosomes 4At and 6At09. The presence of other translocations and rearrangements between T. timopheevii and T. aestivum was demonstrated by a variety of markers mapping to nonhomoeologous positions.
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Affiliation(s)
- Elena A Salina
- Institute of Cytology and Genetics, Lavrentiev ave. 10, Novosibirsk, 630090, Russia.
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45
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Goyal A, Bandopadhyay R, Sourdille P, Endo TR, Balyan HS, Gupta PK. Physical molecular maps of wheat chromosomes. Funct Integr Genomics 2005; 5:260-3. [PMID: 15902544 DOI: 10.1007/s10142-005-0146-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2005] [Revised: 04/10/2005] [Accepted: 04/10/2005] [Indexed: 01/22/2023]
Abstract
In bread wheat, a set of 527 simple sequence repeats (SSRs) were tried on 164 deletion lines, leading to a successful mapping of 270 SSRs on 313 loci covering all 21 chromosomes. A maximum of 119 loci (38%) were located on B subgenome, and a minimum of 90 loci (29%) mapped on D subgenome. Similarly, homoeologous group 7 carried a maximum of 61 loci (19%), and group 4 carried a minimum of 22 loci (7%). Of the cited 270 SSRs, 39 had multiple loci, but only eight of these detected homoeologous loci. Linear order of loci in physical maps largely corresponded with those in the genetic maps. Apparently, distances between each of only 26 pairs of loci significantly differed from the corresponding distances on genetic maps. Some loci, which were genetically mapped close to the centromere, were physically located distally, while other loci that were mapped distally in the genetic maps were located in the proximal bins in the physical maps. This suggested that although the linear order of the loci was largely conserved, variation does exist between genetic and physical distances.
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Affiliation(s)
- Aakash Goyal
- Molecular Biology Laboratory, Department of Genetics & Plant Breeding, Ch. Charan Singh University, Meerut, Uttar Pradesh, 250 004, India
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46
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Dilbirligi M, Erayman M, Gill KS. Analysis of recombination and gene distribution in the 2L1.0 region of wheat (Triticum aestivum L.) and barley (Hordeum vulgare L.). Genomics 2005; 86:47-54. [PMID: 15953539 DOI: 10.1016/j.ygeno.2005.03.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2005] [Revised: 03/05/2005] [Accepted: 03/21/2005] [Indexed: 01/20/2023]
Abstract
Both wheat and barley belong to tribe Triticeae and are closely related. High-density detailed comparison of physical and genetic linkage maps revealed that wheat genes are present in physically small gene-rich regions (GRRs). One of the largest GRRs is located around fraction length 1.0 of the long arm of wheat homoeologous group 2 chromosomes termed the "2L1.0 region." The main objective of this study was to analyze the structural and functional organization of the 2L1.0 region in barley in comparison to wheat. Using the 29 physically mapped RFLP markers for the region, wheat and barley consensus genetic linkage maps of the 2L1.0 region were generated by combining information from 18 wheat and 7 barley genetic linkage maps. Comparative analysis using these consensus maps and other available wheat and barley mapping resources identified 227 DNA markers and ESTs for the region. The region accounted for 58% of the genes and 68% of the arm's recombination in wheat. However, the corresponding region in barley accounted for about 42% of the genes and 81% of the recombination. The kb/cM ratio for the region was 122 in barley compared to 244 in wheat. Distribution of genes and recombination varied between the two species even though the gene order and density were similar.
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Affiliation(s)
- Muharrem Dilbirligi
- Central Research Institute for Field Crops, Pk 226, 0642 Ulus/Ankara, Turkey.
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47
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Zhang D, Choi DW, Wanamaker S, Fenton RD, Chin A, Malatrasi M, Turuspekov Y, Walia H, Akhunov ED, Kianian P, Otto C, Simons K, Deal KR, Echenique V, Stamova B, Ross K, Butler GE, Strader L, Verhey SD, Johnson R, Altenbach S, Kothari K, Tanaka C, Shah MM, Laudencia-Chingcuanco D, Han P, Miller RE, Crossman CC, Chao S, Lazo GR, Klueva N, Gustafson JP, Kianian SF, Dubcovsky J, Walker-Simmons MK, Gill KS, Dvorák J, Anderson OD, Sorrells ME, McGuire PE, Qualset CO, Nguyen HT, Close TJ. Construction and evaluation of cDNA libraries for large-scale expressed sequence tag sequencing in wheat (Triticum aestivum L.). Genetics 2005; 168:595-608. [PMID: 15514038 PMCID: PMC1448820 DOI: 10.1534/genetics.104.034785] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
A total of 37 original cDNA libraries and 9 derivative libraries enriched for rare sequences were produced from Chinese Spring wheat (Triticum aestivum L.), five other hexaploid wheat genotypes (Cheyenne, Brevor, TAM W101, BH1146, Butte 86), tetraploid durum wheat (T. turgidum L.), diploid wheat (T. monococcum L.), and two other diploid members of the grass tribe Triticeae (Aegilops speltoides Tausch and Secale cereale L.). The emphasis in the choice of plant materials for library construction was reproductive development subjected to environmental factors that ultimately affect grain quality and yield, but roots and other tissues were also included. Partial cDNA expressed sequence tags (ESTs) were examined by various measures to assess the quality of these libraries. All ESTs were processed to remove cloning system sequences and contaminants and then assembled using CAP3. Following these processing steps, this assembly yielded 101,107 sequences derived from 89,043 clones, which defined 16,740 contigs and 33,213 singletons, a total of 49,953 "unigenes." Analysis of the distribution of these unigenes among the libraries led to the conclusion that the enrichment methods were effective in reducing the most abundant unigenes and to the observation that the most diverse libraries were from tissues exposed to environmental stresses including heat, drought, salinity, or low temperature.
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Affiliation(s)
- D Zhang
- Department of Plant and Soil Science, Texas Tech University, Lubbock, Texas 79409, USA
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Qi LL, Echalier B, Chao S, Lazo GR, Butler GE, Anderson OD, Akhunov ED, Dvorák J, Linkiewicz AM, Ratnasiri A, Dubcovsky J, Bermudez-Kandianis CE, Greene RA, Kantety R, La Rota CM, Munkvold JD, Sorrells SF, Sorrells ME, Dilbirligi M, Sidhu D, Erayman M, Randhawa HS, Sandhu D, Bondareva SN, Gill KS, Mahmoud AA, Ma XF, Gustafson JP, Conley EJ, Nduati V, Gonzalez-Hernandez JL, Anderson JA, Peng JH, Lapitan NLV, Hossain KG, Kalavacharla V, Kianian SF, Pathan MS, Zhang DS, Nguyen HT, Choi DW, Fenton RD, Close TJ, McGuire PE, Qualset CO, Gill BS. A chromosome bin map of 16,000 expressed sequence tag loci and distribution of genes among the three genomes of polyploid wheat. Genetics 2005; 168:701-12. [PMID: 15514046 PMCID: PMC1448828 DOI: 10.1534/genetics.104.034868] [Citation(s) in RCA: 348] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Because of the huge size of the common wheat (Triticum aestivum L., 2n = 6x = 42, AABBDD) genome of 17,300 Mb, sequencing and mapping of the expressed portion is a logical first step for gene discovery. Here we report mapping of 7104 expressed sequence tag (EST) unigenes by Southern hybridization into a chromosome bin map using a set of wheat aneuploids and deletion stocks. Each EST detected a mean of 4.8 restriction fragments and 2.8 loci. More loci were mapped in the B genome (5774) than in the A (5173) or D (5146) genomes. The EST density was significantly higher for the D genome than for the A or B. In general, EST density increased relative to the physical distance from the centromere. The majority of EST-dense regions are in the distal parts of chromosomes. Most of the agronomically important genes are located in EST-dense regions. The chromosome bin map of ESTs is a unique resource for SNP analysis, comparative mapping, structural and functional analysis, and polyploid evolution, as well as providing a framework for constructing a sequence-ready, BAC-contig map of the wheat genome.
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Affiliation(s)
- L L Qi
- Department of Plant Pathology, Wheat Genetics Resource Center, Kansas State University, Manhattan, Kansas 66506-5502, USA
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Peng JH, Lapitan NLV. Characterization of EST-derived microsatellites in the wheat genome and development of eSSR markers. Funct Integr Genomics 2005; 5:80-96. [PMID: 15650880 DOI: 10.1007/s10142-004-0128-8] [Citation(s) in RCA: 144] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2004] [Revised: 10/27/2004] [Accepted: 10/30/2004] [Indexed: 11/24/2022]
Abstract
EST-derived microsatellites or simple sequence repeats (eSSR) occur in expressed sequence tags (EST). Here we report characteristics of eSSRs in the wheat genome, construction of consensus chromosome bin maps of SSR-containing ESTs ((SSR)ESTs), and development of eSSR markers for the 21 wheat chromosomes. A Perl script known as MISA was used to identify eSSRs in wheat ESTs available in the database http://wheat.pw.usda.gov/cgi-bin/ace/search/wEST ). Among 492,832 ESTs from the database, 36,520 (7.41%) contained 43,598 eSSRs. This is equivalent to 1 eSSR per 5.46 kb EST sequence. About 60% of the eSSRs were trinucleotides, 19.7% were mononucleotide, 16.7% were dinucleotides, and the remaining approximately 3% consisted of tetra-, penta-, and hexanucleotides. Among the identified eSSRs, (CCG/CGG)n is the most frequent (20.5%) followed by (A/T)n at 13.6%, (AAC/GTT)n at 11.7%, and (AG/CT)n at 8.7%. Among ESTs previously mapped to wheat chromosome bins, a total of 1,010 eSSR loci were derived from 341 (SSR)ESTs. Consensus chromosome bin maps showing the chromosome locations of (SSR)ESTs, SSR sequence motif, and cDNA library were constructed. A chi(2) test indicated that the distribution pattern of eSSR loci was generally similar to that of the original mapped ESTs in the wheat genome. Forty-eight (SSR)ESTs were converted into PCR-based eSSR markers, and 266 eSSR loci were mapped to specific chromosome arms using wheat cytogenetic stocks. The average polymorphism information content (0.45+/-0.16) of eSSR markers was lower than that reported for genomic SSRs (0.54+/-0.19), but higher than RFLPs (0.30+/-0.27). The eSSR markers were transferable among related Triticeae species, Triticum aestivum, T. durum, T. dicoccoides, Hordeum spontaneum, H. vulgare, and Secale cereale. The results confirm the presence of SSRs in expressed genes of wheat and demonstrate another application of ESTs in genomics research. eSSRs will be useful for gene tagging, gene cloning, and comparative genomics studies of cereal crops.
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Affiliation(s)
- J H Peng
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523-1170, USA.
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Current Awareness on Comparative and Functional Genomics. Comp Funct Genomics 2005. [PMCID: PMC2447482 DOI: 10.1002/cfg.421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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