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Loginova DB, Silkova OG. The Genome of Bread Wheat Triticum aestivum L.: Unique Structural and Functional Properties. RUSS J GENET+ 2018. [DOI: 10.1134/s1022795418040105] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Winfield MO, Allen AM, Wilkinson PA, Burridge AJ, Barker GL, Coghill J, Waterfall C, Wingen LU, Griffiths S, Edwards KJ. High-density genotyping of the A.E. Watkins Collection of hexaploid landraces identifies a large molecular diversity compared to elite bread wheat. PLANT BIOTECHNOLOGY JOURNAL 2018; 16:165-175. [PMID: 28500796 PMCID: PMC5785351 DOI: 10.1111/pbi.12757] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 05/04/2017] [Accepted: 05/06/2017] [Indexed: 05/03/2023]
Abstract
The importance of wheat as a food crop makes it a major target for agricultural improvements. As one of the most widely grown cereal grains, together with maize and rice, wheat is the leading provider of calories in the global diet, constituting 29% of global cereal production in 2015. In the last few decades, however, yields have plateaued, suggesting that the green revolution, at least for wheat, might have run its course and that new sources of genetic variation are urgently required. The overall aim of our work was to identify novel variation that may then be used to enable the breeding process. As landraces are a potential source of such diversity, here we have characterized the A.E. Watkins Collection alongside a collection of elite accessions using two complementary high-density and high-throughput genotyping platforms. While our results show the importance of using the appropriate SNP collection to compare diverse accessions, they also show that the Watkins Collection contains a substantial amount of novel genetic diversity which has either not been captured in current breeding programmes or which has been lost through previous selection pressures. As a consequence of our analysis, we have identified a number of accessions which carry an array of novel alleles along with a number of interesting chromosome rearrangements which confirm the variable nature of the wheat genome.
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Affiliation(s)
- Mark O. Winfield
- University of BristolBristol Life Sciences Building24 Tyndall AvenueBristolUK
| | - Alexandra M. Allen
- University of BristolBristol Life Sciences Building24 Tyndall AvenueBristolUK
| | - Paul A. Wilkinson
- University of BristolBristol Life Sciences Building24 Tyndall AvenueBristolUK
| | - Amanda J. Burridge
- University of BristolBristol Life Sciences Building24 Tyndall AvenueBristolUK
| | - Gary L.A. Barker
- University of BristolBristol Life Sciences Building24 Tyndall AvenueBristolUK
| | - Jane Coghill
- University of BristolBristol Life Sciences Building24 Tyndall AvenueBristolUK
| | - Christy Waterfall
- University of BristolBristol Life Sciences Building24 Tyndall AvenueBristolUK
| | | | | | - Keith J. Edwards
- University of BristolBristol Life Sciences Building24 Tyndall AvenueBristolUK
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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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Majka M, Kwiatek M, Belter J, Wiśniewska H. Characterization of morphology and resistance to Blumeria graminis of winter triticale monosomic addition lines with chromosome 2D of Aegilops tauschii. PLANT CELL REPORTS 2016; 35:2125-35. [PMID: 27406086 PMCID: PMC5025500 DOI: 10.1007/s00299-016-2023-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 06/29/2016] [Indexed: 05/04/2023]
Abstract
Allocation of the chromosome 2D of Ae. tauschii in triticale background resulted in changes of its organization, what is related to varied expression of genes determining agronomically important traits. Monosomic alien addition lines (MAALs) are crucial for transfer of genes from wild relatives into cultivated varieties. This kind of genetic stocks is used for physical mapping of specific chromosomes and analyzing alien genes expression. The main aim of our study is to improve hexaploid triticale by transferring D-genome chromatin from Aegilops tauschii × Secale cereale (2n = 4x = 28, DDRR). In this paper, we demonstrate the molecular cytogenetics analysis and SSR markers screening combined with phenotype analysis and evaluation of powdery mildew infection of triticale monosomic addition lines carrying chromosome 2D of Ae. tauschii. We confirmed the inheritance of chromosome 2D from the BC2F4 to the BC2F6 generation of triticale hybrids. Moreover, we unveiled a high variable region on the short arm of chromosome 2D, where chromosome rearrangements were mapped. These events had direct influence on plant height of hybrids what might be connected with changes at Rht8 loci. We obtained 20 semi-dwarf plants of BC2F6 generation carrying 2D chromosome with the powdery mildew resistance, without changes in spike morphology, which can be used in the triticale breeding programs.
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Affiliation(s)
- M Majka
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland.
| | - M Kwiatek
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland
| | - J Belter
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland
| | - H Wiśniewska
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland
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Ma J, Gao S, Stiller J, Jiang QT, Lan XJ, Liu YX, Pu ZE, Wang J, Wei Y, Zheng YL. Identification of genes bordering breakpoints of the pericentric inversions on 2B, 4B, and 5A in bread wheat (Triticum aestivum L.). Genome 2015; 58:385-90. [DOI: 10.1139/gen-2015-0060] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Chromosome translocation is an important driving force in shaping genomes during evolution. Detailed knowledge of chromosome translocations in a given species and its close relatives should increase the efficiency and precision of chromosome engineering in crop improvement. To identify genes flanking the breakpoints of translocations and inversions as a step toward identifying breakpoints in bread wheat, we systematically analysed genes in the Brachypodium genome against wheat survey sequences and bin-mapped ESTs (expressed sequence tags) derived from the hexaploid wheat genotype ‘Chinese Spring’. In addition to those well-known translocations between group 4, 5, and 7 chromosomes, this analysis identified genes flanking the three pericentric inversions on chromosomes 2B, 4B, and 5A. However, numerous chromosomal rearrangements reported in early studies could not be confirmed. The genes flanking the breakpoints reported in this study are valuable for isolating these breakpoints.
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Affiliation(s)
- Jian Ma
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China
| | - Shang Gao
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China
| | - Jiri Stiller
- CSIRO Agriculture Flagship, 306 Carmody Road, St Lucia, QLD 4067, Australia
| | - Qian-Tao Jiang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China
| | - Xiu-Jin Lan
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China
| | - Ya-Xi Liu
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China
| | - Zhi-En Pu
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China
| | - Jirui Wang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China
| | - Yuming Wei
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China
| | - You-Liang Zheng
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China
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Ma J, Stiller J, Zheng Z, Wei Y, Zheng YL, Yan G, Doležel J, Liu C. Putative interchromosomal rearrangements in the hexaploid wheat (Triticum aestivum L.) genotype 'Chinese Spring' revealed by gene locations on homoeologous chromosomes. BMC Evol Biol 2015; 15:37. [PMID: 25880815 PMCID: PMC4364500 DOI: 10.1186/s12862-015-0313-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Accepted: 02/20/2015] [Indexed: 01/26/2023] Open
Abstract
Background Chromosomal rearrangements are a major driving force in shaping genome during evolution. Previous studies show that translocated genes could undergo elevated rates of evolution and recombination frequencies around these genes can be altered. Based on the recently released genome sequences of Triticum urartu, Aegilops tauschii, Brachypodium distachyon and bread wheat, an analysis of interchromosomal translocations in the hexaploid wheat genotype ‘Chinese Spring’ (‘CS’) was conducted based on chromosome shotgun sequences from individual chromosome arms of this genotype. Results A total of 720 genes representing putative interchromosomal rearrangements was identified. They were distributed across the 42 chromosome arms. About 59% of these translocated genes were those involved in the well-characterized translocations involving chromosomes 4A, 5A and 7B. The other 41% of the genes represent a large numbers of putative interchromosomal rearrangements which have not yet been described. The number of the putative translocation events in the D subgenome was about half of those presented in either the A or B subgenomes, which agreed well with that the times of interaction between the A and B subgenomes almost doubled that between either of them and the D subgenome. Conclusions The possible existence of a large number of interchromosomal rearrangements detected in this study provide further evidence that caution should be taken when using synteny in ordering sequence contigs or in cloning genes in hexaploid wheat. The identification of these putative translocations in ‘CS’ also provide a base for a systematic evaluation of their presence or absence in the full spectrum of bread wheat and its close relatives, which could have significant implications in a wide array of fields ranging from studies of systematics and evolution to practical breeding. Electronic supplementary material The online version of this article (doi:10.1186/s12862-015-0313-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jian Ma
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China. .,CSIRO Agriculture Flagship, 306 Carmody Road, St Lucia, QLD, 4067, Australia.
| | - Jiri Stiller
- CSIRO Agriculture Flagship, 306 Carmody Road, St Lucia, QLD, 4067, Australia.
| | - Zhi Zheng
- CSIRO Agriculture Flagship, 306 Carmody Road, St Lucia, QLD, 4067, Australia. .,School of Plant Biology, The University of Western Australia, Perth, WA, 6009, Australia.
| | - Yuming Wei
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China.
| | - You-Liang Zheng
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China.
| | - Guijun Yan
- School of Plant Biology, The University of Western Australia, Perth, WA, 6009, Australia.
| | - Jaroslav Doležel
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Šlechtitelů 31, CZ-78371, Olomouc, Czech Republic.
| | - Chunji Liu
- CSIRO Agriculture Flagship, 306 Carmody Road, St Lucia, QLD, 4067, Australia. .,School of Plant Biology, The University of Western Australia, Perth, WA, 6009, Australia.
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Zhan H, Li G, Zhang X, Li X, Guo H, Gong W, Jia J, Qiao L, Ren Y, Yang Z, Chang Z. Chromosomal location and comparative genomics analysis of powdery mildew resistance gene Pm51 in a putative wheat-Thinopyrum ponticum introgression line. PLoS One 2014; 9:e113455. [PMID: 25415194 PMCID: PMC4240596 DOI: 10.1371/journal.pone.0113455] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Accepted: 10/24/2014] [Indexed: 11/18/2022] Open
Abstract
Powdery mildew (PM) is a very destructive disease of wheat (Triticum aestivum L.). Wheat-Thinopyrum ponticum introgression line CH7086 was shown to possess powdery mildew resistance possibly originating from Th. ponticum. Genomic in situ hybridization and molecular characterization of the alien introgression failed to identify alien chromatin. To study the genetics of resistance, CH7086 was crossed with susceptible genotypes. Segregation in F2 populations and F2:3 lines tested with Chinese Bgt race E09 under controlled conditions indicated that CH7086 carries a single dominant gene for powdery mildew resistance. Fourteen SSR and EST-PCR markers linked with the locus were identified. The genetic distances between the locus and the two flanking markers were 1.5 and 3.2 cM, respectively. Based on the locations of the markers by nullisomic-tetrasomic and deletion lines of 'Chinese Spring', the resistance gene was located in deletion bin 2BL-0.89-1.00. Conserved orthologous marker analysis indicated that the genomic region flanking the resistance gene has a high level of collinearity to that of rice chromosome 4 and Brachypodium chromosome 5. Both resistance specificities and tests of allelism suggested the resistance gene in CH7086 was different from previously reported powdery mildew resistance genes on 2BL, and the gene was provisionally designated PmCH86. Molecular analysis of PmCH86 compared with other genes for resistance to Bgt in the 2BL-0.89-1.00 region suggested that PmCH86 may be a new PM resistance gene, and it was therefore designated as Pm51. The closely linked flanking markers could be useful in exploiting this putative wheat-Thinopyrum translocation line for rapid transfer of Pm51 to wheat breeding programs.
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Affiliation(s)
- Haixian Zhan
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
- Crop Science Institute, Shanxi Academy of Agricultural Sciences, Taiyuan, Shanxi, China
| | - Guangrong Li
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Xiaojun Zhang
- Crop Science Institute, Shanxi Academy of Agricultural Sciences, Taiyuan, Shanxi, China
| | - Xin Li
- Crop Science Institute, Shanxi Academy of Agricultural Sciences, Taiyuan, Shanxi, China
| | - Huijuan Guo
- Crop Science Institute, Shanxi Academy of Agricultural Sciences, Taiyuan, Shanxi, China
| | - Wenping Gong
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Juqing Jia
- College of agronomy, Shanxi Agricultural University, Taigu, Shanxi, China
| | - Linyi Qiao
- Crop Science Institute, Shanxi Academy of Agricultural Sciences, Taiyuan, Shanxi, China
| | - Yongkang Ren
- Crop Science Institute, Shanxi Academy of Agricultural Sciences, Taiyuan, Shanxi, China
| | - Zujun Yang
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Zhijian Chang
- Crop Science Institute, Shanxi Academy of Agricultural Sciences, Taiyuan, Shanxi, China
- Key Lab of Crop Gene Resources and Germplasm Enhancement on Loess Plateau, Ministry of Agriculture, Taiyuan, Shanxi, China
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8
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Ma J, Stiller J, Wei Y, Zheng YL, Devos KM, Doležel J, Liu C. Extensive pericentric rearrangements in the bread wheat (Triticum aestivum L.) genotype "Chinese Spring" revealed from chromosome shotgun sequence data. Genome Biol Evol 2014; 6:3039-48. [PMID: 25349265 PMCID: PMC4255769 DOI: 10.1093/gbe/evu237] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The bread wheat (Triticum aestivum L.) genotype "Chinese Spring" ("CS") is the reference base in wheat genetics and genomics. Pericentric rearrangements in this genotype were systematically assessed by analyzing homoeoloci for a set of nonredundant genes from Brachypodium distachyon, Triticum urartu, and Aegilops tauschii in the CS chromosome shotgun sequence obtained from individual chromosome arms flow-sorted from CS aneuploid lines. Based on patterns of their homoeologous arm locations, 551 genes indicated the presence of pericentric inversions in at least 10 of the 21 chromosomes. Available data from deletion bin-mapped expressed sequence tags and genetic mapping in wheat indicated that all inversions had breakpoints in the low-recombinant gene-poor pericentromeric regions. The large number of putative intrachromosomal rearrangements suggests the presence of extensive structural differences among the three subgenomes, at least some of which likely occurred during the production of the aneuploid lines of this hexaploid wheat genotype. These differences could have significant implications in wheat genome research where comparative approaches are used such as in ordering and orientating sequence contigs and in gene cloning.
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Affiliation(s)
- Jian Ma
- CSIRO Agriculture Flagship, St Lucia, Queensland, Australia Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, China
| | - Jiri Stiller
- CSIRO Agriculture Flagship, St Lucia, Queensland, Australia
| | - Yuming Wei
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, China
| | - You-Liang Zheng
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, China
| | - Katrien M Devos
- Department of Crop & Soil Sciences, and Department of Plant Biology, University of Georgia
| | - Jaroslav Doležel
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Šlechtitelů, Olomouc, Czech Republic
| | - Chunji Liu
- CSIRO Agriculture Flagship, St Lucia, Queensland, Australia School of Plant Biology, The University of Western Australia, Perth, Western Australia, Australia
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Map-based analysis of the tenacious glume gene Tg-B1 of wild emmer and its role in wheat domestication. Gene 2014; 542:198-208. [DOI: 10.1016/j.gene.2014.03.034] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Revised: 03/14/2014] [Accepted: 03/18/2014] [Indexed: 12/20/2022]
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Genetic rearrangements of six wheat-agropyron cristatum 6P addition lines revealed by molecular markers. PLoS One 2014; 9:e91066. [PMID: 24595330 PMCID: PMC3942500 DOI: 10.1371/journal.pone.0091066] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2013] [Accepted: 02/07/2014] [Indexed: 01/07/2023] Open
Abstract
Agropyron cristatum (L.) Gaertn. (2n = 4x = 28, PPPP) not only is cultivated as pasture fodder but also could provide many desirable genes for wheat improvement. It is critical to obtain common wheat–A. cristatum alien disomic addition lines to locate the desired genes on the P genome chromosomes. Comparative analysis of the homoeologous relationships between the P genome chromosome and wheat genome chromosomes is a key step in transferring different desirable genes into common wheat and producing the desired alien translocation line while compensating for the loss of wheat chromatin. In this study, six common wheat–A. cristatum disomic addition lines were produced and analyzed by phenotypic examination, genomic in situ hybridization (GISH), SSR markers from the ABD genomes and STS markers from the P genome. Comparative maps, six in total, were generated and demonstrated that all six addition lines belonged to homoeologous group 6. However, chromosome 6P had undergone obvious rearrangements in different addition lines compared with the wheat chromosome, indicating that to obtain a genetic compensating alien translocation line, one should recombine alien chromosomal regions with homoeologous wheat chromosomes. Indeed, these addition lines were classified into four types based on the comparative mapping: 6PI, 6PII, 6PIII, and 6PIV. The different types of chromosome 6P possessed different desirable genes. For example, the 6PI type, containing three addition lines, carried genes conferring high numbers of kernels per spike and resistance to powdery mildew, important traits for wheat improvement. These results may prove valuable for promoting the development of conventional chromosome engineering techniques toward molecular chromosome engineering.
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Lee TG, Kim DY, Johnson JW, Seo YW. A genome-wide analysis of transcripts in a 2BS.2RL wheat-rye translocation during Hessian fly infestation. Genes Genomics 2013. [DOI: 10.1007/s13258-013-0130-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Adamski NM, Bush MS, Simmonds J, Turner AS, Mugford SG, Jones A, Findlay K, Pedentchouk N, von Wettstein-Knowles P, Uauy C. The inhibitor of wax 1 locus (Iw1) prevents formation of β- and OH-β-diketones in wheat cuticular waxes and maps to a sub-cM interval on chromosome arm 2BS. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2013; 74:989-1002. [PMID: 23551421 DOI: 10.1111/tpj.12185] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Revised: 03/21/2013] [Accepted: 03/25/2013] [Indexed: 05/18/2023]
Abstract
Glaucousness is described as the scattering effect of visible light from wax deposited on the cuticle of plant aerial organs. In wheat, two dominant genes lead to non-glaucous phenotypes: Inhibitor of wax 1 (Iw1) and Iw2. The molecular mechanisms and the exact extent (beyond visual assessment) by which these genes affect the composition and quantity of cuticular wax is unclear. To describe the Iw1 locus we used a genetic approach with detailed biochemical characterization of wax compounds. Using synteny and a large number of F2 gametes, Iw1 was fine-mapped to a sub-cM genetic interval on wheat chromosome arm 2BS, which includes a single collinear gene from the corresponding Brachypodium and rice physical maps. The major components of flag leaf and peduncle cuticular waxes included primary alcohols, β-diketones and n-alkanes. Small amounts of C19-C27 alkyl and methylalkylresorcinols that have not previously been described in wheat waxes were identified. Using six pairs of BC2 F3 near-isogenic lines, we show that Iw1 inhibits the formation of β- and hydroxy-β-diketones in the peduncle and flag leaf blade cuticles. This inhibitory effect is independent of genetic background or tissue, and is accompanied by minor but consistent increases in n-alkanes and C24 primary alcohols. No differences were found in cuticle thickness and carbon isotope discrimination in near-isogenic lines differing at Iw1.
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13
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Megyeri M, Molnár-Láng M, Molnár I. Cytomolecular Identification of Individual Wheat-Wheat Chromosome Arm Associations in Wheat-Rye Hybrids. Cytogenet Genome Res 2013; 139:128-36. [DOI: 10.1159/000346047] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/15/2012] [Indexed: 01/13/2023] Open
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14
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Kumar A, Simons K, Iqbal MJ, de Jiménez MM, Bassi FM, Ghavami F, Al-Azzam O, Drader T, Wang Y, Luo MC, Gu YQ, Denton A, Lazo GR, Xu SS, Dvorak J, Kianian PMA, Kianian SF. Physical mapping resources for large plant genomes: radiation hybrids for wheat D-genome progenitor Aegilops tauschii. BMC Genomics 2012. [PMID: 23127207 DOI: 10.1186/1471‐2164‐13‐597] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Development of a high quality reference sequence is a daunting task in crops like wheat with large (~17Gb), highly repetitive (>80%) and polyploid genome. To achieve complete sequence assembly of such genomes, development of a high quality physical map is a necessary first step. However, due to the lack of recombination in certain regions of the chromosomes, genetic mapping, which uses recombination frequency to map marker loci, alone is not sufficient to develop high quality marker scaffolds for a sequence ready physical map. Radiation hybrid (RH) mapping, which uses radiation induced chromosomal breaks, has proven to be a successful approach for developing marker scaffolds for sequence assembly in animal systems. Here, the development and characterization of a RH panel for the mapping of D-genome of wheat progenitor Aegilops tauschii is reported. RESULTS Radiation dosages of 350 and 450 Gy were optimized for seed irradiation of a synthetic hexaploid (AABBDD) wheat with the D-genome of Ae. tauschii accession AL8/78. The surviving plants after irradiation were crossed to durum wheat (AABB), to produce pentaploid RH1s (AABBD), which allows the simultaneous mapping of the whole D-genome. A panel of 1,510 RH1 plants was obtained, of which 592 plants were generated from the mature RH1 seeds, and 918 plants were rescued through embryo culture due to poor germination (<3%) of mature RH1 seeds. This panel showed a homogenous marker loss (2.1%) after screening with SSR markers uniformly covering all the D-genome chromosomes. Different marker systems mostly detected different lines with deletions. Using markers covering known distances, the mapping resolution of this RH panel was estimated to be <140kb. Analysis of only 16 RH lines carrying deletions on chromosome 2D resulted in a physical map with cM/cR ratio of 1:5.2 and 15 distinct bins. Additionally, with this small set of lines, almost all the tested ESTs could be mapped. A set of 399 most informative RH lines with an average deletion frequency of ~10% were identified for developing high density marker scaffolds of the D-genome. CONCLUSIONS The RH panel reported here is the first developed for any wild ancestor of a major cultivated plant species. The results provided insight into various aspects of RH mapping in plants, including the genetically effective cell number for wheat (for the first time) and the potential implementation of this technique in other plant species. This RH panel will be an invaluable resource for mapping gene based markers, developing a complete marker scaffold for the whole genome sequence assembly, fine mapping of markers and functional characterization of genes and gene networks present on the D-genome.
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Affiliation(s)
- Ajay Kumar
- Department of Plant Sciences, North Dakota State University, Fargo, ND 58108, USA
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Kumar A, Simons K, Iqbal MJ, de Jiménez MM, Bassi FM, Ghavami F, Al-Azzam O, Drader T, Wang Y, Luo MC, Gu YQ, Denton A, Lazo GR, Xu SS, Dvorak J, Kianian PMA, Kianian SF. Physical mapping resources for large plant genomes: radiation hybrids for wheat D-genome progenitor Aegilops tauschii. BMC Genomics 2012; 13:597. [PMID: 23127207 PMCID: PMC3542274 DOI: 10.1186/1471-2164-13-597] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2012] [Accepted: 10/31/2012] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND Development of a high quality reference sequence is a daunting task in crops like wheat with large (~17Gb), highly repetitive (>80%) and polyploid genome. To achieve complete sequence assembly of such genomes, development of a high quality physical map is a necessary first step. However, due to the lack of recombination in certain regions of the chromosomes, genetic mapping, which uses recombination frequency to map marker loci, alone is not sufficient to develop high quality marker scaffolds for a sequence ready physical map. Radiation hybrid (RH) mapping, which uses radiation induced chromosomal breaks, has proven to be a successful approach for developing marker scaffolds for sequence assembly in animal systems. Here, the development and characterization of a RH panel for the mapping of D-genome of wheat progenitor Aegilops tauschii is reported. RESULTS Radiation dosages of 350 and 450 Gy were optimized for seed irradiation of a synthetic hexaploid (AABBDD) wheat with the D-genome of Ae. tauschii accession AL8/78. The surviving plants after irradiation were crossed to durum wheat (AABB), to produce pentaploid RH1s (AABBD), which allows the simultaneous mapping of the whole D-genome. A panel of 1,510 RH1 plants was obtained, of which 592 plants were generated from the mature RH1 seeds, and 918 plants were rescued through embryo culture due to poor germination (<3%) of mature RH1 seeds. This panel showed a homogenous marker loss (2.1%) after screening with SSR markers uniformly covering all the D-genome chromosomes. Different marker systems mostly detected different lines with deletions. Using markers covering known distances, the mapping resolution of this RH panel was estimated to be <140kb. Analysis of only 16 RH lines carrying deletions on chromosome 2D resulted in a physical map with cM/cR ratio of 1:5.2 and 15 distinct bins. Additionally, with this small set of lines, almost all the tested ESTs could be mapped. A set of 399 most informative RH lines with an average deletion frequency of ~10% were identified for developing high density marker scaffolds of the D-genome. CONCLUSIONS The RH panel reported here is the first developed for any wild ancestor of a major cultivated plant species. The results provided insight into various aspects of RH mapping in plants, including the genetically effective cell number for wheat (for the first time) and the potential implementation of this technique in other plant species. This RH panel will be an invaluable resource for mapping gene based markers, developing a complete marker scaffold for the whole genome sequence assembly, fine mapping of markers and functional characterization of genes and gene networks present on the D-genome.
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Affiliation(s)
- Ajay Kumar
- Department of Plant Sciences, North Dakota State University, Fargo, ND 58108, USA
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16
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Wang MJ, Zou HD, Lin ZS, Wu Y, Chen X, Yuan YP. Expressed sequence tag-PCR markers for identification of alien barley chromosome 2H in wheat. GENETICS AND MOLECULAR RESEARCH 2012; 11:3452-63. [PMID: 23079838 DOI: 10.4238/2012.september.25.13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
We developed EST-PCR markers specific to barley chromosome 2H, for the purpose of effectively tracing alien chromosomes or chromosome parts in the wheat genetic background. The target alien chromosome 2H confers high resistance to pre-harvest sprouting, which is a worldwide natural disaster in wheat. A total of 120 primer pairs were selected by combining the wheat group 2 chromosomes of the EST database and the genome sequences of the new model plant Brachypodium distachyon. Seventy-seven of 120 primer pairs were polymorphic and 31 of 120 primer pairs were monomorphic between a set of wheat-barley chromosome 2H disomic addition/substitution lines and their parents by agarose gel electrophoresis and polyacrylamide gel electrophoresis. Thirty of 77 polymorphic primer pairs including primer pair P120 derived from the basi gene were chromosome 2H-specific. These markers are expected to be valuable in screening of wheat-barley chromosome 2H recombination lines and pre-harvest sprouting resistant varieties.
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Affiliation(s)
- M J Wang
- College of Plant Science, Jilin University, Changchun, China
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17
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Hazard B, Zhang X, Colasuonno P, Uauy C, Beckles DM, Dubcovsky J. Induced mutations in the starch branching enzyme II ( SBEII) genes increase amylose and resistant starch content in durum wheat. CROP SCIENCE 2012; 52:1754-1766. [PMID: 26924849 PMCID: PMC4768815 DOI: 10.2135/cropsci2012.02.0126] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Starch is the largest component of the wheat (Triticum aestivum L.) grain and consists of approximately 70-80% amylopectin and 20-30% amylose. Amylopectin is a highly-branched, readily digested polysaccharide, whereas amylose has few branches and forms complexes that resist digestion and mimic dietary fiber (resistant starch). Down-regulation of the starch branching enzyme II (SBEII) gene by RNA interference (RNAi) was previously shown to increase amylose content in both hexaploid and tetraploid wheat. We generated ethyl methane sulphonate (EMS) mutants for the SBEIIa-A and SBEIIa-B homoeologs in the tetraploid durum wheat variety Kronos (T. turgidum ssp. durum L.). Single-gene mutants showed non-significant increases in amylose and resistant starch content, but a double mutant combining a SBEIIa-A knock-out mutation with a SBEIIa-B splice-site mutation showed a 22% increase in amylose content (P<0.0001) and a 115% increase in resistant starch content (P<0.0001). In addition, we obtained mutants for the A and B genome copies of the paralogous SBEIIb gene, mapped them 1-2 cM from SBEIIa, and generated double SBEIIa-SBEIIb mutants to study the effect of the SBEIIb gene in the absence of SBEIIa. These mutants are available to those interested in increasing amylose content and resistant starch in durum wheat.
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Affiliation(s)
- Brittany Hazard
- Dept. of Plant Sciences, University of California, Davis, CA 95616, USA
| | - Xiaoqin Zhang
- Dept. of Plant Sciences, University of California, Davis, CA 95616, USA
| | | | - Cristobal Uauy
- Dept. of Plant Sciences, University of California, Davis, CA 95616, USA
| | - Diane M. Beckles
- Dept. of Plant Sciences, University of California, Davis, CA 95616, USA
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18
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Liu Z, Zhu J, Cui Y, Liang Y, Wu H, Song W, Liu Q, Yang T, Sun Q, Liu Z. Identification and comparative mapping of a powdery mildew resistance gene derived from wild emmer (Triticum turgidum var. dicoccoides) on chromosome 2BS. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2012; 124:1041-9. [PMID: 22170431 DOI: 10.1007/s00122-011-1767-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2011] [Accepted: 12/04/2011] [Indexed: 05/18/2023]
Abstract
Powdery mildew, caused by Blumeria graminis f. sp. tritici, is an important foliar disease of wheat worldwide. Wild emmer (Triticum turgidum var. dicoccoides) is a valuable genetic resource for improving disease resistance in common wheat. A powdery mildew resistance gene conferring resistance to B. graminis f. sp. tritici isolate E09 at the seedling and adult stages was identified in wild emmer accession IW170 introduced from Israel. An incomplete dominant gene, temporarily designated MlIW170, was responsible for the resistance. Through molecular marker and bulked segregant analyses of an F(2) population and F(3) families derived from a cross between susceptible durum wheat line 81086A and IW170, MlIW170 was located in the distal chromosome bin 2BS3-0.84-1.00 and flanked by SSR markers Xcfd238 and Xwmc243. MlIW170 co-segregated with Xcau516, an STS marker developed from RFLP marker Xwg516 that co-segregated with powdery mildew resistance gene Pm26 on 2BS. Four EST-STS markers, BE498358, BF201235, BQ160080, and BF146221, were integrated into the genetic linkage map of MlIW170. Three AFLP markers, XPaacMcac, XPagcMcta, XPaacMcag, and seven AFLP-derived SCAR markers, XcauG2, XcauG3, XcauG6, XcauG8, XcauG10, XcauG20, and XcauG25, were linked to MlIW170. XcauG3, a resistance gene analog (RGA)-like sequence, co-segregated with MlIW170. The non-glaucousness locus Iw1 was 18.77 cM distal to MlIW170. By comparative genomics of wheat-Brachypodium-rice genomic co-linearity, four EST-STS markers, CJ658408, CJ945509, BQ169830, CJ945085, and one STS marker XP2430, were developed and MlIW170 was mapped in an 2.69 cM interval that is co-linear with a 131 kb genomic region in Brachypodium and a 105 kb genomic region in rice. Four RGA-like sequences annotated in the orthologous Brachypodium genomic region could serve as chromosome landing target regions for map-based cloning of MlIW170.
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Affiliation(s)
- Ziji Liu
- State Key Laboratory for Agrobiotechnology, Beijing Key Laboratory of Crop Genetic Improvement, Key Laboratory of Crop Heterosis Research and Utilization, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
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19
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Distelfeld A, Pearce SP, Avni R, Scherer B, Uauy C, Piston F, Slade A, Zhao R, Dubcovsky J. Divergent functions of orthologous NAC transcription factors in wheat and rice. PLANT MOLECULAR BIOLOGY 2012; 78:515-24. [PMID: 22278768 PMCID: PMC4773031 DOI: 10.1007/s11103-012-9881-6] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2011] [Accepted: 01/10/2012] [Indexed: 05/18/2023]
Abstract
The wheat GPC-B1 gene located on chromosome 6B is an early regulator of senescence and affects remobilization of protein and minerals to the grain. GPC-B1 is a NAC transcription factor and has a paralogous copy on chromosome 2B in wheat, GPC-B2. The closest rice homolog to both wheat GPC genes is Os07g37920 which is located on rice chromosome 7 and is colinear with GPC-B2. Since rice is a diploid species with a sequenced genome, we initiated the study of Os07g37920 to develop a simpler model to study senescence and mineral remobilization in cereals. We developed eleven independent RNA interference transgenic rice lines (Os07g37920-RNAi) and 10 over-expressing transgenic lines (Os07g37920-OE), but none of them showed differences in senescence. Transgenic Os07g37920-RNAi rice plants had reduced proportions of viable pollen grains and were male-sterile, but were able to produce seeds by cross pollination. Analysis of the flower morphology of the transgenic rice plants showed that anthers failed to dehisce. Transgenic Os07g37920-OE lines showed no sterility or anther dehiscence problems. Os07g37920 transcript levels were higher in stamens compared to leaves and significantly reduced in the transgenic Os07g37920-RNAi plants. Wheat GPC genes showed the opposite transcription profile (higher transcript levels in leaves than in flowers) and plants carrying knock-out mutations of all GPC-1 and GPC-2 genes exhibited delayed senescence but normal anther dehiscence and fertility. These results indicate a functional divergence of the homologous wheat and rice NAC genes and suggest the need for separate studies of the function and targets of these transcription factors in wheat and rice.
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Affiliation(s)
- Assaf Distelfeld
- Dept. of Plant Sciences, University of California, Davis, CA, 95616, USA
- Faculty of Life Sciences, Dept. of Molecular Biology and Ecology of Plants, Tel Aviv University, Israel
| | - Stephen P. Pearce
- Dept. of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Raz Avni
- Faculty of Life Sciences, Dept. of Molecular Biology and Ecology of Plants, Tel Aviv University, Israel
| | - Beatrice Scherer
- Dept. of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Cristobal Uauy
- Dept. of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Fernando Piston
- Dept. of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Ann Slade
- Arcadia Biosciences Inc., Davis, CA, 95616, USA
| | - Rongrong Zhao
- Dept. of Plant Sciences, University of California, Davis, CA, 95616, USA
- College of Resources and Environmental Science, China Agricultural University, Beijing, 100193, P. R. China
| | - Jorge Dubcovsky
- Dept. of Plant Sciences, University of California, Davis, CA, 95616, USA
- Howard Hughes Medical Institute and Gordon & Betty Moore Foundation
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20
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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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21
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Maccaferri M, Ratti C, Rubies-Autonell C, Vallega V, Demontis A, Stefanelli S, Tuberosa R, Sanguineti MC. Resistance to Soil-borne cereal mosaic virus in durum wheat is controlled by a major QTL on chromosome arm 2BS and minor loci. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2011; 123:527-44. [PMID: 21594676 DOI: 10.1007/s00122-011-1605-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2010] [Accepted: 04/26/2011] [Indexed: 05/15/2023]
Abstract
Soil-borne cereal mosaic (SBCM) is a viral disease, which seriously affects hexaploid as well as tetraploid wheat crops in Europe. In durum wheat (Triticum durum Desf.), the elite germplasm is characterized by a wide range of responses to SBCMV, from susceptibility to almost complete resistance. In this study, the genetic analysis of SBCMV resistance was carried out using a population of 181 durum wheat recombinant inbred lines (RILs) obtained from Meridiano (resistant) × Claudio (moderately susceptible), which were profiled with SSR and DArT markers. The RILs were characterized for SBCMV response in the field under severe and uniform SBCMV infection during 2007 and 2008. A wide range of disease reactions (as estimated by symptom severity and DAS-ELISA) was observed. A large portion of the variability for SBCMV response was explained by a major QTL (QSbm.ubo-2BS) located in the distal telomeric region of chromosome 2BS near the marker triplet Xbarc35-Xwmc661-Xgwm210, with R(2) values ranging from 51.6 to 91.6%. The favorable allele was contributed by Meridiano. Several QTLs with minor effects on SBCMV response were also detected. Consistently with the observed transgressive segregation, the resistance alleles at minor QTLs were contributed by both parents. The presence and effects of QSbm.ubo-2BS were validated through association mapping in a panel of 111 elite durum wheat accessions.
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Affiliation(s)
- Marco Maccaferri
- Department of Agroenvironmental Science and Technology, University of Bologna, Viale G. Fanin 44, 40127 Bologna, Italy
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22
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Qin B, Cao A, Wang H, Chen T, You FM, Liu Y, Ji J, Liu D, Chen P, Wang XE. Collinearity-based marker mining for the fine mapping of Pm6, a powdery mildew resistance gene in wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2011; 123:207-18. [PMID: 21468676 DOI: 10.1007/s00122-011-1577-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2010] [Accepted: 03/15/2011] [Indexed: 05/07/2023]
Abstract
The genome sequences of rice (Oryza sativa L.) and Brachypodium distachyon and the comprehensive Triticeae EST (Expressed Sequence Tag) resources provide invaluable information for comparative genomics analysis. The powdery mildew resistance gene, Pm6, which was introgressed into common wheat from Triticum timopheevii, was previously mapped to the wheat chromosome bin of 2BL [fraction length (FL) 0.50-1.00] with limited DNA markers. In this study, we saturated the Pm6 locus in wheat using the collinearity-based markers by extensively exploiting these genomic resources. All wheat ESTs located in the bin 2BL FL 0.50-1.00 and their corresponding orthologous genes on rice chromosome 4 were firstly used to develop STS (Sequence Tagged Site) markers. Those identified markers that flanked the Pm6 locus were then used to identify the collinear regions in the genomes of rice and Brachypodium. Triticeae ESTs with orthologous genes in these collinear regions were further used to develop new conserved markers for the fine mapping of Pm6. Using two F(2) populations derived from crosses of IGVI-465 × Prins and IGVI-466 × Prins, we mapped a total of 29 markers to the Pm6 locus. Among them, 14 markers were co-segregated with Pm6 in the IGVI-466/Prins population. Comparative genome analysis showed that the collinear region of the 29 linked markers covers a ~5.6-Mb region in chromosome 5L of Brachypodium and a ~6.0-Mb region in chromosome 4L of rice. The marker order is conserved between rice and Brachypodium, but re-arrangements are present in wheat. Comparative mapping in the two populations showed that two conserved markers (CINAU123 and CINAU127) flanked the Pm6 locus, and an LRR-receptor-like protein kinase cluster was identified in the collinear regions of Brachypodium and rice. This putative resistance gene cluster provides a potential target site for further fine mapping and cloning of Pm6. Moreover, the newly developed conserved markers closely linked to Pm6 can be used for the marker-assisted selection (MAS) of Pm6 in wheat breeding programs.
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Affiliation(s)
- Bi Qin
- Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
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23
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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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24
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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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25
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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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Comparative physical mapping between wheat chromosome arm 2BL and rice chromosome 4. Genetica 2010; 138:1277-96. [PMID: 21113791 DOI: 10.1007/s10709-010-9528-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2010] [Accepted: 11/11/2010] [Indexed: 10/18/2022]
Abstract
Physical maps of chromosomes provide a framework for organizing and integrating diverse genetic information. DNA microarrays are a valuable technique for physical mapping and can also be used to facilitate the discovery of single feature polymorphisms (SFPs). Wheat chromosome arm 2BL was physically mapped using a Wheat Genome Array onto near-isogenic lines (NILs) with the aid of wheat-rice synteny and mapped wheat EST information. Using high variance probe set (HVP) analysis, 314 HVPs constituting genes present on 2BL were identified. The 314 HVPs were grouped into 3 categories: HVPs that match only rice chromosome 4 (298 HVPs), those that match only wheat ESTs mapped on 2BL (1), and those that match both rice chromosome 4 and wheat ESTs mapped on 2BL (15). All HVPs were converted into gene sets, which represented either unique rice gene models or mapped wheat ESTs that matched identified HVPs. Comparative physical maps were constructed for 16 wheat gene sets and 271 rice gene sets. Of the 271 rice gene sets, 257 were mapped to the 18-35 Mb regions on rice chromosome 4. Based on HVP analysis and sequence similarity between the gene models in the rice chromosomes and mapped wheat ESTs, the outermost rice gene model that limits the translocation breakpoint to orthologous regions was identified.
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Wang MJ, Zhang Y, Lin ZS, Ye XG, Yuan YP, Ma W, Xin ZY. Development of EST-PCR markers for Thinopyrum intermedium chromosome 2Ai#2 and their application in characterization of novel wheat-grass recombinants. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2010; 121:1369-1380. [PMID: 20585749 DOI: 10.1007/s00122-010-1394-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2010] [Accepted: 06/14/2010] [Indexed: 05/29/2023]
Abstract
A series of expressed sequence tags-derived polymerase chain reaction (EST-PCR) markers specific to chromosome 2Ai#2 from Thinopyrum intermedium were developed in this study using a new integrative approach. The target alien chromosome confers high resistance to barley yellow dwarf virus (BYDV), which is a severe virus disease in wheat. To generate markers evenly distributed on 2Ai#2, a total of 105 primer pairs were designed based on mapped ESTs from 8 bins of wheat chromosome 2B with intron-prediction by aligning ESTs with genomic sequences of the new model plant Brachypodium distachyon. Eight and seven polymorphic markers on the short arm and the long arm of chromosome 2Ai#2, respectively, were obtained with a polymorphism rate of 14.3%. These chromosome 2Ai#2-specific EST-PCR markers were then used in tracing and exploring the structural variation of the alien chromosome in the population derived from the immature embryo culture of the cross between N452, a 2Ai#2(2D) substitution line, and common wheat CB037. Two centric fusion of translocations involving 2Ai#2 short or long arm with wheat chromosome 2D and some new genetic stocks including telosomes with the alien chromosome short or long arm were identified in the SC(3) generations, which provided basic materials to further study the mechanism of the BYDV resistance. BYDV tests in two field seasons suggest that the BYDV resistance was mainly conferred by the short arm, gene interaction on both arms of the alien chromosome was discussed.
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Affiliation(s)
- M J Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Key Laboratory of Crop Genetics and Breeding, Ministry of Agriculture, Chinese Academy of Agricultural Sciences (CAAS), Beijing, People's Republic of China
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28
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Yu C, Li Y, Li B, Liu X, Hao L, Chen J, Qian W, Li S, Wang G, Bai S, Ye H, Qin H, Shen Q, Chen L, Zhang A, Wang D. Molecular analysis of phosphomannomutase (PMM) genes reveals a unique PMM duplication event in diverse Triticeae species and the main PMM isozymes in bread wheat tissues. BMC PLANT BIOLOGY 2010; 10:214. [PMID: 20920368 PMCID: PMC3017832 DOI: 10.1186/1471-2229-10-214] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2010] [Accepted: 10/05/2010] [Indexed: 05/06/2023]
Abstract
BACKGROUND Phosphomannomutase (PMM) is an essential enzyme in eukaryotes. However, little is known about PMM gene and function in crop plants. Here, we report molecular evolutionary and biochemical analysis of PMM genes in bread wheat and related Triticeae species. RESULTS Two sets of homologous PMM genes (TaPMM-1 and 2) were found in bread wheat, and two corresponding PMM genes were identified in the diploid progenitors of bread wheat and many other diploid Triticeae species. The duplication event yielding PMM-1 and 2 occurred before the radiation of diploid Triticeae genomes. The PMM gene family in wheat and relatives may evolve largely under purifying selection. Among the six TaPMM genes, the transcript levels of PMM-1 members were comparatively high and their recombinant proteins were all enzymatically active. However, PMM-2 homologs exhibited lower transcript levels, two of which were also inactive. TaPMM-A1, B1 and D1 were probably the main active isozymes in bread wheat tissues. The three isozymes differed from their counterparts in barley and Brachypodium distachyon in being more tolerant to elevated test temperatures. CONCLUSION Our work identified the genes encoding PMM isozymes in bread wheat and relatives, uncovered a unique PMM duplication event in diverse Triticeae species, and revealed the main active PMM isozymes in bread wheat tissues. The knowledge obtained here improves the understanding of PMM evolution in eukaryotic organisms, and may facilitate further investigations of PMM function in the temperature adaptability of bread wheat.
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Affiliation(s)
- Chunmei Yu
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, PR China
- Life Science School, Nantong University, Nantong 226019, PR China
- Graduate University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Yiwen Li
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Bin Li
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, PR China
- Graduate University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Xin Liu
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Lifang Hao
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, PR China
- Graduate University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Jing Chen
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, PR China
- Graduate University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Weiqiang Qian
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, PR China
- Graduate University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Shiming Li
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, PR China
- Graduate University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Guanfeng Wang
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, PR China
- Graduate University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Shiwei Bai
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, PR China
- Graduate University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Hua Ye
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, PR China
- Graduate University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Huanju Qin
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Qianhua Shen
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Liangbiao Chen
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Aimin Zhang
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, PR 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, PR China
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Qi Z, Du P, Qian B, Zhuang L, Chen H, Chen T, Shen J, Guo J, Feng Y, Pei Z. Characterization of a wheat-Thinopyrum bessarabicum (T2JS-2BS.2BL) translocation line. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2010; 121:589-97. [PMID: 20407740 DOI: 10.1007/s00122-010-1332-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2009] [Accepted: 04/01/2010] [Indexed: 05/07/2023]
Abstract
Thinopyrum bessarabicum (2n = 2x = 14, JJ or E(b)E(b)) is an important genetic resource for wheat improvement due to its salinity tolerance and disease resistance. Development of wheat-Th. bessarabicum translocation lines will facilitate its practical utilization in wheat improvement. In this study, a novel wheat-Th. bessarabicum translocation line T2JS-2BS.2BL, which carries a segment of Th. bessarabicum chromosome arm 2JS was identified and further characterized using sequential chromosome C-banding, genomic in situ hybridization (GISH), dual-color fluorescent in situ hybridization (FISH) and DNA markers. The translocation breakpoint was mapped within bin C-2BS1-0.53 of chromosome 2B through marker analysis. Compared to the Chinese Spring (CS) parent and to CS-type lines, the translocation line has more fertile spikes per plant, longer spikes, more grains per spike and higher yield per plant, which suggests that the alien segment carries yield-related genes. However, plants with the translocation are also taller, head later and have lower 1,000-kernel weight than CS or CS-type lines. By using markers specific to the barley photoperiod response gene Ppd-H1, it was determined that the late heading date was conferred by a recessive allele located on the 2JS segment. In addition, four markers specific for the translocated segment were identified, which can be used for marker-aided screening.
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Affiliation(s)
- Zengjun Qi
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China.
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30
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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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31
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YIN GH, LI GY, HE ZH, LIU JJ, WANG H, XIA XC. Molecular Mapping of Powdery Mildew Resistance Gene in Wheat Cultivar Jimai 22. ZUOWU XUEBAO 2009. [DOI: 10.3724/sp.j.1006.2009.01425] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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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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Lee TG, Hong MJ, Johnson JW, Bland DE, Kim DY, Seo YW. Development and functional assessment of EST-derived 2RL-specific markers for 2BS.2RL translocations. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2009; 119:663-673. [PMID: 19543880 DOI: 10.1007/s00122-009-1077-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2009] [Accepted: 05/15/2009] [Indexed: 05/26/2023]
Abstract
ESTs-derived markers are useful for comparative genomic analysis and can also serve as phenotype-linked functional markers. Here, we report the development of EST-derived 2RL-specific markers and the evaluation of the possibility of functional assessment of markers tagging 2RL, which carries Hessian fly resistance genes (loci). To identify transcripts specific to 2RL, unigene sequences in combination with wheat progenitor genomes were used. Total 275 contigs mapped to the long arms of homoeologous group 2 chromosomes were downloaded. To obtain a cluster corresponding to each of the wheat 275 contigs, unigene sequences of wheat, rice, barley, and rye were pooled for cross-species clusters. Out of 275 clusters examined, it was possible to design 112 cross-species primer pairs for genome-specific amplifications. Out of 112 cross-species primer pairs, 45 primer pairs (40%) produced amplicons from at least one species (three wheat progenitors or rye). Among the 45 contigs, 73% were associated with one of known functions and 82% of the contigs associated with known functions were also associated with one of the GO categories. On the basis of the oligonucleotide sequence alignment of each of 45 genome-specific amplifications, 21 amplifications (47%) were suitable for designing RR genome-specific primers, which are specific to translocated rye chromatin 2RL. Six primer pairs (13%) successfully produced amplicons in the 2BS.2RL translocation lines and not in the non-2RLs. Functional assessment of one of the 2RL-specific markers, NSFT03P2_Contig4445, was performed on Hessian fly infested NILs. Under Hessian fly infestation, significantly high expression of a gene tagged by a 2RL-specific marker (NSFT03P2_Contig4445) was observed 1 day after infestation. EST-derived 2RL-specific marker development from this study provides a basis for the development of ESTs-derived markers for detecting wheat-rye translocations. In addition, these markers could be employed in elucidating functional analysis of genes on 2RL.
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Affiliation(s)
- Tong Geon Lee
- College of Life Sciences and Biotechnology, Korea University, Seoul, 136-713, Republic of Korea
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Sood S, Kuraparthy V, Bai G, Gill BS. The major threshability genes soft glume (sog) and tenacious glume (Tg), of diploid and polyploid wheat, trace their origin to independent mutations at non-orthologous loci. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2009; 119:341-51. [PMID: 19421730 DOI: 10.1007/s00122-009-1043-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2008] [Accepted: 04/09/2009] [Indexed: 05/23/2023]
Abstract
Threshability is an important crop domestication trait. The wild wheat progenitors have tough glumes enveloping the floret that make spikes difficult to thresh, whereas cultivated wheats have soft glumes and are free-threshing. In hexaploid wheat, the glume tenacity gene Tg along with the major domestication locus Q control threshability. The Q gene was isolated recently and found to be a member of the AP2 class of transcription factors. However, only a few studies have reported on the tough glume trait. Here, we report comparative mapping of the soft glume (sog) gene of diploid Triticum monococcum L. and tenacious glume (Tg) gene of hexaploid T. aestivum L. using chromosome-specific SSR and RFLP markers. The sog gene was flanked by Xgwm71 and Xbcd120 in a 6.8 cM interval on chromosome 2A(m)S of T. monococcum whereas Tg was targeted to a 8.1 cM interval flanked by Xwmc503 and Xfba88 on chromosome 2DS of T. aestivum. Deletion bin mapping of the flanking markers assigned sog close to the centromere on 2AS, whereas Tg was mapped to the most distal region on 2DS. Both 2AS and 2DS maps were colinear ruling out the role of chromosome rearrangements for their non-syntenic positions. Therefore, sog and Tg are not true orthologues suggesting the possibility of a diverse origin.
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Affiliation(s)
- Shilpa Sood
- Department of Plant Pathology, Wheat Genetic and Genomic Resources Center, Kansas State University, Manhattan, KS 66506-5502, USA.
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Structure-function analysis of the barley genome: the gene-rich region of chromosome 2HL. Funct Integr Genomics 2008; 9:67-79. [PMID: 18958509 DOI: 10.1007/s10142-008-0099-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2008] [Revised: 09/03/2008] [Accepted: 10/13/2008] [Indexed: 10/21/2022]
Abstract
A major gene-rich region on the end of the long arm of Triticeae group 2 chromosomes exhibits high recombination frequencies, making it an attractive region for positional cloning. Traits known to be controlled by this region include chasmogamy/cleistogamy, frost tolerance at flowering, grain yield, head architecture, and resistance to Fusarium head blight and rusts. To assist these cloning efforts, we constructed detailed genetic maps of barley chromosome 2H, including 61 polymerase chain reaction markers. Colinearity with rice occurred in eight distinct blocks, including five blocks in the terminal gene-rich region. Alignment of rice sequences from the junctions of colinear chromosome segments provided no evidence for the involvement of long (>2.5 kb) inverted repeats in generating inversions. However, reuse of some junction sequences in two or three separate evolutionary breakage/fusion events was implicated, suggesting the presence of fragile sites. Sequencing across 91 gene fragments totaling 107 kb from four barley genotypes revealed the highest single nucleotide substitution and insertion-deletion polymorphism levels in the terminal regions of the chromosome arms. The maps will assist in the isolation of genes from the chromosome 2L gene-rich region in barley and wheat by providing markers and accelerating the identification of the corresponding points in the rice genome sequence.
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Ochiai K, Uemura S, Shimizu A, Okumoto Y, Matoh T. Boron toxicity in rice (Oryza sativa L.). I. Quantitative trait locus (QTL) analysis of tolerance to boron toxicity. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2008; 117:125-133. [PMID: 18401574 DOI: 10.1007/s00122-008-0758-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2007] [Accepted: 03/25/2008] [Indexed: 05/26/2023]
Abstract
Boron toxicity tolerance of rice plants was studied. Modern japonica subspecies such as Koshihikari, Nipponbare, and Sasanishiki were tolerant, whereas indica subspecies such as Kasalath and IR36 were intolerant to excessive application of boron (B), even though their shoot B contents under B toxicity were not significantly different. Recombinant inbred lines (RILs) of japonica Nekken-1 and indica IR36 were used for quantitative trait locus (QTL) analysis to identify the gene responsible for B toxicity tolerance. A major QTL that could explain 45% of the phenotypic variation was detected in chromosome 4. The QTL was confirmed using a population derived from a recombinant inbred line which is heterogenic at the QTL region. The QTL was also confirmed in other chromosome segment substitution lines (CSSLs).
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Affiliation(s)
- K Ochiai
- Laboratory of Plant Nutrition, Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
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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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38
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Salse J, Bolot S, Throude M, Jouffe V, Piegu B, Quraishi UM, Calcagno T, Cooke R, Delseny M, Feuillet C. Identification and characterization of shared duplications between rice and wheat provide new insight into grass genome evolution. THE PLANT CELL 2008; 20:11-24. [PMID: 18178768 PMCID: PMC2254919 DOI: 10.1105/tpc.107.056309] [Citation(s) in RCA: 258] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2007] [Revised: 11/21/2007] [Accepted: 12/12/2007] [Indexed: 05/17/2023]
Abstract
The grass family comprises the most important cereal crops and is a good system for studying, with comparative genomics, mechanisms of evolution, speciation, and domestication. Here, we identified and characterized the evolution of shared duplications in the rice (Oryza sativa) and wheat (Triticum aestivum) genomes by comparing 42,654 rice gene sequences with 6426 mapped wheat ESTs using improved sequence alignment criteria and statistical analysis. Intraspecific comparisons identified 29 interchromosomal duplications covering 72% of the rice genome and 10 duplication blocks covering 67.5% of the wheat genome. Using the same methodology, we assessed orthologous relationships between the two genomes and detected 13 blocks of colinearity that represent 83.1 and 90.4% of the rice and wheat genomes, respectively. Integration of the intraspecific duplications data with colinearity relationships revealed seven duplicated segments conserved at orthologous positions. A detailed analysis of the length, composition, and divergence time of these duplications and comparisons with sorghum (Sorghum bicolor) and maize (Zea mays) indicated common and lineage-specific patterns of conservation between the different genomes. This allowed us to propose a model in which the grass genomes have evolved from a common ancestor with a basic number of five chromosomes through a series of whole genome and segmental duplications, chromosome fusions, and translocations.
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Affiliation(s)
- Jérôme Salse
- Institut National de la Recherche Agronomique/Université Blaise Pascal Unité Mixte de Recherche 1095, Amélioration et Santé des Plantes, 63100 Clermont-Ferrand, France
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39
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Qi L, Friebe B, Gill BS. Complex genome rearrangements reveal evolutionary dynamics of pericentromeric regions in the Triticeae. Genome 2007; 49:1628-39. [PMID: 17426778 DOI: 10.1139/g06-123] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Most pericentromeric regions of eukaryotic chromosomes are heterochromatic and are the most rapidly evolving regions of complex genomes. The closely related genomes within hexaploid wheat (Triticum aestivum L., 2n=6x=42, AABBDD), as well as in the related Triticeae taxa, share large conserved chromosome segments and provide a good model for the study of the evolution of pericentromeric regions. Here we report on the comparative analysis of pericentric inversions in the Triticeae, including Triticum aestivum, Aegilops speltoides, Ae. longissima, Ae. searsii, Hordeum vulgare, Secale cereale, and Agropyron elongatum. Previously, 4 pericentric inversions were identified in the hexaploid wheat cultivar 'Chinese Spring' ('CS') involving chromosomes 2B, 4A, 4B, and 5A. In the present study, 2 additional pericentric inversions were detected in chromosomes 3B and 6B of 'CS' wheat. Only the 3B inversion pre-existed in chromosome 3S, 3Sl, and 3Ss of Aegilops species of the Sitopsis section, the remaining inversions occurring after wheat polyploidization. The translocation T2BS/6BS previously reported in 'CS' was detected in the hexaploid variety 'Wichita' but not in other species of the Triticeae. It appears that the B genome is more prone to genome rearrangements than are the A and D genomes. Five different pericentric inversions were detected in rye chromosomes 3R and 4R, 4Sl of Ae. longissima, 4H of barley, and 6E of Ag. elongatum. This indicates that pericentric regions in the Triticeae, especially those of group 4 chromosomes, are undergoing rapid and recurrent rearrangements.
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Affiliation(s)
- Lili Qi
- Wheat Genetic and Genomic Resources Center, Department of Plant Pathology, Throckmorton Hall, Kansas State University, Manhattan, KS 66506-5502, USA
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40
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Francki MG, Walker E, Forster JW, Spangenberg G, Appels R. Fructosyltransferase and invertase genes evolved by gene duplication and rearrangements: rice, perennial ryegrass, and wheat gene families. Genome 2007; 49:1081-91. [PMID: 17110988 DOI: 10.1139/g06-066] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The invertase enzyme family is responsible for carbohydrate metabolism in rice, perennial ryegrass, and wheat. Fructan molecules accumulate in cell vacuoles of perennial ryegrass and wheat and are associated with abiotic stress tolerance. High levels of amino acid similarity between the fructosyltransferases responsible for fructan accumulation indicates that they may have evolved from invertase-like ancestral genes. In this study, we have applied comparative genomics to determine the mechanisms that lead to the evolution of fructosytransferase and invertase genes in rice, perennial ryegrass, and wheat. Duplications and rearrangements have been inferred to generate variant forms of the rice invertases since divergence from a common grass progenitor. The occurrence of multiple copies of fructosyltransferase genes indicated that duplication events continued during evolution of the wheat and perennial ryegrass lineages. Further gene rearrangements were evident in perennial ryegrass genes, albeit at a reduced level compared with the rice invertases. Gene orthologs were largely static after duplication during evolution of the wheat lineage. This study details evolutionary events that contribute to fructosyltransferase and invertase gene variation in grasses.
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Affiliation(s)
- Michael G Francki
- Western Australia Department of Agriculture, 3 Baron-Hay Ct, South Perth, WA 6151, Australia.
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41
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Zhang P, Friebe B, Gill B, Park RF. Cytogenetics in the age of molecular genetics. ACTA ACUST UNITED AC 2007. [DOI: 10.1071/ar07054] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
From the beginning of the 20th Century, we have seen tremendous advances in knowledge and understanding in almost all biological disciplines, including genetics, molecular biology, structural and functional genomics, and biochemistry. Among these advances, cytogenetics has played an important role. This paper details some of the important milestones of modern cytogenetics. Included are the historical role of cytogenetics in genetic studies in general and the genetics stocks produced using cytogenetic techniques. The basic biological questions cytogenetics can address and the important role and practical applications of cytogenetics in applied sciences, such as in agriculture and in breeding for disease resistance in cereals, are also discussed. The goal of this paper is to show that cytogenetics remains important in the age of molecular genetics, because it is inseparable from overall genome analysis. Cytogenetics complements studies in other disciplines within the field of biology and provides the basis for linking genetics, molecular biology and genomics research.
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42
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Huang S, Spielmeyer W, Lagudah ES, James RA, Platten JD, Dennis ES, Munns R. A sodium transporter (HKT7) is a candidate for Nax1, a gene for salt tolerance in durum wheat. PLANT PHYSIOLOGY 2006; 142:1718-27. [PMID: 17071645 PMCID: PMC1676039 DOI: 10.1104/pp.106.088864] [Citation(s) in RCA: 150] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2006] [Accepted: 10/11/2006] [Indexed: 05/12/2023]
Abstract
Durum wheat (Triticum turgidum subsp. durum) is more salt sensitive than bread wheat (Triticum aestivum). A novel source of Na(+) exclusion conferring salt tolerance to durum wheat is present in the durum wheat Line 149 derived from Triticum monococcum C68-101, and a quantitative trait locus contributing to low Na(+) concentration in leaf blades, Nax1, mapped to chromosome 2AL. In this study, we used the rice (Oryza sativa) genome sequence and data from the wheat expressed sequence tag deletion bin mapping project to identify markers and construct a high-resolution map of the Nax1 region. Genes on wheat chromosome 2AL and rice chromosome 4L had good overall colinearity, but there was an inversion of a chromosomal segment that includes the Nax1 locus. Two putative sodium transporter genes (TmHKT7) related to OsHKT7 were mapped to chromosome 2AL. One TmHKT7 member (TmHKT7-A1) was polymorphic between the salt-tolerant and -sensitive lines, and cosegregated with Nax1 in the high-resolution mapping family. The other TmHKT7 member (TmHKT7-A2) was located within the same bacterial artificial chromosome contig of approximately 145 kb as TmHKT7-A1. TmHKT7-A1 and -A2 showed 83% amino acid identity. TmHKT7-A2, but not TmHKT7-A1, was expressed in roots and leaf sheaths of the salt-tolerant durum wheat Line 149. The expression pattern of TmHKT7-A2 was consistent with the physiological role of Nax1 in reducing Na(+) concentration in leaf blades by retaining Na(+) in the sheaths. TmHKT7-A2 could control Na(+) unloading from xylem in roots and sheaths.
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Affiliation(s)
- Shaobai Huang
- CSIRO Plant Industry, Canberra, Australian Capital Territory 2601, Australia.
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43
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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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44
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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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45
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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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46
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Muehlbauer GJ, Bhau BS, Syed NH, Heinen S, Cho S, Marshall D, Pateyron S, Buisine N, Chalhoub B, Flavell AJ. A hAT superfamily transposase recruited by the cereal grass genome. Mol Genet Genomics 2006; 275:553-63. [PMID: 16468023 DOI: 10.1007/s00438-006-0098-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2005] [Accepted: 12/22/2005] [Indexed: 11/30/2022]
Abstract
Transposable elements are ubiquitous genomic parasites with an ancient history of coexistence with their hosts. A few cases have emerged recently where these genetic elements have been recruited for normal function in the host organism. We have identified an expressed hobo/Ac/Tam (hAT) family transposase-like gene in cereal grasses which appears to represent such a case. This gene, which we have called gary, is found in one or two copies in barley, two diverged copies in rice and two very similar copies in hexaploid wheat. No gary homologues are found in Arabidopsis. In all three cereal species, an apparently complete 2.5 kb transposase-like open reading frame is present and nucleotide substitution data show evidence for positive selection, yet the predicted gary protein is probably not an active transposase, as judged by the absence of key amino acids required for transposase function. Gary is expressed in wheat and barley spikes and gary cDNA sequences are also found in rice, oat, rye, maize, sorghum and sugarcane. The short inverted terminal repeats, flanked by an eight-nucleotide host sequence duplication, which are characteristic of a hAT transposon are absent. Genetic mapping in barley shows that gary is located on the distal end of the long arm of chromosome 2H. Wheat homologues of gary map to the same approximate location on the wheat group 2 chromosomes by physical bin-mapping and the more closely related of the two rice garys maps to the syntenic location near the bottom of rice chromosome 4. These data suggest that gary has resided in a single genomic location for at least 60 Myr and has lost the ability to transpose, yet expresses a transposase-related protein that is being conserved under host selection. We propose that the gary transposase-like gene has been recruited by the cereal grasses for an unknown function.
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Affiliation(s)
- Gary J Muehlbauer
- Department of Agronomy and Plant Genetics, University of Minnesota, 411 Borlaug Hall, St. Paul, MN, 55108, USA
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47
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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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48
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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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49
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Kawaura K, Mochida K, Yamazaki Y, Ogihara Y. Transcriptome analysis of salinity stress responses in common wheat using a 22k oligo-DNA microarray. Funct Integr Genomics 2005; 6:132-42. [PMID: 16328439 DOI: 10.1007/s10142-005-0010-3] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2005] [Revised: 08/27/2005] [Accepted: 09/06/2005] [Indexed: 12/16/2022]
Abstract
In this study, we constructed a 22k wheat oligo-DNA microarray. A total of 148,676 expressed sequence tags of common wheat were collected from the database of the Wheat Genomics Consortium of Japan. These were grouped into 34,064 contigs, which were then used to design an oligonucleotide DNA microarray. Following a multistep selection of the sense strand, 21,939 60-mer oligo-DNA probes were selected for attachment on the microarray slide. This 22k oligo-DNA microarray was used to examine the transcriptional response of wheat to salt stress. More than 95% of the probes gave reproducible hybridization signals when targeted with RNAs extracted from salt-treated wheat shoots and roots. With the microarray, we identified 1,811 genes whose expressions changed more than 2-fold in response to salt. These included genes known to mediate response to salt, as well as unknown genes, and they were classified into 12 major groups by hierarchical clustering. These gene expression patterns were also confirmed by real-time reverse transcription-PCR. Many of the genes with unknown function were clustered together with genes known to be involved in response to salt stress. Thus, analysis of gene expression patterns combined with gene ontology should help identify the function of the unknown genes. Also, functional analysis of these wheat genes should provide new insight into the response to salt stress. Finally, these results indicate that the 22k oligo-DNA microarray is a reliable method for monitoring global gene expression patterns in wheat.
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Affiliation(s)
- Kanako Kawaura
- Laboratory of Genetic Engineering, Kyoto Prefectural University, Shimogamo, Kyoto 606-8522, Japan
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50
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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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