51
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Cui F, Zhang N, Fan XL, Zhang W, Zhao CH, Yang LJ, Pan RQ, Chen M, Han J, Zhao XQ, Ji J, Tong YP, Zhang HX, Jia JZ, Zhao GY, Li JM. Utilization of a Wheat660K SNP array-derived high-density genetic map for high-resolution mapping of a major QTL for kernel number. Sci Rep 2017. [PMID: 28630475 DOI: 10.1038/s41598-017-04028-63] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/24/2023] Open
Abstract
In crop plants, a high-density genetic linkage map is essential for both genetic and genomic researches. The complexity and the large size of wheat genome have hampered the acquisition of a high-resolution genetic map. In this study, we report a high-density genetic map based on an individual mapping population using the Affymetrix Wheat660K single-nucleotide polymorphism (SNP) array as a probe in hexaploid wheat. The resultant genetic map consisted of 119 566 loci spanning 4424.4 cM, and 119 001 of those loci were SNP markers. This genetic map showed good collinearity with the 90 K and 820 K consensus genetic maps and was also in accordance with the recently released wheat whole genome assembly. The high-density wheat genetic map will provide a major resource for future genetic and genomic research in wheat. Moreover, a comparative genomics analysis among gramineous plant genomes was conducted based on the high-density wheat genetic map, providing an overview of the structural relationships among theses gramineous plant genomes. A major stable quantitative trait locus (QTL) for kernel number per spike was characterized, providing a solid foundation for the future high-resolution mapping and map-based cloning of the targeted QTL.
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Affiliation(s)
- Fa Cui
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, 050022, China
- Genetic Improvement Centre of Agricultural and Forest Crops, College of Agriculture, Ludong Unversity, Yan'tai, 264025, China
- State Key Laboratory of Plant Cell and Chromosomal Engineering, Chinese Academy of Sciences, Beijing, 100101, China
| | - Na Zhang
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, 050022, China
- University of Chinese Academy of Sciences, Beijing, 10049, China
| | - Xiao-Li Fan
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, 050022, China
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Wei Zhang
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, 050022, China.
- State Key Laboratory of Plant Cell and Chromosomal Engineering, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Chun-Hua Zhao
- Genetic Improvement Centre of Agricultural and Forest Crops, College of Agriculture, Ludong Unversity, Yan'tai, 264025, China
| | - Li-Juan Yang
- Xinxiang Academy of Agricultural Sciences, Xinxiang, 453000, China
| | - Rui-Qing Pan
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, 050022, China
- University of Chinese Academy of Sciences, Beijing, 10049, China
| | - Mei Chen
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, 050022, China
- University of Chinese Academy of Sciences, Beijing, 10049, China
| | - Jie Han
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, 050022, China
- University of Chinese Academy of Sciences, Beijing, 10049, China
| | - Xue-Qiang Zhao
- State Key Laboratory of Plant Cell and Chromosomal Engineering, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jun Ji
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, 050022, China
- State Key Laboratory of Plant Cell and Chromosomal Engineering, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yi-Ping Tong
- State Key Laboratory of Plant Cell and Chromosomal Engineering, Chinese Academy of Sciences, Beijing, 100101, China
| | - Hong-Xia Zhang
- Genetic Improvement Centre of Agricultural and Forest Crops, College of Agriculture, Ludong Unversity, Yan'tai, 264025, China
| | - Ji-Zeng Jia
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Guang-Yao Zhao
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Jun-Ming Li
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, 050022, China.
- State Key Laboratory of Plant Cell and Chromosomal Engineering, Chinese Academy of Sciences, Beijing, 100101, China.
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52
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Utilization of a Wheat660K SNP array-derived high-density genetic map for high-resolution mapping of a major QTL for kernel number. Sci Rep 2017. [PMID: 28630475 PMCID: PMC5476560 DOI: 10.1038/s41598-017-04028-6] [Citation(s) in RCA: 138] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
In crop plants, a high-density genetic linkage map is essential for both genetic and genomic researches. The complexity and the large size of wheat genome have hampered the acquisition of a high-resolution genetic map. In this study, we report a high-density genetic map based on an individual mapping population using the Affymetrix Wheat660K single-nucleotide polymorphism (SNP) array as a probe in hexaploid wheat. The resultant genetic map consisted of 119 566 loci spanning 4424.4 cM, and 119 001 of those loci were SNP markers. This genetic map showed good collinearity with the 90 K and 820 K consensus genetic maps and was also in accordance with the recently released wheat whole genome assembly. The high-density wheat genetic map will provide a major resource for future genetic and genomic research in wheat. Moreover, a comparative genomics analysis among gramineous plant genomes was conducted based on the high-density wheat genetic map, providing an overview of the structural relationships among theses gramineous plant genomes. A major stable quantitative trait locus (QTL) for kernel number per spike was characterized, providing a solid foundation for the future high-resolution mapping and map-based cloning of the targeted QTL.
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53
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High-Resolution Mapping of Crossover Events in the Hexaploid Wheat Genome Suggests a Universal Recombination Mechanism. Genetics 2017; 206:1373-1388. [PMID: 28533438 DOI: 10.1534/genetics.116.196014] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 05/12/2017] [Indexed: 11/18/2022] Open
Abstract
During meiosis, crossovers (COs) create new allele associations by reciprocal exchange of DNA. In bread wheat (Triticum aestivum L.), COs are mostly limited to subtelomeric regions of chromosomes, resulting in a substantial loss of breeding efficiency in the proximal regions, though these regions carry ∼60-70% of the genes. Identifying sequence and/or chromosome features affecting recombination occurrence is thus relevant to improve and drive recombination. Using the recent release of a reference sequence of chromosome 3B and of the draft assemblies of the 20 other wheat chromosomes, we performed fine-scale mapping of COs and revealed that 82% of COs located in the distal ends of chromosome 3B representing 19% of the chromosome length. We used 774 SNPs to genotype 180 varieties representative of the Asian and European genetic pools and a segregating population of 1270 F6 lines. We observed a common location for ancestral COs (predicted through linkage disequilibrium) and the COs derived from the segregating population. We delineated 73 small intervals (<26 kb) on chromosome 3B that contained 252 COs. We observed a significant association of COs with genic features (73 and 54% in recombinant and nonrecombinant intervals, respectively) and with those expressed during meiosis (67% in recombinant intervals and 48% in nonrecombinant intervals). Moreover, while the recombinant intervals contained similar amounts of retrotransposons and DNA transposons (42 and 53%), nonrecombinant intervals had a higher level of retrotransposons (63%) and lower levels of DNA transposons (28%). Consistent with this, we observed a higher frequency of a DNA motif specific to the TIR-Mariner DNA transposon in recombinant intervals.
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54
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Guo Y, Du Z, Chen J, Zhang Z. QTL mapping of wheat plant architectural characteristics and their genetic relationship with seven QTLs conferring resistance to sheath blight. PLoS One 2017; 12:e0174939. [PMID: 28384183 PMCID: PMC5383044 DOI: 10.1371/journal.pone.0174939] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Accepted: 03/17/2017] [Indexed: 11/18/2022] Open
Abstract
Sheath blight is one of the most devastating wheat diseases worldwide. Breeding resistant cultivars is the most powerful strategy to defeat the disease. Plant resistance on “disease escape” works through modulation of morphological traits and shows sustainable resistance to disease. Plant architectural traits have been reported to play a significant role in disease response. Therefore, exploring the genetic relationship between plant architecture and disease resistance is of importance to the understanding of plant resistance via “disease escape”. Using an F9 population of 266 RILs (Recombinant Inbred Lines) derived from the cross of Luke × AQ24788-83, we have generated a linkage map of 631 markers on 21 chromosomes. In this study, we present the QTL identification of fourteen plant architectural characteristics and heading time from two years and analyze their genetic relationships with seven previously published QTLs to sheath blight (QSBs, QSe.cau), including plant height (PH), the space between the flag leaf and penultimate leaf (fdR), heading date (Hd), and other traits. Twelve stable QTLs of the morphological traits were identified with good consistency across five replicates. For the seven previously published QSBs, we found no significant association with plant height. However, some of the QSBs displayed strong associations with plant architectural traits and heading date. Especially, QfdR.cau-1AS, QHd.cau-2BS, QfdR.cau-5DL, and QfdR.cau-6BL were respectively mapped to the same regions as QSe.cau-1AS, QSe.cau-2BS, QSe.cau-5DL, and QSe.cau-6BL. Taken together, we have demonstrated that plant height did not exert a direct influence on the resistance to sheath blight conferred by the seven QSBs and that the plant architecture and heading date did exhibit a tight relationship with the resistance. Therefore, this study provides a novel evidence to help understand sheath blight resistance in wheat. In addition, the linked morphological characteristics and the generated flanking markers will facilitate breeding for resistance to sheath blight in wheat.
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Affiliation(s)
- Yan Guo
- Plant Pathology Department, College of Plant Protection, China Agricultural University, Beijing, China
- * E-mail:
| | - Ziyi Du
- Plant Pathology Department, College of Plant Protection, China Agricultural University, Beijing, China
| | - Jiang Chen
- Plant Pathology Department, College of Plant Protection, China Agricultural University, Beijing, China
| | - Zhongjun Zhang
- Plant Pathology Department, College of Plant Protection, China Agricultural University, Beijing, China
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55
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Pavy N, Lamothe M, Pelgas B, Gagnon F, Birol I, Bohlmann J, Mackay J, Isabel N, Bousquet J. A high-resolution reference genetic map positioning 8.8 K genes for the conifer white spruce: structural genomics implications and correspondence with physical distance. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 90:189-203. [PMID: 28090692 DOI: 10.1111/tpj.13478] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 12/23/2016] [Accepted: 01/03/2017] [Indexed: 05/21/2023]
Abstract
Over the last decade, extensive genetic and genomic resources have been developed for the conifer white spruce (Picea glauca, Pinaceae), which has one of the largest plant genomes (20 Gbp). Draft genome sequences of white spruce and other conifers have recently been produced, but dense genetic maps are needed to comprehend genome macrostructure, delineate regions involved in quantitative traits, complement functional genomic investigations, and assist the assembly of fragmented genomic sequences. A greatly expanded P. glauca composite linkage map was generated from a set of 1976 full-sib progeny, with the positioning of 8793 expressed genes. Regions with significant low or high gene density were identified. Gene family members tended to be mapped on the same chromosomes, with tandemly arrayed genes significantly biased towards specific functional classes. The map was integrated with transcriptome data surveyed across eight tissues. In total, 69 clusters of co-expressed and co-localising genes were identified. A high level of synteny was found with pine genetic maps, which should facilitate the transfer of structural information in the Pinaceae. Although the current white spruce genome sequence remains highly fragmented, dozens of scaffolds encompassing more than one mapped gene were identified. From these, the relationship between genetic and physical distances was examined and the genome-wide recombination rate was found to be much smaller than most estimates reported for angiosperm genomes. This gene linkage map shall assist the large-scale assembly of the next-generation white spruce genome sequence and provide a reference resource for the conifer genomics community.
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Affiliation(s)
- Nathalie Pavy
- Canada Research Chair in Forest Genomics, Forest Research Centre and Institute for Systems and Integrative Biology, Université Laval, Québec, QC, G1V 0A6, Canada
| | - Manuel Lamothe
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, 1055 du P.E.P.S., P.O. Box 10380, Stn. Sainte-Foy, Québec, QC, G1V 4C7, Canada
| | - Betty Pelgas
- Canada Research Chair in Forest Genomics, Forest Research Centre and Institute for Systems and Integrative Biology, Université Laval, Québec, QC, G1V 0A6, Canada
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, 1055 du P.E.P.S., P.O. Box 10380, Stn. Sainte-Foy, Québec, QC, G1V 4C7, Canada
| | - France Gagnon
- Canada Research Chair in Forest Genomics, Forest Research Centre and Institute for Systems and Integrative Biology, Université Laval, Québec, QC, G1V 0A6, Canada
| | - Inanç Birol
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, V5Z 4S6, Canada
| | - Joerg Bohlmann
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - John Mackay
- Canada Research Chair in Forest Genomics, Forest Research Centre and Institute for Systems and Integrative Biology, Université Laval, Québec, QC, G1V 0A6, Canada
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, 0X1 3RB, UK
| | - Nathalie Isabel
- Canada Research Chair in Forest Genomics, Forest Research Centre and Institute for Systems and Integrative Biology, Université Laval, Québec, QC, G1V 0A6, Canada
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, 1055 du P.E.P.S., P.O. Box 10380, Stn. Sainte-Foy, Québec, QC, G1V 4C7, Canada
| | - Jean Bousquet
- Canada Research Chair in Forest Genomics, Forest Research Centre and Institute for Systems and Integrative Biology, Université Laval, Québec, QC, G1V 0A6, Canada
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56
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Uauy C. Wheat genomics comes of age. CURRENT OPINION IN PLANT BIOLOGY 2017; 36:142-148. [PMID: 28346895 DOI: 10.1016/j.pbi.2017.01.007] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Revised: 01/24/2017] [Accepted: 01/30/2017] [Indexed: 05/18/2023]
Abstract
Advances in wheat genomics have lagged behind other major cereals (e.g., rice and maize) due to its highly repetitive and large polyploid genome. Recent technological developments in sequencing and assembly methods, however, have largely overcome these barriers. The community now moves to an era centred on functional characterisation of the genome. This includes understanding sequence and structural variation as well as how information is integrated across multiple homoeologous genomes. This understanding promises to uncover variation previously hidden from natural and human selection due to the often observed functional redundancy between homoeologs. Key functional genomic resources will enable this, including sequenced mutant populations and gene editing technologies which are now available in wheat. Training the next-generation of genomics-enabled researchers will be essential to ensure these advances are quickly translated into farmers' fields.
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Affiliation(s)
- Cristobal Uauy
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom.
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57
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Hao C, Wang Y, Chao S, Li T, Liu H, Wang L, Zhang X. The iSelect 9 K SNP analysis revealed polyploidization induced revolutionary changes and intense human selection causing strong haplotype blocks in wheat. Sci Rep 2017; 7:41247. [PMID: 28134278 PMCID: PMC5278348 DOI: 10.1038/srep41247] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 12/19/2016] [Indexed: 01/05/2023] Open
Abstract
A Chinese wheat mini core collection was genotyped using the wheat 9 K iSelect SNP array. Total 2420 and 2396 polymorphic SNPs were detected on the A and the B genome chromosomes, which formed 878 haplotype blocks. There were more blocks in the B genome, but the average block size was significantly (P < 0.05) smaller than those in the A genome. Intense selection (domestication and breeding) had a stronger effect on the A than on the B genome chromosomes. Based on the genetic pedigrees, many blocks can be traced back to a well-known Strampelli cross, which was made one century ago. Furthermore, polyploidization of wheat (both tetraploidization and hexaploidization) induced revolutionary changes in both the A and the B genomes, with a greater increase of gene diversity compared to their diploid ancestors. Modern breeding has dramatically increased diversity in the gene coding regions, though obvious blocks were formed on most of the chromosomes in both tetraploid and hexaploid wheats. Tag-SNP markers identified in this study can be used for marker assisted selection using haplotype blocks as a wheat breeding strategy. This strategy can also be employed to facilitate genome selection in other self-pollinating crop species.
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Affiliation(s)
- Chenyang Hao
- Key Laboratory of Crop Gene Resources and Germplasm Enhancment, Ministry of Agriculture/The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yuquan Wang
- Key Laboratory of Crop Gene Resources and Germplasm Enhancment, Ministry of Agriculture/The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Shiaoman Chao
- US Department of Agriculture-Agricultural Research Service Biosciences Research Laboratory, Fargo, ND 58102, USA
| | - Tian Li
- Key Laboratory of Crop Gene Resources and Germplasm Enhancment, Ministry of Agriculture/The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Hongxia Liu
- Key Laboratory of Crop Gene Resources and Germplasm Enhancment, Ministry of Agriculture/The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Lanfen Wang
- Key Laboratory of Crop Gene Resources and Germplasm Enhancment, Ministry of Agriculture/The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xueyong Zhang
- Key Laboratory of Crop Gene Resources and Germplasm Enhancment, Ministry of Agriculture/The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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58
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Balcárková B, Frenkel Z, Škopová M, Abrouk M, Kumar A, Chao S, Kianian SF, Akhunov E, Korol AB, Doležel J, Valárik M. A High Resolution Radiation Hybrid Map of Wheat Chromosome 4A. FRONTIERS IN PLANT SCIENCE 2017; 7:2063. [PMID: 28119729 PMCID: PMC5222868 DOI: 10.3389/fpls.2016.02063] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 12/26/2016] [Indexed: 05/18/2023]
Abstract
Bread wheat has a large and complex allohexaploid genome with low recombination level at chromosome centromeric and peri-centromeric regions. This significantly hampers ordering of markers, contigs of physical maps and sequence scaffolds and impedes obtaining of high-quality reference genome sequence. Here we report on the construction of high-density and high-resolution radiation hybrid (RH) map of chromosome 4A supported by high-density chromosome deletion map. A total of 119 endosperm-based RH lines of two RH panels and 15 chromosome deletion bin lines were genotyped with 90K iSelect single nucleotide polymorphism (SNP) array. A total of 2316 and 2695 markers were successfully mapped to the 4A RH and deletion maps, respectively. The chromosome deletion map was ordered in 19 bins and allowed precise identification of centromeric region and verification of the RH panel reliability. The 4A-specific RH map comprises 1080 mapping bins and spans 6550.9 cR with a resolution of 0.13 Mb/cR. Significantly higher mapping resolution in the centromeric region was observed as compared to recombination maps. Relatively even distribution of deletion frequency along the chromosome in the RH panel was observed and putative functional centromere was delimited within a region characterized by two SNP markers.
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Affiliation(s)
- Barbora Balcárková
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural ResearchOlomouc, Czechia
| | - Zeev Frenkel
- Institute of Evolution, University of HaifaHaifa, Israel
| | - Monika Škopová
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural ResearchOlomouc, Czechia
| | - Michael Abrouk
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural ResearchOlomouc, Czechia
| | - Ajay Kumar
- Department of Plant Sciences, North Dakota State University, FargoND, USA
| | - Shiaoman Chao
- Biosciences Research Laboratory, United States Department of Agriculture-Agricultural Research Service, FargoND, USA
| | - Shahryar F. Kianian
- Cereal Disease Laboratory, United States Department of Agriculture-Agricultural Research Service, University of Minnesota, St. PaulMN, USA
| | - Eduard Akhunov
- Department of Plant Pathology, Kansas State University, ManhattanKS, USA
| | | | - Jaroslav Doležel
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural ResearchOlomouc, Czechia
| | - Miroslav Valárik
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural ResearchOlomouc, Czechia
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59
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Deng X, Wang SL, Zhen SM, Zhang WY, Yan YM. Identification and molecular characterization of one novel 1SPl-encoded s-type low molecular weight glutenin B-subunit from 1Sl(1B) substitution line of wheat variety Chinese Spring (Triticum aestivum). Biologia (Bratisl) 2016. [DOI: 10.1515/biolog-2016-0147] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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60
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Nesterov MA, Afonnikov DA, Sergeeva EM, Miroshnichenko LA, Bragina MK, Bragin AO, Vasiliev GV, Salina EA. Identification of microsatellite loci based on BAC sequencing data and their physical mapping into the soft wheat 5B chromosome. ACTA ACUST UNITED AC 2016. [DOI: 10.1134/s2079059716070078] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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61
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Baránek M, Čechová J, Kovacs T, Eichmeier A, Wang S, Raddová J, Nečas T, Ye X. Use of Combined MSAP and NGS Techniques to Identify Differentially Methylated Regions in Somaclones: A Case Study of Two Stable Somatic Wheat Mutants. PLoS One 2016; 11:e0165749. [PMID: 27792769 PMCID: PMC5085084 DOI: 10.1371/journal.pone.0165749] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 10/16/2016] [Indexed: 12/22/2022] Open
Abstract
The appearance of somaclonal variability induced by in vitro cultivation is relatively frequent and can, in some cases, provide a valuable source of new genetic variation for crop improvement. The cause of this phenomenon remains unknown; however, there are a number of reports suggesting that epigenetics, including DNA methylations, are an important factor. In addition to the non-heritable DNA methylation changes caused by transient and reversible stress-responsive gene regulation, recent evidence supports the existence of mitotically and meiotically inherited changes. The induction of phenotypes via stable DNA methylation changes has occasionally great economical value; however, very little is known about the genetic or molecular basis of these phenotypes. We used a novel approach consisting of a standard MSAP analysis followed by deep amplicon sequencing to better understand this phenomenon. Our models included two wheat genotypes, and their somaclones induced using in vitro cultivation with a changed heritable phenotype (shortened stem height and silenced high molecular weight glutenin). Using this novel procedure, we obtained information on the dissimilarity of DNA methylation landscapes between the standard cultivar and its respective somaclones, and we extracted the sequences and genome regions that were differentially methylated between subjects. Transposable elements were identified as the most likely factor for producing changes in somaclone properties. In summary, the novel approach of combining MSAP and NGS is relatively easy and widely applicable, which is a rather unique feature compared with the currently available techniques in the epigenetics field.
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Affiliation(s)
- Miroslav Baránek
- Mendeleum–Department of Genetics, Horticulture Faculty of Mendel University in Brno, Lednice, Czech Republic
- * E-mail:
| | - Jana Čechová
- Mendeleum–Department of Genetics, Horticulture Faculty of Mendel University in Brno, Lednice, Czech Republic
| | | | - Aleš Eichmeier
- Mendeleum–Department of Genetics, Horticulture Faculty of Mendel University in Brno, Lednice, Czech Republic
| | - Shunli Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jana Raddová
- Mendeleum–Department of Genetics, Horticulture Faculty of Mendel University in Brno, Lednice, Czech Republic
| | - Tomáš Nečas
- Department of Fruit Growing, Horticulture Faculty of Mendel University in Brno, Lednice, Czech Republic
| | - Xingguo Ye
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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62
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Chaney L, Sharp AR, Evans CR, Udall JA. Genome Mapping in Plant Comparative Genomics. TRENDS IN PLANT SCIENCE 2016; 21:770-780. [PMID: 27289181 DOI: 10.1016/j.tplants.2016.05.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Revised: 04/27/2016] [Accepted: 05/12/2016] [Indexed: 05/10/2023]
Abstract
Genome mapping produces fingerprints of DNA sequences to construct a physical map of the whole genome. It provides contiguous, long-range information that complements and, in some cases, replaces sequencing data. Recent advances in genome-mapping technology will better allow researchers to detect large (>1kbp) structural variations between plant genomes. Some molecular and informatics complications need to be overcome for this novel technology to achieve its full utility. This technology will be useful for understanding phenotype responses due to DNA rearrangements and will yield insights into genome evolution, particularly in polyploids. In this review, we outline recent advances in genome-mapping technology, including the processes required for data collection and analysis, and applications in plant comparative genomics.
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Affiliation(s)
- Lindsay Chaney
- Plant and Wildlife Sciences Department, Brigham Young University, Provo, UT 84602, USA
| | - Aaron R Sharp
- Plant and Wildlife Sciences Department, Brigham Young University, Provo, UT 84602, USA
| | - Carrie R Evans
- Plant and Wildlife Sciences Department, Brigham Young University, Provo, UT 84602, USA
| | - Joshua A Udall
- Plant and Wildlife Sciences Department, Brigham Young University, Provo, UT 84602, USA.
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63
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Prins R, Dreisigacker S, Pretorius Z, van Schalkwyk H, Wessels E, Smit C, Bender C, Singh D, Boyd LA. Stem Rust Resistance in a Geographically Diverse Collection of Spring Wheat Lines Collected from Across Africa. FRONTIERS IN PLANT SCIENCE 2016; 7:973. [PMID: 27462322 PMCID: PMC4939729 DOI: 10.3389/fpls.2016.00973] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 06/20/2016] [Indexed: 05/08/2023]
Abstract
Following the emergence of the Ug99 lineage of Puccinia graminis f. sp. tritici (Pgt) a collective international effort has been undertaken to identify new sources of wheat stem rust resistance effective against these races. Analyses were undertaken in a collection of wheat genotypes gathered from across Africa to identify stem rust resistance effective against the Pgt races found in Eastern and Southern Africa. The African wheat collection consisted of historic genotypes collected in Kenya, South Africa, Ethiopia, Sudan, Zambia, Morocco, and Tunisia, and current South African breeding lines. Both Bayesian cluster and principal coordinate analyses placed the wheat lines from Sudan in a distinct group, but indicated a degree of genetic relatedness among the other wheat lines despite originating from countries across Africa. Seedling screens with Pgt race PTKST, pedigree information and marker haplotype analysis confirmed the presence of Sr2, Sr36, Sr24, Sr31, and Lr34/Yr18/Sr57 in a number of the lines. A genome-wide association study (GWAS) undertaken with Diversiry Arrays Technology (DArT) and stem rust (Sr) gene associated markers and Stem Area Infected (SAI) and Reaction Type (RT) field phenotypes, collected from trials carried out across two seasons in Kenya in 2009 and in South Africa in 2011, identified 29 marker-trait associations (MTA). Three MTA were in common between SAI and RT, with the biggest effect MTA being found on chromosome 6AS. Two wheat lines, W1406 and W6979 that exhibited high levels of adult plant stem rust resistance were selected to generate bi-parental mapping populations. Only the MTA on chromosomes 6AS and 3BS, and the locus Lr34/Yr18/Sr57 were confirmed following QTL mapping. Additional stem rust resistance QTL, not detected by the GWAS, were found on chromosomes 2BS, 2DL, 3DL, and 4D.
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Affiliation(s)
- Renée Prins
- CenGen (Pty) Ltd.Worcester, South Africa
- Department of Plant Sciences, University of the Free StateBloemfontein, South Africa
| | | | - Zakkie Pretorius
- Department of Plant Sciences, University of the Free StateBloemfontein, South Africa
| | - Hester van Schalkwyk
- CenGen (Pty) Ltd.Worcester, South Africa
- Department of Plant Sciences, University of the Free StateBloemfontein, South Africa
| | | | | | - Cornel Bender
- Department of Plant Sciences, University of the Free StateBloemfontein, South Africa
| | - Davinder Singh
- Faculty of Agriculture and Environment, Plant Breeding Institute Cobbitty, University of SydneyNarellan, NSW, Australia
| | - Lesley A. Boyd
- Department of Genetics and Breeding, National Institute of Agricultural BotanyCambridge, UK
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Beier S, Himmelbach A, Schmutzer T, Felder M, Taudien S, Mayer KFX, Platzer M, Stein N, Scholz U, Mascher M. Multiplex sequencing of bacterial artificial chromosomes for assembling complex plant genomes. PLANT BIOTECHNOLOGY JOURNAL 2016; 14:1511-22. [PMID: 26801048 PMCID: PMC5066668 DOI: 10.1111/pbi.12511] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Revised: 11/11/2015] [Accepted: 11/13/2015] [Indexed: 05/02/2023]
Abstract
Hierarchical shotgun sequencing remains the method of choice for assembling high-quality reference sequences of complex plant genomes. The efficient exploitation of current high-throughput technologies and powerful computational facilities for large-insert clone sequencing necessitates the sequencing and assembly of a large number of clones in parallel. We developed a multiplexed pipeline for shotgun sequencing and assembling individual bacterial artificial chromosomes (BACs) using the Illumina sequencing platform. We illustrate our approach by sequencing 668 barley BACs (Hordeum vulgare L.) in a single Illumina HiSeq 2000 lane. Using a newly designed parallelized computational pipeline, we obtained sequence assemblies of individual BACs that consist, on average, of eight sequence scaffolds and represent >98% of the genomic inserts. Our BAC assemblies are clearly superior to a whole-genome shotgun assembly regarding contiguity, completeness and the representation of the gene space. Our methods may be employed to rapidly obtain high-quality assemblies of a large number of clones to assemble map-based reference sequences of plant and animal species with complex genomes by sequencing along a minimum tiling path.
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Affiliation(s)
- Sebastian Beier
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Stadt Seeland, Germany
| | - Axel Himmelbach
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Stadt Seeland, Germany
| | - Thomas Schmutzer
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Stadt Seeland, Germany
| | - Marius Felder
- Leibniz Institute on Aging-Fritz Lipmann Institute (FLI), Jena, Germany
| | - Stefan Taudien
- Leibniz Institute on Aging-Fritz Lipmann Institute (FLI), Jena, Germany
| | - Klaus F X Mayer
- Plant Genome and System Biology (PGSB), Helmholtz Center Munich, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Matthias Platzer
- Leibniz Institute on Aging-Fritz Lipmann Institute (FLI), Jena, Germany
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Stadt Seeland, Germany
| | - Uwe Scholz
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Stadt Seeland, Germany
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Stadt Seeland, Germany
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Staňková H, Hastie AR, Chan S, Vrána J, Tulpová Z, Kubaláková M, Visendi P, Hayashi S, Luo M, Batley J, Edwards D, Doležel J, Šimková H. BioNano genome mapping of individual chromosomes supports physical mapping and sequence assembly in complex plant genomes. PLANT BIOTECHNOLOGY JOURNAL 2016; 14:1523-31. [PMID: 26801360 PMCID: PMC5066648 DOI: 10.1111/pbi.12513] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Revised: 11/12/2015] [Accepted: 11/13/2015] [Indexed: 05/09/2023]
Abstract
The assembly of a reference genome sequence of bread wheat is challenging due to its specific features such as the genome size of 17 Gbp, polyploid nature and prevalence of repetitive sequences. BAC-by-BAC sequencing based on chromosomal physical maps, adopted by the International Wheat Genome Sequencing Consortium as the key strategy, reduces problems caused by the genome complexity and polyploidy, but the repeat content still hampers the sequence assembly. Availability of a high-resolution genomic map to guide sequence scaffolding and validate physical map and sequence assemblies would be highly beneficial to obtaining an accurate and complete genome sequence. Here, we chose the short arm of chromosome 7D (7DS) as a model to demonstrate for the first time that it is possible to couple chromosome flow sorting with genome mapping in nanochannel arrays and create a de novo genome map of a wheat chromosome. We constructed a high-resolution chromosome map composed of 371 contigs with an N50 of 1.3 Mb. Long DNA molecules achieved by our approach facilitated chromosome-scale analysis of repetitive sequences and revealed a ~800-kb array of tandem repeats intractable to current DNA sequencing technologies. Anchoring 7DS sequence assemblies obtained by clone-by-clone sequencing to the 7DS genome map provided a valuable tool to improve the BAC-contig physical map and validate sequence assembly on a chromosome-arm scale. Our results indicate that creating genome maps for the whole wheat genome in a chromosome-by-chromosome manner is feasible and that they will be an affordable tool to support the production of improved pseudomolecules.
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Affiliation(s)
- Helena Staňková
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | | | - Saki Chan
- BioNano Genomics, San Diego, CA, USA
| | - Jan Vrána
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Zuzana Tulpová
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Marie Kubaláková
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Paul Visendi
- Australian Centre for Plant Functional Genomics, University of Queensland, Brisbane, QLD, Australia
| | - Satomi Hayashi
- School of Agriculture and Food Sciences, University of Queensland, Brisbane, QLD, Australia
| | - Mingcheng Luo
- Department of Plant Sciences, University of California, Davis, CA, USA
| | - Jacqueline Batley
- School of Agriculture and Food Sciences, University of Queensland, Brisbane, QLD, Australia
- School of Plant Biology, University of Western Australia, Crawley, WA, Australia
| | - David Edwards
- School of Plant Biology, University of Western Australia, Crawley, WA, Australia
| | - Jaroslav Doležel
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Hana Šimková
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
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Ribeiro T, Barrela RM, Bergès H, Marques C, Loureiro J, Morais-Cecílio L, Paiva JAP. Advancing Eucalyptus Genomics: Cytogenomics Reveals Conservation of Eucalyptus Genomes. FRONTIERS IN PLANT SCIENCE 2016; 7:510. [PMID: 27148332 PMCID: PMC4840385 DOI: 10.3389/fpls.2016.00510] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Accepted: 03/31/2016] [Indexed: 05/30/2023]
Abstract
The genus Eucalyptus encloses several species with high ecological and economic value, being the subgenus Symphyomyrtus one of the most important. Species such as E. grandis and E. globulus are well characterized at the molecular level but knowledge regarding genome and chromosome organization is very scarce. Here we characterized and compared the karyotypes of three economically important species, E. grandis, E. globulus, and E. calmadulensis, and three with ecological relevance, E. pulverulenta, E. cornuta, and E. occidentalis, through an integrative approach including genome size estimation, fluorochrome banding, rDNA FISH, and BAC landing comprising genes involved in lignin biosynthesis. All karyotypes show a high degree of conservation with pericentromeric 35S and 5S rDNA loci in the first and third pairs, respectively. GC-rich heterochromatin was restricted to the 35S rDNA locus while the AT-rich heterochromatin pattern was species-specific. The slight differences in karyotype formulas and distribution of AT-rich heterochromatin, along with genome sizes estimations, support the idea of Eucalyptus genome evolution by local expansions of heterochromatin clusters. The unusual co-localization of both rDNA with AT-rich heterochromatin was attributed mainly to the presence of silent transposable elements in those loci. The cinnamoyl CoA reductase gene (CCR1) previously assessed to linkage group 10 (LG10) was clearly localized distally at the long arm of chromosome 9 establishing an unexpected correlation between the cytogenetic chromosome 9 and the LG10. Our work is novel and contributes to the understanding of Eucalyptus genome organization which is essential to develop successful advanced breeding strategies for this genus.
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Affiliation(s)
- Teresa Ribeiro
- Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, University of LisbonLisboa, Portugal
| | - Ricardo M. Barrela
- Plant Cell Biotechnology Laboratory, Instituto de Biologia Experimental e TecnológicaOeiras, Portugal
| | - Hélène Bergès
- Institut National de la Recherche Agronomique, Centre National de Ressources Génomiques VégétalesCastanet-Tolosan, France
| | - Cristina Marques
- RAIZ, Instituto de Investigação da Floresta e PapelAveiro, Portugal
| | - João Loureiro
- Centre for Functional Ecology, Department of Life Sciences, University of CoimbraCoimbra, Portugal
| | - Leonor Morais-Cecílio
- Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, University of LisbonLisboa, Portugal
| | - Jorge A. P. Paiva
- Plant Cell Biotechnology Laboratory, Instituto de Biologia Experimental e TecnológicaOeiras, Portugal
- Department of Integrative Plant Biology, Instytut Genetyki Roślin, Polskiej Akademii NaukPoznań, Poland
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Tiwari VK, Heesacker A, Riera-Lizarazu O, Gunn H, Wang S, Wang Y, Gu YQ, Paux E, Koo DH, Kumar A, Luo MC, Lazo G, Zemetra R, Akhunov E, Friebe B, Poland J, Gill BS, Kianian S, Leonard JM. A whole-genome, radiation hybrid mapping resource of hexaploid wheat. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 86:195-207. [PMID: 26945524 DOI: 10.1111/tpj.13153] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Revised: 02/04/2016] [Accepted: 02/22/2016] [Indexed: 06/05/2023]
Abstract
Generating a contiguous, ordered reference sequence of a complex genome such as hexaploid wheat (2n = 6x = 42; approximately 17 GB) is a challenging task due to its large, highly repetitive, and allopolyploid genome. In wheat, ordering of whole-genome or hierarchical shotgun sequencing contigs is primarily based on recombination and comparative genomics-based approaches. However, comparative genomics approaches are limited to syntenic inference and recombination is suppressed within the pericentromeric regions of wheat chromosomes, thus, precise ordering of physical maps and sequenced contigs across the whole-genome using these approaches is nearly impossible. We developed a whole-genome radiation hybrid (WGRH) resource and tested it by genotyping a set of 115 randomly selected lines on a high-density single nucleotide polymorphism (SNP) array. At the whole-genome level, 26 299 SNP markers were mapped on the RH panel and provided an average mapping resolution of approximately 248 Kb/cR1500 with a total map length of 6866 cR1500 . The 7296 unique mapping bins provided a five- to eight-fold higher resolution than genetic maps used in similar studies. Most strikingly, the RH map had uniform bin resolution across the entire chromosome(s), including pericentromeric regions. Our research provides a valuable and low-cost resource for anchoring and ordering sequenced BAC and next generation sequencing (NGS) contigs. The WGRH developed for reference wheat line Chinese Spring (CS-WGRH), will be useful for anchoring and ordering sequenced BAC and NGS based contigs for assembling a high-quality, reference sequence of hexaploid wheat. Additionally, this study provides an excellent model for developing similar resources for other polyploid species.
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Affiliation(s)
- Vijay K Tiwari
- Department of Plant Pathology, Wheat Genetics Resource Center, Kansas State University, Manhattan, KS, USA
| | - Adam Heesacker
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR, USA
| | | | - Hilary Gunn
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR, USA
| | - Shichen Wang
- Department of Plant Pathology, Wheat Genetics Resource Center, Kansas State University, Manhattan, KS, USA
| | - Yi Wang
- Crop Improvement and Genetics Research Unit, USDA-ARS, Albany, NY, USA
| | - Young Q Gu
- Crop Improvement and Genetics Research Unit, USDA-ARS, Albany, NY, USA
| | - Etienne Paux
- Diversité et Ecophysiologie des Céréales, INRA, UMR 1095 Génétique, 5 chemin de Beaulieu, F-63039, Clermont-Ferrand, France
- Diversité et Ecophysiologie des Céréales, UMR 1095 Génétique, Université Blaise Pascal, F-63177, Aubière Cedex, France
| | - Dal-Hoe Koo
- Department of Plant Pathology, Wheat Genetics Resource Center, Kansas State University, Manhattan, KS, USA
| | - Ajay Kumar
- Department of Plant Sciences, North Dakota State University, Fargo, ND, USA
| | - Ming-Cheng Luo
- Department of Plant Sciences, University of California, Davis, CA, USA
| | - Gerard Lazo
- Crop Improvement and Genetics Research Unit, USDA-ARS, Albany, NY, USA
| | - Robert Zemetra
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR, USA
| | - Eduard Akhunov
- Department of Plant Pathology, Wheat Genetics Resource Center, Kansas State University, Manhattan, KS, USA
| | - Bernd Friebe
- Department of Plant Pathology, Wheat Genetics Resource Center, Kansas State University, Manhattan, KS, USA
| | - Jesse Poland
- Department of Plant Pathology, Wheat Genetics Resource Center, Kansas State University, Manhattan, KS, USA
| | - Bikram S Gill
- Department of Plant Pathology, Wheat Genetics Resource Center, Kansas State University, Manhattan, KS, USA
| | - Shahryar Kianian
- Cereal Disease Laboratory, University of Minnesota, Saint Paul, MN, USA
| | - Jeffrey M Leonard
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR, USA
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Arruda MP, Brown P, Brown-Guedira G, Krill AM, Thurber C, Merrill KR, Foresman BJ, Kolb FL. Genome-Wide Association Mapping of Fusarium Head Blight Resistance in Wheat using Genotyping-by-Sequencing. THE PLANT GENOME 2016; 9. [PMID: 27898754 DOI: 10.3835/plantgenome2015.04.0028] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Fusarium head blight (FHB) is one of the most important wheat ( L.) diseases worldwide, and host resistance displays complex genetic control. A genome-wide association study (GWAS) was performed on 273 winter wheat breeding lines from the midwestern and eastern regions of the United States to identify chromosomal regions associated with FHB resistance. Genotyping-by-sequencing (GBS) was used to identify 19,992 single-nucleotide polymorphisms (SNPs) covering all 21 wheat chromosomes. Marker-trait associations were performed with different statistical models, the most appropriate being a compressed mixed linear model (cMLM) controlling for relatedness and population structure. Ten significant SNP-trait associations were detected on chromosomes 4A, 6A, 7A, 1D, 4D, and 7D, and multiple SNPs were associated with on chromosome 3B. Although combination of favorable alleles of these SNPs resulted in lower levels of severity (SEV), incidence (INC), and deoxynivalenol concentration (DON), lines carrying multiple beneficial alleles were in very low frequency for most traits. These SNPs can now be used for creating new breeding lines with different combinations of favorable alleles. This is one of the first GWAS using genomic resources from the International Wheat Genome Sequencing Consortium (IWGSC).
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Lu P, Liang Y, Li D, Wang Z, Li W, Wang G, Wang Y, Zhou S, Wu Q, Xie J, Zhang D, Chen Y, Li M, Zhang Y, Sun Q, Han C, Liu Z. Fine genetic mapping of spot blotch resistance gene Sb3 in wheat (Triticum aestivum). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2016; 129:577-89. [PMID: 26747045 DOI: 10.1007/s00122-015-2649-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Accepted: 12/08/2015] [Indexed: 05/19/2023]
Abstract
Spot blotch disease resistance gene Sb3 was mapped to a 0.15 centimorgan (cM) genetic interval spanning a 602 kb physical genomic region on chromosome 3BS. Wheat spot blotch disease, caused by B. sorokiniana, is a devastating disease that can cause severe yield losses. Although inoculum levels can be reduced by planting disease-free seed, treatment of plants with fungicides and crop rotation, genetic resistance is likely to be a robust, economical and environmentally friendly tool in the control of spot blotch. The winter wheat line 621-7-1 confers immune resistance against B. sorokiniana. Genetic analysis indicates that the spot blotch resistance of 621-7-1 is controlled by a single dominant gene, provisionally designated Sb3. Bulked segregant analysis (BSA) and simple sequence repeat (SSR) mapping showed that Sb3 is located on chromosome arm 3BS linked with markers Xbarc133 and Xbarc147. Seven and twelve new polymorphic markers were developed from the Chinese Spring 3BS shotgun survey sequence contigs and 3BS reference sequences, respectively. Finally, Sb3 was mapped in a 0.15 cM genetic interval spanning a 602 kb physical genomic region of Chinese Spring chromosome 3BS. The genetic and physical maps of Sb3 provide a framework for map-based cloning and marker-assisted selection (MAS) of the spot blotch resistance.
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Affiliation(s)
- Ping Lu
- State Key Laboratory for Agrobiotechnology/Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Yong Liang
- State Key Laboratory for Agrobiotechnology/Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Delin Li
- State Key Laboratory for Agrobiotechnology/Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Zhengzhong Wang
- China Rural Technology Development Center, Beijing, 100045, China
| | - Wenbin Li
- State Key Laboratory for Agrobiotechnology/Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Guoxin Wang
- State Key Laboratory for Agrobiotechnology/Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Yong Wang
- State Key Laboratory for Agrobiotechnology/Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Shenghui Zhou
- State Key Laboratory for Agrobiotechnology/Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Qiuhong Wu
- State Key Laboratory for Agrobiotechnology/Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Jingzhong Xie
- State Key Laboratory for Agrobiotechnology/Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Deyun Zhang
- State Key Laboratory for Agrobiotechnology/Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Yongxing Chen
- State Key Laboratory for Agrobiotechnology/Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Miaomiao Li
- State Key Laboratory for Agrobiotechnology/Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Yan Zhang
- State Key Laboratory for Agrobiotechnology/Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Qixin Sun
- State Key Laboratory for Agrobiotechnology/Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Chenggui Han
- State Key Laboratory for Agrobiotechnology/Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Zhiyong Liu
- State Key Laboratory for Agrobiotechnology/Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China.
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Ono H, Ishii K, Kozaki T, Ogiwara I, Kanekatsu M, Yamada T. Removal of redundant contigs from de novo RNA-Seq assemblies via homology search improves accurate detection of differentially expressed genes. BMC Genomics 2015; 16:1031. [PMID: 26637306 PMCID: PMC4670531 DOI: 10.1186/s12864-015-2247-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Accepted: 11/26/2015] [Indexed: 12/31/2022] Open
Abstract
Background For plant species with unsequenced genomes, cDNA contigs created by de novo assembly of RNA-Seq reads are used as reference sequences for comparative analysis of RNA-Seq datasets and the detection of differentially expressed genes (DEGs). Redundancies in such contigs are evident in previous RNA-Seq studies, and such redundancies can lead to difficulties in subsequent analysis. Nevertheless, the effects of removing redundancy from contig assemblies on comparative RNA-Seq analysis have not been evaluated. Results Here we describe a method for removing redundancy from raw contigs that were primarily created by de novo assembly of Arabidopsis thaliana RNA-Seq reads. Specifically, the contigs with the highest bit scores were selected from raw contigs by a homology search against the gene dataset in the TAIR10 database. The two existing methods for removal of redundancy based on contig length or clustering analysis used to eliminate redundancies from raw contigs. Contig number was reduced most effectively with the method based on homology search. In a comparative analysis of RNA-Seq datasets, DEGs detected in contigs that underwent redundancy removal via the homology search method showed the highest identity to the DEGs detected when the TAIR10 gene dataset was used as an exact reference. Redundancy in raw contigs could also be removed by a homology search against integrated protein datasets from several plant species other than A. thaliana. DEGs detected using contigs that underwent such redundancy-removed also showed high homology to DEGs detected using the TAIR10 gene dataset. Conclusion Here we describe a method for removing redundant contigs within raw contigs; this method involves a homology search against a gene or protein database. In principal, this method can be used with unsequenced plant genomes that lack a well-developed gene database. Redundant contigs were not removed adequately via either of two existing methods, but our method allowed for removal of all redundant contigs. To our knowledge, this is the first reported improvement in accurate detection of DEGs via comparative RNA-Seq analysis that involved preparation of a non-redundant reference sequence. This method could be used to rapidly and cost-effectively detect useful genes in unsequenced plants.
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Affiliation(s)
- Hanako Ono
- United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, 183-8509, Japan.
| | - Kazuo Ishii
- Department of Applied Biological Science, Faculty of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, 183-8509, Japan.
| | - Toshinori Kozaki
- Department of Applied Biological Science, Faculty of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, 183-8509, Japan.
| | - Isao Ogiwara
- United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, 183-8509, Japan.
| | - Motoki Kanekatsu
- United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, 183-8509, Japan.
| | - Tetsuya Yamada
- United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, 183-8509, Japan.
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Borrill P, Adamski N, Uauy C. Genomics as the key to unlocking the polyploid potential of wheat. THE NEW PHYTOLOGIST 2015; 208:1008-22. [PMID: 26108556 DOI: 10.1111/nph.13533] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 05/31/2015] [Indexed: 05/19/2023]
Abstract
Polyploidy has played a central role in plant genome evolution and in the formation of new species such as tetraploid pasta wheat and hexaploid bread wheat. Until recently, the high sequence conservation between homoeologous genes, together with the large genome size of polyploid wheat, had hindered genomic analyses in this important crop species. In the past 5 yr, however, the advent of next-generation sequencing has radically changed the wheat genomics landscape. Here, we review a series of advances in genomic resources and tools for functional genomics that are shifting the paradigm of what is possible in wheat molecular genetics and breeding. We discuss how understanding the relationship between homoeologues can inform approaches to modulate the response of quantitative traits in polyploid wheat; we also argue that functional redundancy has 'locked up' a wide range of phenotypic variation in wheat. We explore how genomics provides key tools to inform targeted manipulation of multiple homoeologues, thereby allowing researchers and plant breeders to unlock the full polyploid potential of wheat.
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Affiliation(s)
| | - Nikolai Adamski
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Cristobal Uauy
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
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Barabaschi D, Magni F, Volante A, Gadaleta A, Šimková H, Scalabrin S, Prazzoli ML, Bagnaresi P, Lacrima K, Michelotti V, Desiderio F, Orrù L, Mazzamurro V, Fricano A, Mastrangelo A, Tononi P, Vitulo N, Jurman I, Frenkel Z, Cattonaro F, Morgante M, Blanco A, Doležel J, Delledonne M, Stanca AM, Cattivelli L, Valè G. Physical Mapping of Bread Wheat Chromosome 5A: An Integrated Approach. THE PLANT GENOME 2015; 8:eplantgenome2015.03.0011. [PMID: 33228274 DOI: 10.3835/plantgenome2015.03.0011] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Accepted: 06/21/2015] [Indexed: 06/11/2023]
Abstract
The huge size, redundancy, and highly repetitive nature of the bread wheat [Triticum aestivum (L.)] genome, makes it among the most difficult species to be sequenced. To overcome these limitations, a strategy based on the separation of individual chromosomes or chromosome arms and the subsequent production of physical maps was established within the frame of the International Wheat Genome Sequence Consortium (IWGSC). A total of 95,812 bacterial artificial chromosome (BAC) clones of short-arm chromosome 5A (5AS) and long-arm chromosome 5A (5AL) arm-specific BAC libraries were fingerprinted and assembled into contigs by complementary analytical approaches based on the FingerPrinted Contig (FPC) and Linear Topological Contig (LTC) tools. Combined anchoring approaches based on polymerase chain reaction (PCR) marker screening, microarray, and sequence homology searches applied to several genomic tools (i.e., genetic maps, deletion bin map, neighbor maps, BAC end sequences (BESs), genome zipper, and chromosome survey sequences) allowed the development of a high-quality physical map with an anchored physical coverage of 75% for 5AS and 53% for 5AL with high portions (64 and 48%, respectively) of contigs ordered along the chromosome. In the genome of grasses, Brachypodium [Brachypodium distachyon (L.) Beauv.], rice (Oryza sativa L.), and sorghum [Sorghum bicolor (L.) Moench] homologs of genes on wheat chromosome 5A were separated into syntenic blocks on different chromosomes as a result of translocations and inversions during evolution. The physical map presented represents an essential resource for fine genetic mapping and map-based cloning of agronomically relevant traits and a reference for the 5A sequencing projects.
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Affiliation(s)
- Delfina Barabaschi
- Council for Agricultural Research and Economics (CREA)-Genomics Research Centre, Fiorenzuola d'Arda, Piacenza, I-29017
| | | | - Andrea Volante
- Council for Agricultural Research and Economics (CREA)-Genomics Research Centre, Fiorenzuola d'Arda, Piacenza, I-29017
| | - Agata Gadaleta
- Dep. of Soil, Plant and Food Sciences, Section of Genetic and Plant Breeding, Univ. of Bari, Bari, I-70126
| | - Hana Šimková
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, CZ-77200
| | | | - Maria Lucia Prazzoli
- Council for Agricultural Research and Economics (CREA)-Genomics Research Centre, Fiorenzuola d'Arda, Piacenza, I-29017
| | - Paolo Bagnaresi
- Council for Agricultural Research and Economics (CREA)-Genomics Research Centre, Fiorenzuola d'Arda, Piacenza, I-29017
| | - Katia Lacrima
- Council for Agricultural Research and Economics (CREA)-Genomics Research Centre, Fiorenzuola d'Arda, Piacenza, I-29017
| | - Vania Michelotti
- Council for Agricultural Research and Economics (CREA)-Genomics Research Centre, Fiorenzuola d'Arda, Piacenza, I-29017
| | - Francesca Desiderio
- Council for Agricultural Research and Economics (CREA)-Genomics Research Centre, Fiorenzuola d'Arda, Piacenza, I-29017
| | - Luigi Orrù
- Council for Agricultural Research and Economics (CREA)-Genomics Research Centre, Fiorenzuola d'Arda, Piacenza, I-29017
| | - Valentina Mazzamurro
- Dep. of Life Sciences, Univ. of Modena and Reggio Emilia, Reggio Emilia, I-42100
| | | | - AnnaMaria Mastrangelo
- Council for Agricultural Research and Economics (CREA)-Cereal Research Centre, Foggia, I-71122
| | - Paola Tononi
- Dep. of Biotechnology, Univ. of Verona, Verona, I-37129
| | - Nicola Vitulo
- CRIBI Biotechnology Center, Univ. of Padova, Padova, I-35121
| | | | - Zeev Frenkel
- Institute of Evolution and Dep. of Evolutionary and Environmental Biology, Univ. of Haifa, Haifa, IL-3498838
| | | | | | - Antonio Blanco
- Dep. of Soil, Plant and Food Sciences, Section of Genetic and Plant Breeding, Univ. of Bari, Bari, I-70126
| | - Jaroslav Doležel
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, CZ-77200
| | | | - Antonio M Stanca
- Council for Agricultural Research and Economics (CREA)-Genomics Research Centre, Fiorenzuola d'Arda, Piacenza, I-29017
- Dep. of Life Sciences, Univ. of Modena and Reggio Emilia, Reggio Emilia, I-42100
| | - Luigi Cattivelli
- Council for Agricultural Research and Economics (CREA)-Genomics Research Centre, Fiorenzuola d'Arda, Piacenza, I-29017
| | - Giampiero Valè
- Council for Agricultural Research and Economics (CREA)-Genomics Research Centre, Fiorenzuola d'Arda, Piacenza, I-29017
- Council for Agricultural Research and Economics (CREA)-Rice Research Unit, Vercelli, I-13100
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Tiwari VK, Wang S, Danilova T, Koo DH, Vrána J, Kubaláková M, Hribova E, Rawat N, Kalia B, Singh N, Friebe B, Doležel J, Akhunov E, Poland J, Sabir JSM, Gill BS. Exploring the tertiary gene pool of bread wheat: sequence assembly and analysis of chromosome 5M(g) of Aegilops geniculata. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 84:733-46. [PMID: 26408103 DOI: 10.1111/tpj.13036] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Revised: 09/03/2015] [Accepted: 09/14/2015] [Indexed: 05/07/2023]
Abstract
Next-generation sequencing (NGS) provides a powerful tool for the discovery of important genes and alleles in crop plants and their wild relatives. Despite great advances in NGS technologies, whole-genome shotgun sequencing is cost-prohibitive for species with complex genomes. An attractive option is to reduce genome complexity to a single chromosome prior to sequencing. This work describes a strategy for studying the genomes of distant wild relatives of wheat by isolating single chromosomes from addition or substitution lines, followed by chromosome sorting using flow cytometry and sequencing of chromosomal DNA by NGS technology. We flow-sorted chromosome 5M(g) from a wheat/Aegilops geniculata disomic substitution line [DS5M(g) (5D)] and sequenced it using an Illumina HiSeq 2000 system at approximately 50 × coverage. Paired-end sequences were assembled and used for structural and functional annotation. A total of 4236 genes were annotated on 5M(g) , in close agreement with the predicted number of genes on wheat chromosome 5D (4286). Single-gene FISH indicated no major chromosomal rearrangements between chromosomes 5M(g) and 5D. Comparing chromosome 5M(g) with model grass genomes identified synteny blocks in Brachypodium distachyon, rice (Oryza sativa), sorghum (Sorghum bicolor) and barley (Hordeum vulgare). Chromosome 5M(g) -specific SNPs and cytogenetic probe-based resources were developed and validated. Deletion bin-mapped and ordered 5M(g) SNP markers will be useful to track 5M-specific introgressions and translocations. This study provides a detailed sequence-based analysis of the composition of a chromosome from a distant wild relative of bread wheat, and opens up opportunities to develop genomic resources for wild germplasm to facilitate crop improvement.
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Affiliation(s)
- Vijay K Tiwari
- Department of Plant Pathology, Wheat Genetics Resource Center, Kansas State University Manhattan, Manhattan, KS, 66506, USA
| | - Shichen Wang
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66502, USA
| | - Tatiana Danilova
- Department of Plant Pathology, Wheat Genetics Resource Center, Kansas State University Manhattan, Manhattan, KS, 66506, USA
| | - Dal Hoe Koo
- Department of Plant Pathology, Wheat Genetics Resource Center, Kansas State University Manhattan, Manhattan, KS, 66506, USA
| | - Jan Vrána
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, CZ 78371, Olomouc, Czech Republic
| | - Marie Kubaláková
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, CZ 78371, Olomouc, Czech Republic
| | - Eva Hribova
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, CZ 78371, Olomouc, Czech Republic
| | - Nidhi Rawat
- Department of Plant Pathology, Wheat Genetics Resource Center, Kansas State University Manhattan, Manhattan, KS, 66506, USA
| | - Bhanu Kalia
- Department of Plant Pathology, Wheat Genetics Resource Center, Kansas State University Manhattan, Manhattan, KS, 66506, USA
| | - Narinder Singh
- Department of Plant Pathology, Wheat Genetics Resource Center, Kansas State University Manhattan, Manhattan, KS, 66506, USA
| | - Bernd Friebe
- Department of Plant Pathology, Wheat Genetics Resource Center, Kansas State University Manhattan, Manhattan, KS, 66506, USA
| | - Jaroslav Doležel
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, CZ 78371, Olomouc, Czech Republic
| | - Eduard Akhunov
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66502, USA
| | - Jesse Poland
- Department of Plant Pathology, Wheat Genetics Resource Center, Kansas State University Manhattan, Manhattan, KS, 66506, USA
| | - Jamal S M Sabir
- Biotechnology Research Group, Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - Bikram S Gill
- Department of Plant Pathology, Wheat Genetics Resource Center, Kansas State University Manhattan, Manhattan, KS, 66506, USA
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74
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Cápal P, Blavet N, Vrána J, Kubaláková M, Doležel J. Multiple displacement amplification of the DNA from single flow-sorted plant chromosome. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 84:838-844. [PMID: 26400218 DOI: 10.1111/tpj.13035] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Revised: 09/13/2015] [Accepted: 09/17/2015] [Indexed: 06/05/2023]
Abstract
A protocol is described for production of micrograms of DNA from single copies of flow-sorted plant chromosomes. Of 183 single copies of wheat chromosome 3B, 118 (64%) were successfully amplified. Sequencing DNA amplification products using an Illumina HiSeq 2000 system to 10× coverage and merging sequences from three separate amplifications resulted in 60% coverage of the chromosome 3B reference, entirely covering 30% of its genes. The merged sequences permitted de novo assembly of 19% of chromosome 3B genes, with 10% of genes contained in a single contig, and 39% of genes covered for at least 80% of their length. The chromosome-derived sequences allowed identification of missing genic sequences in the chromosome 3B reference and short sequences similar to 3B in survey sequences of other wheat chromosomes. These observations indicate that single-chromosome sequencing is suitable to identify genic sequences on particular chromosomes, to develop chromosome-specific DNA markers, to verify assignment of DNA sequence contigs to individual pseudomolecules, and to validate whole-genome assemblies. The protocol expands the potential of chromosome genomics, which may now be applied to any plant species from which chromosome samples suitable for flow cytometry can be prepared, and opens new avenues for studies on chromosome structural heterozygosity and haplotype phasing in plants.
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Affiliation(s)
- Petr Cápal
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371, Olomouc, Czech Republic
| | - Nicolas Blavet
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371, Olomouc, Czech Republic
- Palacký University Olomouc, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 27, CZ-78371, Olomouc, Czech Republic
| | - Jan Vrána
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371, Olomouc, Czech Republic
| | - Marie Kubaláková
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371, Olomouc, Czech Republic
| | - Jaroslav Doležel
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371, Olomouc, Czech Republic
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75
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Zheng Z, Ma J, Stiller J, Zhao Q, Feng Q, Choulet F, Feuillet C, Zheng YL, Wei Y, Han B, Yan G, Manners JM, Liu C. Fine mapping of a large-effect QTL conferring Fusarium crown rot resistance on the long arm of chromosome 3B in hexaploid wheat. BMC Genomics 2015; 16:850. [PMID: 26493707 PMCID: PMC4618961 DOI: 10.1186/s12864-015-2105-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 10/16/2015] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND Fusarium crown rot (FCR) is a major cereal disease in semi-arid areas worldwide. Of the various QTL reported, the one on chromosome arm 3BL (Qcrs.cpi-3B) has the largest effect that can be consistently detected in different genetic backgrounds. Nine sets of near isogenic lines (NILs) for this locus were made available in a previous study. To identify markers that could be reliably used in tagging the Qcrs.cpi-3B locus, a NIL-derived population consisting of 774 F10 lines were generated and exploited to assess markers selected from the existing linkage map and generated from sequences of the 3B pseudomolecule. RESULTS This is the first report on fine mapping a QTL conferring FCR resistance in wheat. By three rounds of linkage mapping using the NILs and the NIL-derived population, the Qcrs.cpi-3B locus was mapped to an interval of 0.7 cM covering a physical distance of about 1.5 Mb. Seven markers co-segregating with the locus were developed. This interval contains a total of 63 gene-coding sequences based on the 3B pseudomolecule, and six of them were known to encode disease resistance proteins. Several of the genes in this interval were among those responsive to FCR infection detected in an earlier study. CONCLUSIONS The accurate localization of the Qcrs.cpi-3B locus and the development of the markers co-segregating with it should facilitate the incorporation of this large-effect QTL conferring FCR resistance into breeding programs as well as the cloning of the gene(s) underlying the QTL.
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Affiliation(s)
- Zhi Zheng
- CSIRO Agriculture, 306 Carmody Road, St Lucia, QLD, 4067, Australia.
- School of Plant Biology, Faculty of Science and The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, 6009, Australia.
- National Foxtail Millet Improvement Centre, Institute of Millet Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, China.
| | - Jian Ma
- CSIRO Agriculture, 306 Carmody Road, St Lucia, QLD, 4067, Australia.
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China.
| | - Jiri Stiller
- CSIRO Agriculture, 306 Carmody Road, St Lucia, QLD, 4067, Australia.
| | - Qiang Zhao
- National Center for Gene Research, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 500 Caobao Road, Shanghai, 200233, China.
| | - Qi Feng
- National Center for Gene Research, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 500 Caobao Road, Shanghai, 200233, China.
| | - Frédéric Choulet
- INRA-UBP Joint Research Unit 1095, Genetics, Diversity and Ecophysiology of Cereals Clermont-Ferrand, Clermont-Ferrand, F-63100, France.
| | - Catherine Feuillet
- INRA-UBP Joint Research Unit 1095, Genetics, Diversity and Ecophysiology of Cereals Clermont-Ferrand, Clermont-Ferrand, F-63100, France.
| | - You-Liang Zheng
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China.
| | - Yuming Wei
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China.
| | - Bin Han
- National Center for Gene Research, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 500 Caobao Road, Shanghai, 200233, China.
| | - Guijun Yan
- National Foxtail Millet Improvement Centre, Institute of Millet Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, China.
| | - John M Manners
- CSIRO Agriculture, 306 Carmody Road, St Lucia, QLD, 4067, Australia.
| | - Chunji Liu
- CSIRO Agriculture, 306 Carmody Road, St Lucia, QLD, 4067, Australia.
- School of Plant Biology, Faculty of Science and The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, 6009, Australia.
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Kumar A, Seetan R, Mergoum M, Tiwari VK, Iqbal MJ, Wang Y, Al-Azzam O, Šimková H, Luo MC, Dvorak J, Gu YQ, Denton A, Kilian A, Lazo GR, Kianian SF. Radiation hybrid maps of the D-genome of Aegilops tauschii and their application in sequence assembly of large and complex plant genomes. BMC Genomics 2015; 16:800. [PMID: 26475137 PMCID: PMC4609151 DOI: 10.1186/s12864-015-2030-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Accepted: 10/09/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The large and complex genome of bread wheat (Triticum aestivum L., ~17 Gb) requires high resolution genome maps with saturated marker scaffolds to anchor and orient BAC contigs/ sequence scaffolds for whole genome assembly. Radiation hybrid (RH) mapping has proven to be an excellent tool for the development of such maps for it offers much higher and more uniform marker resolution across the length of the chromosome compared to genetic mapping and does not require marker polymorphism per se, as it is based on presence (retention) vs. absence (deletion) marker assay. METHODS In this study, a 178 line RH panel was genotyped with SSRs and DArT markers to develop the first high resolution RH maps of the entire D-genome of Ae. tauschii accession AL8/78. To confirm map order accuracy, the AL8/78-RH maps were compared with:1) a DArT consensus genetic map constructed using more than 100 bi-parental populations, 2) a RH map of the D-genome of reference hexaploid wheat 'Chinese Spring', and 3) two SNP-based genetic maps, one with anchored D-genome BAC contigs and another with anchored D-genome sequence scaffolds. Using marker sequences, the RH maps were also anchored with a BAC contig based physical map and draft sequence of the D-genome of Ae. tauschii. RESULTS A total of 609 markers were mapped to 503 unique positions on the seven D-genome chromosomes, with a total map length of 14,706.7 cR. The average distance between any two marker loci was 29.2 cR which corresponds to 2.1 cM or 9.8 Mb. The average mapping resolution across the D-genome was estimated to be 0.34 Mb (Mb/cR) or 0.07 cM (cM/cR). The RH maps showed almost perfect agreement with several published maps with regard to chromosome assignments of markers. The mean rank correlations between the position of markers on AL8/78 maps and the four published maps, ranged from 0.75 to 0.92, suggesting a good agreement in marker order. With 609 mapped markers, a total of 2481 deletions for the whole D-genome were detected with an average deletion size of 42.0 Mb. A total of 520 markers were anchored to 216 Ae. tauschii sequence scaffolds, 116 of which were not anchored earlier to the D-genome. CONCLUSION This study reports the development of first high resolution RH maps for the D-genome of Ae. tauschii accession AL8/78, which were then used for the anchoring of unassigned sequence scaffolds. This study demonstrates how RH mapping, which offered high and uniform resolution across the length of the chromosome, can facilitate the complete sequence assembly of the large and complex plant genomes.
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Affiliation(s)
- Ajay Kumar
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58102, USA
| | - Raed Seetan
- Department of Computer Sciences, North Dakota State University, Fargo, ND, 58102, USA
- Department of Computer Science, Slippery Rock University, Slippery Rock, PA, 16057, USA
| | - Mohamed Mergoum
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58102, USA
| | - Vijay K Tiwari
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506-5502, USA
| | - Muhammad J Iqbal
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58102, USA
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Yi Wang
- USDA-ARS, Western Regional Research Center, Albany, CA, 94710, USA
| | - Omar Al-Azzam
- Department of Computer Sciences, North Dakota State University, Fargo, ND, 58102, USA
- Department of Computer Science and Information Technology, St. Cloud State University, St. Cloud, MN, 56301, USA
| | - Hana Šimková
- Faculty of Science, Palacký University, 783 71, Olomouc, Czech Republic
- Institute of Experimental Botany, Šlechtitelů 31, 783-71, Olomouc, Czech Republic
| | - Ming-Cheng Luo
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Jan Dvorak
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Yong Q Gu
- USDA-ARS, Western Regional Research Center, Albany, CA, 94710, USA
| | - Anne Denton
- Department of Computer Sciences, North Dakota State University, Fargo, ND, 58102, USA
| | - Andrzej Kilian
- Diversity Arrays Technology Pty Limited, 1 Wilf Crane Crescent, Yarralumla, ACT2600, Australia
| | - Gerard R Lazo
- USDA-ARS, Western Regional Research Center, Albany, CA, 94710, USA
| | - Shahryar F Kianian
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58102, USA.
- USDA-ARS, Cereal Disease Laboratory, University of Minnesota, St. Paul, MN, 55108, USA.
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Ishihara A, Mizuno N, Islam RAKM, Doležel J, Endo TR, Nasuda S. Dissection of barley chromosomes 1H and 6H by the gametocidal system. Genes Genet Syst 2015; 89:203-14. [PMID: 25832747 DOI: 10.1266/ggs.89.203] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
We dissected barley chromosomes 1H and 6H added to common wheat by the gametocidal system and identified structural changes of the chromosomes by fluorescence in situ hybridization and genomic in situ hybridization. We found five aberrations of chromosome 1H, all of which lacked the long arm: one small fragment with the subtelomeric HvT01 sequence, one terminal deletion, and three telocentric chromosomes of the short arm. We established 33 dissection lines carrying single aberrant 6H chromosomes, of which 15 were deletions, 16 were translocations and two were isochromosomes. We conducted PCR analysis of the aberrant barley chromosomes using 75 and 81 EST markers specific to chromosomes 1H and 6H, respectively. This enabled us to construct a cytological map of chromosome 6H and to compare it to the previously reported genetic map and also to the physical map, which were released by the International Barley Genome Sequencing Consortium. The marker orders on the three maps were largely in agreement. The cytological map had better resolution in the proximal region of chromosome 6H than the corresponding genetic map. We discuss some of the discrepancies in marker order between the three maps that might be due to intraspecific polymorphism and gene duplication, as well as to technical problems inherent in the physical mapping process.
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Affiliation(s)
- Ayaka Ishihara
- Laboratory of Plant Genetics, Graduate School of Agriculture, Kyoto University
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Li T, Ma L, Geng Y, Hao C, Chen X, Zhang X. Small RNA and Degradome Sequencing Reveal Complex Roles of miRNAs and Their Targets in Developing Wheat Grains. PLoS One 2015; 10:e0139658. [PMID: 26426440 PMCID: PMC4591353 DOI: 10.1371/journal.pone.0139658] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2015] [Accepted: 09/16/2015] [Indexed: 11/19/2022] Open
Abstract
Plant microRNAs (miRNAs) have been shown to play critical roles in plant development. In this study, we employed small RNA combined with degradome sequencing to survey development-related miRNAs and their validated targets during wheat grain development. A total of 186 known miRNAs and 37 novel miRNAs were identified in four small RNA libraries. Moreover, a miRNA-like long hairpin locus was first identified to produce 21~22-nt phased siRNAs that act in trans to cleave target mRNAs. A comparison of the miRNAomes revealed that 55 miRNA families were differentially expressed during the grain development. Predicted and validated targets of these development-related miRNAs are involved in different cellular responses and metabolic processes including cell proliferation, auxin signaling, nutrient metabolism and gene expression. This study provides insight into the complex roles of miRNAs and their targets in regulating wheat grain development.
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Affiliation(s)
- Tian Li
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture / Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lin Ma
- Shaanxi Key Laboratory of Genetic Engineering for Plant Breeding, College of Agronomy, Northwest A & F University, Yangling, Shaanxi, China
| | - Yuke Geng
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture / Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Chenyang Hao
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture / Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xinhong Chen
- Shaanxi Key Laboratory of Genetic Engineering for Plant Breeding, College of Agronomy, Northwest A & F University, Yangling, Shaanxi, China
| | - Xueyong Zhang
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture / Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
- * E-mail:
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79
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Wang Y, Drader T, Tiwari VK, Dong L, Kumar A, Huo N, Ghavami F, Iqbal MJ, Lazo GR, Leonard J, Gill BS, Kianian SF, Luo MC, Gu YQ. Development of a D genome specific marker resource for diploid and hexaploid wheat. BMC Genomics 2015; 16:646. [PMID: 26315263 PMCID: PMC4552153 DOI: 10.1186/s12864-015-1852-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Accepted: 08/17/2015] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Mapping and map-based cloning of genes that control agriculturally and economically important traits remain great challenges for plants with complex highly repetitive genomes such as those within the grass tribe, Triticeae. Mapping limitations in the Triticeae are primarily due to low frequencies of polymorphic gene markers and poor genetic recombination in certain genetic regions. Although the abundance of repetitive sequence may pose common problems in genome analysis and sequence assembly of large and complex genomes, they provide repeat junction markers with random and unbiased distribution throughout chromosomes. Hence, development of a high-throughput mapping technology that combine both gene-based and repeat junction-based markers is needed to generate maps that have better coverage of the entire genome. RESULTS In this study, the available genomics resource of the diploid Aegilop tauschii, the D genome donor of bread wheat, were used to develop genome specific markers that can be applied for mapping in modern hexaploid wheat. A NimbleGen array containing both gene-based and repeat junction probe sequences derived from Ae. tauschii was developed and used to map the Chinese Spring nullisomic-tetrasomic lines and deletion bin lines of the D genome chromosomes. Based on these mapping data, we have now anchored 5,171 repeat junction probes and 10,892 gene probes, corresponding to 5,070 gene markers, to the delineated deletion bins of the D genome. The order of the gene-based markers within the deletion bins of the Chinese Spring can be inferred based on their positions on the Ae. tauschii genetic map. Analysis of the probe sequences against the Chinese Spring chromosome sequence assembly database facilitated mapping of the NimbleGen probes to the sequence contigs and allowed assignment or ordering of these sequence contigs within the deletion bins. The accumulated length of anchored sequence contigs is about 155 Mb, representing ~ 3.2 % of the D genome. A specific database was developed to allow user to search or BLAST against the probe sequence information and to directly download PCR primers for mapping specific genetic loci. CONCLUSIONS In bread wheat, aneuploid stocks have been extensively used to assign markers linked with genes/traits to chromosomes, chromosome arms, and their specific bins. Through this study, we added thousands of markers to the existing wheat chromosome bin map, representing a significant step forward in providing a resource to navigate the wheat genome. The database website ( http://probes.pw.usda.gov/ATRJM/ ) provides easy access and efficient utilization of the data. The resources developed herein can aid map-based cloning of traits of interest and the sequencing of the D genome of hexaploid wheat.
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Affiliation(s)
- Yi Wang
- Western Regional Research Center, USDA-ARS, Albany, CA, 94710, USA. .,Department of Plant Sciences, University of California, Davis, CA, 95616, USA.
| | - Thomas Drader
- Western Regional Research Center, USDA-ARS, Albany, CA, 94710, USA.
| | - Vijay K Tiwari
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR, 97331, USA. .,Wheat Genetic Resource Center, Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA.
| | - Lingli Dong
- Western Regional Research Center, USDA-ARS, Albany, CA, 94710, USA. .,Department of Plant Sciences, University of California, Davis, CA, 95616, USA.
| | - Ajay Kumar
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA. ajay.kumar.2.@ndsu.edu
| | - Naxin Huo
- Western Regional Research Center, USDA-ARS, Albany, CA, 94710, USA.,Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Farhad Ghavami
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA.,Molecular Breeding and Genomics Technology Laboratory, BioDiagnostics Inc., River Falls, WI, 54022, USA
| | - M Javed Iqbal
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA
| | - Gerard R Lazo
- Western Regional Research Center, USDA-ARS, Albany, CA, 94710, USA.
| | - Jeff Leonard
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR, 97331, USA.
| | - Bikram S Gill
- Wheat Genetic Resource Center, Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA.
| | | | - Ming-Cheng Luo
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA.
| | - Yong Q Gu
- Western Regional Research Center, USDA-ARS, Albany, CA, 94710, USA.
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80
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Kobayashi F, Wu J, Kanamori H, Tanaka T, Katagiri S, Karasawa W, Kaneko S, Watanabe S, Sakaguchi T, Hanawa Y, Fujisawa H, Kurita K, Abe C, Iehisa JCM, Ohno R, Šafář J, Šimková H, Mukai Y, Hamada M, Saito M, Ishikawa G, Katayose Y, Endo TR, Takumi S, Nakamura T, Sato K, Ogihara Y, Hayakawa K, Doležel J, Nasuda S, Matsumoto T, Handa H. A high-resolution physical map integrating an anchored chromosome with the BAC physical maps of wheat chromosome 6B. BMC Genomics 2015; 16:595. [PMID: 26265254 PMCID: PMC4534020 DOI: 10.1186/s12864-015-1803-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Accepted: 07/31/2015] [Indexed: 11/10/2022] Open
Abstract
Background A complete genome sequence is an essential tool for the genetic improvement of wheat. Because the wheat genome is large, highly repetitive and complex due to its allohexaploid nature, the International Wheat Genome Sequencing Consortium (IWGSC) chose a strategy that involves constructing bacterial artificial chromosome (BAC)-based physical maps of individual chromosomes and performing BAC-by-BAC sequencing. Here, we report the construction of a physical map of chromosome 6B with the goal of revealing the structural features of the third largest chromosome in wheat. Results We assembled 689 informative BAC contigs (hereafter reffered to as contigs) representing 91 % of the entire physical length of wheat chromosome 6B. The contigs were integrated into a radiation hybrid (RH) map of chromosome 6B, with one linkage group consisting of 448 loci with 653 markers. The order and direction of 480 contigs, corresponding to 87 % of the total length of 6B, were determined. We also characterized the contigs that contained a part of the nucleolus organizer region or centromere based on their positions on the RH map and the assembled BAC clone sequences. Analysis of the virtual gene order along 6B using the information collected for the integrated map revealed the presence of several chromosomal rearrangements, indicating evolutionary events that occurred on chromosome 6B. Conclusions We constructed a reliable physical map of chromosome 6B, enabling us to analyze its genomic structure and evolutionary progression. More importantly, the physical map should provide a high-quality and map-based reference sequence that will serve as a resource for wheat chromosome 6B. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1803-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Fuminori Kobayashi
- Plant Genome Research Unit, National Institute of Agrobiological Sciences, Tsukuba, 305-8602, Japan.
| | - Jianzhong Wu
- Plant Genome Research Unit, National Institute of Agrobiological Sciences, Tsukuba, 305-8602, Japan. .,Advanced Genomics Laboratory, National Institute of Agrobiological Sciences, Tsukuba, 305-8602, Japan.
| | - Hiroyuki Kanamori
- Plant Genome Research Unit, National Institute of Agrobiological Sciences, Tsukuba, 305-8602, Japan.
| | - Tsuyoshi Tanaka
- Bioinformatics Research Unit, National Institute of Agrobiological Sciences, Tsukuba, 305-8602, Japan.
| | - Satoshi Katagiri
- Advanced Genomics Laboratory, National Institute of Agrobiological Sciences, Tsukuba, 305-8602, Japan.
| | - Wataru Karasawa
- Advanced Genomics Laboratory, National Institute of Agrobiological Sciences, Tsukuba, 305-8602, Japan.
| | - Satoko Kaneko
- Laboratory of Plant Genetics, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan.
| | - Shota Watanabe
- Laboratory of Plant Genetics, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan.
| | - Toyotaka Sakaguchi
- Laboratory of Plant Genetics, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan.
| | - Yumiko Hanawa
- Advanced Genomics Laboratory, National Institute of Agrobiological Sciences, Tsukuba, 305-8602, Japan.
| | - Hiroko Fujisawa
- Advanced Genomics Laboratory, National Institute of Agrobiological Sciences, Tsukuba, 305-8602, Japan.
| | - Kanako Kurita
- Plant Genome Research Unit, National Institute of Agrobiological Sciences, Tsukuba, 305-8602, Japan.
| | - Chikako Abe
- Cereal Science Research Center of Tsukuba, Nisshin Flour Milling Inc., Tsukuba, 300-2611, Japan.
| | - Julio C M Iehisa
- Laboratory of Plant Genetics, Graduate School of Agricultural Science, Kobe University, Kobe, 657-8501, Japan.
| | - Ryoko Ohno
- Core Research Division, Organization of Advanced Science and Technology, Kobe University, Kobe, 657-8501, Japan.
| | - Jan Šafář
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, CZ-78371, Olomouc, Czech Republic.
| | - Hana Šimková
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, CZ-78371, Olomouc, Czech Republic.
| | - Yoshiyuki Mukai
- Advanced Genomics Laboratory, National Institute of Agrobiological Sciences, Tsukuba, 305-8602, Japan.
| | - Masao Hamada
- Advanced Genomics Laboratory, National Institute of Agrobiological Sciences, Tsukuba, 305-8602, Japan.
| | - Mika Saito
- Wheat Breeding Group, NARO Tohoku Agricultural Research Center, Morioka, 020-0198, Japan.
| | - Goro Ishikawa
- Wheat Breeding Group, NARO Tohoku Agricultural Research Center, Morioka, 020-0198, Japan.
| | - Yuichi Katayose
- Advanced Genomics Laboratory, National Institute of Agrobiological Sciences, Tsukuba, 305-8602, Japan.
| | - Takashi R Endo
- Laboratory of Plant Genetics, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan.
| | - Shigeo Takumi
- Laboratory of Plant Genetics, Graduate School of Agricultural Science, Kobe University, Kobe, 657-8501, Japan.
| | - Toshiki Nakamura
- Wheat Breeding Group, NARO Tohoku Agricultural Research Center, Morioka, 020-0198, Japan.
| | - Kazuhiro Sato
- Institute of Plant Science and Resources, Okayama University, Kurashiki, 710-0046, Japan.
| | - Yasunari Ogihara
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, 244-0813, Japan.
| | - Katsuyuki Hayakawa
- Cereal Science Research Center of Tsukuba, Nisshin Flour Milling Inc., Tsukuba, 300-2611, Japan.
| | - Jaroslav Doležel
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, CZ-78371, Olomouc, Czech Republic.
| | - Shuhei Nasuda
- Laboratory of Plant Genetics, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan.
| | - Takashi Matsumoto
- Plant Genome Research Unit, National Institute of Agrobiological Sciences, Tsukuba, 305-8602, Japan.
| | - Hirokazu Handa
- Plant Genome Research Unit, National Institute of Agrobiological Sciences, Tsukuba, 305-8602, Japan.
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81
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Suzuki T, Murai MN, Hayashi T, Nasuda S, Yoshimura Y, Komatsuda T. Resistance to wheat yellow mosaic virus in Madsen wheat is controlled by two major complementary QTLs. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2015; 128:1569-78. [PMID: 25957645 DOI: 10.1007/s00122-015-2532-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 04/27/2015] [Indexed: 05/15/2023]
Abstract
Wheat yellow mosaic virus resistance of Madsen is governed by two complementary QTLs, Qym1 and Qym2 , located on chromosome arms 2DL and 3BS. Wheat yellow mosaic, caused by Wheat yellow mosaic virus (WYMV), is one of the most serious wheat diseases in East Asia. In this study, recombinant inbred lines (RILs, F9) from a cross between cultivars Madsen (resistant) and Hokushin (susceptible) grown in a WYMV-infected nursery field were tested for the presence of WYMV in leaves by enzyme-linked immunosorbent assay (ELISA) and genotyped by using genome-wide molecular markers. Two major QTLs were detected: Qym1 located between Xgwm539 and Xgwm349 on chromosome 2DL and Qym2 located between Xbarc147 and Xwmc623 on chromosome 3BS. The resistance alleles for both QTLs originated from Madsen. The third QTL Qym3 located near Xwmc457 on chromosome 4D, where the resistant allele for this QTL originated from Hokushin. Although the Qym3 was rather minor, it was essential to complement Qym1 and Qym2 for complete avoidance of WYMV infection. Near-isogenic lines carrying the resistance QTLs were developed by repeated backcrosses using Madsen as the donor parent and Hokushin as the recurrent parent. The lines that were resistant to WYMV (as tested by ELISA) were homozygous for the Madsen alleles at both Qym1 and Qym2. Qym1 dominance was partial, whereas that of Qym2 was nearly complete. Qym1 was closely linked to Xwmc41; Qym2 was closely linked to Xwmc754. These markers will be useful in marker-assisted selection in wheat breeding for WYMV resistance; this study will facilitate cloning the WYMV resistance genes.
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Affiliation(s)
- Takako Suzuki
- Agricultural Research Department, Hokkaido Research Organization, Chuo Agricultural Experiment Station, Higashi-6, Kita-15, Naganuma, Hokkaido, 069-1395, Japan,
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82
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Molnár I, Vrána J, Farkas A, Kubaláková M, Cseh A, Molnár-Láng M, Doležel J. Flow sorting of C-genome chromosomes from wild relatives of wheat Aegilops markgrafii, Ae. triuncialis and Ae. cylindrica, and their molecular organization. ANNALS OF BOTANY 2015; 116:189-200. [PMID: 26043745 PMCID: PMC4512188 DOI: 10.1093/aob/mcv073] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 03/27/2015] [Accepted: 04/15/2015] [Indexed: 05/18/2023]
Abstract
BACKGROUND AND AIMS Aegilops markgrafii (CC) and its natural hybrids Ae. triuncialis (U(t)U(t)C(t)C(t)) and Ae. cylindrica (D(c)D(c)C(c)C(c)) represent a rich reservoir of useful genes for improvement of bread wheat (Triticum aestivum), but the limited information available on their genome structure and the shortage of molecular (cyto-) genetic tools hamper the utilization of the extant genetic diversity. This study provides the complete karyotypes in the three species obtained after fluorescent in situ hybridization (FISH) with repetitive DNA probes, and evaluates the potential of flow cytometric chromosome sorting. METHODS The flow karyotypes obtained after the analysis of 4',6-diamidino-2-phenylindole (DAPI)-stained chromosomes were characterized and the chromosome content of the peaks on the flow karyotypes was determined by FISH. Twenty-nine conserved orthologous set (COS) markers covering all seven wheat homoeologous chromosome groups were used for PCR with DNA amplified from flow-sorted chromosomes and genomic DNA. KEY RESULTS FISH with repetitive DNA probes revealed that chromosomes 4C, 5C, 7C(t), T6U(t)S.6U(t)L-5C(t)L, 1C(c) and 5D(c) could be sorted with purities ranging from 66 to 91 %, while the remaining chromosomes could be sorted in groups of 2-5. This identified a partial wheat-C-genome homology for group 4 and 5 chromosomes. In addition, 1C chromosomes were homologous with group 1 of wheat; a small segment from group 2 indicated 1C-2C rearrangement. An extensively rearranged structure of chromosome 7C relative to wheat was also detected. CONCLUSIONS The possibility of purifying Aegilops chromosomes provides an attractive opportunity to investigate the structure and evolution of the Aegilops C genome and to develop molecular tools to facilitate the identification of alien chromatin and support alien introgression breeding in bread wheat.
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Affiliation(s)
- István Molnár
- Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, Brunszvik u. 2, H-2462 Martonvásár, Hungary and
| | - Jan Vrána
- Centre of the Region Hana for Biotechnological and Agricultural Research, Institute of Experimental Botany, Šlechtitelů 31, CZ-78371 Olomouc, Czech Republic
| | - András Farkas
- Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, Brunszvik u. 2, H-2462 Martonvásár, Hungary and
| | - Marie Kubaláková
- Centre of the Region Hana for Biotechnological and Agricultural Research, Institute of Experimental Botany, Šlechtitelů 31, CZ-78371 Olomouc, Czech Republic
| | - András Cseh
- Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, Brunszvik u. 2, H-2462 Martonvásár, Hungary and
| | - Márta Molnár-Láng
- Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, Brunszvik u. 2, H-2462 Martonvásár, Hungary and
| | - Jaroslav Doležel
- Centre of the Region Hana for Biotechnological and Agricultural Research, Institute of Experimental Botany, Šlechtitelů 31, CZ-78371 Olomouc, Czech Republic
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83
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Mazaheri M, Kianian P, Kumar A, Mergoum M, Seetan R, Soltani A, Lund LI, Pirseyedi SM, Denton AM, Kianian SF. Radiation Hybrid Map of Barley Chromosome 3H. THE PLANT GENOME 2015; 8:eplantgenome2015.02.0005. [PMID: 33228309 DOI: 10.3835/plantgenome2015.02.0005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Accepted: 04/14/2015] [Indexed: 06/11/2023]
Abstract
Assembly of the barley (Hordeum vulgare L.) genome is complicated by its large size (5.1 Gb) and proportion of repetitive elements (84%). This process is facilitated by high resolution maps for aligning bacterial artificial chromosome (BAC) contigs along chromosomes. Available genetic maps, however, do not provide accurate information on the physical position of a large portion of the genome located in recombination-poor regions. Radiation hybrid (RH) mapping is an alternative approach, which is based on radiation-induced deletions along the length of chromosomes. In this study, the first RH map for barley chromosome 3H was developed. In total, 373 in vivo RH lines were generated by irradiating wheat (Triticum aestivum L.)-barley chromosome 3H addition lines and crossing them to a normal wheat cultivar. Each RH informative line (containing deletions) had, on average, three deletions. The induced deletion size varied from 36.58 Kb to 576.00 Mb, with an average length of 52.42 Mb. This initial chromosome 3H radiation hybrid (3H-RH) map had a 9.53× higher resolution than an analogous genetic map, reaching a maximum of >262.40× resolution in regions around the centromere. The final RH map was 3066.1 cR in length, with a 0.76 Mb resolution. It was estimated that the map resolution can be improved to an average of 30.34 Kb by saturating the 3H-RH map with molecular markers. The generated RH panel enabled alignment of BAC and sequenced contigs as small as 1.50 Kb in size. The high resolution and the coverage of poor-recombination regions make RH maps an ideal resource for barley genome assembly, as well as other genetic studies.
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Affiliation(s)
- Mona Mazaheri
- Dep. of Plant Sciences, North Dakota State Univ., Fargo, ND, 58108
| | - Penny Kianian
- Dep. of Horticultural Science, Univ. of Minnesota, St. Paul, MN, 55108
| | - Ajay Kumar
- Dep. of Plant Sciences, North Dakota State Univ., Fargo, ND, 58108
| | - Mohamed Mergoum
- Dep. of Plant Sciences, North Dakota State Univ., Fargo, ND, 58108
| | - Raed Seetan
- Dep. of Math, Science, and Technology, Univ. of Minnesota, Crookston, MN
| | - Ali Soltani
- Dep. of Plant Sciences, North Dakota State Univ., Fargo, ND, 58108
| | - Lucy I Lund
- Dep. of Plant Sciences, North Dakota State Univ., Fargo, ND, 58108
| | | | - Anne M Denton
- Dep. of Computer Sciences, North Dakota State Univ., Fargo, ND, 58108
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84
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Akpinar BA, Magni F, Yuce M, Lucas SJ, Šimková H, Šafář J, Vautrin S, Bergès H, Cattonaro F, Doležel J, Budak H. The physical map of wheat chromosome 5DS revealed gene duplications and small rearrangements. BMC Genomics 2015; 16:453. [PMID: 26070810 PMCID: PMC4465308 DOI: 10.1186/s12864-015-1641-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Accepted: 05/19/2015] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND The substantially large bread wheat genome, organized into highly similar three sub-genomes, renders genomic research challenging. The construction of BAC-based physical maps of individual chromosomes reduces the complexity of this allohexaploid genome, enables elucidation of gene space and evolutionary relationships, provides tools for map-based cloning, and serves as a framework for reference sequencing efforts. In this study, we constructed the first comprehensive physical map of wheat chromosome arm 5DS, thereby exploring its gene space organization and evolution. RESULTS The physical map of 5DS was comprised of 164 contigs, of which 45 were organized into 21 supercontigs, covering 176 Mb with an N50 value of 2,173 kb. Fifty-eight of the contigs were larger than 1 Mb, with the largest contig spanning 6,649 kb. A total of 1,864 molecular markers were assigned to the map at a density of 10.5 markers/Mb, anchoring 100 of the 120 contigs (>5 clones) that constitute ~95 % of the cumulative length of the map. Ordering of 80 contigs along the deletion bins of chromosome arm 5DS revealed small-scale breaks in syntenic blocks. Analysis of the gene space of 5DS suggested an increasing gradient of genes organized in islands towards the telomere, with the highest gene density of 5.17 genes/Mb in the 0.67-0.78 deletion bin, 1.4 to 1.6 times that of all other bins. CONCLUSIONS Here, we provide a chromosome-specific view into the organization and evolution of the D genome of bread wheat, in comparison to one of its ancestors, revealing recent genome rearrangements. The high-quality physical map constructed in this study paves the way for the assembly of a reference sequence, from which breeding efforts will greatly benefit.
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Affiliation(s)
- Bala Ani Akpinar
- Sabanci University Nanotechnology Research and Application Centre (SUNUM), Sabanci University, Universite Cad. Orta Mah. No: 27, Tuzla, 34956, Istanbul, Turkey.
| | - Federica Magni
- Instituto di Genomica Applicata, Via J.Linussio 51, Udine, 33100, Italy.
| | - Meral Yuce
- Sabanci University Nanotechnology Research and Application Centre (SUNUM), Sabanci University, Universite Cad. Orta Mah. No: 27, Tuzla, 34956, Istanbul, Turkey.
| | - Stuart J Lucas
- Sabanci University Nanotechnology Research and Application Centre (SUNUM), Sabanci University, Universite Cad. Orta Mah. No: 27, Tuzla, 34956, Istanbul, Turkey.
| | - Hana Šimková
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, CZ-78371, Olomouc, Czech Republic.
| | - Jan Šafář
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, CZ-78371, Olomouc, Czech Republic.
| | - Sonia Vautrin
- Centre Nationales Ressources Génomiques Végétales, INRA UPR 1258, 24 Chemin de Borde Rouge - Auzeville 31326, Castanet-Tolosan, France.
| | - Hélène Bergès
- Centre Nationales Ressources Génomiques Végétales, INRA UPR 1258, 24 Chemin de Borde Rouge - Auzeville 31326, Castanet-Tolosan, France.
| | - Federica Cattonaro
- Instituto di Genomica Applicata, Via J.Linussio 51, Udine, 33100, Italy.
| | - Jaroslav Doležel
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, CZ-78371, Olomouc, Czech Republic.
| | - Hikmet Budak
- Sabanci University Nanotechnology Research and Application Centre (SUNUM), Sabanci University, Universite Cad. Orta Mah. No: 27, Tuzla, 34956, Istanbul, Turkey.
- Molecular Biology, Genetics and Bioengineering Program, Sabanci University, 34956, Istanbul, Turkey.
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85
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Wang M, Wang S, Xia G. From genome to gene: a new epoch for wheat research? TRENDS IN PLANT SCIENCE 2015; 20:380-387. [PMID: 25887708 DOI: 10.1016/j.tplants.2015.03.010] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Revised: 03/18/2015] [Accepted: 03/18/2015] [Indexed: 06/04/2023]
Abstract
Genetic research for bread wheat (Triticum aestivum), a staple crop around the world, has been impeded by its complex large hexaploid genome that contains a high proportion of repetitive DNA. Recent advances in sequencing technology have now overcome these challenges and led to genome drafts for bread wheat and its progenitors as well as high-resolution transcriptomes. However, the exploitation of these data for identifying agronomically important genes in wheat is lagging behind. We review recent wheat genome sequencing achievements and focus on four aspects of strategies and future hotspots for wheat improvement: positional cloning, 'omics approaches, combining forward and reverse genetics, and epigenetics.
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Affiliation(s)
- Meng Wang
- The Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Sciences, Shandong University, Jinan 250100, P.R. China
| | - Shubin Wang
- The Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Sciences, Shandong University, Jinan 250100, P.R. China
| | - Guangmin Xia
- The Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Sciences, Shandong University, Jinan 250100, P.R. China.
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86
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Li AL, Geng SF, Zhang LQ, Liu DC, Mao L. Making the Bread: Insights from Newly Synthesized Allohexaploid Wheat. MOLECULAR PLANT 2015; 8:847-59. [PMID: 25747845 DOI: 10.1016/j.molp.2015.02.016] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Revised: 02/13/2015] [Accepted: 02/25/2015] [Indexed: 05/27/2023]
Abstract
Bread wheat (or common wheat, Triticum aestivum) is an allohexaploid (AABBDD, 2n = 6x = 42) that arose by hybridization between a cultivated tetraploid wheat T. turgidum (AABB, 2n = 4x = 28) and the wild goatgrass Aegilops tauschii (DD, 2n = 2x = 14). Polyploidization provided niches for rigorous genome modification at cytogenetic, genetic, and epigenetic levels, rendering a broader spread than its progenitors. This review summarizes the latest advances in understanding gene regulation mechanisms in newly synthesized allohexaploid wheat and possible correlation with polyploid growth vigor and adaptation. Cytogenetic studies reveal persistent association of whole-chromosome aneuploidy with nascent allopolyploids, in contrast to the genetic stability in common wheat. Transcriptome analysis of the euploid wheat shows that small RNAs are driving forces for homoeo-allele expression regulation via genetic and epigenetic mechanisms. The ensuing non-additively expressed genes and those with expression level dominance to the respective progenitor may play distinct functions in growth vigor and adaptation in nascent allohexaploid wheat. Further genetic diploidization of allohexaploid wheat is not random. Regional asymmetrical gene distribution, rather than subgenome dominance, is observed in both synthetic and natural allohexaploid wheats. The combinatorial effects of diverged genomes, subsequent selection of specific gene categories, and subgenome-specific traits are essential for the successful establishment of common wheat.
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Affiliation(s)
- Ai-li Li
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Shuai-Feng Geng
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Lian-quan Zhang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Deng-cai Liu
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Long Mao
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
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87
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Novoselskaya-Dragovich AY. Genetics and genomics of wheat: Storage proteins, ecological plasticity, and immunity. RUSS J GENET+ 2015. [DOI: 10.1134/s102279541505004x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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88
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Harris MO, Friesen TL, Xu SS, Chen MS, Giron D, Stuart JJ. Pivoting from Arabidopsis to wheat to understand how agricultural plants integrate responses to biotic stress. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:513-531. [PMID: 25504642 DOI: 10.1093/jxb/eru465] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
In this review, we argue for a research initiative on wheat's responses to biotic stress. One goal is to begin a conversation between the disparate communities of plant pathology and entomology. Another is to understand how responses to a variety of agents of biotic stress are integrated in an important crop. We propose gene-for-gene interactions as the focus of the research initiative. On the parasite's side is an Avirulence (Avr) gene that encodes one of the many effector proteins the parasite applies to the plant to assist with colonization. On the plant's side is a Resistance (R) gene that mediates a surveillance system that detects the Avr protein directly or indirectly and triggers effector-triggered plant immunity. Even though arthropods are responsible for a significant proportion of plant biotic stress, they have not been integrated into important models of plant immunity that come from plant pathology. A roadblock has been the absence of molecular evidence for arthropod Avr effectors. Thirty years after this evidence was discovered in a plant pathogen, there is now evidence for arthropods with the cloning of the Hessian fly's vH13 Avr gene. After reviewing the two models of plant immunity, we discuss how arthropods could be incorporated. We end by showing features that make wheat an interesting system for plant immunity, including 479 resistance genes known from agriculture that target viruses, bacteria, fungi, nematodes, insects, and mites. It is not likely that humans will be subsisting on Arabidopsis in the year 2050. It is time to start understanding how agricultural plants integrate responses to biotic stress.
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Affiliation(s)
- M O Harris
- Department of Entomology, North Dakota State University, Fargo, ND 58105, USA
| | - T L Friesen
- USDA-ARS, Cereal Crops Research Unit, Fargo, ND USA
| | - S S Xu
- USDA-ARS, Cereal Crops Research Unit, Fargo, ND USA
| | - M S Chen
- USDA-ARS, Hard Winter Wheat Genetics Research Unit, Kansas State University, Manhattan, KS, USA
| | - D Giron
- Institut de Recherche sur la Biologie de l'Insecte UMR 7261 CNRS/Université François-Rabelais de Tours, Tours, France
| | - J J Stuart
- Department of Entomology, Purdue University, West Lafayette, IN, USA
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89
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Chapman JA, Mascher M, Buluç A, Barry K, Georganas E, Session A, Strnadova V, Jenkins J, Sehgal S, Oliker L, Schmutz J, Yelick KA, Scholz U, Waugh R, Poland JA, Muehlbauer GJ, Stein N, Rokhsar DS. A whole-genome shotgun approach for assembling and anchoring the hexaploid bread wheat genome. Genome Biol 2015. [PMID: 25637298 DOI: 10.1186/s13059‐015‐0582‐8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Polyploid species have long been thought to be recalcitrant to whole-genome assembly. By combining high-throughput sequencing, recent developments in parallel computing, and genetic mapping, we derive, de novo, a sequence assembly representing 9.1 Gbp of the highly repetitive 16 Gbp genome of hexaploid wheat, Triticum aestivum, and assign 7.1 Gb of this assembly to chromosomal locations. The genome representation and accuracy of our assembly is comparable or even exceeds that of a chromosome-by-chromosome shotgun assembly. Our assembly and mapping strategy uses only short read sequencing technology and is applicable to any species where it is possible to construct a mapping population.
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Affiliation(s)
- Jarrod A Chapman
- Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA.
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466, Stadt Seeland, Germany.
| | - Aydın Buluç
- Computational Research Division and National Energy Research Supercomputing Center (NERSC), Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
| | - Kerrie Barry
- Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA.
| | - Evangelos Georganas
- Computational Research Division and National Energy Research Supercomputing Center (NERSC), Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA. .,Department of Electrical Engineering and Computer Science, Computer Science Division, University of California, Berkeley, CA, 94720, USA.
| | - Adam Session
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94720, USA.
| | - Veronika Strnadova
- Department of Computer Science, University of California, Santa Barbara, CA, 93106, USA.
| | - Jerry Jenkins
- Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA. .,HudsonAlpha Institute of Biotechnology, Huntsville, AL, 35806, USA.
| | - Sunish Sehgal
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 65506, USA. .,Present address: Department of Plant Science, South Dakota State University, Brookings, SD, 57007, USA.
| | - Leonid Oliker
- Computational Research Division and National Energy Research Supercomputing Center (NERSC), Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
| | - Jeremy Schmutz
- Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA. .,HudsonAlpha Institute of Biotechnology, Huntsville, AL, 35806, USA.
| | - Katherine A Yelick
- Computational Research Division and National Energy Research Supercomputing Center (NERSC), Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA. .,Department of Electrical Engineering and Computer Science, Computer Science Division, University of California, Berkeley, CA, 94720, USA.
| | - Uwe Scholz
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466, Stadt Seeland, Germany.
| | - Robbie Waugh
- Division of Plant Sciences, University of Dundee & The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK.
| | - Jesse A Poland
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 65506, USA.
| | - Gary J Muehlbauer
- Departments of Agronomy and Plant Genetics, and Plant Biology, University of Minnesota, St Paul, MN, 55108, USA.
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466, Stadt Seeland, Germany.
| | - Daniel S Rokhsar
- Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA. .,Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94720, USA.
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90
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Chapman JA, Mascher M, Buluç A, Barry K, Georganas E, Session A, Strnadova V, Jenkins J, Sehgal S, Oliker L, Schmutz J, Yelick KA, Scholz U, Waugh R, Poland JA, Muehlbauer GJ, Stein N, Rokhsar DS. A whole-genome shotgun approach for assembling and anchoring the hexaploid bread wheat genome. Genome Biol 2015; 16:26. [PMID: 25637298 PMCID: PMC4373400 DOI: 10.1186/s13059-015-0582-8] [Citation(s) in RCA: 162] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Accepted: 01/06/2015] [Indexed: 11/10/2022] Open
Abstract
Polyploid species have long been thought to be recalcitrant to whole-genome assembly. By combining high-throughput sequencing, recent developments in parallel computing, and genetic mapping, we derive, de novo, a sequence assembly representing 9.1 Gbp of the highly repetitive 16 Gbp genome of hexaploid wheat, Triticum aestivum, and assign 7.1 Gb of this assembly to chromosomal locations. The genome representation and accuracy of our assembly is comparable or even exceeds that of a chromosome-by-chromosome shotgun assembly. Our assembly and mapping strategy uses only short read sequencing technology and is applicable to any species where it is possible to construct a mapping population.
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Affiliation(s)
- Jarrod A Chapman
- Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA.
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466, Stadt Seeland, Germany.
| | - Aydın Buluç
- Computational Research Division and National Energy Research Supercomputing Center (NERSC), Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
| | - Kerrie Barry
- Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA.
| | - Evangelos Georganas
- Computational Research Division and National Energy Research Supercomputing Center (NERSC), Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA. .,Department of Electrical Engineering and Computer Science, Computer Science Division, University of California, Berkeley, CA, 94720, USA.
| | - Adam Session
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94720, USA.
| | - Veronika Strnadova
- Department of Computer Science, University of California, Santa Barbara, CA, 93106, USA.
| | - Jerry Jenkins
- Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA. .,HudsonAlpha Institute of Biotechnology, Huntsville, AL, 35806, USA.
| | - Sunish Sehgal
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 65506, USA. .,Present address: Department of Plant Science, South Dakota State University, Brookings, SD, 57007, USA.
| | - Leonid Oliker
- Computational Research Division and National Energy Research Supercomputing Center (NERSC), Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
| | - Jeremy Schmutz
- Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA. .,HudsonAlpha Institute of Biotechnology, Huntsville, AL, 35806, USA.
| | - Katherine A Yelick
- Computational Research Division and National Energy Research Supercomputing Center (NERSC), Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA. .,Department of Electrical Engineering and Computer Science, Computer Science Division, University of California, Berkeley, CA, 94720, USA.
| | - Uwe Scholz
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466, Stadt Seeland, Germany.
| | - Robbie Waugh
- Division of Plant Sciences, University of Dundee & The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK.
| | - Jesse A Poland
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 65506, USA.
| | - Gary J Muehlbauer
- Departments of Agronomy and Plant Genetics, and Plant Biology, University of Minnesota, St Paul, MN, 55108, USA.
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466, Stadt Seeland, Germany.
| | - Daniel S Rokhsar
- Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA. .,Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94720, USA.
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91
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Muthamilarasan M, Prasad M. An overview of wheat genome sequencing and its implications for crop improvement. J Genet 2015; 93:619-22. [PMID: 25572220 DOI: 10.1007/s12041-014-0455-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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92
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Mago R, Tabe L, Vautrin S, Šimková H, Kubaláková M, Upadhyaya N, Berges H, Kong X, Breen J, Doležel J, Appels R, Ellis JG, Spielmeyer W. Major haplotype divergence including multiple germin-like protein genes, at the wheat Sr2 adult plant stem rust resistance locus. BMC PLANT BIOLOGY 2014; 14:379. [PMID: 25547135 PMCID: PMC4305260 DOI: 10.1186/s12870-014-0379-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2014] [Accepted: 12/11/2014] [Indexed: 05/20/2023]
Abstract
BACKGROUND The adult plant stem rust resistance gene Sr2 was introgressed into hexaploid wheat cultivar (cv) Marquis from tetraploid emmer wheat cv Yaroslav, to generate stem rust resistant cv Hope in the 1920s. Subsequently, Sr2 has been widely deployed and has provided durable partial resistance to all known races of Puccinia graminis f. sp. tritici. This report describes the physical map of the Sr2-carrying region on the short arm of chromosome 3B of cv Hope and compares the Hope haplotype with non-Sr2 wheat cv Chinese Spring. RESULTS Sr2 was located to a region of 867 kb on chromosome 3B in Hope, which corresponded to a region of 567 kb in Chinese Spring. The Hope Sr2 region carried 34 putative genes but only 17 were annotated in the comparable region of Chinese Spring. The two haplotypes differed by extensive DNA sequence polymorphisms between flanking markers as well as by a major insertion/deletion event including ten Germin-Like Protein (GLP) genes in Hope that were absent in Chinese Spring. Haplotype analysis of a limited number of wheat genotypes of interest showed that all wheat genotypes carrying Sr2 possessed the GLP cluster; while, of those lacking Sr2, some, including Marquis, possessed the cluster, while some lacked it. Thus, this region represents a common presence-absence polymorphism in wheat, with presence of the cluster not correlated with presence of Sr2. Comparison of Hope and Marquis GLP genes on 3BS found no polymorphisms in the coding regions of the ten genes but several SNPs in the shared promoter of one divergently transcribed GLP gene pair and a single SNP downstream of the transcribed region of a second GLP. CONCLUSION Physical mapping and sequence comparison showed major haplotype divergence at the Sr2 locus between Hope and Chinese Spring. Candidate genes within the Sr2 region of Hope are being evaluated for the ability to confer stem rust resistance. Based on the detailed mapping and sequencing of the locus, we predict that Sr2 does not belong to the NB-LRR gene family and is not related to previously cloned, race non-specific rust resistance genes Lr34 and Yr36.
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Affiliation(s)
- Rohit Mago
- />CSIRO Agriculture Flagship, Canberra, ACT 2601 Australia
| | - Linda Tabe
- />CSIRO Agriculture Flagship, Canberra, ACT 2601 Australia
| | - Sonia Vautrin
- />INRA – CNRGV, 24 Chemin de Borde Rouge, Auzeville, CS 52627, 31326 Castanet Tolosan Cedex, France
| | - Hana Šimková
- />Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371 Olomouc, Czech Republic
| | - Marie Kubaláková
- />Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371 Olomouc, Czech Republic
| | | | - Hélène Berges
- />INRA – CNRGV, 24 Chemin de Borde Rouge, Auzeville, CS 52627, 31326 Castanet Tolosan Cedex, France
| | - Xiuying Kong
- />Key Laboratory of Crop Germplasm Resources and Utilization, MOA/Institute of Crop Sciences, CAAS/The Key Facility for Crop Gene Resources and Genetic Improvement, Beijing, 100081 PR China
| | - James Breen
- />Centre for Comparative Genomics, Murdoch University, Murdoch, 6150 WA Australia
- />Current address: Australian Centre for Ancient DNA (ACAD), University of Adelaide, Adelaide, SA 5005 Australia
| | - Jaroslav Doležel
- />Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371 Olomouc, Czech Republic
| | - Rudi Appels
- />Centre for Comparative Genomics, Murdoch University, Murdoch, 6150 WA Australia
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93
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Nussbaumer T, Kugler KG, Schweiger W, Bader KC, Gundlach H, Spannagl M, Poursarebani N, Pfeifer M, Mayer KFX. chromoWIZ: a web tool to query and visualize chromosome-anchored genes from cereal and model genomes. BMC PLANT BIOLOGY 2014; 14:348. [PMID: 25491094 PMCID: PMC4266971 DOI: 10.1186/s12870-014-0348-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Accepted: 11/24/2014] [Indexed: 05/04/2023]
Abstract
BACKGROUND Over the last years reference genome sequences of several economically and scientifically important cereals and model plants became available. Despite the agricultural significance of these crops only a small number of tools exist that allow users to inspect and visualize the genomic position of genes of interest in an interactive manner. DESCRIPTION We present chromoWIZ, a web tool that allows visualizing the genomic positions of relevant genes and comparing these data between different plant genomes. Genes can be queried using gene identifiers, functional annotations, or sequence homology in four grass species (Triticum aestivum, Hordeum vulgare, Brachypodium distachyon, Oryza sativa). The distribution of the anchored genes is visualized along the chromosomes by using heat maps. Custom gene expression measurements, differential expression information, and gene-to-group mappings can be uploaded and can be used for further filtering. CONCLUSIONS This tool is mainly designed for breeders and plant researchers, who are interested in the location and the distribution of candidate genes as well as in the syntenic relationships between different grass species. chromoWIZ is freely available and online accessible at http://mips.helmholtz-muenchen.de/plant/chromoWIZ/index.jsp.
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Affiliation(s)
- Thomas Nussbaumer
- />Plant Genome and System Biology (PGSB), Helmholtz Center Munich, D-85764 Neuherberg, Germany
| | - Karl G Kugler
- />Plant Genome and System Biology (PGSB), Helmholtz Center Munich, D-85764 Neuherberg, Germany
| | - Wolfgang Schweiger
- />Institute for Biotechnology in Plant Production, IFA-Tulln, University of
Natural Resources and Life Sciences, A-3430 Tulln, Austria
| | - Kai C Bader
- />Plant Genome and System Biology (PGSB), Helmholtz Center Munich, D-85764 Neuherberg, Germany
| | - Heidrun Gundlach
- />Plant Genome and System Biology (PGSB), Helmholtz Center Munich, D-85764 Neuherberg, Germany
| | - Manuel Spannagl
- />Plant Genome and System Biology (PGSB), Helmholtz Center Munich, D-85764 Neuherberg, Germany
| | - Naser Poursarebani
- />Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstraße 3, D-06466 Stadt Seeland, Germany
| | - Matthias Pfeifer
- />Plant Genome and System Biology (PGSB), Helmholtz Center Munich, D-85764 Neuherberg, Germany
| | - Klaus FX Mayer
- />Plant Genome and System Biology (PGSB), Helmholtz Center Munich, D-85764 Neuherberg, Germany
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94
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Cao W, Fu B, Wu K, Li N, Zhou Y, Gao Z, Lin M, Li G, Wu X, Ma Z, Jia H. Construction and characterization of three wheat bacterial artificial chromosome libraries. Int J Mol Sci 2014; 15:21896-912. [PMID: 25464379 PMCID: PMC4284684 DOI: 10.3390/ijms151221896] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Revised: 11/22/2014] [Accepted: 11/24/2014] [Indexed: 11/29/2022] Open
Abstract
We have constructed three bacterial artificial chromosome (BAC) libraries of wheat cultivar Triticum aestivum Wangshuibai, germplasms T. monococcum TA2026 and TA2033. A total of 1,233,792,170,880 and 263,040 clones were picked and arrayed in 384-well plates. On the basis of genome sizes of 16.8 Gb for hexaploid wheat and 5.6 Gb for diploid wheat, the three libraries represented 9.05-, 2.60-, and 3.71-fold coverage of the haploid genomes, respectively. An improved descending pooling system for BAC libraries screening was established. This improved strategy can save 80% of the time and 68% of polymerase chain reaction (PCR) with the same successful rate as the universal 6D pooling strategy.
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Affiliation(s)
- Wenjin Cao
- College of Agricultural Sciences, Nanjing Agricultural University, Nanjing 210095, China.
| | - Bisheng Fu
- College of Agricultural Sciences, Nanjing Agricultural University, Nanjing 210095, China.
| | - Kun Wu
- College of Agricultural Sciences, Nanjing Agricultural University, Nanjing 210095, China.
| | - Na Li
- College of Agricultural Sciences, Nanjing Agricultural University, Nanjing 210095, China.
| | - Yan Zhou
- College of Agricultural Sciences, Nanjing Agricultural University, Nanjing 210095, China.
| | - Zhongxia Gao
- College of Agricultural Sciences, Nanjing Agricultural University, Nanjing 210095, China.
| | - Musen Lin
- College of Agricultural Sciences, Nanjing Agricultural University, Nanjing 210095, China.
| | - Guoqiang Li
- College of Agricultural Sciences, Nanjing Agricultural University, Nanjing 210095, China.
| | - Xinyi Wu
- College of Agricultural Sciences, Nanjing Agricultural University, Nanjing 210095, China.
| | - Zhengqiang Ma
- College of Agricultural Sciences, Nanjing Agricultural University, Nanjing 210095, China.
| | - Haiyan Jia
- College of Agricultural Sciences, Nanjing Agricultural University, Nanjing 210095, China.
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95
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Garsed DW, Marshall OJ, Corbin VDA, Hsu A, Di Stefano L, Schröder J, Li J, Feng ZP, Kim BW, Kowarsky M, Lansdell B, Brookwell R, Myklebost O, Meza-Zepeda L, Holloway AJ, Pedeutour F, Choo KHA, Damore MA, Deans AJ, Papenfuss AT, Thomas DM. The architecture and evolution of cancer neochromosomes. Cancer Cell 2014; 26:653-67. [PMID: 25517748 DOI: 10.1016/j.ccell.2014.09.010] [Citation(s) in RCA: 128] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/05/2013] [Revised: 05/15/2014] [Accepted: 09/19/2014] [Indexed: 01/21/2023]
Abstract
We isolated and analyzed, at single-nucleotide resolution, cancer-associated neochromosomes from well- and/or dedifferentiated liposarcomas. Neochromosomes, which can exceed 600 Mb in size, initially arise as circular structures following chromothripsis involving chromosome 12. The core of the neochromosome is amplified, rearranged, and corroded through hundreds of breakage-fusion-bridge cycles. Under selective pressure, amplified oncogenes are overexpressed, while coamplified passenger genes may be silenced epigenetically. New material may be captured during punctuated chromothriptic events. Centromeric corrosion leads to crisis, which is resolved through neocentromere formation or native centromere capture. Finally, amplification terminates, and the neochromosome core is stabilized in linear form by telomere capture. This study investigates the dynamic mutational processes underlying the life history of a special form of cancer mutation.
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Affiliation(s)
- Dale W Garsed
- Cancer Genomics, Peter MacCallum Cancer Centre, East Melbourne, VIC 3002, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, VIC 3010, Australia; Department of Pathology, University of Melbourne, VIC 3010, Australia
| | - Owen J Marshall
- Chromosome Research, Murdoch Childrens Research Institute, and Department of Paediatrics, Royal Children's Hospital, University of Melbourne, Parkville, VIC 3052, Australia
| | - Vincent D A Corbin
- Bioinformatics Division, The Walter & Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, VIC 3010, Australia; Bioinformatics and Cancer Genomics, Peter MacCallum Cancer Centre, East Melbourne, VIC, 3002, Australia
| | - Arthur Hsu
- Bioinformatics Division, The Walter & Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Leon Di Stefano
- Bioinformatics Division, The Walter & Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Jan Schröder
- Bioinformatics Division, The Walter & Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, VIC 3010, Australia
| | - Jason Li
- Cancer Genomics, Peter MacCallum Cancer Centre, East Melbourne, VIC 3002, Australia
| | - Zhi-Ping Feng
- Bioinformatics Division, The Walter & Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, VIC 3010, Australia
| | - Bo W Kim
- Chromosome Research, Murdoch Childrens Research Institute, and Department of Paediatrics, Royal Children's Hospital, University of Melbourne, Parkville, VIC 3052, Australia
| | - Mark Kowarsky
- Bioinformatics Division, The Walter & Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Ben Lansdell
- Bioinformatics Division, The Walter & Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Ross Brookwell
- Sullivan Nicolaides Pathology, Indooroopilly, QLD 4068, Australia
| | - Ola Myklebost
- Department of Tumor Biology, Oslo University Hospital, Norwegian Radium Hospital, Oslo 0424, Norway
| | - Leonardo Meza-Zepeda
- Department of Tumor Biology, Oslo University Hospital, Norwegian Radium Hospital, Oslo 0424, Norway
| | - Andrew J Holloway
- Cancer Genomics, Peter MacCallum Cancer Centre, East Melbourne, VIC 3002, Australia
| | - Florence Pedeutour
- Laboratory of Solid Tumors Genetics, Nice University Hospital, Nice 06107, France
| | - K H Andy Choo
- Chromosome Research, Murdoch Childrens Research Institute, and Department of Paediatrics, Royal Children's Hospital, University of Melbourne, Parkville, VIC 3052, Australia
| | | | | | - Anthony T Papenfuss
- Bioinformatics Division, The Walter & Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, VIC 3010, Australia; Department of Mathematics and Statistics, University of Melbourne, VIC, 3010, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, VIC 3010, Australia; Bioinformatics and Cancer Genomics, Peter MacCallum Cancer Centre, East Melbourne, VIC, 3002, Australia.
| | - David M Thomas
- Cancer Genomics, Peter MacCallum Cancer Centre, East Melbourne, VIC 3002, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, VIC 3010, Australia; The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia.
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96
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Garcia-Oliveira AL, Martins-Lopes P, Tolrá R, Poschenrieder C, Tarquis M, Guedes-Pinto H, Benito C. Molecular characterization of the citrate transporter gene TaMATE1 and expression analysis of upstream genes involved in organic acid transport under Al stress in bread wheat (Triticum aestivum). PHYSIOLOGIA PLANTARUM 2014; 152:441-52. [PMID: 24588850 DOI: 10.1111/ppl.12179] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2013] [Revised: 01/27/2014] [Accepted: 01/28/2014] [Indexed: 05/25/2023]
Abstract
In bread wheat, besides malate, the importance of citrate efflux for Al tolerance has also been reported. For better understanding the Al tolerance mechanism in bread wheat, here, we performed both a molecular characterization of the citrate transporter gene TaMATE1 and an investigation on the upstream variations in citrate and malate transporter genes. TaMATE1 belong to multidrug transporter protein family, which are located on the long arm of homoeologous group 4 chromosomes (TaMATE1-4A, TaMATE1-4B TaMATE1-4D). TaMATE1 homoeologues transcript expression study exhibited the preponderance of homoeologue TaMATE1-4B followed by TaMATE1-4D whereas homoeologue TaMATE1-4A seemed to be silenced. TaMATE1, particularly homoeologue TaMATE1-4B and TaALMT1 transcripts were much more expressed in the root apices than in shoots of Al tolerant genotype Barbela 7/72/92 under both control and Al stress conditions. In addition, in both tissues of Barbela 7/72/92, higher basal levels of these gene transcripts were observed than in Anahuac (Al sensitive). Noticeably, the presence of a transposon in the upstream of TaMATE1-4B in Barbela 7/72/92 seems to be responsible for its higher transcript expression where it may confer citrate efflux. Thus, promoter variations (transposon in TaMATE1-4B upstream and type VI promoter in TaALMT1) associated with higher basal transcript expression of TaMATE1-4B and TaALMT1 clearly show how different mechanisms for Al tolerance operate simultaneously in a single genotype. In conclusion, our results demonstrate that Barbela 7/72/92 has favorable alleles for these organic acids transporter genes which could be utilized through genomic assisted selection to develop improved cultivars for acidic soils.
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Affiliation(s)
- Ana Luísa Garcia-Oliveira
- Centro de Genómica e Biotecnologia, Instituto de Biotecnologia e Bioengenharia (CGB/IBB), Universidade de Trás-os-Montes e Alto Douro (UTAD), PO Box 1013, 5001-801, Vila Real, Portugal; Departamento de Genética, Facultad de Biología, Universidad Complutense de Madrid (UCM), 28040 Madrid, Spain
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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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Maccaferri M, Cane' MA, Sanguineti MC, Salvi S, Colalongo MC, Massi A, Clarke F, Knox R, Pozniak CJ, Clarke JM, Fahima T, Dubcovsky J, Xu S, Ammar K, Karsai I, Vida G, Tuberosa R. A consensus framework map of durum wheat (Triticum durum Desf.) suitable for linkage disequilibrium analysis and genome-wide association mapping. BMC Genomics 2014; 15:873. [PMID: 25293821 PMCID: PMC4287192 DOI: 10.1186/1471-2164-15-873] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2014] [Accepted: 09/23/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Durum wheat (Triticum durum Desf.) is a tetraploid cereal grown in the medium to low-precipitation areas of the Mediterranean Basin, North America and South-West Asia. Genomics applications in durum wheat have the potential to boost exploitation of genetic resources and to advance understanding of the genetics of important complex traits (e.g. resilience to environmental and biotic stresses). A dense and accurate consensus map specific for T. durum will greatly facilitate genetic mapping, functional genomics and marker-assisted improvement. RESULTS High quality genotypic data from six core recombinant inbred line populations were used to obtain a consensus framework map of 598 simple sequence repeats (SSR) and Diversity Array Technology® (DArT) anchor markers (common across populations). Interpolation of unique markers from 14 maps allowed us to position a total of 2,575 markers in a consensus map of 2,463 cM. The T. durum A and B genomes were covered in their near totality based on the reference SSR hexaploid wheat map. The consensus locus order compared to those of the single component maps showed good correspondence, (average Spearman's rank correlation rho ρ value of 0.96). Differences in marker order and local recombination rate were observed between the durum and hexaploid wheat consensus maps. The consensus map was used to carry out a whole-genome search for genetic differentiation signatures and association to heading date in a panel of 183 accessions adapted to the Mediterranean areas. Linkage disequilibrium was found to decay below the r2 threshold=0.3 within 2.20 cM, on average. Strong molecular differentiations among sub-populations were mapped to 87 chromosome regions. A genome-wide association scan for heading date from 27 field trials in the Mediterranean Basin and in Mexico yielded 50 chromosome regions with evidences of association in multiple environments. CONCLUSIONS The consensus map presented here was used as a reference for genetic diversity and mapping analyses in T. durum, providing nearly complete genome coverage and even marker density. Markers previously mapped in hexaploid wheat constitute a strong link between the two species. The consensus map provides the basis for high-density single nucleotide polymorphic (SNP) marker implementation in durum wheat.
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Affiliation(s)
- Marco Maccaferri
- Department of Agricultural Sciences (DipSA), Viale Fanin 44, University of Bologna, 40127 Bologna, Italy.
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Zheng M, Sun X, Zhang M, Qian M, Zheng Y, Li M, Cretoiu SM, Chen C, Chen L, Cretoiu D, Popescu LM, Fang H, Wang X. Variations of chromosomes 2 and 3 gene expression profiles among pulmonary telocytes, pneumocytes, airway cells, mesenchymal stem cells and lymphocytes. J Cell Mol Med 2014; 18:2044-60. [PMID: 25278030 PMCID: PMC4244019 DOI: 10.1111/jcmm.12429] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Accepted: 08/18/2014] [Indexed: 01/11/2023] Open
Abstract
Telocytes (TCs) were identified as a distinct cellular type of the interstitial tissue and defined as cells with extremely long telopodes (Tps). Our previous data demonstrated patterns of mouse TC-specific gene profiles on chromosome 1. The present study focuses on the identification of characters and patterns of TC-specific or TC-dominated gene expression profiles in chromosome 2 and 3, the network of principle genes and potential functional association. We compared gene expression profiles of pulmonary TCs, mesenchymal stem cells, fibroblasts, alveolar type II cells, airway basal cells, proximal airway cells, CD8+T cells from bronchial lymph nodes (T-BL), and CD8+ T cells from lungs (T-LL). We identified that 26 or 80 genes of TCs in chromosome 2 and 13 or 59 genes of TCs up-or down-regulated in chromosome 3, as compared with other cells respectively. Obvious overexpression of Myl9 in chromosome 2 of TCs different from other cells, indicates that biological functions of TCs are mainly associated with tissue/organ injury and ageing, while down-expression of Pltp implies that TCs may be associated with inhibition or reduction of inflammation in the lung. Dominant overexpression of Sh3glb1, Tm4sf1 or Csf1 in chromosome 3 of TCs is mainly associated with tumour promotion in lung cancer, while most down-expression of Pde5 may be involved in the development of pulmonary fibrosis and other acute and chronic interstitial lung disease.
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Affiliation(s)
- Minghuan Zheng
- Biomedical Research Center, Minhang Hospital & Zhongshan Hospital, Fudan University Center for Clinical Bioinformatics, Shanghai, China
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Girin T, David LC, Chardin C, Sibout R, Krapp A, Ferrario-Méry S, Daniel-Vedele F. Brachypodium: a promising hub between model species and cereals. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:5683-96. [PMID: 25262566 DOI: 10.1093/jxb/eru376] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Brachypodium distachyon was proposed as a model species for genetics and molecular genomics in cereals less than 10 years ago. It is now established as a standard for research on C3 cereals on a variety of topics, due to its close phylogenetic relationship with Triticeae crops such as wheat and barley, and to its simple genome, its minimal growth requirement, and its short life cycle. In this review, we first highlight the tools and resources for Brachypodium that are currently being developed and made available by the international community. We subsequently describe how this species has been used for comparative genomic studies together with cereal crops, before illustrating major research fields in which Brachypodium has been successfully used as a model: cell wall synthesis, plant-pathogen interactions, root architecture, and seed development. Finally, we discuss the usefulness of research on Brachypodium in order to improve nitrogen use efficiency in cereals, with the aim of reducing the amount of applied fertilizer while increasing the grain yield. Several paths are considered, namely an improvement of either nitrogen remobilization from the vegetative organs, nitrate uptake from the soil, or nitrate assimilation by the plant. Altogether, these examples position the research on Brachypodium as at an intermediate stage between basic research, carried out mainly in Arabidopsis, and applied research carried out on wheat and barley, enabling a complementarity of the studies and reciprocal benefits.
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Affiliation(s)
- Thomas Girin
- Institut National de la Recherche Agronomique (INRA), UMR1318, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, RD10, F-78000 Versailles, France AgroParisTech, Institut Jean-Pierre Bourgin, RD10, F-78000 Versailles, France
| | - Laure C David
- Institut National de la Recherche Agronomique (INRA), UMR1318, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, RD10, F-78000 Versailles, France AgroParisTech, Institut Jean-Pierre Bourgin, RD10, F-78000 Versailles, France
| | - Camille Chardin
- Institut National de la Recherche Agronomique (INRA), UMR1318, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, RD10, F-78000 Versailles, France AgroParisTech, Institut Jean-Pierre Bourgin, RD10, F-78000 Versailles, France
| | - Richard Sibout
- Institut National de la Recherche Agronomique (INRA), UMR1318, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, RD10, F-78000 Versailles, France AgroParisTech, Institut Jean-Pierre Bourgin, RD10, F-78000 Versailles, France
| | - Anne Krapp
- Institut National de la Recherche Agronomique (INRA), UMR1318, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, RD10, F-78000 Versailles, France AgroParisTech, Institut Jean-Pierre Bourgin, RD10, F-78000 Versailles, France
| | - Sylvie Ferrario-Méry
- Institut National de la Recherche Agronomique (INRA), UMR1318, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, RD10, F-78000 Versailles, France AgroParisTech, Institut Jean-Pierre Bourgin, RD10, F-78000 Versailles, France
| | - Françoise Daniel-Vedele
- Institut National de la Recherche Agronomique (INRA), UMR1318, Institut Jean-Pierre Bourgin, Saclay Plant Sciences, RD10, F-78000 Versailles, France AgroParisTech, Institut Jean-Pierre Bourgin, RD10, F-78000 Versailles, France
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