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Tolmay VL, Sydenham SL, Sikhakhane TN, Nhlapho BN, Tsilo TJ. Elusive Diagnostic Markers for Russian Wheat Aphid Resistance in Bread Wheat: Deliberating and Reviewing the Status Quo. Int J Mol Sci 2020; 21:ijms21218271. [PMID: 33158282 PMCID: PMC7663459 DOI: 10.3390/ijms21218271] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 08/22/2020] [Accepted: 08/24/2020] [Indexed: 12/13/2022] Open
Abstract
Russian wheat aphid, Diuraphis noxia (Kurdjumov), is a severe pest of wheat, Triticum aestivum L., throughout the world. Resistant cultivars are viewed as the most economical and environmentally viable control available. Studies to identify molecular markers to facilitate resistance breeding started in the 1990s, and still continue. This paper reviews and discusses the literature pertaining to the D. noxia R-genes on chromosome 7D, and markers reported to be associated with them. Individual plants with known phenotypes from a panel of South African wheat accessions are used as examples. Despite significant inputs from various research groups over many years, diagnostic markers for resistance to D. noxia remain elusive. Factors that may have impeded critical investigation, thus blurring the accumulation of a coherent body of information applicable to Dn resistance, are discussed. This review calls for a more fastidious approach to the interpretation of results, especially considering the growing evidence pointing to the complex regulation of aphid resistance response pathways in plants. Appropriate reflection on prior studies, together with emerging knowledge regarding the complexity and specificity of the D. noxia–wheat resistance interaction, should enable scientists to address the challenges of protecting wheat against this pest in future.
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Affiliation(s)
- Vicki L. Tolmay
- Agricultural Research Council, Small Grain, Private Bag X29, Bethlehem 9700, South Africa; (S.L.S.); (T.N.S.); (B.N.N.); (T.J.T.)
- Department of Life and Consumer Sciences, University of South Africa, Pretoria 0002, South Africa
- Correspondence:
| | - Scott L. Sydenham
- Agricultural Research Council, Small Grain, Private Bag X29, Bethlehem 9700, South Africa; (S.L.S.); (T.N.S.); (B.N.N.); (T.J.T.)
| | - Thandeka N. Sikhakhane
- Agricultural Research Council, Small Grain, Private Bag X29, Bethlehem 9700, South Africa; (S.L.S.); (T.N.S.); (B.N.N.); (T.J.T.)
- Department of Life and Consumer Sciences, University of South Africa, Pretoria 0002, South Africa
| | - Bongiwe N. Nhlapho
- Agricultural Research Council, Small Grain, Private Bag X29, Bethlehem 9700, South Africa; (S.L.S.); (T.N.S.); (B.N.N.); (T.J.T.)
| | - Toi J. Tsilo
- Agricultural Research Council, Small Grain, Private Bag X29, Bethlehem 9700, South Africa; (S.L.S.); (T.N.S.); (B.N.N.); (T.J.T.)
- Department of Life and Consumer Sciences, University of South Africa, Pretoria 0002, South Africa
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Feng K, Cui L, Wang L, Shan D, Tong W, Deng P, Yan Z, Wang M, Zhan H, Wu X, He W, Zhou X, Ji J, Zhang G, Mao L, Karafiátová M, Šimková H, Doležel J, Du X, Zhao S, Luo M, Han D, Zhang C, Kang Z, Appels R, Edwards D, Nie X, Weining S. The improved assembly of 7DL chromosome provides insight into the structure and evolution of bread wheat. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:732-742. [PMID: 31471988 PMCID: PMC7004910 DOI: 10.1111/pbi.13240] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 07/27/2019] [Accepted: 08/15/2019] [Indexed: 05/03/2023]
Abstract
Wheat is one of the most important staple crops worldwide and also an excellent model species for crop evolution and polyploidization studies. The breakthrough of sequencing the bread wheat genome and progenitor genomes lays the foundation to decipher the complexity of wheat origin and evolutionary process as well as the genetic consequences of polyploidization. In this study, we sequenced 3286 BACs from chromosome 7DL of bread wheat cv. Chinese Spring and integrated the unmapped contigs from IWGSC v1 and available PacBio sequences to close gaps present in the 7DL assembly. In total, 8043 out of 12 825 gaps, representing 3 491 264 bp, were closed. We then used the improved assembly of 7DL to perform comparative genomic analysis of bread wheat (Ta7DL) and its D donor, Aegilops tauschii (At7DL), to identify domestication signatures. Results showed a strong syntenic relationship between Ta7DL and At7DL, although some small rearrangements were detected at the distal regions. A total of 53 genes appear to be lost genes during wheat polyploidization, with 23% (12 genes) as RGA (disease resistance gene analogue). Furthermore, 86 positively selected genes (PSGs) were identified, considered to be domestication-related candidates. Finally, overlapping of QTLs obtained from GWAS analysis and PSGs indicated that TraesCS7D02G321000 may be one of the domestication genes involved in grain morphology. This study provides comparative information on the sequence, structure and organization between bread wheat and Ae. tauschii from the perspective of the 7DL chromosome, which contribute to better understanding of the evolution of wheat, and supports wheat crop improvement.
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Affiliation(s)
- Kewei Feng
- State Key Laboratory of Crop Stress Biology in Arid AreasCollege of Agronomy and Yangling Branch of China Wheat Improvement CenterNorthwest A&F UniversityYanglingShaanxiChina
| | - Licao Cui
- State Key Laboratory of Crop Stress Biology in Arid AreasCollege of Agronomy and Yangling Branch of China Wheat Improvement CenterNorthwest A&F UniversityYanglingShaanxiChina
- College of Bioscience and EngineeringJiangxi Agricultural UniversityNanchangJiangxiChina
| | - Le Wang
- Department of Plant SciencesUniversity of CaliforniaDavisCAUSA
| | - Dai Shan
- BGI GenomicsBGI‐ShenzhenShenzhenChina
| | - Wei Tong
- State Key Laboratory of Crop Stress Biology in Arid AreasCollege of Agronomy and Yangling Branch of China Wheat Improvement CenterNorthwest A&F UniversityYanglingShaanxiChina
| | - Pingchuan Deng
- State Key Laboratory of Crop Stress Biology in Arid AreasCollege of Agronomy and Yangling Branch of China Wheat Improvement CenterNorthwest A&F UniversityYanglingShaanxiChina
| | - Zhaogui Yan
- College of Horticulture and Forestry Sciences/Hubei Engineering Technology Research Center for Forestry InformationHuazhong Agricultural UniversityWuhanChina
| | - Mengxing Wang
- State Key Laboratory of Crop Stress Biology in Arid AreasCollege of Agronomy and Yangling Branch of China Wheat Improvement CenterNorthwest A&F UniversityYanglingShaanxiChina
| | - Haoshuang Zhan
- State Key Laboratory of Crop Stress Biology in Arid AreasCollege of Agronomy and Yangling Branch of China Wheat Improvement CenterNorthwest A&F UniversityYanglingShaanxiChina
| | - Xiaotong Wu
- State Key Laboratory of Crop Stress Biology in Arid AreasCollege of Agronomy and Yangling Branch of China Wheat Improvement CenterNorthwest A&F UniversityYanglingShaanxiChina
| | | | | | | | | | - Long Mao
- Key Laboratory of Crop Gene Resources and Germplasm EnhancementMinistry of AgricultureThe National Key Facility for Crop Gene Resources and Genetic ImprovementInstitute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Miroslava Karafiátová
- Centre of the Region Haná for Biotechnological and Agricultural ResearchInstitute of Experimental BotanyOlomoucCzech Republic
| | - Hana Šimková
- Centre of the Region Haná for Biotechnological and Agricultural ResearchInstitute of Experimental BotanyOlomoucCzech Republic
| | - Jaroslav Doležel
- Centre of the Region Haná for Biotechnological and Agricultural ResearchInstitute of Experimental BotanyOlomoucCzech Republic
| | - Xianghong Du
- State Key Laboratory of Crop Stress Biology in Arid AreasCollege of Agronomy and Yangling Branch of China Wheat Improvement CenterNorthwest A&F UniversityYanglingShaanxiChina
| | - Shancen Zhao
- BGI Institute of Applied AgricultureBGI‐ShenzhenShenzhenChina
| | - Ming‐Cheng Luo
- Department of Plant SciencesUniversity of CaliforniaDavisCAUSA
| | - Dejun Han
- State Key Laboratory of Crop Stress Biology in Arid AreasCollege of Agronomy and Yangling Branch of China Wheat Improvement CenterNorthwest A&F UniversityYanglingShaanxiChina
| | - Chi Zhang
- BGI GenomicsBGI‐ShenzhenShenzhenChina
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of Plant ProtectionNorthwest A&F UniversityYanglingShaanxiChina
| | - Rudi Appels
- State Agriculture Biotechnology CentreSchool of Veterinary and Life SciencesAustralia Export Grains Innovation CentreMurdoch UniversityPerthWAAustralia
| | - David Edwards
- School of Biological Sciences and Institute of AgricultureThe University of Western AustraliaPerthWAAustralia
| | - Xiaojun Nie
- State Key Laboratory of Crop Stress Biology in Arid AreasCollege of Agronomy and Yangling Branch of China Wheat Improvement CenterNorthwest A&F UniversityYanglingShaanxiChina
| | - Song Weining
- State Key Laboratory of Crop Stress Biology in Arid AreasCollege of Agronomy and Yangling Branch of China Wheat Improvement CenterNorthwest A&F UniversityYanglingShaanxiChina
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Tulpová Z, Toegelová H, Lapitan NLV, Peairs FB, Macas J, Novák P, Lukaszewski AJ, Kopecký D, Mazáčová M, Vrána J, Holušová K, Leroy P, Doležel J, Šimková H. Accessing a Russian Wheat Aphid Resistance Gene in Bread Wheat by Long-Read Technologies. THE PLANT GENOME 2019; 12. [PMID: 31290924 DOI: 10.3835/plantgenome2018.09.0065] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Russian wheat aphid (RWA) ( Kurdjumov) is a serious invasive pest of small-grain cereals and many grass species. An efficient strategy to defy aphid attacks is to identify sources of natural resistance and transfer resistance genes into susceptible crop cultivars. Revealing the genes helps understand plant defense mechanisms and engineer plants with durable resistance to the pest. To date, more than 15 RWA resistance genes have been identified in wheat ( L.) but none of them has been cloned. Previously, we genetically mapped the RWA resistance gene into an interval of 0.83 cM on the short arm of chromosome 7D and spanned it with five bacterial artificial chromosome (BAC) clones. Here, we used a targeted strategy combining traditional approaches toward gene cloning (genetic mapping and sequencing of BAC clones) with novel technologies, including optical mapping and long-read nanopore sequencing. The latter, with reads spanning the entire length of a BAC insert, enabled us to assemble the whole region, a task that was not achievable with short reads. Long-read optical mapping validated the DNA sequence in the interval and revealed a difference in the locus organization between resistant and susceptible genotypes. The complete and accurate sequence of the region facilitated the identification of new markers and precise annotation of the interval, revealing six high-confidence genes. Identification of as the most likely candidate opens an avenue for its validation through functional genomics approaches.
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Kapustová V, Tulpová Z, Toegelová H, Novák P, Macas J, Karafiátová M, Hřibová E, Doležel J, Šimková H. The Dark Matter of Large Cereal Genomes: Long Tandem Repeats. Int J Mol Sci 2019; 20:E2483. [PMID: 31137466 PMCID: PMC6567227 DOI: 10.3390/ijms20102483] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Revised: 05/15/2019] [Accepted: 05/16/2019] [Indexed: 01/08/2023] Open
Abstract
Reference genomes of important cereals, including barley, emmer wheat and bread wheat, were released recently. Their comparison with genome size estimates obtained by flow cytometry indicated that the assemblies represent not more than 88-98% of the complete genome. This work is aimed at identifying the missing parts in two cereal genomes and proposing techniques to make the assemblies more complete. We focused on tandemly organised repetitive sequences, known to be underrepresented in genome assemblies generated from short-read sequence data. Our study found arrays of three tandem repeats with unit sizes of 1242 to 2726 bp present in the bread wheat reference genome generated from short reads. However, this and another wheat genome assembly employing long PacBio reads failed in integrating correctly the 2726-bp repeat in the pseudomolecule context. This suggests that tandem repeats of this size, frequently incorporated in unassigned scaffolds, may contribute to shrinking of pseudomolecules without reducing size of the entire assembly. We demonstrate how this missing information may be added to the pseudomolecules with the aid of nanopore sequencing of individual BAC clones and optical mapping. Using the latter technique, we identified and localised a 470-kb long array of 45S ribosomal DNA absent from the reference genome of barley.
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Affiliation(s)
- Veronika Kapustová
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371 Olomouc, Czech Republic.
| | - Zuzana Tulpová
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371 Olomouc, Czech Republic.
| | - Helena Toegelová
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371 Olomouc, Czech Republic.
| | - Petr Novák
- Biology Centre, Czech Academy of Sciences, Institute of Plant Molecular Biology, Branišovská 31, CZ-37005 České Budějovice, Czech Republic.
| | - Jiří Macas
- Biology Centre, Czech Academy of Sciences, Institute of Plant Molecular Biology, Branišovská 31, CZ-37005 České Budějovice, Czech Republic.
| | - Miroslava Karafiátová
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371 Olomouc, Czech Republic.
| | - Eva Hřibová
- 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.
| | - Hana Šimková
- 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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Janáková E, Jakobson I, Peusha H, Abrouk M, Škopová M, Šimková H, Šafář J, Vrána J, Doležel J, Järve K, Valárik M. Divergence between bread wheat and Triticum militinae in the powdery mildew resistance QPm.tut-4A locus and its implications for cloning of the resistance gene. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:1061-1072. [PMID: 30535646 PMCID: PMC6449310 DOI: 10.1007/s00122-018-3259-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 12/03/2018] [Indexed: 06/09/2023]
Abstract
A segment of Triticum militinae chromosome 7G harbors a gene(s) conferring powdery mildew resistance which is effective at both the seedling and the adult plant stages when transferred into bread wheat (T. aestivum). The introgressed segment replaces a piece of wheat chromosome arm 4AL. An analysis of segregating materials generated to positionally clone the gene highlighted that in a plant heterozygous for the introgression segment, only limited recombination occurs between the introgressed region and bread wheat 4A. Nevertheless, 75 genetic markers were successfully placed within the region, thereby confining the gene to a 0.012 cM window along the 4AL arm. In a background lacking the Ph1 locus, the localized rate of recombination was raised 33-fold, enabling the reduction in the length of the region containing the resistance gene to a 480 kbp stretch harboring 12 predicted genes. The substituted segment in the reference sequence of bread wheat cv. Chinese Spring is longer (640 kbp) and harbors 16 genes. A comparison of the segments' sequences revealed a high degree of divergence with respect to both their gene content and nucleotide sequence. Of the 12 T. militinae genes, only four have a homolog in cv. Chinese Spring. Possible candidate genes for the resistance have been identified based on function predicted from their sequence.
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Affiliation(s)
- Eva Janáková
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 78371, Olomouc, Czech Republic
| | - Irena Jakobson
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Akadeemia tee 15, 19086, Tallinn, Estonia
| | - Hilma Peusha
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Akadeemia tee 15, 19086, Tallinn, Estonia
| | - Michael Abrouk
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 78371, Olomouc, Czech Republic
- Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Monika Škopová
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 78371, Olomouc, Czech Republic
- Limagrain Central Europe Cereals, s.r.o., Hrubčice 111, 79821, Bedihošť, Czech Republic
| | - Hana Šimková
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 78371, Olomouc, Czech Republic
| | - Jan Šafář
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 78371, Olomouc, Czech Republic
| | - Jan Vrána
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 78371, Olomouc, Czech Republic
| | - Jaroslav Doležel
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 78371, Olomouc, Czech Republic
| | - Kadri Järve
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Akadeemia tee 15, 19086, Tallinn, Estonia
| | - Miroslav Valárik
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 78371, Olomouc, Czech Republic.
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6
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Salina EA, Nesterov MA, Frenkel Z, Kiseleva AA, Timonova EM, Magni F, Vrána J, Šafář J, Šimková H, Doležel J, Korol A, Sergeeva EM. Features of the organization of bread wheat chromosome 5BS based on physical mapping. BMC Genomics 2018; 19:80. [PMID: 29504906 PMCID: PMC5836826 DOI: 10.1186/s12864-018-4470-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND The IWGSC strategy for construction of the reference sequence of the bread wheat genome is based on first obtaining physical maps of the individual chromosomes. Our aim is to develop and use the physical map for analysis of the organization of the short arm of wheat chromosome 5B (5BS) which bears a number of agronomically important genes, including genes conferring resistance to fungal diseases. RESULTS A physical map of the 5BS arm (290 Mbp) was constructed using restriction fingerprinting and LTC software for contig assembly of 43,776 BAC clones. The resulting physical map covered ~ 99% of the 5BS chromosome arm (111 scaffolds, N50 = 3.078 Mb). SSR, ISBP and zipper markers were employed for anchoring the BAC clones, and from these 722 novel markers were developed based on previously obtained data from partial sequencing of 5BS. The markers were mapped using a set of Chinese Spring (CS) deletion lines, and F2 and RICL populations from a cross of CS and CS-5B dicoccoides. Three approaches have been used for anchoring BAC contigs on the 5BS chromosome, including clone-by-clone screening of BACs, GenomeZipper analysis, and comparison of BAC-fingerprints with in silico fingerprinting of 5B pseudomolecules of T. dicoccoides. These approaches allowed us to reach a high level of BAC contig anchoring: 96% of 5BS BAC contigs were located on 5BS. An interesting pattern was revealed in the distribution of contigs along the chromosome. Short contigs (200-999 kb) containing markers for the regions interrupted by tandem repeats, were mainly localized to the 5BS subtelomeric block; whereas the distribution of larger 1000-3500 kb contigs along the chromosome better correlated with the distribution of the regions syntenic to rice, Brachypodium, and sorghum, as detected by the Zipper approach. CONCLUSION The high fingerprinting quality, LTC software and large number of BAC clones selected by the informative markers in screening of the 43,776 clones allowed us to significantly increase the BAC scaffold length when compared with the published physical maps for other wheat chromosomes. The genetic and bioinformatics resources developed in this study provide new possibilities for exploring chromosome organization and for breeding applications.
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Affiliation(s)
- Elena A Salina
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia.
| | - Mikhail A Nesterov
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
| | | | - Antonina A Kiseleva
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
| | - Ekaterina M Timonova
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
| | | | - Jan Vrána
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Jan Šafář
- 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
| | - Jaroslav Doležel
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | | | - Ekaterina M Sergeeva
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
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7
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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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8
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Visendi P, Berkman PJ, Hayashi S, Golicz AA, Bayer PE, Ruperao P, Hurgobin B, Montenegro J, Chan CKK, Staňková H, Batley J, Šimková H, Doležel J, Edwards D. An efficient approach to BAC based assembly of complex genomes. PLANT METHODS 2016; 12:2. [PMID: 26793268 PMCID: PMC4719536 DOI: 10.1186/s13007-016-0107-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 01/08/2016] [Indexed: 05/27/2023]
Abstract
BACKGROUND There has been an exponential growth in the number of genome sequencing projects since the introduction of next generation DNA sequencing technologies. Genome projects have increasingly involved assembly of whole genome data which produces inferior assemblies compared to traditional Sanger sequencing of genomic fragments cloned into bacterial artificial chromosomes (BACs). While whole genome shotgun sequencing using next generation sequencing (NGS) is relatively fast and inexpensive, this method is extremely challenging for highly complex genomes, where polyploidy or high repeat content confounds accurate assembly, or where a highly accurate 'gold' reference is required. Several attempts have been made to improve genome sequencing approaches by incorporating NGS methods, to variable success. RESULTS We present the application of a novel BAC sequencing approach which combines indexed pools of BACs, Illumina paired read sequencing, a sequence assembler specifically designed for complex BAC assembly, and a custom bioinformatics pipeline. We demonstrate this method by sequencing and assembling BAC cloned fragments from bread wheat and sugarcane genomes. CONCLUSIONS We demonstrate that our assembly approach is accurate, robust, cost effective and scalable, with applications for complete genome sequencing in large and complex genomes.
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Affiliation(s)
- Paul Visendi
- />School of Agriculture and Food Science, University of Queensland, Brisbane, QLD 4072 Australia
- />Centre for Biotechnology and Bioinformatics, College of Biological and Physical Sciences, University of Nairobi, P. O. Box 30197, Nairobi, 00100 Kenya
| | | | - Satomi Hayashi
- />School of Agriculture and Food Science, University of Queensland, Brisbane, QLD 4072 Australia
| | - Agnieszka A. Golicz
- />School of Agriculture and Food Science, University of Queensland, Brisbane, QLD 4072 Australia
| | - Philipp E. Bayer
- />School of Agriculture and Food Science, University of Queensland, Brisbane, QLD 4072 Australia
- />School of Plant Biology, University of Western Australia, Perth, WA 6009 Australia
| | - Pradeep Ruperao
- />School of Agriculture and Food Science, University of Queensland, Brisbane, QLD 4072 Australia
- />School of Plant Biology, University of Western Australia, Perth, WA 6009 Australia
| | - Bhavna Hurgobin
- />School of Agriculture and Food Science, University of Queensland, Brisbane, QLD 4072 Australia
- />School of Plant Biology, University of Western Australia, Perth, WA 6009 Australia
| | - Juan Montenegro
- />School of Agriculture and Food Science, University of Queensland, Brisbane, QLD 4072 Australia
| | - Chon-Kit Kenneth Chan
- />School of Agriculture and Food Science, University of Queensland, Brisbane, QLD 4072 Australia
- />School of Plant Biology, University of Western Australia, Perth, WA 6009 Australia
| | - Helena Staňková
- />Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 78371 Olomouc, Czech Republic
| | - Jacqueline Batley
- />School of Agriculture and Food Science, University of Queensland, Brisbane, QLD 4072 Australia
- />School of Plant Biology, University of Western Australia, Perth, WA 6009 Australia
| | - Hana Šimková
- />Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 78371 Olomouc, Czech Republic
| | - Jaroslav Doležel
- />Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 78371 Olomouc, Czech Republic
| | - David Edwards
- />School of Agriculture and Food Science, University of Queensland, Brisbane, QLD 4072 Australia
- />School of Plant Biology, University of Western Australia, Perth, WA 6009 Australia
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9
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Abstract
Nuclear genomes of many important plant species are tremendously complicated to map and sequence. The ability to isolate single chromosomes, which represent small units of nuclear genome, is priceless in many areas of plant research including cytogenetics, genomics, and proteomics. Flow cytometry is the only technique which can provide large quantities of pure chromosome fractions suitable for downstream applications including physical mapping, preparation of chromosome-specific BAC libraries, sequencing, and optical mapping. Here, we describe step-by-step procedure of preparation of liquid suspensions of intact mitotic metaphase chromosomes and their flow cytometric analysis and sorting.
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Affiliation(s)
- Jan Vrána
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Šlechtitelů 31, 783 71, Olomouc, Czech Republic.
| | - Petr Cápal
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Šlechtitelů 31, 783 71, Olomouc, Czech Republic
| | - Jarmila Číhalíková
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Šlechtitelů 31, 783 71, Olomouc, Czech Republic
| | - Marie Kubaláková
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Šlechtitelů 31, 783 71, Olomouc, Czech Republic
| | - Jaroslav Doležel
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Šlechtitelů 31, 783 71, Olomouc, Czech Republic
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10
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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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11
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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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12
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Staňková H, Valárik M, Lapitan NLV, Berkman PJ, Batley J, Edwards D, Luo MC, Tulpová Z, Kubaláková M, Stein N, Doležel J, Šimková H. Chromosomal genomics facilitates fine mapping of a Russian wheat aphid resistance gene. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2015; 128:1373-1383. [PMID: 25862680 DOI: 10.1007/s00122-015-2512-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Accepted: 03/27/2015] [Indexed: 06/04/2023]
Abstract
Making use of wheat chromosomal resources, we developed 11 gene-associated markers for the region of interest, which allowed reducing gene interval and spanning it by four BAC clones. Positional gene cloning and targeted marker development in bread wheat are hampered by high complexity and polyploidy of its nuclear genome. Aiming to clone a Russian wheat aphid resistance gene Dn2401 located on wheat chromosome arm 7DS, we have developed a strategy overcoming problems due to polyploidy and enabling efficient development of gene-associated markers from the region of interest. We employed information gathered by GenomeZipper, a synteny-based tool combining sequence data of rice, Brachypodium, sorghum and barley, and took advantage of a high-density linkage map of Aegilops tauschii. To ensure genome- and locus-specificity of markers, we made use of survey sequence assemblies of isolated wheat chromosomes 7A, 7B and 7D. Despite the low level of polymorphism of the wheat D subgenome, our approach allowed us to add in an efficient and cost-effective manner 11 new gene-associated markers in the Dn2401 region and narrow down the target interval to 0.83 cM. Screening 7DS-specific BAC library with the flanking markers revealed a contig of four BAC clones that span the Dn2401 region in wheat cultivar 'Chinese Spring'. With the availability of sequence assemblies and GenomeZippers for each of the wheat chromosome arms, the proposed strategy can be applied for focused marker development in any region of the wheat genome.
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Affiliation(s)
- Helena Staňková
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Šlechtitelů 31, 783 71, Olomouc, Czech Republic
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13
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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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14
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Li G, Wang Y, Chen MS, Edae E, Poland J, Akhunov E, Chao S, Bai G, Carver BF, Yan L. Precisely mapping a major gene conferring resistance to Hessian fly in bread wheat using genotyping-by-sequencing. BMC Genomics 2015; 16:108. [PMID: 25765046 PMCID: PMC4347651 DOI: 10.1186/s12864-015-1297-7] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2014] [Accepted: 01/29/2015] [Indexed: 11/20/2022] Open
Abstract
Background One of the reasons hard red winter wheat cultivar ‘Duster’ (PI 644016) is widely grown in the southern Great Plains is that it confers a consistently high level of resistance to biotype GP of Hessian fly (Hf). However, little is known about the genetic mechanism underlying Hf resistance in Duster. This study aimed to unravel complex structures of the Hf region on chromosome 1AS in wheat by using genotyping-by-sequencing (GBS) markers and single nucleotide polymorphism (SNP) markers. Results Doubled haploid (DH) lines generated from a cross between two winter wheat cultivars, ‘Duster’ and ‘Billings’ , were used to identify genes in Duster responsible for effective and consistent resistance to Hf. Segregation in reaction of the 282 DH lines to Hf biotype GP fit a one-gene model. The DH population was genotyped using 2,358 markers developed using the GBS approach. A major QTL, explaining 88% of the total phenotypic variation, was mapped to a chromosome region that spanned 178 cM and contained 205 GBS markers plus 1 SSR marker and 1 gene marker, with 0.86 cM per marker in genetic distance. The analyses of GBS marker sequences and further mapping of SSR and gene markers enabled location of the QTL-containing linkage group on the short arm of chromosome 1A. Comparative mapping of the common markers for the gene for QHf.osu-1Ad in Duster and the Hf-resistance gene for QHf.osu-1A74 in cultivar ‘2174’ showed that the two Hf resistance genes are located on the same chromosome arm 1AS, only 11.2 cM apart in genetic distance. The gene at QHf.osu-1Ad in Duster has been delimited within a 2.7 cM region. Conclusion Two distinct resistance genes exist on the short arm of chromosome 1A as found in the two hard red winter cultivars, 2174 and Duster. Whereas the Hf resistance gene in 2174 is likely allelic to one or more of the previously mapped resistance genes (H9, H10, H11, H16, or H17) in wheat, the gene in Duster is novel and confers a more consistent phenotype than 2174 in response to biotype GP infestation in controlled-environment assays. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1297-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Genqiao Li
- Department of Plant and Soil Sciences, Oklahoma State University, 368 AG Hall, Stillwater, OK, 74078, USA.
| | - Ying Wang
- Department of Plant and Soil Sciences, Oklahoma State University, 368 AG Hall, Stillwater, OK, 74078, USA.
| | - Ming-Shun Chen
- Hard Winter Wheat Genetics Research Unit, USDA-ARS, Manhattan, KS, 66506, USA.
| | - Erena Edae
- Hard Winter Wheat Genetics Research Unit, USDA-ARS, Manhattan, KS, 66506, USA.
| | - Jesse Poland
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA.
| | - Edward Akhunov
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA.
| | - Shiaoman Chao
- United States Department of Agriculture, Agricultural Research Service, Cereal Crops Research Unit, Fargo, ND, 58102, USA.
| | - Guihua Bai
- Hard Winter Wheat Genetics Research Unit, USDA-ARS, Manhattan, KS, 66506, USA.
| | - Brett F Carver
- Department of Plant and Soil Sciences, Oklahoma State University, 368 AG Hall, Stillwater, OK, 74078, USA.
| | - Liuling Yan
- Department of Plant and Soil Sciences, Oklahoma State University, 368 AG Hall, Stillwater, OK, 74078, USA.
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15
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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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Barghini E, Natali L, Giordani T, Cossu RM, Scalabrin S, Cattonaro F, Šimková H, Vrána J, Doležel J, Morgante M, Cavallini A. LTR retrotransposon dynamics in the evolution of the olive (Olea europaea) genome. DNA Res 2014; 22:91-100. [PMID: 25428895 PMCID: PMC4379980 DOI: 10.1093/dnares/dsu042] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Improved knowledge of genome composition, especially of its repetitive component, generates important information for both theoretical and applied research. The olive repetitive component is made up of two main classes of sequences: tandem repeats and retrotransposons (REs). In this study, we provide characterization of a sample of 254 unique full-length long terminal repeat (LTR) REs. In the sample, Ty1-Copia elements were more numerous than Ty3-Gypsy elements. Mapping a large set of Illumina whole-genome shotgun reads onto the identified retroelement set revealed that Gypsy elements are more redundant than Copia elements. The insertion time of intact retroelements was estimated based on sister LTR’s divergence. Although some elements inserted relatively recently, the mean insertion age of the isolated retroelements is around 18 million yrs. Gypsy and Copia retroelements showed different waves of transposition, with Gypsy elements especially active between 10 and 25 million yrs ago and nearly inactive in the last 7 million yrs. The occurrence of numerous solo-LTRs related to isolated full-length retroelements was ascertained for two Gypsy elements and one Copia element. Overall, the results reported in this study show that RE activity (both retrotransposition and DNA loss) has impacted the olive genome structure in more ancient times than in other angiosperms.
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Affiliation(s)
- Elena Barghini
- Department of Agricultural, Food, and Environmental Sciences, University of Pisa, Pisa I-56124, Italy
| | - Lucia Natali
- Department of Agricultural, Food, and Environmental Sciences, University of Pisa, Pisa I-56124, Italy
| | - Tommaso Giordani
- Department of Agricultural, Food, and Environmental Sciences, University of Pisa, Pisa I-56124, Italy
| | - Rosa Maria Cossu
- Department of Agricultural, Food, and Environmental Sciences, University of Pisa, Pisa I-56124, Italy Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa, Italy
| | | | | | - Hana Šimková
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Jan Vrána
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Jaroslav Doležel
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Michele Morgante
- Department of Crop and Environmental Sciences, University of Udine, Udine, Italy Institute of Applied Genomics, Udine, Italy
| | - Andrea Cavallini
- Department of Agricultural, Food, and Environmental Sciences, University of Pisa, Pisa I-56124, Italy
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Poursarebani N, Nussbaumer T, Šimková H, Šafář J, Witsenboer H, van Oeveren J, Doležel J, Mayer KFX, Stein N, Schnurbusch T. Whole-genome profiling and shotgun sequencing delivers an anchored, gene-decorated, physical map assembly of bread wheat chromosome 6A. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2014; 79:334-47. [PMID: 24813060 PMCID: PMC4241024 DOI: 10.1111/tpj.12550] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Revised: 04/25/2014] [Accepted: 05/01/2014] [Indexed: 05/08/2023]
Abstract
Bread wheat (Triticum aestivum L.) is the most important staple food crop for 35% of the world's population. International efforts are underway to facilitate an increase in wheat production, of which the International Wheat Genome Sequencing Consortium (IWGSC) plays an important role. As part of this effort, we have developed a sequence-based physical map of wheat chromosome 6A using whole-genome profiling (WGP™). The bacterial artificial chromosome (BAC) contig assembly tools fingerprinted contig (fpc) and linear topological contig (ltc) were used and their contig assemblies were compared. A detailed investigation of the contigs structure revealed that ltc created a highly robust assembly compared with those formed by fpc. The ltc assemblies contained 1217 contigs for the short arm and 1113 contigs for the long arm, with an L50 of 1 Mb. To facilitate in silico anchoring, WGP™ tags underlying BAC contigs were extended by wheat and wheat progenitor genome sequence information. Sequence data were used for in silico anchoring against genetic markers with known sequences, of which almost 79% of the physical map could be anchored. Moreover, the assigned sequence information led to the 'decoration' of the respective physical map with 3359 anchored genes. Thus, this robust and genetically anchored physical map will serve as a framework for the sequencing of wheat chromosome 6A, and is of immediate use for map-based isolation of agronomically important genes/quantitative trait loci located on this chromosome.
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Affiliation(s)
- Naser Poursarebani
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Corrensstr. 3, D-06466, Stadt Seeland (OT) Gatersleben, Germany
- * For correspondence (e-mails and )
| | - Thomas Nussbaumer
- MIPS/IBIS German Research Center for Environmental HealthD-85764, Neuherberg, Germany
- † These authors contributed equally to this work
| | - Hana Šimková
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural ResearchCZ-78371, Olomouc, Czech Republic
| | - Jan Šafář
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural ResearchCZ-78371, Olomouc, Czech Republic
| | | | - Jan van Oeveren
- Keygene N.V.Agro Business Park 90, 6708 PW, Wageningen, The Netherlands
| | - Jaroslav Doležel
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural ResearchCZ-78371, Olomouc, Czech Republic
| | - Klaus FX Mayer
- MIPS/IBIS German Research Center for Environmental HealthD-85764, Neuherberg, Germany
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Corrensstr. 3, D-06466, Stadt Seeland (OT) Gatersleben, Germany
| | - Thorsten Schnurbusch
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Corrensstr. 3, D-06466, Stadt Seeland (OT) Gatersleben, Germany
- * For correspondence (e-mails and )
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Zeng Q, Yuan F, Xu X, Shi X, Nie X, Zhuang H, Chen X, Wang Z, Wang X, Huang L, Han D, Kang Z. Construction and characterization of a bacterial artificial chromosome library for the hexaploid wheat line 92R137. BIOMED RESEARCH INTERNATIONAL 2014; 2014:845806. [PMID: 24895618 PMCID: PMC4026951 DOI: 10.1155/2014/845806] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Revised: 03/26/2014] [Accepted: 04/18/2014] [Indexed: 11/18/2022]
Abstract
For map-based cloning of genes conferring important traits in the hexaploid wheat line 92R137, a bacterial artificial chromosome (BAC) library, including two sublibraries, was constructed using the genomic DNA of 92R137 digested with restriction enzymes HindIII and BamHI. The BAC library was composed of total 765,696 clones, of which 390,144 were from the HindIII digestion and 375,552 from the BamHI digestion. Through pulsed-field gel electrophoresis (PFGE) analysis of 453 clones randomly selected from the HindIII sublibrary and 573 clones from the BamHI sublibrary, the average insert sizes were estimated as 129 and 113 kb, respectively. Thus, the HindIII sublibrary was estimated to have a 3.01-fold coverage and the BamHI sublibrary a 2.53-fold coverage based on the estimated hexaploid wheat genome size of 16,700 Mb. The 765,696 clones were arrayed in 1,994 384-well plates. All clones were also arranged into plate pools and further arranged into 5-dimensional (5D) pools. The probability of identifying a clone corresponding to any wheat DNA sequence (such as gene Yr26 for stripe rust resistance) from the library was estimated to be more than 99.6%. Through polymerase chain reaction screening the 5D pools with Xwe173, a marker tightly linked to Yr26, six BAC clones were successfully obtained. These results demonstrate that the BAC library is a valuable genomic resource for positional cloning of Yr26 and other genes of interest.
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Affiliation(s)
- Qingdong Zeng
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Fengping Yuan
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xin Xu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xue Shi
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xiaojun Nie
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Hua Zhuang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xianming Chen
- Wheat Genetics, Quality, Physiology, and Disease Research Unit, Agricultural Research Service, United States Department of Agriculture, and Department of Plant Pathology, Washington State University, Pullman, WA 99164-6430, USA
| | - Zhonghua Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xiaojie Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Lili Huang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Dejun Han
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
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Doležel J, Vrána J, Cápal P, Kubaláková M, Burešová V, Šimková H. Advances in plant chromosome genomics. Biotechnol Adv 2014; 32:122-36. [DOI: 10.1016/j.biotechadv.2013.12.011] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Revised: 12/20/2013] [Accepted: 12/21/2013] [Indexed: 01/09/2023]
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Raats D, Frenkel Z, Krugman T, Dodek I, Sela H, Simková H, Magni F, Cattonaro F, Vautrin S, Bergès H, Wicker T, Keller B, Leroy P, Philippe R, Paux E, Doležel J, Feuillet C, Korol A, Fahima T. The physical map of wheat chromosome 1BS provides insights into its gene space organization and evolution. Genome Biol 2013; 14:R138. [PMID: 24359668 PMCID: PMC4053865 DOI: 10.1186/gb-2013-14-12-r138] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Accepted: 12/20/2013] [Indexed: 11/16/2022] Open
Abstract
Background The wheat genome sequence is an essential tool for advanced genomic research and improvements. The generation of a high-quality wheat genome sequence is challenging due to its complex 17 Gb polyploid genome. To overcome these difficulties, sequencing through the construction of BAC-based physical maps of individual chromosomes is employed by the wheat genomics community. Here, we present the construction of the first comprehensive physical map of chromosome 1BS, and illustrate its unique gene space organization and evolution. Results Fingerprinted BAC clones were assembled into 57 long scaffolds, anchored and ordered with 2,438 markers, covering 83% of chromosome 1BS. The BAC-based chromosome 1BS physical map and gene order of the orthologous regions of model grass species were consistent, providing strong support for the reliability of the chromosome 1BS assembly. The gene space for chromosome 1BS spans the entire length of the chromosome arm, with 76% of the genes organized in small gene islands, accompanied by a two-fold increase in gene density from the centromere to the telomere. Conclusions This study provides new evidence on common and chromosome-specific features in the organization and evolution of the wheat genome, including a non-uniform distribution of gene density along the centromere-telomere axis, abundance of non-syntenic genes, the degree of colinearity with other grass genomes and a non-uniform size expansion along the centromere-telomere axis compared with other model cereal genomes. The high-quality physical map constructed in this study provides a solid basis for the assembly of a reference sequence of chromosome 1BS and for breeding applications.
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21
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Breen J, Wicker T, Shatalina M, Frenkel Z, Bertin I, Philippe R, Spielmeyer W, Šimková H, Šafář J, Cattonaro F, Scalabrin S, Magni F, Vautrin S, Bergès H, Paux E, Fahima T, Doležel J, Korol A, Feuillet C, Keller B. A physical map of the short arm of wheat chromosome 1A. PLoS One 2013; 8:e80272. [PMID: 24278269 PMCID: PMC3836966 DOI: 10.1371/journal.pone.0080272] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2013] [Accepted: 10/11/2013] [Indexed: 12/31/2022] Open
Abstract
Bread wheat (Triticum aestivum) has a large and highly repetitive genome which poses major technical challenges for its study. To aid map-based cloning and future genome sequencing projects, we constructed a BAC-based physical map of the short arm of wheat chromosome 1A (1AS). From the assembly of 25,918 high information content (HICF) fingerprints from a 1AS-specific BAC library, 715 physical contigs were produced that cover almost 99% of the estimated size of the chromosome arm. The 3,414 BAC clones constituting the minimum tiling path were end-sequenced. Using a gene microarray containing ∼40 K NCBI UniGene EST clusters, PCR marker screening and BAC end sequences, we arranged 160 physical contigs (97 Mb or 35.3% of the chromosome arm) in a virtual order based on synteny with Brachypodium, rice and sorghum. BAC end sequences and information from microarray hybridisation was used to anchor 3.8 Mbp of Illumina sequences from flow-sorted chromosome 1AS to BAC contigs. Comparison of genetic and synteny-based physical maps indicated that ∼50% of all genetic recombination is confined to 14% of the physical length of the chromosome arm in the distal region. The 1AS physical map provides a framework for future genetic mapping projects as well as the basis for complete sequencing of chromosome arm 1AS.
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Affiliation(s)
- James Breen
- Institute of Plant Biology, University of Zurich, Zurich, Switzerland
| | - Thomas Wicker
- Institute of Plant Biology, University of Zurich, Zurich, Switzerland
| | | | - Zeev Frenkel
- Institute of Evolution, University of Haifa, Haifa, Israel
| | - Isabelle Bertin
- INRA UMR 1095, Genetique Diversite et Ecophysiologie des Cereales, Clermont-Ferrand, France
| | - Romain Philippe
- INRA UMR 1095, Genetique Diversite et Ecophysiologie des Cereales, Clermont-Ferrand, France
| | | | - Hana Šimková
- Centre of the Region Hana for Biotechnological and Agricultural Research, Institute of Experimental Botany, Olomouc, Czech Republic
| | - Jan Šafář
- Centre of the Region Hana for Biotechnological and Agricultural Research, Institute of Experimental Botany, Olomouc, Czech Republic
| | | | | | | | | | | | | | - Etienne Paux
- INRA UMR 1095, Genetique Diversite et Ecophysiologie des Cereales, Clermont-Ferrand, France
| | - Tzion Fahima
- Institute of Evolution, University of Haifa, Haifa, Israel
| | - Jaroslav Doležel
- Centre of the Region Hana for Biotechnological and Agricultural Research, Institute of Experimental Botany, Olomouc, Czech Republic
| | - Abraham Korol
- Institute of Evolution, University of Haifa, Haifa, Israel
| | - Catherine Feuillet
- INRA UMR 1095, Genetique Diversite et Ecophysiologie des Cereales, Clermont-Ferrand, France
| | - Beat Keller
- Institute of Plant Biology, University of Zurich, Zurich, Switzerland
- * E-mail:
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22
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Philippe R, Paux E, Bertin I, Sourdille P, Choulet F, Laugier C, Šimková H, Šafář J, Bellec A, Vautrin S, Frenkel Z, Cattonaro F, Magni F, Scalabrin S, Martis MM, Mayer KFX, Korol A, Bergès H, Doležel J, Feuillet C. A high density physical map of chromosome 1BL supports evolutionary studies, map-based cloning and sequencing in wheat. Genome Biol 2013; 14:R64. [PMID: 23800011 PMCID: PMC4054855 DOI: 10.1186/gb-2013-14-6-r64] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Revised: 05/24/2013] [Accepted: 06/25/2013] [Indexed: 01/31/2023] Open
Abstract
BACKGROUND As for other major crops, achieving a complete wheat genome sequence is essential for the application of genomics to breeding new and improved varieties. To overcome the complexities of the large, highly repetitive and hexaploid wheat genome, the International Wheat Genome Sequencing Consortium established a chromosome-based strategy that was validated by the construction of the physical map of chromosome 3B. Here, we present improved strategies for the construction of highly integrated and ordered wheat physical maps, using chromosome 1BL as a template, and illustrate their potential for evolutionary studies and map-based cloning. RESULTS Using a combination of novel high throughput marker assays and an assembly program, we developed a high quality physical map representing 93% of wheat chromosome 1BL, anchored and ordered with 5,489 markers including 1,161 genes. Analysis of the gene space organization and evolution revealed that gene distribution and conservation along the chromosome results from the superimposition of the ancestral grass and recent wheat evolutionary patterns, leading to a peak of synteny in the central part of the chromosome arm and an increased density of non-collinear genes towards the telomere. With a density of about 11 markers per Mb, the 1BL physical map provides 916 markers, including 193 genes, for fine mapping the 40 QTLs mapped on this chromosome. CONCLUSIONS Here, we demonstrate that high marker density physical maps can be developed in complex genomes such as wheat to accelerate map-based cloning, gain new insights into genome evolution, and provide a foundation for reference sequencing.
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Affiliation(s)
- Romain Philippe
- INRA-UBP UMR 1095 Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu 63039 Clermont-Ferrand, France
| | - Etienne Paux
- INRA-UBP UMR 1095 Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu 63039 Clermont-Ferrand, France
| | - Isabelle Bertin
- INRA-UBP UMR 1095 Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu 63039 Clermont-Ferrand, France
| | - Pierre Sourdille
- INRA-UBP UMR 1095 Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu 63039 Clermont-Ferrand, France
| | - Fréderic Choulet
- INRA-UBP UMR 1095 Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu 63039 Clermont-Ferrand, France
| | - Christel Laugier
- INRA-UBP UMR 1095 Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu 63039 Clermont-Ferrand, France
| | - Hana Šimková
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Sokolovska 6, CZ-77200 Olomouc, Czech Republic
| | - Jan Šafář
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Sokolovska 6, CZ-77200 Olomouc, Czech Republic
| | - Arnaud Bellec
- Centre National des Ressources Génomiques Végétales, INRA UPR 1258, 24 Chemin de Borde Rouge - Auzeville 31326 Castalnet Tolosan, France
| | - Sonia Vautrin
- Centre National des Ressources Génomiques Végétales, INRA UPR 1258, 24 Chemin de Borde Rouge - Auzeville 31326 Castalnet Tolosan, France
| | - Zeev Frenkel
- University of Haifa, Institute of Evolution and Department of Evolutionary and Environmental Biology, Haifa 31905, Israel
| | - Federica Cattonaro
- Instituto di Genomica Applicata, Via J. Linussio 51, Udine, 33100, Italy
| | - Federica Magni
- Instituto di Genomica Applicata, Via J. Linussio 51, Udine, 33100, Italy
| | - Simone Scalabrin
- Instituto di Genomica Applicata, Via J. Linussio 51, Udine, 33100, Italy
| | | | - Klaus FX Mayer
- MIPS/IBIS; Helmholtz-Zentrum München, 85764 Neuherberg, Germany
| | - Abraham Korol
- University of Haifa, Institute of Evolution and Department of Evolutionary and Environmental Biology, Haifa 31905, Israel
| | - Hélène Bergès
- Centre National des Ressources Génomiques Végétales, INRA UPR 1258, 24 Chemin de Borde Rouge - Auzeville 31326 Castalnet Tolosan, France
| | - Jaroslav Doležel
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Sokolovska 6, CZ-77200 Olomouc, Czech Republic
| | - Catherine Feuillet
- INRA-UBP UMR 1095 Genetics, Diversity and Ecophysiology of Cereals, 5 Chemin de Beaulieu 63039 Clermont-Ferrand, France
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Tan CT, Carver BF, Chen MS, Gu YQ, Yan L. Genetic association of OPR genes with resistance to Hessian fly in hexaploid wheat. BMC Genomics 2013; 14:369. [PMID: 23724909 PMCID: PMC3674912 DOI: 10.1186/1471-2164-14-369] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2013] [Accepted: 05/17/2013] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Hessian fly (Mayetiola destructor) is one of the most destructive pests of wheat. The genes encoding 12-oxo-phytodienoic acid reductase (OPR) and lipoxygenase (LOX) play critical roles in insect resistance pathways in higher plants, but little is known about genes controlling resistance to Hessian fly in wheat. RESULTS In this study, 154 F6:8 recombinant inbred lines (RILs) generated from a cross between two cultivars, 'Jagger' and '2174' of hexaploid wheat (2n = 6 × =42; AABBDD), were used to map genes associated with resistance to Hessian fly. Two QTLs were identified. The first one was a major QTL on chromosome 1A (QHf.osu-1A), which explained 70% of the total phenotypic variation. The resistant allele at this locus in cultivar 2174 could be orthologous to one or more of the previously mapped resistance genes (H9, H10, H11, H16, and H17) in tetraploid wheat. The second QTL was a minor QTL on chromosome 2A (QHf.osu-2A), which accounted for 18% of the total phenotypic variation. The resistant allele at this locus in 2174 is collinear to an Yr17-containing-fragment translocated from chromosome 2N of Triticum ventricosum (2n = 4 × =28; DDNN) in Jagger. Genetic mapping results showed that two OPR genes, TaOPR1-A and TaOPR2-A, were tightly associated with QHf.osu-1A and QHf.osu-2A, respectively. Another OPR gene and three LOX genes were mapped but not associated with Hessian fly resistance in the segregating population. CONCLUSIONS This study has located two major QTLs/genes in bread wheat that can be directly used in wheat breeding programs and has also provided insights for the genetic association and disassociation of Hessian fly resistance with OPR and LOX genes in wheat.
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Affiliation(s)
- Chor Tee Tan
- Department of Plant and Soil Sciences, Oklahoma State University, Stillwater, OK 74078, USA
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Ye Q, He K, Wu SY, Wan QH. Isolation of a 97-kb minimal essential MHC B locus from a new reverse-4D BAC library of the golden pheasant. PLoS One 2012; 7:e32154. [PMID: 22403630 PMCID: PMC3293878 DOI: 10.1371/journal.pone.0032154] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2011] [Accepted: 01/19/2012] [Indexed: 12/02/2022] Open
Abstract
The bacterial artificial chromosome (BAC) system is widely used in isolation of large genomic fragments of interest. Construction of a routine BAC library requires several months for picking clones and arraying BACs into superpools in order to employ 4D-PCR to screen positive BACs, which might be time-consuming and laborious. The major histocompatibility complex (MHC) is a cluster of genes involved in the vertebrate immune system, and the classical avian MHC-B locus is a minimal essential one, occupying a 100-kb genomic region. In this study, we constructed a more effective reverse-4D BAC library for the golden pheasant, which first creates sub-libraries and then only picks clones of positive sub-libraries, and identified several MHC clones within thirty days. The full sequencing of a 97-kb reverse-4D BAC demonstrated that the golden pheasant MHC-B locus contained 20 genes and showed good synteny with that of the chicken. The notable differences between these two species were the numbers of class II B loci and NK genes and the inversions of the TAPBP gene and the TAP1-TAP2 region. Furthermore, the inverse TAP2-TAP1 was unique in the golden pheasant in comparison with that of chicken, turkey, and quail. The newly defined genomic structure of the golden pheasant MHC will give an insight into the evolutionary history of the avian MHC.
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Affiliation(s)
| | | | - Shao-Ying Wu
- The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education and State Conservation Center for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Qiu-Hong Wan
- The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education and State Conservation Center for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou, China
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Azhaguvel P, Rudd JC, Ma Y, Luo MC, Weng Y. Fine genetic mapping of greenbug aphid-resistance gene Gb3 in Aegilops tauschii. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2012; 124:555-64. [PMID: 22038487 DOI: 10.1007/s00122-011-1728-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2011] [Accepted: 10/07/2011] [Indexed: 05/11/2023]
Abstract
The greenbug, Schizaphis graminum (Rondani), is an important aphid pest of small grain crops especially wheat (Triticum aestivum L., 2n = 6x = 42, genomes AABBDD) in many parts of the world. The greenbug-resistance gene Gb3 originated from Aegilops tauschii Coss. (2n = 2x = 14, genome D(t)D(t)) has shown consistent and durable resistance against prevailing greenbug biotypes in wheat fields. We previously mapped Gb3 in a recombination-rich, telomeric bin of wheat chromosome arm 7DL. In this study, high-resolution genetic mapping was carried out using an F(2:3) segregating population derived from two Ae. tauschii accessions, the resistant PI 268210 (original donor of Gb3 in the hexaploid wheat germplasm line 'Largo') and susceptible AL8/78. Molecular markers were developed by exploring bin-mapped wheat RFLPs, SSRs, ESTs and the Ae. tauschii physical map (BAC contigs). Wheat EST and Ae. tauschii BAC end sequences located in the deletion bin 7DL3-0.82-1.00 were used to design STS (sequence tagged site) or CAPS (Cleaved Amplified Polymorphic Sequence) markers. Forty-five PCR-based markers were developed and mapped to the chromosomal region spanning the Gb3 locus. The greenbug-resistance gene Gb3 now was delimited in an interval of 1.1 cM by two molecular markers (HI067J6-R and HI009B3-R). This localized high-resolution genetic map with markers closely linked to Gb3 lays a solid foundation for map based cloning of Gb3 and marker-assisted selection of this gene in wheat breeding.
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Affiliation(s)
- Perumal Azhaguvel
- Texas AgriLife Research, 6500 Amarillo Blvd W, Amarillo, TX 79106, USA.
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26
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Rustenholz C, Choulet F, Laugier C, Šafář J, Šimková H, Doležel J, Magni F, Scalabrin S, Cattonaro F, Vautrin S, Bellec A, Bergès H, Feuillet C, Paux E. A 3,000-loci transcription map of chromosome 3B unravels the structural and functional features of gene islands in hexaploid wheat. PLANT PHYSIOLOGY 2011; 157:1596-608. [PMID: 22034626 PMCID: PMC3327205 DOI: 10.1104/pp.111.183921] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
To improve our understanding of the organization and regulation of the wheat (Triticum aestivum) gene space, we established a transcription map of a wheat chromosome (3B) by hybridizing a newly developed wheat expression microarray with bacterial artificial chromosome pools from a new version of the 3B physical map as well as with cDNA probes derived from 15 RNA samples. Mapping data for almost 3,000 genes showed that the gene space spans the whole chromosome 3B with a 2-fold increase of gene density toward the telomeres due to an increase in the number of genes in islands. Comparative analyses with rice (Oryza sativa) and Brachypodium distachyon revealed that these gene islands are composed mainly of genes likely originating from interchromosomal gene duplications. Gene Ontology and expression profile analyses for the 3,000 genes located along the chromosome revealed that the gene islands are enriched significantly in genes sharing the same function or expression profile, thereby suggesting that genes in islands acquired shared regulation during evolution. Only a small fraction of these clusters of cofunctional and coexpressed genes was conserved with rice and B. distachyon, indicating a recent origin. Finally, genes with the same expression profiles in remote islands (coregulation islands) were identified suggesting long-distance regulation of gene expression along the chromosomes in wheat.
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MESH Headings
- Base Sequence
- Brachypodium/genetics
- Centromere/genetics
- Chromosomes, Artificial, Bacterial/genetics
- Chromosomes, Plant/genetics
- DNA, Intergenic/genetics
- DNA, Plant/chemistry
- DNA, Plant/genetics
- Evolution, Molecular
- Gene Duplication
- Gene Expression Profiling
- Gene Expression Regulation, Plant/genetics
- Genes, Plant/genetics
- Genome, Plant/genetics
- Genomic Islands/genetics
- Genomic Islands/physiology
- Molecular Sequence Data
- Multigene Family
- Oligonucleotide Array Sequence Analysis
- Oryza/genetics
- Physical Chromosome Mapping/methods
- Polyploidy
- Sequence Analysis, DNA
- Telomere/genetics
- Transcriptome
- Triticum/genetics
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27
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Functional features of a single chromosome arm in wheat (1AL) determined from its structure. Funct Integr Genomics 2011; 12:173-82. [PMID: 21892730 DOI: 10.1007/s10142-011-0250-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2011] [Revised: 07/22/2011] [Accepted: 08/16/2011] [Indexed: 10/17/2022]
Abstract
Bread wheat (Triticum aestivum L.) is one of the most important crops globally and a high priority for genetic improvement, but its large and complex genome has been seen as intractable to whole genome sequencing. Isolation of individual wheat chromosome arms has facilitated large-scale sequence analyses. However, so far there is no such survey of sequences from the A genome of wheat. Greater understanding of an A chromosome could facilitate wheat improvement and future sequencing of the entire genome. We have constructed BAC library from the long arm of T. aestivum chromosome 1A (1AL) and obtained BAC end sequences from 7,470 clones encompassing the arm. We obtained 13,445 (89.99%) useful sequences with a cumulative length of 7.57 Mb, representing 1.43% of 1AL and about 0.14% of the entire A genome. The GC content of the sequences was 44.7%, and 90% of the chromosome was estimated to comprise repeat sequences, while just over 1% encoded expressed genes. From the sequence data, we identified a large number of sites suitable for development of molecular markers (362 SSR and 6,948 ISBP) which will have utility for mapping this chromosome and for marker assisted breeding. From 44 putative ISBP markers tested 23 (52.3%) were found to be useful. The BAC end sequence data also enabled the identification of genes and syntenic blocks specific to chromosome 1AL, suggesting regions of particular functional interest and targets for future research.
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