1
|
Buerstmayr M, Steiner B, Wagner C, Schwarz P, Brugger K, Barabaschi D, Volante A, Valè G, Cattivelli L, Buerstmayr H. High-resolution mapping of the pericentromeric region on wheat chromosome arm 5AS harbouring the Fusarium head blight resistance QTL Qfhs.ifa-5A. Plant Biotechnol J 2018; 16:1046-1056. [PMID: 29024288 PMCID: PMC5902775 DOI: 10.1111/pbi.12850] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 09/17/2017] [Accepted: 10/08/2017] [Indexed: 05/24/2023]
Abstract
The Qfhs.ifa-5A allele, contributing to enhanced Fusarium head blight resistance in wheat, resides in a low-recombinogenic region of chromosome 5A close to the centromere. A near-isogenic RIL population segregating for the Qfhs.ifa-5A resistance allele was developed and among 3650 lines as few as four recombined within the pericentromeric C-5AS1-0.40 bin, yielding only a single recombination point. Genetic mapping of the pericentromeric region using a recombination-dependent approach was thus not successful. To facilitate fine-mapping the physically large Qfhs.ifa-5A interval, two gamma-irradiated deletion panels were generated: (i) seeds of line NIL3 carrying the Qfhs.ifa-5A resistance allele in an otherwise susceptible background were irradiated and plants thereof were selfed to obtain deletions in homozygous state and (ii) a radiation hybrid panel was produced using irradiated pollen of the wheat line Chinese Spring (CS) for pollinating the CS-nullisomic5Atetrasomic5B. In total, 5157 radiation selfing and 276 radiation hybrid plants were screened for deletions on 5AS and plants containing deletions were analysed using 102 5AS-specific markers. Combining genotypic information of both panels yielded an 817-fold map improvement (cR/cM) for the centromeric bin and was 389-fold increased across the Qfhs.ifa-5A interval compared to the genetic map, with an average map resolution of 0.77 Mb/cR. We successfully proved that the RH mapping technique can effectively resolve marker order in low-recombining regions, including pericentromeric intervals, and simultaneously allow developing an in vivo panel of sister lines differing for induced deletions across the Qfhs.ifa-5A interval that can be used for phenotyping.
Collapse
Affiliation(s)
- Maria Buerstmayr
- Department of Agrobiotechnology TullnBOKU ‐ University of Natural Resources and Life Sciences, ViennaTullnAustria
| | - Barbara Steiner
- Department of Agrobiotechnology TullnBOKU ‐ University of Natural Resources and Life Sciences, ViennaTullnAustria
| | - Christian Wagner
- Department of Agrobiotechnology TullnBOKU ‐ University of Natural Resources and Life Sciences, ViennaTullnAustria
| | - Petra Schwarz
- Department of Agrobiotechnology TullnBOKU ‐ University of Natural Resources and Life Sciences, ViennaTullnAustria
| | - Klaus Brugger
- Department of Agrobiotechnology TullnBOKU ‐ University of Natural Resources and Life Sciences, ViennaTullnAustria
| | - Delfina Barabaschi
- Council for Agricultural Research and Economics (CREA)Genomics Research CentreFiorenzuola d'ArdaItaly
| | - Andrea Volante
- Council for Agricultural Research and Economics (CREA)Research Centre for Cereal and Industrial CropsVercelliItaly
| | - Giampiero Valè
- Council for Agricultural Research and Economics (CREA)Research Centre for Cereal and Industrial CropsVercelliItaly
| | - Luigi Cattivelli
- Council for Agricultural Research and Economics (CREA)Genomics Research CentreFiorenzuola d'ArdaItaly
| | - Hermann Buerstmayr
- Department of Agrobiotechnology TullnBOKU ‐ University of Natural Resources and Life Sciences, ViennaTullnAustria
| |
Collapse
|
2
|
Kumar A, Seetan R, Mergoum M, Tiwari VK, Iqbal MJ, Wang Y, Al-Azzam O, Šimková H, Luo MC, Dvorak J, Gu YQ, Denton A, Kilian A, Lazo GR, Kianian SF. Radiation hybrid maps of the D-genome of Aegilops tauschii and their application in sequence assembly of large and complex plant genomes. BMC Genomics 2015; 16:800. [PMID: 26475137 PMCID: PMC4609151 DOI: 10.1186/s12864-015-2030-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Accepted: 10/09/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The large and complex genome of bread wheat (Triticum aestivum L., ~17 Gb) requires high resolution genome maps with saturated marker scaffolds to anchor and orient BAC contigs/ sequence scaffolds for whole genome assembly. Radiation hybrid (RH) mapping has proven to be an excellent tool for the development of such maps for it offers much higher and more uniform marker resolution across the length of the chromosome compared to genetic mapping and does not require marker polymorphism per se, as it is based on presence (retention) vs. absence (deletion) marker assay. METHODS In this study, a 178 line RH panel was genotyped with SSRs and DArT markers to develop the first high resolution RH maps of the entire D-genome of Ae. tauschii accession AL8/78. To confirm map order accuracy, the AL8/78-RH maps were compared with:1) a DArT consensus genetic map constructed using more than 100 bi-parental populations, 2) a RH map of the D-genome of reference hexaploid wheat 'Chinese Spring', and 3) two SNP-based genetic maps, one with anchored D-genome BAC contigs and another with anchored D-genome sequence scaffolds. Using marker sequences, the RH maps were also anchored with a BAC contig based physical map and draft sequence of the D-genome of Ae. tauschii. RESULTS A total of 609 markers were mapped to 503 unique positions on the seven D-genome chromosomes, with a total map length of 14,706.7 cR. The average distance between any two marker loci was 29.2 cR which corresponds to 2.1 cM or 9.8 Mb. The average mapping resolution across the D-genome was estimated to be 0.34 Mb (Mb/cR) or 0.07 cM (cM/cR). The RH maps showed almost perfect agreement with several published maps with regard to chromosome assignments of markers. The mean rank correlations between the position of markers on AL8/78 maps and the four published maps, ranged from 0.75 to 0.92, suggesting a good agreement in marker order. With 609 mapped markers, a total of 2481 deletions for the whole D-genome were detected with an average deletion size of 42.0 Mb. A total of 520 markers were anchored to 216 Ae. tauschii sequence scaffolds, 116 of which were not anchored earlier to the D-genome. CONCLUSION This study reports the development of first high resolution RH maps for the D-genome of Ae. tauschii accession AL8/78, which were then used for the anchoring of unassigned sequence scaffolds. This study demonstrates how RH mapping, which offered high and uniform resolution across the length of the chromosome, can facilitate the complete sequence assembly of the large and complex plant genomes.
Collapse
Affiliation(s)
- Ajay Kumar
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58102, USA
| | - Raed Seetan
- Department of Computer Sciences, North Dakota State University, Fargo, ND, 58102, USA
- Department of Computer Science, Slippery Rock University, Slippery Rock, PA, 16057, USA
| | - Mohamed Mergoum
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58102, USA
| | - Vijay K Tiwari
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506-5502, USA
| | - Muhammad J Iqbal
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58102, USA
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Yi Wang
- USDA-ARS, Western Regional Research Center, Albany, CA, 94710, USA
| | - Omar Al-Azzam
- Department of Computer Sciences, North Dakota State University, Fargo, ND, 58102, USA
- Department of Computer Science and Information Technology, St. Cloud State University, St. Cloud, MN, 56301, USA
| | - Hana Šimková
- Faculty of Science, Palacký University, 783 71, Olomouc, Czech Republic
- Institute of Experimental Botany, Šlechtitelů 31, 783-71, Olomouc, Czech Republic
| | - Ming-Cheng Luo
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Jan Dvorak
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Yong Q Gu
- USDA-ARS, Western Regional Research Center, Albany, CA, 94710, USA
| | - Anne Denton
- Department of Computer Sciences, North Dakota State University, Fargo, ND, 58102, USA
| | - Andrzej Kilian
- Diversity Arrays Technology Pty Limited, 1 Wilf Crane Crescent, Yarralumla, ACT2600, Australia
| | - Gerard R Lazo
- USDA-ARS, Western Regional Research Center, Albany, CA, 94710, USA
| | - Shahryar F Kianian
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58102, USA.
- USDA-ARS, Cereal Disease Laboratory, University of Minnesota, St. Paul, MN, 55108, USA.
| |
Collapse
|
3
|
Abstract
Radiation hybrid (RH) mapping has become one of the most well-established techniques for economically and efficiently navigating genomes of interest. The success of the technique relies on random chromosome breakage of a target genome, which is then captured by recipient cells missing a preselected marker. Selection for hybrid cells that have DNA fragments bearing the marker of choice, plus a random set of DNA fragments from the initial irradiation, generates a set of cell lines that recapitulates the genome of the target organism several-fold. Markers or genes of interest are analyzed by PCR using DNA isolated from each cell line. Statistical tools are applied to determine both the linear order of markers on each chromosome, and the confidence of each placement. The resolution of the resulting map relies on many factors, most notably the degree of breakage from the initial radiation as well as the number of hybrid clones and mean retention value.A high-resolution RH map of a genome derived from low pass or survey sequencing (coverage from 1 to 2 times) can provide essentially the same comparative data on gene order that is derived from high-coverage (greater than x7) genome sequencing. When combined with fluorescence in situ hybridization, RH maps are complete and ordered blueprints for each chromosome. They give information about the relative order and spacing of genes and markers, and allow investigators to move between target and reference genomes, such as those of mouse or human, with ease although the approach is not limited to mammal genomes.
Collapse
Affiliation(s)
- Christophe Hitte
- IGDR, Institut de Génétique et Développement de Rennes
CNRS : UMR6061Université Rennes IIFR140Faculté de Médecine - CS 34317
2 Av du Professeur Léon Bernard
35043 RENNES CEDEX,FR
| | - Ewen F. Kirkness
- TIGR, The Institute for Genomic Research
JCVI J. Craig Venter InstituteRockville, MD,FR
| | | | - Francis Galibert
- IGDR, Institut de Génétique et Développement de Rennes
CNRS : UMR6061Université Rennes IIFR140Faculté de Médecine - CS 34317
2 Av du Professeur Léon Bernard
35043 RENNES CEDEX,FR
| |
Collapse
|