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Vidal A, Gauthier F, Rodrigez W, Guiglielmoni N, Leroux D, Chevrolier N, Jasson S, Tourrette E, Martin OC, Falque M. SeSAM: software for automatic construction of order-robust linkage maps. BMC Bioinformatics 2022; 23:499. [PMCID: PMC9675223 DOI: 10.1186/s12859-022-05045-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 11/08/2022] [Indexed: 11/21/2022] Open
Abstract
Background Genotyping and sequencing technologies produce increasingly large numbers of genetic markers with potentially high rates of missing or erroneous data. Therefore, the construction of linkage maps is more and more complex. Moreover, the size of segregating populations remains constrained by cost issues and is less and less commensurate with the numbers of SNPs available. Thus, guaranteeing a statistically robust marker order requires that maps include only a carefully selected subset of SNPs. Results In this context, the SeSAM software allows automatic genetic map construction using seriation and placement approaches, to produce (1) a high-robustness framework map which includes as many markers as possible while keeping the order robustness beyond a given statistical threshold, and (2) a high-density total map including the framework plus almost all polymorphic markers. During this process, care is taken to limit the impact of genotyping errors and of missing data on mapping quality. SeSAM can be used with a wide range of biparental populations including from outcrossing species for which phases are inferred on-the-fly by maximum-likelihood during map elongation. The package also includes functions to simulate data sets, convert data formats, detect putative genotyping errors, visualize data and map quality (including graphical genotypes), and merge several maps into a consensus. SeSAM is also suitable for interactive map construction, by providing lower-level functions for 2-point and multipoint EM analyses. The software is implemented in a R package including functions in C++. Conclusions SeSAM is a fully automatic linkage mapping software designed to (1) produce a framework map as robust as desired by optimizing the selection of a subset of markers, and (2) produce a high-density map including almost all polymorphic markers. The software can be used with a wide range of biparental mapping populations including cases from outcrossing. SeSAM is freely available under a GNU GPL v3 license and works on Linux, Windows, and macOS platforms. It can be downloaded together with its user-manual and quick-start tutorial from ForgeMIA (SeSAM project) at https://forgemia.inra.fr/gqe-acep/sesam/-/releases Supplementary Information The online version contains supplementary material available at 10.1186/s12859-022-05045-7.
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Affiliation(s)
- Adrien Vidal
- grid.460789.40000 0004 4910 6535Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE - Le Moulon, 91190 Gif-sur-Yvette, France
| | - Franck Gauthier
- grid.460789.40000 0004 4910 6535Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE - Le Moulon, 91190 Gif-sur-Yvette, France
| | - Willy Rodrigez
- grid.460789.40000 0004 4910 6535Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE - Le Moulon, 91190 Gif-sur-Yvette, France
| | - Nadège Guiglielmoni
- grid.460789.40000 0004 4910 6535Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE - Le Moulon, 91190 Gif-sur-Yvette, France
| | - Damien Leroux
- grid.507621.7INRAE, Unité de Mathématiques et Informatique Appliquées - Toulouse, Toulouse, France
| | - Nicolas Chevrolier
- grid.460789.40000 0004 4910 6535Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE - Le Moulon, 91190 Gif-sur-Yvette, France
| | - Sylvain Jasson
- grid.507621.7INRAE, Unité de Mathématiques et Informatique Appliquées - Toulouse, Toulouse, France
| | - Elise Tourrette
- grid.460789.40000 0004 4910 6535Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE - Le Moulon, 91190 Gif-sur-Yvette, France
| | - Olivier C. Martin
- grid.460789.40000 0004 4910 6535Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE - Le Moulon, 91190 Gif-sur-Yvette, France ,grid.503243.3Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif-sur-Yvette, France ,Université Paris Cité, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif-sur-Yvette, France
| | - Matthieu Falque
- grid.460789.40000 0004 4910 6535Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE - Le Moulon, 91190 Gif-sur-Yvette, France
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Sari E, Knox RE, Ruan Y, Henriquez MA, Kumar S, Burt AJ, Cuthbert RD, Konkin DJ, Walkowiak S, Campbell HL, Singh AK, Ross J, Lokuruge P, Hsueh E, Boyle K, Sidebottom C, Condie J, Yates S, Pozniak CJ, Fobert PR. Historic recombination in a durum wheat breeding panel enables high-resolution mapping of Fusarium head blight resistance quantitative trait loci. Sci Rep 2020; 10:7567. [PMID: 32372012 PMCID: PMC7200731 DOI: 10.1038/s41598-020-64399-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 04/15/2020] [Indexed: 11/09/2022] Open
Abstract
The durum wheat line DT696 is a source of moderate Fusarium head blight (FHB) resistance. Previous analysis using a bi-parental population identified two FHB resistance quantitative trait loci (QTL) on chromosome 5A: 5A1 was co-located with a plant height QTL, and 5A2 with a major maturity QTL. A Genome-Wide Association Study (GWAS) of DT696 derivative lines from 72 crosses based on multi-environment FHB resistance, plant height, and maturity phenotypic data was conducted to improve the mapping resolution and further elucidate the genetic relationship of height and maturity with FHB resistance. The Global Tetraploid Wheat Collection (GTWC) was exploited to identify durum wheat lines with DT696 allele and additional recombination events. The 5A2 QTL was confirmed in the derivatives, suggesting the expression stability of the 5A2 QTL in various genetic backgrounds. The GWAS led to an improved mapping resolution rendering the 5A2 interval 10 Mbp shorter than the bi-parental QTL mapping interval. Haplotype analysis using SNPs within the 5A2 QTL applied to the GTWC identified novel haplotypes and recombination breakpoints, which could be exploited for further improvement of the mapping resolution. This study suggested that GWAS of derivative breeding lines is a credible strategy for improving mapping resolution.
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Affiliation(s)
- Ehsan Sari
- Aquatic and Crop Resource Development Centre, National Research Council, Saskatoon, SK, Canada.,Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, Canada
| | - Ron E Knox
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, Swift Current, SK, Canada.
| | - Yuefeng Ruan
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, Swift Current, SK, Canada.
| | - Maria Antonia Henriquez
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB, Canada
| | - Santosh Kumar
- Brandon Research and Development Centre, Agriculture and Agri-Food Canada, Brandon, MB, Canada
| | - Andrew J Burt
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Richard D Cuthbert
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, Swift Current, SK, Canada
| | - David J Konkin
- Aquatic and Crop Resource Development Centre, National Research Council, Saskatoon, SK, Canada
| | - Sean Walkowiak
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, Canada.,Canadian Grain Commission, Winnipeg, MB, Canada
| | - Heather L Campbell
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, Swift Current, SK, Canada
| | - Asheesh K Singh
- Department of Agronomy, Iowa State University, Ames, Iowa, United States of America
| | - Jay Ross
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, Swift Current, SK, Canada
| | - Prabhath Lokuruge
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, Swift Current, SK, Canada
| | - Emma Hsueh
- Aquatic and Crop Resource Development Centre, National Research Council, Saskatoon, SK, Canada
| | - Kerry Boyle
- Aquatic and Crop Resource Development Centre, National Research Council, Saskatoon, SK, Canada
| | - Christine Sidebottom
- Aquatic and Crop Resource Development Centre, National Research Council, Saskatoon, SK, Canada
| | - Janet Condie
- Aquatic and Crop Resource Development Centre, National Research Council, Saskatoon, SK, Canada
| | - Shawn Yates
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, Swift Current, SK, Canada
| | - Curtis J Pozniak
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, Canada
| | - Pierre R Fobert
- Aquatic and Crop Resource Development Centre, National Research Council, Ottawa, ON, Canada
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3
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Guan P, Di N, Mu Q, Shen X, Wang Y, Wang X, Yu K, Song W, Chen Y, Xin M, Hu Z, Guo W, Yao Y, Ni Z, Sun Q, Peng H. Use of near-isogenic lines to precisely map and validate a major QTL for grain weight on chromosome 4AL in bread wheat (Triticum aestivum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:2367-2379. [PMID: 31119311 DOI: 10.1007/s00122-019-03359-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 05/08/2019] [Indexed: 06/09/2023]
Abstract
This study precisely mapped and validated a major quantitative trait locus (QTL) on chromosome 4AL for thousand-grain weight in wheat using multiple near-isogenic lines. Thousand-grain weight (TGW) is an essential yield component. Following the previous identification of a major QTL for TGW within the interval of 15.7 cM (92.7-108.4 cM) on chromosome 4AL using the Nongda3338 (ND3338)/Jingdong6 (JD6) doubled haploid population, the aim of this study was to perform more precise mapping and validate the genetic effect of the QTL. Multiple near-isogenic lines (NILs) were developed using ND3338 as the recurrent parent through marker-assisted selection. Based on five independent BC3F3:4 segregating populations derived from BC3F3 plants with different heterozygous segments for the target QTL site and the results of genotyping analysis performed using the Wheat660 K SNP array, it was possible to delimit the QTL region to a physical interval of approximately 6.5 Mb (677.11-683.61 Mb, IWGSC Ref Seq v1.0). Field trials across multiple environments showed that NILsJD6 had a consistent effect on increasing the TGW by 5.16-27.48% and decreasing the grain number per spike (GNS) by 3.98-32.91% compared to the corresponding NILsND3338, which exhibited locus-specific TGW-GNS trade-offs. Moreover, by using RNA sequencing (RNA-Seq) of whole grains at 10 days after pollination stage of multiple NILs, we found that differentially expressed genes between the NIL pairs were significantly enriched for cell cycle and the replication of chromosome-related genes, hence affecting cell division and cell proliferation. Overall, our results provide a basis for map-based cloning of the major QTL and determining the mechanisms underlying TGW-GNS trade-offs in wheat, which would help to fine-tune these two components and maximize the grain yield for breeders.
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Affiliation(s)
- Panfeng Guan
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement/College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
- College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Na Di
- College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Qing Mu
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement/College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Xueyi Shen
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement/College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Yongfa Wang
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement/College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Xiaobo Wang
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement/College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Kuohai Yu
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement/College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Wanjun Song
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement/College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Yongming Chen
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement/College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Mingming Xin
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement/College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Zhaorong Hu
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement/College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Weilong Guo
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement/College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Yingyin Yao
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement/College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Zhongfu Ni
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement/College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Qixin Sun
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement/College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Huiru Peng
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement/College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China.
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4
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Dvorak J, Wang L, Zhu T, Jorgensen CM, Luo MC, Deal KR, Gu YQ, Gill BS, Distelfeld A, Devos KM, Qi P, McGuire PE. Reassessment of the evolution of wheat chromosomes 4A, 5A, and 7B. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2018; 131:2451-2462. [PMID: 30141064 PMCID: PMC6208953 DOI: 10.1007/s00122-018-3165-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Accepted: 08/13/2018] [Indexed: 05/02/2023]
Abstract
Comparison of genome sequences of wild emmer wheat and Aegilops tauschii suggests a novel scenario of the evolution of rearranged wheat chromosomes 4A, 5A, and 7B. Past research suggested that wheat chromosome 4A was subjected to a reciprocal translocation T(4AL;5AL)1 that occurred in the diploid progenitor of the wheat A subgenome and to three major rearrangements that occurred in polyploid wheat: pericentric inversion Inv(4AS;4AL)1, paracentric inversion Inv(4AL;4AL)1, and reciprocal translocation T(4AL;7BS)1. Gene collinearity along the pseudomolecules of tetraploid wild emmer wheat (Triticum turgidum ssp. dicoccoides, subgenomes AABB) and diploid Aegilops tauschii (genomes DD) was employed to confirm these rearrangements and to analyze the breakpoints. The exchange of distal regions of chromosome arms 4AS and 4AL due to pericentric inversion Inv(4AS;4AL)1 was detected, and breakpoints were validated with an optical Bionano genome map. Both breakpoints contained satellite DNA. The breakpoints of reciprocal translocation T(4AL;7BS)1 were also found. However, the breakpoints that generated paracentric inversion Inv(4AL;4AL)1 appeared to be collocated with the 4AL breakpoints that had produced Inv(4AS;4AL)1 and T(4AL;7BS)1. Inv(4AS;4AL)1, Inv(4AL;4AL)1, and T(4AL;7BS)1 either originated sequentially, and Inv(4AL;4AL)1 was produced by recurrent chromosome breaks at the same breakpoints that generated Inv(4AS;4AL)1 and T(4AL;7BS)1, or Inv(4AS;4AL)1, Inv(4AL;4AL)1, and T(4AL;7BS)1 originated simultaneously. We prefer the latter hypothesis since it makes fewer assumptions about the sequence of events that produced these chromosome rearrangements.
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Affiliation(s)
- Jan Dvorak
- Department of Plant Sciences, University of California, Davis, CA USA
| | - Le Wang
- Department of Plant Sciences, University of California, Davis, CA USA
| | - Tingting Zhu
- Department of Plant Sciences, University of California, Davis, CA USA
| | - Chad M. Jorgensen
- Department of Plant Sciences, University of California, Davis, CA USA
| | - Ming-Cheng Luo
- Department of Plant Sciences, University of California, Davis, CA USA
| | - Karin R. Deal
- Department of Plant Sciences, University of California, Davis, CA USA
| | - Yong Q. Gu
- Crop Improvement and Genetics Research, USDA-ARS, Albany, CA USA
| | - Bikram S. Gill
- Department of Plant Pathology, Kansas State University, Manhattan, KS USA
| | - Assaf Distelfeld
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
| | - Katrien M. Devos
- Institute of Plant Breeding, Genetics and Genomics, Department of Crop and Soil Sciences, University of Georgia, Athens, GA USA
- Department of Plant Biology, University of Georgia, Athens, GA USA
| | - Peng Qi
- Institute of Plant Breeding, Genetics and Genomics, Department of Crop and Soil Sciences, University of Georgia, Athens, GA USA
- Department of Plant Biology, University of Georgia, Athens, GA USA
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5
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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 BIOTECHNOLOGY JOURNAL 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] [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.
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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
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Loginova DB, Silkova OG. The Genome of Bread Wheat Triticum aestivum L.: Unique Structural and Functional Properties. RUSS J GENET+ 2018. [DOI: 10.1134/s1022795418040105] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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7
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Jorgensen C, Luo MC, Ramasamy R, Dawson M, Gill BS, Korol AB, Distelfeld A, Dvorak J. A High-Density Genetic Map of Wild Emmer Wheat from the Karaca Dağ Region Provides New Evidence on the Structure and Evolution of Wheat Chromosomes. FRONTIERS IN PLANT SCIENCE 2017; 8:1798. [PMID: 29104581 PMCID: PMC5655018 DOI: 10.3389/fpls.2017.01798] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 10/03/2017] [Indexed: 05/05/2023]
Abstract
Wild emmer (Triticum turgidum ssp. dicoccoides) is a progenitor of all cultivated wheat grown today. It has been hypothesized that emmer was domesticated in the Karaca Dağ region in southeastern Turkey. A total of 445 recombinant inbred lines of T. turgidum ssp. durum cv. 'Langdon' x wild emmer accession PI 428082 from this region was developed and genotyped with the Illumina 90K single nucleotide polymorphism Infinium assay. A genetic map comprising 2,650 segregating markers was constructed. The order of the segregating markers and an additional 8,264 co-segregating markers in the Aegilops tauschii reference genome sequence was used to compare synteny of the tetraploid wheat with the Brachypodium distachyon, rice, and sorghum. These comparisons revealed the presence of 15 structural chromosome rearrangements, in addition to the already known 4A-5A-7B rearrangements. The most common type was an intra-chromosomal translocation in which the translocated segment was short and was translocated only a short distance along the chromosome. A large reciprocal translocation, one small non-reciprocal translocation, and three large and one small paracentric inversions were also discovered. The use of inversions for a phylogeny reconstruction in the Triticum-Aegilops alliance was illustrated. The genetic map was inconsistent with the current model of evolution of the rearranged chromosomes 4A-5A-7B. Genetic diversity in the rearranged chromosome 4A showed that the rearrangements might have been contemporary with wild emmer speciation. A selective sweep was found in the centromeric region of chromosome 4A in Karaca Dağ wild emmer but not in 4A of T. aestivum. The absence of diversity from a large portion of chromosome 4A of wild emmer, believed to be ancestral to all domesticated wheat, is puzzling.
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Affiliation(s)
- Chad Jorgensen
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States
| | - Ming-Cheng Luo
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States
| | - Ramesh Ramasamy
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States
| | - Mathew Dawson
- Department of Statistics, University of California, Davis, Davis, CA, United States
| | - Bikram S. Gill
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States
| | | | - Assaf Distelfeld
- Institute for Cereal Crops Improvement, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Jan Dvorak
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States
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Shorinola O, Balcárková B, Hyles J, Tibbits JFG, Hayden MJ, Holušova K, Valárik M, Distelfeld A, Torada A, Barrero JM, Uauy C. Haplotype Analysis of the Pre-harvest Sprouting Resistance Locus Phs-A1 Reveals a Causal Role of TaMKK3-A in Global Germplasm. FRONTIERS IN PLANT SCIENCE 2017; 8:1555. [PMID: 28955352 PMCID: PMC5602128 DOI: 10.3389/fpls.2017.01555] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 08/25/2017] [Indexed: 05/03/2023]
Abstract
Pre-harvest sprouting (PHS) is an important cause of quality loss in many cereal crops and is particularly prevalent and damaging in wheat. Resistance to PHS is therefore a valuable target trait in many breeding programs. The Phs-A1 locus on wheat chromosome arm 4AL has been consistently shown to account for a significant proportion of natural variation to PHS in diverse mapping populations. However, the deployment of sprouting resistance is confounded by the fact that different candidate genes, including the tandem duplicated Plasma Membrane 19 (PM19) genes and the mitogen-activated protein kinase kinase 3 (TaMKK3-A) gene, have been proposed to underlie Phs-A1. To further define the Phs-A1 locus, we constructed a physical map across this interval in hexaploid and tetraploid wheat. We established close proximity of the proposed candidate genes which are located within a 1.2 Mb interval. Genetic characterization of diverse germplasm used in previous genetic mapping studies suggests that TaMKK3-A, and not PM19, is the major gene underlying the Phs-A1 effect in European, North American, Australian and Asian germplasm. We identified the non-dormant TaMKK3-A allele at low frequencies within the A-genome diploid progenitor Triticum urartu genepool, and show an increase in the allele frequency in modern varieties. In United Kingdom varieties, the frequency of the dormant TaMKK3-A allele was significantly higher in bread-making quality varieties compared to feed and biscuit-making cultivars. Analysis of exome capture data from 58 diverse hexaploid wheat accessions identified fourteen haplotypes across the extended Phs-A1 locus and four haplotypes for TaMKK3-A. Analysis of these haplotypes in a collection of United Kingdom and Australian cultivars revealed distinct major dormant and non-dormant Phs-A1 haplotypes in each country, which were either rare or absent in the opposing germplasm set. The diagnostic markers and haplotype information reported in the study will help inform the choice of germplasm and breeding strategies for the deployment of Phs-A1 resistance into breeding germplasm.
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Affiliation(s)
| | - Barbara Balcárková
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural ResearchOlomouc, Czechia
| | - Jessica Hyles
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Agriculture and Food, CanberraACT, Australia
| | - Josquin F. G. Tibbits
- Department of Economic Development, Jobs, Transport and Resources, Centre for AgriBioscience, BundooraVIC, Australia
| | - Matthew J. Hayden
- Department of Economic Development, Jobs, Transport and Resources, Centre for AgriBioscience, BundooraVIC, Australia
| | - Katarina Holušova
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural ResearchOlomouc, Czechia
| | - Miroslav Valárik
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural ResearchOlomouc, Czechia
| | - Assaf Distelfeld
- The Institute for Cereal Crop Improvement, Tel Aviv UniversityTel Aviv, Israel
| | | | - Jose M. Barrero
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Agriculture and Food, CanberraACT, Australia
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