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Hussain B, Akpınar BA, Alaux M, Algharib AM, Sehgal D, Ali Z, Aradottir GI, Batley J, Bellec A, Bentley AR, Cagirici HB, Cattivelli L, Choulet F, Cockram J, Desiderio F, Devaux P, Dogramaci M, Dorado G, Dreisigacker S, Edwards D, El-Hassouni K, Eversole K, Fahima T, Figueroa M, Gálvez S, Gill KS, Govta L, Gul A, Hensel G, Hernandez P, Crespo-Herrera LA, Ibrahim A, Kilian B, Korzun V, Krugman T, Li Y, Liu S, Mahmoud AF, Morgounov A, Muslu T, Naseer F, Ordon F, Paux E, Perovic D, Reddy GVP, Reif JC, Reynolds M, Roychowdhury R, Rudd J, Sen TZ, Sukumaran S, Ozdemir BS, Tiwari VK, Ullah N, Unver T, Yazar S, Appels R, Budak H. Capturing Wheat Phenotypes at the Genome Level. FRONTIERS IN PLANT SCIENCE 2022; 13:851079. [PMID: 35860541 PMCID: PMC9289626 DOI: 10.3389/fpls.2022.851079] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Accepted: 05/19/2022] [Indexed: 06/15/2023]
Abstract
Recent technological advances in next-generation sequencing (NGS) technologies have dramatically reduced the cost of DNA sequencing, allowing species with large and complex genomes to be sequenced. Although bread wheat (Triticum aestivum L.) is one of the world's most important food crops, efficient exploitation of molecular marker-assisted breeding approaches has lagged behind that achieved in other crop species, due to its large polyploid genome. However, an international public-private effort spanning 9 years reported over 65% draft genome of bread wheat in 2014, and finally, after more than a decade culminated in the release of a gold-standard, fully annotated reference wheat-genome assembly in 2018. Shortly thereafter, in 2020, the genome of assemblies of additional 15 global wheat accessions was released. As a result, wheat has now entered into the pan-genomic era, where basic resources can be efficiently exploited. Wheat genotyping with a few hundred markers has been replaced by genotyping arrays, capable of characterizing hundreds of wheat lines, using thousands of markers, providing fast, relatively inexpensive, and reliable data for exploitation in wheat breeding. These advances have opened up new opportunities for marker-assisted selection (MAS) and genomic selection (GS) in wheat. Herein, we review the advances and perspectives in wheat genetics and genomics, with a focus on key traits, including grain yield, yield-related traits, end-use quality, and resistance to biotic and abiotic stresses. We also focus on reported candidate genes cloned and linked to traits of interest. Furthermore, we report on the improvement in the aforementioned quantitative traits, through the use of (i) clustered regularly interspaced short-palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9)-mediated gene-editing and (ii) positional cloning methods, and of genomic selection. Finally, we examine the utilization of genomics for the next-generation wheat breeding, providing a practical example of using in silico bioinformatics tools that are based on the wheat reference-genome sequence.
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Affiliation(s)
- Babar Hussain
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
- Department of Biotechnology, Faculty of Life Sciences, University of Central Punjab, Lahore, Pakistan
| | | | - Michael Alaux
- Université Paris-Saclay, INRAE, URGI, Versailles, France
| | - Ahmed M. Algharib
- Department of Environment and Bio-Agriculture, Faculty of Agriculture, Al-Azhar University, Cairo, Egypt
| | - Deepmala Sehgal
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - Zulfiqar Ali
- Institute of Plant Breeding and Biotechnology, MNS University of Agriculture, Multan, Pakistan
| | - Gudbjorg I. Aradottir
- Department of Pathology, The National Institute of Agricultural Botany, Cambridge, United Kingdom
| | - Jacqueline Batley
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, WA, Australia
| | - Arnaud Bellec
- French Plant Genomic Resource Center, INRAE-CNRGV, Castanet Tolosan, France
| | - Alison R. Bentley
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - Halise B. Cagirici
- Crop Improvement and Genetics Research, USDA, Agricultural Research Service, Albany, CA, United States
| | - Luigi Cattivelli
- Council for Agricultural Research and Economics-Research Centre for Genomics and Bioinformatics, Fiorenzuola d’Arda, Italy
| | - Fred Choulet
- French National Research Institute for Agriculture, Food and the Environment, INRAE, GDEC, Clermont-Ferrand, France
| | - James Cockram
- The John Bingham Laboratory, The National Institute of Agricultural Botany, Cambridge, United Kingdom
| | - Francesca Desiderio
- Council for Agricultural Research and Economics-Research Centre for Genomics and Bioinformatics, Fiorenzuola d’Arda, Italy
| | - Pierre Devaux
- Research & Innovation, Florimond Desprez Group, Cappelle-en-Pévèle, France
| | - Munevver Dogramaci
- USDA, Agricultural Research Service, Edward T. Schafer Agricultural Research Center, Fargo, ND, United States
| | - Gabriel Dorado
- Department of Bioquímica y Biología Molecular, Campus Rabanales C6-1-E17, Campus de Excelencia Internacional Agroalimentario (ceiA3), Universidad de Córdoba, Córdoba, Spain
| | | | - David Edwards
- University of Western Australia, Perth, WA, Australia
| | - Khaoula El-Hassouni
- State Plant Breeding Institute, The University of Hohenheim, Stuttgart, Germany
| | - Kellye Eversole
- International Wheat Genome Sequencing Consortium (IWGSC), Bethesda, MD, United States
| | - Tzion Fahima
- Institute of Evolution and Department of Environmental and Evolutionary Biology, University of Haifa, Haifa, Israel
| | - Melania Figueroa
- Commonwealth Scientific and Industrial Research Organization, Agriculture and Food, Canberra, ACT, Australia
| | - Sergio Gálvez
- Department of Languages and Computer Science, ETSI Informática, Campus de Teatinos, Universidad de Málaga, Andalucía Tech, Málaga, Spain
| | - Kulvinder S. Gill
- Department of Crop Science, Washington State University, Pullman, WA, United States
| | - Liubov Govta
- Institute of Evolution and Department of Environmental and Evolutionary Biology, University of Haifa, Haifa, Israel
| | - Alvina Gul
- Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Goetz Hensel
- Center of Plant Genome Engineering, Heinrich-Heine-Universität, Düsseldorf, Germany
- Division of Molecular Biology, Centre of Region Haná for Biotechnological and Agriculture Research, Czech Advanced Technology and Research Institute, Palacký University, Olomouc, Czechia
| | - Pilar Hernandez
- Institute for Sustainable Agriculture (IAS-CSIC), Consejo Superior de Investigaciones Científicas (CSIC), Córdoba, Spain
| | | | - Amir Ibrahim
- Crop and Soil Science, Texas A&M University, College Station, TX, United States
| | | | | | - Tamar Krugman
- Institute of Evolution and Department of Environmental and Evolutionary Biology, University of Haifa, Haifa, Israel
| | - Yinghui Li
- Institute of Evolution and Department of Environmental and Evolutionary Biology, University of Haifa, Haifa, Israel
| | - Shuyu Liu
- Crop and Soil Science, Texas A&M University, College Station, TX, United States
| | - Amer F. Mahmoud
- Department of Plant Pathology, Faculty of Agriculture, Assiut University, Assiut, Egypt
| | - Alexey Morgounov
- Food and Agriculture Organization of the United Nations, Riyadh, Saudi Arabia
| | - Tugdem Muslu
- Molecular Biology, Genetics and Bioengineering, Sabanci University, Istanbul, Turkey
| | - Faiza Naseer
- Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Frank Ordon
- Institute for Resistance Research and Stress Tolerance, Julius Kühn Institute, Quedlinburg, Germany
| | - Etienne Paux
- French National Research Institute for Agriculture, Food and the Environment, INRAE, GDEC, Clermont-Ferrand, France
| | - Dragan Perovic
- Institute for Resistance Research and Stress Tolerance, Julius Kühn Institute, Quedlinburg, Germany
| | - Gadi V. P. Reddy
- USDA-Agricultural Research Service, Southern Insect Management Research Unit, Stoneville, MS, United States
| | - Jochen Christoph Reif
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Matthew Reynolds
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - Rajib Roychowdhury
- Institute of Evolution and Department of Environmental and Evolutionary Biology, University of Haifa, Haifa, Israel
| | - Jackie Rudd
- Crop and Soil Science, Texas A&M University, College Station, TX, United States
| | - Taner Z. Sen
- Crop Improvement and Genetics Research, USDA, Agricultural Research Service, Albany, CA, United States
| | | | | | | | - Naimat Ullah
- Institute of Biological Sciences (IBS), Gomal University, D. I. Khan, Pakistan
| | - Turgay Unver
- Ficus Biotechnology, Ostim Teknopark, Ankara, Turkey
| | - Selami Yazar
- General Directorate of Research, Ministry of Agriculture, Ankara, Turkey
| | | | - Hikmet Budak
- Montana BioAgriculture, Inc., Missoula, MT, United States
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Gogolev YV, Ahmar S, Akpinar BA, Budak H, Kiryushkin AS, Gorshkov VY, Hensel G, Demchenko KN, Kovalchuk I, Mora-Poblete F, Muslu T, Tsers ID, Yadav NS, Korzun V. OMICs, Epigenetics, and Genome Editing Techniques for Food and Nutritional Security. PLANTS (BASEL, SWITZERLAND) 2021; 10:1423. [PMID: 34371624 PMCID: PMC8309286 DOI: 10.3390/plants10071423] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 06/30/2021] [Accepted: 07/07/2021] [Indexed: 12/22/2022]
Abstract
The incredible success of crop breeding and agricultural innovation in the last century greatly contributed to the Green Revolution, which significantly increased yields and ensures food security, despite the population explosion. However, new challenges such as rapid climate change, deteriorating soil, and the accumulation of pollutants require much faster responses and more effective solutions that cannot be achieved through traditional breeding. Further prospects for increasing the efficiency of agriculture are undoubtedly associated with the inclusion in the breeding strategy of new knowledge obtained using high-throughput technologies and new tools in the future to ensure the design of new plant genomes and predict the desired phenotype. This article provides an overview of the current state of research in these areas, as well as the study of soil and plant microbiomes, and the prospective use of their potential in a new field of microbiome engineering. In terms of genomic and phenomic predictions, we also propose an integrated approach that combines high-density genotyping and high-throughput phenotyping techniques, which can improve the prediction accuracy of quantitative traits in crop species.
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Affiliation(s)
- Yuri V. Gogolev
- Federal Research Center Kazan Scientific Center of Russian Academy of Sciences, Kazan Institute of Biochemistry and Biophysics, 420111 Kazan, Russia;
- Federal Research Center Kazan Scientific Center of Russian Academy of Sciences, Laboratory of Plant Infectious Diseases, 420111 Kazan, Russia;
| | - Sunny Ahmar
- Institute of Biological Sciences, University of Talca, 1 Poniente 1141, Talca 3460000, Chile; (S.A.); (F.M.-P.)
| | | | - Hikmet Budak
- Montana BioAg Inc., Missoula, MT 59802, USA; (B.A.A.); (H.B.)
| | - Alexey S. Kiryushkin
- Laboratory of Cellular and Molecular Mechanisms of Plant Development, Komarov Botanical Institute of the Russian Academy of Sciences, 197376 Saint Petersburg, Russia; (A.S.K.); (K.N.D.)
| | - Vladimir Y. Gorshkov
- Federal Research Center Kazan Scientific Center of Russian Academy of Sciences, Kazan Institute of Biochemistry and Biophysics, 420111 Kazan, Russia;
- Federal Research Center Kazan Scientific Center of Russian Academy of Sciences, Laboratory of Plant Infectious Diseases, 420111 Kazan, Russia;
| | - Goetz Hensel
- Centre for Plant Genome Engineering, Institute of Plant Biochemistry, Heinrich-Heine-University, 40225 Dusseldorf, Germany;
- Centre of the Region Haná for Biotechnological and Agricultural Research, Czech Advanced Technology and Research Institute, Palacký University Olomouc, 78371 Olomouc, Czech Republic
| | - Kirill N. Demchenko
- Laboratory of Cellular and Molecular Mechanisms of Plant Development, Komarov Botanical Institute of the Russian Academy of Sciences, 197376 Saint Petersburg, Russia; (A.S.K.); (K.N.D.)
| | - Igor Kovalchuk
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada; (I.K.); (N.S.Y.)
| | - Freddy Mora-Poblete
- Institute of Biological Sciences, University of Talca, 1 Poniente 1141, Talca 3460000, Chile; (S.A.); (F.M.-P.)
| | - Tugdem Muslu
- Faculty of Engineering and Natural Sciences, Sabanci University, 34956 Istanbul, Turkey;
| | - Ivan D. Tsers
- Federal Research Center Kazan Scientific Center of Russian Academy of Sciences, Laboratory of Plant Infectious Diseases, 420111 Kazan, Russia;
| | - Narendra Singh Yadav
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada; (I.K.); (N.S.Y.)
| | - Viktor Korzun
- Federal Research Center Kazan Scientific Center of Russian Academy of Sciences, Laboratory of Plant Infectious Diseases, 420111 Kazan, Russia;
- KWS SAAT SE & Co. KGaA, Grimsehlstr. 31, 37555 Einbeck, Germany
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Said M, Holušová K, Farkas A, Ivanizs L, Gaál E, Cápal P, Abrouk M, Martis-Thiele MM, Kalapos B, Bartoš J, Friebe B, Doležel J, Molnár I. Development of DNA Markers From Physically Mapped Loci in Aegilops comosa and Aegilops umbellulata Using Single-Gene FISH and Chromosome Sequences. FRONTIERS IN PLANT SCIENCE 2021; 12:689031. [PMID: 34211490 PMCID: PMC8240756 DOI: 10.3389/fpls.2021.689031] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 05/19/2021] [Indexed: 05/31/2023]
Abstract
Breeding of agricultural crops adapted to climate change and resistant to diseases and pests is hindered by a limited gene pool because of domestication and thousands of years of human selection. One way to increase genetic variation is chromosome-mediated gene transfer from wild relatives by cross hybridization. In the case of wheat (Triticum aestivum), the species of genus Aegilops are a particularly attractive source of new genes and alleles. However, during the evolution of the Aegilops and Triticum genera, diversification of the D-genome lineage resulted in the formation of diploid C, M, and U genomes of Aegilops. The extent of structural genome alterations, which accompanied their evolution and speciation, and the shortage of molecular tools to detect Aegilops chromatin hamper gene transfer into wheat. To investigate the chromosome structure and help develop molecular markers with a known physical position that could improve the efficiency of the selection of desired introgressions, we developed single-gene fluorescence in situ hybridization (FISH) maps for M- and U-genome progenitors, Aegilops comosa and Aegilops umbellulata, respectively. Forty-three ortholog genes were located on 47 loci in Ae. comosa and on 52 loci in Ae. umbellulata using wheat cDNA probes. The results obtained showed that M-genome chromosomes preserved collinearity with those of wheat, excluding 2 and 6M containing an intrachromosomal rearrangement and paracentric inversion of 6ML, respectively. While Ae. umbellulata chromosomes 1, 3, and 5U maintained collinearity with wheat, structural reorganizations in 2, 4, 6, and 7U suggested a similarity with the C genome of Aegilops markgrafii. To develop molecular markers with exact physical positions on chromosomes of Aegilops, the single-gene FISH data were validated in silico using DNA sequence assemblies from flow-sorted M- and U-genome chromosomes. The sequence similarity search of cDNA sequences confirmed 44 out of the 47 single-gene loci in Ae. comosa and 40 of the 52 map positions in Ae. umbellulata. Polymorphic regions, thus, identified enabled the development of molecular markers, which were PCR validated using wheat-Aegilops disomic chromosome addition lines. The single-gene FISH-based approach allowed the development of PCR markers specific for cytogenetically mapped positions on Aegilops chromosomes, substituting as yet unavailable segregating map. The new knowledge and resources will support the efforts for the introgression of Aegilops genes into wheat and their cloning.
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Affiliation(s)
- Mahmoud Said
- Institute of Experimental Botany of the Czech Academy of Sciences, Center of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czechia
- Agricultural Research Centre, Field Crops Research Institute, Cairo, Egypt
| | - Katerina Holušová
- Institute of Experimental Botany of the Czech Academy of Sciences, Center of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czechia
| | - András Farkas
- ELKH Centre for Agricultural Research, Agricultural Institute, Martonvásár, Hungary
| | - László Ivanizs
- ELKH Centre for Agricultural Research, Agricultural Institute, Martonvásár, Hungary
| | - Eszter Gaál
- ELKH Centre for Agricultural Research, Agricultural Institute, Martonvásár, Hungary
| | - Petr Cápal
- Institute of Experimental Botany of the Czech Academy of Sciences, Center of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czechia
| | - Michael Abrouk
- Biological and Environmental Science and Engineering Division, Center for Desert Agriculture, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Mihaela M. Martis-Thiele
- NBIS (National Bioinformatics Infrastructure Sweden, Science for Life Laboratory), Division of Cell Biology, Department of Clinical and Experimental Medicine, Faculty of Medicine and Health Sciences, Linköping University, Linköping, Sweden
| | - Balázs Kalapos
- ELKH Centre for Agricultural Research, Agricultural Institute, Martonvásár, Hungary
| | - Jan Bartoš
- Institute of Experimental Botany of the Czech Academy of Sciences, Center of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czechia
| | - Bernd Friebe
- Wheat Genetics Resource Center, Kansas State University, Manhattan, KS, United States
| | - Jaroslav Doležel
- Institute of Experimental Botany of the Czech Academy of Sciences, Center of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czechia
| | - István Molnár
- Institute of Experimental Botany of the Czech Academy of Sciences, Center of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czechia
- ELKH Centre for Agricultural Research, Agricultural Institute, Martonvásár, Hungary
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Zwyrtková J, Šimková H, Doležel J. Chromosome genomics uncovers plant genome organization and function. Biotechnol Adv 2020; 46:107659. [PMID: 33259907 DOI: 10.1016/j.biotechadv.2020.107659] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 10/10/2020] [Accepted: 11/13/2020] [Indexed: 02/07/2023]
Abstract
The identification of causal genomic loci and their interactions underlying various traits in plants has been greatly aided by progress in understanding the organization of the nuclear genome. This provides clues to the responses of plants to environmental stimuli at the molecular level. Apart from other uses, these insights are needed to fully explore the potential of new breeding techniques that rely on genome editing. However, genome analysis and sequencing is not straightforward in the many agricultural crops and their wild relatives that possess large and complex genomes. Chromosome genomics streamlines this task by dissecting the genome to single chromosomes whose DNA is then used instead of nuclear DNA. This results in a massive and lossless reduction in DNA sample complexity, reduces the time and cost of the experiment, and simplifies data interpretation. Flow cytometric sorting of condensed mitotic chromosomes makes it possible to purify single chromosomes in large quantities, and as the DNA remains intact this process can be coupled successfully with many techniques in molecular biology and genomics. Since the first experiments with flow cytometric sorting in the late 1980s, numerous applications have been developed, and chromosome genomics has been having a significant impact in many areas of research, including the sequencing of complex genomes of important crops and gene cloning. This review discusses these applications, describes their contribution to advancements in plant genome analysis and gene cloning, and outlines future directions.
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Affiliation(s)
- Jana Zwyrtková
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-77900 Olomouc, 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, CZ-77900 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, CZ-77900 Olomouc, Czech Republic.
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Scarrow M, Wang Y, Sun G. Molecular regulatory mechanisms underlying the adaptability of polyploid plants. Biol Rev Camb Philos Soc 2020; 96:394-407. [PMID: 33098261 DOI: 10.1111/brv.12661] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 10/13/2020] [Accepted: 10/15/2020] [Indexed: 12/11/2022]
Abstract
Polyploidization influences the genetic composition and gene expression of an organism. This multi-level genetic change allows the formation of new regulatory pathways leading to increased adaptability. Although both forms of polyploidization provide advantages, autopolyploids were long thought to have little impact on plant divergence compared to allopolyploids due to their formation through genome duplication only, rather than in combination with hybridization. Recent advances have begun to clarify the molecular regulatory mechanisms such as microRNAs, alternative splicing, RNA-binding proteins, histone modifications, chromatin remodelling, DNA methylation, and N6 -methyladenosine (m6A) RNA methylation underlying the evolutionary success of polyploids. Such research is expanding our understanding of the evolutionary adaptability of polyploids and the regulatory pathways that allow adaptive plasticity in a variety of plant species. Herein we review the roles of individual molecular regulatory mechanisms and their potential synergistic pathways underlying plant evolution and adaptation. Notably, increasing interest in m6A methylation has provided a new component in potential mechanistic coordination that is still predominantly unexplored. Future research should attempt to identify and functionally characterize the evolutionary impact of both individual and synergistic pathways in polyploid plant species.
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Affiliation(s)
- Margaret Scarrow
- Department of Biology, Saint Mary's University, Halifax, Nova Scotia, B3H 3C3, Canada
| | - Yiling Wang
- College of Life Science, Shanxi Normal University, Linfen, Shanxi, 041000, China
| | - Genlou Sun
- Department of Biology, Saint Mary's University, Halifax, Nova Scotia, B3H 3C3, Canada
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Highly efficient synchronization of sheep skin fibroblasts at G2/M phase and isolation of sheep Y chromosomes by flow cytometric sorting. Sci Rep 2020; 10:9933. [PMID: 32555328 PMCID: PMC7303189 DOI: 10.1038/s41598-020-66905-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Accepted: 05/29/2020] [Indexed: 01/08/2023] Open
Abstract
At present, based on whole genome sequencing, sequences and genes annotation of the sheep (Ovis aries) Y chromosome are still absent. The isolation of Y chromosomes followed by sequencing has been approved as an effective approach to analyze this complex chromosome in other species. In this study, we established a highly efficient synchronization method for G2/M phase of sheep fibroblasts, which was successfully applied to flow-sorting chromosomes of sheep, with a focus on isolation and sequencing of the ovine Y chromosome. The isolated (~80,000) Y chromosomes were verified by fluorescence quantitative real-time polymerase chain reaction, further confirmed by fluorescence in situ hybridization, and amplified by the MALBAC method before next-generation sequencing. The sequence results indicated that 68.90% of reads were Y chromosome-related sequences as they are homologous to the bovine Y chromosome. The remaining 31.1% of reads were aligned to the sheep reference genome, including 13.57% reads to chromosome X and 6.68% to chromosome 17. Importantly, the paired-end reads that are properly aligned to the bovine Y sequence assembly accounted for 46.49%, indicating the success in the ovine Y chromosome isolation and the high quality of the Y chromosome sequences. This study not only set up a foundation for future sequencing, assembly and annotation of the ovine Y chromosome, but also provide a validated approach to overcoming difficulties in sequencing Y chromosome in other mammalian species.
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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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8
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He Q, Wang X, He L, Yang L, Wang S, Bi Y. Alternative respiration pathway is involved in the response of highland barley to salt stress. PLANT CELL REPORTS 2019; 38:295-309. [PMID: 30542981 DOI: 10.1007/s00299-018-2366-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 12/05/2018] [Indexed: 06/09/2023]
Abstract
Alternative respiration pathway is involved in the response of highland barley to salt stress. The response of two barley seedlings to salt stress was investigated. Results showed that the growth of highland barley (Kunlun 14) and barley (Ganpi 6) had no obvious difference under low concentrations (50, 100 and 200 mM) of NaCl treatment. However, high concentrations of NaCl treatment (300 and 400 mM) severely affected the growth of two barley cultivars. Under 300 mM NaCl treatment, the fresh weight, relative water content (RWC), pigments and K+ content reduced more in Ganpi 6 than in Kunlun 14. In contrast, the electrolyte leakage and the content of MDA, Na+, H2O2 and O2- increased more in Ganpi 6 than in Kunlun 14. The gene expression of AOX1a, HvNHX1, HvNHX3, HvHVP1, HvHVA, H+-ATPase, the alternative respiration capacity (Valt) and the enzymatic activity of SOD, POD, CAT, APX and H+-ATPase increased more in Kunlun14 than in Ganpi6 under 300 mM NaCl treatment, whereas the cytochrome respiration capacity (Vcyt) decreased similarly in both barley cultivars. Western blot analysis showed that the protein level of the alternative oxidase (AOX) increased more in Kunlun 14 than in Ganpi 6 under 300 mM NaCl treatment. Inhibition of the alternative respiration by salicylhydroxamic acid (SHAM) decreased the fresh weight, K+ content, Valt, H+-ATPase activity and the gene expression of AOX1a, HvNHX1, HvNHX3, HvHVP1, HvHVA, H+-ATPase, but increased the electrolyte leakage, MDA and Na+ content in both cultivars under 300 mM NaCl treatment. In short, alternative respiration is involved in the tolerance of highland barley to salt stress.
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Affiliation(s)
- Qiang He
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, People's Republic of China
| | - Xiaomin Wang
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, People's Republic of China
| | - Li He
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, People's Republic of China
| | - Lei Yang
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, People's Republic of China
| | - Shengwang Wang
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, People's Republic of China
| | - Yurong Bi
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, People's Republic of China.
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9
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Akpinar BA, Biyiklioglu S, Alptekin B, Havránková M, Vrána J, Doležel J, Distelfeld A, Hernandez P, Budak H. Chromosome-based survey sequencing reveals the genome organization of wild wheat progenitor Triticum dicoccoides. PLANT BIOTECHNOLOGY JOURNAL 2018; 16:2077-2087. [PMID: 29729062 PMCID: PMC6230948 DOI: 10.1111/pbi.12940] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 04/11/2018] [Accepted: 04/20/2018] [Indexed: 05/20/2023]
Abstract
Wild emmer wheat (Triticum turgidum ssp. dicoccoides) is the progenitor of wheat. We performed chromosome-based survey sequencing of the 14 chromosomes, examining repetitive sequences, protein-coding genes, miRNA/target pairs and tRNA genes, as well as syntenic relationships with related grasses. We found considerable differences in the content and distribution of repetitive sequences between the A and B subgenomes. The gene contents of individual chromosomes varied widely, not necessarily correlating with chromosome size. We catalogued candidate agronomically important loci, along with new alleles and flanking sequences that can be used to design exome sequencing. Syntenic relationships and virtual gene orders revealed several small-scale evolutionary rearrangements, in addition to providing evidence for the 4AL-5AL-7BS translocation in wild emmer wheat. Chromosome-based sequence assemblies contained five novel miRNA families, among 59 families putatively encoded in the entire genome which provide insight into the domestication of wheat and an overview of the genome content and organization.
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Affiliation(s)
- Bala Ani Akpinar
- Department of Plant Sciences and Plant PathologyCereal Genomics LabMontana State UniversityBozemanMTUSA
| | - Sezgi Biyiklioglu
- Department of Plant Sciences and Plant PathologyCereal Genomics LabMontana State UniversityBozemanMTUSA
| | - Burcu Alptekin
- Department of Plant Sciences and Plant PathologyCereal Genomics LabMontana State UniversityBozemanMTUSA
| | - Miroslava Havránková
- Centre of the Region Haná for Biotechnological and Agricultural ResearchInstitute of Experimental BotanyOlomoucCzech Republic
| | - Jan Vrána
- 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
| | - Assaf Distelfeld
- Department of Molecular Biology and Ecology of PlantsFaculty of Life SciencesTel Aviv UniversityTel AvivIsrael
| | - Pilar Hernandez
- Instituto de Agricultura Sostenible (IAS)Consejo Superior de Investigaciones Científicas (CSIC)CordobaSpain
| | - The IWGSC
- International Wheat Genome Sequencing ConsortiumBethesdaMDUSA
| | - Hikmet Budak
- Department of Plant Sciences and Plant PathologyCereal Genomics LabMontana State UniversityBozemanMTUSA
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10
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Complete chloroplast genome sequence and comparative analysis of loblolly pine (Pinus taeda L.) with related species. PLoS One 2018; 13:e0192966. [PMID: 29596414 PMCID: PMC5875761 DOI: 10.1371/journal.pone.0192966] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 02/01/2018] [Indexed: 12/14/2022] Open
Abstract
Pinaceae, the largest family of conifers, has a diversified organization of chloroplast (cp) genomes with two typical highly reduced inverted repeats (IRs). In the current study, we determined the complete sequence of the cp genome of an economically and ecologically important conifer tree, the loblolly pine (Pinus taeda L.), using Illumina paired-end sequencing and compared the sequence with those of other pine species. The results revealed a genome size of 121,531 base pairs (bp) containing a pair of 830-bp IR regions, distinguished by a small single copy (42,258 bp) and large single copy (77,614 bp) region. The chloroplast genome of P. taeda encodes 120 genes, comprising 81 protein-coding genes, four ribosomal RNA genes, and 35 tRNA genes, with 151 randomly distributed microsatellites. Approximately 6 palindromic, 34 forward, and 22 tandem repeats were found in the P. taeda cp genome. Whole cp genome comparison with those of other Pinus species exhibited an overall high degree of sequence similarity, with some divergence in intergenic spacers. Higher and lower numbers of indels and single-nucleotide polymorphism substitutions were observed relative to P. contorta and P. monophylla, respectively. Phylogenomic analyses based on the complete genome sequence revealed that 60 shared genes generated trees with the same topologies, and P. taeda was closely related to P. contorta in the subgenus Pinus. Thus, the complete P. taeda genome provided valuable resources for population and evolutionary studies of gymnosperms and can be used to identify related species.
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11
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Rasheed A, Mujeeb-Kazi A, Ogbonnaya FC, He Z, Rajaram S. Wheat genetic resources in the post-genomics era: promise and challenges. ANNALS OF BOTANY 2018; 121:603-616. [PMID: 29240874 PMCID: PMC5852999 DOI: 10.1093/aob/mcx148] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Accepted: 10/13/2017] [Indexed: 05/18/2023]
Abstract
Background Wheat genetic resources have been used for genetic improvement since 1876, when Stephen Wilson (Transactions and Proceedings of the Botanical Society of Edinburgh 12: 286) consciously made the first wide hybrid involving wheat and rye in Scotland. Wide crossing continued with sporadic attempts in the first half of 19th century and became a sophisticated scientific discipline during the last few decades with considerable impact in farmers' fields. However, a large diversity of untapped genetic resources could contribute in meeting future wheat production challenges. Perspectives and Conclusion Recently the complete reference genome of hexaploid (Chinese Spring) and tetraploid (Triticum turgidum ssp. dicoccoides) wheat became publicly available coupled with on-going international efforts on wheat pan-genome sequencing. We anticipate that an objective appraisal is required in the post-genomics era to prioritize genetic resources for use in the improvement of wheat production if the goal of doubling yield by 2050 is to be met. Advances in genomics have resulted in the development of high-throughput genotyping arrays, improved and efficient methods of gene discovery, genomics-assisted selection and gene editing using endonucleases. Likewise, ongoing advances in rapid generation turnover, improved phenotyping, envirotyping and analytical methods will significantly accelerate exploitation of exotic genes and increase the rate of genetic gain in breeding. We argue that the integration of these advances will significantly improve the precision and targeted identification of potentially useful variation in the wild relatives of wheat, providing new opportunities to contribute to yield and quality improvement, tolerance to abiotic stresses, resistance to emerging biotic stresses and resilience to weather extremes.
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Affiliation(s)
- Awais Rasheed
- International Maize and Wheat Improvement Center (CIMMYT), c/o Chinese Academy of Agricultural Sciences (CAAS), China
- Institute of Crop Sciences, CAAS, China
| | | | | | - Zhonghu He
- International Maize and Wheat Improvement Center (CIMMYT), c/o Chinese Academy of Agricultural Sciences (CAAS), China
- Institute of Crop Sciences, CAAS, China
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12
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Hussain B, Lucas SJ, Ozturk L, Budak H. Mapping QTLs conferring salt tolerance and micronutrient concentrations at seedling stagein wheat. Sci Rep 2017. [PMID: 29142238 DOI: 10.1038/s41598‐017‐15726‐6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Soil salinization and degradation is one of the consequences of climate change. Identification of major salt tolerance genes and marker assisted selection (MAS) can accelerate wheat breeding for this trait. We genotyped 154 wheat F2 lines derived from a cross between salt tolerant and susceptible cultivars using the Axiom Wheat Breeder's Genotyping Array. A high-density linkage map of 988 single nucleotide polymorphisms (SNPs) was constructed and utilized for quantitative trait loci (QTL) mapping for salt tolerance traits and mineral concentrations under salinity. Of 49 mapped QTLs, six were for Na+ exclusion (NAX) and two QTLs (qSNAX.2 A.1, qSNAX.2 A.2) on chromosome 2 A coincided with a reported major NAX QTL (Nax1 or HKT1;4). Two other major NAX QTLs were mapped on 7 A, which contributed 11.23 and 18.79% of the salt tolerance respectively. In addition to Ca+2 and Mg+2 QTLs, twenty-seven QTLs for tissue Phosphorus, Zinc, Iron, Manganese, Copper, Sulphur and Boron concentrations under salinity were also mapped. The 1293 segregating SNPs were annotated/located within genes for various ion channels, signalling pathways, transcription factors (TFs), metabolic pathways and 258 of them showed differential expression in silico under salinity. These findings will create new opportunities for salt tolerance breeding programs.
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Affiliation(s)
- Babar Hussain
- Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
| | - Stuart James Lucas
- SU Nanotechnology Research and Application Centre, Sabanci University, Istanbul, Turkey
| | - Levent Ozturk
- Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
| | - Hikmet Budak
- Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey. .,Cereal genomics Lab, Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT, USA.
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13
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Mapping QTLs conferring salt tolerance and micronutrient concentrations at seedling stagein wheat. Sci Rep 2017; 7:15662. [PMID: 29142238 PMCID: PMC5688110 DOI: 10.1038/s41598-017-15726-6] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 11/01/2017] [Indexed: 11/16/2022] Open
Abstract
Soil salinization and degradation is one of the consequences of climate change. Identification of major salt tolerance genes and marker assisted selection (MAS) can accelerate wheat breeding for this trait. We genotyped 154 wheat F2 lines derived from a cross between salt tolerant and susceptible cultivars using the Axiom Wheat Breeder’s Genotyping Array. A high-density linkage map of 988 single nucleotide polymorphisms (SNPs) was constructed and utilized for quantitative trait loci (QTL) mapping for salt tolerance traits and mineral concentrations under salinity. Of 49 mapped QTLs, six were for Na+ exclusion (NAX) and two QTLs (qSNAX.2 A.1, qSNAX.2 A.2) on chromosome 2 A coincided with a reported major NAX QTL (Nax1 or HKT1;4). Two other major NAX QTLs were mapped on 7 A, which contributed 11.23 and 18.79% of the salt tolerance respectively. In addition to Ca+2 and Mg+2 QTLs, twenty-seven QTLs for tissue Phosphorus, Zinc, Iron, Manganese, Copper, Sulphur and Boron concentrations under salinity were also mapped. The 1293 segregating SNPs were annotated/located within genes for various ion channels, signalling pathways, transcription factors (TFs), metabolic pathways and 258 of them showed differential expression in silico under salinity. These findings will create new opportunities for salt tolerance breeding programs.
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14
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Massive expansion and differential evolution of small heat shock proteins with wheat (Triticum aestivum L.) polyploidization. Sci Rep 2017; 7:2581. [PMID: 28566710 PMCID: PMC5451465 DOI: 10.1038/s41598-017-01857-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 04/03/2017] [Indexed: 12/13/2022] Open
Abstract
Wheat (Triticum aestivum), one of the world’s most important crops, is facing unprecedented challenges due to global warming. To evaluate the gene resources for heat adaptation in hexaploid wheat, small heat shock proteins (sHSPs), the key plant heat protection genes, were comprehensively analysed in wheat and related species. We found that the sHSPs of hexaploid wheat were massively expanded in A and B subgenomes with intrachromosomal duplications during polyploidization. These expanded sHSPs were under similar purifying selection and kept the expressional patterns with the original copies. Generally, a strong purifying selection acted on the α-crystallin domain (ACD) and theoretically constrain conserved function. Meanwhile, weaker purifying selection and strong positive selection acted on the N-terminal region, which conferred sHSP flexibility, allowing adjustments to a wider range of substrates in response to genomic and environmental changes. Notably, in CI, CV, ER, MI and MII subfamilies, gene duplications, expression variations and functional divergence occurred before wheat polyploidization. Our results indicate the massive expansion of active sHSPs in hexaploid wheat may also provide more raw materials for evolving functional novelties and generating genetic diversity to face future global climate changes, and highlight the expansion of stress response genes with wheat polyploidization.
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15
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Lucas SJ, Salantur A, Yazar S, Budak H. High-throughput SNP genotyping of modern and wild emmer wheat for yield and root morphology using a combined association and linkage analysis. Funct Integr Genomics 2017; 17:667-685. [PMID: 28550605 DOI: 10.1007/s10142-017-0563-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Revised: 05/11/2017] [Accepted: 05/12/2017] [Indexed: 11/24/2022]
Abstract
Durum wheat (Triticum turgidum var. durum Desf.) is a major world crop that is grown primarily in areas of the world that experience periodic drought, and therefore, breeding climate-resilient durum wheat is a priority. High-throughput single nucleotide polymorphism (SNP) genotyping techniques have greatly increased the power of linkage and association mapping analyses for bread wheat, but as yet there is no durum wheat-specific platform available. In this study, we evaluate the new 384HT Wheat Breeders Array for its usefulness in tetraploid wheat breeding by genotyping a breeding population of F6 hybrids, derived from multiple crosses between T. durum cultivars and wild and cultivated emmer wheat accessions. Using a combined linkage and association mapping approach, we generated a genetic map including 1345 SNP markers, and identified markers linked to 6 QTLs for coleoptile length (2), heading date (1), anthocyanin accumulation (1) and osmotic stress tolerance (2). We also developed a straightforward approach for combining genetic data from multiple families of limited size that will be useful for evaluating and mapping pre-existing breeding material.
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Affiliation(s)
- Stuart J Lucas
- SU Nanotechnology Research and Application Centre, Sabanci University, 34956, Tuzla, İstanbul, Turkey.
| | - Ayten Salantur
- Breeding and Genetics, Field Crops Central Research Institute, Ankara, Turkey
| | - Selami Yazar
- Breeding and Genetics, Field Crops Central Research Institute, Ankara, Turkey
| | - Hikmet Budak
- Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey. .,412 Leon Johnson Hall, Cereal Genomics Lab, Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT, USA.
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16
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Mochizuki T, Tanizawa Y, Fujisawa T, Ohta T, Nikoh N, Shimizu T, Toyoda A, Fujiyama A, Kurata N, Nagasaki H, Kaminuma E, Nakamura Y. DNApod: DNA polymorphism annotation database from next-generation sequence read archives. PLoS One 2017; 12:e0172269. [PMID: 28234924 PMCID: PMC5325239 DOI: 10.1371/journal.pone.0172269] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 02/02/2017] [Indexed: 01/18/2023] Open
Abstract
With the rapid advances in next-generation sequencing (NGS), datasets for DNA polymorphisms among various species and strains have been produced, stored, and distributed. However, reliability varies among these datasets because the experimental and analytical conditions used differ among assays. Furthermore, such datasets have been frequently distributed from the websites of individual sequencing projects. It is desirable to integrate DNA polymorphism data into one database featuring uniform quality control that is distributed from a single platform at a single place. DNA polymorphism annotation database (DNApod; http://tga.nig.ac.jp/dnapod/) is an integrated database that stores genome-wide DNA polymorphism datasets acquired under uniform analytical conditions, and this includes uniformity in the quality of the raw data, the reference genome version, and evaluation algorithms. DNApod genotypic data are re-analyzed whole-genome shotgun datasets extracted from sequence read archives, and DNApod distributes genome-wide DNA polymorphism datasets and known-gene annotations for each DNA polymorphism. This new database was developed for storing genome-wide DNA polymorphism datasets of plants, with crops being the first priority. Here, we describe our analyzed data for 679, 404, and 66 strains of rice, maize, and sorghum, respectively. The analytical methods are available as a DNApod workflow in an NGS annotation system of the DNA Data Bank of Japan and a virtual machine image. Furthermore, DNApod provides tables of links of identifiers between DNApod genotypic data and public phenotypic data. To advance the sharing of organism knowledge, DNApod offers basic and ubiquitous functions for multiple alignment and phylogenetic tree construction by using orthologous gene information.
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Affiliation(s)
- Takako Mochizuki
- Genome Informatics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Yasuhiro Tanizawa
- Genome Informatics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Takatomo Fujisawa
- Genome Informatics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Tazro Ohta
- Database Center for Life Science, Joint Support-Center for Data Science Research, Research Organization of Information and Systems, Mishima, Shizuoka, Japan
| | - Naruo Nikoh
- Department of Liberal Arts, The Open University of Japan, Chiba, Chiba, Japan
| | - Tokurou Shimizu
- Division of Citrus Research, Institute of Fruit Tree and Tea Science, NARO, Shimizu, Shizuoka, Japan
| | - Atsushi Toyoda
- Comparative Genomics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan
- Advanced Genomics Center, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Asao Fujiyama
- Advanced Genomics Center, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Nori Kurata
- Plant Genetics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Hideki Nagasaki
- Genome Informatics Group, Department of Technology Development, Kazusa DNA Research Institute, Kisarazu, Chiba, Japan
| | - Eli Kaminuma
- Genome Informatics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan
- * E-mail:
| | - Yasukazu Nakamura
- Genome Informatics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan
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17
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Akpinar BA, Lucas S, Budak H. A large-scale chromosome-specific SNP discovery guideline. Funct Integr Genomics 2016; 17:97-105. [PMID: 27900504 DOI: 10.1007/s10142-016-0536-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Revised: 11/06/2016] [Accepted: 11/09/2016] [Indexed: 12/01/2022]
Abstract
Single-nucleotide polymorphisms (SNPs) are the most prevalent type of variation in genomes that are increasingly being used as molecular markers in diversity analyses, mapping and cloning of genes, and germplasm characterization. However, only a few studies reported large-scale SNP discovery in Aegilops tauschii, restricting their potential use as markers for the low-polymorphic D genome. Here, we report 68,592 SNPs found on the gene-related sequences of the 5D chromosome of Ae. tauschii genotype MvGB589 using genomic and transcriptomic sequences from seven Ae. tauschii accessions, including AL8/78, the only genotype for which a draft genome sequence is available at present. We also suggest a workflow to compare SNP positions in homologous regions on the 5D chromosome of Triticum aestivum, bread wheat, to mark single nucleotide variations between these closely related species. Overall, the identified SNPs define a density of 4.49 SNPs per kilobyte, among the highest reported for the genic regions of Ae. tauschii so far. To our knowledge, this study also presents the first chromosome-specific SNP catalog in Ae. tauschii that should facilitate the association of these SNPs with morphological traits on chromosome 5D to be ultimately targeted for wheat improvement.
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Affiliation(s)
- Bala Ani Akpinar
- Sabanci University Nanotechnology Research and Application Center (SUNUM), Sabanci University, Orhanlı, 34956, Tuzla, Istanbul, Turkey
| | - Stuart Lucas
- Sabanci University Nanotechnology Research and Application Center (SUNUM), Sabanci University, Orhanlı, 34956, Tuzla, Istanbul, Turkey
| | - Hikmet Budak
- Sabanci University Nanotechnology Research and Application Center (SUNUM), Sabanci University, Orhanlı, 34956, Tuzla, Istanbul, Turkey. .,Cereal Genomics Lab, Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT, 59717, USA.
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18
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Dong Y, Liu J, Zhang Y, Geng H, Rasheed A, Xiao Y, Cao S, Fu L, Yan J, Wen W, Zhang Y, Jing R, Xia X, He Z. Genome-Wide Association of Stem Water Soluble Carbohydrates in Bread Wheat. PLoS One 2016; 11:e0164293. [PMID: 27802269 PMCID: PMC5089554 DOI: 10.1371/journal.pone.0164293] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 09/22/2016] [Indexed: 11/18/2022] Open
Abstract
Water soluble carbohydrates (WSC) in stems play an important role in buffering grain yield in wheat against biotic and abiotic stresses; however, knowledge of genes controlling WSC is very limited. We conducted a genome-wide association study (GWAS) using a high-density 90K SNP array to better understand the genetic basis underlying WSC, and to explore marker-based breeding approaches. WSC was evaluated in an association panel comprising 166 Chinese bread wheat cultivars planted in four environments. Fifty two marker-trait associations (MTAs) distributed across 23 loci were identified for phenotypic best linear unbiased estimates (BLUEs), and 11 MTAs were identified in two or more environments. Liner regression showed a clear dependence of WSC BLUE scores on numbers of favorable (increasing WSC content) and unfavorable alleles (decreasing WSC), indicating that genotypes with higher numbers of favorable or lower numbers of unfavorable alleles had higher WSC content. In silico analysis of flanking sequences of trait-associated SNPs revealed eight candidate genes related to WSC content grouped into two categories based on the type of encoding proteins, namely, defense response proteins and proteins triggered by environmental stresses. The identified SNPs and candidate genes related to WSC provide opportunities for breeding higher WSC wheat cultivars.
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Affiliation(s)
- Yan Dong
- Institute of Crop Science/National Wheat Improvement Center, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jindong Liu
- Institute of Crop Science/National Wheat Improvement Center, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yan Zhang
- Institute of Crop Science/National Wheat Improvement Center, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hongwei Geng
- College of Agronomy, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi, Xinjiang, 830052, China
| | - Awais Rasheed
- Institute of Crop Science/National Wheat Improvement Center, Chinese Academy of Agricultural Sciences, Beijing, China
- International Maize and Wheat Improvement Center (CIMMYT) China Office, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yonggui Xiao
- Institute of Crop Science/National Wheat Improvement Center, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shuanghe Cao
- Institute of Crop Science/National Wheat Improvement Center, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Luping Fu
- Institute of Crop Science/National Wheat Improvement Center, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jun Yan
- Cotton Research Institute, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
| | - Weie Wen
- Institute of Crop Science/National Wheat Improvement Center, Chinese Academy of Agricultural Sciences, Beijing, China
- College of Agronomy, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi, Xinjiang, 830052, China
| | - Yong Zhang
- Institute of Crop Science/National Wheat Improvement Center, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ruilian Jing
- Institute of Crop Science/National Wheat Improvement Center, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xianchun Xia
- Institute of Crop Science/National Wheat Improvement Center, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhonghu He
- Institute of Crop Science/National Wheat Improvement Center, Chinese Academy of Agricultural Sciences, Beijing, China
- International Maize and Wheat Improvement Center (CIMMYT) China Office, Chinese Academy of Agricultural Sciences, Beijing, China
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19
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Vrána J, Cápal P, Šimková H, Karafiátová M, Čížková J, Doležel J. Flow Analysis and Sorting of Plant Chromosomes. CURRENT PROTOCOLS IN CYTOMETRY 2016; 78:5.3.1-5.3.43. [PMID: 27723090 DOI: 10.1002/cpcy.9] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Analysis and sorting of plant chromosomes (plant flow cytogenetics) is a special application of flow cytometry in plant genomics and its success depends critically on sample quality. This unit describes the methodology in a stepwise manner, starting with the induction of cell cycle synchrony and accumulation of dividing cells in mitotic metaphase, and continues with the preparation of suspensions of intact mitotic chromosomes, flow analysis and sorting of chromosomes, and finally processing of the sorted chromosomes. Each step of the protocol is described in detail as some procedures have not been used widely. Supporting histograms are presented as well as hints on dealing with plant material; the utility of sorted chromosomes for plant genomics is also discussed. © 2016 by John Wiley & Sons, Inc.
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Affiliation(s)
- Jan Vrána
- Institute of Experimental Botany, Center of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Petr Cápal
- Institute of Experimental Botany, Center of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Hana Šimková
- Institute of Experimental Botany, Center of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Miroslava Karafiátová
- Institute of Experimental Botany, Center of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Jana Čížková
- Institute of Experimental Botany, Center of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Jaroslav Doležel
- Institute of Experimental Botany, Center of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
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20
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Xie J, Huo N, Zhou S, Wang Y, Guo G, Deal KR, Ouyang S, Liang Y, Wang Z, Xiao L, Zhu T, Hu T, Tiwari V, Zhang J, Li H, Ni Z, Yao Y, Peng H, Zhang S, Anderson OD, McGuire PE, Dvorak J, Luo MC, Liu Z, Gu YQ, Sun Q. Sequencing and comparative analyses of Aegilops tauschii chromosome arm 3DS reveal rapid evolution of Triticeae genomes. J Genet Genomics 2016; 44:51-61. [PMID: 27765484 DOI: 10.1016/j.jgg.2016.09.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Revised: 09/26/2016] [Accepted: 09/27/2016] [Indexed: 11/18/2022]
Abstract
Bread wheat (Triticum aestivum, AABBDD) is an allohexaploid species derived from two rounds of interspecific hybridizations. A high-quality genome sequence assembly of diploid Aegilops tauschii, the donor of the wheat D genome, will provide a useful platform to study polyploid wheat evolution. A combined approach of BAC pooling and next-generation sequencing technology was employed to sequence the minimum tiling path (MTP) of 3176 BAC clones from the short arm of Ae. tauschii chromosome 3 (At3DS). The final assembly of 135 super-scaffolds with an N50 of 4.2 Mb was used to build a 247-Mb pseudomolecule with a total of 2222 predicted protein-coding genes. Compared with the orthologous regions of rice, Brachypodium, and sorghum, At3DS contains 38.67% more genes. In comparison to At3DS, the short arm sequence of wheat chromosome 3B (Ta3BS) is 95-Mb large in size, which is primarily due to the expansion of the non-centromeric region, suggesting that transposable element (TE) bursts in Ta3B likely occurred there. Also, the size increase is accompanied by a proportional increase in gene number in Ta3BS. We found that in the sequence of short arm of wheat chromosome 3D (Ta3DS), there was only less than 0.27% gene loss compared to At3DS. Our study reveals divergent evolution of grass genomes and provides new insights into sequence changes in the polyploid wheat genome.
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Affiliation(s)
- Jingzhong Xie
- State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing 100193, China
| | - Naxin Huo
- USDA-ARS West Regional Research Center, Albany, CA 94710, USA; Department of Plant Sciences, University of California at Davis, Davis, CA 95616, USA
| | - Shenghui Zhou
- State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing 100193, China
| | - Yi Wang
- USDA-ARS West Regional Research Center, Albany, CA 94710, USA
| | - Guanghao Guo
- State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing 100193, China
| | - Karin R Deal
- Department of Plant Sciences, University of California at Davis, Davis, CA 95616, USA
| | - Shuhong Ouyang
- State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing 100193, China
| | - Yong Liang
- State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing 100193, China
| | - Zhenzhong Wang
- State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing 100193, China
| | - Lichan Xiao
- Department of Plant Sciences, University of California at Davis, Davis, CA 95616, USA
| | - Tingting Zhu
- Department of Plant Sciences, University of California at Davis, Davis, CA 95616, USA
| | - Tiezhu Hu
- USDA-ARS West Regional Research Center, Albany, CA 94710, USA
| | - Vijay Tiwari
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, USA
| | - Jianwei Zhang
- Arizona Genomics Institute, School of Plant Science, University of Arizona, Tucson, AZ 85721, USA
| | - Hongxia Li
- USDA-ARS West Regional Research Center, Albany, CA 94710, USA
| | - Zhongfu Ni
- State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing 100193, China
| | - Yingyin Yao
- State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing 100193, China
| | - Huiru Peng
- State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing 100193, China
| | - Shengli Zhang
- USDA-ARS West Regional Research Center, Albany, CA 94710, USA
| | - Olin D Anderson
- USDA-ARS West Regional Research Center, Albany, CA 94710, USA
| | - Patrick E McGuire
- Department of Plant Sciences, University of California at Davis, Davis, CA 95616, USA
| | - Jan Dvorak
- Department of Plant Sciences, University of California at Davis, Davis, CA 95616, USA.
| | - Ming-Cheng Luo
- Department of Plant Sciences, University of California at Davis, Davis, CA 95616, USA.
| | - Zhiyong Liu
- State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing 100193, China.
| | - Yong Q Gu
- USDA-ARS West Regional Research Center, Albany, CA 94710, USA.
| | - Qixin Sun
- State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing 100193, China.
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21
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Jia YY, Wu HN, Fang L, Liu Y, Cheng L, Liu G, Zhang ML, Huang Y. Sorting of chromosomes on FACSAriaTMSORP for the preparation of painting probes. Cytometry A 2016; 89:844-51. [DOI: 10.1002/cyto.a.22934] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Revised: 06/14/2016] [Accepted: 08/08/2016] [Indexed: 11/10/2022]
Affiliation(s)
- Yu-Yan Jia
- State Key Laboratory of Medical Molecular Biology, Department of Medical Genetics; Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College; Beijing 100005 People's Republic of China
| | - Hou-Nan Wu
- Peking University Medical and Health Analytical Center, Peking University Health Sciences Center; Beijing 100191 People's Republic of China
| | - Liang Fang
- BD Biosciences; Beijing 100025 People's Republic of China
| | - Yun Liu
- Peking University Medical and Health Analytical Center, Peking University Health Sciences Center; Beijing 100191 People's Republic of China
| | - Li Cheng
- State Key Laboratory of Medical Molecular Biology, Department of Medical Genetics; Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College; Beijing 100005 People's Republic of China
| | - Guang Liu
- State Key Laboratory of Medical Molecular Biology, Department of Medical Genetics; Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College; Beijing 100005 People's Republic of China
| | - Mei-Li Zhang
- State Key Laboratory of Medical Molecular Biology, Department of Medical Genetics; Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College; Beijing 100005 People's Republic of China
| | - Yue Huang
- State Key Laboratory of Medical Molecular Biology, Department of Medical Genetics; Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College; Beijing 100005 People's Republic of China
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22
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Alptekin B, Budak H. Wheat miRNA ancestors: evident by transcriptome analysis of A, B, and D genome donors. Funct Integr Genomics 2016; 17:171-187. [PMID: 27032785 DOI: 10.1007/s10142-016-0487-y] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 03/06/2016] [Accepted: 03/14/2016] [Indexed: 12/24/2022]
Abstract
MicroRNAs are critical players of post-transcriptional gene regulation with profound effects on the fundamental processes of cellular life. Their identification and characterization, together with their targets, hold great significance in exploring and exploiting their roles on a functional context, providing valuable clues into the regulation of important biological processes, such as stress tolerance or environmental adaptation. Wheat is a hardy crop, extensively harvested in temperate regions, and is a major component of the human diet. With the advent of the next generation sequencing technologies considerably decreasing sequencing costs per base-pair, genomic, and transcriptomic data from several wheat species, including the progenitors and wild relatives have become available. In this study, we performed in silico identification and comparative analysis of microRNA repertoires of bread wheat (Triticum aestivum L.) and its diploid progenitors and relatives, Aegilops sharonensis, Aegilops speltoides, Aegilops tauschii, Triticum monococcum, and Triticum urartu through the utilization of publicly available transcriptomic data. Over 200 miRNA families were identified, majority of which have not previously been reported. Ancestral relationships expanded our understanding of wheat miRNA evolution, while T. monococcum miRNAs delivered important clues on the effects of domestication on miRNA expression. Comparative analyses on wild Ae. sharonensis accessions highlighted candidate miRNAs that can be linked to stress tolerance. The miRNA repertoires of bread wheat and its diploid progenitors and relatives provide important insight into the diversification and distribution of miRNA genes, which should contribute to the elucidation of miRNA evolution of Poaceae family. A thorough understanding of the convergent and divergent expression profiles of miRNAs in different genetic backgrounds can provide unique opportunities to modulation of gene regulation for better crop performance.
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Affiliation(s)
- Burcu Alptekin
- Molecular Biology, Genetics and Bioengineering Program, Sabanci University, 34956, Istanbul, Turkey
| | - Hikmet Budak
- Molecular Biology, Genetics and Bioengineering Program, Sabanci University, 34956, Istanbul, Turkey.
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT, 59717, USA.
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23
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Shaaf S, Sharma R, Baloch FS, Badaeva ED, Knüpffer H, Kilian B, Özkan H. The grain Hardness locus characterized in a diverse wheat panel (Triticum aestivum L.) adapted to the central part of the Fertile Crescent: genetic diversity, haplotype structure, and phylogeny. Mol Genet Genomics 2016; 291:1259-75. [DOI: 10.1007/s00438-016-1180-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Accepted: 02/03/2016] [Indexed: 12/27/2022]
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24
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Akpinar BA, Budak H. Dissecting miRNAs in Wheat D Genome Progenitor, Aegilops tauschii. FRONTIERS IN PLANT SCIENCE 2016; 7:606. [PMID: 27200073 PMCID: PMC4855405 DOI: 10.3389/fpls.2016.00606] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 04/20/2016] [Indexed: 05/09/2023]
Abstract
As the post-transcriptional regulators of gene expression, microRNAs or miRNAs comprise an integral part of understanding how genomes function. Although miRNAs have been a major focus of recent efforts, miRNA research is still in its infancy in most plant species. Aegilops tauschii, the D genome progenitor of bread wheat, is a wild diploid grass exhibiting remarkable population diversity. Due to the direct ancestry and the diverse gene pool, A. tauschii is a promising source for bread wheat improvement. In this study, a total of 87 Aegilops miRNA families, including 51 previously unknown, were computationally identified both at the subgenomic level, using flow-sorted A. tauschii 5D chromosome, and at the whole genome level. Predictions at the genomic and subgenomic levels suggested A. tauschii 5D chromosome as rich in pre-miRNAs that are highly associated with Class II DNA transposons. In order to gain insights into miRNA evolution, putative 5D chromosome miRNAs were compared to its modern ortholog, Triticum aestivum 5D chromosome, revealing that 48 of the 58 A. tauschii 5D miRNAs were conserved in orthologous T. aestivum 5D chromosome. The expression profiles of selected miRNAs (miR167, miR5205, miR5175, miR5523) provided the first experimental evidence for miR5175, miR5205 and miR5523, and revealed differential expressional changes in response to drought in different genetic backgrounds for miR167 and miR5175. Interestingly, while miR5523 coding regions were present and expressed as pre-miR5523 in both T. aestivum and A. tauschii, the expression of mature miR5523 was observed only in A. tauschii under normal conditions, pointing out to an interference at the downstream processing of pre-miR5523 in T. aestivum. Overall, this study expands our knowledge on the miRNA catalog of A. tauschii, locating a subset specifically to the 5D chromosome, with ample functional and comparative insight which should contribute to and complement efforts to develop drought tolerant wheat varieties.
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Affiliation(s)
- Bala A. Akpinar
- Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci UniversityIstanbul, Turkey
| | - Hikmet Budak
- Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci UniversityIstanbul, Turkey
- Department of Plant Sciences and Plant Pathology, Montana State UniversityBozeman, MT, USA
- *Correspondence: Hikmet Budak,
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25
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Han B, Wang C, Tang Z, Ren Y, Li Y, Zhang D, Dong Y, Zhao X. Genome-Wide Analysis of Microsatellite Markers Based on Sequenced Database in Chinese Spring Wheat (Triticum aestivum L.). PLoS One 2015; 10:e0141540. [PMID: 26536014 PMCID: PMC4633229 DOI: 10.1371/journal.pone.0141540] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Accepted: 10/10/2015] [Indexed: 12/12/2022] Open
Abstract
Microsatellites or simple sequence repeats (SSRs) are distributed across both prokaryotic and eukaryotic genomes and have been widely used for genetic studies and molecular marker-assisted breeding in crops. Though an ordered draft sequence of hexaploid bread wheat have been announced, the researches about systemic analysis of SSRs for wheat still have not been reported so far. In the present study, we identified 364,347 SSRs from among 10,603,760 sequences of the Chinese spring wheat (CSW) genome, which were present at a density of 36.68 SSR/Mb. In total, we detected 488 types of motifs ranging from di- to hexanucleotides, among which dinucleotide repeats dominated, accounting for approximately 42.52% of the genome. The density of tri- to hexanucleotide repeats was 24.97%, 4.62%, 3.25% and 24.65%, respectively. AG/CT, AAG/CTT, AGAT/ATCT, AAAAG/CTTTT and AAAATT/AATTTT were the most frequent repeats among di- to hexanucleotide repeats. Among the 21 chromosomes of CSW, the density of repeats was highest on chromosome 2D and lowest on chromosome 3A. The proportions of di-, tri-, tetra-, penta- and hexanucleotide repeats on each chromosome, and even on the whole genome, were almost identical. In addition, 295,267 SSR markers were successfully developed from the 21 chromosomes of CSW, which cover the entire genome at a density of 29.73 per Mb. All of the SSR markers were validated by reverse electronic-Polymerase Chain Reaction (re-PCR); 70,564 (23.9%) were found to be monomorphic and 224,703 (76.1%) were found to be polymorphic. A total of 45 monomorphic markers were selected randomly for validation purposes; 24 (53.3%) amplified one locus, 8 (17.8%) amplified multiple identical loci, and 13 (28.9%) did not amplify any fragments from the genomic DNA of CSW. Then a dendrogram was generated based on the 24 monomorphic SSR markers among 20 wheat cultivars and three species of its diploid ancestors showing that monomorphic SSR markers represented a promising source to increase the number of genetic markers available for the wheat genome. The results of this study will be useful for investigating the genetic diversity and evolution among wheat and related species. At the same time, the results will facilitate comparative genomic studies and marker-assisted breeding (MAS) in plants.
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Affiliation(s)
- Bin Han
- College of Bio-engineering, Shanxi University, Taiyuan, China
| | - Changbiao Wang
- Biotechnology Research Center, Shanxi Academy of Agricultural Sciences, Taiyuan, China
- * E-mail: (ZHT); (DYZ); (CBW)
| | - Zhaohui Tang
- Biotechnology Research Center, Shanxi Academy of Agricultural Sciences, Taiyuan, China
- * E-mail: (ZHT); (DYZ); (CBW)
| | - Yongkang Ren
- Institute of Crop Science, Shanxi Academy of Agricultural Sciences, Taiyuan, China
| | - Yali Li
- Biotechnology Research Center, Shanxi Academy of Agricultural Sciences, Taiyuan, China
| | - Dayong Zhang
- Provincial Key Laboratory of Agrobiology, Institute of Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, China
- * E-mail: (ZHT); (DYZ); (CBW)
| | - Yanhui Dong
- Biotechnology Research Center, Shanxi Academy of Agricultural Sciences, Taiyuan, China
| | - Xinghua Zhao
- Biotechnology Research Center, Shanxi Academy of Agricultural Sciences, Taiyuan, China
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26
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Molecular organization and comparative analysis of chromosome 5B of the wild wheat ancestor Triticum dicoccoides. Sci Rep 2015; 5:10763. [PMID: 26084265 PMCID: PMC4471722 DOI: 10.1038/srep10763] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Accepted: 04/28/2015] [Indexed: 12/13/2022] Open
Abstract
Wild emmer wheat, Triticum turgidum ssp. dicoccoides is the wild relative of Triticum turgidum, the progenitor of durum and bread wheat, and maintains a rich allelic diversity among its wild populations. The lack of adequate genetic and genomic resources, however, restricts its exploitation in wheat improvement. Here, we report next-generation sequencing of the flow-sorted chromosome 5B of T. dicoccoides to shed light into its genome structure, function and organization by exploring the repetitive elements, protein-encoding genes and putative microRNA and tRNA coding sequences. Comparative analyses with its counterparts in modern and wild wheats suggest clues into the B-genome evolution. Syntenic relationships of chromosome 5B with the model grasses can facilitate further efforts for fine-mapping of traits of interest. Mapping of 5B sequences onto the root transcriptomes of two additional T. dicoccoides genotypes, with contrasting drought tolerances, revealed several thousands of single nucleotide polymorphisms, of which 584 shared polymorphisms on 228 transcripts were specific to the drought-tolerant genotype. To our knowledge, this study presents the largest genomics resource currently available for T. dicoccoides, which, we believe, will encourage the exploitation of its genetic and genomic potential for wheat improvement to meet the increasing demand to feed the world.
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27
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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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28
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Budak H, Kantar M. Harnessing NGS and Big Data Optimally: Comparison of miRNA Prediction from Assembled versus Non-assembled Sequencing Data--The Case of the Grass Aegilops tauschii Complex Genome. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2015; 19:407-15. [PMID: 26061358 DOI: 10.1089/omi.2015.0038] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
MicroRNAs (miRNAs) are small, endogenous, non-coding RNA molecules that regulate gene expression at the post-transcriptional level. As high-throughput next generation sequencing (NGS) and Big Data rapidly accumulate for various species, efforts for in silico identification of miRNAs intensify. Surprisingly, the effect of the input genomics sequence on the robustness of miRNA prediction was not evaluated in detail to date. In the present study, we performed a homology-based miRNA and isomiRNA prediction of the 5D chromosome of bread wheat progenitor, Aegilops tauschii, using two distinct sequence data sets as input: (1) raw sequence reads obtained from 454-GS FLX Titanium sequencing platform and (2) an assembly constructed from these reads. We also compared this method with a number of available plant sequence datasets. We report here the identification of 62 and 22 miRNAs from raw reads and the assembly, respectively, of which 16 were predicted with high confidence from both datasets. While raw reads promoted sensitivity with the high number of miRNAs predicted, 55% (12 out of 22) of the assembly-based predictions were supported by previous observations, bringing specificity forward compared to the read-based predictions, of which only 37% were supported. Importantly, raw reads could identify several repeat-related miRNAs that could not be detected with the assembly. However, raw reads could not capture 6 miRNAs, for which the stem-loops could only be covered by the relatively longer sequences from the assembly. In summary, the comparison of miRNA datasets obtained by these two strategies revealed that utilization of raw reads, as well as assemblies for in silico prediction, have distinct advantages and disadvantages. Consideration of these important nuances can benefit future miRNA identification efforts in the current age of NGS and Big Data driven life sciences innovation.
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Affiliation(s)
- Hikmet Budak
- Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University , Istanbul, Turkey
| | - Melda Kantar
- Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University , Istanbul, Turkey
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29
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Han B, Wang C, Tang Z, Ren Y, Li Y, Zhang D, Dong Y, Zhao X. Genome-Wide Analysis of Microsatellite Markers Based on Sequenced Database in Chinese Spring Wheat (Triticum aestivum L.). PLoS One 2015; 10:e0141540. [PMID: 26536014 DOI: 10.1371/journal.pone.0141540.t006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Accepted: 10/10/2015] [Indexed: 05/21/2023] Open
Abstract
Microsatellites or simple sequence repeats (SSRs) are distributed across both prokaryotic and eukaryotic genomes and have been widely used for genetic studies and molecular marker-assisted breeding in crops. Though an ordered draft sequence of hexaploid bread wheat have been announced, the researches about systemic analysis of SSRs for wheat still have not been reported so far. In the present study, we identified 364,347 SSRs from among 10,603,760 sequences of the Chinese spring wheat (CSW) genome, which were present at a density of 36.68 SSR/Mb. In total, we detected 488 types of motifs ranging from di- to hexanucleotides, among which dinucleotide repeats dominated, accounting for approximately 42.52% of the genome. The density of tri- to hexanucleotide repeats was 24.97%, 4.62%, 3.25% and 24.65%, respectively. AG/CT, AAG/CTT, AGAT/ATCT, AAAAG/CTTTT and AAAATT/AATTTT were the most frequent repeats among di- to hexanucleotide repeats. Among the 21 chromosomes of CSW, the density of repeats was highest on chromosome 2D and lowest on chromosome 3A. The proportions of di-, tri-, tetra-, penta- and hexanucleotide repeats on each chromosome, and even on the whole genome, were almost identical. In addition, 295,267 SSR markers were successfully developed from the 21 chromosomes of CSW, which cover the entire genome at a density of 29.73 per Mb. All of the SSR markers were validated by reverse electronic-Polymerase Chain Reaction (re-PCR); 70,564 (23.9%) were found to be monomorphic and 224,703 (76.1%) were found to be polymorphic. A total of 45 monomorphic markers were selected randomly for validation purposes; 24 (53.3%) amplified one locus, 8 (17.8%) amplified multiple identical loci, and 13 (28.9%) did not amplify any fragments from the genomic DNA of CSW. Then a dendrogram was generated based on the 24 monomorphic SSR markers among 20 wheat cultivars and three species of its diploid ancestors showing that monomorphic SSR markers represented a promising source to increase the number of genetic markers available for the wheat genome. The results of this study will be useful for investigating the genetic diversity and evolution among wheat and related species. At the same time, the results will facilitate comparative genomic studies and marker-assisted breeding (MAS) in plants.
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Affiliation(s)
- Bin Han
- College of Bio-engineering, Shanxi University, Taiyuan, China
| | - Changbiao Wang
- Biotechnology Research Center, Shanxi Academy of Agricultural Sciences, Taiyuan, China
| | - Zhaohui Tang
- Biotechnology Research Center, Shanxi Academy of Agricultural Sciences, Taiyuan, China
| | - Yongkang Ren
- Institute of Crop Science, Shanxi Academy of Agricultural Sciences, Taiyuan, China
| | - Yali Li
- Biotechnology Research Center, Shanxi Academy of Agricultural Sciences, Taiyuan, China
| | - Dayong Zhang
- Provincial Key Laboratory of Agrobiology, Institute of Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Yanhui Dong
- Biotechnology Research Center, Shanxi Academy of Agricultural Sciences, Taiyuan, China
| | - Xinghua Zhao
- Biotechnology Research Center, Shanxi Academy of Agricultural Sciences, Taiyuan, China
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