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Ubi BE, Gorafi YSA, Yaakov B, Monden Y, Kashkush K, Tsujimoto H. Exploiting the miniature inverted-repeat transposable elements insertion polymorphisms as an efficient DNA marker system for genome analysis and evolutionary studies in wheat and related species. FRONTIERS IN PLANT SCIENCE 2022; 13:995586. [PMID: 36119578 PMCID: PMC9479669 DOI: 10.3389/fpls.2022.995586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Accepted: 08/09/2022] [Indexed: 06/15/2023]
Abstract
Transposable elements (TEs) constitute ~80% of the complex bread wheat genome and contribute significantly to wheat evolution and environmental adaptation. We studied 52 TE insertion polymorphism markers to ascertain their efficiency as a robust DNA marker system for genetic studies in wheat and related species. Significant variation was found in miniature inverted-repeat transposable element (MITE) insertions in relation to ploidy with the highest number of "full site" insertions occurring in the hexaploids (32.6 ± 3.8), while the tetraploid and diploid progenitors had 22.3 ± 0.6 and 15.0 ± 3.5 "full sites," respectively, which suggested a recent rapid activation of these transposons after the formation of wheat. Constructed phylogenetic trees were consistent with the evolutionary history of these species which clustered mainly according to ploidy and genome types (SS, AA, DD, AABB, and AABBDD). The synthetic hexaploids sub-clustered near the tetraploid species from which they were re-synthesized. Preliminary genotyping in 104 recombinant inbred lines (RILs) showed predominantly 1:1 segregation for simplex markers, with four of these markers already integrated into our current DArT-and SNP-based linkage map. The MITE insertions also showed stability with no single excision observed. The MITE insertion site polymorphisms uncovered in this study are very promising as high-potential evolutionary markers for genomic studies in wheat.
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Affiliation(s)
- Benjamin Ewa Ubi
- Molecular Breeding Laboratory, Arid Land Research Center, Tottori University, Tottori, Japan
- Department of Biotechnology, Ebonyi State University, Abakaliki, Abakaliki, Ebonyi, Nigeria
| | - Yasir Serag Alnor Gorafi
- International Platform for Dryland Research and Education, Tottori University, Tottori, Japan
- Agricultural Research Corporation, Wad Medani, Sudan
| | - Beery Yaakov
- French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Yuki Monden
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | - Khalil Kashkush
- Department of Life Sciences, Ben-Gurion University, Beer-Sheva, Israel
| | - Hisashi Tsujimoto
- Molecular Breeding Laboratory, Arid Land Research Center, Tottori University, Tottori, Japan
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Li C, Wang J, Li L, Li J, Zhuang M, Li B, Li Q, Huang J, Du Y, Wang J, Fan Z, Mao X, Jing R. TaMOR is essential for root initiation and improvement of root system architecture in wheat. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:862-875. [PMID: 34890129 PMCID: PMC9055823 DOI: 10.1111/pbi.13765] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 10/25/2021] [Accepted: 12/07/2021] [Indexed: 05/13/2023]
Abstract
Optimal root system architecture is beneficial for water-fertilizer use efficiency, stress tolerance and yield improvement of crops. However, because of the complexity of root traits and difficulty in phenotyping deep roots, the study on mechanisms of root development is rarely reported in wheat (Triticum aestivum L.). In this study, we identified that the LBD (LATERAL ORGAN BOUNDARIES DOMAIN) gene TaMOR (MORE ROOT in wheat) determines wheat crown root initiation. The mor mutants exhibited less or even no crown root, dwarfism, less grain number and lodging caused by few roots. The observation of cross sections showed that crown root initiation is inhibited in the mor mutants. Molecular assays revealed that TaMOR interacts with the auxin response factor ARF5 to directly induce the expression of the auxin transporter gene PIN2 (PIN-FORMED 2) in the root base to regulate crown root initiation. In addition, a 159-bp MITE (miniature inverted-repeat transposable element) insertion causing DNA methylation and lower expression of TaMOR-B was identified in TaMOR-B promoter, which is associated with lower root dry weight and shorter plant height. The results bring new light into regulation mechanisms of crown root initiation and offer a new target for the improvement of root system architecture in wheat.
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Affiliation(s)
- Chaonan Li
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Jingyi Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Long Li
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Jialu Li
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Mengjia Zhuang
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Bo Li
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Qiaoru Li
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Junfang Huang
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Yan Du
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Jinping Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Zipei Fan
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Xinguo Mao
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Ruilian Jing
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
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Wang J, Li L, Li C, Yang X, Xue Y, Zhu Z, Mao X, Jing R. A transposon in the vacuolar sorting receptor gene TaVSR1-B promoter region is associated with wheat root depth at booting stage. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:1456-1467. [PMID: 33555662 PMCID: PMC8313126 DOI: 10.1111/pbi.13564] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 01/06/2021] [Accepted: 01/28/2021] [Indexed: 05/14/2023]
Abstract
Root depth, as an important component of root architecture, plays a significant role in growth, grain yield determination and abiotic stress tolerance in crop plants, but its genetic basis remains poorly elucidated. In this study, a panel composed of 323 wheat (Triticum aestivum L.) accessions was assessed for variation in root depth and genotyped with the Wheat 660K SNP Array. GWAS (genome-wide association study) detected significant association between a 125 bp miniature inverted-repeat transposable element (MITE) in the promoter of the TaVSR1-B gene with root depth at the booting stage. We showed that the MITE repressed TaVSR1-B expression by DNA methylation and H3K27 tri-methylation. The roles of TaVSR1-B in root growth were verified by altered expression of the gene in transgenic wheat, rice and a tavsr1 TILLING mutant. Increased TaVSR1-B expression made the root elongation zone shorter and the differentiation zone longer, leading to deeper root. This work provides novel insight into the genetic basis of variation in root depth and a promising target for genetic improvement of root architecture in wheat.
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Affiliation(s)
- Jingyi Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Long Li
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Chaonan Li
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Xi Yang
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Yinghong Xue
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Zhi Zhu
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Xinguo Mao
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Ruilian Jing
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
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Edet OU, Kim JS, Okamoto M, Hanada K, Takeda T, Kishii M, Gorafi YSA, Tsujimoto H. Efficient anchoring of alien chromosome segments introgressed into bread wheat by new Leymus racemosus genome-based markers. BMC Genet 2018; 19:18. [PMID: 29587653 PMCID: PMC5872505 DOI: 10.1186/s12863-018-0603-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 03/13/2018] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND The tertiary gene pool of bread wheat, to which Leymus racemosus belongs, has remained underutilized due to the current limited genomic resources of the species that constitute it. Continuous enrichment of public databases with useful information regarding these species is, therefore, needed to provide insights on their genome structures and aid successful utilization of their genes to develop improved wheat cultivars for effective management of environmental stresses. RESULTS We generated de novo DNA and mRNA sequence information of L. racemosus and developed 110 polymorphic PCR-based markers from the data, and to complement the PCR markers, DArT-seq genotyping was applied to develop additional 9990 SNP markers. Approximately 52% of all the markers enabled us to clearly genotype 22 wheat-L. racemosus chromosome introgression lines, and L. racemosus chromosome-specific markers were highly efficient in detailed characterization of the translocation and recombination lines analyzed. A further analysis revealed remarkable transferability of the PCR markers to three other important Triticeae perennial species: L. mollis, Psathyrostachys huashanica and Elymus ciliaris, indicating their suitability for characterizing wheat-alien chromosome introgressions carrying chromosomes of these genomes. CONCLUSION The efficiency of the markers in characterizing wheat-L. racemosus chromosome introgression lines proves their reliability, and their high transferability further broadens their scope of application. This is the first report on sequencing and development of markers from L. racemosus genome and the application of DArT-seq to develop markers from a perennial wild relative of wheat, marking a paradigm shift from the seeming concentration of the technology on cultivated species. Integration of these markers with appropriate cytogenetic methods would accelerate development and characterization of wheat-alien chromosome introgression lines.
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Affiliation(s)
- Offiong Ukpong Edet
- Arid Land Research Center, Tottori University, Tottori, Japan
- United Graduate School of Agricultural Sciences, Tottori University, Tottori, Japan
| | - June-Sik Kim
- RIKEN Center for Sustainable Resource Science, Tsukuba, Ibaraki, 305-0074 Japan
| | - Masanori Okamoto
- Center for Bioscience Research and Education, Utsunomiya University, Utsunomiya, Japan
| | - Kousuke Hanada
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Kitakyushu, Japan
| | - Tomoyuki Takeda
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Kitakyushu, Japan
| | - Masahiro Kishii
- International Maize and Wheat Improvement Center (CIMMYT), El Batan, Mexico
| | - Yasir Serag Alnor Gorafi
- Arid Land Research Center, Tottori University, Tottori, Japan
- Agricultural Research Corporation (ARC), Wad Madani, Sudan
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Wang H, Zhang H, Li B, Yu Z, Li G, Zhang J, Yang Z. Molecular Cytogenetic Characterization of New Wheat- Dasypyrum breviaristatum Introgression Lines for Improving Grain Quality of Wheat. FRONTIERS IN PLANT SCIENCE 2018; 9:365. [PMID: 29616071 PMCID: PMC5868130 DOI: 10.3389/fpls.2018.00365] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 03/05/2018] [Indexed: 05/22/2023]
Abstract
As an important relative of wheat (Triticum aestivum L), Dasypyrum breviaristatum contains novel high molecular weight glutenin subunits (HMW-GSs) encoded by Glu-1Vb genes. We identified new wheat-D. breviaristatum chromosome introgression lines including chromosomes 1Vb and 1VbL.5VbL by fluorescence in situ hybridization (FISH) combined with molecular markers. We found that chromosome changes occurred in the wheat-D. breviaristatum introgression lines and particularly induced the deletion of 5BS terminal repeats and formation of a new type of 5B-7B reciprocal translocation. The results imply that the D. breviaristatum chromosome 1Vb may contain genes which induce chromosomal recombination in wheat background. Ten putative high molecular weight glutenin subunit (HMW-GS) genes from D. breviaristatum and wheat-D. breviaristatum introgression lines were isolated. The lengths of the HMW-GS genes in Dasypyrum were significantly shorter than typical HMW-GS of common wheat. A new y-type HMW-GS gene, named Glu-Vb1y, was characterized in wheat-D. breviaristatum 1Vb introgression lines. The new wheat-D. breviaristatum germplasm displayed reduced plant height, increased tillers and superior grain protein and gluten contents, improved gluten performance index. The results showed considerable potential for utilization of D. breviaristatum chromosome 1Vb segments in future wheat improvement.
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Affiliation(s)
- Hongjin Wang
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
| | - Hongjun Zhang
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
| | - Bin Li
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
| | - Zhihui Yu
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
| | - Guangrong Li
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
- Center of Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Jie Zhang
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
| | - Zujun Yang
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
- Center of Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
- *Correspondence: Zujun Yang,
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