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Ghorbel M, Zribi I, Haddaji N, Siddiqui AJ, Bouali N, Brini F. Genome-Wide Identification and Expression Analysis of Catalase Gene Families in Triticeae. PLANTS (BASEL, SWITZERLAND) 2023; 13:11. [PMID: 38202319 PMCID: PMC10781083 DOI: 10.3390/plants13010011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 12/03/2023] [Accepted: 12/11/2023] [Indexed: 01/12/2024]
Abstract
Aerobic metabolism in plants results in the production of hydrogen peroxide (H2O2), a significant and comparatively stable non-radical reactive oxygen species (ROS). H2O2 is a signaling molecule that regulates particular physiological and biological processes (the cell cycle, photosynthesis, plant growth and development, and plant responses to environmental challenges) at low concentrations. Plants may experience oxidative stress and ultimately die from cell death if excess H2O2 builds up. Triticum dicoccoides, Triticum urartu, and Triticum spelta are different ancient wheat species that present different interesting characteristics, and their importance is becoming more and more clear. In fact, due to their interesting nutritive health, flavor, and nutritional values, as well as their resistance to different parasites, the cultivation of these species is increasingly important. Thus, it is important to understand the mechanisms of plant tolerance to different biotic and abiotic stresses by studying different stress-induced gene families such as catalases (CAT), which are important H2O2-metabolizing enzymes found in plants. Here, we identified seven CAT-encoding genes (TdCATs) in Triticum dicoccoides, four genes in Triticum urartu (TuCATs), and eight genes in Triticum spelta (TsCATs). The accuracy of the newly identified wheat CAT gene members in different wheat genomes is confirmed by the gene structures, phylogenetic relationships, protein domains, and subcellular location analyses discussed in this article. In fact, our analysis showed that the identified genes harbor the following two conserved domains: a catalase domain (pfam00199) and a catalase-related domain (pfam06628). Phylogenetic analyses showed that the identified wheat CAT proteins were present in an analogous form in durum wheat and bread wheat. Moreover, the identified CAT proteins were located essentially in the peroxisome, as revealed by in silico analyses. Interestingly, analyses of CAT promoters in those species revealed the presence of different cis elements related to plant development, maturation, and plant responses to different environmental stresses. According to RT-qPCR, Triticum CAT genes showed distinctive expression designs in the studied organs and in response to different treatments (salt, heat, cold, mannitol, and ABA). This study completed a thorough analysis of the CAT genes in Triticeae, which advances our knowledge of CAT genes and establishes a framework for further functional analyses of the wheat gene family.
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Affiliation(s)
- Mouna Ghorbel
- Department of Biology, College of Sciences, University of Hail, P.O. Box 2440, Ha’il City 81451, Saudi Arabia; (M.G.); (N.H.); (A.J.S.); (N.B.)
| | - Ikram Zribi
- Laboratory of Biotechnology and Plant Improvement, Center of Biotechnology of Sfax, P.O. Box 1177, Sfax 3018, Tunisia;
| | - Najla Haddaji
- Department of Biology, College of Sciences, University of Hail, P.O. Box 2440, Ha’il City 81451, Saudi Arabia; (M.G.); (N.H.); (A.J.S.); (N.B.)
| | - Arif Jamal Siddiqui
- Department of Biology, College of Sciences, University of Hail, P.O. Box 2440, Ha’il City 81451, Saudi Arabia; (M.G.); (N.H.); (A.J.S.); (N.B.)
| | - Nouha Bouali
- Department of Biology, College of Sciences, University of Hail, P.O. Box 2440, Ha’il City 81451, Saudi Arabia; (M.G.); (N.H.); (A.J.S.); (N.B.)
| | - Faiçal Brini
- Laboratory of Biotechnology and Plant Improvement, Center of Biotechnology of Sfax, P.O. Box 1177, Sfax 3018, Tunisia;
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Sha Y, Li Y, Zhang D, Lv R, Wang H, Wang R, Ji H, Li S, Gong L, Li N, Liu B. Genome shock in a synthetic allotetraploid wheat invokes subgenome-partitioned gene regulation, meiotic instability, and karyotype variation. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:5547-5563. [PMID: 37379452 DOI: 10.1093/jxb/erad247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 06/27/2023] [Indexed: 06/30/2023]
Abstract
It is becoming increasingly evident that interspecific hybridization at the homoploid level or coupled with whole-genome duplication (i.e. allopolyploidization) has played a major role in biological evolution. However, the direct impacts of hybridization and allopolyploidization on genome structure and function, phenotype, and fitness remains to be fully understood. Synthetic hybrids and allopolyploids are trackable experimental systems that can be used to address this issue. In this study, we resynthesized a pair of reciprocal F1 hybrids and corresponding reciprocal allotetraploids using the two diploid progenitor species of bread wheat (Triticum aestivum, BBAADD), namely T. urartu (AA) and Aegilops tauschii (DD). By comparing phenotypes related to growth, development, and fitness, and by analysing genome expression in both hybrids and allotetraploids in relation to the parents, we found that the types and trends of karyotype variation in the immediately formed allotetraploids were correlated with both instability of meiosis and chromosome- and subgenome-biased expression. We determined clear advantages of allotetraploids over diploid F1 hybrids in several morphological traits including fitness that mirrored the tissue- and developmental stage-dependent subgenome-partitioning of the allotetraploids. The allotetraploids were meiotically unstable primarily due to homoeologous pairing that varied dramatically among the chromosomes. Nonetheless, the manifestation of organismal karyotype variation and the occurrence of meiotic irregularity were not concordant, suggesting a role of functional constraints probably imposed by subgenome- and chromosome-biased gene expression. Our results provide new insights into the direct impacts and consequences of hybridization and allopolyploidization that are relevant to evolution and likely to be informative for future crop improvement approaches using synthetic polyploids.
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Affiliation(s)
- Yan Sha
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Yang Li
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Deshi Zhang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Ruili Lv
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Han Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Ruisi Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Heyu Ji
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Shuhang Li
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Lei Gong
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Ning Li
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
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Liu G, Xue G, Zhao T, Li Y, Yue L, Song H, Liu Q. Population structure and phylogeography of three closely related tree peonies. Ecol Evol 2023; 13:e10073. [PMID: 37274151 PMCID: PMC10234759 DOI: 10.1002/ece3.10073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 04/23/2023] [Accepted: 04/25/2023] [Indexed: 06/06/2023] Open
Abstract
Paeonia decomposita, Paeonia rotundiloba, and Paeonia rockii are three closely related species of Sect. Moutan is distributed in the montane area of the Eastern Hengduan Mountain region. Understanding the population history of these three tree peony species could contribute to unraveling the evolutionary patterns of undergrowth species in this hotspot area. We used one nuclear DNA marker (internal transcribed spacer region, ITS) and two chloroplast DNA markers (matK, ycf1) to reconstruct the phylogeographic pattern of the populations. In total, 228 individuals from 17 populations of the three species were analyzed in this study. Three nuclear clades (Clade I - Clade III) and four maternal clades (Clade A - Clade D) were reconstructed. Molecular dating suggested that young lineages diverged during the late Pliocene and early Pleistocene, younger than the uplift of the Hengduan Mountains but older than the last glacial maximum (LGM). Significant population and phylogeographic structures were detected at both markers. Furthermore, the populations of these tree peonies were overall at equilibrium during the climatic oscillations of the Pleistocene. The simulated palaeoranges of the three species during the LGM period mostly overlapped, which could have led to cross-breeding events. We propose an evolutionary scenario in which mountain orogenesis around the Hengduan Mountain area triggered parapatric isolation between maternal lineages of tree peonies. Subsequent climatic fluctuations drove migration and range recontact of these populations along the valleys. This detailed evolutionary history provides new insights into the phylogeographic pattern of species from mountain-valley systems.
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Affiliation(s)
- Guangli Liu
- College of Landscape ArchitectureSichuan Agricultural UniversityChengduChina
| | - Ge Xue
- College of Landscape ArchitectureSichuan Agricultural UniversityChengduChina
| | - Tingting Zhao
- College of Landscape ArchitectureSichuan Agricultural UniversityChengduChina
| | - Yang Li
- College of Landscape ArchitectureSichuan Agricultural UniversityChengduChina
| | - Liangliang Yue
- National Plateau Wetlands Research Center, College of WetlandsSouthwest Forestry UniversityKunmingChina
| | - Huixing Song
- College of Landscape ArchitectureSichuan Agricultural UniversityChengduChina
| | - Qinglin Liu
- College of Landscape ArchitectureSichuan Agricultural UniversityChengduChina
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Yang Y, Cui L, Lu Z, Li G, Yang Z, Zhao G, Kong C, Li D, Chen Y, Xie Z, Chen Z, Zhang L, Xia C, Liu X, Jia J, Kong X. Genome sequencing of Sitopsis species provides insights into their contribution to the B subgenome of bread wheat. PLANT COMMUNICATIONS 2023:100567. [PMID: 36855304 PMCID: PMC10363506 DOI: 10.1016/j.xplc.2023.100567] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 02/14/2023] [Accepted: 02/23/2023] [Indexed: 06/18/2023]
Abstract
Wheat (Triticum aestivum, BBAADD) is an allohexaploid species that originated from two polyploidization events. The progenitors of the A and D subgenomes have been identified as Triticum urartu and Aegilops tauschii, respectively. Current research suggests that Aegilops speltoides is the closest but not the direct ancestor of the B subgenome. However, whether Ae. speltoides has contributed genomically to the wheat B subgenome and which chromosome regions are conserved between Ae. speltoides and the B subgenome remain unclear. Here, we assembled a high-quality reference genome for Ae. speltoides, resequenced 53 accessions from seven species (Aegilops bicornis, Aegilops longissima, Aegilops searsii, Aegilops sharonensis, Ae. speltoides, Aegilops mutica [syn. Amblyopyrum muticum], and Triticum dicoccoides) and revealed their genomic contributions to the wheat B subgenome. Our results showed that centromeric regions were particularly conserved between Aegilops and Triticum and revealed 0.17 Gb of conserved blocks between Ae. speltoides and the B subgenome. We classified five groups of conserved and non-conserved genes between Aegilops and Triticum, revealing their biological characteristics, differentiation in gene expression patterns, and collinear relationships between Ae. speltoides and the wheat B subgenome. We also identified gene families that expanded in Ae. speltoides during its evolution and 789 genes specific to Ae. speltoides. These genes can serve as genetic resources for improvement of adaptability to biotic and abiotic stress. The newly constructed reference genome and large-scale resequencing data for Sitopsis species will provide a valuable genomic resource for wheat genetic improvement and genomic studies.
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Affiliation(s)
- Yuxin Yang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Licao Cui
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zefu Lu
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Guangrong Li
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Zujun Yang
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Guangyao Zhao
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Chuizheng Kong
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Danping Li
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yaoyu Chen
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zhencheng Xie
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zhongxu Chen
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Lichao Zhang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Chuan Xia
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xu Liu
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Jizeng Jia
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Xiuying Kong
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
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Zeibig F, Kilian B, Frei M. The grain quality of wheat wild relatives in the evolutionary context. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:4029-4048. [PMID: 34919152 PMCID: PMC9729140 DOI: 10.1007/s00122-021-04013-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 12/06/2021] [Indexed: 05/17/2023]
Abstract
We evaluated the potential of wheat wild relatives for the improvement in grain quality characteristics including micronutrients (Fe, Zn) and gluten and identified diploid wheats and the timopheevii lineage as the most promising resources. Domestication enabled the advancement of civilization through modification of plants according to human requirements. Continuous selection and cultivation of domesticated plants induced genetic bottlenecks. However, ancient diversity has been conserved in crop wild relatives. Wheat (Triticum aestivum L.; Triticum durum Desf.) is one of the most important staple foods and was among the first domesticated crop species. Its evolutionary diversity includes diploid, tetraploid and hexaploid species from the Triticum and Aegilops taxa and different genomes, generating an AA, BBAA/GGAA and BBAADD/GGAAAmAm genepool, respectively. Breeding and improvement in wheat altered its grain quality. In this review, we identified evolutionary patterns and the potential of wheat wild relatives for quality improvement regarding the micronutrients Iron (Fe) and Zinc (Zn), the gluten storage proteins α-gliadins and high molecular weight glutenin subunits (HMW-GS), and the secondary metabolite phenolics. Generally, the timopheevii lineage has been neglected to date regarding grain quality studies. Thus, the timopheevii lineage should be subject to grain quality research to explore the full diversity of the wheat gene pool.
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Affiliation(s)
- Frederike Zeibig
- Department of Agronomy and Crop Physiology, Institute of Agronomy and Plant Breeding I, Justus-Liebig-University, 35392, Giessen, Germany
| | | | - Michael Frei
- Department of Agronomy and Crop Physiology, Institute of Agronomy and Plant Breeding I, Justus-Liebig-University, 35392, Giessen, Germany.
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6
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Estimation of Nuclear DNA Content in Some Aegilops Species: Best Analyzed Using Flow Cytometry. Genes (Basel) 2022; 13:genes13111980. [DOI: 10.3390/genes13111980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 10/13/2022] [Accepted: 10/24/2022] [Indexed: 11/16/2022] Open
Abstract
The genera Triticum and Aegilops have been considered as the main gene pool of wheat due to their features, such as tolerance of all types of abiotic and biotic stresses. This study was conducted to evaluate the cytogenetic analyses in 115 native and wild populations from eleven Aegilops species using their nuclear DNA quantification. Mean 2C nuclear DNA contents of different ploidy levels in the wild wheat of Turkey and Iran were measured using the flow cytometry technique. The obtained results showed that the mean nuclear DNA content in diploid species varied from 10.09 pg/2C (Ae. umbellulata) to 10.95 pg/2C (Ae. speltoides var. ligustica) in Turkey. In Iranian diploids, the mean nuclear DNA content varied from 10.20 pg/2C (Ae. taushii) to 11.56 pg/2C (Ae. speltoides var. ligustica). This index in the tetraploid species of Turkey varied from 18.09 pg/2C (Ae. cylindrica) to 21.65 pg/2C (Ae. triaristata), and in Iranian species, it was from 18.61 pg/2C (Ae. cylindrica) to 21.75 pg/2C (Ae. columnaris). On the other hand, in the hexaploid species of Turkey, this index varied from 31.59 pg/2C (Ae. crassa) to 31.81 pg/2C (Ae. cylindrica); in the Iranian species, it varied from 32.58 pg/2C (Ae. cylindrica) to 33.97 pg/2C (Ae. crassa). There was a significant difference in the DNA content of Turkey and Iran diploid as well as tetraploid species; however, in hexaploid species, the difference was not significant. It was concluded that the variation in intraspecific genome size was very low in diploid and tetraploid populations; this means that the low variation is not dependent on geographic and climatic parameters. On the other hand, the interspecific variation is significant at the diploid and tetraploid populations. It is generally very difficult to distinguish Aegilops species from each other in natural conditions; meanwhile, in this study, all species could be, easily, quickly and unambiguously, distinguished and separated using the FCM technique.
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Li LF, Zhang ZB, Wang ZH, Li N, Sha Y, Wang XF, Ding N, Li Y, Zhao J, Wu Y, Gong L, Mafessoni F, Levy AA, Liu B. Genome sequences of five Sitopsis species of Aegilops and the origin of polyploid wheat B subgenome. MOLECULAR PLANT 2022; 15:488-503. [PMID: 34979290 DOI: 10.1016/j.molp.2021.12.019] [Citation(s) in RCA: 61] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 12/11/2021] [Accepted: 12/28/2021] [Indexed: 05/23/2023]
Abstract
Common wheat (Triticum aestivum, BBAADD) is a major staple food crop worldwide. The diploid progenitors of the A and D subgenomes have been unequivocally identified; that of B, however, remains ambiguous and controversial but is suspected to be related to species of Aegilops, section Sitopsis. Here, we report the assembly of chromosome-level genome sequences of all five Sitopsis species, namely Aegilops bicornis, Ae. longissima, Ae. searsii, Ae. sharonensis, and Ae. speltoides, as well as the partial assembly of the Amblyopyrum muticum (synonym Aegilops mutica) genome for phylogenetic analysis. Our results reveal that the donor of the common wheat B subgenome is a distinct, and most probably extinct, diploid species that diverged from an ancestral progenitor of the B lineage to which the still extant Ae. speltoides and Am. muticum belong. In addition, we identified interspecific genetic introgressions throughout the evolution of the Triticum/Aegilops species complex. The five Sitopsis species have various assembled genome sizes (4.11-5.89 Gb) with high proportions of repetitive sequences (85.99%-89.81%); nonetheless, they retain high collinearity with other genomes or subgenomes of species in the Triticum/Aegilops complex. Differences in genome size were primarily due to independent post-speciation amplification of transposons. We also identified a set of Sitopsis genes pertinent to important agronomic traits that can be harnessed for wheat breeding. These newly assembled genome resources provide a new roadmap for evolutionary and genetic studies of the Triticum/Aegilops complex, as well as for wheat improvement.
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Affiliation(s)
- Lin-Feng Li
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China; Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China.
| | - Zhi-Bin Zhang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China; Department of Plant and Environmental Sciences, The Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Zhen-Hui Wang
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130118, China
| | - Ning Li
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Yan Sha
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Xin-Feng Wang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Ning Ding
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Yang Li
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Jing Zhao
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Ying Wu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Lei Gong
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Fabrizio Mafessoni
- Department of Plant and Environmental Sciences, The Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Avraham A Levy
- Department of Plant and Environmental Sciences, The Weizmann Institute of Science, 76100 Rehovot, Israel.
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China.
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Badaeva ED, Konovalov FA, Knüpffer H, Fricano A, Ruban AS, Kehel Z, Zoshchuk SA, Surzhikov SA, Neumann K, Graner A, Hammer K, Filatenko A, Bogaard A, Jones G, Özkan H, Kilian B. Genetic diversity, distribution and domestication history of the neglected GGA tA t genepool of wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:755-776. [PMID: 34283259 PMCID: PMC8942905 DOI: 10.1007/s00122-021-03912-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 07/07/2021] [Indexed: 05/03/2023]
Abstract
We present a comprehensive survey of cytogenetic and genomic diversity of the GGAtAt genepool of wheat, thereby unlocking these plant genetic resources for wheat improvement. Wheat yields are stagnating around the world and new sources of genes for resistance or tolerances to abiotic traits are required. In this context, the tetraploid wheat wild relatives are among the key candidates for wheat improvement. Despite its potential huge value for wheat breeding, the tetraploid GGAtAt genepool is largely neglected. Understanding the population structure, native distribution range, intraspecific variation of the entire tetraploid GGAtAt genepool and its domestication history would further its use for wheat improvement. The paper provides the first comprehensive survey of genomic and cytogenetic diversity sampling the full breadth and depth of the tetraploid GGAtAt genepool. According to the results obtained, the extant GGAtAt genepool consists of three distinct lineages. We provide detailed insights into the cytogenetic composition of GGAtAt wheats, revealed group- and population-specific markers and show that chromosomal rearrangements play an important role in intraspecific diversity of T. araraticum. The origin and domestication history of the GGAtAt lineages is discussed in the context of state-of-the-art archaeobotanical finds. We shed new light on the complex evolutionary history of the GGAtAt wheat genepool and provide the basis for an increased use of the GGAtAt wheat genepool for wheat improvement. The findings have implications for our understanding of the origins of agriculture in southwest Asia.
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Affiliation(s)
- Ekaterina D Badaeva
- N.I. Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia.
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.
| | - Fedor A Konovalov
- Independent Clinical Bioinformatics Laboratory, Moscow, Russia
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Helmut Knüpffer
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Agostino Fricano
- Council for Agricultural Research and Economics - Research Centre for Genomics & Bioinformatics, Fiorenzuola d'Arda (PC), Italy
| | - Alevtina S Ruban
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
- KWS SAAT SE & Co. KGaA, Einbeck, Germany
| | - Zakaria Kehel
- International Center for the Agricultural Research in the Dry Areas (ICARDA), Rabat, Morocco
| | - Svyatoslav A Zoshchuk
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Sergei A Surzhikov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Kerstin Neumann
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Andreas Graner
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Karl Hammer
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Anna Filatenko
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
- Independent Researcher, St. Petersburg, Russia
| | | | - Glynis Jones
- Department of Archaeology, University of Sheffield, Sheffield, UK
| | - Hakan Özkan
- Department of Field Crops, Faculty of Agriculture, University of Çukurova, Adana, Turkey
| | - Benjamin Kilian
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
- Global Crop Diversity Trust, Bonn, Germany
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9
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Keilwagen J, Lehnert H, Berner T, Badaeva E, Himmelbach A, Börner A, Kilian B. Detecting major introgressions in wheat and their putative origins using coverage analysis. Sci Rep 2022; 12:1908. [PMID: 35115645 PMCID: PMC8813953 DOI: 10.1038/s41598-022-05865-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 01/12/2022] [Indexed: 12/11/2022] Open
Abstract
Introgressions from crop wild relatives (CWRs) have been used to introduce beneficial traits into cultivated plants. Introgressions have traditionally been detected using cytological methods. Recently, single nucleotide polymorphism (SNP)-based methods have been proposed to detect introgressions in crosses for which both parents are known. However, for unknown material, no method was available to detect introgressions and predict the putative donor species. Here, we present a method to detect introgressions and the putative donor species. We demonstrate the utility of this method using 10 publicly available wheat genome sequences and identify nine major introgressions. We show that the method can distinguish different introgressions at the same locus. We trace introgressions to early wheat cultivars and show that natural introgressions were utilised in early breeding history and still influence elite lines today. Finally, we provide evidence that these introgressions harbour resistance genes.
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Affiliation(s)
| | | | | | - Ekaterina Badaeva
- N.I. Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia.,The Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), Novosibirsk, Russia
| | - Axel Himmelbach
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Andreas Börner
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
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10
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Keilwagen J, Lehnert H, Berner T, Badaeva E, Himmelbach A, Börner A, Kilian B. Detecting major introgressions in wheat and their putative origins using coverage analysis. Sci Rep 2022; 12:1908. [PMID: 35115645 DOI: 10.21203/rs.3.rs-910879/v1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 01/12/2022] [Indexed: 05/26/2023] Open
Abstract
Introgressions from crop wild relatives (CWRs) have been used to introduce beneficial traits into cultivated plants. Introgressions have traditionally been detected using cytological methods. Recently, single nucleotide polymorphism (SNP)-based methods have been proposed to detect introgressions in crosses for which both parents are known. However, for unknown material, no method was available to detect introgressions and predict the putative donor species. Here, we present a method to detect introgressions and the putative donor species. We demonstrate the utility of this method using 10 publicly available wheat genome sequences and identify nine major introgressions. We show that the method can distinguish different introgressions at the same locus. We trace introgressions to early wheat cultivars and show that natural introgressions were utilised in early breeding history and still influence elite lines today. Finally, we provide evidence that these introgressions harbour resistance genes.
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Affiliation(s)
| | | | | | - Ekaterina Badaeva
- N.I. Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
- The Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), Novosibirsk, Russia
| | - Axel Himmelbach
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Andreas Börner
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
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11
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Wicker T, Stritt C, Sotiropoulos AG, Poretti M, Pozniak C, Walkowiak S, Gundlach H, Stein N. Transposable Element Populations Shed Light on the Evolutionary History of Wheat and the Complex Co-Evolution of Autonomous and Non-Autonomous Retrotransposons. ADVANCED GENETICS (HOBOKEN, N.J.) 2021; 3:2100022. [PMID: 36619351 PMCID: PMC9744471 DOI: 10.1002/ggn2.202100022] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Indexed: 01/11/2023]
Abstract
Wheat has one of the largest and most repetitive genomes among major crop plants, containing over 85% transposable elements (TEs). TEs populate genomes much in the way that individuals populate ecosystems, diversifying into different lineages, sub-families and sub-populations. The recent availability of high-quality, chromosome-scale genome sequences from ten wheat lines enables a detailed analysis how TEs evolved in allohexaploid wheat, its diploids progenitors, and in various chromosomal haplotype segments. LTR retrotransposon families evolved into distinct sub-populations and sub-families that were active in waves lasting several hundred thousand years. Furthermore, It is shown that different retrotransposon sub-families were active in the three wheat sub-genomes, making them useful markers to study and date polyploidization events and chromosomal rearrangements. Additionally, haplotype-specific TE sub-families are used to characterize chromosomal introgressions in different wheat lines. Additionally, populations of non-autonomous TEs co-evolved over millions of years with their autonomous partners, leading to complex systems with multiple types of autonomous, semi-autonomous and non-autonomous elements. Phylogenetic and TE population analyses revealed the relationships between non-autonomous elements and their mobilizing autonomous partners. TE population analysis provided insights into genome evolution of allohexaploid wheat and genetic diversity of species, and may have implication for future crop breeding.
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Affiliation(s)
- Thomas Wicker
- Department of Plant and Microbial BiologyUniversity of ZurichZurich8008Switzerland
| | - Christoph Stritt
- Department of Plant and Microbial BiologyUniversity of ZurichZurich8008Switzerland,Present address:
Department of Medical Parasitology and Infection BiologySwiss Tropical and Public Health InstituteBasel4123Switzerland,Present address:
University of BaselBasel4001Switzerland
| | | | - Manuel Poretti
- Department of Plant and Microbial BiologyUniversity of ZurichZurich8008Switzerland
| | - Curtis Pozniak
- Crop Development CentreUniversity of SaskatchewanSaskatoonSaskatchewanSK S7N 5A8Canada
| | - Sean Walkowiak
- Crop Development CentreUniversity of SaskatchewanSaskatoonSaskatchewanSK S7N 5A8Canada,Grain Research LaboratoryCanadian Grain CommissionWinnipegManitobaR3C 3G8Canada
| | - Heidrun Gundlach
- PGSB Plant Genome and Systems BiologyHelmholtz Center MunichGerman Research Center for Environmental HealthNeuherberg85764Germany
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Seeland06466Germany,Center of Integrated Breeding Research (CiBreed)Department of Crop SciencesGeorg‐August‐UniversityGöttingen37075Germany
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12
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Elisafenko EA, Evtushenko EV, Vershinin AV. The origin and evolution of a two-component system of paralogous genes encoding the centromeric histone CENH3 in cereals. BMC PLANT BIOLOGY 2021; 21:541. [PMID: 34794377 PMCID: PMC8603533 DOI: 10.1186/s12870-021-03264-3] [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: 03/21/2021] [Accepted: 10/12/2021] [Indexed: 06/07/2023]
Abstract
BACKGROUND The cereal family Poaceae is one of the largest and most diverse angiosperm families. The central component of centromere specification and function is the centromere-specific histone H3 (CENH3). Some cereal species (maize, rice) have one copy of the gene encoding this protein, while some (wheat, barley, rye) have two. We applied a homology-based approach to sequenced cereal genomes, in order to finally trace the mutual evolution of the structure of the CENH3 genes and the nearby regions in various tribes. RESULTS We have established that the syntenic group or the CENH3 locus with the CENH3 gene and the boundaries defined by the CDPK2 and bZIP genes first appeared around 50 Mya in a common ancestor of the subfamilies Bambusoideae, Oryzoideae and Pooideae. This locus came to Pooideae with one copy of CENH3 in the most ancient tribes Nardeae and Meliceae. The βCENH3 gene as a part of the locus appeared in the tribes Stipeae and Brachypodieae around 35-40 Mya. The duplication was accompanied by changes in the exon-intron structure. Purifying selection acts mostly on αCENH3s, while βCENH3s form more heterogeneous structures, in which clade-specific amino acid motifs are present. In barley species, the βCENH3 gene assumed an inverted orientation relative to αCENH3 and the CDPK2 gene was substituted with LHCB-l. As the evolution and domestication of plant species went on, the locus was growing in size due to an increasing distance between αCENH3 and βCENH3 because of a massive insertion of the main LTR-containing retrotransposon superfamilies, gypsy and copia, without any evolutionary preference on either of them. A comparison of the molecular structure of the locus in the A, B and D subgenomes of the hexaploid wheat T. aestivum showed that invasion by mobile elements and concomitant rearrangements took place in an independent way even in evolutionarily close species. CONCLUSIONS The CENH3 duplication in cereals was accompanied by changes in the exon-intron structure of the βCENH3 paralog. The observed general tendency towards the expansion of the CENH3 locus reveals an amazing diversity of ways in which different species implement the scenario described in this paper.
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Affiliation(s)
- Evgeny A Elisafenko
- Institute of Cytology and Genetics, SB RAS, Novosibirsk, 630090, Russia
- Institute of Molecular and Cellular Biology, SB RAS, Novosibirsk, 630090, Russia
| | - Elena V Evtushenko
- Institute of Molecular and Cellular Biology, SB RAS, Novosibirsk, 630090, Russia
| | - Alexander V Vershinin
- Institute of Molecular and Cellular Biology, SB RAS, Novosibirsk, 630090, Russia.
- Novosibirsk State University, Novosibirsk, 630090, Russia.
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13
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Alemu SK, Huluka AB, Tesfaye K, Haileselassie T, Uauy C. Genome-wide association mapping identifies yellow rust resistance loci in Ethiopian durum wheat germplasm. PLoS One 2021; 16:e0243675. [PMID: 33999918 PMCID: PMC8128278 DOI: 10.1371/journal.pone.0243675] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 04/16/2021] [Indexed: 12/28/2022] Open
Abstract
Durum wheat is an important cereal grown in Ethiopia, a country which is also its center for genetic diversity. Yellow (stripe) rust caused by Puccinia striiformis fsp tritici is one of the most devastating diseases threatening Ethiopian wheat production. To identify sources of genetic resistance and combat this pathogen, we conducted a genome wide association study of yellow rust resistance on 300 durum wheat accessions comprising 261 landraces and 39 cultivars. The accessions were evaluated for their field resistance using a modified Cobb scale at Meraro, Kulumsa and Chefe Donsa in the 2015 and 2016 main growing seasons. Analysis of the 35K Axiom Array genotyping data of the panel resulted in a total of 8,797 polymorphic SNPs of which 7,093 were used in subsequent analyses. Population structure analysis suggested two groups in which the cultivars clearly stood out separately from the landraces. Eleven SNPs significantly associated with yellow rust resistance were identified on four chromosomes (1A, 1B, 2B, and 5A) which defined at least five genomic loci. Six of the SNPs were consistently identified on chromosome 1B singly at each and combined overall environments which explained 62.6–64.0% of the phenotypic variation (R2). Resistant allele frequency ranged from 14.0–71.0%; Zooming in to the identified resistance loci revealed the presence of disease resistance related genes involved in the plant defense system such as the ABC transporter gene family, disease resistance protein RPM1 (NBS-LRR class), Receptor kinases and Protein kinases. This study has provided SNPs for tracking the loci associated with yellow rust resistance and a diversity panel which can be used for association study of other agriculturally important traits in durum wheat.
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Affiliation(s)
- Sisay Kidane Alemu
- National Agricultural Biotechnology Research Center, Holeta, Ethiopian Institute of Agricultural Research, Addis Ababa, Ethiopia
- * E-mail:
| | - Ayele Badebo Huluka
- International Maize and Wheat Improvement Center (CIMMYT), Addis Ababa, Ethiopia
| | - Kassahun Tesfaye
- Institute of Biotechnology and DMCMB, Addis Ababa University, Addis Ababa, Ethiopia
| | | | - Cristobal Uauy
- John Innes Centre, Norwich Research Park, Norwich, United Kingdom
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14
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Zhang W, Zhao J, He J, Kang L, Wang X, Zhang F, Hao C, Ma X, Chen D. Functional gene assessment of bread wheat: breeding implications in Ningxia Province. BMC PLANT BIOLOGY 2021; 21:103. [PMID: 33602134 PMCID: PMC7893757 DOI: 10.1186/s12870-021-02870-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 02/01/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND The overall genetic distribution and divergence of cloned genes among bread wheat varieties that have occurred during the breeding process over the past few decades in Ningxia Province, China, are poorly understood. Here, we report the genetic diversities of 44 important genes related to grain yield, quality, adaptation and resistance in 121 Ningxia and 86 introduced wheat cultivars and advanced lines. RESULTS The population structure indicated characteristics of genetic components of Ningxia wheat, including landraces of particular genetic resources, introduced varieties with rich genetic diversities and modern cultivars in different periods. Analysis of allele frequencies showed that the dwarfing alleles Rht-B1b at Rht-B1 and Rht-D1b at Rht-D1, 1BL/1RS translocation, Hap-1 at GW2-6B and Hap-H at Sus2-2B are very frequently present in modern Ningxia cultivars and in introduced varieties from other regions but absent in landraces. This indicates that the introduced wheat germplasm with numerous beneficial genes is vital for broadening the genetic diversity of Ningxia wheat varieties. Large population differentiation between modern cultivars and landraces has occurred in adaptation genes. Founder parents carry excellent allele combinations of important genes, with a higher number of favorable alleles than modern cultivars. Gene flow analysis showed that six founder parents have greatly contributed to breeding improvement in Ningxia Province, particularly Zhou 8425B, for yield-related genes. CONCLUSIONS Varieties introduced from other regions with rich genetic diversity and landraces with well-adapted genetic resources have been applied to improve modern cultivars. Founder parents, particularly Zhou 8425B, for yield-related genes have contributed greatly to wheat breeding improvement in Ningxia Province. These findings will greatly benefit bread wheat breeding in Ningxia Province as well as other areas with similar ecological environments.
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Affiliation(s)
- Weijun Zhang
- Crop Research Institute, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, 750002 Ningxia China
| | - Junjie Zhao
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 Henan China
| | - Jinshang He
- Crop Research Institute, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, 750002 Ningxia China
| | - Ling Kang
- Crop Research Institute, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, 750002 Ningxia China
| | - Xiaoliang Wang
- Crop Research Institute, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, 750002 Ningxia China
| | - Fuguo Zhang
- Crop Research Institute, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, 750002 Ningxia China
| | - Chenyang Hao
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs/The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Xiongfeng Ma
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 Henan China
| | - Dongsheng Chen
- Crop Research Institute, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, 750002 Ningxia China
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15
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Dai Y, Huang S, Sun G, Li H, Chen S, Gao Y, Chen J. Origins and chromosome differentiation of Thinopyrum elongatum revealed by PepC and Pgk1 genes and ND-FISH. Genome 2021; 64:901-913. [PMID: 33596125 DOI: 10.1139/gen-2019-0176] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Thinopyrum elongatum is an important gene pool for wheat genetic improvement. However, the origins of the Thinopyrum genomes and the nature of the genus' intraspecific relationships are still controversial. In this study, we used single-copy nuclear genes and non-denaturing fluorescence in situ hybridization (ND-FISH) to characterize genome constitution and chromosome differentiation in Th. elongatum. According to phylogenetic analyses based on PepC and Pgk1 genes, there was an E genome with three versions (Ee, Eb, Ex) and St genomes in the polyploid Th. elongatum. The ND-FISH results of pSc119.2 and pAs1 revealed that the karyotypes of diploid Th. elongatum and Th. bessarabicum were different, and the chromosome differentiation occurred among accessions of the diploid Th. elongatum. In addition, the tetraploid Th. elongatum has two groups of ND-FISH karyotype, indicating that the tetraploid Th. elongatum might be a segmental allotetraploid. In summary, our results suggested that the diploid Th. elongatum, Th. Bessarabicum, and Pseudoroegneria were the donors of the Ee, Eb, and St genomes to the polyploid Th. elongatum, respectively.
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Affiliation(s)
- Yi Dai
- Joint International Research Laboratory of Agriculture and Agri-product Safety, the Ministry of Education of China, Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou 225009, China.,Jiangsu Key Laboratories of Crop Genetics and Physiology and Plant Functional Genomics of the Ministry of Education, Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province, Yangzhou University, Yangzhou 225009, China
| | - Shuai Huang
- Jiangsu Key Laboratories of Crop Genetics and Physiology and Plant Functional Genomics of the Ministry of Education, Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province, Yangzhou University, Yangzhou 225009, China
| | - Genlou Sun
- Department of Biology, Saint Mary's University, Halifax, NS B3H 3C3, Canada
| | - Haifeng Li
- Yangzhou Polytechnic College, Yangzhou 225009, China
| | - Shiqiang Chen
- Institute of Agricultural Sciences, Lixia River Region, Yangzhou 225009, China
| | - Yong Gao
- Jiangsu Key Laboratories of Crop Genetics and Physiology and Plant Functional Genomics of the Ministry of Education, Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province, Yangzhou University, Yangzhou 225009, China
| | - Jianmin Chen
- Jiangsu Key Laboratories of Crop Genetics and Physiology and Plant Functional Genomics of the Ministry of Education, Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province, Yangzhou University, Yangzhou 225009, China
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16
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Distinct nucleotide patterns among three subgenomes of bread wheat and their potential origins during domestication after allopolyploidization. BMC Biol 2020; 18:188. [PMID: 33267868 PMCID: PMC7713161 DOI: 10.1186/s12915-020-00917-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 11/05/2020] [Indexed: 11/13/2022] Open
Abstract
Background The speciation and fast global domestication of bread wheat have made a great impact on three subgenomes of bread wheat. DNA base composition is an essential genome feature, which follows the individual-strand base equality rule and [AT]-increase pattern at the genome, chromosome, and polymorphic site levels among thousands of species. Systematic analyses on base compositions of bread wheat and its wild progenitors could facilitate further understanding of the evolutionary pattern of genome/subgenome-wide base composition of allopolyploid species and its potential causes. Results Genome/subgenome-wide base-composition patterns were investigated by using the data of polymorphic site in 93 accessions from worldwide populations of bread wheat, its diploid and tetraploid progenitors, and their corresponding reference genome sequences. Individual-strand base equality rule and [AT]-increase pattern remain in recently formed hexaploid species bread wheat at the genome, subgenome, chromosome, and polymorphic site levels. However, D subgenome showed the fastest [AT]-increase across polymorphic site from Aegilops tauschii to bread wheat than that on A and B subgenomes from wild emmer to bread wheat. The fastest [AT]-increase could be detected almost all chromosome windows on D subgenome, suggesting different mechanisms between D and other two subgenomes. Interestingly, the [AT]-increase is mainly contributed by intergenic regions at non-selective sweeps, especially the fastest [AT]-increase of D subgenome. Further transition frequency and sequence context analysis indicated that three subgenomes shared same mutation type, but D subgenome owns the highest mutation rate on high-frequency mutation type. The highest mutation rate on D subgenome was further confirmed by using a bread-wheat-private SNP set. The exploration of loci/genes related to the [AT] value of D subgenome suggests the fastest [AT]-increase of D subgenome could be involved in DNA repair systems distributed on three subgenomes of bread wheat. Conclusions The highest mutation rate is detected on D subgenome of bread wheat during domestication after allopolyploidization, leading to the fastest [AT]-increase pattern of D subgenome. The phenomenon may come from the joint action of multiple repair systems inherited from its wild progenitors. Supplementary information The online version contains supplementary material available at 10.1186/s12915-020-00917-x.
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17
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Muñoz-Ramírez CP, Barnes DKA, Cárdenas L, Meredith MP, Morley SA, Roman-Gonzalez A, Sands CJ, Scourse J, Brante A. Gene flow in the Antarctic bivalve Aequiyoldia eightsii (Jay, 1839) suggests a role for the Antarctic Peninsula Coastal Current in larval dispersal. ROYAL SOCIETY OPEN SCIENCE 2020; 7:200603. [PMID: 33047024 PMCID: PMC7540763 DOI: 10.1098/rsos.200603] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 08/21/2020] [Indexed: 05/12/2023]
Abstract
The Antarctic Circumpolar Current (ACC) dominates the open-ocean circulation of the Southern Ocean, and both isolates and connects the Southern Ocean biodiversity. However, the impact on biological processes of other Southern Ocean currents is less clear. Adjacent to the West Antarctic Peninsula (WAP), the ACC flows offshore in a northeastward direction, whereas the Antarctic Peninsula Coastal Current (APCC) follows a complex circulation pattern along the coast, with topographically influenced deflections depending on the area. Using genomic data, we estimated genetic structure and migration rates between populations of the benthic bivalve Aequiyoldia eightsii from the shallows of southern South America and the WAP to test the role of the ACC and the APCC in its dispersal. We found strong genetic structure across the ACC (between southern South America and Antarctica) and moderate structure between populations of the WAP. Migration rates along the WAP were consistent with the APCC being important for species dispersal. Along with supporting current knowledge about ocean circulation models at the WAP, migration from the tip of the Antarctic Peninsula to the Bellingshausen Sea highlights the complexities of Southern Ocean circulation. This study provides novel biological evidence of a role of the APCC as a driver of species dispersal and highlights the power of genomic data for aiding in the understanding of the influence of complex oceanographic processes in shaping the population structure of marine species.
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Affiliation(s)
- Carlos P. Muñoz-Ramírez
- Instituto de Entomología, Facultad de Ciencias Básicas, Universidad Metropolitana de Ciencias de la Educación, Santiago, Chile
- Facultad de Ciencias, Universidad Católica de la Santísima Concepción, Concepción, Chile
- Centro de Investigación en Biodiversidad y Ambientes Sustentables (CIBAS), Universidad Católica de la Santísima Concepción, Concepción, Chile
| | - David K. A. Barnes
- British Antarctic Survey, Natural Environment Research Council, Cambridge, UK
| | - Leyla Cárdenas
- Centro FONDAP de Investigación Dinámica de Ecosistemas Marinos de Altas Latitudes (IDEAL), Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, UniversidadAustral de Chile, Valdivia, Chile
| | - Michael P. Meredith
- British Antarctic Survey, Natural Environment Research Council, Cambridge, UK
| | - Simon A. Morley
- British Antarctic Survey, Natural Environment Research Council, Cambridge, UK
| | | | - Chester J. Sands
- British Antarctic Survey, Natural Environment Research Council, Cambridge, UK
| | - James Scourse
- College of Life and Environmental Sciences, University of Exeter, Penryn, Cornwall TR10 9EZ, UK
| | - Antonio Brante
- Facultad de Ciencias, Universidad Católica de la Santísima Concepción, Concepción, Chile
- Centro de Investigación en Biodiversidad y Ambientes Sustentables (CIBAS), Universidad Católica de la Santísima Concepción, Concepción, Chile
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18
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Zhang J, Yang F, Jiang Y, Guo Y, Wang Y, Zhu X, Li J, Wan H, Wang Q, Deng Z, Xuan P, Yang W. Preferential Subgenome Elimination and Chromosomal Structural Changes Occurring in Newly Formed Tetraploid Wheat- Aegilops ventricosa Amphiploid (AABBD vD vN vN v). Front Genet 2020; 11:330. [PMID: 32477398 PMCID: PMC7235383 DOI: 10.3389/fgene.2020.00330] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 03/20/2020] [Indexed: 11/15/2022] Open
Abstract
Artificial allopolyploids derived from the genera Triticum and Aegilops have been used as genetic resources for wheat improvement and are a classic example of evolution via allopolyploidization. In this study, we investigated chromosomes and subgenome transmission behavior in the newly formed allopolyploid of wheat group via multicolor Fluorescence in situ hybridization (mc-FISH), using pSc119.2, pTa535, and (GAA)7 as probe combinations, to enabled us to precisely identify individual chromosomes in 381 S3 and S4 generations plants derived from reciprocal crosses between Ae. ventricosa (DvDvNvNv) and T. turgidum (AABB). A higher rate of aneuploidy, constituting 66.04–86.41% individuals, was observed in these two early generations. Of the four constituent subgenomes, Dv showed the highest frequency of elimination, followed by Nv and B, while A was the most stable. In addition, structural chromosomal changes occurred ubiquitously in the selfed progenies of allopolyploids. Among the constituent subgenomes, B showed the highest number of aberrations. In terms of chromosomal dynamics, there was no significant association between the chromosomal behavior model and the cytoplasm, with the exception of chromosomal loss in the Dv subgenome. The chromosome loss frequency in the Dv subgenome was significantly higher in the T. turgidum × Ae. ventricosa cross than in the Ae. ventricosa × T. turgidum cross. This result indicates that, although the D subgenome showed great instability, allopolyploids containing D subgenome could probably be maintained after a certain hybridization in which the D subgenome donor was used as the maternal parent at its onset stage. Our findings provide valuable information pertaining to the behavior patterns of subgenomes during allopolyploidization. Moreover, the allopolyploids developed here could be used as potential resources for the genetic improvement of wheat.
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Affiliation(s)
- Jie Zhang
- Institute of Biotechnology and Nuclear Technology Research, Sichuan Academy of Agricultural Sciences, Chengdu, China.,Key Laboratory of Wheat Biology and Genetic Improvement on Southwestern China (Ministry of Agriculture), Chengdu, China
| | - Fan Yang
- Institute of Crop Research, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Yun Jiang
- Institute of Biotechnology and Nuclear Technology Research, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Yuanlin Guo
- Institute of Biotechnology and Nuclear Technology Research, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Ying Wang
- Institute of Biotechnology and Nuclear Technology Research, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - XinGuo Zhu
- Institute of Crop Research, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Jun Li
- Key Laboratory of Wheat Biology and Genetic Improvement on Southwestern China (Ministry of Agriculture), Chengdu, China.,Institute of Crop Research, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Hongshen Wan
- Key Laboratory of Wheat Biology and Genetic Improvement on Southwestern China (Ministry of Agriculture), Chengdu, China.,Institute of Crop Research, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Qin Wang
- Institute of Crop Research, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Ziyuan Deng
- Institute of Biotechnology and Nuclear Technology Research, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Pu Xuan
- Institute of Agro-products Processing Science and Technology, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - WuYun Yang
- Key Laboratory of Wheat Biology and Genetic Improvement on Southwestern China (Ministry of Agriculture), Chengdu, China.,Institute of Crop Research, Sichuan Academy of Agricultural Sciences, Chengdu, China
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Wan W, Xiao J, Li M, Tang X, Wen M, Cheruiyot AK, Li Y, Wang H, Wang X. Fine mapping of wheat powdery mildew resistance gene Pm6 using 2B/2G homoeologous recombinants induced by the ph1b mutant. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:1265-1275. [PMID: 31974668 DOI: 10.1007/s00122-020-03546-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 01/13/2020] [Indexed: 05/07/2023]
Abstract
Using the ph1b mutant, the recombination frequency between the homoeologous region of 2B and 2G was significantly increased. By this, we narrowed Pm6 to a 0.9 Mb physical region. The powdery mildew (Pm) resistance gene Pm6 from Triticum timopheevii (2n = 48, AAGG) was mapped to the long arm of chromosome 2G and introduced into common wheat in the form of 2B-2G introgressions. The introgression line IGV1-465 has the shortest 2G segment, which is estimated 37 Mb in size when referring to 2BL genome reference of Chinese Spring (CS). The further fine mapping of Pm6 was impeded by the inhibition of allogeneic chromosome recombination between 2B and 2G in the Pm6 region. In the present study, to overcome 2B/2G recombination suppression, a ph1b-based strategy was employed to produce introgressions with reduced 2G fragments for the fine mapping of Pm6. IGV1-465 was crossed and backcrossed to the CSph1b mutant to produce plants with increased 2B/2G chromosome pairing frequency at the Pm6 region. A total of 182 allogeneic recombinants were obtained through two-round screening, i.e., first round of screening of 820 BC1F2:3 progenies using the flanking markers CIT02g-14/CIT02g-19 and second round of screening of 642 BC1F2:4 progenies using the flanking markers CIT02g-13/CIT02g-18, respectively. Through marker analysis using 30 chromosome 2G-specific markers located in the Pm6 region, the identified recombinants were divided into 14 haplotypes. Pm resistance evaluation of these haplotypes enabled us to narrow Pm6 to a 0.9 Mb physical region of 2BL, flanked by markers CIT02g-20 and CIT02g-18. Six wheat varieties containing Pm6 were identified from a natural population, and they showed increased Pm resistance. This implied Pm6 is still effective, especially when used in combination with other Pm resistance genes.
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Affiliation(s)
- Wentao Wan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095, Jiangsu, China
| | - Jin Xiao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095, Jiangsu, China
| | - Mengli Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095, Jiangsu, China
| | - Xiong Tang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095, Jiangsu, China
| | - Mingxing Wen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095, Jiangsu, China
- Zhenjiang Institute of Agricultural Sciences, Jurong, 212400, Jiangsu, China
| | - Antony Kibet Cheruiyot
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095, Jiangsu, China
| | - Yingbo Li
- Biotech Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai, 201106, China
| | - Haiyan Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095, Jiangsu, China.
| | - Xiue Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095, Jiangsu, China.
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20
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Interaction between serine carboxypeptidase-like protein TtGS5 and Annexin D1 in developing seeds of Triticum timopheevi. J Appl Genet 2020; 61:151-162. [PMID: 31970663 DOI: 10.1007/s13353-020-00539-7] [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: 01/07/2019] [Revised: 12/20/2019] [Accepted: 01/08/2020] [Indexed: 01/18/2023]
Abstract
GS5 encoding a serine carboxypeptidase-like protein positively regulates grain size and weight through the regulation of grain width and filling and is helpful in improving cereal yields. Grain width variation determined by GS5 is associated with cell number and size, but the actual underlying mechanism is still unclear. Two orthologs of GS5, TtGS5-3A-G and TtGS5-3G-G, were cloned from the Triticum timopheevi accession no. CWI17006. To identify the proteins that interacted with TtGS5-3A-G and TtGS5-3G-G in premature grains, we performed pull-down assays followed by liquid chromatography-mass spectrometry/mass spectrometry analysis. The analyses revealed 18 proteins were present in both the TtGS5-3A-G and TtGS5-3G-G interactomes. Among five candidates selected, only Annexin D1 interacted with both TtGS5-3A-G and TtGS5-3G-G in yeast. Annexin D1, TtGS5-3A-G, and TtGS5-3G-G were located on the cytoplasmic membranes of Arabidopsis protoplasts and onion epidermal cells, and interactions between Annexin D1 and TtGS5-3A-G, as well as TtGS5-3G-G, were shown by bimolecular fluorescence complementation assays. Annexin D1 was expressed widely in different tissues, and it co-expressed with TtGS5-3A-G/TtGS5-3G-G at the grain enlargement phase. These results indicated that Annexin D1 interacted with TtGS5-3A-G and TtGS5-3G-G in premature grains. Together with the structural similarities of Annexin D1 to known fiber elongation factors, we proposed that TtGS5 might regulate the cell size by interacting with Annexin D1. The results provide significant new information for understanding the roles that GS5 plays in regulating grain size, which may be useful in improving crop yields.
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Hyun DY, Sebastin R, Lee KJ, Lee GA, Shin MJ, Kim SH, Lee JR, Cho GT. Genotyping-by-Sequencing Derived Single Nucleotide Polymorphisms Provide the First Well-Resolved Phylogeny for the Genus Triticum (Poaceae). FRONTIERS IN PLANT SCIENCE 2020; 11:688. [PMID: 32625218 PMCID: PMC7311657 DOI: 10.3389/fpls.2020.00688] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 04/30/2020] [Indexed: 05/17/2023]
Abstract
Wheat (Triticum spp.) has been an important staple food crop for mankind since the beginning of agriculture. The genus Triticum L. is composed of diploid, tetraploid, and hexaploid species, majority of which have not yet been discriminated clearly, and hence their phylogeny and classification remain unresolved. Genotyping-by-sequencing (GBS) is an easy and affordable method that allows us to generate genome-wide single nucleotide polymorphism (SNP) markers. In this study, we used GBS to obtain SNPs covering all seven chromosomes from 283 accessions of Triticum-related genera. After filtering low-quality and redundant SNPs based on haplotype information, the GBS assay provided 14,188 high-quality SNPs that were distributed across the A (71%), B (26%), and D (2.4%) genomes. Cluster analysis and discriminant analysis of principal components (DAPC) allowed us to distinguish six distinct groups that matched well with Triticum species complexity. We constructed a Bayesian phylogenetic tree using 14,188 SNPs, in which 17 Triticum species and subspecies were discriminated. Dendrogram analysis revealed that the polyploid wheat species could be divided into groups according to the presence of A, B, D, and G genomes with strong nodal support and provided new insight into the evolution of spelt wheat. A total of 2,692 species-specific SNPs were identified to discriminate the common (T. aestivum) and durum (T. turgidum) wheat cultivar and landraces. In principal component analysis grouping, the two wheat species formed individual clusters and the SNPs were able to distinguish up to nine groups of 10 subspecies. This study demonstrated that GBS-derived SNPs could be used efficiently in genebank management to classify Triticum species and subspecies that are very difficult to distinguish by their morphological characters.
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22
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Ivanizs L, Monostori I, Farkas A, Megyeri M, Mikó P, Türkösi E, Gaál E, Lenykó-Thegze A, Szőke-Pázsi K, Szakács É, Darkó É, Kiss T, Kilian A, Molnár I. Unlocking the Genetic Diversity and Population Structure of a Wild Gene Source of Wheat, Aegilops biuncialis Vis., and Its Relationship With the Heading Time. FRONTIERS IN PLANT SCIENCE 2019; 10:1531. [PMID: 31824545 PMCID: PMC6882925 DOI: 10.3389/fpls.2019.01531] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 11/01/2019] [Indexed: 06/02/2023]
Abstract
Understanding the genetic diversity of Aegilops biuncialis, a valuable source of agronomical useful genes, may significantly facilitate the introgression breeding of wheat. The genetic diversity and population structure of 86 Ae. biuncialis genotypes were investigated by 32700 DArT markers with the simultaneous application of three statistical methods- neighbor-joining clustering, Principal Coordinate Analysis, and the Bayesian approach to classification. The collection of Ae. biuncialis accessions was divided into five groups that correlated well with their eco-geographic habitat: A (North Africa), B (mainly from Balkans), C (Kosovo and Near East), D (Turkey, Crimea, and Peloponnese), and E (Azerbaijan and the Levant region). The diversity between the Ae. biuncialis accessions for a phenological trait (heading time), which is of decisive importance in the adaptation of plants to different eco-geographical environments, was studied over 3 years. A comparison of the intraspecific variation in the heading time trait by means of analysis of variance and principal component analysis revealed four phenotypic categories showing association with the genetic structure and geographic distribution, except for minor differences. The detailed exploration of genetic and phenologic divergence provides an insight into the adaptation capacity of Ae. biuncialis, identifying promising genotypes that could be utilized for wheat improvement.
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Affiliation(s)
- László Ivanizs
- Agricultural Institute, Centre for Agricultural Research, Martonvásár, Hungary
| | - István Monostori
- Agricultural Institute, Centre for Agricultural Research, Martonvásár, Hungary
| | - András Farkas
- Agricultural Institute, Centre for Agricultural Research, Martonvásár, Hungary
| | - Mária Megyeri
- Agricultural Institute, Centre for Agricultural Research, Martonvásár, Hungary
| | - Péter Mikó
- Agricultural Institute, Centre for Agricultural Research, Martonvásár, Hungary
| | - Edina Türkösi
- Agricultural Institute, Centre for Agricultural Research, Martonvásár, Hungary
| | - Eszter Gaál
- Agricultural Institute, Centre for Agricultural Research, Martonvásár, Hungary
| | | | - Kitti Szőke-Pázsi
- Agricultural Institute, Centre for Agricultural Research, Martonvásár, Hungary
| | - Éva Szakács
- Agricultural Institute, Centre for Agricultural Research, Martonvásár, Hungary
| | - Éva Darkó
- Agricultural Institute, Centre for Agricultural Research, Martonvásár, Hungary
| | - Tibor Kiss
- Agricultural Institute, Centre for Agricultural Research, Martonvásár, Hungary
| | - Andrzej Kilian
- University of Canberra, Diversity Array Technologies, Canberra, ACT, Australia
| | - István Molnár
- Agricultural Institute, Centre for Agricultural Research, Martonvásár, Hungary
- Institute of Experimental Botany, Center of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czechia
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23
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Gholamian F, Etminan A, Changizi M, Khaghani S, Gomarian M. Assessment of genetic diversity inTriticum urartuThumanjan ex Gandilyan accessions using start codon targeted polymorphism (SCoT) and CAAT-box derived polymorphism (CBDP) markers. BIOTECHNOL BIOTEC EQ 2019. [DOI: 10.1080/13102818.2019.1691466] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Affiliation(s)
- Fataneh Gholamian
- Department of Agronomy and Plant Breeding, Arak Branch, Islamic Azad University, Arak, Iran
| | - Alireza Etminan
- Department of Plant Breeding and Biotechnology, Kermanshah Branch, Islamic Azad University, Kermanshah, Iran
| | - Mahdi Changizi
- Department of Agronomy and Plant Breeding, Arak Branch, Islamic Azad University, Arak, Iran
| | - Shahab Khaghani
- Department of Agronomy and Plant Breeding, Arak Branch, Islamic Azad University, Arak, Iran
| | - Masoud Gomarian
- Department of Agronomy and Plant Breeding, Arak Branch, Islamic Azad University, Arak, Iran
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24
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Cheng H, Liu J, Wen J, Nie X, Xu L, Chen N, Li Z, Wang Q, Zheng Z, Li M, Cui L, Liu Z, Bian J, Wang Z, Xu S, Yang Q, Appels R, Han D, Song W, Sun Q, Jiang Y. Frequent intra- and inter-species introgression shapes the landscape of genetic variation in bread wheat. Genome Biol 2019; 20:136. [PMID: 31300020 PMCID: PMC6624984 DOI: 10.1186/s13059-019-1744-x] [Citation(s) in RCA: 100] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 06/22/2019] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Bread wheat is one of the most important and broadly studied crops. However, due to the complexity of its genome and incomplete genome collection of wild populations, the bread wheat genome landscape and domestication history remain elusive. RESULTS By investigating the whole-genome resequencing data of 93 accessions from worldwide populations of bread wheat and its diploid and tetraploid progenitors, together with 90 published exome-capture data, we find that the B subgenome has more variations than A and D subgenomes, including SNPs and deletions. Population genetics analyses support a monophyletic origin of domesticated wheat from wild emmer in northern Levant, with substantial introgressed genomic fragments from southern Levant. Southern Levant contributes more than 676 Mb in AB subgenomes and enriched in the pericentromeric regions. The AB subgenome introgression happens at the early stage of wheat speciation and partially contributes to their greater genetic diversity. Furthermore, we detect massive alien introgressions that originated from distant species through natural and artificial hybridizations, resulting in the reintroduction of ~ 709 Mb and ~ 1577 Mb sequences into bread wheat landraces and varieties, respectively. A large fraction of these intra- and inter-introgression fragments are associated with quantitative trait loci of important traits, and selection events are also identified. CONCLUSION We reveal the significance of multiple introgressions from distant wild populations and alien species in shaping the genetic components of bread wheat, and provide important resources and new perspectives for future wheat breeding.
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Affiliation(s)
- Hong Cheng
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100 China
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 China
| | - Jing Liu
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 China
- Department of Molecular Evolution and Development, University of Vienna, Vienna, Austria
| | - Jia Wen
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 China
| | - Xiaojun Nie
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100 China
| | - Luohao Xu
- Department of Molecular Evolution and Development, University of Vienna, Vienna, Austria
| | - Ningbo Chen
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 China
| | - Zhongxing Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, 712100 China
| | - Qilin Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100 China
| | - Zhuqing Zheng
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 China
| | - Ming Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 China
| | - Licao Cui
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100 China
| | - Zihua Liu
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 China
| | - Jianxin Bian
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100 China
| | - Zhonghua Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100 China
| | - Shengbao Xu
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100 China
| | - Qin Yang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100 China
| | - Rudi Appels
- AgriBio, Centre for AgriBioscience, Department of Economic Development, Jobs, Transport, and Resources, La Trobe University, 5 Ring Road, Bundoora, VIC 3083 Australia
| | - Dejun Han
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100 China
| | - Weining Song
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100 China
| | - Qixin Sun
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100 China
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193 China
| | - Yu Jiang
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 China
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Radchuk V, Sharma R, Potokina E, Radchuk R, Weier D, Munz E, Schreiber M, Mascher M, Stein N, Wicker T, Kilian B, Borisjuk L. The highly divergent Jekyll genes, required for sexual reproduction, are lineage specific for the related grass tribes Triticeae and Bromeae. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 98:961-974. [PMID: 31021020 PMCID: PMC6851964 DOI: 10.1111/tpj.14363] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 03/27/2019] [Accepted: 04/04/2019] [Indexed: 05/26/2023]
Abstract
Phylogenetically related groups of species contain lineage-specific genes that exhibit no sequence similarity to any genes outside the lineage. We describe here that the Jekyll gene, required for sexual reproduction, exists in two much diverged allelic variants, Jek1 and Jek3. Despite low similarity, the Jek1 and Jek3 proteins share identical signal peptides, conserved cysteine positions and direct repeats. The Jek1/Jek3 sequences are located at the same chromosomal locus and inherited in a monogenic Mendelian fashion. Jek3 has a similar expression as Jek1 and complements the Jek1 function in Jek1-deficient plants. Jek1 and Jek3 allelic variants were almost equally distributed in a collection of 485 wild and domesticated barley accessions. All domesticated barleys harboring the Jek1 allele belong to single haplotype J1-H1 indicating a genetic bottleneck during domestication. Domesticated barleys harboring the Jek3 allele consisted of three haplotypes. Jekyll-like sequences were found only in species of the closely related tribes Bromeae and Triticeae but not in other Poaceae. Non-invasive magnetic resonance imaging revealed intrinsic grain structure in Triticeae and Bromeae, associated with the Jekyll function. The emergence of Jekyll suggests its role in the separation of the Bromeae and Triticeae lineages within the Poaceae and identifies the Jekyll genes as lineage-specific.
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Affiliation(s)
- Volodymyr Radchuk
- Leibniz‐Institute of Plant Genetics and Crop Plant Research (IPK)06466GaterslebenGermany
| | - Rajiv Sharma
- Leibniz‐Institute of Plant Genetics and Crop Plant Research (IPK)06466GaterslebenGermany
- Present address:
Division of Plant SciencesSchool of Life SciencesUniversity of DundeeThe James Hutton InstituteInvergowrie, DundeeDD2 5DAUK
| | - Elena Potokina
- Leibniz‐Institute of Plant Genetics and Crop Plant Research (IPK)06466GaterslebenGermany
- Vavilov Institute of Plant Genetic Resources (VIR)St. Petersburg190000Russian Federation
| | - Ruslana Radchuk
- Leibniz‐Institute of Plant Genetics and Crop Plant Research (IPK)06466GaterslebenGermany
| | - Diana Weier
- Leibniz‐Institute of Plant Genetics and Crop Plant Research (IPK)06466GaterslebenGermany
| | - Eberhard Munz
- Leibniz‐Institute of Plant Genetics and Crop Plant Research (IPK)06466GaterslebenGermany
- Department of Experimental Physics 5University of WürzburgWürzburgGermany
| | | | - Martin Mascher
- Leibniz‐Institute of Plant Genetics and Crop Plant Research (IPK)06466GaterslebenGermany
| | - Nils Stein
- Leibniz‐Institute of Plant Genetics and Crop Plant Research (IPK)06466GaterslebenGermany
| | - Thomas Wicker
- Department of Plant and Microbial BiologyUniversity of ZürichZürichSwitzerland
| | - Benjamin Kilian
- Leibniz‐Institute of Plant Genetics and Crop Plant Research (IPK)06466GaterslebenGermany
- Present address:
Global Crop Diversity Trust53113BonnGermany
| | - Ljudmilla Borisjuk
- Leibniz‐Institute of Plant Genetics and Crop Plant Research (IPK)06466GaterslebenGermany
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26
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Xu Y, Sun FY, Ji C, Hu QW, Wang CY, Wu DX, Sun G. Nucleotide diversity patterns at the DREB1 transcriptional factor gene in the genome donor species of wheat (Triticum aestivum L). PLoS One 2019; 14:e0217081. [PMID: 31136598 PMCID: PMC6538315 DOI: 10.1371/journal.pone.0217081] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 05/05/2019] [Indexed: 11/19/2022] Open
Abstract
Bread wheat (AABBDD) originated from the diploid progenitor Triticum urartu (AA), a relative of Aegilops speltoides (BB), and Ae. tauschii (DD). The DREB1 transcriptional factor plays key regulatory role in low-temperature tolerance. The modern breeding strategies resulted in serious decrease of the agricultural biodiversity, which led to a loss of elite genes underlying abiotic stress tolerance in crops. However, knowledge of this gene's natural diversity is largely unknown in the genome donor species of wheat. We characterized the dehydration response element binding protein 1 (DREB1) gene-diversity pattern in Ae. speltoides, Ae. tauschii, T. monococcum and T. urartu. The highest nucleotide diversity value was detected in Ae. speltoides, followed by Ae. tauschii and T. monococcum. The lowest nucleotide diversity value was observed in T. urartu. Nucleotide diversity and haplotype data might suggest no reduction of nucleotide diversity during T. monococcum domestication. Alignment of the 68 DREB1 sequences found a large-size (70 bp) insertion/deletion in the accession PI486264 of Ae. speltoides, which was different from the copy of sequences from other accessions of Ae. speltoides, suggesting a likely existence of two different ancestral Ae. speltoides forms. Implication of sequences variation of Ae. speltoides on origination of B genome in wheat was discussed.
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Affiliation(s)
- Yi Xu
- College of Agronomy, Anhui Agricultural University, Hefei, Anhui, China
| | - Fang-Yao Sun
- College of Agronomy, Anhui Agricultural University, Hefei, Anhui, China
| | - Chun Ji
- College of Agronomy, Anhui Agricultural University, Hefei, Anhui, China
| | - Quan-Wen Hu
- College of Agronomy, Anhui Agricultural University, Hefei, Anhui, China
| | - Cheng-Yu Wang
- College of Agronomy, Anhui Agricultural University, Hefei, Anhui, China
| | - De-Xiang Wu
- College of Agronomy, Anhui Agricultural University, Hefei, Anhui, China
| | - Genlou Sun
- College of Agronomy, Anhui Agricultural University, Hefei, Anhui, China
- Biology Department, Saint Mary’s University, Halifax, NS, Canada
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Kishii M. An Update of Recent Use of Aegilops Species in Wheat Breeding. FRONTIERS IN PLANT SCIENCE 2019; 10:585. [PMID: 31143197 PMCID: PMC6521781 DOI: 10.3389/fpls.2019.00585] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 04/18/2019] [Indexed: 05/16/2023]
Abstract
Aegilops species have significantly contributed to wheat breeding despite the difficulties involved in the handling of wild species, such as crossability and incompatibility. A number of biotic resistance genes have been identified and incorporated into wheat varieties from Aegilops species, and this genus is also contributing toward improvement of complex traits such as yield and abiotic tolerance for drought and heat. The D genome diploid species of Aegilops tauschii has been utilized most often in wheat breeding programs. Other Aegilops species are more difficult to utilize in the breeding because of lower meiotic recombination frequencies; generally they can be utilized only after extensive and time-consuming procedures in the form of translocation/introgression lines. After the emergence of Ug99 stem rust and wheat blast threats, Aegilops species gathered more attention as a form of new resistance sources. This article aims to update recent progress on Aegilops species, as well as to cover new topics around their use in wheat breeding.
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Affiliation(s)
- Masahiro Kishii
- Global Wheat Program, International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
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28
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He F, Pasam R, Shi F, Kant S, Keeble-Gagnere G, Kay P, Forrest K, Fritz A, Hucl P, Wiebe K, Knox R, Cuthbert R, Pozniak C, Akhunova A, Morrell PL, Davies JP, Webb SR, Spangenberg G, Hayes B, Daetwyler H, Tibbits J, Hayden M, Akhunov E. Exome sequencing highlights the role of wild-relative introgression in shaping the adaptive landscape of the wheat genome. Nat Genet 2019; 51:896-904. [PMID: 31043759 DOI: 10.1038/s41588-019-0382-2] [Citation(s) in RCA: 153] [Impact Index Per Article: 30.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 02/26/2019] [Indexed: 11/09/2022]
Abstract
Introgression is a potential source of beneficial genetic diversity. The contribution of introgression to adaptive evolution and improvement of wheat as it was disseminated worldwide remains unknown. We used targeted re-sequencing of 890 diverse accessions of hexaploid and tetraploid wheat to identify wild-relative introgression. Introgression, and selection for improvement and environmental adaptation, each reduced deleterious allele burden. Introgression increased diversity genome wide and in regions harboring major agronomic genes, and contributed alleles explaining a substantial proportion of phenotypic variation. These results suggest that historic gene flow from wild relatives made a substantial contribution to the adaptive diversity of modern bread wheat.
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Affiliation(s)
- Fei He
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
| | - Raj Pasam
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, Victoria, Australia
| | - Fan Shi
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, Victoria, Australia
| | - Surya Kant
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, Victoria, Australia
| | | | - Pippa Kay
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, Victoria, Australia
| | - Kerrie Forrest
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, Victoria, Australia
| | - Allan Fritz
- Department of Agronomy, Kansas State University, Manhattan, KS, USA
| | - Pierre Hucl
- Crop Development Centre, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Krystalee Wiebe
- Crop Development Centre, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Ron Knox
- Swift Current Research and Development Centre, Swift Current, Saskatchewan, Canada
| | - Richard Cuthbert
- Swift Current Research and Development Centre, Swift Current, Saskatchewan, Canada
| | - Curtis Pozniak
- Crop Development Centre, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Alina Akhunova
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA.,Integrated Genomics Facility, Kansas State University, Manhattan, KS, USA
| | - Peter L Morrell
- Department of Agronomy and Plant Genetics, University of Minnesota, St Paul, MN, USA
| | - John P Davies
- Corteva Agriscience, Agriculture Division of DowDuPont, Indianapolis, IN, USA
| | - Steve R Webb
- Corteva Agriscience, Agriculture Division of DowDuPont, Indianapolis, IN, USA
| | - German Spangenberg
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, Victoria, Australia.,School of Applied Systems Biology, La Trobe University, Bundoora, Victoria, Australia
| | - Ben Hayes
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, Victoria, Australia.,Queensland Alliance for Agriculture and Food Innovation, Centre for Animal Science, University of Queensland, St Lucia, Queensland, Australia
| | - Hans Daetwyler
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, Victoria, Australia.,School of Applied Systems Biology, La Trobe University, Bundoora, Victoria, Australia
| | - Josquin Tibbits
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, Victoria, Australia.,School of Applied Systems Biology, La Trobe University, Bundoora, Victoria, Australia
| | - Matthew Hayden
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, Victoria, Australia. .,School of Applied Systems Biology, La Trobe University, Bundoora, Victoria, Australia.
| | - Eduard Akhunov
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA.
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29
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Miki Y, Yoshida K, Mizuno N, Nasuda S, Sato K, Takumi S. Origin of wheat B-genome chromosomes inferred from RNA sequencing analysis of leaf transcripts from section Sitopsis species of Aegilops. DNA Res 2019; 26:171-182. [PMID: 30715317 PMCID: PMC6476730 DOI: 10.1093/dnares/dsy047] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 12/22/2018] [Indexed: 12/16/2022] Open
Abstract
Dramatic changes occasionally occur in intergenic regions leading to genomic alterations during speciation and will consequently obscure the ancestral species that have contributed to the formation of allopolyploid organisms. The S genome of five species of section Sitopsis of genus Aegilops is considered to be an origin of B-genome in cultivated tetraploid and hexaploid wheat species, although its actual donor is still unclear. Here, we attempted to elucidate phylogenetic relationship among Sitopsis species by performing RNA sequencing of the coding regions of each chromosome. Thus, genome-wide polymorphisms were extensively analyzed in 19 accessions of the Sitopsis species in reference to the tetraploid and hexaploid wheat B genome sequences and consequently were efficiently anchored to the B-genome chromosomes. The results of our genome-wide exon sequencing and resultant phylogenetic analysis indicate that Ae. speltoides is likely to be the direct donor of all chromosomes of the wheat B genome. Our results also indicate that the genome differentiation during wheat allopolyploidization from S to B proceeds at different speeds over the chromosomes rather than at constant rate and recombination could be a factor determining the speed. This observation is potentially generalized to genome differentiation during plant allopolyploid evolution.
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Affiliation(s)
- Yuka Miki
- Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | - Kentaro Yoshida
- Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | - Nobuyuki Mizuno
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Shuhei Nasuda
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Kazuhiro Sato
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
| | - Shigeo Takumi
- Graduate School of Agricultural Science, Kobe University, Kobe, Japan
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30
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Gou X, Bian Y, Zhang A, Zhang H, Wang B, Lv R, Li J, Zhu B, Gong L, Liu B. Transgenerationally Precipitated Meiotic Chromosome Instability Fuels Rapid Karyotypic Evolution and Phenotypic Diversity in an Artificially Constructed Allotetraploid Wheat (AADD). Mol Biol Evol 2019; 35:1078-1091. [PMID: 29365173 PMCID: PMC5913668 DOI: 10.1093/molbev/msy009] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Although a distinct karyotype with defined chromosome number and structure characterizes each biological species, it is intrinsically labile. Polyploidy or whole-genome duplication has played a pervasive and ongoing role in the evolution of all eukaryotes, and is the most dramatic force known to cause rapid karyotypic reconfiguration, especially at the initial stage. However, issues concerning transgenerational propagation of karyotypic heterogeneity and its translation to phenotypic diversity in nascent allopolyploidy, at the population level, have yet to be studied in detail. Here, we report a large-scale examination of transgenerationally propagated karyotypic heterogeneity and its phenotypic manifestation in an artificially constructed allotetraploid with a genome composition of AADD, that is, involving two of the three progenitor genomes of polyploid wheat. Specifically, we show that 1) massive organismal karyotypic heterogeneity is precipitated after 12 consecutive generations of selfing from a single euploid founder individual, 2) there exist dramatic differences in aptitudes between subgenomes and among chromosomes for whole-chromosome gain and/or loss and structural variations, 3) majority of the numerical and structural chromosomal variations are concurrent due to mutual contingency and possible functional constraint, 4) purposed and continuous selection and propagation for euploidy over generations did not result in enhanced karyotype stabilization, and 5) extent of karyotypic variation correlates with variability of phenotypic manifestation. Together, our results document that allopolyploidization catalyzes rampant and transgenerationally heritable organismal karyotypic heterogeneity that drives population-level phenotypic diversification, which lends fresh empirical support to the still contentious notion that whole-genome duplication enhances organismal evolvability.
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Affiliation(s)
- Xiaowan Gou
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, People's Republic of China
| | - Yao Bian
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, People's Republic of China
| | - Ai Zhang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, People's Republic of China
| | - Huakun Zhang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, People's Republic of China
| | - Bin Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, People's Republic of China
| | - Ruili Lv
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, People's Republic of China
| | - Juzuo Li
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, People's Republic of China
| | - Bo Zhu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, People's Republic of China
| | - Lei Gong
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, People's Republic of China
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, People's Republic of China
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31
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Peng Y, Zhou P, Zhao J, Li J, Lai S, Tinker NA, Liao S, Yan H. Phylogenetic relationships in the genus Avena based on the nuclear Pgk1 gene. PLoS One 2018; 13:e0200047. [PMID: 30408035 PMCID: PMC6224039 DOI: 10.1371/journal.pone.0200047] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 10/29/2018] [Indexed: 11/18/2022] Open
Abstract
The phylogenetic relationships among 76 Avena taxa, representing 14 diploids, eight tetraploids, and four hexaploids were investigated by using the nuclear plastid 3-phosphoglycerate kinase gene (Pgk1). A significant deletion (131 bp) was detected in all the C genome homoeologues which reconfirmed a major structural divergence between the A and C genomes. Phylogenetic analysis indicated the Cp genome is more closely related to the polyploid species than is the Cv genome. Two haplotypes of Pgk1 gene were obtained from most of the AB genome tetraploids. Both types of the barbata group showed a close relationship with the As genome diploid species, supporting the hypothesis that both the A and B genomes are derived from an As genome. Two haplotypes were also detected in A. agadiriana, which showed close relationships with the As genome diploid and the Ac genome diploid, respectively, emphasizing the important role of the Ac genome in the evolution of A. agadiriana. Three homoeologues of the Pgk1 gene were detected in five hexaploid accessions. The homoeologues that might represent the D genome were tightly clustered with the tetraploids A. maroccana and A. murphyi, but did not show a close relationship with any extant diploid species.
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Affiliation(s)
- Yuanying Peng
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, People’s Republic of China
| | - Pingping Zhou
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, People’s Republic of China
- Collaborative Innovation Center of Tissue Repair Material of Sichuan Province, China West Normal University, Nanchong, People’s Republic of China
| | - Jun Zhao
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, People’s Republic of China
| | - Junzhuo Li
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, People’s Republic of China
| | - Shikui Lai
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, People’s Republic of China
| | - Nicholas A. Tinker
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, Canada
| | - Shu Liao
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, People’s Republic of China
| | - Honghai Yan
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, People’s Republic of China
- Collaborative Innovation Center of Tissue Repair Material of Sichuan Province, China West Normal University, Nanchong, People’s Republic of China
- * E-mail:
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32
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Edet OU, Gorafi YSA, Nasuda S, Tsujimoto H. DArTseq-based analysis of genomic relationships among species of tribe Triticeae. Sci Rep 2018; 8:16397. [PMID: 30401925 PMCID: PMC6219600 DOI: 10.1038/s41598-018-34811-y] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 10/26/2018] [Indexed: 11/10/2022] Open
Abstract
Precise utilization of wild genetic resources to improve the resistance of their cultivated relatives to environmental growth limiting factors, such as salinity stress and diseases, requires a clear understanding of their genomic relationships. Although seriously criticized, analyzing these relationships in tribe Triticeae has largely been based on meiotic chromosome pairing in hybrids of wide crosses, a specialized and labourious strategy. In this study, DArTseq, an efficient genotyping-by-sequencing platform, was applied to analyze the genomes of 34 Triticeae species. We reconstructed the phylogenetic relationships among diploid and polyploid Aegilops and Triticum species, including hexaploid wheat. Tentatively, we have identified the diploid genomes that are likely to have been involved in the evolution of five polyploid species of Aegilops, which have remained unresolved for decades. Explanations which cast light on the progenitor of the A genomes and the complex genomic status of the B/G genomes of polyploid Triticum species in the Emmer and Timopheevi lineages of wheat have also been provided. This study has, therefore, demonstrated that DArTseq genotyping can be effectively applied to analyze the genomes of plants, especially where their genome sequence information are not available.
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Affiliation(s)
- Offiong U Edet
- Arid Land Research Center, Tottori University, Tottori, 680-0001, Japan.,United Graduate School of Agricultural Sciences, Tottori University, Tottori, 680-8553, Japan
| | - Yasir S A Gorafi
- Arid Land Research Center, Tottori University, Tottori, 680-0001, Japan.,Agricultural Research Corporation (ARC), P. O. Box 126, Wad Madani, Sudan
| | - Shuhei Nasuda
- Laboratory of Plant Genetics, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan
| | - Hisashi Tsujimoto
- Arid Land Research Center, Tottori University, Tottori, 680-0001, Japan.
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33
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Luo W, Qin N, Mu Y, Tang H, Deng M, Liu Y, Chen G, Jiang Q, Chen G, Wei Y, Zheng Y, Lan X, Ma J. Variation and diversity of the breakpoint sequences on 4AL for the 4AL/5AL translocation in Triticum. Genome 2018; 61:635-641. [PMID: 29962237 DOI: 10.1139/gen-2018-0060] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The translocation of 4AL/5AL in Triticum, which occurred before the differentiation of T. urartu and einkorn, is an important chromosomal rearrangement. Recently, the first identification of breakpoint sequence on 4AL for this translocation provides the opportunity to analyze the variation and diversity of breakpoints in Triticum. In this study, the breakpoint regions of 52 accessions from 21 species were isolated and further characterized. The sequences were divided into 12 types based on their lengths, which ranged from 2009 to 2552 bp. Cluster analysis showed that they were further divided into three groups. Interesting evolutionary relationships among a few of the species were observed and discussed. Multiple sequence alignment of the 52 sequences made it possible to detect 13 insertion and deletion length polymorphisms (InDels) and 101 single nucleotide polymorphisms (SNPs). Furthermore, several species- or accession-specific SNPs or InDels were also identified. Based on BLAST analysis of the conserved sequences, the breakpoint was narrowed down to a 125 bp fragment. Taken together, the results obtained in this study enrich our understanding of chromosomal breakpoints and will be useful for the identification of other breakpoints in wheat.
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Affiliation(s)
- Wei Luo
- a Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Nana Qin
- a Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Yang Mu
- a Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Huaping Tang
- a Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Mei Deng
- a Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Yaxi Liu
- a Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Guangdeng Chen
- b Institute of Ecological and Environmental Sciences, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China
| | - Qiantao Jiang
- a Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Guoyue Chen
- a Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Yuming Wei
- a Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Youliang Zheng
- a Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Xiujin Lan
- a Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Jian Ma
- a Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
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34
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Huang S, Steffenson BJ, Sela H, Stinebaugh K. Resistance of Aegilops longissima to the Rusts of Wheat. PLANT DISEASE 2018; 102:1124-1135. [PMID: 30673435 DOI: 10.1094/pdis-06-17-0880-re] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Stem rust (caused by Puccinia graminis f. sp. tritici), leaf rust (P. triticina), and stripe rust (P. striiformis f. sp. tritici) rank among the most important diseases of wheat worldwide. The development of resistant cultivars is the preferred method of controlling rust diseases because it is environmentally benign and also cost effective. However, new virulence types often arise in pathogen populations, rendering such cultivars vulnerable to losses. The identification of new sources of resistance is key to providing long-lasting disease control against the rapidly evolving rust pathogens. Thus, the objective of this research was to evaluate the wild wheat relative Aegilops longissima for resistance to stem rust, leaf rust, and stripe rust at the seedling stage in the greenhouse. A diverse collection of 394 accessions of the species, mostly from Israel, was assembled for the study, but the total number included in any one rust evaluation ranged from 308 to 379. With respect to stem rust resistance, 18.2 and 80.8% of accessions were resistant to the widely virulent U.S. and Kenyan P. graminis f. sp. tritici races of TTTTF and TTKSK, respectively. The percentage of accessions exhibiting resistance to the U.S. P. triticina races of THBJ and BBBD was 65.9 and 52.2%, respectively. Over half (50.1%) of the Ae. longissima accessions were resistant to the U.S. P. striiformis f. sp. tritici race PSTv-37. Ten accessions (AEG-683-23, AEG-725-15, AEG-803-49, AEG-1274-20, AEG-1276-22, AEG-1471-15, AEG-1475-19, AEG-2974-0, AEG-4005-20, and AEG-8705-10) were resistant to all races of the three rust pathogens used in this study. Distinct differences in the geographic distribution of resistance and susceptibility were found in Ae. longissima accessions from Israel in response to some rust races. To P. graminis f. sp. tritici race TTKSK, populations with a very high frequency of resistance were concentrated in the central and northern part of Israel, whereas populations with a comparatively higher frequency of susceptibility were concentrated in the southern part of the country. The reverse trend was observed with respect to P. striiformis f. sp. tritici race PSTv-37. The results from this study demonstrate that Ae. longissima is a rich source of rust resistance genes for wheat improvement.
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Affiliation(s)
- Shuyi Huang
- Department of Plant Pathology, University of Minnesota, St. Paul, 55108
| | | | - Hanan Sela
- Institute for Cereal Crops Improvement, Tel Aviv University, Tel Aviv 6139001, Israel
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35
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Luo G, Song S, Zhao L, Shen L, Song Y, Wang X, Yu K, Liu Z, Li Y, Yang W, Li X, Zhan K, Zhang A, Liu D. Mechanisms, origin and heredity of Glu-1Ay silencing in wheat evolution and domestication. THEORETICAL AND APPLIED GENETICS 2018; 131:1561-1575. [PMID: 29696298 DOI: 10.1007/s00122-018-3098-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 04/13/2018] [Indexed: 01/10/2023]
Abstract
KEY MESSAGE Allotetraploidization drives Glu-1Ay silencing in polyploid wheat. The high-molecular-weight glutenin subunit gene, Glu-1Ay, is always silenced in common wheat via elusive mechanisms. To investigate its silencing and heredity during wheat polyploidization and domestication, the Glu-1Ay gene was characterized in 1246 accessions containing diploid and polyploid wheat worldwide. Eight expressed Glu-1Ay alleles (in 71.81% accessions) and five silenced alleles with a premature termination codon (PTC) were identified in Triticum urartu; 4 expressed alleles (in 41.21% accessions), 13 alleles with PTCs and 1 allele with a WIS 2-1A retrotransposon were present in wild tetraploid wheat; and only silenced alleles with PTC or WIS 2-1A were in cultivated tetra- and hexaploid wheat. Both the PTC number and position in T. urartu Glu-1Ay alleles (one in the N-terminal region) differed from its progeny wild tetraploid wheat (1-5 PTCs mainly in the repetitive domain). The WIS 2-1A insertion occurred ~ 0.13 million years ago in wild tetraploid wheat, much later than the allotetraploidization event. The Glu-1Ay alleles with PTCs or WIS 2-1A that arose in wild tetraploid wheat were fully succeeded to cultivated tetraploid and hexaploid wheat. In addition, the Glu-1Ay gene in wild einkorn inherited to cultivated einkorn. Our data demonstrated that the silencing of Glu-1Ay in tetraploid and hexaploid wheat was attributed to the new PTCs and WIS 2-1A insertion in wild tetraploid wheat, and most silenced alleles were delivered to the cultivated tetraploid and hexaploid wheat, providing a clear evolutionary history of the Glu-1Ay gene in the wheat polyploidization and domestication processes.
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Affiliation(s)
- Guangbin Luo
- State Key Laboratory of Plant Cell and Chromosome Engineering, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 1 West Beichen Road, Chaoyang District, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shuyi Song
- State Key Laboratory of Plant Cell and Chromosome Engineering, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 1 West Beichen Road, Chaoyang District, Beijing, 100101, China.,College of Agronomy, The Collaborative Innovation Center of Grain Crops in Henan, Henan Agricultural University, 63 Nongye Road, Zhengzhou, 450002, China
| | - Liru Zhao
- State Key Laboratory of Plant Cell and Chromosome Engineering, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 1 West Beichen Road, Chaoyang District, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lisha Shen
- State Key Laboratory of Plant Cell and Chromosome Engineering, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 1 West Beichen Road, Chaoyang District, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yanhong Song
- State Key Laboratory of Plant Cell and Chromosome Engineering, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 1 West Beichen Road, Chaoyang District, Beijing, 100101, China.,College of Agronomy, The Collaborative Innovation Center of Grain Crops in Henan, Henan Agricultural University, 63 Nongye Road, Zhengzhou, 450002, China
| | - Xin Wang
- State Key Laboratory of Plant Cell and Chromosome Engineering, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 1 West Beichen Road, Chaoyang District, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Kang Yu
- State Key Laboratory of Plant Cell and Chromosome Engineering, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 1 West Beichen Road, Chaoyang District, Beijing, 100101, China.,Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Fragrant Hill, Beijing, 100093, China
| | - Zhiyong Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 1 West Beichen Road, Chaoyang District, Beijing, 100101, China
| | - Yiwen Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 1 West Beichen Road, Chaoyang District, Beijing, 100101, China
| | - Wenlong Yang
- State Key Laboratory of Plant Cell and Chromosome Engineering, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 1 West Beichen Road, Chaoyang District, Beijing, 100101, China
| | - Xin Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 1 West Beichen Road, Chaoyang District, Beijing, 100101, China
| | - Kehui Zhan
- College of Agronomy, The Collaborative Innovation Center of Grain Crops in Henan, Henan Agricultural University, 63 Nongye Road, Zhengzhou, 450002, China
| | - Aimin Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 1 West Beichen Road, Chaoyang District, Beijing, 100101, China. .,College of Agronomy, The Collaborative Innovation Center of Grain Crops in Henan, Henan Agricultural University, 63 Nongye Road, Zhengzhou, 450002, China.
| | - Dongcheng Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 1 West Beichen Road, Chaoyang District, Beijing, 100101, China.
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36
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Zhang W, Zhang M, Zhu X, Cao Y, Sun Q, Ma G, Chao S, Yan C, Xu SS, Cai X. Molecular cytogenetic and genomic analyses reveal new insights into the origin of the wheat B genome. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2018; 131:365-375. [PMID: 29094182 DOI: 10.1007/s00122-017-3007-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 10/26/2017] [Indexed: 05/18/2023]
Abstract
This work pinpointed the goatgrass chromosomal segment in the wheat B genome using modern cytogenetic and genomic technologies, and provided novel insights into the origin of the wheat B genome. Wheat is a typical allopolyploid with three homoeologous subgenomes (A, B, and D). The donors of the subgenomes A and D had been identified, but not for the subgenome B. The goatgrass Aegilops speltoides (genome SS) has been controversially considered a possible candidate for the donor of the wheat B genome. However, the relationship of the Ae. speltoides S genome with the wheat B genome remains largely obscure. The present study assessed the homology of the B and S genomes using an integrative cytogenetic and genomic approach, and revealed the contribution of Ae. speltoides to the origin of the wheat B genome. We discovered noticeable homology between wheat chromosome 1B and Ae. speltoides chromosome 1S, but not between other chromosomes in the B and S genomes. An Ae. speltoides-originated segment spanning a genomic region of approximately 10.46 Mb was detected on the long arm of wheat chromosome 1B (1BL). The Ae. speltoides-originated segment on 1BL was found to co-evolve with the rest of the B genome. Evidently, Ae. speltoides had been involved in the origin of the wheat B genome, but should not be considered an exclusive donor of this genome. The wheat B genome might have a polyphyletic origin with multiple ancestors involved, including Ae. speltoides. These novel findings will facilitate genome studies in wheat and other polyploids.
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Affiliation(s)
- Wei Zhang
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108-6050, USA
| | - Mingyi Zhang
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108-6050, USA
| | - Xianwen Zhu
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108-6050, USA
| | - Yaping Cao
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108-6050, USA
| | - Qing Sun
- Department of Computer Science, North Dakota State University, Fargo, ND, 58108-6050, USA
| | - Guojia Ma
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108-6050, USA
| | - Shiaoman Chao
- The Red River Valley Agricultural Research Center, USDA-ARS, Fargo, ND, 58102, USA
| | - Changhui Yan
- Department of Computer Science, North Dakota State University, Fargo, ND, 58108-6050, USA
| | - Steven S Xu
- The Red River Valley Agricultural Research Center, USDA-ARS, Fargo, ND, 58102, USA
| | - Xiwen Cai
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108-6050, USA.
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37
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Ruban AS, Badaeva ED. Evolution of the S-Genomes in Triticum-Aegilops Alliance: Evidences From Chromosome Analysis. FRONTIERS IN PLANT SCIENCE 2018; 9:1756. [PMID: 30564254 PMCID: PMC6288319 DOI: 10.3389/fpls.2018.01756] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 11/12/2018] [Indexed: 05/20/2023]
Abstract
Five diploid Aegilops species of the Sitopsis section: Ae. speltoides, Ae. longissima, Ae. sharonensis, Ae. searsii, and Ae. bicornis, two tetraploid species Ae. peregrina (= Ae. variabilis) and Ae. kotschyi (Aegilops section) and hexaploid Ae. vavilovii (Vertebrata section) carry the S-genomes. The B- and G-genomes of polyploid wheat are also the derivatives of the S-genome. Evolution of the S-genome species was studied using Giemsa C-banding and fluorescence in situ hybridization (FISH) with DNA probes representing 5S (pTa794) and 18S-5.8S-26S (pTa71) rDNAs as well as nine tandem repeats: pSc119.2, pAesp_SAT86, Spelt-1, Spelt-52, pAs1, pTa-535, and pTa-s53. To correlate the C-banding and FISH patterns we used the microsatellites (CTT)10 and (GTT)9, which are major components of the C-banding positive heterochromatin in wheat. According to the results obtained, diploid species split into two groups corresponding to Emarginata and Truncata sub-sections, which differ in the C-banding patterns, distribution of rDNA and other repeats. The B- and G-genomes of polyploid wheat are most closely related to the S-genome of Ae. speltoides. The genomes of allopolyploid wheat have been evolved as a result of different species-specific chromosome translocations, sequence amplification, elimination and re-patterning of repetitive DNA sequences. These events occurred independently in different wheat species and in Ae. speltoides . The 5S rDNA locus of chromosome 1S was probably lost in ancient Ae. speltoides prior to formation of Timopheevii wheat, but after the emergence of ancient emmer. Evolution of Emarginata species was associated with an increase of C-banding and (CTT)10-positive heterochromatin, amplification of Spelt-52, re-pattering of the pAesp_SAT86, and a gradual decrease in the amount of the D-genome-specific repeats pAs1, pTa-535, and pTa-s53. The emergence of Ae. peregrina and Ae. kotschyi did not lead to significant changes of the S*-genomes. However, partial elimination of 45S rDNA repeats from 5S* and 6S* chromosomes and alterations of C-banding and FISH-patterns have been detected. Similarity of the Sv-genome of Ae. vavilovii with the Ss genome of diploid Ae. searsii confirmed the origin of this hexaploid. A model of the S-genome evolution is suggested.
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Affiliation(s)
- Alevtina S. Ruban
- Laboratory of Chromosome Structure and Function, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Ekaterina D. Badaeva
- Laboratory of Genetic Basis of Plant Identification, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
- Laboratory of Molecular Karyology, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
- *Correspondence: Ekaterina D. Badaeva
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Yang Y, Fan X, Wang L, Zhang HQ, Sha LN, Wang Y, Kang HY, Zeng J, Yu XF, Zhou YH. Phylogeny and maternal donors of Elytrigia Desv. sensu lato (Triticeae; Poaceae) inferred from nuclear internal-transcribed spacer and trnL-F sequences. BMC PLANT BIOLOGY 2017; 17:207. [PMID: 29157213 PMCID: PMC5697114 DOI: 10.1186/s12870-017-1163-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/02/2017] [Accepted: 11/08/2017] [Indexed: 06/07/2023]
Abstract
BACKGROUND Elytrigia Desv. is a genus with a varied array of morphology, cytology, ecology, and distribution in Triticeae. Classification and systematic position of Elytrigia remain controversial. We used nuclear internal-transcribed spacer (nrITS) sequences and chloroplast trnL-F region to study the relationships of phylogenetic and maternal genome donor of Elytrigia Desv. sensu lato. RESULTS (1) E, F, P, St, and W genomes bear close relationship with one another and are distant from H and Ns genomes. Ee and Eb are homoeologous. (2) In ESt genome species, E genome is the origin of diploid Elytrigia species with E genome, St genome is the origin of Pseudoroegneria. (3) Diploid species Et. elongata were differentiated. (4) Et. stipifolia and Et. varnensis sequences are diverse based on nrITS data. (5) Et. lolioides contains St and H genomes and belongs to Elymus s. l. (6) E genome diploid species in Elytrigia serve as maternal donors of E genome for Et. nodosa (PI547344), Et. farcta, Et. pontica, Et. pycnantha, Et. scirpea, and Et. scythica. At least two species act as maternal donor of allopolyploids (ESt and EStP genomes). CONCLUSIONS Our results suggested that Elytrigia s. l. species contain different genomes, which should be divided into different genera. However, the genomes of Elytrigia species had close relationships with one another. Diploid species were differentiated, because of introgression and different geographical sources. The results also suggested that the same species and the same genomes of different species have different maternal donor. Further study of molecular biology and cytology could facilitate the evaluation of our results of phylogenetic in a more specific and accurate way.
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Affiliation(s)
- Yan Yang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, 611130 Chengdu, Sichuan People’s Republic of China
- College of Environmental Science and Engineering, China West Normal University, Nanchong, 637009 Sichuan People’s Republic of China
| | - Xing Fan
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, 611130 Chengdu, Sichuan People’s Republic of China
| | - Long Wang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, 611130 Chengdu, Sichuan People’s Republic of China
| | - Hai-Qin Zhang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, 611130 Chengdu, Sichuan People’s Republic of China
| | - Li-Na Sha
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, 611130 Chengdu, Sichuan People’s Republic of China
| | - Yi Wang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, 611130 Chengdu, Sichuan People’s Republic of China
| | - Hou-Yang Kang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, 611130 Chengdu, Sichuan People’s Republic of China
| | - Jian Zeng
- College of Resources, Sichuan Agricultural University, Wenjiang, 611130 Chengdu, Sichuan People’s Republic of China
| | - Xiao-Fang Yu
- College of Landscape Architecture, Sichuan Agricultural University, Wenjiang, 611130 Chengdu, Sichuan People’s Republic of China
| | - Yong-Hong Zhou
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, 611130 Chengdu, Sichuan People’s Republic of China
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Danilova TV, Akhunova AR, Akhunov ED, Friebe B, Gill BS. Major structural genomic alterations can be associated with hybrid speciation in Aegilops markgrafii (Triticeae). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 92:317-330. [PMID: 28776783 DOI: 10.1111/tpj.13657] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 07/21/2017] [Accepted: 07/31/2017] [Indexed: 05/19/2023]
Abstract
During evolutionary history many grasses from the tribe Triticeae have undergone interspecific hybridization, resulting in allopolyploidy; whereas homoploid hybrid speciation was found only in rye. Homoeologous chromosomes within the Triticeae preserved cross-species macrocolinearity, except for a few species with rearranged genomes. Aegilops markgrafii, a diploid wild relative of wheat (2n = 2x = 14), has a highly asymmetrical karyotype that is indicative of chromosome rearrangements. Molecular cytogenetics and next-generation sequencing were used to explore the genome organization. Fluorescence in situ hybridization with a set of wheat cDNAs allowed the macrostructure and cross-genome homoeology of the Ae. markgrafii chromosomes to be established. Two chromosomes maintained colinearity, whereas the remaining were highly rearranged as a result of inversions and inter- and intrachromosomal translocations. We used sets of barley and wheat orthologous gene sequences to compare discrete parts of the Ae. markgrafii genome involved in the rearrangements. Analysis of sequence identity profiles and phylogenic relationships grouped chromosome blocks into two distinct clusters. Chromosome painting revealed the distribution of transposable elements and differentiated chromosome blocks into two groups consistent with the sequence analyses. These data suggest that introgressive hybridization accompanied by gross chromosome rearrangements might have had an impact on karyotype evolution and homoploid speciation in Ae. markgrafii.
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Affiliation(s)
- Tatiana V Danilova
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
| | - Alina R Akhunova
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
| | - Eduard D Akhunov
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
| | - Bernd Friebe
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
| | - Bikram S Gill
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
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Klindworth DL, Saini J, Long Y, Rouse MN, Faris JD, Jin Y, Xu SS. Physical mapping of DNA markers linked to stem rust resistance gene Sr47 in durum wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2017; 130:1135-1154. [PMID: 28286900 DOI: 10.1007/s00122-017-2875-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Accepted: 02/07/2017] [Indexed: 06/06/2023]
Abstract
Markers linked to stem rust resistance gene Sr47 were physically mapped in three small Aegilops speltoides chromosomal bins. Five markers, including two PCR-based SNP markers, were validated for marker-assisted selection. In durum wheat (Triticum turgidum subsp. durum), the gene Sr47 derived from Aegilops speltoides conditions resistance to race TTKSK (Ug99) of the stem rust pathogen (Puccinia graminis f. sp. tritici). Sr47 is carried on small interstitial translocation chromosomes (Ti2BL-2SL-2BL·2BS) in which the Ae. speltoides chromosome 2S segments are divided into four bins in genetic stocks RWG35, RWG36, and RWG37. Our objective was to physically map molecular markers to bins and to determine if any of the molecular markers would be useful in marker-assisted selection (MAS). Durum cultivar Joppa was used as the recurrent parent to produce three BC2F2 populations. Each BC2F2 plant was genotyped with markers to detect the segment carrying Sr47, and stem rust testing of BC2F3 progeny with race TTKSK confirmed the genotyping. Forty-nine markers from published sources, four new SSR markers, and five new STARP (semi-thermal asymmetric reverse PCR) markers, were evaluated in BC2F2 populations for assignment of markers to bins. Sr47 was mapped to bin 3 along with 13 markers. No markers were assigned to bin 1; however, 7 and 13 markers were assigned to bins 2 and 4, respectively. Markers Xrwgs38a, Xmag1729, Xwmc41, Xtnac3119, Xrwgsnp1, and Xrwgsnp4 were found to be useful for MAS of Sr47. However, STARP markers Xrwgsnp1 and Xrwgsnp4 can be used in gel-free systems, and are the preferred markers for high-throughput MAS. The physical mapping data from this study will also be useful for pyramiding Sr47 with other Sr genes on chromosome 2B.
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Affiliation(s)
- Daryl L Klindworth
- USDA-ARS, Northern Crop Science Laboratory, Cereal Crops Research Unit, Red River Valley Agricultural Research Center, 1605 Albrecht Blvd. North, Fargo, ND, 58102-2765, USA
| | - Jyoti Saini
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA
| | - Yunming Long
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA
| | - Matthew N Rouse
- USDA-ARS, Cereal Disease Laboratory, and Department of Plant Pathology, University of Minnesota, St. Paul, MN, 55108, USA
| | - Justin D Faris
- USDA-ARS, Northern Crop Science Laboratory, Cereal Crops Research Unit, Red River Valley Agricultural Research Center, 1605 Albrecht Blvd. North, Fargo, ND, 58102-2765, USA
| | - Yue Jin
- USDA-ARS, Cereal Disease Laboratory, and Department of Plant Pathology, University of Minnesota, St. Paul, MN, 55108, USA
| | - Steven S Xu
- USDA-ARS, Northern Crop Science Laboratory, Cereal Crops Research Unit, Red River Valley Agricultural Research Center, 1605 Albrecht Blvd. North, Fargo, ND, 58102-2765, USA.
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Sadigov GB, Trifonova AA, Kudryavtsev AM. Genetic diversity in collection of cultivars and varieties of Triticum durum Desf. from Azerbaijan. RUSS J GENET+ 2017. [DOI: 10.1134/s1022795417050088] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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El Baidouri M, Murat F, Veyssiere M, Molinier M, Flores R, Burlot L, Alaux M, Quesneville H, Pont C, Salse J. Reconciling the evolutionary origin of bread wheat (Triticum aestivum). THE NEW PHYTOLOGIST 2017; 213:1477-1486. [PMID: 27551821 DOI: 10.1111/nph.14113] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 06/18/2016] [Indexed: 05/26/2023]
Abstract
The origin of bread wheat (Triticum aestivum; AABBDD) has been a subject of controversy and of intense debate in the scientific community over the last few decades. In 2015, three articles published in New Phytologist discussed the origin of hexaploid bread wheat (AABBDD) from the diploid progenitors Triticum urartu (AA), a relative of Aegilops speltoides (BB) and Triticum tauschii (DD). Access to new genomic resources since 2013 has offered the opportunity to gain novel insights into the paleohistory of modern bread wheat, allowing characterization of its origin from its diploid progenitors at unprecedented resolution. We propose a reconciled evolutionary scenario for the modern bread wheat genome based on the complementary investigation of transposable element and mutation dynamics between diploid, tetraploid and hexaploid wheat. In this scenario, the structural asymmetry observed between the A, B and D subgenomes in hexaploid bread wheat derives from the cumulative effect of diploid progenitor divergence, the hybrid origin of the D subgenome, and subgenome partitioning following the polyploidization events.
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Affiliation(s)
- Moaine El Baidouri
- INRA/UBP UMR 1095 GDEC (Genetics, Diversity and Ecophysiology of Cereals), 5 chemin de Beaulieu, Clermont Ferrand, 63100, France
| | - Florent Murat
- INRA/UBP UMR 1095 GDEC (Genetics, Diversity and Ecophysiology of Cereals), 5 chemin de Beaulieu, Clermont Ferrand, 63100, France
| | - Maeva Veyssiere
- INRA/UBP UMR 1095 GDEC (Genetics, Diversity and Ecophysiology of Cereals), 5 chemin de Beaulieu, Clermont Ferrand, 63100, France
| | - Mélanie Molinier
- INRA/UBP UMR 1095 GDEC (Genetics, Diversity and Ecophysiology of Cereals), 5 chemin de Beaulieu, Clermont Ferrand, 63100, France
| | - Raphael Flores
- INRA UR1164 URGI (Research Unit in Genomics-Info), Université Paris-Saclay, Versailles, 78026, France
| | - Laura Burlot
- INRA UR1164 URGI (Research Unit in Genomics-Info), Université Paris-Saclay, Versailles, 78026, France
| | - Michael Alaux
- INRA UR1164 URGI (Research Unit in Genomics-Info), Université Paris-Saclay, Versailles, 78026, France
| | - Hadi Quesneville
- INRA UR1164 URGI (Research Unit in Genomics-Info), Université Paris-Saclay, Versailles, 78026, France
| | - Caroline Pont
- INRA/UBP UMR 1095 GDEC (Genetics, Diversity and Ecophysiology of Cereals), 5 chemin de Beaulieu, Clermont Ferrand, 63100, France
| | - Jérôme Salse
- INRA/UBP UMR 1095 GDEC (Genetics, Diversity and Ecophysiology of Cereals), 5 chemin de Beaulieu, Clermont Ferrand, 63100, France
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Tang Y, Kang HY, Tang L, Diao CD, Li DY, Zhu W, Fan X, Wang Y, Zeng J, Xu LL, Sha LN, Yu XF, Zhang HQ, Zhou YH. Phylogenetic analysis of tetraploid wheat based on nuclear DMC1 gene. BIOCHEM SYST ECOL 2017. [DOI: 10.1016/j.bse.2016.10.022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Qin L, Zhao J, Li T, Hou J, Zhang X, Hao C. TaGW2, a Good Reflection of Wheat Polyploidization and Evolution. FRONTIERS IN PLANT SCIENCE 2017; 8:318. [PMID: 28326096 PMCID: PMC5339256 DOI: 10.3389/fpls.2017.00318] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Accepted: 02/22/2017] [Indexed: 05/04/2023]
Abstract
Hexaploid wheat consists of three subgenomes, namely, A, B, and D. These well-characterized ancestral genomes also exist at the diploid and tetraploid levels, thereby rendering wheat as a good model species for studying polyploidization. Here, we performed intra- and inter-species comparative analyses of wheat and its relatives to dissect polymorphism and differentiation of the TaGW2 genes. Our results showed that genetic diversity of TaGW2 decreased with progression from the diploids to tetraploids and hexaploids. The strongest selection occurred in the promoter regions of TaGW2-6A and TaGW2-6B. Phylogenetic trees clearly indicated that Triticum urartu and Ae. speltoides were the donors of the A and B genomes in tetraploid and hexaploid wheats. Haplotypes detected among hexaploid genotypes traced back to the tetraploid level. Fst and π values revealed that the strongest selection on TaGW2 occurred at the tetraploid level rather than in hexaploid wheat. This infers that grain size enlargement, especially increased kernel width, mainly occurred in tetraploid genotypes. In addition, relative expression levels of TaGW2s significantly declined from the diploid level to tetraploids and hexaploids, further indicating that these genes negatively regulate kernel size. Our results also revealed that the polyploidization events possibly caused much stronger differentiation than domestication and breeding.
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Affiliation(s)
- Lin Qin
- Crop Genomics and Bioinformatics Center and National Key Lab of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural UniversityNanjing, China
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture/The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Science, Chinese Academy of Agricultural SciencesBeijing, China
| | - Junjie Zhao
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture/The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Science, Chinese Academy of Agricultural SciencesBeijing, China
| | - Tian Li
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture/The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Science, Chinese Academy of Agricultural SciencesBeijing, China
| | - Jian Hou
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture/The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Science, Chinese Academy of Agricultural SciencesBeijing, China
| | - Xueyong Zhang
- Crop Genomics and Bioinformatics Center and National Key Lab of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural UniversityNanjing, China
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture/The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Science, Chinese Academy of Agricultural SciencesBeijing, China
- *Correspondence: Xueyong Zhang
| | - Chenyang Hao
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture/The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Science, Chinese Academy of Agricultural SciencesBeijing, China
- Chenyang Hao
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Liu W, Koo DH, Friebe B, Gill BS. A set of Triticum aestivum-Aegilops speltoides Robertsonian translocation lines. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2016; 129:2359-2368. [PMID: 27558595 DOI: 10.1007/s00122-016-2774-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 08/12/2016] [Indexed: 06/06/2023]
Abstract
Here we report the production of a set of wheat - Aegilops speltoides Robertsonian translocations covering all Ae. speltoides chromosome arms except the long arm of the homoeologous group 4 chromosome. Aegilops speltoides of the Poaceae family is the most probable donor of the B and G genomes of polyploid Triticum species and also an important source of resistance to diseases and pests of wheat. Previously, we reported the production of a complete set of T aestivum-Ae. speltoides chromosome addition lines and a set of disomic S(B/A)-genome chromosome substitution lines. The isolation of compensating Robertsonian translocations (RobTs) composed of alien chromosome arms translocated to homoeologous wheat chromosome arms is the important next step to exploit the genetic variation of a wild relative of wheat. Here, we report the development of molecular markers specific for the S-genome chromosomes and their use in the isolation of a set of 13 compensating wheat-Ae. speltoides RobTs covering the S genome of Ae. speltoides except for the long arm of chromosome 4S. Most of the RobTs were fully fertile and will facilitate mapping of genes to specific chromosome arms and also will accelerate the introgression of agronomically useful traits from Ae. speltoides into wheat by homologous recombination.
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Affiliation(s)
- Wenxuan Liu
- Laboratory of Cell and Chromosome Engineering, College of Life Sciences, Henan Agricultural University, Zhengzhou, Henan, 450002, People's Republic of China
| | - Dal-Hoe Koo
- Wheat Genetics Resource Center, Department of Plant Pathology, Throckmorton Plant Sciences Center, Kansas State University, Manhattan, KS, 66506-5502, USA
| | - Bernd Friebe
- Wheat Genetics Resource Center, Department of Plant Pathology, Throckmorton Plant Sciences Center, Kansas State University, Manhattan, KS, 66506-5502, USA.
| | - Bikram S Gill
- Wheat Genetics Resource Center, Department of Plant Pathology, Throckmorton Plant Sciences Center, Kansas State University, Manhattan, KS, 66506-5502, USA
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Shcherban AB, Schichkina AA, Salina EA. The occurrence of spring forms in tetraploid Timopheevi wheat is associated with variation in the first intron of the VRN-A1 gene. BMC PLANT BIOLOGY 2016; 16:236. [PMID: 28105942 PMCID: PMC5123382 DOI: 10.1186/s12870-016-0925-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
BACKGROUND Triticum araraticum and Triticum timopheevii are tetraploid species of the Timopheevi group. The former includes both winter and spring forms with a predominance of winter forms, whereas T. timopheevii is considered a spring species. In order to clarify the origin of the spring growth habit in T. timopheevii, allelic variability of the VRN-1 gene was investigated in a set of accessions of both tetraploid species, together with the diploid species Ae. speltoides, presumed donor of the G genome to these tetraploids. RESULTS The promoter region of the VRN-A1 locus in all studied tetraploid accessions of both T. araraticum and T. timopheevii represents the previously described allele VRN-A1f with a 50 bp deletion near the start codon. Three additional alleles were identified namely, VRN-A1f-del, VRN-A1f-ins and VRN-A1f-del/ins, which contained large mutations in the first (1st) intron of VRN-A1. The first allele, carrying a deletion of 2.7 kb in a central part of intron 1, occurred in a few accessions of T. araraticum and no accessions of T. timopheevii. The VRN-A1f-ins allele, containing the insertion of a 0.4 kb MITE element about 0.4 kb upstream from the start of intron 1, and allele VRN-A1f-del/ins having this insertion coupled with a deletion of 2.7 kb are characteristic only for T. timopheevii. Allelic variation at the VRN-G1 locus includes the previously described allele VRN-G1a (with the insertion of a 0.2 kb MITE in the promoter) found in a few accessions of both tetraploid species. We showed that alleles VRN-A1f-del and VRN-G1a have no association with the spring growth habit, while in all accessions of T. timopheevii this habit was associated with the dominant VRN-A1f-ins and VRN-A1f-del/ins alleles. None of the Ae. speltoides accessions included in this study had changes in the promoter or 1st intron regions of VRN-1 which might confer a spring growth habit. The VRN-1 promoter sequences analyzed herein and downloaded from databases have been used to construct a phylogram to assess the time of divergence of Ae. speltoides in relation to other wheat species. CONCLUSIONS Among accessions of T. araraticum, the preferentially winter predecessor of T. timopheevii, two large mutations were found in both VRN-A1 and VRN-G1 loci (VRN-A1f-del and VRN-G1a) that were found to have no effect on vernalization requirements. Spring tetraploid T. timopheevii had one VRN-1 allele in common for two species (VRN-G1a), and two that were specific (VRN-A1f-ins, VRN-A1f-del/ins). The latter alleles include mutations in the 1st intron of VRN-A1 and also share a 0.4 kb MITE insertion near the start of intron 1. We suggested that this insertion resulted in a spring growth habit in a progenitor of T. timopheevii which has probably been selected during subsequent domestication. The phylogram constructed on the basis of the VRN-1 promoter sequences confirmed the early divergence (~3.5 MYA) of the ancestor(s) of the B/G genomes from Ae. speltoides.
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Affiliation(s)
- Andrey Borisovich Shcherban
- The Federal Research Center "Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences", Lavrentiev ave. 10, Novosibirsk, 630090, Russia.
| | | | - Elena Artemovna Salina
- The Federal Research Center "Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences", Lavrentiev ave. 10, Novosibirsk, 630090, Russia
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Zhao L, Ning S, Yu J, Hao M, Zhang L, Yuan Z, Zheng Y, Liu D. Cytological identification of an Aegilops variabilis chromosome carrying stripe rust resistance in wheat. BREEDING SCIENCE 2016; 66:522-529. [PMID: 27795677 PMCID: PMC5010304 DOI: 10.1270/jsbbs.16011] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Accepted: 04/23/2016] [Indexed: 05/19/2023]
Abstract
Aegilops variabilis (UUSvSv), an important sources for wheat improvement, originated from chromosome doubling of a natural hybrid between Ae. umbellulata (UU) with Ae. longissima (SlSl). The Ae. variabilis karyotype was poorly characterized by fluorescent in situ hybridization (FISH). The FISH probe combination of pSc119.2, pTa71 and pTa-713 identified each of the 14 pairs of Ae. variabilis chromosomes. Our FISH ideogram was further used to detect an Ae. variabilis chromosome carrying stripe rust resistance in the background of wheat lines developed from crosses of the stripe rust susceptible bread wheat cultivar Yiyuan 2 with a resistant Ae. variabilis accession. Among the 15 resistant BC1F7 lines, three were 2Sv + 4Sv addition lines (2n = 46) and 12 were 2Sv(2B) or 2Sv(2D) substitution lines that were confirmed with SSR markers. SSR marker gwm148 can be used to trace 2Sv in common wheat background. Chromosome 2Sv probably carries gametocidal(Gc) gene(s) since cytological instability and chromosome structural variations, including non-homologous translocations, were observed in some lines with this chromosome. Due to the effects of photoperiod genes, substitution lines 2Sv(2D) and 2Sv(2B) exhibited late heading with 2Sv(2D) lines being later than 2Sv(2B) lines. 2Sv(2D) substitution lines were also taller and exhibited higher spikelet numbers and longer spikes.
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Affiliation(s)
| | | | - Jianjun Yu
- Triticeae Research Institute, Sichuan Agricultural University,
Chengdu, Sichuan 611130,
China
| | - Ming Hao
- Triticeae Research Institute, Sichuan Agricultural University,
Chengdu, Sichuan 611130,
China
| | - Lianquan Zhang
- Triticeae Research Institute, Sichuan Agricultural University,
Chengdu, Sichuan 611130,
China
| | - Zhongwei Yuan
- Triticeae Research Institute, Sichuan Agricultural University,
Chengdu, Sichuan 611130,
China
| | - Youliang Zheng
- Triticeae Research Institute, Sichuan Agricultural University,
Chengdu, Sichuan 611130,
China
| | - Dengcai Liu
- Triticeae Research Institute, Sichuan Agricultural University,
Chengdu, Sichuan 611130,
China
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48
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Liu F, Si H, Wang C, Sun G, Zhou E, Chen C, Ma C. Molecular evolution of Wcor15 gene enhanced our understanding of the origin of A, B and D genomes in Triticum aestivum. Sci Rep 2016; 6:31706. [PMID: 27526862 PMCID: PMC4985644 DOI: 10.1038/srep31706] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 07/25/2016] [Indexed: 11/29/2022] Open
Abstract
The allohexaploid bread wheat originally derived from three closely related species with A, B and D genome. Although numerous studies were performed to elucidate its origin and phylogeny, no consensus conclusion has reached. In this study, we cloned and sequenced the genes Wcor15-2A, Wcor15-2B and Wcor15-2D in 23 diploid, 10 tetraploid and 106 hexaploid wheat varieties and analyzed their molecular evolution to reveal the origin of the A, B and D genome in Triticum aestivum. Comparative analyses of sequences in diploid, tetraploid and hexaploid wheats suggest that T. urartu, Ae. speltoides and Ae. tauschii subsp. strangulata are most likely the donors of the Wcor15-2A, Wcor15-2B and Wcor15-2D locus in common wheat, respectively. The Wcor15 genes from subgenomes A and D were very conservative without insertion and deletion of bases during evolution of diploid, tetraploid and hexaploid. Non-coding region of Wcor15-2B gene from B genome might mutate during the first polyploidization from Ae. speltoides to tetraploid wheat, however, no change has occurred for this gene during the second allopolyploidization from tetraploid to hexaploid. Comparison of the Wcor15 gene shed light on understanding of the origin of the A, B and D genome of common wheat.
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Affiliation(s)
- Fangfang Liu
- School of Agronomy, Anhui Agricultural University, Hefei 230036, China.,Key Laboratory of Wheat Biology and Genetic Improvement on South Yellow &Huai River Valley, Ministry of Agriculture, Hefei 230036, China
| | - Hongqi Si
- School of Agronomy, Anhui Agricultural University, Hefei 230036, China.,Key Laboratory of Wheat Biology and Genetic Improvement on South Yellow &Huai River Valley, Ministry of Agriculture, Hefei 230036, China
| | - Chengcheng Wang
- School of Agronomy, Anhui Agricultural University, Hefei 230036, China.,Key Laboratory of Wheat Biology and Genetic Improvement on South Yellow &Huai River Valley, Ministry of Agriculture, Hefei 230036, China
| | - Genlou Sun
- School of Agronomy, Anhui Agricultural University, Hefei 230036, China.,Biology Department, Saint Mary's University, Halifax, NS, B3H 3C3 Canada
| | - Erting Zhou
- School of Agronomy, Anhui Agricultural University, Hefei 230036, China
| | - Can Chen
- School of Agronomy, Anhui Agricultural University, Hefei 230036, China
| | - Chuanxi Ma
- School of Agronomy, Anhui Agricultural University, Hefei 230036, China.,Key Laboratory of Wheat Biology and Genetic Improvement on South Yellow &Huai River Valley, Ministry of Agriculture, Hefei 230036, China.,National United Engineering Laboratory for Crop Stress Resistance Breeding, Hefei 230036, China.,Anhui Key Laboratory of Crop Biology, Hefei 230036, China
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49
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Bassi FM, Ghavami F, Hayden MJ, Wang Y, Forrest KL, Kong S, Dizon R, Michalak de Jimenez MK, Meinhardt SW, Mergoum M, Gu YQ, Kianian SF. Fast-forward genetics by radiation hybrids to saturate the locus regulating nuclear-cytoplasmic compatibility in Triticum. PLANT BIOTECHNOLOGY JOURNAL 2016; 14:1716-1726. [PMID: 26915753 PMCID: PMC5067624 DOI: 10.1111/pbi.12532] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Revised: 11/24/2015] [Accepted: 12/24/2015] [Indexed: 05/29/2023]
Abstract
The nuclear-encoded species cytoplasm specific (scs) genes control nuclear-cytoplasmic compatibility in wheat (genus Triticum). Alloplasmic cells, which have nucleus and cytoplasm derived from different species, produce vigorous and vital organisms only when the correct version of scs is present in their nucleus. In this study, bulks of in vivo radiation hybrids segregating for the scs phenotype have been genotyped by sequencing with over 1.9 million markers. The high marker saturation obtained for a critical region of chromosome 1D allowed identification of 3318 reads that mapped in close proximity of the scs. A novel in silico approach was deployed to extend these short reads to sequences of up to 70 Kb in length and identify candidate open reading frames (ORFs). Markers were developed to anchor the short contigs containing ORFs to a radiation hybrid map of 650 individuals with resolution of 288 Kb. The region containing the scs locus was narrowed to a single Bacterial Artificial Chromosome (BAC) contig of Aegilops tauschii. Its sequencing and assembly by nano-mapping allowed rapid identification of a rhomboid gene as the only ORF existing within the refined scs locus. Resequencing of this gene from multiple germplasm sources identified a single nucleotide mutation, which gives rise to a functional amino acid change. Gene expression characterization revealed that an active copy of this rhomboid exists on all homoeologous chromosomes of wheat, and depending on the specific cytoplasm each copy is preferentially expressed. Therefore, a new methodology was applied to unique genetic stocks to rapidly identify a strong candidate gene for the control of nuclear-cytoplasmic compatibility in wheat.
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Affiliation(s)
- Filippo M Bassi
- Department of Plant Sciences, North Dakota State University, Fargo, ND, USA
- International Center for the Agricultural Research in the Dry Areas (ICARDA), Rabat, Morocco
| | - Farhad Ghavami
- Department of Plant Sciences, North Dakota State University, Fargo, ND, USA
- Eurofins BioDiagnostics, Inc., River Falls, WI, USA
| | - Matthew J Hayden
- Department of Environment and Primary Industries, AgriBiosciences Center, Bundoora, Vic, Australia
| | - Yi Wang
- USDA-ARS, Western Regional Research Center, Albany, CA, USA
| | - Kerrie L Forrest
- Department of Environment and Primary Industries, AgriBiosciences Center, Bundoora, Vic, Australia
| | - Stephan Kong
- Department of Environment and Primary Industries, AgriBiosciences Center, Bundoora, Vic, Australia
| | - Rhoderissa Dizon
- Department of Plant Sciences, North Dakota State University, Fargo, ND, USA
| | | | - Steven W Meinhardt
- Department of Plant Pathology, North Dakota State University, Fargo, ND, USA
| | - Mohamed Mergoum
- Department of Plant Sciences, North Dakota State University, Fargo, ND, USA
| | - Yong Q Gu
- USDA-ARS, Western Regional Research Center, Albany, CA, USA
| | - Shahryar F Kianian
- Department of Plant Sciences, North Dakota State University, Fargo, ND, USA
- USDA-ARS Cereal Disease Laboratory, University of Minnesota, Saint Paul, MN, USA
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50
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Diversification of the Homoeologous Lr34 Sequences in Polyploid Wheat Species and Their Diploid Progenitors. J Mol Evol 2016; 82:291-302. [PMID: 27300207 DOI: 10.1007/s00239-016-9748-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 06/04/2016] [Indexed: 10/21/2022]
Abstract
Allopolyploidization induces a multiple processes of genomic reorganization, including the structurally functional diversification of the homoeologous genes. An example of such diversification is the appearance of the Lr34 gene on chromosome 7D of bread wheat T. aestivum (BAD), the gene conferring durable, race non-specific protection against three fungal pathogens. In this study, we focused on the variability of a functionally critical region between exons 10-12 of Lr34 among diploid progenitors of wheat genomes and their respective polyploids. In the diploid A-genome species, two basic forms of the studied region have been revealed: (1) non-functional forms containing stop codons, or/and frameshifts (T. monococcum/T. urartu) and (2) forms with no such a mutations (T. boeoticum). The Lr34 sequence of T. urartu containing a TGA stop codon was inherited by the first tetraploid T. dicoccoides (BA), and then reorganized in some accessions of this species due to the insertion of an LTR retroelement in exon 10. Besides T. boeoticum, the second form of the Lr34 sequence is also characteristic of A. speltoides, which presumably donated this form to all polyploid descendants bearing B-genome. No differences were found between the D-genome-specific Lr34 sequences studied here and downloaded from databases, implying the highest level of conservation of the Lr34 predecessor throughout evolution. The sequence data were later used to construct phylograms, and apparent peculiarities in the evolution of the studied region of Lr34 genes discussed.
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