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Said M, Gaál E, Farkas A, Molnár I, Bartoš J, Doležel J, Cabrera A, Endo TR. Gametocidal genes: from a discovery to the application in wheat breeding. Front Plant Sci 2024; 15:1396553. [PMID: 38711610 PMCID: PMC11070591 DOI: 10.3389/fpls.2024.1396553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 04/02/2024] [Indexed: 05/08/2024]
Abstract
Some species of the genus Aegilops, a wild relative of wheat, carry chromosomes that after introducing to wheat exhibit preferential transmission to progeny. Their selective retention is a result of the abortion of gametes lacking them due to induced chromosomal aberrations. These chromosomes are termed Gametocidal (Gc) and, based on their effects, they are categorized into three types: mild, intense or severe, and very strong. Gc elements within the same homoeologous chromosome groups of Aegilops (II, III, or IV) demonstrate similar Gc action. This review explores the intriguing dynamics of Gc chromosomes and encompasses comprehensive insights into their source species, behavioral aspects, mode of action, interactions, suppressions, and practical applications of the Gc system in wheat breeding. By delving into these areas, this work aims to contribute to the development of novel plant genetic resources for wheat breeding. The insights provided herein shed light on the utilization of Gc chromosomes to produce chromosomal rearrangements in wheat and its wild relatives, thereby facilitating the generation of chromosome deletions, translocations, and telosomic lines. The Gc approach has significantly advanced various aspects of wheat genetics, including the introgression of novel genes and alleles, molecular markers and gene mapping, and the exploration of homoeologous relationships within Triticeae species. The mystery lies in why gametes possessing Gc genes maintain their normality while those lacking Gc genes suffer abnormalities, highlighting an unresolved research gap necessitating deeper investigation.
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Affiliation(s)
- Mahmoud Said
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Olomouc, Czechia
- Field Crops Research Institute, Agricultural Research Centre, Giza, Egypt
| | - Eszter Gaál
- Agricultural Institute, Hungarian Research Network (HUN-REN) Centre for Agricultural Research, Martonvásár, Hungary
| | - András Farkas
- Agricultural Institute, Hungarian Research Network (HUN-REN) Centre for Agricultural Research, Martonvásár, Hungary
| | - István Molnár
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Olomouc, Czechia
- Agricultural Institute, Hungarian Research Network (HUN-REN) Centre for Agricultural Research, Martonvásár, Hungary
| | - Jan Bartoš
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Olomouc, Czechia
| | - Jaroslav Doležel
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Olomouc, Czechia
| | - Adoración Cabrera
- Genetics Department, Escuela Técnica Superior de Ingeniería Agronómica y de Montes (ETSIAM), Agrifood Campus of International Excellence (ceiA3), University of Córdoba, Córdoba, Spain
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Kaur H, Sharma P, Kumar J, Singh VK, Vasistha NK, Gahlaut V, Tyagi V, Verma SK, Singh S, Dhaliwal HS, Sheikh I. Genetic analysis of iron, zinc and grain yield in wheat- Aegilops derivatives using multi-locus GWAS. Mol Biol Rep 2023; 50:9191-9202. [PMID: 37776411 DOI: 10.1007/s11033-023-08800-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 09/05/2023] [Indexed: 10/02/2023]
Abstract
BACKGROUND Wheat is a major staple crop and helps to reduce worldwide micronutrient deficiency. Investigating the genetics that control the concentrations of iron (Fe) and zinc (Zn) in wheat is crucial. Hence, we undertook a comprehensive study aimed at elucidating the genomic regions linked to the contents of Fe and Zn in the grain. METHODS AND RESULTS We performed the multi-locus genome-wide association (ML-GWAS) using a panel of 161 wheat-Aegilops substitution and addition lines to dissect the genomic regions controlling grain iron (GFeC), and grain zinc (GZnC) contents. The wheat panel was genotyped using 10,825 high-quality SNPs and phenotyped in three different environments (E1-E3) during 2017-2019. A total of 111 marker-trait associations (MTAs) (at p-value < 0.001) were detected that belong to all three sub-genomes of wheat. The highest number of MTAs were identified for GFeC (58), followed by GZnC (44) and yield (9). Further, six stable MTAs were identified for these three traits and also two pleiotropic MTAs were identified for GFeC and GZnC. A total of 1291 putative candidate genes (CGs) were also identified for all three traits. These CGs encode a diverse set of proteins, including heavy metal-associated (HMA), bZIP family protein, AP2/ERF, and protein previously associated with GFeC, GZnC, and grain yield. CONCLUSIONS The significant MTAs and CGs pinpointed in this current study are poised to play a pivotal role in enhancing both the nutritional quality and yield of wheat, utilizing marker-assisted selection (MAS) techniques.
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Affiliation(s)
- Harneet Kaur
- Department of Genetics-Plant Breeding and Biotechnology, Dr. Khem Singh Gill Akal College of Agriculture, Eternal University, Baru Sahib, Sirmaur, 173101, India
| | - Prachi Sharma
- Department of Genetics-Plant Breeding and Biotechnology, Dr. Khem Singh Gill Akal College of Agriculture, Eternal University, Baru Sahib, Sirmaur, 173101, India
| | - Jitendra Kumar
- National Agri-Food Biotechnology Institute, Sector-81, Mohali, Punjab, 140306, India
| | - Vikas Kumar Singh
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, U.P., 250004, India
| | - Neeraj Kumar Vasistha
- Department of Genetics-Plant Breeding and Biotechnology, Dr. Khem Singh Gill Akal College of Agriculture, Eternal University, Baru Sahib, Sirmaur, 173101, India
- Department of Genetics and Plant Breeding, Rajiv Gandhi University, Itanagar, India
| | - Vijay Gahlaut
- Department of Biotechnology, Chandigarh University, Gharuan, Mohali, Punjab, 140413, India.
- University Center for Research and Development, Chandigarh University, Gharuan, Mohali, Punjab, 140413, India.
| | - Vikrant Tyagi
- Department of Genetics-Plant Breeding and Biotechnology, Dr. Khem Singh Gill Akal College of Agriculture, Eternal University, Baru Sahib, Sirmaur, 173101, India
| | | | - Sukhwinder Singh
- International Maize and Wheat Improvement Center (CIMMYT), El Batan, Texcoco, Mexico
- USDA-ARS, Southeast Area, Subtropical Horticulture Research Station, 13601 Old Cutler Road, Miami, FL, 33158, USA
| | - H S Dhaliwal
- Department of Genetics-Plant Breeding and Biotechnology, Dr. Khem Singh Gill Akal College of Agriculture, Eternal University, Baru Sahib, Sirmaur, 173101, India
| | - Imran Sheikh
- Department of Genetics-Plant Breeding and Biotechnology, Dr. Khem Singh Gill Akal College of Agriculture, Eternal University, Baru Sahib, Sirmaur, 173101, India.
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Adhikari L, Raupp J, Wu S, Koo DH, Friebe B, Poland J. Genomic characterization and gene bank curation of Aegilops: the wild relatives of wheat. Front Plant Sci 2023; 14:1268370. [PMID: 37915516 PMCID: PMC10616851 DOI: 10.3389/fpls.2023.1268370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 09/25/2023] [Indexed: 11/03/2023]
Abstract
Genetic diversity found in crop wild relatives is critical to preserve and utilize for crop improvement to achieve sustainable food production amid climate change and increased demand. We genetically characterized a large collection of 1,041 Aegilops accessions distributed among 23 different species using more than 45K single nucleotide polymorphisms identified by genotyping-by-sequencing. The Wheat Genetics Resource Center (WGRC) Aegilops germplasm collection was curated through the identification of misclassified and redundant accessions. There were 49 misclassified and 28 sets of redundant accessions within the four diploid species. The curated germplasm sets now have improved utility for genetic studies and wheat improvement. We constructed a phylogenetic tree and principal component analysis cluster for all Aegilops species together, giving one of the most comprehensive views of Aegilops. The Sitopsis section and the U genome Aegilops clade were further scrutinized with in-depth population analysis. The genetic relatedness among the pair of Aegilops species provided strong evidence for the species evolution, speciation, and diversification. We inferred genome symbols for two species Ae. neglecta and Ae. columnaris based on the sequence read mapping and the presence of segregating loci on the pertinent genomes as well as genetic clustering. The high genetic diversity observed among Aegilops species indicated that the genus could play an even greater role in providing the critical need for untapped genetic diversity for future wheat breeding and improvement. To fully characterize these Aegilops species, there is an urgent need to generate reference assemblies for these wild wheats, especially for the polyploid Aegilops.
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Affiliation(s)
- Laxman Adhikari
- Plant Breeding and Genetics Lab, Center for Desert Agriculture, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Wheat Genetics Resource Center, Department of Plant Pathology, Kansas State University, Manhattan, KS, United States
| | - John Raupp
- Wheat Genetics Resource Center, Department of Plant Pathology, Kansas State University, Manhattan, KS, United States
| | - Shuangye Wu
- Wheat Genetics Resource Center, Department of Plant Pathology, Kansas State University, Manhattan, KS, United States
| | - Dal-Hoe Koo
- Wheat Genetics Resource Center, Department of Plant Pathology, Kansas State University, Manhattan, KS, United States
| | - Bernd Friebe
- Wheat Genetics Resource Center, Department of Plant Pathology, Kansas State University, Manhattan, KS, United States
| | - Jesse Poland
- Plant Breeding and Genetics Lab, Center for Desert Agriculture, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Wheat Genetics Resource Center, Department of Plant Pathology, Kansas State University, Manhattan, KS, United States
- Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
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Kroupin PY, Badaeva ED, Sokolova VM, Chikida NN, Belousova MK, Surzhikov SA, Nikitina EA, Kocheshkova AA, Ulyanov DS, Ermolaev AS, Khuat TML, Razumova OV, Yurkina AI, Karlov GI, Divashuk MG. Erratum: Aegilops crassa Boiss. repeatome characterized using low-coverage NGS as a source of new FISH markers: application in phylogenetic studies of the Triticeae. Front Plant Sci 2023; 14:1207880. [PMID: 37521923 PMCID: PMC10374421 DOI: 10.3389/fpls.2023.1207880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 05/04/2023] [Indexed: 08/01/2023]
Abstract
[This corrects the article DOI: 10.3389/fpls.2022.980764.].
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Affiliation(s)
- Pavel Yu. Kroupin
- All-Russia Research Institute of Agricultural Biotechnology, Kurchatov Genomics Centre – ARRIAB, Moscow, Russia
| | - 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
| | - Victoria M. Sokolova
- All-Russia Research Institute of Agricultural Biotechnology, Kurchatov Genomics Centre – ARRIAB, Moscow, Russia
| | - Nadezhda N. Chikida
- All-Russian Institute of Plant Genetic Resources (VIR), Department of Wheat Genetic Resources, St. Petersburg, Russia
| | - Maria Kh. Belousova
- All-Russian Institute of Plant Genetic Resources (VIR), Department of Wheat Genetic Resources, St. Petersburg, Russia
| | - Sergei A. Surzhikov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Ekaterina A. Nikitina
- All-Russia Research Institute of Agricultural Biotechnology, Kurchatov Genomics Centre – ARRIAB, Moscow, Russia
| | - Alina A. Kocheshkova
- All-Russia Research Institute of Agricultural Biotechnology, Kurchatov Genomics Centre – ARRIAB, Moscow, Russia
| | - Daniil S. Ulyanov
- All-Russia Research Institute of Agricultural Biotechnology, Kurchatov Genomics Centre – ARRIAB, Moscow, Russia
| | - Aleksey S. Ermolaev
- All-Russia Research Institute of Agricultural Biotechnology, Kurchatov Genomics Centre – ARRIAB, Moscow, Russia
| | - Thi Mai Luong Khuat
- Agricultural Genetics Institute, Department of Molecular Biology, Hanoi, Vietnam
| | - Olga V. Razumova
- All-Russia Research Institute of Agricultural Biotechnology, Kurchatov Genomics Centre – ARRIAB, Moscow, Russia
| | - Anna I. Yurkina
- All-Russia Research Institute of Agricultural Biotechnology, Kurchatov Genomics Centre – ARRIAB, Moscow, Russia
| | - Gennady I. Karlov
- All-Russia Research Institute of Agricultural Biotechnology, Kurchatov Genomics Centre – ARRIAB, Moscow, Russia
| | - Mikhail G. Divashuk
- All-Russia Research Institute of Agricultural Biotechnology, Kurchatov Genomics Centre – ARRIAB, Moscow, Russia
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Jabari M, Golparvar A, Sorkhilalehloo B, Shams M. Investigation of genetic diversity of Iranian wild relatives of bread wheat using ISSR and SSR markers. J Genet Eng Biotechnol 2023; 21:73. [PMID: 37382843 DOI: 10.1186/s43141-023-00526-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 06/08/2023] [Indexed: 06/30/2023]
Abstract
BACKGROUND Wild relatives of wheat are one of the most important genetic resources to use in wheat breeding programs. Therefore, identifying wild relatives of wheat and being aware of their diversity, is undeniably effective in expanding the richness of the gene pool and the genetic base of new cultivars and can be a useful tool for breeders in the future. The present study was performed to evaluate the molecular diversity among 49 accessions of the genera Aegilops and Triticum in the National Plant Gene Bank of Iran using two DNA-based markers, i.e., SSR and ISSR. Also, the present study aimed to examine the relationships among the accessions studied belonging to different genetic backgrounds. RESULTS Ten SSR and tan ISSR primers produced 2065 and 1524 polymorphism bands, respectively. The number of Polymorphic Bands (NPB), the Polymorphism Information Content (PIC), Marker Index (MI), and Resolving Power (Rp) in SSR marker was 162 to 317, 0.830 to 0.919, 1.326 to 3.167, and 3.169 to 5.692, respectively, and in the ISSR marker, it was from 103 to 185, 0.377 to 0.441, 0.660 to 1.151, and 3.169 to 5.693, respectively. This indicates the efficiency of both markers in detecting polymorphism among the accessions studied. The ISSR marker had a higher polymorphism rate, MI, and Rp than the SSR marker. Molecular analysis of variance for both DNA-based markers showed that the genetic variation within the species was more than the genetic diversity between them. The high level of genomic diversity discovered in the Aegilops and Triticum species proved to provide an ideal gene pool for discovering genes useful for wheat breeding. The accessions were classified into eight groups based on SSR and ISSR markers using the UPGMA method of cluster analysis. According to the cluster analysis results, despite similarities between the accessions of a given province, in most cases, the geographical pattern was not in accordance with that observed using the molecular clustering. Based on the coordinate analysis, neighboring groups showed the maximum similarities, and distant ones revealed the maximum genetic distance from each other. The genetic structure analysis successfully separated accessions for their ploidy levels. CONCLUSIONS Both markers provided a comprehensive model of genetic diversity between Iranian accessions of Aegilops and Triticum genera. Primers used in the present study were effective, informative, and genome-specific which could be used in genome explanatory experiments.
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Affiliation(s)
- Maryam Jabari
- Department of Agronomy and Plant Breeding, College of Agriculture, Islamic Azad University, Isfahan (Khorasgan) Isfahan Branch, Iran
| | - Ahmadreza Golparvar
- Department of Agronomy and Plant Breeding, College of Agriculture, Islamic Azad University, Isfahan (Khorasgan) Isfahan Branch, Iran
| | - Behzad Sorkhilalehloo
- Genetic Research Department and the National Plant Genebank of Iran, Seed and Plant Improvement Institute, Agricultural Research, Education and Extension Organization, AREEO, Karaj, Iran.
| | - Majid Shams
- Department of Agronomy and Plant Breeding, College of Agriculture, Islamic Azad University, Isfahan (Khorasgan) Isfahan Branch, Iran
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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 Commun 2023:100567. [PMID: 36855304 PMCID: PMC10363506 DOI: 10.1016/j.xplc.2023.100567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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Kroupin PY, Badaeva ED, Sokolova VM, Chikida NN, Belousova MK, Surzhikov SA, Nikitina EA, Kocheshkova AA, Ulyanov DS, Ermolaev AS, Khuat TML, Razumova OV, Yurkina AI, Karlov GI, Divashuk MG. Aegilops crassa Boiss. repeatome characterized using low-coverage NGS as a source of new FISH markers: Application in phylogenetic studies of the Triticeae. Front Plant Sci 2022; 13:980764. [PMID: 36325551 PMCID: PMC9621091 DOI: 10.3389/fpls.2022.980764] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 08/29/2022] [Indexed: 06/13/2023]
Abstract
Aegilops crassa Boiss. is polyploid grass species that grows in the eastern part of the Fertile Crescent, Afghanistan, and Middle Asia. It consists of tetraploid (4x) and hexaploid (6x) cytotypes (2n = 4x = 28, D1D (Abdolmalaki et al., 2019) XcrXcr and 2n = 6x = 42, D1D (Abdolmalaki et al., 2019) XcrXcrD2D (Adams and Wendel, 2005), respectively) that are similar morphologically. Although many Aegilops species were used in wheat breeding, the genetic potential of Ae. crassa has not yet been exploited due to its uncertain origin and significant genome modifications. Tetraploid Ae. crassa is thought to be the oldest polyploid Aegilops species, the subgenomes of which still retain some features of its ancient diploid progenitors. The D1 and D2 subgenomes of Ae. crassa were contributed by Aegilops tauschii (2n = 2x = 14, DD), while the Xcr subgenome donor is still unknown. Owing to its ancient origin, Ae. crassa can serve as model for studying genome evolution. Despite this, Ae. crassa is poorly studied genetically and no genome sequences were available for this species. We performed low-coverage genome sequencing of 4x and 6x cytotypes of Ae. crassa, and four Ae. tauschii accessions belonging to different subspecies; diploid wheatgrass Thinopyrum bessarabicum (Jb genome), which is phylogenetically close to D (sub)genome species, was taken as an outgroup. Subsequent data analysis using the pipeline RepeatExplorer2 allowed us to characterize the repeatomes of these species and identify several satellite sequences. Some of these sequences are novel, while others are found to be homologous to already known satellite sequences of Triticeae species. The copy number of satellite repeats in genomes of different species and their subgenome (D1 or Xcr) affinity in Ae. crassa were assessed by means of comparative bioinformatic analysis combined with quantitative PCR (qPCR). Fluorescence in situ hybridization (FISH) was performed to map newly identified satellite repeats on chromosomes of common wheat, Triticum aestivum, 4x and 6x Ae. crassa, Ae. tauschii, and Th. bessarabicum. The new FISH markers can be used in phylogenetic analyses of the Triticeae for chromosome identification and the assessment of their subgenome affinities and for evaluation of genome/chromosome constitution of wide hybrids or polyploid species.
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Affiliation(s)
- Pavel Yu. Kroupin
- All-Russia Research Institute of Agricultural Biotechnology, Kurchatov Genomics Centre – ARRIAB, Moscow, Russia
| | - 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
| | - Victoria M. Sokolova
- All-Russia Research Institute of Agricultural Biotechnology, Kurchatov Genomics Centre – ARRIAB, Moscow, Russia
| | - Nadezhda N. Chikida
- All-Russian Institute of Plant Genetic Resources (VIR), Department of Wheat Genetic Resources, St. Petersburg, Russia
| | - Maria Kh. Belousova
- All-Russian Institute of Plant Genetic Resources (VIR), Department of Wheat Genetic Resources, St. Petersburg, Russia
| | - Sergei A. Surzhikov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Ekaterina A. Nikitina
- All-Russia Research Institute of Agricultural Biotechnology, Kurchatov Genomics Centre – ARRIAB, Moscow, Russia
| | - Alina A. Kocheshkova
- All-Russia Research Institute of Agricultural Biotechnology, Kurchatov Genomics Centre – ARRIAB, Moscow, Russia
| | - Daniil S. Ulyanov
- All-Russia Research Institute of Agricultural Biotechnology, Kurchatov Genomics Centre – ARRIAB, Moscow, Russia
| | - Aleksey S. Ermolaev
- All-Russia Research Institute of Agricultural Biotechnology, Kurchatov Genomics Centre – ARRIAB, Moscow, Russia
| | - Thi Mai Luong Khuat
- Agricultural Genetics Institute, Department of Molecular Biology, Hanoi, Vietnam
| | - Olga V. Razumova
- All-Russia Research Institute of Agricultural Biotechnology, Kurchatov Genomics Centre – ARRIAB, Moscow, Russia
| | - Anna I. Yurkina
- All-Russia Research Institute of Agricultural Biotechnology, Kurchatov Genomics Centre – ARRIAB, Moscow, Russia
| | - Gennady I. Karlov
- All-Russia Research Institute of Agricultural Biotechnology, Kurchatov Genomics Centre – ARRIAB, Moscow, Russia
| | - Mikhail G. Divashuk
- All-Russia Research Institute of Agricultural Biotechnology, Kurchatov Genomics Centre – ARRIAB, Moscow, Russia
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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. Mol Plant 2022; 15:488-503. [PMID: 34979290 DOI: 10.1016/j.molp.2021.12.019] [Citation(s) in RCA: 51] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 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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9
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Khan MK, Pandey A, Hamurcu M, Avsaroglu ZZ, Ozbek M, Omay AH, Elbasan F, Omay MR, Gokmen F, Topal A, Gezgin S. Variability in Physiological Traits Reveals Boron Toxicity Tolerance in Aegilops Species. Front Plant Sci 2021; 12:736614. [PMID: 34777419 PMCID: PMC8585849 DOI: 10.3389/fpls.2021.736614] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 09/30/2021] [Indexed: 05/31/2023]
Abstract
Boron (B) is an important micronutrient required for the normal growth and development of plants. However, its excess in the soil causes severe damage to plant tissues, which affects the final yield. Wheat, one of the main staple crops, has been reported to be largely affected by B toxicity stress in arid and semi-arid regions of the world. The prevalence of B toxicity stress can be addressed by utilizing wild wheat genotypes with a variant level of stress tolerance. Wild wheat relatives have been identified as a prominent source of several abiotic stress-tolerant genes. However, Aegilops species in the tertiary gene pool of wheat have not been well exploited as a source of B toxicity tolerance. This study explores the root and shoot growth, proline induction, and extent of lipid peroxidation in 19 Aegilops accessions comprising 6 different species and the B-tolerant check wheat cultivar Bolal 2973 grown under Control (3.1 μM B), toxic (1 mM B), and highly toxic (10 mM B) B stress treatment. B toxicity stress had a more decisive impact on growth parameters as compared to the malondialdehyde (MDA) and proline content. The obtained results suggested that even the genotypes with high shoot B (SB) accumulation can be tolerant to B toxicity stress, and the mechanism of B redistribution in leaves should be studied in detail. It has been proposed that the studied Aegilops accessions can be potentially used for genetically improving the B toxicity-tolerance trait due to a high level of variation in the response toward high B toxicity. Though a number of accessions showed suppression in the root and shoot growth, very few accessions with stress adaptive plasticity to B toxicity stress leading to an improvement of shoot growth parameters could be determined. The two accessions, Aegilops biuncialis accession TGB 026219 and Aegilops columnaris accession TGB 000107, were identified as the potential genotypes with B toxicity stress tolerance and can be utilized for developing a pre-breeding material in B tolerance-based breeding programs.
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Affiliation(s)
- Mohd. Kamran Khan
- Department of Soil Science and Plant Nutrition, Faculty of Agriculture, Selcuk University, Konya, Turkey
| | - Anamika Pandey
- Department of Soil Science and Plant Nutrition, Faculty of Agriculture, Selcuk University, Konya, Turkey
| | - Mehmet Hamurcu
- Department of Soil Science and Plant Nutrition, Faculty of Agriculture, Selcuk University, Konya, Turkey
| | - Zuhal Zeynep Avsaroglu
- Department of Soil Science and Plant Nutrition, Faculty of Agriculture, Selcuk University, Konya, Turkey
| | - Merve Ozbek
- Department of Soil Science and Plant Nutrition, Faculty of Agriculture, Selcuk University, Konya, Turkey
| | - Ayse Humeyra Omay
- Department of Soil Science and Plant Nutrition, Faculty of Agriculture, Selcuk University, Konya, Turkey
| | - Fevzi Elbasan
- Department of Soil Science and Plant Nutrition, Faculty of Agriculture, Selcuk University, Konya, Turkey
| | - Makbule Rumeysa Omay
- Department of Soil Science and Plant Nutrition, Faculty of Agriculture, Selcuk University, Konya, Turkey
| | - Fatma Gokmen
- Department of Soil Science and Plant Nutrition, Faculty of Agriculture, Selcuk University, Konya, Turkey
| | - Ali Topal
- Department of Field Crops, Faculty of Agriculture, Selcuk University, Konya, Turkey
| | - Sait Gezgin
- Department of Soil Science and Plant Nutrition, Faculty of Agriculture, Selcuk University, Konya, Turkey
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10
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Sharma S, Schulthess AW, Bassi FM, Badaeva ED, Neumann K, Graner A, Özkan H, Werner P, Knüpffer H, Kilian B. Introducing Beneficial Alleles from Plant Genetic Resources into the Wheat Germplasm. Biology (Basel) 2021; 10:982. [PMID: 34681081 PMCID: PMC8533267 DOI: 10.3390/biology10100982] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 09/24/2021] [Accepted: 09/24/2021] [Indexed: 12/02/2022]
Abstract
Wheat (Triticum sp.) is one of the world's most important crops, and constantly increasing its productivity is crucial to the livelihoods of millions of people. However, more than a century of intensive breeding and selection processes have eroded genetic diversity in the elite genepool, making new genetic gains difficult. Therefore, the need to introduce novel genetic diversity into modern wheat has become increasingly important. This review provides an overview of the plant genetic resources (PGR) available for wheat. We describe the most important taxonomic and phylogenetic relationships of these PGR to guide their use in wheat breeding. In addition, we present the status of the use of some of these resources in wheat breeding programs. We propose several introgression schemes that allow the transfer of qualitative and quantitative alleles from PGR into elite germplasm. With this in mind, we propose the use of a stage-gate approach to align the pre-breeding with main breeding programs to meet the needs of breeders, farmers, and end-users. Overall, this review provides a clear starting point to guide the introgression of useful alleles over the next decade.
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Affiliation(s)
- Shivali Sharma
- Global Crop Diversity Trust, Platz der Vereinten Nationen 7, D-53113 Bonn, Germany; (S.S.); (P.W.)
| | - Albert W. Schulthess
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstr. 3, D-06466 Seeland, Germany; (A.W.S.); (K.N.); (A.G.); (H.K.)
| | - Filippo M. Bassi
- International Center for Agricultural Research in the Dry Areas (ICARDA), Rabat 10112, Morocco;
| | - Ekaterina D. Badaeva
- N.I. Vavilov Institute of General Genetics, Russian Academy of Sciences, 119991 Moscow, Russia;
- The Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), 630090 Novosibirsk, Russia
| | - Kerstin Neumann
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstr. 3, D-06466 Seeland, Germany; (A.W.S.); (K.N.); (A.G.); (H.K.)
| | - Andreas Graner
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstr. 3, D-06466 Seeland, Germany; (A.W.S.); (K.N.); (A.G.); (H.K.)
| | - Hakan Özkan
- Department of Field Crops, Faculty of Agriculture, University of Çukurova, Adana 01330, Turkey;
| | - Peter Werner
- Global Crop Diversity Trust, Platz der Vereinten Nationen 7, D-53113 Bonn, Germany; (S.S.); (P.W.)
| | - Helmut Knüpffer
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstr. 3, D-06466 Seeland, Germany; (A.W.S.); (K.N.); (A.G.); (H.K.)
| | - Benjamin Kilian
- Global Crop Diversity Trust, Platz der Vereinten Nationen 7, D-53113 Bonn, Germany; (S.S.); (P.W.)
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11
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Sato K, Yoshida K, Takumi S. RNA-Seq-based DNA marker analysis of the genetics and molecular evolution of Triticeae species. Funct Integr Genomics 2021; 21:535-42. [PMID: 34405283 DOI: 10.1007/s10142-021-00799-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 01/08/2021] [Accepted: 07/23/2021] [Indexed: 10/20/2022]
Abstract
The release of high-quality chromosome-level genome sequences of members of the Triticeae tribe has greatly facilitated genetic and genomic analyses of important crops such as wheat (Triticum aestivum) and barley (Hordeum vulgare). Due to the large diploid genome size of Triticeae plants (ca. 5 Gbp), transcript analysis is an important method for identifying genetic and genomic differences among Triticeae species. In this review, we summarize our results of RNA-Seq analyses of diploid wheat accessions belonging to the genera Aegilops and Triticum. We also describe studies of the molecular relationships among these accessions and provide insight into the evolution of common hexaploid wheat. DNA markers based on polymorphisms within species can be used to map loci of interest. Even though the genome sequence of diploid Aegilops tauschii, the D-genome donor of common wheat, has been released, the diploid barley genome continues to provide key information about the physical structures of diploid wheat genomes. We describe how a series of RNA-Seq analyses of wheat relatives has helped uncover the structural and evolutionary features of genomic and genetic systems in wild and cultivated Triticeae species.
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12
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Kwiatek MT, Belter J, Ulaszewski W, Skowrońska R, Noweiska A, Wiśniewska H. Molecular identification of triticale introgression lines carrying leaf rust resistance genes transferred from Aegilops kotschyi Boiss. and Ae. tauschii Coss. J Appl Genet 2021; 62:431-439. [PMID: 33990930 PMCID: PMC8357765 DOI: 10.1007/s13353-021-00635-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 04/20/2021] [Accepted: 04/22/2021] [Indexed: 11/28/2022]
Abstract
Triticale (× Triticosecale Wittmack) is a commercial hybrid harboring wheat (Triticum sp.) and rye (Secale cereale L.) genomes. The limited genetic diversity of this crop resulted in the collapse of fungal disease resistance. Leaf rust disease, caused by Puccinia triticina Eriks., is reported to reduce the triticale yield significantly (more than 30%). There is a need to enlarge the genetic variability of this crop including leaf resistance genes. The main aim of this research was to evaluate the leaf rust resistance of the offspring of translocation lines of triticale carrying chromatin of Ae. tauschii and Ae. kotschyi. A reaction of seedlings of 200 plants of two triticale-Aegilops translocation lines (Bogo-2Dt.2R and Sekundo-2Sk.2R) was compared after inoculation with a natural mixture of P. triticina races, specific to triticale in controlled condition. Before inoculation, each plant was screened using molecular cytogenetics and molecular markers linked to leaf rust resistance genes. The presence of Aegilops chromosome segments was confirmed using genomic in situ hybridization (GISH). Lr39 and Lr54 leaf rust resistance genes were identified using Xgdm35 and S14 molecular markers, respectively. After inoculation, a significant improvement of resistance severity was observed in Sekundo-2Sk.2R in comparison with triticale cv. Sekundo plants. The resistance level of Bogo-2Dt.2R did not differ compared with triticale cv. Bogo plants. It was shown that Lr39 gene did not increase the leaf rust resistance level of triticale cv. Bogo.
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Affiliation(s)
- Michał T Kwiatek
- Department of Genomics, Institute of Plant Genetics of the Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland. .,Department of Genetics and Plant Breeding, Poznan University of Life Sciences, Dojazd 11, 60-632, Poznań, Poland.
| | - Jolanta Belter
- Department of Genomics, Institute of Plant Genetics of the Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland
| | - Waldemar Ulaszewski
- Department of Genomics, Institute of Plant Genetics of the Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland
| | - Roksana Skowrońska
- Department of Genetics and Plant Breeding, Poznan University of Life Sciences, Dojazd 11, 60-632, Poznań, Poland
| | - Aleksandra Noweiska
- Department of Genetics and Plant Breeding, Poznan University of Life Sciences, Dojazd 11, 60-632, Poznań, Poland
| | - Halina Wiśniewska
- Department of Genomics, Institute of Plant Genetics of the Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland
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13
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Ito N, Mori N, Miyashita NT. Rhizospheric bacterial community structure of Triticum and Aegilops revealed by pyrosequencing analysis of the 16S rRNA gene: dominance of the A genome over the B and D genomes. Genes Genet Syst 2020; 95:249-268. [PMID: 33298661 DOI: 10.1266/ggs.20-00006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
This study examined the relationship between host plant and rhizospheric bacterial community structure, including composition and diversity, in Triticum and Aegilops species (12 and two accessions, respectively) as well as three closely related species, barley, rye and oat (four accessions), to explore the possibility that wheat root and rhizosphere interaction can be utilized for wheat breeding and biotechnology in the future. For this purpose, DNA was isolated from rhizospheric soil samples and one control non-rhizospheric soil sample, and the 16S rRNA gene region was amplified and subjected to DNA pyrosequencing. A total of 132,888 amplicons were analyzed. Bacterial composition at the phylum level was similar among the 18 rhizospheric samples; however, the proportion of Acidobacteria was much lower in these samples than in the control non-rhizospheric soil sample, indicating that rhizospheres influenced the bacterial composition even at the higher taxonomic level. Across host plant genome types (three levels of ploidy and three major genomes, A, B and D), there was no detectable difference in phylum composition or species diversity. Estimated bacterial species diversity was higher in the control soil sample than in plant rhizospheric soils, implying that bacterial species diversity was reduced in rhizospheres. A PCoA plot and UPGMA dendrogram based on the bacterial species composition showed that control soil was distantly located from the plant rhizospheric samples and that Triticum, Aegilops and related species were well separated. PERMANOVA analysis detected statistically significant differentiation among these four groups. Clustering of Triticum species suggested that the A genome was dominant over the B and D genomes, with respect to the influence on rhizospheric bacterial species composition. Although the cause was not investigated in this study, these results clearly indicated that the genetic constitution of the plant host exerted a strong influence on rhizospheric bacterial community structure.
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Affiliation(s)
- Natsumi Ito
- Laboratory of Plant Genetics, Graduate School of Agriculture, Kyoto University
| | - Naoki Mori
- Laboratory of Plant Genetics, Graduate School of Agriculture, Kobe University
| | - Naohiko T Miyashita
- Laboratory of Plant Genetics, Graduate School of Agriculture, Kyoto University
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14
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Vavilova V, Konopatskaia I, Blinov A, Kondratenko EY, Kruchinina YV, Goncharov NP. Genetic variability of spelt factor gene in Triticum and Aegilops species. BMC Plant Biol 2020; 20:310. [PMID: 33050874 PMCID: PMC7556929 DOI: 10.1186/s12870-020-02536-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 06/29/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Threshability, rachis fragility and spike shape are critical traits for the domestication and evolution of wheat, determining the crop yield and efficiency of the harvest. Spelt factor gene Q controls a wide range of domestication-related traits in polyploid wheats, including those mentioned above. The main goal of the present study was to characterise the Q gene for uninvestigated accessions of wheats, including four endemics, and Aegilops accessions, and to analyze the species evolution based on differences in Q gene sequences. RESULTS We have studied the spike morphology for 15 accessions of wheat species, including four endemics, namely Triticum macha, T. tibetanum, T. aestivum ssp. petropavlovskyi and T. spelta ssp. yunnanense, and 24 Aegilops accessions, which are donors of B and D genomes for polyploid wheat. The Q-5A, q-5D and q-5S genes were investigated, and a novel allele of the Q-5A gene was found in accessions of T. tibetanum (KU510 and KU515). This allele was similar to the Q allele of T. aestivum cv. Chinese Spring but had an insertion 161 bp in length within exon 5. This insertion led to a frameshift and premature stop codon formation. Thus, the T. tibetanum have spelt spikes, which is probably determined by the gene Tg, rather than Q. We determined the variability within the q-5D genes among hexaploid wheat and their D genome donor Aegilops tauschii. Moreover, we studied the accessions C21-5129, KU-2074, and K-1100 of Ae. tauschii ssp. strangulata, which could be involved in the origin of hexaploid wheats. CONCLUSIONS The variability and phylogenetic relationships of the Q gene sequences studied allowed us to clarify the relationships between species of the genus Triticum and to predict the donor of the D genome among the Ae. tauschii accessions. Ae. tauschii ssp. strangulata accessions C21-5129, KU-2074 and K-1100 are the most interesting among the analysed accessions, since their partial sequence of q-5D is identical to the q-5D of T. aestivum cv. Chinese Spring. This result indicates that the donor is Ae. tauschii ssp. strangulata but not Ae. tauschii ssp. tauschii. Our analysis allowed us to clarify the phylogenetic relationships in the genus Triticum.
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Affiliation(s)
- Valeriya Vavilova
- Institute of Cytology and Genetics SB RAS, Novosibirsk, Russian Federation.
| | - Irina Konopatskaia
- Institute of Cytology and Genetics SB RAS, Novosibirsk, Russian Federation
| | - Alexandr Blinov
- Institute of Cytology and Genetics SB RAS, Novosibirsk, Russian Federation
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15
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Sun X, Kosman E, Sharon A. Stem Endophytic Mycobiota in Wild and Domesticated Wheat: Structural Differences and Hidden Resources for Wheat Improvement. J Fungi (Basel) 2020; 6:jof6030180. [PMID: 32962177 PMCID: PMC7557378 DOI: 10.3390/jof6030180] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 09/12/2020] [Accepted: 09/15/2020] [Indexed: 12/23/2022] Open
Abstract
Towards the identification of entophytic fungal taxa with potential for crop improvement, we characterized and compared fungal endophyte communities (FECs) from domesticated bread wheat and two wheat ancestors, Aegilopssharonensis and Triticumdicoccoides. Data generated by next generation sequencing identified a total of 1666 taxa. The FECs in the three plant species contained high proportions of random taxa with low abundance. At plant species level, the majority of abundant taxa were common to all host plants, and the collective FECs of each of the three plant species had similar diversity. However, FECs from the wild plants in specific sites were more diverse and had greater richness than wheat FECs from corresponding specific fields. The wild plants also had higher numbers of differentially abundant fungal taxa than wheat, with Alternaria infectoria being the most abundant species in wild plants and Candida sake the most abundant in wheat. Network analysis on co-occurrence association revealed a small number of taxa with a relatively high number of co-occurrence associations, which might be important in community assembly. Our results show that the actual endophytic cargo in cultivated wheat plants is limited relative to wild plants, and highlight putative functional and hub fungal taxa with potential for wheat improvement.
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16
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Zuo Y, Xiang Q, Dai S, Song Z, Bao T, Hao M, Zhang L, Liu G, Li J, Liu D, Wei Y, Zheng Y, Yan Z. Development and characterization of Triticum turgidum - Aegilops comosa and T. turgidum - Ae. markgrafii amphidiploids. Genome 2020; 63:263-273. [PMID: 32160479 DOI: 10.1139/gen-2019-0215] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Aegilops comosa and Ae. markgrafii are diploid progenitors of polyploidy species of Aegilops sharing M and C genomes, respectively. Transferring valuable genes/traits from Aegilops into wheat is an alternative strategy for wheat genetic improvement. The amphidiploids between diploid species of Aegilops and tetraploid wheat can act as bridges to overcome obstacles from direct hybridization and can be developed by the union of unreduced gametes. In this study, we developed seven Triticum turgidum - Ae. comosa and two T. turgidum - Ae. markgrafii amphidiploids. The unreduced gametes mechanisms, including first-division restitution (FDR) and single-division meiosis (SDM), were observed in triploid F1 hybrids of T. turgidum - Ae. comosa (STM) and T. turgidum - Ae. markgrafii (STC). Only FDR was observed in STC hybrids, whereas FDR or both FDR and SDM were detected in the STM hybrids. All seven pairs of M chromosomes of Ae. comosa and C chromosomes of Ae. markgrafii were distinguished by fluorescent in situ hybridization (FISH) probes pSc119.2 and pTa71 combinations with pTa-535 and (CTT)12/(ACT)7, respectively. Meanwhile, the chromosomes of tetraploid wheat and diploid Aegilops parents were distinguished by the same FISH probes. The amphidiploids possessed specific valuable traits such as multiple tillers, large seed size related traits, and stripe rust resistance that could be utilized in the genetic improvement of wheat.
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Affiliation(s)
- Yuanyuan Zuo
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Wenjiang, Chengdu 611130, Sichuan, P.R. China.,Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu 611130, Sichuan, P.R. China
| | - Qin Xiang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Wenjiang, Chengdu 611130, Sichuan, P.R. China.,Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu 611130, Sichuan, P.R. China
| | - Shoufen Dai
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Wenjiang, Chengdu 611130, Sichuan, P.R. China.,Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu 611130, Sichuan, P.R. China
| | - Zhongping Song
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Wenjiang, Chengdu 611130, Sichuan, P.R. China.,Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu 611130, Sichuan, P.R. China
| | - Tingyu Bao
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Wenjiang, Chengdu 611130, Sichuan, P.R. China.,Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu 611130, Sichuan, P.R. China
| | - Ming Hao
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Wenjiang, Chengdu 611130, Sichuan, P.R. China.,Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu 611130, Sichuan, P.R. China
| | - Lianquan Zhang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Wenjiang, Chengdu 611130, Sichuan, P.R. China.,Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu 611130, Sichuan, P.R. China
| | - Gang Liu
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu 611130, Sichuan, P.R. China
| | - Jian Li
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu 611130, Sichuan, P.R. China
| | - Dengcai Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Wenjiang, Chengdu 611130, Sichuan, P.R. China.,Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu 611130, Sichuan, P.R. China
| | - Yuming Wei
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Wenjiang, Chengdu 611130, Sichuan, P.R. China.,Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu 611130, Sichuan, P.R. China
| | - Youliang Zheng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Wenjiang, Chengdu 611130, Sichuan, P.R. China.,Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu 611130, Sichuan, P.R. China
| | - Zehong Yan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Wenjiang, Chengdu 611130, Sichuan, P.R. China.,Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu 611130, Sichuan, P.R. China
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17
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Fatima F, McCallum BD, Pozniak CJ, Hiebert CW, McCartney CA, Fedak G, You FM, Cloutier S. Identification of New Leaf Rust Resistance Loci in Wheat and Wild Relatives by Array-Based SNP Genotyping and Association Genetics. Front Plant Sci 2020; 11:583738. [PMID: 33304363 PMCID: PMC7701059 DOI: 10.3389/fpls.2020.583738] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Accepted: 10/15/2020] [Indexed: 05/22/2023]
Abstract
Leaf rust caused by Puccinia triticina is the most widespread rust disease of wheat. As pathogen populations are constantly evolving, identification of novel sources of resistance is necessary to maintain disease resistance and stay ahead of this plant-pathogen evolutionary arms race. The wild genepool of wheat is a rich source of genetic diversity, accounting for 44% of the Lr genes identified. Here we performed a genome-wide association study (GWAS) on a diverse germplasm of 385 accessions, including 27 different Triticum and Aegilops species. Genetic characterization using the wheat 90 K array and subsequent filtering identified a set of 20,501 single nucleotide polymorphic (SNP) markers. Of those, 9,570 were validated using exome capture and mapped onto the Chinese Spring reference sequence v1.0. Phylogenetic analyses illustrated four major clades, clearly separating the wild species from the T. aestivum and T. turgidum species. GWAS was conducted using eight statistical models for infection types against six leaf rust isolates and leaf rust severity rated in field trials for 3-4 years at 2-3 locations in Canada. Functional annotation of genes containing significant quantitative trait nucleotides (QTNs) identified 96 disease-related loci associated with leaf rust resistance. A total of 21 QTNs were in haplotype blocks or within flanking markers of at least 16 known Lr genes. The remaining significant QTNs were considered loci that putatively harbor new Lr resistance genes. Isolation of these candidate genes will contribute to the elucidation of their role in leaf rust resistance and promote their usefulness in marker-assisted selection and introgression.
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Affiliation(s)
- Fizza Fatima
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
- Department of Biology, University of Ottawa, Ottawa, ON, Canada
| | - Brent D. McCallum
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Curtis J. Pozniak
- Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Colin W. Hiebert
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Curt A. McCartney
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - George Fedak
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Frank M. You
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Sylvie Cloutier
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
- Department of Biology, University of Ottawa, Ottawa, ON, Canada
- *Correspondence: Sylvie Cloutier,
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18
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Blume YB. A journey through a plant cytoskeleton: Hot spots in signaling and functioning. Cell Biol Int 2019; 44:1262-1266. [PMID: 31486567 DOI: 10.1002/cbin.11224] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 08/03/2019] [Indexed: 01/20/2023]
Abstract
This survey paper contains a brief analysis of publications included in the special issue of the scientific journal Cell Biology International titled "Plant Cytoskeleton Structure, Dynamics and Functions". The manuscripts in this special issue reflect some new aspects of plant cytoskeleton organization, signaling and functioning, and results from different Ukrainian research groups, and focuses on bringing together scientists working across different instrumental scales.
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Affiliation(s)
- Yaroslav B Blume
- Department of Genomics and Molecular Biotechnology, Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, Osypovskoho Str., 2a, Kyiv, 04123, Ukraine
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19
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Domb K, Keidar-Friedman D, Kashkush K. A novel miniature transposon-like element discovered in the coding sequence of a gene that encodes for 5-formyltetrahydrofolate in wheat. BMC Plant Biol 2019; 19:461. [PMID: 31675912 PMCID: PMC6824096 DOI: 10.1186/s12870-019-2034-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 09/12/2019] [Indexed: 05/02/2023]
Abstract
BACKGROUND Transposable elements (TEs) comprise over 80% of the wheat genome and usually possess unique features for specific super-families and families. However, the role of TEs in wheat evolution and reshaping the wheat genome remains largely unclear. RESULTS In this study, we discovered a miniature (307 bp in length) TE-like sequence in exon 6 of a gene that encodes for 5-formyltetrahydrofolate, in two accessions of wild emmer wheat (T. turgidum ssp. dicoccoides) and has interfered with the gene translation by creating a shorter reading frame as a result of a stop codon. The sequence that was termed Mariam, does not show any structural similarity to known TEs. It does not possess terminal inverted repeats (TIRs) that would allow us to assign this element to one of the TIR DNA super-families, and it does not possess characteristic features of SINE, such as a Pol-III promotor or a poly-A tail. In-silico analysis of five publicly available genome drafts of Triticum and Aegilops species revealed that Mariam element appears in a very low copy number (1-3 insertions) in diploid wheat species and ~ 12 insertions in tetraploid and hexaploidy wheat species. In addition, Mariam element was found to be unique to wheat, as it was not found in other plant genomes. The dynamic nature of Mariam in the wheat genome was assessed by site-specific PCR analysis and revealed that it retained activity in wild emmer populations in a population-specific manner. CONCLUSIONS This study provides additional insight into the evolutionary impact of TEs in wheat.
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Affiliation(s)
- Katherine Domb
- Present Address: Department of Molecular Biology and Ecology of Plants, Tel-Aviv University, Tel Aviv, Israel
| | | | - Khalil Kashkush
- Department of Life Sciences, Ben-Gurion University, 84105, Beer-Sheva, Israel.
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20
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Affiliation(s)
- Yaroslav B Blume
- Department of Genomics and Molecular Biotechnology, Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, Osypovskoho Str., 2a, Kyiv, 04123, Ukraine
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21
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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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22
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Kumar A, Kapoor P, Chunduri V, Sharma S, Garg M. Potential of Aegilops sp. for Improvement of Grain Processing and Nutritional Quality in Wheat ( Triticum aestivum). Front Plant Sci 2019; 10:308. [PMID: 30936886 PMCID: PMC6431632 DOI: 10.3389/fpls.2019.00308] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 02/26/2019] [Indexed: 06/09/2023]
Abstract
Wheat is one of the most important staple crops in the world and good source of calories and nutrition. Its flour and dough have unique physical properties and can be processed to make unique products like bread, cakes, biscuits, pasta, noodles etc., which is not possible from other staple crops. Due to domestication, the genetic variability of the genes coding for different economically important traits in wheat is narrow. This genetic variability can be increased by utilizing its wild relatives. Its closest relative, genus Aegilops can be an important source of new alleles. Aegilops has played a very important role in evolution of tetraploid and hexaploid wheat. It consists of 22 species with C, D, M, N, S, T and U genomes with high allelic diversity relative to wheat. Its utilization for wheat improvement for various abiotic and biotic stresses has been reported by various scientific publications. Here in, for the first time, we review the potential of Aegilops for improvement of processing and nutritional traits in wheat. Among processing quality related gluten proteins; high molecular weight glutenins (HMW GS), being easiest to study have been explored in highest number of accessions or lines i.e., 681 belonging to 13 species and selected ones like Ae. searsii, Ae. geniculata and Ae. longissima have been linked with improved bread making quality of wheat. Gliadins and low molecular weight glutenins (LMW GS) have also been extensively explored for wheat improvement and Ae. umbellulata specific LMW GS have been linked with wheat bread making quality improvement. Aegilops has been explored for seed texture diversity and proteins like puroindolins (Pin) and grain softness proteins (GSP). For nutrition quality improvement, it has been screened for essential micronutrients like Fe, Zn, phytochemicals like carotenoids and dietary fibers like arabinoxylan and β-glucan. Ae. kotschyi and Ae. biuncialis transfer in wheat have been associated with higher Fe, Zn content. In this article we have tried to compile information available on exploration of nutritional and processing quality related traits in Aegilops section and their utilization for wheat improvement by different approaches.
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23
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Abstract
Background Flavonoid compounds are secondary plant metabolites, having a functional importance in plant development, protection from pathogens and unfavorable environmental factors. Chalcone synthase (CHS) is a key enzyme in the biosynthesis of flavonoids; it is involved in biosynthesis of all classes of flavonoid compounds. Nevertheless, the Chs gene family in bread wheat (Triticum aestivum L.) has been not characterized yet. The aim of the current study was to investigate structural and functional organization of the Chs genes and evolution of this gene family in bread wheat and relative species. Results The nucleotide sequences of the eight Chs copies in T. aestivum were identified. Among them, two homoeologous sets of the Chs genes were located on the short (Chs-A1, −B1, −D1) and the long (Chs-A4, −B4, −D4) arms of homoeologous group 2 chromosomes. Two paralogous gene copies in the B-genome (Chs-B2, −B3) were located in the distal regions of 2BS chromosome. To clarify the origin of Chs duplications in the B-genome the phylogenetic analysis with the Chs sequences of Triticum and Aegilops species carrying ancestral genomes was conducted. It was estimated that the first duplication event occurred in the genome of the common ancestor of Triticum and Aegilops genera about 10–12 million years ago (MYA), then another copy was formed in the ancestor of the B-genome about 6–7 MYA. A homology modeling revealed high sequence similarity of bread wheat CHS enzymes. A number of short deletions in coding regions of some Chs sequences are not expected to have any significant functional effects. Estimation of transcriptional activity of the Chs copies along with a comparative analysis of their promoters structure suggested their functional specialization, which likely contributed to the maintaining of the duplicated Chs genes in wheat genome. Conclusions From possible ten Chs copies in bread wheat genome, eight members of this family retained their intact structure and activity, while two copies appear to be lost at the level of diploid and tetraploid ancestors. Transcriptional assay along with a comparative analysis of the cis-regulatory elements revealed their functional diversification. The multiple functions supported by the Chs family are assumed to be a driving force for duplications of the Chs gene and their retention in plant genome. Electronic supplementary material The online version of this article (10.1186/s12863-019-0727-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Nikita V Ivanisenko
- Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia.,Novosibirsk State University, Novosibirsk, Russia
| | - Elena K Khlestkina
- Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia.,Novosibirsk State University, Novosibirsk, Russia.,N.I. Vavilov All-Russian Research Institute of Plant Genetic Resources (VIR), Saint-Petersburg, Russia
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24
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Przewieslik-Allen AM, Burridge AJ, Wilkinson PA, Winfield MO, Shaw DS, McAusland L, King J, King IP, Edwards KJ, Barker GLA. Developing a High-Throughput SNP-Based Marker System to Facilitate the Introgression of Traits From Aegilops Species Into Bread Wheat ( Triticum aestivum). Front Plant Sci 2019; 9:1993. [PMID: 30733728 PMCID: PMC6354564 DOI: 10.3389/fpls.2018.01993] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 12/21/2018] [Indexed: 06/09/2023]
Abstract
The genus Aegilops contains a diverse collection of wild species exhibiting variation in geographical distribution, ecological adaptation, ploidy and genome organization. Aegilops is the most closely related genus to Triticum which includes cultivated wheat, a globally important crop that has a limited gene pool for modern breeding. Aegilops species are a potential future resource for wheat breeding for traits, such as adaptation to different ecological conditions and pest and disease resistance. This study describes the development and application of the first high-throughput genotyping platform specifically designed for screening wheat relative species. The platform was used to screen multiple accessions representing all species in the genus Aegilops. Firstly, the data was demonstrated to be useful for screening diversity and examining relationships within and between Aegilops species. Secondly, markers able to characterize and track introgressions from Aegilops species in hexaploid wheat were identified and validated using two different approaches.
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Affiliation(s)
| | | | | | | | - Daniel S. Shaw
- Life Sciences, University of Bristol, Bristol, United Kingdom
| | - Lorna McAusland
- Plant Sciences, Sutton Bonington Campus, Leicestershire, United Kingdom
| | - Julie King
- Plant Sciences, Sutton Bonington Campus, Leicestershire, United Kingdom
| | - Ian P. King
- Plant Sciences, Sutton Bonington Campus, Leicestershire, United Kingdom
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25
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Strygina KV, Khlestkina EK. [MYC gene family in cereals: Transformations during evolution of hexaploid bread wheat and its relatives]. Mol Biol (Mosk) 2018; 51:772-779. [PMID: 29116063 DOI: 10.7868/s0026898417050032] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Accepted: 12/05/2016] [Indexed: 11/23/2022]
Abstract
The transcription factors of the MYC gene family are an integral part of the MYB + MYC + WD40 regulatory complex required to activate the genes of plant flavonoid biosynthesis. The TaMyc1 gene, which controls the synthesis of flavonoid pigments in the grain pericarp, is known in bread wheat (Triticum aestivum L., BBAADD genome, 2n = 6x = 42). In the present work, we identified 10 copies of this gene in the T. aestivum genome, 22 copies in the nearest bread wheat relatives (T. durum, T. urartu, T. monococcum, Aegilops speltoides, Ae. sharonensis, Ae. tauschii). The analysis of genetic similarity of all these genes demonstrated that the MYC gene duplication occurred for the first time in the common diploid ancestor of the Triticeae tribe with the formation of copies in the second and fourth chromosomes. In the members of the Triticum and Aegilops genera, these genes underwent from two to four duplication acts that resulted in the formation of paralogous copies. The orthologs of the MYC genes obtained from ancestral diploid species exist in polyploid species of the Triticum genus (in addition to paralogues). The time of the emergence of individual MYC family members was calculated based on the average speed of accumulation of nucleotide substitutions (k) in the MYC genes (established in this work) and certain number of synonymous substitutions between individual copies.
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Affiliation(s)
- K V Strygina
- Federal Research Center Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Novosibirsk, 630090 Russia.,
| | - E K Khlestkina
- Federal Research Center Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Novosibirsk, 630090 Russia.,Novosibirsk State University, Novosibirsk, 630090 Russia
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26
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Brestic M, Zivcak M, Hauptvogel P, Misheva S, Kocheva K, Yang X, Li X, Allakhverdiev SI. Wheat plant selection for high yields entailed improvement of leaf anatomical and biochemical traits including tolerance to non-optimal temperature conditions. Photosynth Res 2018; 136:245-255. [PMID: 29383631 DOI: 10.1007/s11120-018-0486-z] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Accepted: 01/23/2018] [Indexed: 05/11/2023]
Abstract
Assessment of photosynthetic traits and temperature tolerance was performed on field-grown modern genotype (MG), and the local landrace (LR) of wheat (Triticum aestivum L.) as well as the wild relative species (Aegilops cylindrica Host.). The comparison was based on measurements of the gas exchange (A/ci, light and temperature response curves), slow and fast chlorophyll fluorescence kinetics, and some growth and leaf parameters. In MG, we observed the highest CO2 assimilation rate [Formula: see text] electron transport rate (Jmax) and maximum carboxylation rate [Formula: see text]. The Aegilops leaves had substantially lower values of all photosynthetic parameters; this fact correlated with its lower biomass production. The mesophyll conductance was almost the same in Aegilops and MG, despite the significant differences in leaf phenotype. In contrary, in LR with a higher dry mass per leaf area, the half mesophyll conductance (gm) values indicated more limited CO2 diffusion. In Aegilops, we found much lower carboxylation capacity; this can be attributed mainly to thin leaves and lower Rubisco activity. The difference in CO2 assimilation rate between MG and others was diminished because of its higher mitochondrial respiration activity indicating more intense metabolism. Assessment of temperature response showed lower temperature optimum and a narrow ecological valence (i.e., the range determining the tolerance limits of a species to an environmental factor) in Aegilops. In addition, analysis of photosynthetic thermostability identified the LR as the most sensitive. Our results support the idea that the selection for high yields was accompanied by the increase of photosynthetic productivity through unintentional improvement of leaf anatomical and biochemical traits including tolerance to non-optimal temperature conditions.
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Affiliation(s)
- Marian Brestic
- Department of Plant Physiology, Slovak Agricultural University, Tr. A. Hlinku 2, 949 76, Nitra, Slovakia.
| | - Marek Zivcak
- Department of Plant Physiology, Slovak Agricultural University, Tr. A. Hlinku 2, 949 76, Nitra, Slovakia
| | - Pavol Hauptvogel
- National Agricultural and Food Centre, Research Institute of Plant Production, Piešťany, Slovakia
| | - Svetlana Misheva
- Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, Acad. Georgi Bonchev Street, Bldg. 21, 1113, Sofia, Bulgaria
| | - Konstantina Kocheva
- Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, Acad. Georgi Bonchev Street, Bldg. 21, 1113, Sofia, Bulgaria
| | - Xinghong Yang
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, China
| | - Xiangnan Li
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, China
| | - Suleyman I Allakhverdiev
- Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya Street 35, Moscow, Russia, 127276.
- Institute of Basic Biological Problems, Russian Academy of Sciences, Pushchino, Moscow Region, Russia, 142290.
- Department of Plant Physiology, Faculty of Biology, M.V. Lomonosov Moscow State University, Leninskie Gory 1-12, Moscow, Russia, 119991.
- Moscow Institute of Physics and Technology, Institutsky lane 9, Dolgoprudny, Moscow Region, Russia, 141700.
- Institute of Molecular Biology and Biotechnology, Azerbaijan National Academy of Sciences, Matbuat Avenue 2a, 1073, Baku, Azerbaijan.
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27
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Ruban AS, Badaeva ED. Evolution of the S-Genomes in Triticum-Aegilops Alliance: Evidences From Chromosome Analysis. Front Plant Sci 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] [What about the content of this article? (0)] [Affiliation(s)] [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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28
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B Shcherban A, A Salina E. Dataset of the HOX1 gene sequences of the wheat polyploids and their diploid relatives. Data Brief 2017; 16:147-153. [PMID: 29201982 PMCID: PMC5699892 DOI: 10.1016/j.dib.2017.11.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Revised: 10/09/2017] [Accepted: 11/02/2017] [Indexed: 10/31/2022] Open
Abstract
The TaHOX-1 gene of common wheat Triticum aestivum L. (BAD-genome) encodes transcription factor (HD-Zip I) which is characterized by the presence of a DNA-binding homeodomain (HD) with an adjacent Leucine zipper (LZ) motif. This gene can play a role in adapting plant to a variety of abiotic stresses, such as drought, cold, salinity etc., which strongly affect wheat production. However, it's both functional role in stress resistance and divergence during wheat evolution has not yet been elucidated. This data in brief article is associated with the research paper "Structural and functional divergence of homoeologous copies of the TaHOX-1 gene in polyploid wheats and their diploid ancestors". The data set represents a recent survey of the primary HOX-1 gene sequences isolated from the first wheat allotetraploids (BA-genome) and their corresponding Triticum and Aegilops diploid relatives. Specifically, we provide detailed information about the HOX-1 nucleotide sequences of the promoter region and both nucleotide and amino acid sequences of the gene. The sequencing data used here is available at DDBJ/EMBL/GenBank under the accession numbers MG000630-MG000698.
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Affiliation(s)
- Andrey B Shcherban
- The Federal Research Center "The Institute of Cytology and Genetics SB RAS", Russian Federation
| | - Elena A Salina
- The Federal Research Center "The Institute of Cytology and Genetics SB RAS", Russian Federation
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29
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Rabokon A, Demkovych A, Sozinov A, Kozub N, Sozinov I, Pirko Y, Blume Y. Intron length polymorphism of β-tubulin genes of Aegilops biuncialis Vis. Cell Biol Int 2017; 43:1031-1039. [PMID: 29024189 DOI: 10.1002/cbin.10886] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 10/08/2017] [Indexed: 12/13/2022]
Abstract
Intron-specific DNA polymorphism is present among plant β-tubulin gene family members and is considered to be one of the molecular markers based on the difference of tubulin introns length assayed both separately (TBP: 1st intron) or in combination (h-TBP: 1st and 2nd introns). These two approaches are possibly useful for wheat breeding programs, since TBP and h-TBP help to differentiate between the accessions of Aegilops biuncialis Vis., a wild relative of wheat. PCR-derived polymorphic fragments were resolved by PAGE electrophoresis. The length of amplicons varied significantly (395-3900 bp for TBP and 466-3440 bp for h-TBP), while the numbers of polymorphic bands were 21 for TBP and 23 for h-TBP, respectively. PIC mean value was circa 0.3. Dendrograms constructed on the basis of the Nei and Li coefficient with the high bootstrap support reveal a similar order of hierarchy for the samples analyzed using both methods. Thus, both techniques uncover DNA polymorphism level sufficiently high to distinguish different accessions of Ae. biuncialis Vis.
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Affiliation(s)
- Anastasiia Rabokon
- Institute of Food Biotechnology and Genomics, Osipovskogo St., 2a, Kyiv-123, 04123, Ukraine
| | - Andrii Demkovych
- Institute of Food Biotechnology and Genomics, Osipovskogo St., 2a, Kyiv-123, 04123, Ukraine
| | - Alexei Sozinov
- Institute of Food Biotechnology and Genomics, Osipovskogo St., 2a, Kyiv-123, 04123, Ukraine
| | - Natalia Kozub
- Institute of Food Biotechnology and Genomics, Osipovskogo St., 2a, Kyiv-123, 04123, Ukraine.,Institute of Plant Protection, Vasylkivska St., 33, Kyiv-022, 03022, Ukraine
| | - Igor Sozinov
- Institute of Plant Protection, Vasylkivska St., 33, Kyiv-022, 03022, Ukraine
| | - Yaroslav Pirko
- Institute of Food Biotechnology and Genomics, Osipovskogo St., 2a, Kyiv-123, 04123, Ukraine
| | - Yaroslav Blume
- Institute of Food Biotechnology and Genomics, Osipovskogo St., 2a, Kyiv-123, 04123, Ukraine
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Rakszegi M, Molnár I, Lovegrove A, Darkó É, Farkas A, Láng L, Bedő Z, Doležel J, Molnár-Láng M, Shewry P. Addition of Aegilops U and M Chromosomes Affects Protein and Dietary Fiber Content of Wholemeal Wheat Flour. Front Plant Sci 2017; 8:1529. [PMID: 28932231 PMCID: PMC5592229 DOI: 10.3389/fpls.2017.01529] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 08/21/2017] [Indexed: 05/22/2023]
Abstract
Cereal grain fiber is an important health-promoting component in the human diet. One option to improve dietary fiber content and composition in wheat is to introduce genes from its wild relatives Aegilops biuncialis and Aegilops geniculata. This study showed that the addition of chromosomes 2Ug, 4Ug, 5Ug, 7Ug, 2Mg, 5Mg, and 7Mg of Ae. geniculata and 3Ub, 2Mb, 3Mb, and 7Mb of Ae. biuncialis into bread wheat increased the seed protein content. Chromosomes 1Ug and 1Mg increased the proportion of polymeric glutenin proteins, while the addition of chromosomes 1Ub and 6Ub led to its decrease. Both Aegilops species had higher proportions of β-glucan compared to arabinoxylan (AX) than wheat lines, and elevated β-glucan content was also observed in wheat chromosome addition lines 5U, 7U, and 7M. The AX content in wheat was increased by the addition of chromosomes 5Ug, 7Ug, and 1Ub while water-soluble AX was increased by the addition of chromosomes 5U, 5M, and 7M, and to a lesser extent by chromosomes 3, 4, 6Ug, and 2Mb. Chromosomes 5Ug and 7Mb also affected the structure of wheat AX, as shown by the pattern of oligosaccharides released by digestion with endoxylanase. These results will help to map genomic regions responsible for edible fiber content in Aegilops and will contribute to the efficient transfer of wild alleles in introgression breeding programs to obtain wheat varieties with improved health benefits. Key Message: Addition of Aegilops U- and M-genome chromosomes 5 and 7 improves seed protein and fiber content and composition in wheat.
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Affiliation(s)
- Marianna Rakszegi
- Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of SciencesMartonvásár, Hungary
| | - István Molnár
- Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of SciencesMartonvásár, Hungary
| | - Alison Lovegrove
- Department of Plant Science, Rothamsted ResearchHarpenden, United Kingdom
| | - Éva Darkó
- Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of SciencesMartonvásár, Hungary
| | - András Farkas
- Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of SciencesMartonvásár, Hungary
| | - László Láng
- Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of SciencesMartonvásár, Hungary
| | - Zoltán Bedő
- Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of SciencesMartonvásár, Hungary
| | - Jaroslav Doležel
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural ResearchOlomouc, Czechia
| | - Márta Molnár-Láng
- Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of SciencesMartonvásár, Hungary
| | - Peter Shewry
- Department of Plant Science, Rothamsted ResearchHarpenden, United Kingdom
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31
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Izan S, Esselink D, Visser RGF, Smulders MJM, Borm T. De Novo Assembly of Complete Chloroplast Genomes from Non-model Species Based on a K-mer Frequency-Based Selection of Chloroplast Reads from Total DNA Sequences. Front Plant Sci 2017; 8:1271. [PMID: 28824658 PMCID: PMC5539191 DOI: 10.3389/fpls.2017.01271] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 07/05/2017] [Indexed: 05/11/2023]
Abstract
Whole Genome Shotgun (WGS) sequences of plant species often contain an abundance of reads that are derived from the chloroplast genome. Up to now these reads have generally been identified and assembled into chloroplast genomes based on homology to chloroplasts from related species. This re-sequencing approach may select against structural differences between the genomes especially in non-model species for which no close relatives have been sequenced before. The alternative approach is to de novo assemble the chloroplast genome from total genomic DNA sequences. In this study, we used k-mer frequency tables to identify and extract the chloroplast reads from the WGS reads and assemble these using a highly integrated and automated custom pipeline. Our strategy includes steps aimed at optimizing assemblies and filling gaps which are left due to coverage variation in the WGS dataset. We have successfully de novo assembled three complete chloroplast genomes from plant species with a range of nuclear genome sizes to demonstrate the universality of our approach: Solanum lycopersicum (0.9 Gb), Aegilops tauschii (4 Gb) and Paphiopedilum henryanum (25 Gb). We also highlight the need to optimize the choice of k and the amount of data used. This new and cost-effective method for de novo short read assembly will facilitate the study of complete chloroplast genomes with more accurate analyses and inferences, especially in non-model plant genomes.
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Affiliation(s)
- Shairul Izan
- Plant Breeding, Wageningen University and ResearchWageningen, Netherlands
- Department of Crop Science, Faculty of Agriculture, Universiti Putra MalaysiaSerdang, Malaysia
| | - Danny Esselink
- Plant Breeding, Wageningen University and ResearchWageningen, Netherlands
| | | | | | - Theo Borm
- Plant Breeding, Wageningen University and ResearchWageningen, Netherlands
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32
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Abstract
An interesting and possibly unique pattern of genome evolution following polyploidy can be observed among allopolyploids of the Triticum and Aegilops genera (wheat group). Most polyploids in this group are presumed to share a common unaltered (pivotal) subgenome (U, D, or A) together with one or two modified (differential) subgenomes, a status that has been referred to as 'pivotal-differential' genome evolution. In this review we discuss various mechanisms that could be responsible for this evolutionary pattern, as well as evidence for and against the putative evolutionary mechanisms involved. We suggest that, in light of recent advances in genome sequencing and related technologies in the wheat group, the time has come to reopen the investigation into pivotal-differential genome evolution.
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Affiliation(s)
- Ghader Mirzaghaderi
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, University of Kurdistan, PO Box 416, Sanandaj, Iran
| | - Annaliese S Mason
- Department of Plant Breeding, Justus Liebig University, Research Center for Biosystems, Land Use, and Nutrition (IFZ), Heinrich-Buff-Ring 26-32, Giessen 35392, Germany.
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33
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Onishi K, Yamane M, Yamaji N, Tokui M, Kanamori H, Wu J, Komatsuda T, Sato K. Sequence differences in the seed dormancy gene Qsd1 among various wheat genomes. BMC Genomics 2017; 18:497. [PMID: 28662630 PMCID: PMC5492916 DOI: 10.1186/s12864-017-3880-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 06/20/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Pre-harvest sprouting frequently occurs in Triticum aestivum (wheat) and Hordeum vulgare (barley) at the end of the maturity period due to high rainfall, particularly in Asian monsoon areas. Seed dormancy is a major mechanism preventing pre-harvest sprouting in these crops. RESULTS We identified orthologous sequences of the major Hordeum vulgare (barley) seed dormancy gene Qsd1 in hexaploid wheat cv. Chinese Spring by performing genomic clone sequencing, followed by transcript sequencing. We detected 13 non-synonymous amino acid substitutions among the three sub-genomes of wheat and found that the Qsd1 sequence in the B sub-genome is most similar to that in barley. The Qsd1 sequence in A genome diploid wheat is highly similar to that in the hexaploid A sub-genome. Wheat orthologs of Qsd1 showed closer similarities to barley Qsd1 than did those of other accessions in the DNA database. Like barley Qsd1, all three wheat Qsd1s showed embryo-specific gene expression patterns, indicating that barley and wheat Qsd1 share an orthologous origin. The alignment of four hexaploid wheat cultivars indicated that the amino acid sequences of three spring cultivars, Chinese Spring, Haruyo Koi, and Fielder, are exactly the same in each sub-genome. Only Kitahonami has three amino acid substitutions at the B sub-genome. CONCLUSIONS Kitahonami has a longer seed dormancy period than does Chinese Spring. Sequence polymorphisms between Chiniese Spring and Kitahonami in the B sub-genome may underlie the phenotypic differences in seed dormancy between these hexaploid wheat cultivars.
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Affiliation(s)
- Kazumitsu Onishi
- Obihiro University of Agriculture and Veterinary Medicine, Obihiro, 080-8555, Japan
| | - Miki Yamane
- Institute of Plant Science and Resources, Okayama University, Kurashiki, 710-0046, Japan
| | - Nami Yamaji
- Institute of Plant Science and Resources, Okayama University, Kurashiki, 710-0046, Japan
| | - Mayumi Tokui
- Obihiro University of Agriculture and Veterinary Medicine, Obihiro, 080-8555, Japan
| | - Hiroyuki Kanamori
- Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba, 305-8634, Japan
| | - Jianzhong Wu
- Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba, 305-8634, Japan
| | - Takao Komatsuda
- Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba, 305-8634, Japan
| | - Kazuhiro Sato
- Institute of Plant Science and Resources, Okayama University, Kurashiki, 710-0046, Japan.
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Abstract
Aegilops is a genus belonging to the family Poaceace, which have played an indispensible role in the evolution of bread wheat and continues to do so by transferring genes by wide hybridization. Being the secondary gene pool of wheat, gene transfer from Aegilops poses difficulties and segregation distortion is common. Gametocidal genes are the most well characterized class of segregation distorters reported in interspecific crosses of wheat with Aegilops. These "selfish" genetic elements ensure their preferential transmission to progeny at the cost of gametes lacking them without providing any phenotypic benefits to the plant, thereby causing a proportional reduction in fertility. Gametocidal genes (Gc) have been reported in different species of Aegilops belonging to the sections Aegilops (Ae. geniculata and Ae. triuncialis), Cylindropyrum (Ae. caudata and Ae. cylindrica), and Sitopsis (Ae. longissima, Ae. sharonensis, and Ae. speltoides). Gametocidal activity is mostly confined to 2, 3, and 4 homeologous groups of C, S, S1, Ssh, and Mg genomes. Removal of such genes is necessary for successful alien gene introgression and can be achieved by mutagenesis or allosyndetic pairing. However, there are some instances where Gc genes are constructively utilized for development of deletion stocks in wheat, improving genetic variability and chromosome engineering.
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Affiliation(s)
- M Niranjana
- Indian Agricultural Research Institute, New Delhi, India.,Indian Agricultural Research Institute, New Delhi, India
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Bernhardt N, Brassac J, Kilian B, Blattner FR. Dated tribe-wide whole chloroplast genome phylogeny indicates recurrent hybridizations within Triticeae. BMC Evol Biol 2017; 17:141. [PMID: 28622761 PMCID: PMC5474006 DOI: 10.1186/s12862-017-0989-9] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Accepted: 06/03/2017] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Triticeae, the tribe of wheat grasses, harbours the cereals barley, rye and wheat and their wild relatives. Although economically important, relationships within the tribe are still not understood. We analysed the phylogeny of chloroplast lineages among nearly all monogenomic Triticeae taxa and polyploid wheat species aiming at a deeper understanding of the tribe's evolution. We used on- and off-target reads of a target-enrichment experiment followed by Illumina sequencing. RESULTS The read data was used to assemble the plastid locus ndhF for 194 individuals and the whole chloroplast genome for 183 individuals, representing 53 Triticeae species and 15 genera. We conducted Bayesian and multispecies coalescent analyses to infer relationships and estimate divergence times of the taxa. We present the most comprehensive dated Triticeae chloroplast phylogeny and review previous hypotheses in the framework of our results. Monophyly of Triticeae chloroplasts could not be confirmed, as either Bromus or Psathyrostachys captured a chloroplast from a lineage closely related to a Bromus-Triticeae ancestor. The most recent common ancestor of Triticeae occurred approximately between ten and 19 million years ago. CONCLUSIONS The comparison of the chloroplast phylogeny with available nuclear data in several cases revealed incongruences indicating past hybridizations. Recent events of chloroplast capture were detected as individuals grouped apart from con-specific accessions in otherwise monopyhletic groups.
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Affiliation(s)
- Nadine Bernhardt
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany.
| | - Jonathan Brassac
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Benjamin Kilian
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
- Present address: Crop Trust, Bonn, Germany
| | - Frank R Blattner
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
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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 Biol 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] [What about the content of this article? (0)] [Affiliation(s)] [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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Majka M, Kwiatek M, Belter J, Wiśniewska H. Characterization of morphology and resistance to Blumeria graminis of winter triticale monosomic addition lines with chromosome 2D of Aegilops tauschii. Plant Cell Rep 2016; 35:2125-35. [PMID: 27406086 PMCID: PMC5025500 DOI: 10.1007/s00299-016-2023-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 06/29/2016] [Indexed: 05/04/2023]
Abstract
Allocation of the chromosome 2D of Ae. tauschii in triticale background resulted in changes of its organization, what is related to varied expression of genes determining agronomically important traits. Monosomic alien addition lines (MAALs) are crucial for transfer of genes from wild relatives into cultivated varieties. This kind of genetic stocks is used for physical mapping of specific chromosomes and analyzing alien genes expression. The main aim of our study is to improve hexaploid triticale by transferring D-genome chromatin from Aegilops tauschii × Secale cereale (2n = 4x = 28, DDRR). In this paper, we demonstrate the molecular cytogenetics analysis and SSR markers screening combined with phenotype analysis and evaluation of powdery mildew infection of triticale monosomic addition lines carrying chromosome 2D of Ae. tauschii. We confirmed the inheritance of chromosome 2D from the BC2F4 to the BC2F6 generation of triticale hybrids. Moreover, we unveiled a high variable region on the short arm of chromosome 2D, where chromosome rearrangements were mapped. These events had direct influence on plant height of hybrids what might be connected with changes at Rht8 loci. We obtained 20 semi-dwarf plants of BC2F6 generation carrying 2D chromosome with the powdery mildew resistance, without changes in spike morphology, which can be used in the triticale breeding programs.
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Affiliation(s)
- M Majka
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland.
| | - M Kwiatek
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland
| | - J Belter
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland
| | - H Wiśniewska
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland
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Ofek-Lalzar M, Gur Y, Ben-Moshe S, Sharon O, Kosman E, Mochli E, Sharon A. Diversity of fungal endophytes in recent and ancient wheat ancestors Triticum dicoccoides and Aegilops sharonensis. FEMS Microbiol Ecol 2016; 92:fiw152. [PMID: 27402714 DOI: 10.1093/femsec/fiw152] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/05/2016] [Indexed: 01/29/2023] Open
Abstract
Endophytes have profound impacts on plants, including beneficial effects on agriculturally important traits. We hypothesized that endophytes in wild plants include beneficial endophytes that are absent or underrepresented in domesticated crops. In this work, we studied the structure of endophyte communities in wheat-related grasses, Triticum dicoccoides and Aegilops sharonensis, and compared it to an endophyte community from wheat (T. aeastivum). Endophytes were isolated by cultivation and by cultivation-independent methods. In total, 514 intergenic spacer region sequences from single cultures were analyzed. Categorization at 97% sequence similarity resulted in 67 operational taxonomic units (OTUs) that were evenly distributed between the different plant species. A narrow core community of Alternaria spp. was found in all samples, but each plant species also contained a significant portion of unique endophytes. The cultivation-independent analysis identified a larger number of OTUs than the cultivation method, half of which were singletons or doubletons. For OTUs with a relative abundance >0.5%, similar numbers were obtained by both methods. Collectively, our data show that wild grass relatives of wheat contain a wealth of taxonomically diverse fungal endophytes that are not found in modern wheat, some of which belong to taxa with known beneficial effects.
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Affiliation(s)
- Maya Ofek-Lalzar
- Institute of Cereal Crop Improvement, Department of Molecular Biology and Ecology of Plants, Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv 6997, Israel
| | - Yonatan Gur
- Institute of Cereal Crop Improvement, Department of Molecular Biology and Ecology of Plants, Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv 6997, Israel
| | - Sapir Ben-Moshe
- Institute of Cereal Crop Improvement, Department of Molecular Biology and Ecology of Plants, Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv 6997, Israel
| | - Or Sharon
- Institute of Cereal Crop Improvement, Department of Molecular Biology and Ecology of Plants, Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv 6997, Israel
| | - Evsey Kosman
- Institute of Cereal Crop Improvement, Department of Molecular Biology and Ecology of Plants, Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv 6997, Israel
| | - Elad Mochli
- Institute of Cereal Crop Improvement, Department of Molecular Biology and Ecology of Plants, Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv 6997, Israel
| | - Amir Sharon
- Institute of Cereal Crop Improvement, Department of Molecular Biology and Ecology of Plants, Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv 6997, Israel
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Kwiatek M, Belter J, Majka M, Wiśniewska H. Allocation of the S-genome chromosomes of Aegilops variabilis Eig. carrying powdery mildew resistance in triticale (× Triticosecale Wittmack). Protoplasma 2016; 253:329-43. [PMID: 25868512 PMCID: PMC4783449 DOI: 10.1007/s00709-015-0813-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Accepted: 03/25/2015] [Indexed: 05/15/2023]
Abstract
It has been hypothesized that the powdery mildew adult plant resistance (APR) controlled by the Pm13 gene in Aegilops longissima Schweinf. & Muschl. (S(l)S(l)) has been evolutionary transferred to Aegilops variabilis Eig. (UUSS). The molecular marker analysis and the visual evaluation of powdery mildew symptoms in Ae. variabilis and the Ae. variabilis × Secale cereale amphiploid forms (2n = 6x = 42, UUSSRR) showed the presence of product that corresponded to Pm13 marker and the lower infection level compared to susceptible model, respectively. This study also describes the transfer of Ae. variabilis Eig. (2n = 4x = 28, U(v)U(v)S(v)S(v)) chromosomes, carrying powdery mildew resistance, into triticale (× Triticosecale Wittm., 2n = 6x = 42, AABBRR) using Ae. variabilis × S. cereale amphiploid forms. The individual chromosomes of Ae. variabilis, triticale 'Lamberto' and hybrids were characterized by genomic and fluorescence in situ hybridization (GISH/FISH). The chromosome configurations of obtained hybrid forms were studied at first metaphase of meiosis of pollen mother cells (PMCs) using GISH. The statistical analysis showed that the way of S-genome chromosome pairing and transmission to subsequent hybrid generations was diploid-like and had no influence on chromosome pairing of triticale chromosomes. The cytogenetic study of hybrid forms were supported by the marker-assisted selection using Pm13 marker and visual evaluation of natural infection by Blumeria graminis, that allowed to select the addition or substitution lines of hybrids carrying chromosome 3S(v) which were tolerant to the powdery mildew infection.
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Affiliation(s)
- M Kwiatek
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland.
| | - J Belter
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland.
| | - M Majka
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland.
| | - H Wiśniewska
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland.
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40
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Prins A, Orr DJ, Andralojc PJ, Reynolds MP, Carmo-Silva E, Parry MAJ. Rubisco catalytic properties of wild and domesticated relatives provide scope for improving wheat photosynthesis. J Exp Bot 2016; 67:1827-38. [PMID: 26798025 PMCID: PMC4783365 DOI: 10.1093/jxb/erv574] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Rubisco is a major target for improving crop photosynthesis and yield, yet natural diversity in catalytic properties of this enzyme is poorly understood. Rubisco from 25 genotypes of the Triticeae tribe, including wild relatives of bread wheat (Triticum aestivum), were surveyed to identify superior enzymes for improving photosynthesis in this crop. In vitro Rubisco carboxylation velocity (V c), Michaelis-Menten constants for CO2 (K c) and O2 (K o) and specificity factor (S c/o) were measured at 25 and 35 °C. V c and K c correlated positively, while V c and S c/o were inversely related. Rubisco large subunit genes (rbcL) were sequenced, and predicted corresponding amino acid differences analysed in relation to the corresponding catalytic properties. The effect of replacing native wheat Rubisco with counterparts from closely related species was analysed by modelling the response of photosynthesis to varying CO2 concentrations. The model predicted that two Rubisco enzymes would increase photosynthetic performance at 25 °C while only one of these also increased photosynthesis at 35 °C. Thus, under otherwise identical conditions, catalytic variation in the Rubiscos analysed is predicted to improve photosynthetic rates at physiological CO2 concentrations. Naturally occurring Rubiscos with superior properties amongst the Triticeae tribe can be exploited to improve wheat photosynthesis and crop productivity.
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Affiliation(s)
- Anneke Prins
- Plant Biology and Crop Science Department, Rothamsted Research, Harpenden AL5 2JQ UK
| | - Douglas J Orr
- Plant Biology and Crop Science Department, Rothamsted Research, Harpenden AL5 2JQ UK
| | - P John Andralojc
- Plant Biology and Crop Science Department, Rothamsted Research, Harpenden AL5 2JQ UK
| | - Matthew P Reynolds
- International Maize and Wheat Improvement Center (CIMMYT), El Batán, Texcoco CP 56130, Mexico
| | - Elizabete Carmo-Silva
- Plant Biology and Crop Science Department, Rothamsted Research, Harpenden AL5 2JQ UK
| | - Martin A J Parry
- Plant Biology and Crop Science Department, Rothamsted Research, Harpenden AL5 2JQ UK
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41
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Gogniashvili M, Jinjikhadze T, Maisaia I, Akhalkatsi M, Kotorashvili A, Kotaria N, Beridze T, Dudnikov AJ. Complete chloroplast genomes of Aegilops tauschii Coss. and Ae. cylindrica Host sheds light on plasmon D evolution. Curr Genet 2016; 62:791-798. [PMID: 26923563 DOI: 10.1007/s00294-016-0583-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2015] [Revised: 02/11/2016] [Accepted: 02/13/2016] [Indexed: 10/22/2022]
Abstract
Hexaploid wheat (Triticum aestivum L., genomes AABBDD) originated in South Caucasus by allopolyploidization of the cultivated Emmer wheat T. dicoccum (genomes AABB) with the Caucasian Ae. tauschii ssp strangulata (genomes DD). Genetic variation of Ae. tauschii is an important natural resource, that is why it is of particular importance to investigate how this variation was formed during Ae. tauschii evolutionary history and how it is presented through the species area. The D genome is also found in tetraploid Ae. cylindrica Host (2n = 28, CCDD). The plasmon diversity that exists in Triticum and Aegilops species is of great significance for understanding the evolution of these genera. In the present investigation the complete nucleotide sequence of plasmon D (chloroplast DNA) of nine accessions of Ae. tauschii and two accessions of Ae. cylindrica are presented. Twenty-eight SNPs are characteristic for both TauL1 and TauL2 accessions of Ae. tauschii using TauL3 as a reference. Four SNPs are additionally observed for TauL2 lineage. The longest (27 bp) indel is located in the intergenic spacer Rps15-ndhF of SSC. This indel can be used for simple determination of TauL3 lineage among Ae. tauschii accessions. In the case of Ae. cylindrica additionally 7 SNPs were observed. The phylogeny tree shows that chloroplast DNA of TauL1 and TauL2 diverged from the TauL3 lineage. TauL1 lineage is relatively older then TauL2. The position of Ae. cylindrica accessions on Ae. tauschii phylogeny tree constructed on chloroplast DNA variation data is intermediate between TauL1 and TauL2. The complete nucleotide sequence of chloroplast DNA of Ae. tauschii and Ae. cylindrica allows to refine the origin and evolution of D plasmon of genus Aegilops.
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Affiliation(s)
- Mari Gogniashvili
- Institute of Molecular Genetics, Agricultural University of Georgia, #240 D. Agmashenebeli Alley, 0159, Tbilisi, Georgia.
| | | | - Inesa Maisaia
- Institute of Botany, Ilia State University, Tbilisi, Georgia
| | - Maia Akhalkatsi
- Institute of Botany, Ilia State University, Tbilisi, Georgia
| | - Adam Kotorashvili
- National Centre for Disease Control and Public Health, Tbilisi, Georgia
| | - Nato Kotaria
- National Centre for Disease Control and Public Health, Tbilisi, Georgia
| | - Tengiz Beridze
- Institute of Molecular Genetics, Agricultural University of Georgia, #240 D. Agmashenebeli Alley, 0159, Tbilisi, Georgia
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Kwiatek M, Majka M, Ślusarkiewicz-Jarzina A, Ponitka A, Pudelska H, Belter J, Wiśniewska H. Transmission of the Aegilops ovata chromosomes carrying gametocidal factors in hexaploid triticale (×Triticosecale Wittm.) hybrids. J Appl Genet 2016; 57:305-15. [PMID: 26825077 PMCID: PMC4963450 DOI: 10.1007/s13353-015-0332-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Revised: 12/08/2015] [Accepted: 12/10/2015] [Indexed: 12/28/2022]
Abstract
The main aim of this work was to induce the chromosome rearrangements between Aegilops ovata (UUMM) and hexaploid triticale (AABBRR) by expression of the gametocidal factor located on the chromosome 4M. The Aegilops ovata × Secale cereale (UUMMRR) amphiploids and triticale ‘Moreno’ were used to produce hybrids by reciprocal crosses. Chromosome dynamics was observed in subsequent generations of hybrids during mitotic metaphase of root meristems and first metaphase of meiosis of pollen mother cells. Chromosomes were identified by genomic in situ hybridisation (GISH) and fluorescence in situ hybridisation (FISH) using pTa71, pTa791, pSc119.2 and pAs1 DNA probes. It has been shown that the origin of the genetic background had an influence on Aegilops chromosome transmission. Moreover, it has been reported that the preferential transmission of chromosome 4M appeared during both androgenesis and gynogenesis. It is also hypothesised that the expression of the triticale Gc gene suppressor had an influence on the semi-fertility of hybrids but did not inhibit the chromosome rearrangements. This paper also describes the double haploid production, which enabled to obtain plants with two identical copies of triticale chromosomes with translocations of Aegilops chromatin segments.
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Affiliation(s)
- M Kwiatek
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland.
| | - M Majka
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland
| | - A Ślusarkiewicz-Jarzina
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland
| | - A Ponitka
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland
| | - H Pudelska
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland
| | - J Belter
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland
| | - H Wiśniewska
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland
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43
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Senerchia N, Felber F, Parisod C. Genome reorganization in F1 hybrids uncovers the role of retrotransposons in reproductive isolation. Proc Biol Sci 2015; 282:20142874. [PMID: 25716787 DOI: 10.1098/rspb.2014.2874] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Interspecific hybridization leads to new interactions among divergent genomes, revealing the nature of genetic incompatibilities having accumulated during and after the origin of species. Conflicts associated with misregulation of transposable elements (TEs) in hybrids expectedly result in their activation and genome-wide changes that may be key to species boundaries. Repetitive genomes of wild wheats have diverged under differential dynamics of specific long terminal repeat retrotransposons (LTR-RTs), offering unparalleled opportunities to address the underpinnings of plant genome reorganization by selfish sequences. Using reciprocal F1 hybrids between three Aegilops species, restructuring and epigenetic repatterning was assessed at random and LTR-RT sequences with amplified fragment length polymorphism and sequence-specific amplified polymorphisms as well as their methylation-sensitive counterparts, respectively. Asymmetrical reorganization of LTR-RT families predicted to cause conflicting interactions matched differential survival of F1 hybrids. Consistent with the genome shock model, increasing divergence of merged LTR-RTs yielded higher levels of changes in corresponding genome fractions and lead to repeated reorganization of LTR-RT sequences in F1 hybrids. Such non-random reorganization of hybrid genomes is coherent with the necessary repression of incompatible TE loci in support of hybrid viability and indicates that TE-driven genomic conflicts may represent an overlooked factor supporting reproductive isolation.
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Affiliation(s)
- Natacha Senerchia
- Laboratory of Evolutionary Botany, Institute of Biology, University of Neuchâtel, Rue Emile Argand 11, Neuchâtel 2000, Switzerland
| | - François Felber
- Laboratory of Evolutionary Botany, Institute of Biology, University of Neuchâtel, Rue Emile Argand 11, Neuchâtel 2000, Switzerland Musée et Jardins Botaniques Cantonaux, Lausanne 1007, Switzerland
| | - Christian Parisod
- Laboratory of Evolutionary Botany, Institute of Biology, University of Neuchâtel, Rue Emile Argand 11, Neuchâtel 2000, Switzerland
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44
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Li LF, Liu B, Olsen KM, Wendel JF. Multiple rounds of ancient and recent hybridizations have occurred within the Aegilops-Triticum complex. New Phytol 2015; 208:11-2. [PMID: 26147650 DOI: 10.1111/nph.13563] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Affiliation(s)
- Lin-Feng Li
- Key Laboratory of Molecular Epigenetics of Ministry of Education, Northeast Normal University, #5268 Renmin Str., Changchun, 130024, China
- Department of Biology, Washington University in St Louis, St Louis, MO, 63130, USA
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of Ministry of Education, Northeast Normal University, #5268 Renmin Str., Changchun, 130024, China
| | - Kenneth M Olsen
- Department of Biology, Washington University in St Louis, St Louis, MO, 63130, USA
| | - Jonathan F Wendel
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA, 50011, USA
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Li LF, Liu B, Olsen KM, Wendel JF. A re-evaluation of the homoploid hybrid origin of Aegilops tauschii, the donor of the wheat D-subgenome. New Phytol 2015; 208:4-8. [PMID: 25612061 DOI: 10.1111/nph.13294] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Affiliation(s)
- Lin-Feng Li
- Key Laboratory of Molecular Epigenetics of Ministry of Education, Northeast Normal University, No. 5268 Renmin Str., Changchun, 130024, China
- Department of Biology, Washington University in St Louis, St Louis, MO, 63130, USA
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of Ministry of Education, Northeast Normal University, No. 5268 Renmin Str., Changchun, 130024, China
| | - Kenneth M Olsen
- Department of Biology, Washington University in St Louis, St Louis, MO, 63130, USA
| | - Jonathan F Wendel
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA, 50011, USA
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46
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Hairat S, Khurana P. Evaluation of Aegilops tauschii and Aegilops speltoides for acquired thermotolerance: Implications in wheat breeding programmes. Plant Physiol Biochem 2015; 95:65-74. [PMID: 26188500 DOI: 10.1016/j.plaphy.2015.07.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Revised: 06/30/2015] [Accepted: 07/06/2015] [Indexed: 06/04/2023]
Abstract
Severe and frequent heat waves are predicted in the near future having dramatic and far-reaching ecological and social impact. The aim of this study was to examine acquired thermotolerance of two Aegilops species: Aegilops tauschii and Aegilops speltoides and study their potential adaptive mechanisms. The effect of two episodes of high heat stress (45 °C/12 h) with a day of recovery period was investigated on their physiology. As compared to A. speltoides, A. tauschii suffered less inhibition of photosystem II efficiency and net photosynthetic rate (Pn). Although A. tauschii showed nearly complete recovery of PSII, the adverse effect was more pronounced in A. speltoides. Measurement of the minimum fluorescence (Fo) versus temperature curves revealed a higher inflection temperature of Fo for A. tauschii than A. speltoides, reflecting greater thermo stability of the photosynthetic apparatus. Absorbed light energy distribution revealed that A. speltoides showed increased steady state fluorescence and a lower absorbed light allocated to photosynthetic chemistry (ɸPSII) relative to A. tauschii. However, A. tauschii showed higher ability to scavenge free radicals as compared to A. speltoides. This was further validated by higher expression of ascorbate peroxidase gene. These results suggest that A. tauschii showed faster recovery and a better thermostability of its photosynthetic apparatus under severe stress conditions along with a better regulation of energy channeling of PSII complexes to minimize oxidative damage and thus retains greater capability of carbon assimilation. These factors aid in imparting a greater heat tolerance to A. tauschii as compared to A. speltoides and thus make it a better candidate for alien species introgression in wheat breeding programs for thermotolerance in wheat.
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Affiliation(s)
- Suboot Hairat
- Department of Plant Molecular Biology, University of Delhi, South Campus, Benito Juarez Road, Dhaula Kuan, New Delhi 110 021, India
| | - Paramjit Khurana
- Department of Plant Molecular Biology, University of Delhi, South Campus, Benito Juarez Road, Dhaula Kuan, New Delhi 110 021, India.
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47
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Nemeth C, Yang CY, Kasprzak P, Hubbart S, Scholefield D, Mehra S, Skipper E, King I, King J. Generation of amphidiploids from hybrids of wheat and related species from the genera Aegilops, Secale, Thinopyrum, and Triticum as a source of genetic variation for wheat improvement. Genome 2015; 58:71-9. [PMID: 26053312 DOI: 10.1139/gen-2015-0002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
We aim to improve diversity of domesticated wheat by transferring genetic variation for important target traits from related wild and cultivated grass species. The present study describes the development of F1 hybrids between wheat and related species from the genera Aegilops, Secale, Thinopyrum, and Triticum and production of new amphidiploids. Amphidiploid lines were produced from 20 different distant relatives. Both colchicine and caffeine were successfully used to double the chromosome numbers. The genomic constitution of the newly formed amphidiploids derived from seven distant relatives was determined using genomic in situ hybridization (GISH). Altogether, 42 different plants were analysed, 19 using multicolour GISH separating the chromosomes from the A, B, and D genomes of wheat, as well as the distant relative, and 23 using single colour GISH. Restructuring of the allopolyploid genome, both chromosome losses and aneuploidy, was detected in all the genomes contained by the amphidiploids. From the observed chromosome numbers there is an indication that in amphidiploids the B genome of wheat suffers chromosome losses less frequently than the other wheat genomes. Phenotyping to realize the full potential of the wheat-related grass germplasm is underway, linking the analyzed genotypes to agronomically important target traits.
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Affiliation(s)
- Csilla Nemeth
- a Plant and Crop Sciences Division, School of Biosciences, The University of Nottingham, Sutton Bonington Campus, LE12 5RD, UK
| | - Cai-yun Yang
- a Plant and Crop Sciences Division, School of Biosciences, The University of Nottingham, Sutton Bonington Campus, LE12 5RD, UK
| | - Paul Kasprzak
- a Plant and Crop Sciences Division, School of Biosciences, The University of Nottingham, Sutton Bonington Campus, LE12 5RD, UK
| | - Stella Hubbart
- a Plant and Crop Sciences Division, School of Biosciences, The University of Nottingham, Sutton Bonington Campus, LE12 5RD, UK
| | - Duncan Scholefield
- a Plant and Crop Sciences Division, School of Biosciences, The University of Nottingham, Sutton Bonington Campus, LE12 5RD, UK
| | - Surbhi Mehra
- a Plant and Crop Sciences Division, School of Biosciences, The University of Nottingham, Sutton Bonington Campus, LE12 5RD, UK
| | - Emma Skipper
- b East Malling Research, New Road, East Malling, Kent, ME19 6BJ, UK
| | - Ian King
- a Plant and Crop Sciences Division, School of Biosciences, The University of Nottingham, Sutton Bonington Campus, LE12 5RD, UK
| | - Julie King
- a Plant and Crop Sciences Division, School of Biosciences, The University of Nottingham, Sutton Bonington Campus, LE12 5RD, UK
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48
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Demir P, Onde S, Severcan F. Phylogeny of cultivated and wild wheat species using ATR-FTIR spectroscopy. Spectrochim Acta A Mol Biomol Spectrosc 2015; 135:757-763. [PMID: 25145919 DOI: 10.1016/j.saa.2014.07.025] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Revised: 07/02/2014] [Accepted: 07/15/2014] [Indexed: 06/03/2023]
Abstract
Within the last decade, an increasing amount of genetic data has been used to clarify the problems inherent in wheat taxonomy. The techniques for obtaining and analyzing these data are not only cumbersome, but also expensive and technically demanding. In the present study, we introduce infrared spectroscopy as a method for a sensitive, rapid and low cost phylogenetic analysis tool for wheat seed samples. For this purpose, 12 Triticum and Aegilops species were studied by Attenuated Total Reflection-Fourier Transform Infrared (ATR-FTIR) spectroscopy. Hierarchical cluster analysis and principal component analysis clearly revealed that the lignin band (1525-1505 cm(-1)) discriminated the species at the genus level. However, the species were clustered according to their genome commonalities when the whole spectra were used (4000-650 cm(-1)). The successful differentiation of Triticum and its closely related genus Aegilops clearly demonstrated the power of ATR-FTIR spectroscopy as a suitable tool for phylogenetic research.
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Affiliation(s)
- Pinar Demir
- Department of Biology, Middle East Technical University, 06800 Ankara, Turkey
| | - Sertac Onde
- Department of Biology, Middle East Technical University, 06800 Ankara, Turkey.
| | - Feride Severcan
- Department of Biology, Middle East Technical University, 06800 Ankara, Turkey
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49
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Gornicki P, Zhu H, Wang J, Challa GS, Zhang Z, Gill BS, Li W. The chloroplast view of the evolution of polyploid wheat. New Phytol 2014; 204:704-714. [PMID: 25059383 DOI: 10.1111/nph.12931] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Accepted: 06/07/2014] [Indexed: 05/20/2023]
Abstract
Polyploid wheats comprise four species: Triticum turgidum (AABB genomes) and T. aestivum (AABBDD) in the Emmer lineage, and T. timopheevii (AAGG) and T. zhukovskyi (AAGGA(m) A(m) ) in the Timopheevi lineage. Genetic relationships between chloroplast genomes were studied to trace the evolutionary history of the species. Twenty-five chloroplast genomes were sequenced, and 1127 plant accessions were genotyped, representing 13 Triticum and Aegilops species. The A. speltoides (SS genome) diverged before the divergence of T. urartu (AA), A. tauschii (DD) and the Aegilops species of the Sitopsis section. Aegilops speltoides forms a monophyletic clade with the polyploid Emmer and Timopheevi wheats, which originated within the last 0.7 and 0.4 Myr, respectively. The geographic distribution of chloroplast haplotypes of the wild tetraploid wheats and A. speltoides illustrates the possible geographic origin of the Emmer lineage in the southern Levant and the Timopheevi lineage in northern Iraq. Aegilops speltoides is the closest relative of the diploid donor of the chloroplast (cytoplasm), as well as the B and G genomes to Timopheevi and Emmer lineages. Chloroplast haplotypes were often shared by species or subspecies within major lineages and between the lineages, indicating the contribution of introgression to the evolution and domestication of polyploid wheats.
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Affiliation(s)
- Piotr Gornicki
- Department of Molecular Genetics and Cell Biology, University of Chicago, 920 E 58th St, Chicago, IL, 60637, USA
| | - Huilan Zhu
- Department of Biology and Microbiology, South Dakota State University, 252 North Plain Biostress, Brookings, SD, 57007, USA
| | - Junwei Wang
- Department of Biology and Microbiology, South Dakota State University, 252 North Plain Biostress, Brookings, SD, 57007, USA
| | - Ghana S Challa
- Department of Biology and Microbiology, South Dakota State University, 252 North Plain Biostress, Brookings, SD, 57007, USA
| | - Zhengzhi Zhang
- Department of Biology and Microbiology, South Dakota State University, 252 North Plain Biostress, Brookings, SD, 57007, USA
| | - Bikram S Gill
- Wheat Genetics Resource Center, Department of Plant Pathology, Kansas State University, 4024 Throckmorton Hall, Manhattan, KS, 66506, USA
- Biotechnology Section, Faculty of Sciences, King Abdulaziz University, Jeddeh, Saudi Arabia
| | - Wanlong Li
- Department of Biology and Microbiology, South Dakota State University, 252 North Plain Biostress, Brookings, SD, 57007, USA
- Department of Plant Science, South Dakota State University, 247 North Plain Biostress, Brookings, SD, 57007, USA
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50
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Senerchia N, Felber F, Parisod C. Contrasting evolutionary trajectories of multiple retrotransposons following independent allopolyploidy in wild wheats. New Phytol 2014; 202:975-985. [PMID: 24548250 DOI: 10.1111/nph.12731] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Accepted: 01/09/2014] [Indexed: 06/03/2023]
Abstract
Transposable elements (TEs) are expectedly central to genome evolution. To assess the impact of TEs in driving genome turnover, we used allopolyploid genomes, showing considerable deviation from the predicted additivity of their diploid progenitors and thus having undergone major restructuring. Genome survey sequencing was used to select 17 putatively active families of long terminal repeat retrotransposons. Genome-wide TE insertions were genotyped with sequence-specific amplified polymorphism (SSAP) in diploid progenitors and their derived polyploids, and compared with changes in random sequences to assess restructuring of four independent Aegilops allotetraploid genomes. Generally, TEs with different evolutionary trajectories from those of random sequences were identified. Thus, TEs presented family-specific and species-specific dynamics following polyploidy, as illustrated by Sabine showing proliferation in particular polyploids, but massive elimination in others. Contrasting with that, only a few families (BARE1 and Romani) showed proliferation in all polyploids. Overall, TE divergence between progenitors was strongly correlated with the degree of restructuring in polyploid TE fractions. TE families present evolutionary trajectories that are decoupled from genome-wide changes after allopolyploidy and have a pervasive impact on their restructuring.
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Affiliation(s)
- Natacha Senerchia
- Laboratory of Evolutionary Botany, Institute of Biology, University of Neuchâtel, Rue Emile-Argand 11, 2000, Neuchâtel, Switzerland
| | - François Felber
- Laboratory of Evolutionary Botany, Institute of Biology, University of Neuchâtel, Rue Emile-Argand 11, 2000, Neuchâtel, Switzerland
- Musée et Jardins botaniques cantonaux, Avenue de Cour 14bis, 1007, Lausanne, Switzerland
| | - Christian Parisod
- Laboratory of Evolutionary Botany, Institute of Biology, University of Neuchâtel, Rue Emile-Argand 11, 2000, Neuchâtel, Switzerland
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