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Zhang Z, Zhao J, Li J, Yao J, Wang B, Ma Y, Li N, Wang H, Wang T, Liu B, Gong L. Evolutionary trajectory of organelle-derived nuclear DNAs in the Triticum/Aegilops complex species. PLANT PHYSIOLOGY 2024; 194:918-935. [PMID: 37847157 PMCID: PMC10828211 DOI: 10.1093/plphys/kiad552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 08/18/2023] [Accepted: 09/23/2023] [Indexed: 10/18/2023]
Abstract
Organelle-derived nuclear DNAs, nuclear plastid DNAs (NUPTs), and nuclear mitochondrial DNAs (NUMTs) have been identified in plants. Most, if not all, genes residing in NUPTs/NUMTs (NUPGs/NUMGs) are known to be inactivated and pseudogenized. However, the role of epigenetic control in silencing NUPGs/NUMGs and the dynamic evolution of NUPTs/NUMTs with respect to organismal phylogeny remain barely explored. Based on the available nuclear and organellar genomic resources of wheat (genus Triticum) and goat grass (genus Aegilops) within Triticum/Aegilops complex species, we investigated the evolutionary fates of NUPTs/NUMTs in terms of their epigenetic silencing and their dynamic occurrence rates in the nuclear diploid genomes and allopolyploid subgenomes. NUPTs and NUMTs possessed similar genomic atlas, including (i) predominantly located in intergenic regions and preferential integration to gene regulation regions and (ii) generating sequence variations in the nuclear genome. Unlike nuclear indigenous genes, the alien NUPGs/NUMGs were associated with repressive epigenetic signals, namely high levels of DNA methylation and low levels of active histone modifications. Phylogenomic analyses suggested that the species-specific and gradual accumulation of NUPTs/NUMTs accompanied the speciation processes. Moreover, based on further pan-genomic analyses, we found significant subgenomic asymmetry in the NUPT/NUMT occurrence, which accumulated during allopolyploid wheat evolution. Our findings provide insight into the dynamic evolutionary fates of organelle-derived nuclear DNA in plants.
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Affiliation(s)
- Zhibin Zhang
- 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
| | - Juzuo Li
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Jinyang Yao
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Bin Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Yiqiao Ma
- Jilin Academy of Vegetable and Flower Science, Changchun 130033, China
| | - Ning Li
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Hongyan Wang
- Laboratory of Plant Epigenetics and Evolution, School of Life Science, Liaoning University, Shenyang 110036, China
| | - Tianya Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Lei Gong
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
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Banouh M, Armisen D, Bouguennec A, Huneau C, Sow MD, Pont C, Salse J, Civáň P. Low impact of polyploidization on the transcriptome of synthetic allohexaploid wheat. BMC Genomics 2023; 24:255. [PMID: 37170217 PMCID: PMC10173476 DOI: 10.1186/s12864-023-09324-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 04/20/2023] [Indexed: 05/13/2023] Open
Abstract
BACKGROUND Bread wheat is a recent allohexaploid (genomic constitution AABBDD) that emerged through a hybridization between tetraploid Triticum turgidum (AABB) and diploid Aegilops tauschii (DD) less than 10,000 years ago. The hexaploidization can be re-created artificially, producing synthetic wheat that has been used to study immediate genomic responses to polyploidization. The scale of the consequences of polyploidization, and their mechanism of establishment, remain uncertain. RESULTS Here we sampled several synthetic wheats from alternative parental genotypes and reciprocal crosses, and examined transcriptomes from two different tissues and successive generations. We did not detect any massive reprogramming in gene expression, with only around 1% of expressed genes showing significant differences compared to their lower-ploidy parents. Most of this differential expression is located on the D subgenome, without consistency in the direction of the expression change. Homoeolog expression bias in synthetic wheat is similar to the pattern observed in the parents. Both differential expression and homoeolog bias are tissue-specific. While up to three families of transposable elements became upregulated in wheat synthetics, their position and distance are not significantly associated with expression changes in proximal genes. DISCUSSION While only a few genes change their expression pattern after polyploidization, they can be involved in agronomically important pathways. Alternative parental combinations can lead to opposite changes on the same subset of D-located genes, which is relevant for harnessing new diversity in wheat breeding. Tissue specificity of the polyploidization-triggered expression changes indicates the remodelling of transcriptomes in synthetic wheat is plastic and likely caused by regulome interactions rather than permanent changes. We discuss the pitfalls of transcriptomic comparisons across ploidy levels that can inflate the de-regulation signal. CONCLUSIONS Transcriptomic response to polyploidization in synthetic AABBDD wheat is modest and much lower than some previous estimates. Homoeolog expression bias in wheat allohexaploids is mostly attributed to parental legacy, with polyploidy having a mild balancing effect.
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Grants
- PolyBléD Fonds de Soutien à l'Obtention Végétale
- SeedEX, SeedENCODE, MethylWheat Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement
- SeedEX, SeedENCODE, MethylWheat Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement
- SeedEX, SeedENCODE, MethylWheat Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement
- SeedEX, SeedENCODE, MethylWheat Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement
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Affiliation(s)
- Meriem Banouh
- INRAE/UCA UMR 1095, 5 Chemin de Beaulieu, Clermont Ferrand, 63100, France
| | - David Armisen
- Institut de Génomique Fonctionnelle de Lyon, CNRS UMR 5242, 46 allée d'Italie, Lyon, 69364, France
| | - Annaig Bouguennec
- INRAE/UCA UMR 1095, 5 Chemin de Beaulieu, Clermont Ferrand, 63100, France
| | - Cécile Huneau
- INRAE/UCA UMR 1095, 5 Chemin de Beaulieu, Clermont Ferrand, 63100, France
| | - Mamadou Dia Sow
- INRAE/UCA UMR 1095, 5 Chemin de Beaulieu, Clermont Ferrand, 63100, France
| | - Caroline Pont
- INRAE/UCA UMR 1095, 5 Chemin de Beaulieu, Clermont Ferrand, 63100, France
| | - Jérôme Salse
- INRAE/UCA UMR 1095, 5 Chemin de Beaulieu, Clermont Ferrand, 63100, France
| | - Peter Civáň
- INRAE/UCA UMR 1095, 5 Chemin de Beaulieu, Clermont Ferrand, 63100, France.
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Dong C, Wang S, Zhang H, Liu J, Li M. Karyotype evolution of the Asterids insights from the first genome sequences of the family Cornaceae. DNA Res 2022; 30:6912218. [PMID: 36521020 PMCID: PMC9835862 DOI: 10.1093/dnares/dsac051] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 11/25/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022] Open
Abstract
Cornaceae is a core representative family in Cornales, the earliest branching lineage in the Asterids on the life tree of angiosperms. This family includes the only genus Cornus, a group of ~55 species. These species occur widely in Northern Hemisphere and have been used as resources for horticultural ornaments, medicinal and industrial manufacturing. However, no any genome sequences are available for this family. Here, we reported a chromosome-level genome for Cornus controversa. This was generated using high-fidelity plus Hi-C sequencing, and totally ~771.80 Mb assembled sequences and 39,886 protein-coding genes were obtained. We provided evidence for a whole-genome duplication event (WGD) unique to C. controversa. The evolutionary features of this genome indicated that the expanded and unique genes might have contributed to response to stress, stimulus and defense. By using chromosome-level syntenic blocks shared between eight living genomes, we found high degrees of genomic diversification from the ancestral core-eudicot genome to the present-day genomes, suggesting an important role of WGD in genomic plasticity that leads to speciation and diversification. These results provide foundational insights on the evolutionary history of Cornaceae, as well as on the Asterids diversification.
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Affiliation(s)
| | | | - Han Zhang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Jianquan Liu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China,Key Laboratory of BioResource and EcoEnvironment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Minjie Li
- To whom correspondence should be addressed. (M.L.)
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Shahid S, Ali Q, Ali S, Al-Misned FA, Maqbool S. Water Deficit Stress Tolerance Potential of Newly Developed Wheat Genotypes for Better Yield Based on Agronomic Traits and Stress Tolerance Indices: Physio-Biochemical Responses, Lipid Peroxidation and Antioxidative Defense Mechanism. PLANTS 2022; 11:plants11030466. [PMID: 35161446 PMCID: PMC8839292 DOI: 10.3390/plants11030466] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Revised: 12/31/2021] [Accepted: 01/13/2022] [Indexed: 12/03/2022]
Abstract
Changing environmental conditions, fresh water shortages for irrigation and the rapid increase in world population have created the problems of food insecurity and malnutrition. Different strategies, including the development of water stress-tolerant, high-yielding genotypes through breeding are used to fulfil the world food demand. The present study was conducted for the selection of high-yielding, drought-tolerant wheat genotypes, considering different morpho-physio-biochemical, agronomic and yield attributes in relation to the stress tolerance indices (STI). The experiment was carried out in field in a split-plot arrangement. Water deficit stress was maintained based on the number of irrigations. All genotypes showed a differential decreasing trend in different agronomic traits. However, the increasing or decreasing trend in leaf photosynthetic pigments, non-enzymatic and enzymatic antioxidants under limited water supply also found to be genotype-specific. Genotypes MP1, MP3, MP5, MP8 and MP10 performed better regarding the yield performance under water deficit stress, which was associated with their better maintenance of water relations, photosynthetic pigments and antioxidative defense mechanisms. In conclusion, the physio-biochemical mechanisms should also be considered as the part of breeding programs for the selection of stress-tolerant genotypes, along with agronomic traits, in wheat.
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Affiliation(s)
- Sumreena Shahid
- Department of Botany, Government College University, Faisalabad 38000, Pakistan;
| | - Qasim Ali
- Department of Botany, Government College University, Faisalabad 38000, Pakistan;
- Correspondence: (Q.A.); (S.A.)
| | - Shafaqat Ali
- Department of Environmental Sciences and Engineering, Government College University, Allama Iqbal Road, Faisalabad 38000, Pakistan
- Department of Biological Sciences and Technology, China Medical University, Taichung 40402, Taiwan
- Correspondence: (Q.A.); (S.A.)
| | - Fahad A. Al-Misned
- Department of Zoology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia;
| | - Saliha Maqbool
- Department of Soil, Water, and Climate, University of Minnesota, Saint Paul, MN 55108, USA;
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5
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Conover JL, Wendel JF. Deleterious Mutations Accumulate Faster in Allopolyploid than Diploid Cotton (Gossypium) and Unequally between Subgenomes. Mol Biol Evol 2022; 39:6517786. [PMID: 35099532 PMCID: PMC8841602 DOI: 10.1093/molbev/msac024] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Whole genome duplication (polyploidization) is among the most dramatic mutational processes in nature, so understanding how natural selection differs in polyploids relative to diploids is an important goal. Population genetics theory predicts that recessive deleterious mutations accumulate faster in allopolyploids than diploids due to the masking effect of redundant gene copies, but this prediction is hitherto unconfirmed. Here, we use the cotton genus (Gossypium), which contains seven allopolyploids derived from a single polyploidization event 1-2 million years ago, to investigate deleterious mutation accumulation. We use two methods of identifying deleterious mutations at the nucleotide and amino acid level, along with whole-genome resequencing of 43 individuals spanning six allopolyploid species and their two diploid progenitors, to demonstrate that deleterious mutations accumulate faster in allopolyploids than in their diploid progenitors. We find that, unlike what would be expected under models of demographic changes alone, strongly deleterious mutations show the biggest difference between ploidy levels, and this effect diminishes for moderately and mildly deleterious mutations. We further show that the proportion of nonsynonymous mutations that are deleterious differs between the two co-resident subgenomes in the allopolyploids, suggesting that homoeologous masking acts unequally between subgenomes. Our results provide a genome-wide perspective on classic notions of the significance of gene duplication that likely are broadly applicable to allopolyploids, with implications for our understanding of the evolutionary fate of deleterious mutations. Finally, we note that some measures of selection (e.g. dN/dS, πN/πS) may be biased when species of different ploidy levels are compared.
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Affiliation(s)
- Justin L Conover
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, 50011, USA
| | - Jonathan F Wendel
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, 50011, USA
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Muslu T, Akpinar BA, Biyiklioglu-Kaya S, Yuce M, Budak H. Comparative Analysis of Coding and Non-Coding Features within Insect Tolerance Loci in Wheat with Their Homologs in Cereal Genomes. Int J Mol Sci 2021; 22:ijms222212349. [PMID: 34830231 PMCID: PMC8623949 DOI: 10.3390/ijms222212349] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 11/08/2021] [Accepted: 11/10/2021] [Indexed: 12/14/2022] Open
Abstract
Food insecurity and malnutrition have reached critical levels with increased human population, climate fluctuations, water shortage; therefore, higher-yielding crops are in the spotlight of numerous studies. Abiotic factors affect the yield of staple food crops; among all, wheat stem sawfly (Cephus cinctus Norton) and orange wheat blossom midge (Sitodiplosis mosellana) are two of the most economically and agronomically harmful insect pests which cause yield loss in cereals, especially in wheat in North America. There is no effective strategy for suppressing this pest damage yet, and only the plants with intrinsic tolerance mechanisms such as solid stem phenotypes for WSS and antixenosis and/or antibiosis mechanisms for OWBM can limit damage. A major QTL and a causal gene for WSS resistance were previously identified in wheat, and 3 major QTLs and a causal gene for OWBM resistance. Here, we present a comparative analysis of coding and non-coding features of these loci of wheat across important cereal crops, barley, rye, oat, and rice. This research paves the way for our cloning and editing of additional WSS and OWBM tolerance gene(s), proteins, and metabolites.
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Affiliation(s)
- Tugdem Muslu
- Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul 34956, Turkey; (T.M.); (S.B.-K.)
| | | | - Sezgi Biyiklioglu-Kaya
- Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul 34956, Turkey; (T.M.); (S.B.-K.)
| | - Meral Yuce
- Sabanci University Nanotechnology Research and Application Centre (SUNUM), Istanbul 34956, Turkey;
| | - Hikmet Budak
- Montana BioAgriculture, Inc., Missoula, MT 59802, USA;
- Correspondence:
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Karyotype Reorganization in Wheat-Rye Hybrids Obtained via Unreduced Gametes: Is There a Limit to the Chromosome Number in Triticale? PLANTS 2021; 10:plants10102052. [PMID: 34685861 PMCID: PMC8538156 DOI: 10.3390/plants10102052] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 09/20/2021] [Accepted: 09/23/2021] [Indexed: 11/25/2022]
Abstract
To date, few data have been accumulated on the contribution of meiotic restitution to the formation of Triticum aestivum hybrid karyotypes. In this study, based on FISH and C-banding, karyotype reorganization was observed in three groups of F5 wheat–rye hybrids 1R(1A) × R. Aberrations, including aneuploidy, telocentrics, and Robertsonian translocations, were detected in all groups. Some of the Group 1 plants and all of the Group 2 plants only had a 4R4R pair (in addition to 1R1R), which was either added or substituted for its homeolog in ABD subgenomes. In about 82% of meiocytes, 4R4R formed bivalents, which indicates its competitiveness. The rest of the Group 1 plants had 2R and 7R chromosomes in addition to 1R1R. Group 3 retained all their rye chromosomes, with a small aneuploidy on the wheat chromosomes. A feature of the meiosis in the Group 3 plants was asynchronous cell division and omission of the second division. Diploid gametes did not form because of the significant disturbances during gametogenesis. As a result, the frequency of occurrence of the formed dyads was negatively correlated (r = −0.73) with the seed sets. Thus, meiotic restitution in the 8n triticale does not contribute to fertility or increased ploidy in subsequent generations.
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Chalopin D, Clark LG, Wysocki WP, Park M, Duvall MR, Bennetzen JL. Integrated Genomic Analyses From Low-Depth Sequencing Help Resolve Phylogenetic Incongruence in the Bamboos (Poaceae: Bambusoideae). FRONTIERS IN PLANT SCIENCE 2021; 12:725728. [PMID: 34567039 PMCID: PMC8456298 DOI: 10.3389/fpls.2021.725728] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 08/13/2021] [Indexed: 06/13/2023]
Abstract
The bamboos (Bambusoideae, Poaceae) comprise a major grass lineage with a complex evolutionary history involving ancient hybridization and allopolyploidy. About 1700 described species are classified into three tribes, Olyreae (herbaceous bamboos), Bambuseae (tropical woody bamboos), and Arundinarieae (temperate woody bamboos). Nuclear analyses strongly support monophyly of the woody tribes, whereas plastome analyses strongly support paraphyly, with Bambuseae sister to Olyreae. Our objectives were to clarify the origin(s) of the woody bamboo tribes and resolve the nuclear vs. plastid conflict using genomic tools. For the first time, plastid and nuclear genomic information from the same bamboo species were combined in a single study. We sampled 51 species of bamboos representing the three tribes, estimated their genome sizes and generated low-depth sample sequence data, from which plastomes were assembled and nuclear repeats were analyzed. The distribution of repeat families was found to agree with nuclear gene phylogenies, but also provides novel insights into nuclear evolutionary history. We infer two early, independent hybridization events, one between an Olyreae ancestor and a woody ancestor giving rise to the two Bambuseae lineages, and another between two woody ancestors giving rise to the Arundinarieae. Retention of the Olyreae plastome associated with differential dominance of nuclear genomes and subsequent diploidization in some lineages explains the paraphyly observed in plastome phylogenetic estimations. We confirm ancient hybridization and allopolyploidy in the origins of the extant woody bamboo lineages and propose biased fractionation and diploidization as important factors in their evolution.
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Affiliation(s)
- Domitille Chalopin
- Department of Genetics, University of Georgia, Athens, GA, United States
| | - Lynn G. Clark
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, United States
| | - William P. Wysocki
- Center for Translational Data Science, University of Chicago, Chicago, IL, United States
| | - Minkyu Park
- Department of Genetics, University of Georgia, Athens, GA, United States
| | - Melvin R. Duvall
- Department of Biology and Institute for the Study of the Environment, Sustainability, and Energy, Northern Illinois University, DeKalb, IL, United States
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Xu J, Hu P, Tao Y, Song P, Gao H, Guan Y. Genome-wide identification and characterization of the Lateral Organ Boundaries Domain ( LBD) gene family in polyploid wheat and related species. PeerJ 2021; 9:e11811. [PMID: 34447619 PMCID: PMC8364319 DOI: 10.7717/peerj.11811] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Accepted: 06/27/2021] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Wheat (Triticum aestivum) originated from three different diploid ancestral grass species and experienced two rounds of polyploidization. Exploring how certain wheat gene subfamilies have expanded during the evolutionary process is of great importance. The Lateral Organ Boundaries Domain (LBD) gene family encodes plant-specific transcription factors that share a highly conserved LOB domain and are prime candidates for this, as they are involved in plant growth, development, secondary metabolism and stress in various species. METHODS Using a genome-wide analysis of high-quality polyploid wheat and related species genome sequences, a total of 228 LBD members from five Triticeae species were identified, and phylogenetic relationship analysis of LBD members classified them into two main classes (classes I and II) and seven subgroups (classes I a-e, II a and II b). RESULTS The gene structure and motif composition analyses revealed that genes that had a closer phylogenetic relationship in the same subgroup also had a similar gene structure. Macrocollinearity and microcollinearity analyses of Triticeae species suggested that some LBD genes from wheat produced gene pairs across subgenomes of chromosomes 4A and 5A and that the complex evolutionary history of TaLBD4B-9 homologs was a combined result of chromosome translocation, polyploidization, gene loss and duplication events. Public RNA-seq data were used to analyze the expression patterns of wheat LBD genes in various tissues, different developmental stages and following abiotic and biotic stresses. Furthermore, qRT-PCR results suggested that some TaLBDs in class II responded to powdery mildew, regulated reproductive growth and were involved in embryo sac development in common wheat.
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Affiliation(s)
- Jun Xu
- Henan Institute of Science and Technology, Xinxiang, China
| | - Ping Hu
- Henan Institute of Science and Technology, Xinxiang, China
- Henan Engineering Research Center of Crop/ Henan International Joint Laboratory of Plant Genetic Improvement and Soil Remediation Genome Editing, Xinxiang, China
| | - Ye Tao
- Henan Institute of Science and Technology, Xinxiang, China
- Henan Engineering Research Center of Crop/ Henan International Joint Laboratory of Plant Genetic Improvement and Soil Remediation Genome Editing, Xinxiang, China
| | - Puwen Song
- Henan Institute of Science and Technology, Xinxiang, China
- Henan Engineering Research Center of Crop/ Henan International Joint Laboratory of Plant Genetic Improvement and Soil Remediation Genome Editing, Xinxiang, China
| | - Huanting Gao
- Henan Institute of Science and Technology, Xinxiang, China
- Henan Engineering Research Center of Crop/ Henan International Joint Laboratory of Plant Genetic Improvement and Soil Remediation Genome Editing, Xinxiang, China
| | - Yuanyuan Guan
- Henan Institute of Science and Technology, Xinxiang, China
- Henan Engineering Research Center of Crop/ Henan International Joint Laboratory of Plant Genetic Improvement and Soil Remediation Genome Editing, Xinxiang, China
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Meziani S, Nadaud I, Tasleem-Tahir A, Nurit E, Benguella R, Branlard G. Wheat aleurone layer: A site enriched with nutrients and bioactive molecules with potential nutritional opportunities for breeding. J Cereal Sci 2021. [DOI: 10.1016/j.jcs.2021.103225] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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He G, Zhang Y, Liu P, Jing Y, Zhang L, Zhu Y, Kong X, Zhao H, Zhou Y, Sun J. The transcription factor TaLAX1 interacts with Q to antagonistically regulate grain threshability and spike morphogenesis in bread wheat. THE NEW PHYTOLOGIST 2021; 230:988-1002. [PMID: 33521967 DOI: 10.1111/nph.17235] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 01/19/2021] [Indexed: 06/12/2023]
Abstract
The domestication gene Q is largely responsible for the widespread cultivation of wheat because it confers multiple domestication traits. However, the underlying molecular mechanisms of how Q regulates these domestication traits remain unclear. In this study, we identify a Q-interacting protein TaLAX1, a basic helix-loop-helix transcription factor, through yeast two-hybrid assays. Using biochemical and genetic approaches, we explore the roles of TaLAX1 in regulating wheat domestication traits. Overexpression of TaLAX1 produces phenotypes, reminiscent of the q allele; loss-of-function Talax1 mutations confer compact spikes, largely similar to the Q-overexpression wheat lines. The two transcription factors TaLAX1 and Q disturb each other's activity to antagonistically regulate the expression of the lignin biosynthesis-related gene TaKNAT7-4D. More interestingly, a natural variation (InDel, +/- TATA), which occurs in the promoter of TaLAX1, is associated with the promoter activity difference between the D subgenome of bread wheat and its ancestor Aegilops tauschii accession T093. This study reveals that the transcription factor TaLAX1 physically interacts with Q to antagonistically regulate wheat domestication traits and a natural variation (InDel, +/- TATA) is associated with the diversification of TaLAX1 promoter activity.
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Affiliation(s)
- Guanhua He
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Yunwei Zhang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Pan Liu
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yexing Jing
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Lichao Zhang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yingfang Zhu
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475001, China
| | - Xiuying Kong
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Huixian Zhao
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
- State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Yun Zhou
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475001, China
| | - Jiaqiang Sun
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
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Juery C, Concia L, De Oliveira R, Papon N, Ramírez-González R, Benhamed M, Uauy C, Choulet F, Paux E. New insights into homoeologous copy number variations in the hexaploid wheat genome. THE PLANT GENOME 2021; 14:e20069. [PMID: 33155760 DOI: 10.1002/tpg2.20069] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 10/11/2020] [Indexed: 06/11/2023]
Abstract
Bread wheat is an allohexaploid species originating from two successive and recent rounds of hybridization between three diploid species that were very similar in terms of chromosome number, genome size, TE content, gene content and synteny. As a result, it has long been considered that most of the genes were in three pairs of homoeologous copies. However, these so-called triads represent only one half of wheat genes, while the remaining half belong to homoeologous groups with various number of copies across subgenomes. In this study, we examined and compared the distribution, conservation, function, expression and epigenetic profiles of triads with homoeologous groups having undergone a deletion (dyads) or a duplication (tetrads) in one subgenome. We show that dyads and tetrads are mostly located in distal regions and have lower expression level and breadth than triads. Moreover, they are enriched in functions related to adaptation and more associated with the repressive H3K27me3 modification. Altogether, these results suggest that triads mainly correspond to housekeeping genes and are part of the core genome, while dyads and tetrads belong to the Triticeae dispensable genome. In addition, by comparing the different categories of dyads and tetrads, we hypothesize that, unlike most of the allopolyploid species, subgenome dominance and biased fractionation are absent in hexaploid wheat. Differences observed between the three subgenomes are more likely related to two successive and ongoing waves of post-polyploid diploidization, that had impacted A and B more significantly than D, as a result of the evolutionary history of hexaploid wheat.
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Affiliation(s)
- Caroline Juery
- Université Clermont Auvergne, INRAE, GDEC, Clermont-Ferrand, 63000, France
| | - Lorenzo Concia
- Institute of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Orsay, 91405, France
- Current address: Institut de biologie de l'Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, Université PSL, Paris, 75005, France
| | - Romain De Oliveira
- Université Clermont Auvergne, INRAE, GDEC, Clermont-Ferrand, 63000, France
| | - Nathan Papon
- Université Clermont Auvergne, INRAE, GDEC, Clermont-Ferrand, 63000, France
| | | | - Moussa Benhamed
- Institute of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Orsay, 91405, France
| | - Cristobal Uauy
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Frédéric Choulet
- Université Clermont Auvergne, INRAE, GDEC, Clermont-Ferrand, 63000, France
| | - Etienne Paux
- Université Clermont Auvergne, INRAE, GDEC, Clermont-Ferrand, 63000, France
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13
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Ma QH, Han JQ. Identification of monocot chimeric jacalin family reveals functional diversity in wheat. PLANTA 2021; 253:30. [PMID: 33423087 DOI: 10.1007/s00425-020-03548-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 12/22/2020] [Indexed: 06/12/2023]
Abstract
MAIN CONCLUSION 46 monocot chimeric jacalins (MCJs) were mined from wheat genome. They were divided into three subfamilies with the activity of mannose-specific lectins and had effects on dehydration tolerance or disease resistance. Monocot chimeric jacalin (MCJ) is a newly identified subfamily of plant lectins that exclusively exists in Poaceae. The MCJs are modular proteins consisting of a dirigent domain and a jacalin-related lectin domain. Their unique evolution and various functions are not fully understood as only few members of MCJ have so for been investigated. From wheat, 46 MCJs were identified and phylogenetically classified into three subfamilies, in which subfamily I represented the early evolutionary cluster. MCJ genes are evenly distributed among three subgenomes of wheat, indicating that MCJ might be an ancient gene in Poaceae. qRT-PCR analysis showed that TaMCJ1 and TaMCJ2 were mainly expressed in leaves while TaMCJ3 in root tissues. All these TaMCJ genes are JA or ABA inducible. All three proteins exhibited agglutinating activity but different preference to mannose-binding. The overexpression of TaMCJ3 in tobacco increased dehydration tolerance, while TaMCJ1 enhanced wildfire disease resistance. The lignin biosynthetic genes were temporarily induced after pathogen inoculation in transgenic tobacco overexpressing TaMCJ, but the specific association with TaMCJ was not established. This evidence argued against the notion that the dirigent domain in TaMCJ is directly linked with lignin metabolism. Taken together, these results pave the way for a better understanding of the manifold functionality of MCJs and offer important insights to the evolutionary history of MCJ.
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Affiliation(s)
- Qing-Hu Ma
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Xiangshan, Beijing, 100093, China.
| | - Jia-Qi Han
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Xiangshan, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
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14
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Genome-Wide Analysis of LysM-Containing Gene Family in Wheat: Structural and Phylogenetic Analysis during Development and Defense. Genes (Basel) 2020; 12:genes12010031. [PMID: 33383636 PMCID: PMC7823900 DOI: 10.3390/genes12010031] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 12/19/2020] [Accepted: 12/23/2020] [Indexed: 11/17/2022] Open
Abstract
The lysin motif (LysM) family comprise a number of defense proteins that play important roles in plant immunity. The LysM family includes LysM-containing receptor-like proteins (LYP) and LysM-containing receptor-like kinase (LYK). LysM generally recognizes the chitin and peptidoglycan derived from bacteria and fungi. Approximately 4000 proteins with the lysin motif (Pfam PF01476) are found in prokaryotes and eukaryotes. Our study identified 57 LysM genes and 60 LysM proteins in wheat and renamed these genes and proteins based on chromosome distribution. According to the phylogenetic and gene structure of intron-exon distribution analysis, the 60 LysM proteins were classified into seven groups. Gene duplication events had occurred among the LysM family members during the evolution process, resulting in an increase in the LysM gene family. Synteny analysis suggested the characteristics of evolution of the LysM family in wheat and other species. Systematic analysis of these species provided a foundation of LysM genes in crop defense. A comprehensive analysis of the expression and cis-elements of LysM gene family members suggested that they play an essential role in defending against plant pathogens. The present study provides an overview of the LysM family in the wheat genome as well as information on systematic, phylogenetic, gene duplication, and intron-exon distribution analyses that will be helpful for future functional analysis of this important protein family, especially in Gramineae species.
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15
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Chen Y, Song W, Xie X, Wang Z, Guan P, Peng H, Jiao Y, Ni Z, Sun Q, Guo W. A Collinearity-Incorporating Homology Inference Strategy for Connecting Emerging Assemblies in the Triticeae Tribe as a Pilot Practice in the Plant Pangenomic Era. MOLECULAR PLANT 2020; 13:1694-1708. [PMID: 32979565 DOI: 10.1016/j.molp.2020.09.019] [Citation(s) in RCA: 111] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 09/03/2020] [Accepted: 09/21/2020] [Indexed: 05/18/2023]
Abstract
Plant genome sequencing has dramatically increased, and some species even have multiple high-quality reference versions. Demands for clade-specific homology inference and analysis have increased in the pangenomic era. Here we present a novel method, GeneTribe (https://chenym1.github.io/genetribe/), for homology inference among genetically similar genomes that incorporates gene collinearity and shows better performance than traditional sequence-similarity-based methods in terms of accuracy and scalability. The Triticeae tribe is a typical allopolyploid-rich clade with complex species relationships that includes many important crops, such as wheat, barley, and rye. We built Triticeae-GeneTribe (http://wheat.cau.edu.cn/TGT/), a homology database, by integrating 12 Triticeae genomes and 3 outgroup model genomes and implemented versatile analysis and visualization functions. With macrocollinearity analysis, we were able to construct a refined model illustrating the structural rearrangements of the 4A-5A-7B chromosomes in wheat as two major translocation events. With collinearity analysis at both the macro- and microscale, we illustrated the complex evolutionary history of homologs of the wheat vernalization gene Vrn2, which evolved as a combined result of genome translocation, duplication, and polyploidization and gene loss events. Our work provides a useful practice for connecting emerging genome assemblies, with awareness of the extensive polyploidy in plants, and will help researchers efficiently exploit genome sequence resources.
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Affiliation(s)
- Yongming Chen
- Key Laboratory of Crop Heterosis and Utilization, State Key Laboratory for Agrobiotechnology, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Wanjun Song
- Key Laboratory of Crop Heterosis and Utilization, State Key Laboratory for Agrobiotechnology, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China; Beijing Geek Gene Technology Co Ltd, Beijing 100193, China
| | - Xiaoming Xie
- Key Laboratory of Crop Heterosis and Utilization, State Key Laboratory for Agrobiotechnology, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Zihao Wang
- Key Laboratory of Crop Heterosis and Utilization, State Key Laboratory for Agrobiotechnology, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Panfeng Guan
- Key Laboratory of Crop Heterosis and Utilization, State Key Laboratory for Agrobiotechnology, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Huiru Peng
- Key Laboratory of Crop Heterosis and Utilization, State Key Laboratory for Agrobiotechnology, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Yuannian Jiao
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhongfu Ni
- Key Laboratory of Crop Heterosis and Utilization, State Key Laboratory for Agrobiotechnology, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Qixin Sun
- Key Laboratory of Crop Heterosis and Utilization, State Key Laboratory for Agrobiotechnology, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Weilong Guo
- Key Laboratory of Crop Heterosis and Utilization, State Key Laboratory for Agrobiotechnology, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China.
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16
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Babu P, Baranwal DK, Harikrishna, Pal D, Bharti H, Joshi P, Thiyagarajan B, Gaikwad KB, Bhardwaj SC, Singh GP, Singh A. Application of Genomics Tools in Wheat Breeding to Attain Durable Rust Resistance. FRONTIERS IN PLANT SCIENCE 2020; 11:567147. [PMID: 33013989 PMCID: PMC7516254 DOI: 10.3389/fpls.2020.567147] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 08/12/2020] [Indexed: 11/13/2023]
Abstract
Wheat is an important source of dietary protein and calories for the majority of the world's population. It is one of the largest grown cereal in the world occupying over 215 M ha. Wheat production globally is challenged by biotic stresses such as pests and diseases. Of the 50 diseases of wheat that are of economic importance, the three rust diseases are the most ubiquitous causing significant yield losses in the majority of wheat production environments. Under severe epidemics they can lead to food insecurity threats amid the continuous evolution of new races of the pathogens, shifts in population dynamics and their virulence patterns, thereby rendering several effective resistance genes deployed in wheat breeding programs vulnerable. This emphasizes the need to identify, characterize, and deploy effective rust-resistant genes from diverse sources into pre-breeding lines and future wheat varieties. The use of genetic resistance has been marked as eco-friendly and to curb the further evolution of rust pathogens. Deployment of multiple rust resistance genes including major and minor genes in wheat lines could enhance the durability of resistance thereby reducing pathogen evolution. Advances in next-generation sequencing (NGS) platforms and associated bioinformatics tools have revolutionized wheat genomics. The sequence alignment of the wheat genome is the most important landmark which will enable genomics to identify marker-trait associations, candidate genes and enhanced breeding values in genomic selection (GS) studies. High throughput genotyping platforms have demonstrated their role in the estimation of genetic diversity, construction of the high-density genetic maps, dissecting polygenic traits, and better understanding their interactions through GWAS (genome-wide association studies) and QTL mapping, and isolation of R genes. Application of breeder's friendly KASP assays in the wheat breeding program has expedited the identification and pyramiding of rust resistance alleles/genes in elite lines. The present review covers the evolutionary trends of the rust pathogen and contemporary wheat varieties, and how these research strategies galvanized to control the wheat killer genus Puccinia. It will also highlight the outcome and research impact of cost-effective NGS technologies and cloning of rust resistance genes amid the public availability of common and tetraploid wheat reference genomes.
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Affiliation(s)
- Prashanth Babu
- Indian Agricultural Research Institute (ICAR), New Delhi, India
| | | | - Harikrishna
- Indian Agricultural Research Institute (ICAR), New Delhi, India
| | - Dharam Pal
- Indian Agricultural Research Institute (ICAR), New Delhi, India
| | - Hemlata Bharti
- Directorate of Medicinal and Aromatic Plants Research (ICAR), Anand, India
| | - Priyanka Joshi
- Department of Plant Pathology, Washington State University, Pullman, WA, United States
| | | | | | | | | | - Anupam Singh
- DCM SHRIRAM-Bioseed Research India, ICRISAT, Hyderabad, India
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17
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Parisod C, Badaeva ED. Chromosome restructuring among hybridizing wild wheats. THE NEW PHYTOLOGIST 2020; 226:1263-1273. [PMID: 31913521 DOI: 10.1111/nph.16415] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 12/29/2019] [Indexed: 06/10/2023]
Abstract
The wheat group offers an outstanding system to address the interplay between hybridization, chromosomal evolution and biological diversification. Most diploid wild wheats originated following hybridization between the A-genome lineage and the B-genome lineage some 4 Myr ago, resulting in an admixed D-genome lineage that presented dramatic radiation accompanied by considerable changes in genome size and chromosomal rearrangements. Comparative profiling of low-copy genes, repeated sequences and transposable elements among those divergent species characterized by different karyotypes highlights high genome dynamics and sheds new light on the processes underlying chromosomal evolution in wild wheats. One of the hybrid clades presents upsizing of metacentric chromosomes going along with the proliferation of specific repeats (i.e. 'genomic obesity'), whereas other species show stable genome size associated with increasing chromosomal asymmetry. Genetic and ecological variation in those specialized species suggest that genome restructuring was coupled with adaptive processes to support the evolution of a majority of acrocentric chromosomes. This synthesis of current knowledge on genome restructuring across the diversity of wild wheats paves the way towards surveys based on latest sequencing technologies to characterize valuable resources and address the significance of chromosomal evolution in species with complex genomes.
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Affiliation(s)
- Christian Parisod
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, Bern, 3013, Switzerland
| | - Ekaterina D Badaeva
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Gubkin St. 3, Moscow, 119991, Russia
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18
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Concia L, Veluchamy A, Ramirez-Prado JS, Martin-Ramirez A, Huang Y, Perez M, Domenichini S, Rodriguez Granados NY, Kim S, Blein T, Duncan S, Pichot C, Manza-Mianza D, Juery C, Paux E, Moore G, Hirt H, Bergounioux C, Crespi M, Mahfouz MM, Bendahmane A, Liu C, Hall A, Raynaud C, Latrasse D, Benhamed M. Wheat chromatin architecture is organized in genome territories and transcription factories. Genome Biol 2020; 21:104. [PMID: 32349780 PMCID: PMC7189446 DOI: 10.1186/s13059-020-01998-1] [Citation(s) in RCA: 91] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 03/12/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Polyploidy is ubiquitous in eukaryotic plant and fungal lineages, and it leads to the co-existence of several copies of similar or related genomes in one nucleus. In plants, polyploidy is considered a major factor in successful domestication. However, polyploidy challenges chromosome folding architecture in the nucleus to establish functional structures. RESULTS We examine the hexaploid wheat nuclear architecture by integrating RNA-seq, ChIP-seq, ATAC-seq, Hi-C, and Hi-ChIP data. Our results highlight the presence of three levels of large-scale spatial organization: the arrangement into genome territories, the diametrical separation between facultative and constitutive heterochromatin, and the organization of RNA polymerase II around transcription factories. We demonstrate the micro-compartmentalization of transcriptionally active genes determined by physical interactions between genes with specific euchromatic histone modifications. Both intra- and interchromosomal RNA polymerase-associated contacts involve multiple genes displaying similar expression levels. CONCLUSIONS Our results provide new insights into the physical chromosome organization of a polyploid genome, as well as on the relationship between epigenetic marks and chromosome conformation to determine a 3D spatial organization of gene expression, a key factor governing gene transcription in polyploids.
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Affiliation(s)
- Lorenzo Concia
- Institute of Plant Sciences Paris of Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Orsay, France
| | - Alaguraj Veluchamy
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Juan S Ramirez-Prado
- Institute of Plant Sciences Paris of Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Orsay, France
| | | | - Ying Huang
- Institute of Plant Sciences Paris of Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Orsay, France
| | - Magali Perez
- Institute of Plant Sciences Paris of Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Orsay, France
| | - Severine Domenichini
- Institute of Plant Sciences Paris of Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Orsay, France
| | | | - Soonkap Kim
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Thomas Blein
- Institute of Plant Sciences Paris of Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Orsay, France
| | - Susan Duncan
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UG, UK
| | - Clement Pichot
- Institute of Plant Sciences Paris of Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Orsay, France
| | - Deborah Manza-Mianza
- Institute of Plant Sciences Paris of Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Orsay, France
| | - Caroline Juery
- INRA UMR1095 Genetics, Diversity and Ecophysiology of Cereals, 5 chemin de Beaulieu, 63039, Clermont-Ferrand, France
| | - Etienne Paux
- INRA UMR1095 Genetics, Diversity and Ecophysiology of Cereals, 5 chemin de Beaulieu, 63039, Clermont-Ferrand, France
| | - Graham Moore
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Heribert Hirt
- Institute of Plant Sciences Paris of Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Orsay, France
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Catherine Bergounioux
- Institute of Plant Sciences Paris of Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Orsay, France
| | - Martin Crespi
- Institute of Plant Sciences Paris of Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Orsay, France
| | - Magdy M Mahfouz
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Abdelhafid Bendahmane
- Institute of Plant Sciences Paris of Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Orsay, France
| | - Chang Liu
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Auf der Morgenstelle 32, 72076, Tübingen, Germany
| | - Anthony Hall
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UG, UK
| | - Cécile Raynaud
- Institute of Plant Sciences Paris of Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Orsay, France
| | - David Latrasse
- Institute of Plant Sciences Paris of Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Orsay, France
| | - Moussa Benhamed
- Institute of Plant Sciences Paris of Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Orsay, France.
- Institut Universitaire de France (IUF), Paris, France.
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19
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Dmochowska-Boguta M, Kloc Y, Zielezinski A, Werecki P, Nadolska-Orczyk A, Karlowski WM, Orczyk W. TaWAK6 encoding wall-associated kinase is involved in wheat resistance to leaf rust similar to adult plant resistance. PLoS One 2020; 15:e0227713. [PMID: 31929605 PMCID: PMC6957155 DOI: 10.1371/journal.pone.0227713] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 12/25/2019] [Indexed: 11/19/2022] Open
Abstract
In wheat, adult plant resistance (APR) to leaf rust (Puccinia triticina), is effective in restricting pathogen growth and provides durable resistance against a wide range of virulent forms of P. triticina. Despite the importance, there is limited knowledge on the molecular basis of this type of resistance. We isolated and characterized the wall-associated kinase encoding gene in wheat, and assigned it as TaWAK6. Localization of TaWAK6 homeologs in A and B wheat subgenomes was consistent with the presence of the gene's orthologs in T. urartu (AA) and T. dicoccoides (AABB) and with the absence of its orthologs in Aegilops tauschii (DD). Overexpression of TaWAK6 did not change the wheat phenotype, nor did it affect seedling resistance. However, the adult plants overexpressing TaWAK6 showed that important parameters of APR were significantly elevated. Infection types scored on the first (flag), second and third leaves indicated elevated resistance, which significantly correlated with expression of TaWAK6. Analysis of plant-pathogen interactions showed a lower number of uredinia and higher rates of necrosis at the infection sites and this was associated with smaller size of uredinia and a longer latent period. The results indicated a role of TaWAK6 in quantitative partial resistance similar to APR in wheat. It is proposed that TaWAK6, which is a non-arginine-aspartate (non-RD) kinase, represents a novel class of quantitative immune receptors in monocots.
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Affiliation(s)
- Marta Dmochowska-Boguta
- Department of Genetic Engineering, Plant Breeding and Acclimatization Institute-National Research Institute, Radzikow, Blonie, Poland
| | - Yuliya Kloc
- Department of Genetic Engineering, Plant Breeding and Acclimatization Institute-National Research Institute, Radzikow, Blonie, Poland
| | - Andrzej Zielezinski
- Department of Computational Biology, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland
| | - Przemysław Werecki
- Department of Genetic Engineering, Plant Breeding and Acclimatization Institute-National Research Institute, Radzikow, Blonie, Poland
| | - Anna Nadolska-Orczyk
- Department of Functional Genomics, Plant Breeding and Acclimatization Institute-National Research Institute, Radzikow, Blonie, Poland
| | - Wojciech M. Karlowski
- Department of Computational Biology, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland
| | - Wacław Orczyk
- Department of Genetic Engineering, Plant Breeding and Acclimatization Institute-National Research Institute, Radzikow, Blonie, Poland
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20
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Comparative linkage mapping of diploid, tetraploid, and hexaploid Avena species suggests extensive chromosome rearrangement in ancestral diploids. Sci Rep 2019; 9:12298. [PMID: 31444367 DOI: 10.1038/s41598-019-48639-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 07/10/2019] [Indexed: 12/30/2022] Open
Abstract
The genus Avena (oats) contains diploid, tetraploid and hexaploid species that evolved through hybridization and polyploidization. Four genome types (named A through D) are generally recognized. We used GBS markers to construct linkage maps of A genome diploid (Avena strigosa x A. wiestii, 2n = 14), and AB genome tetraploid (A. barbata 2n = 28) oats. These maps greatly improve coverage from older marker systems. Seven linkage groups in the tetraploid showed much stronger homology and synteny with the A genome diploids than did the other seven, implying an allopolyploid hybrid origin of A. barbata from distinct A and B genome diploid ancestors. Inferred homeologies within A. barbata revealed that the A and B genomes are differentiated by several translocations between chromosomes within each subgenome. However, no translocation exchanges were observed between A and B genomes. Comparison to a consensus map of ACD hexaploid A. sativa (2n = 42) revealed that the A and D genomes of A. sativa show parallel rearrangements when compared to the A genomes of the diploids and tetraploids. While intergenomic translocations are well known in polyploid Avena, our results are most parsimoniously explained if translocations also occurred in the A, B and D genome diploid ancestors of polyploid Avena.
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21
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Venske E, dos Santos RS, Busanello C, Gustafson P, Costa de Oliveira A. Bread wheat: a role model for plant domestication and breeding. Hereditas 2019; 156:16. [PMID: 31160891 PMCID: PMC6542105 DOI: 10.1186/s41065-019-0093-9] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 05/20/2019] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Bread wheat is one of the most important crops in the world. Its domestication coincides with the beginning of agriculture and since then, it has been constantly under selection by humans. Its breeding has followed millennia of cultivation, sometimes with unintended selection on adaptive traits, and later by applying intentional but empirical selective pressures. For more than one century, wheat breeding has been based on science, and has been constantly evolving due to on farm agronomy and breeding program improvements. The aim of this work is to briefly review wheat breeding, with emphasis on the current advances. DISCUSSION Improving yield potential, resistance/tolerance to biotic and abiotic stresses, and baking quality, have been priorities for breeding this cereal, however, new objectives are arising, such as biofortification enhancement. The narrow genetic diversity and complexity of its genome have hampered the breeding progress and the application of biotechnology. Old approaches, such as the introgression from relative species, mutagenesis, and hybrid breeding are strongly reappearing, motivated by an accumulation of knowledge and new technologies. A revolution has taken place regarding the use of molecular markers whereby thousands of plants can be routinely genotyped for thousands of loci. After 13 years, the wheat reference genome sequence and annotation has finally been completed, and is currently available to the scientific community. Transgenics, an unusual approach for wheat improvement, still represents a potential tool, however it is being replaced by gene editing, whose technology along with genomic selection, speed breeding, and high-throughput phenotyping make up the most recent frontiers for future wheat improvement. FINAL CONSIDERATION Agriculture and plant breeding are constantly evolving, wheat has played a major role in these processes and will continue through decades to come.
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Affiliation(s)
- Eduardo Venske
- Plant Genomics and Breeding Center, Crop Science Department, Eliseu Maciel College of Agronomy, Federal University of Pelotas, Capão do Leão Campus, Capão do Leão, Rio Grande do Sul 96010-610 Brazil
| | - Railson Schreinert dos Santos
- Plant Genomics and Breeding Center, Crop Science Department, Eliseu Maciel College of Agronomy, Federal University of Pelotas, Capão do Leão Campus, Capão do Leão, Rio Grande do Sul 96010-610 Brazil
| | - Carlos Busanello
- Plant Genomics and Breeding Center, Crop Science Department, Eliseu Maciel College of Agronomy, Federal University of Pelotas, Capão do Leão Campus, Capão do Leão, Rio Grande do Sul 96010-610 Brazil
| | - Perry Gustafson
- Plant Sciences Division, 1–32 Agriculture, University of Missouri, Columbia, MO 65211 USA
| | - Antonio Costa de Oliveira
- Plant Genomics and Breeding Center, Crop Science Department, Eliseu Maciel College of Agronomy, Federal University of Pelotas, Capão do Leão Campus, Capão do Leão, Rio Grande do Sul 96010-610 Brazil
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Wang S, Chen Y. Fine-Tuning the Expression of Duplicate Genes by Translational Regulation in Arabidopsis and Maize. FRONTIERS IN PLANT SCIENCE 2019; 10:534. [PMID: 31156655 PMCID: PMC6530396 DOI: 10.3389/fpls.2019.00534] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 04/05/2019] [Indexed: 06/01/2023]
Abstract
Plant genomes are extensively shaped by various types of gene duplication. However, in this active area of investigation, the vast majority of studies focus on the sequence and transcription of duplicate genes, leaving open the question of how translational regulation impacts the expression and evolution of duplicate genes. We explored this issue by analyzing the ribo- and mRNA-seq data sets across six tissue types and stress conditions in Arabidopsis thaliana and maize (Zea mays). We dissected the relative contributions of transcriptional and translational regulation to the divergence in the abundance of ribosome footprint (RF) for different types of duplicate genes. We found that the divergence in RF abundance was largely programmed at the transcription level and that translational regulation plays more of a modulatory role. Intriguingly, translational regulation is characterized by its strong directionality, with the divergence in translational efficiency (TE) globally counteracting the divergence in mRNA abundance, indicating partial buffering of the transcriptional divergence between paralogs by translational regulation. Divergence in TE was associated with several sequence features. The faster-evolving copy in a duplicate pair was more likely to show lower RF abundance, which possibly results from relaxed purifying selection compared with its paralog. A considerable proportion of duplicates displayed differential TE across tissue types and stress conditions, most of which were enriched in photosynthesis, energy production, and translation-related processes. Additionally, we constructed a database TDPDG-DB (http://www.plantdupribo.tk), providing an online platform for data exploration. Overall, our study illustrates the roles of translational regulation in fine-tuning duplicate gene expression in plants.
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Affiliation(s)
- Sishuo Wang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- Department of Botany, Faculty of Science, The University of British Columbia, Vancouver, BC, Canada
- School of Life Sciences, The Chinese University of Hong Kong, Sha Tin, Hong Kong
| | - Youhua Chen
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
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23
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Haas M, Schreiber M, Mascher M. Domestication and crop evolution of wheat and barley: Genes, genomics, and future directions. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2019; 61:204-225. [PMID: 30414305 DOI: 10.1111/jipb.12737] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 10/27/2018] [Indexed: 05/02/2023]
Abstract
Wheat and barley are two of the founder crops of the agricultural revolution that took place 10,000 years ago in the Fertile Crescent and both crops remain among the world's most important crops. Domestication of these crops from their wild ancestors required the evolution of traits useful to humans, rather than survival in their natural environment. Of these traits, grain retention and threshability, yield improvement, changes to photoperiod sensitivity and nutritional value are most pronounced between wild and domesticated forms. Knowledge about the geographical origins of these crops and the genes responsible for domestication traits largely pre-dates the era of next-generation sequencing, although sequencing will lead to new insights. Molecular markers were initially used to calculate distance (relatedness), genetic diversity and to generate genetic maps which were useful in cloning major domestication genes. Both crops are characterized by large, complex genomes which were long thought to be beyond the scope of whole-genome sequencing. However, advances in sequencing technologies have improved the state of genomic resources for both wheat and barley. The availability of reference genomes for wheat and some of its progenitors, as well as for barley, sets the stage for answering unresolved questions in domestication genomics of wheat and barley.
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Affiliation(s)
- Matthew Haas
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstraße 3, 06466 Seeland, Germany
| | - Mona Schreiber
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstraße 3, 06466 Seeland, Germany
- Palaeogenetics Group, Institute of Organismic and Molecular Evolution, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstraße 3, 06466 Seeland, Germany
- German Center for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103 Leipzig, Germany
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24
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Pont C, Wagner S, Kremer A, Orlando L, Plomion C, Salse J. Paleogenomics: reconstruction of plant evolutionary trajectories from modern and ancient DNA. Genome Biol 2019; 20:29. [PMID: 30744646 PMCID: PMC6369560 DOI: 10.1186/s13059-019-1627-1] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
How contemporary plant genomes originated and evolved is a fascinating question. One approach uses reference genomes from extant species to reconstruct the sequence and structure of their common ancestors over deep timescales. A second approach focuses on the direct identification of genomic changes at a shorter timescale by sequencing ancient DNA preserved in subfossil remains. Merged within the nascent field of paleogenomics, these complementary approaches provide insights into the evolutionary forces that shaped the organization and regulation of modern genomes and open novel perspectives in fostering genetic gain in breeding programs and establishing tools to predict future population changes in response to anthropogenic pressure and global warming.
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Affiliation(s)
- Caroline Pont
- INRA-UCA UMR 1095 Génétique Diversité et Ecophysiologie des Céréales, 63100, Clermont-Ferrand, France
| | - Stefanie Wagner
- Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthèse, CNRS UMR 5288, allées Jules Guesde, Bâtiment A, 31000, Toulouse, France.,INRA-Université Bordeaux UMR1202, Biodiversité Gènes et Communautés, 33610, Cestas, France
| | - Antoine Kremer
- INRA-Université Bordeaux UMR1202, Biodiversité Gènes et Communautés, 33610, Cestas, France
| | - Ludovic Orlando
- Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthèse, CNRS UMR 5288, allées Jules Guesde, Bâtiment A, 31000, Toulouse, France.,Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade, 1350K, Copenhagen, Denmark
| | - Christophe Plomion
- INRA-Université Bordeaux UMR1202, Biodiversité Gènes et Communautés, 33610, Cestas, France
| | - Jerome Salse
- INRA-UCA UMR 1095 Génétique Diversité et Ecophysiologie des Céréales, 63100, Clermont-Ferrand, France.
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Abundant Small Genetic Alterations after Upland Cotton Domestication. BIOMED RESEARCH INTERNATIONAL 2018; 2018:9254302. [PMID: 30631774 PMCID: PMC6312614 DOI: 10.1155/2018/9254302] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 11/10/2018] [Accepted: 12/03/2018] [Indexed: 11/24/2022]
Abstract
Domestication has long been recognized as the most direct and effective way to intentionally influence morphological and physiological phenotypes in plants and animals. Consequently, understanding how small genetic alterations contribute to domestication is of considerable importance. In this study, we resequenced the genome of the wild upland cotton variety Gossypium hirsutum var. yucatanense, the putative wild ancestor of cultivated upland cotton, and then compared single nucleotide polymorphism (SNP) and short insertion and deletion (InDel) variations of the genome with the cultivated accession (TM-1) of G. hirsutum. We found approximately 6.6 million SNPs and 0.7 million InDels between the two genomes. Most of the small genetic variations were anchored in the noncoding regions. With regard to potential coding genes, we found 24,035 genes with nonsynonymous SNPs. Interestingly, 2603 genes in domesticated cotton are found that have changed the positions of stop codons or shifted reading frames from that in G. hirsutum var. yucatanense. This suggests that domestication may have been selected for mutations that restored gene function or that wild cotton has undergone a number of gene inactivation events since its divergence from cultivated cotton. The former scenario seems most likely due to the intense selective pressure applied during the domestication process. These results demonstrate that, within a relatively short period of time, the cotton genome has been readjusted through small genetic changes. The current study provides useful clues for seeking interesting genes for cotton improvement.
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Weeks DP. Gene Editing in Polyploid Crops: Wheat, Camelina, Canola, Potato, Cotton, Peanut, Sugar Cane, and Citrus. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2017; 149:65-80. [PMID: 28712501 DOI: 10.1016/bs.pmbts.2017.05.002] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Polyploid crops make up a significant portion of the major food and fiber crops of the world and include wheat, potato, cotton, apple, peanut, citrus, and brassica oilseeds such as rape, canola, and Camelina. The presence of three sets of chromosomes in triploids, four sets in tetraploids, and six sets in hexaploids present significant challenges to conventional plant breeding and, potentially, to efficient use of rapidly emerging gene and genome-editing systems such as zinc finger nucleases, single-stranded oligonucleotides, TALE effector nucleases, and clustered regularly interspaced short palindromic repeats (CRISPR/Cas9). However, recent studies with each of these techniques in several polyploid crops have demonstrated facile editing of some or all of the genes targeted for modification on homeologous chromosomes. These modifications have allowed improvements in food nutrition, seed oil composition, disease resistance, weed protection, plant breeding procedures, and food safety. Plants and plant products exhibiting useful new traits created through gene editing but lacking foreign DNA may face reduced regulatory restrictions. Such plants can be obtained either by simply selecting for null segregants that have lost their editing transgenes during plant breeding or, even more attractively, by delivery of biodegradable Cas9/sgRNA ribonucleoprotein complexes (i.e., no DNA) into plant cells where they are expressed only transiently but allow for efficient gene editing-a system that has been recently demonstrated in at least two polyploid crops. Such systems that create precise mutations but leave no transgene footprint hold potential promise for assisting with the elimination or great diminution of regulatory processes that presently burden approvals of conventional transgenic crops.
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27
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Reconstructing the genome of the most recent common ancestor of flowering plants. Nat Genet 2017; 49:490-496. [DOI: 10.1038/ng.3813] [Citation(s) in RCA: 143] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 02/14/2017] [Indexed: 01/24/2023]
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Quraishi UM, Pont C, Ain QU, Flores R, Burlot L, Alaux M, Quesneville H, Salse J. Combined Genomic and Genetic Data Integration of Major Agronomical Traits in Bread Wheat ( Triticum aestivum L.). FRONTIERS IN PLANT SCIENCE 2017; 8:1843. [PMID: 29184557 PMCID: PMC5694560 DOI: 10.3389/fpls.2017.01843] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 10/10/2017] [Indexed: 05/18/2023]
Abstract
The high resolution integration of bread wheat genetic and genomic resources accumulated during the last decades offers the opportunity to unveil candidate genes driving major agronomical traits to an unprecedented scale. We combined 27 public quantitative genetic studies and four genetic maps to deliver an exhaustive consensus map consisting of 140,315 molecular markers hosting 221, 73, and 82 Quantitative Trait Loci (QTL) for respectively yield, baking quality, and grain protein content (GPC) related traits. Projection of the consensus genetic map and associated QTLs onto the wheat syntenome made of 99,386 genes ordered on the 21 chromosomes delivered a complete and non-redundant repertoire of 18, 8, 6 metaQTLs for respectively yield, baking quality and GPC, altogether associated to 15,772 genes (delivering 28,630 SNP-based makers) including 37 major candidates. Overall, this study illustrates a translational research approach in transferring information gained from grass relatives to dissect the genomic regions hosting major loci governing key agronomical traits in bread wheat, their flanking markers and associated candidate genes to be now considered as a key resource for breeding programs.
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Affiliation(s)
- Umar M. Quraishi
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad, Pakistan
- Institut National de la Recherche Agronomique, Université Clermont Auvergne, UMR 1095 Génétique, Diversité et Ecophysiologie des Céréales, Clermont-Ferrand, France
- *Correspondence: Umar M. Quraishi ;
| | - Caroline Pont
- Institut National de la Recherche Agronomique, Université Clermont Auvergne, UMR 1095 Génétique, Diversité et Ecophysiologie des Céréales, Clermont-Ferrand, France
| | - Qurat-ul Ain
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Raphael Flores
- Institut National de la Recherche Agronomique UR1164 URGI (Research Unit in Genomics-Info), Université Paris-Saclay, Versailles, France
| | - Laura Burlot
- Institut National de la Recherche Agronomique UR1164 URGI (Research Unit in Genomics-Info), Université Paris-Saclay, Versailles, France
| | - Michael Alaux
- Institut National de la Recherche Agronomique UR1164 URGI (Research Unit in Genomics-Info), Université Paris-Saclay, Versailles, France
| | - Hadi Quesneville
- Institut National de la Recherche Agronomique UR1164 URGI (Research Unit in Genomics-Info), Université Paris-Saclay, Versailles, France
| | - Jerome Salse
- Institut National de la Recherche Agronomique, Université Clermont Auvergne, UMR 1095 Génétique, Diversité et Ecophysiologie des Céréales, Clermont-Ferrand, France
- Jerome Salse
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