1
|
Grewal S, Yang CY, Scholefield D, Ashling S, Ghosh S, Swarbreck D, Collins J, Yao E, Sen TZ, Wilson M, Yant L, King IP, King J. Chromosome-scale genome assembly of bread wheat's wild relative Triticum timopheevii. Sci Data 2024; 11:420. [PMID: 38653999 PMCID: PMC11039740 DOI: 10.1038/s41597-024-03260-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 04/15/2024] [Indexed: 04/25/2024] Open
Abstract
Wheat (Triticum aestivum) is one of the most important food crops with an urgent need for increase in its production to feed the growing world. Triticum timopheevii (2n = 4x = 28) is an allotetraploid wheat wild relative species containing the At and G genomes that has been exploited in many pre-breeding programmes for wheat improvement. In this study, we report the generation of a chromosome-scale reference genome assembly of T. timopheevii accession PI 94760 based on PacBio HiFi reads and chromosome conformation capture (Hi-C). The assembly comprised a total size of 9.35 Gb, featuring a contig N50 of 42.4 Mb and included the mitochondrial and plastid genome sequences. Genome annotation predicted 166,325 gene models including 70,365 genes with high confidence. DNA methylation analysis showed that the G genome had on average more methylated bases than the At genome. In summary, the T. timopheevii genome assembly provides a valuable resource for genome-informed discovery of agronomically important genes for food security.
Collapse
Affiliation(s)
- Surbhi Grewal
- Wheat Research Centre, Department of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Loughborough, LE12 5RD, UK.
| | - Cai-Yun Yang
- Wheat Research Centre, Department of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Loughborough, LE12 5RD, UK
| | - Duncan Scholefield
- Wheat Research Centre, Department of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Loughborough, LE12 5RD, UK
| | - Stephen Ashling
- Wheat Research Centre, Department of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Loughborough, LE12 5RD, UK
| | - Sreya Ghosh
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK
| | - David Swarbreck
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK
| | - Joanna Collins
- Genome Reference Informatics Team, Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1RQ, UK
| | - Eric Yao
- University of California, Department of Bioengineering, Berkeley, CA, 94720, USA
- United States Department of Agriculture-Agricultural Research Service, Western Regional Research Center, Crop Improvement and Genetics Research Unit, 800 Buchanan St., Albany, CA, 94710, USA
| | - Taner Z Sen
- University of California, Department of Bioengineering, Berkeley, CA, 94720, USA
- United States Department of Agriculture-Agricultural Research Service, Western Regional Research Center, Crop Improvement and Genetics Research Unit, 800 Buchanan St., Albany, CA, 94710, USA
| | - Michael Wilson
- University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Levi Yant
- University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Ian P King
- Wheat Research Centre, Department of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Loughborough, LE12 5RD, UK
| | - Julie King
- Wheat Research Centre, Department of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Loughborough, LE12 5RD, UK
| |
Collapse
|
2
|
Session AM. Allopolyploid subgenome identification and implications for evolutionary analysis. Trends Genet 2024:S0168-9525(24)00070-2. [PMID: 38637269 DOI: 10.1016/j.tig.2024.03.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 03/21/2024] [Accepted: 03/21/2024] [Indexed: 04/20/2024]
Abstract
Whole-genome duplications (WGDs) are widespread genomic events in eukaryotes that are hypothesized to contribute to the evolutionary success of many lineages, including flowering plants, Saccharomyces yeast, and vertebrates. WGDs generally can be classified into autopolyploids (ploidy increase descended from one species) or allopolyploids (ploidy increase descended from multiple species). Assignment of allopolyploid progenitor species (called subgenomes in the polyploid) is important to understanding the biology and evolution of polyploids, including the asymmetric subgenome evolution following hybridization (biased fractionation). Here, I review the different methodologies used to identify the ancestors of allopolyploid subgenomes, discuss the advantages and disadvantages of these methods, and outline the implications of how these methods affect the subsequent evolutionary analysis of these genomes.
Collapse
Affiliation(s)
- Adam M Session
- Department of Biological Sciences, Binghamton University, Binghamton, NY 13902, USA.
| |
Collapse
|
3
|
Boehm J, Cai X. Enrichment and Diversification of the Wheat Genome via Alien Introgression. PLANTS (BASEL, SWITZERLAND) 2024; 13:339. [PMID: 38337872 PMCID: PMC10857235 DOI: 10.3390/plants13030339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 01/08/2024] [Accepted: 01/19/2024] [Indexed: 02/12/2024]
Abstract
Wheat, including durum and common wheat, respectively, is an allopolyploid with two or three homoeologous subgenomes originating from diploid wild ancestral species. The wheat genome's polyploid origin consisting of just three diploid ancestors has constrained its genetic variation, which has bottlenecked improvement. However, wheat has a large number of relatives, including cultivated crop species (e.g., barley and rye), wild grass species, and ancestral species. Moreover, each ancestor and relative has many other related subspecies that have evolved to inhabit specific geographic areas. Cumulatively, they represent an invaluable source of genetic diversity and variation available to enrich and diversify the wheat genome. The ancestral species share one or more homologous genomes with wheat, which can be utilized in breeding efforts through typical meiotic homologous recombination. Additionally, genome introgressions of distant relatives can be moved into wheat using chromosome engineering-based approaches that feature induced meiotic homoeologous recombination. Recent advances in genomics have dramatically improved the efficacy and throughput of chromosome engineering for alien introgressions, which has served to boost the genetic potential of the wheat genome in breeding efforts. Here, we report research strategies and progress made using alien introgressions toward the enrichment and diversification of the wheat genome in the genomics era.
Collapse
Affiliation(s)
- Jeffrey Boehm
- USDA-ARS, Wheat, Sorghum & Forage Research Unit, Lincoln, NE 68583, USA;
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE 68583, USA
| | - Xiwen Cai
- USDA-ARS, Wheat, Sorghum & Forage Research Unit, Lincoln, NE 68583, USA;
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE 68583, USA
| |
Collapse
|
4
|
Ghorbel M, Zribi I, Haddaji N, Siddiqui AJ, Bouali N, Brini F. Genome-Wide Identification and Expression Analysis of Catalase Gene Families in Triticeae. PLANTS (BASEL, SWITZERLAND) 2023; 13:11. [PMID: 38202319 PMCID: PMC10781083 DOI: 10.3390/plants13010011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 12/03/2023] [Accepted: 12/11/2023] [Indexed: 01/12/2024]
Abstract
Aerobic metabolism in plants results in the production of hydrogen peroxide (H2O2), a significant and comparatively stable non-radical reactive oxygen species (ROS). H2O2 is a signaling molecule that regulates particular physiological and biological processes (the cell cycle, photosynthesis, plant growth and development, and plant responses to environmental challenges) at low concentrations. Plants may experience oxidative stress and ultimately die from cell death if excess H2O2 builds up. Triticum dicoccoides, Triticum urartu, and Triticum spelta are different ancient wheat species that present different interesting characteristics, and their importance is becoming more and more clear. In fact, due to their interesting nutritive health, flavor, and nutritional values, as well as their resistance to different parasites, the cultivation of these species is increasingly important. Thus, it is important to understand the mechanisms of plant tolerance to different biotic and abiotic stresses by studying different stress-induced gene families such as catalases (CAT), which are important H2O2-metabolizing enzymes found in plants. Here, we identified seven CAT-encoding genes (TdCATs) in Triticum dicoccoides, four genes in Triticum urartu (TuCATs), and eight genes in Triticum spelta (TsCATs). The accuracy of the newly identified wheat CAT gene members in different wheat genomes is confirmed by the gene structures, phylogenetic relationships, protein domains, and subcellular location analyses discussed in this article. In fact, our analysis showed that the identified genes harbor the following two conserved domains: a catalase domain (pfam00199) and a catalase-related domain (pfam06628). Phylogenetic analyses showed that the identified wheat CAT proteins were present in an analogous form in durum wheat and bread wheat. Moreover, the identified CAT proteins were located essentially in the peroxisome, as revealed by in silico analyses. Interestingly, analyses of CAT promoters in those species revealed the presence of different cis elements related to plant development, maturation, and plant responses to different environmental stresses. According to RT-qPCR, Triticum CAT genes showed distinctive expression designs in the studied organs and in response to different treatments (salt, heat, cold, mannitol, and ABA). This study completed a thorough analysis of the CAT genes in Triticeae, which advances our knowledge of CAT genes and establishes a framework for further functional analyses of the wheat gene family.
Collapse
Affiliation(s)
- Mouna Ghorbel
- Department of Biology, College of Sciences, University of Hail, P.O. Box 2440, Ha’il City 81451, Saudi Arabia; (M.G.); (N.H.); (A.J.S.); (N.B.)
| | - Ikram Zribi
- Laboratory of Biotechnology and Plant Improvement, Center of Biotechnology of Sfax, P.O. Box 1177, Sfax 3018, Tunisia;
| | - Najla Haddaji
- Department of Biology, College of Sciences, University of Hail, P.O. Box 2440, Ha’il City 81451, Saudi Arabia; (M.G.); (N.H.); (A.J.S.); (N.B.)
| | - Arif Jamal Siddiqui
- Department of Biology, College of Sciences, University of Hail, P.O. Box 2440, Ha’il City 81451, Saudi Arabia; (M.G.); (N.H.); (A.J.S.); (N.B.)
| | - Nouha Bouali
- Department of Biology, College of Sciences, University of Hail, P.O. Box 2440, Ha’il City 81451, Saudi Arabia; (M.G.); (N.H.); (A.J.S.); (N.B.)
| | - Faiçal Brini
- Laboratory of Biotechnology and Plant Improvement, Center of Biotechnology of Sfax, P.O. Box 1177, Sfax 3018, Tunisia;
| |
Collapse
|
5
|
Bian Y, Li L, Tian X, Xu D, Sun M, Li F, Xie L, Liu S, Liu B, Xia X, He Z, Cao S. Rht12b, a widely used ancient allele of TaGA2oxA13, reduces plant height and enhances yield potential in wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:253. [PMID: 37989964 DOI: 10.1007/s00122-023-04502-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Accepted: 11/10/2023] [Indexed: 11/23/2023]
Abstract
KEY MESSAGE We identified a new wheat dwarfing allele Rht12b conferring reduced height and higher grain yield, pinpointed its causal variations, developed a breeding-applicable marker, and traced its origin and worldwide distribution. Plant height control is essential to optimize lodging resistance and yield gain in crops. RHT12 is a reduced height (Rht) locus that is identified in a mutationally induced dwarfing mutant and encodes a gibberellin 2-oxidase TaGA2oxA13. However, the artificial dwarfing allele is not used in wheat breeding due to excessive height reduction. Here, we confirmed a stable Rht locus, overlapping with RHT12, in a panel of wheat cultivars and its dwarfing allele reduced plant height by 5.4-8.2 cm, equivalent to Rht12b, a new allele of RHT12. We validated the effect of Rht12b on plant height in a bi-parent mapping population. Importantly, wheat cultivars carrying Rht12b had higher grain yield than those with the contrasting Rht12a allele. Rht12b conferred higher expression level of TaGA2oxA13. Transient activation assays defined SNP-390(C/A) in the promoter of TaGA2oxA13 as the causal variation. An efficient kompetitive allele-specific PCR marker was developed to diagnose Rht12b. Conjoint analysis showed that Rht12b plus the widely used Rht-D1b, Rht8 and Rht24b was the predominant Rht combination and conferred a moderate plant height in tested wheat cultivars. Evolutionary tracking uncovered that RHT12 locus arose from a tandem duplication event with Rht12b firstly appearing in wild emmer. The frequency of Rht12b was approximately 70% (700/1005) in a worldwide wheat panel and comparable to or higher than those of other widely used Rht genes, suggesting it had been subjected to positive selection. These findings not only identify a valuable Rht gene for wheat improvement but also develop a functionally diagnostic tool for marker-assisted breeding.
Collapse
Affiliation(s)
- Yingjie Bian
- National Wheat Improvement Center, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Lingli Li
- National Wheat Improvement Center, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Xiuling Tian
- National Wheat Improvement Center, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Dengan Xu
- National Wheat Improvement Center, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
- College of Agronomy, Qingdao Agricultural University, Qingdao, 266109, China
| | - Mengjing Sun
- National Wheat Improvement Center, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Faji Li
- Crop Research Institute, Shandong Academy of Agricultural Sciences, 202 Gongye North Road, Jinan, 250100, Shandong, China
| | - Lina Xie
- National Wheat Improvement Center, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Siyang Liu
- National Wheat Improvement Center, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Bingyan Liu
- National Wheat Improvement Center, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Xianchun Xia
- National Wheat Improvement Center, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Zhonghu He
- National Wheat Improvement Center, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China.
- International Maize and Wheat Improvement Center China Office, c/o Chinese Academy Agricultural Sciences, Beijing, 100081, China.
| | - Shuanghe Cao
- National Wheat Improvement Center, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China.
| |
Collapse
|
6
|
Orlovskaya ОA, Leonova IN, Solovey LA, Dubovets NI. Molecular cytological analysis of alien introgressions in common wheat lines created by crossing of Triticum aestivum with T. dicoccoides and T. dicoccum. Vavilovskii Zhurnal Genet Selektsii 2023; 27:553-564. [PMID: 38023811 PMCID: PMC10643109 DOI: 10.18699/vjgb-23-67] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 05/24/2023] [Accepted: 05/26/2023] [Indexed: 12/01/2023] Open
Abstract
Wild and domesticated emmer (ВВАА, 2n = 28) are of significant interest for expanding the genetic diversity of common wheat as sources of a high protein and microelement grain content, resistance to many biotic and abiotic factors. Particular interest in these species is also determined by their close relationship with Triticum aestivum L., which facilitates interspecific hybridization. The objective of this work was to analyze the nature of alien introgressions in hybrid lines from crossing common wheat varieties with T. dicoccoides and T. dicoccum, and to assess the effect of their genome fragments on the cytological stability of introgression lines. A C-banding technique and genotyping with SNP and SSR markers were used to determine localization and length of introgression fragments. Assessment of cytological stability was carried out on the basis of chromosome behavior in microsporogenesis. A molecular cytogenetic analysis of introgression wheat lines indicated that the inclusion of the genetic material of wild and domesticated emmer was carried out mainly in the form of whole arms or large fragments in the chromosomes of the B genome and less extended inserts in the A genome. At the same time, the highest frequency of introgressions of the emmer genome was observed in chromosomes 1A, 1B, 2B, and 3B. The analysis of the final stage of meiosis showed a high level of cytological stability in the vast majority of introgression wheat lines (meiotic index was 83.0-99.0 %), which ensures the formation of functional gametes in an amount sufficient for successful reproduction. These lines are of interest for the selection of promising material with agronomically valuable traits and their subsequent inclusion in the breeding process.
Collapse
Affiliation(s)
- О A Orlovskaya
- Institute of Genetics and Cytology of the National Academy of Sciences of Belarus, Minsk, Belarus
| | - I N Leonova
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Department of Genetics and Selection, Novosibirsk State Agricultural University, Novosibirsk, Russia
| | - L A Solovey
- Institute of Genetics and Cytology of the National Academy of Sciences of Belarus, Minsk, Belarus
| | - N I Dubovets
- Institute of Genetics and Cytology of the National Academy of Sciences of Belarus, Minsk, Belarus
| |
Collapse
|
7
|
Huang Y, Liu Y, Guo X, Fan C, Yi C, Shi Q, Su H, Liu C, Yuan J, Liu D, Yang W, Han F. New insights on the evolution of nucleolar dominance in newly resynthesized hexaploid wheat Triticum zhukovskyi. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 115:1298-1315. [PMID: 37246611 DOI: 10.1111/tpj.16320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 05/11/2023] [Accepted: 05/23/2023] [Indexed: 05/30/2023]
Abstract
Nucleolar dominance (ND) is a widespread epigenetic phenomenon in hybridizations where nucleolus transcription fails at the nucleolus organizer region (NOR). However, the dynamics of NORs during the formation of Triticum zhukovskyi (GGAu Au Am Am ), another evolutionary branch of allohexaploid wheat, remains poorly understood. Here, we elucidated genetic and epigenetic changes occurring at the NOR loci within the Am , G, and D subgenomes during allopolyploidization by synthesizing hexaploid wheat GGAu Au Am Am and GGAu Au DD. In T. zhukovskyi, Au genome NORs from T. timopheevii (GGAu Au ) were lost, while the second incoming NORs from T. monococcum (Am Am ) were retained. Analysis of the synthesized T. zhukovskyi revealed that rRNA genes from the Am genome were silenced in F1 hybrids (GAu Am ) and remained inactive after genome doubling and subsequent self-pollinations. We observed increased DNA methylation accompanying the inactivation of NORs in the Am genome and found that silencing of NORs in the S1 generation could be reversed by a cytidine methylase inhibitor. Our findings provide insights into the ND process during the evolutionary period of T. zhukovskyi and highlight that inactive rDNA units may serve as a 'first reserve' in the form of R-loops, contributing to the successful evolution of T. zhukovskyi.
Collapse
Affiliation(s)
- Yuhong Huang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yang Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xianrui Guo
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Chaolan Fan
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Congyang Yi
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qinghua Shi
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Handong Su
- Huazhong Agricultural University, Hubei, 430070, China
| | - Chang Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jing Yuan
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Dengcai Liu
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Wuyun Yang
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, China
| | - Fangpu Han
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| |
Collapse
|
8
|
Yadav IS, Singh N, Wu S, Raupp J, Wilson DL, Rawat N, Gill BS, Poland J, Tiwari VK. Exploring genetic diversity of wild and related tetraploid wheat species Triticum turgidum and Triticum timopheevii. J Adv Res 2023; 48:47-60. [PMID: 36084813 PMCID: PMC10248793 DOI: 10.1016/j.jare.2022.08.020] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 08/25/2022] [Accepted: 08/31/2022] [Indexed: 11/27/2022] Open
Abstract
INTRODUCTION The domestication bottleneck has reduced genetic diversity inwheat, necessitating the use of wild relatives in breeding programs. Wild tetraploid wheat are widely used in the breeding programs but with morphological characters, it is difficult to distinguish these, resulting in misclassification/mislabeling or duplication of accessions in the Gene bank. OBJECTIVES The study aims to exploreGenotyping by sequencing (GBS) to characterize wild and domesticated tetraploid wheat accessions to generate a core set of accessions to be used in the breeding program. METHODS TASSEL-GBS pipeline was used for SNP discovery, fastStructure was used to determine the population structure and PowerCore was used to generate a core sets. Nucleotide diversity matrices of Nie's and F-statistics (FST) index were used to determine the center of genetic diversity. RESULTS We found 65 % and 47 % duplicated accessions in Triticum timopheevii and T. turgidum respectively. Genome-wide nucleotide diversity and FST scan uncovered a lower intra and higher inter-species differentiation. Distinct FST regions were identified in genomic regions belonging to domestication genes: non-brittle rachis (Btr1) and vernalization (VRN-1).Our results suggest that Israel, Jordan, Syria, and Lebanonas the hub of genetic diversity of wild emmer;Turkey, and Georgia for T. durum; and Iraq, Azerbaijan, and Armenia for theT. timopheevii. Identified core set accessions preserved more than 93 % of the available genetic diversity. Genome wide association study (GWAS) indicated the potential chromosomal segment for resistance to leaf rust in T. timopheevii. CONCLUSION The present study explored the potential of GBS technology in data reduction while maintaining the significant genetic diversity of the species. Wild germplasm showed more differentiation than domesticated accessions, indicating the availability of sufficient diversity for crop improvement. With reduced complexity, the core set preserves the genetic diversity of the gene bank collections and will aid in a more robust characterization of wild germplasm.
Collapse
Affiliation(s)
- Inderjit S. Yadav
- Department of Plant Sciences and Landscape Architecture, University of Maryland, College Park, MD 20742, USA
| | | | - Shuangye Wu
- Department of Plant Pathology and Wheat Genetics Resource Center, Kansas State University, 1712 Claflin Road, Manhattan, KS 66506, USA
| | - Jon Raupp
- Department of Plant Pathology and Wheat Genetics Resource Center, Kansas State University, 1712 Claflin Road, Manhattan, KS 66506, USA
| | - Duane L. Wilson
- Department of Plant Pathology and Wheat Genetics Resource Center, Kansas State University, 1712 Claflin Road, Manhattan, KS 66506, USA
| | - Nidhi Rawat
- Department of Plant Sciences and Landscape Architecture, University of Maryland, College Park, MD 20742, USA
| | - Bikram S. Gill
- Department of Plant Pathology and Wheat Genetics Resource Center, Kansas State University, 1712 Claflin Road, Manhattan, KS 66506, USA
| | - Jesse Poland
- Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, 4700 KAUST, Thuwal 23955-6900, Saudi Arabia
| | - Vijay K. Tiwari
- Department of Plant Sciences and Landscape Architecture, University of Maryland, College Park, MD 20742, USA
| |
Collapse
|
9
|
Ma H, Lin J, Mei F, Mao H, Li QQ. Differential alternative polyadenylation of homoeologous genes of allohexaploid wheat ABD subgenomes during drought stress response. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 114:499-518. [PMID: 36786697 DOI: 10.1111/tpj.16150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 02/08/2023] [Accepted: 02/10/2023] [Indexed: 05/10/2023]
Abstract
Because allohexaploid wheat genome contains ABD subgenomes, how the expression of homoeologous genes is coordinated remains largely unknown, particularly at the co-transcriptional level. Alternative polyadenylation (APA) is an important part of co-transcriptional regulation, which is crucial in developmental processes and stress responses. Drought stress is a major threat to the stable yield of wheat. Focusing on APA, we used poly(A) tag sequencing to track poly(A) site dynamics in wheat under drought stress. The results showed that drought stress led to extensive APA involving 37-47% of differentially expressed genes in wheat. Significant poly(A) site switching was found in stress-responsive genes. Interestingly, homoeologous genes exhibit unequal numbers of poly(A) sites, divergent APA patterns with tissue specificity and time-course dynamics, and distinct 3'-UTR length changes. Moreover, differentially expressed transcripts in leaves and roots used different poly(A) signals, the up- and downregulated isoforms had distinct preferences for non-canonical poly(A) sites. Genes that encode key polyadenylation factors showed differential expression patterns under drought stress. In summary, poly(A) signals and the changes in core poly(A) factors may widely affect the selection of poly(A) sites and gene expression levels during the response to drought stress, and divergent APA patterns among homoeologous genes add extensive plasticity to this responsive network. These results not only reveal the significant role of APA in drought stress response, but also provide a fresh perspective on how homoeologous genes contribute to adaptability through transcriptome diversity. In addition, this work provides information about the ends of transcripts for a better annotation of the wheat genome.
Collapse
Affiliation(s)
- Hui Ma
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystem, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, 361102, China
- Biomedical Sciences, College of Dental Medicine, Western University of Health Sciences, Pomona, CA, 91766, USA
| | - Juncheng Lin
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystem, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, 361102, China
| | - Fangming Mei
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shanxi, 712100, China
| | - Hude Mao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shanxi, 712100, China
| | - Qingshun Q Li
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystem, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, 361102, China
- Biomedical Sciences, College of Dental Medicine, Western University of Health Sciences, Pomona, CA, 91766, USA
| |
Collapse
|
10
|
Yang Y, Cui L, Lu Z, Li G, Yang Z, Zhao G, Kong C, Li D, Chen Y, Xie Z, Chen Z, Zhang L, Xia C, Liu X, Jia J, Kong X. Genome sequencing of Sitopsis species provides insights into their contribution to the B subgenome of bread wheat. PLANT COMMUNICATIONS 2023:100567. [PMID: 36855304 PMCID: PMC10363506 DOI: 10.1016/j.xplc.2023.100567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 02/14/2023] [Accepted: 02/23/2023] [Indexed: 06/18/2023]
Abstract
Wheat (Triticum aestivum, BBAADD) is an allohexaploid species that originated from two polyploidization events. The progenitors of the A and D subgenomes have been identified as Triticum urartu and Aegilops tauschii, respectively. Current research suggests that Aegilops speltoides is the closest but not the direct ancestor of the B subgenome. However, whether Ae. speltoides has contributed genomically to the wheat B subgenome and which chromosome regions are conserved between Ae. speltoides and the B subgenome remain unclear. Here, we assembled a high-quality reference genome for Ae. speltoides, resequenced 53 accessions from seven species (Aegilops bicornis, Aegilops longissima, Aegilops searsii, Aegilops sharonensis, Ae. speltoides, Aegilops mutica [syn. Amblyopyrum muticum], and Triticum dicoccoides) and revealed their genomic contributions to the wheat B subgenome. Our results showed that centromeric regions were particularly conserved between Aegilops and Triticum and revealed 0.17 Gb of conserved blocks between Ae. speltoides and the B subgenome. We classified five groups of conserved and non-conserved genes between Aegilops and Triticum, revealing their biological characteristics, differentiation in gene expression patterns, and collinear relationships between Ae. speltoides and the wheat B subgenome. We also identified gene families that expanded in Ae. speltoides during its evolution and 789 genes specific to Ae. speltoides. These genes can serve as genetic resources for improvement of adaptability to biotic and abiotic stress. The newly constructed reference genome and large-scale resequencing data for Sitopsis species will provide a valuable genomic resource for wheat genetic improvement and genomic studies.
Collapse
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.
| |
Collapse
|
11
|
Bekkering CS, Yu S, Isaka NN, Sproul BW, Dubcovsky J, Tian L. Genetic dissection of the roles of β-hydroxylases in carotenoid metabolism, photosynthesis, and plant growth in tetraploid wheat (Triticum turgidum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:8. [PMID: 36656368 PMCID: PMC9852137 DOI: 10.1007/s00122-023-04276-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 01/09/2023] [Indexed: 06/17/2023]
Abstract
Functional redundancy and subfunctionalization of β-hydroxylases in tetraploid wheat tissues open up opportunities for manipulation of carotenoid metabolism for trait improvement. The genetic diversity provided by subgenome homoeologs in allopolyploid wheat can be leveraged for developing improved wheat varieties with modified chemical traits, including profiles of carotenoids, which play critical roles in photosynthesis, photoprotection, and growth regulation. Carotenoid profiles are greatly influenced by hydroxylation catalyzed by β-hydroxylases (HYDs). To genetically dissect the contribution of HYDs to carotenoid metabolism and wheat growth and yield, we isolated loss-of-function mutants of the two homoeologs of HYD1 (HYD-A1 and HYD-B1) and HYD2 (HYD-A2 and HYD-B2) from the sequenced ethyl methanesulfonate mutant population of the tetraploid wheat cultivar Kronos, and generated various mutant combinations. Although functional redundancy between HYD1 and HYD2 paralogs was observed in leaves, HYD1 homoeologs contributed more than HYD2 homoeologs to carotenoid β-ring hydroxylation in this tissue. By contrast, the HYD2 homoeologs functioned toward production of lutein, the major carotenoid in mature grains, whereas HYD1 homoeologs had a limited role. These results collectively suggested subfunctionalization of HYD genes and homoeologs in different tissues of tetraploid wheat. Despite reduced photoprotective responses observed in the triple hyd-A1 hyd-B1 hyd-A2 and the quadruple hyd-A1 hyd-B1 hyd-A2 hyd-B2 combinatorial mutants, comprehensive plant phenotyping analysis revealed that all mutants analyzed were comparable to the control for growth, yield, and fertility, except for a slight delay in anthesis and senescence as well as accelerated germination in the quadruple mutant. Overall, this research takes steps toward untangling the functions of HYDs in wheat and has implications for improving performance and consumer traits of this economically important global crop.
Collapse
Affiliation(s)
- Cody S Bekkering
- Department of Plant Sciences, University of California, Mail Stop 3, Davis, CA, 95616, USA
| | - Shu Yu
- Department of Plant Sciences, University of California, Mail Stop 3, Davis, CA, 95616, USA
| | - Nina N Isaka
- Department of Plant Sciences, University of California, Mail Stop 3, Davis, CA, 95616, USA
| | - Benjamin W Sproul
- Department of Plant Sciences, University of California, Mail Stop 3, Davis, CA, 95616, USA
| | - Jorge Dubcovsky
- Department of Plant Sciences, University of California, Mail Stop 3, Davis, CA, 95616, USA
| | - Li Tian
- Department of Plant Sciences, University of California, Mail Stop 3, Davis, CA, 95616, USA.
| |
Collapse
|
12
|
Steed A, King J, Grewal S, Yang CY, Clarke M, Devi U, King IP, Nicholson P. Identification of Fusarium Head Blight Resistance in Triticum timopheevii Accessions and Characterization of Wheat- T. timopheevii Introgression Lines for Enhanced Resistance. FRONTIERS IN PLANT SCIENCE 2022; 13:943211. [PMID: 35874002 PMCID: PMC9298666 DOI: 10.3389/fpls.2022.943211] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 06/15/2022] [Indexed: 06/15/2023]
Abstract
A diverse panel of wheat wild relative species was screened for resistance to Fusarium head blight (FHB) by spray inoculation. The great majority of species and accessions were susceptible or highly susceptible to FHB. Accessions of Triticum timopheevii (P95-99.1-1), Agropyron desertorum (9439957), and Elymus vaillantianus (531552) were highly resistant to FHB while additional accessions of T. timopheevii were found to be susceptible to FHB. A combination of spray and point inoculation assessments over two consecutive seasons indicated that the resistance in accession P95-99.1-1 was due to enhanced resistance to initial infection of the fungus (type 1 resistance), and not to reduction in spread (type 2 resistance). A panel of wheat-T. timopheevii (accession P95-99.1-1) introgression lines was screened for FHB resistance over two consecutive seasons using spray inoculation. Most introgression lines were similar in susceptibility to FHB as the wheat recipient (Paragon) but substitution of the terminal portion of chromosome 3BS of wheat with a similar-sized portion of 3G of T. timopheevii significantly enhanced FHB resistance in the wheat background.
Collapse
Affiliation(s)
- Andrew Steed
- Department of Crop Genetics, John Innes Centre, Norwich, United Kingdom
| | - Julie King
- Department of Plant and Crop Sciences, School of Biosciences, Nottingham BBSRC Wheat Research Centre, University of Nottingham, Loughborough, United Kingdom
| | - Surbhi Grewal
- Department of Plant and Crop Sciences, School of Biosciences, Nottingham BBSRC Wheat Research Centre, University of Nottingham, Loughborough, United Kingdom
| | - Cai-yun Yang
- Department of Plant and Crop Sciences, School of Biosciences, Nottingham BBSRC Wheat Research Centre, University of Nottingham, Loughborough, United Kingdom
| | - Martha Clarke
- Department of Crop Genetics, John Innes Centre, Norwich, United Kingdom
| | - Urmila Devi
- Department of Plant and Crop Sciences, School of Biosciences, Nottingham BBSRC Wheat Research Centre, University of Nottingham, Loughborough, United Kingdom
| | - Ian P. King
- Department of Plant and Crop Sciences, School of Biosciences, Nottingham BBSRC Wheat Research Centre, University of Nottingham, Loughborough, United Kingdom
| | - Paul Nicholson
- Department of Crop Genetics, John Innes Centre, Norwich, United Kingdom
| |
Collapse
|
13
|
Assessing the Heat Tolerance of Meiosis in Spanish Landraces of Tetraploid Wheat Triticum turgidum. PLANTS 2022; 11:plants11131661. [PMID: 35807613 PMCID: PMC9268776 DOI: 10.3390/plants11131661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 06/20/2022] [Accepted: 06/22/2022] [Indexed: 11/17/2022]
Abstract
Heat stress alters the number and distribution of meiotic crossovers in wild and cultivated plant species. Hence, global warming may have a negative impact on meiosis, fertility, and crop productions. Assessment of germplasm collections to identify heat-tolerant genotypes is a priority for future crop improvement. Durum wheat, Triticum turgidum, is an important cultivated cereal worldwide and given the genetic diversity of the durum wheat Spanish landraces core collection, we decided to analyse the heat stress effect on chiasma formation in a sample of 16 landraces of T. turgidum ssp. turgidum and T. turgidum ssp. durum, from localities with variable climate conditions. Plants of each landrace were grown at 18–22 °C and at 30 °C during the premeiotic temperature-sensitive stage. The number of chiasmata was not affected by heat stress in three genotypes, but decreased by 0.3–2 chiasmata in ten genotypes and more than two chiasmata in the remaining three ones. Both thermotolerant and temperature-sensitive genotypes were found in the two subspecies, and in some of the agroecological zones studied, which supports that genotypes conferring a heat tolerant meiotic phenotype are not dependent on subspecies or geographical origin. Implications of heat adaptive genotypes in future research and breeding are discussed.
Collapse
|
14
|
Türkösi E, Ivanizs L, Farkas A, Gaál E, Kruppa K, Kovács P, Szakács É, Szőke-Pázsi K, Said M, Cápal P, Griffiths S, Doležel J, Molnár I. Transfer of the ph1b Deletion Chromosome 5B From Chinese Spring Wheat Into a Winter Wheat Line and Induction of Chromosome Rearrangements in Wheat- Aegilops biuncialis Hybrids. FRONTIERS IN PLANT SCIENCE 2022; 13:875676. [PMID: 35769292 PMCID: PMC9234525 DOI: 10.3389/fpls.2022.875676] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 05/09/2022] [Indexed: 06/10/2023]
Abstract
Effective utilization of genetic diversity in wild relatives to improve wheat requires recombination between wheat and alien chromosomes. However, this is suppressed by the Pairing homoeologous gene, Ph1, on the long arm of wheat chromosome 5B. A deletion mutant of the Ph1 locus (ph1b) has been used widely to induce homoeologous recombination in wheat × alien hybrids. However, the original ph1b mutation, developed in Chinese Spring (CS) background has poor agronomic performance. Hence, alien introgression lines are first backcrossed with adapted wheat genotypes and after this step, alien chromosome segments are introduced into breeding lines. In this work, the ph1b mutation was transferred from two CSph1b mutants into winter wheat line Mv9kr1. Homozygous genotypes Mv9kr1 ph1b/ph1b exhibited improved plant and spike morphology compared to Chinese Spring. Flow cytometric chromosome analysis confirmed reduced DNA content of the mutant 5B chromosome in both wheat genotype relative to the wild type chromosome. The ph1b mutation in the Mv9kr1 genotype allowed wheat-alien chromosome pairing in meiosis of Mv9kr1ph1b_K × Aegilops biuncialis F1 hybrids, predominantly with the Mb-genome chromosomes of Aegilops relative to those of the Ub genome. High frequency of wheat-Aegilops chromosome interactions resulted in rearranged chromosomes identified in the new Mv9kr1ph1b × Ae. Biuncialis amphiploids, making these lines valuable sources for alien introgressions. The new Mv9kr1ph1b mutant genotype is a unique resource to support alien introgression breeding of hexaploid wheat.
Collapse
Affiliation(s)
- Edina Türkösi
- Department of Biological Resources, Centre for Agricultural Research, Eötvös Loránd Research Network, Martonvásár, Hungary
| | - László Ivanizs
- Department of Biological Resources, Centre for Agricultural Research, Eötvös Loránd Research Network, Martonvásár, Hungary
| | - András Farkas
- Department of Biological Resources, Centre for Agricultural Research, Eötvös Loránd Research Network, Martonvásár, Hungary
| | - Eszter Gaál
- Department of Biological Resources, Centre for Agricultural Research, Eötvös Loránd Research Network, Martonvásár, Hungary
| | - Klaudia Kruppa
- Department of Biological Resources, Centre for Agricultural Research, Eötvös Loránd Research Network, Martonvásár, Hungary
| | - Péter Kovács
- Department of Biological Resources, Centre for Agricultural Research, Eötvös Loránd Research Network, Martonvásár, Hungary
- Institute of Genetics and Biotechnology, Szent István Campus, MATE, Gödöllő, Hungary
| | - Éva Szakács
- Department of Biological Resources, Centre for Agricultural Research, Eötvös Loránd Research Network, Martonvásár, Hungary
| | - Kitti Szőke-Pázsi
- Department of Biological Resources, Centre for Agricultural Research, Eötvös Loránd Research Network, Martonvásár, Hungary
| | - Mahmoud Said
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute for Experimental Botany of the Czech Academy of Sciences, Olomouc, Czechia
- Field Crops Research Institute, Agricultural Research Centre, Giza, Egypt
| | - Petr Cápal
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute for Experimental Botany of the Czech Academy of Sciences, Olomouc, Czechia
| | | | - Jaroslav Doležel
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute for Experimental Botany of the Czech Academy of Sciences, Olomouc, Czechia
| | - István Molnár
- Department of Biological Resources, Centre for Agricultural Research, Eötvös Loránd Research Network, Martonvásár, Hungary
| |
Collapse
|
15
|
Wang X, Hu Y, He W, Yu K, Zhang C, Li Y, Yang W, Sun J, Li X, Zheng F, Zhou S, Kong L, Ling H, Zhao S, Liu D, Zhang A. Whole-genome resequencing of the wheat A subgenome progenitor Triticum urartu provides insights into its demographic history and geographic adaptation. PLANT COMMUNICATIONS 2022; 3:100345. [PMID: 35655430 PMCID: PMC9483109 DOI: 10.1016/j.xplc.2022.100345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/02/2022] [Revised: 04/23/2022] [Accepted: 05/30/2022] [Indexed: 01/17/2023]
Abstract
Triticum urartu is the progenitor of the A subgenome in tetraploid and hexaploid wheat. Uncovering the landscape of genetic variations in T. urartu will help us understand the evolutionary and polyploid characteristics of wheat. Here, we investigated the population genomics of T. urartu by genome-wide sequencing of 59 representative accessions collected around the world. A total of 42.2 million high-quality single-nucleotide polymorphisms and 3 million insertions and deletions were obtained by mapping reads to the reference genome. The ancient T. urartu population experienced a significant reduction in effective population size (Ne) from ∼3 000 000 to ∼140 000 and subsequently split into eastern Mediterranean coastal and Mesopotamian-Transcaucasian populations during the Younger Dryas period. A map of allelic drift paths displayed splits and mixtures between different geographic groups, and a strong genetic drift towards hexaploid wheat was also observed, indicating that the direct donor of the A subgenome originated from northwestern Syria. Genetic changes were revealed between the eastern Mediterranean coastal and Mesopotamian-Transcaucasian populations in genes orthologous to those regulating plant development and stress responses. A genome-wide association study identified two single-nucleotide polymorphisms in the exonic regions of the SEMI-DWARF 37 ortholog that corresponded to the different T. urartu ecotype groups. Our study provides novel insights into the origin and genetic legacy of the A subgenome in polyploid wheat and contributes a gene repertoire for genomics-enabled improvements in wheat breeding.
Collapse
Affiliation(s)
- Xin Wang
- State Key Laboratory of Plant Cell and Chromosome Engineering, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology/Innovation Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China; Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Yafei Hu
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Weiming He
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Kang Yu
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China; BGI Institute of Applied Agriculture, BGI-Agro, Shenzhen, 518120, China
| | - Chi Zhang
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Yiwen Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology/Innovation Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Wenlong Yang
- State Key Laboratory of Plant Cell and Chromosome Engineering, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology/Innovation Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jiazhu Sun
- State Key Laboratory of Plant Cell and Chromosome Engineering, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology/Innovation Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xin Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology/Innovation Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Fengya Zheng
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Shengjun Zhou
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Lingrang Kong
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, 271018, China
| | - Hongqing Ling
- State Key Laboratory of Plant Cell and Chromosome Engineering, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology/Innovation Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Shancen Zhao
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China; BGI Institute of Applied Agriculture, BGI-Agro, Shenzhen, 518120, China.
| | - Dongcheng Liu
- State Key Laboratory of North China Crop Improvement and Regulation, College of Agronomy, Hebei Agricultural University, Baoding, 071001, China.
| | - Aimin Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology/Innovation Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China; State Key Laboratory of North China Crop Improvement and Regulation, College of Agronomy, Hebei Agricultural University, Baoding, 071001, China.
| |
Collapse
|
16
|
Nocente F, Galassi E, Taddei F, Natale C, Gazza L. Ancient Caucasian Wheats: A Contribution for Sustainable Diets and Food Diversity. Foods 2022; 11:foods11091209. [PMID: 35563931 PMCID: PMC9104265 DOI: 10.3390/foods11091209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 04/14/2022] [Accepted: 04/19/2022] [Indexed: 12/10/2022] Open
Abstract
Through the centuries, the domestication and modern breeding of wheat led to a significant loss of genetic variation in the cultivated gene pool with a consequent decrease in food diversity. Current trends towards low-input and sustainable agriculture call for the revitalization and exploitation of ancient wheats, which represent a reservoir of biodiversity useful to ensure sustainable wheat production in the context of climate change and low-input farming systems. Ancient Caucasian wheat species, such as the hulled wheats Triticum timopheevii (tetraploid AuAuGG) and Triticum zhukovskyi (hexaploid AuAuAmAmGG), are still grown to a limited extent in the Caucasus for the production of traditional foods. These Caucasian wheats were grown in Italy and were analyzed for physical, nutritional and technological characteristics and compared to durum wheat. Both Caucasian species revealed a high protein content (on average 18.5%) associated with a low gluten index, mainly in T. zhukovskyi, and test weight values comparable to commercial wheats. The total antioxidant capacity was revealed to be the double of that in durum wheat, suggesting the use of ancient Caucasian wheats for the production of healthy foods. Finally, the technological and rheological results indicated that Caucasian wheats could be potential raw material for the formulation of flat breads, biscuits and pasta.
Collapse
|
17
|
Adhikari L, Raupp J, Wu S, Wilson D, Evers B, Koo DH, Singh N, Friebe B, Poland J. Genetic characterization and curation of diploid A-genome wheat species. PLANT PHYSIOLOGY 2022; 188:2101-2114. [PMID: 35134208 PMCID: PMC8968256 DOI: 10.1093/plphys/kiac006] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 12/17/2021] [Indexed: 06/14/2023]
Abstract
A-genome diploid wheats represent the earliest domesticated and cultivated wheat species in the Fertile Crescent and include the donor of the wheat A sub-genome. The A-genome species encompass the cultivated einkorn (Triticum monococcum L. subsp. monococcum), wild einkorn (T. monococcum L. subsp. aegilopoides (Link) Thell.), and Triticum urartu. We evaluated the collection of 930 accessions in the Wheat Genetics Resource Center (WGRC) using genotyping by sequencing and identified 13,860 curated single-nucleotide polymorphisms. Genomic analysis detected misclassified and genetically identical (>99%) accessions, with most of the identical accessions originating from the same or nearby locations. About 56% (n = 520) of the WGRC A-genome species collections were genetically identical, supporting the need for genomic characterization for effective curation and maintenance of these collections. Population structure analysis confirmed the morphology-based classifications of the accessions and reflected the species geographic distributions. We also showed that T. urartu is the closest A-genome diploid to the A-subgenome in common wheat (Triticum aestivum L.) through phylogenetic analysis. Population analysis within the wild einkorn group showed three genetically distinct clusters, which corresponded with wild einkorn races α, β, and γ described previously. The T. monococcum genome-wide FST scan identified candidate genomic regions harboring a domestication selection signature at the Non-brittle rachis 1 (Btr1) locus on the short arm of chromosome 3Am at ∼70 Mb. We established an A-genome core set (79 accessions) based on allelic diversity, geographical distribution, and available phenotypic data. The individual species core set maintained at least 79% of allelic variants in the A-genome collection and constituted a valuable genetic resource to improve wheat and domesticated einkorn in breeding programs.
Collapse
Affiliation(s)
- Laxman Adhikari
- Department of Plant Pathology, Kansas State University, Manhattan, Kansas 66502, USA
- Wheat Genetic Resource Center (WGRC), Kansas State University, Manhattan, Kansas 66502, USA
- Center for Desert Agriculture, King Abdullah University of Science and Technology, Thuwal 23955, Saudi Arabia
| | - John Raupp
- Department of Plant Pathology, Kansas State University, Manhattan, Kansas 66502, USA
- Wheat Genetic Resource Center (WGRC), Kansas State University, Manhattan, Kansas 66502, USA
| | - Shuangye Wu
- Department of Plant Pathology, Kansas State University, Manhattan, Kansas 66502, USA
- Wheat Genetic Resource Center (WGRC), Kansas State University, Manhattan, Kansas 66502, USA
| | - Duane Wilson
- Department of Plant Pathology, Kansas State University, Manhattan, Kansas 66502, USA
- Wheat Genetic Resource Center (WGRC), Kansas State University, Manhattan, Kansas 66502, USA
| | - Byron Evers
- Department of Plant Pathology, Kansas State University, Manhattan, Kansas 66502, USA
- Wheat Genetic Resource Center (WGRC), Kansas State University, Manhattan, Kansas 66502, USA
| | - Dal-Hoe Koo
- Department of Plant Pathology, Kansas State University, Manhattan, Kansas 66502, USA
- Wheat Genetic Resource Center (WGRC), Kansas State University, Manhattan, Kansas 66502, USA
| | | | - Bernd Friebe
- Department of Plant Pathology, Kansas State University, Manhattan, Kansas 66502, USA
- Wheat Genetic Resource Center (WGRC), Kansas State University, Manhattan, Kansas 66502, USA
| | | |
Collapse
|
18
|
Li LF, Zhang ZB, Wang ZH, Li N, Sha Y, Wang XF, Ding N, Li Y, Zhao J, Wu Y, Gong L, Mafessoni F, Levy AA, Liu B. Genome sequences of five Sitopsis species of Aegilops and the origin of polyploid wheat B subgenome. MOLECULAR PLANT 2022; 15:488-503. [PMID: 34979290 DOI: 10.1016/j.molp.2021.12.019] [Citation(s) in RCA: 61] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 12/11/2021] [Accepted: 12/28/2021] [Indexed: 05/23/2023]
Abstract
Common wheat (Triticum aestivum, BBAADD) is a major staple food crop worldwide. The diploid progenitors of the A and D subgenomes have been unequivocally identified; that of B, however, remains ambiguous and controversial but is suspected to be related to species of Aegilops, section Sitopsis. Here, we report the assembly of chromosome-level genome sequences of all five Sitopsis species, namely Aegilops bicornis, Ae. longissima, Ae. searsii, Ae. sharonensis, and Ae. speltoides, as well as the partial assembly of the Amblyopyrum muticum (synonym Aegilops mutica) genome for phylogenetic analysis. Our results reveal that the donor of the common wheat B subgenome is a distinct, and most probably extinct, diploid species that diverged from an ancestral progenitor of the B lineage to which the still extant Ae. speltoides and Am. muticum belong. In addition, we identified interspecific genetic introgressions throughout the evolution of the Triticum/Aegilops species complex. The five Sitopsis species have various assembled genome sizes (4.11-5.89 Gb) with high proportions of repetitive sequences (85.99%-89.81%); nonetheless, they retain high collinearity with other genomes or subgenomes of species in the Triticum/Aegilops complex. Differences in genome size were primarily due to independent post-speciation amplification of transposons. We also identified a set of Sitopsis genes pertinent to important agronomic traits that can be harnessed for wheat breeding. These newly assembled genome resources provide a new roadmap for evolutionary and genetic studies of the Triticum/Aegilops complex, as well as for wheat improvement.
Collapse
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.
| |
Collapse
|
19
|
Grewal S, Coombes B, Joynson R, Hall A, Fellers J, Yang CY, Scholefield D, Ashling S, Isaac P, King IP, King J. Chromosome-specific KASP markers for detecting Amblyopyrum muticum segments in wheat introgression lines. THE PLANT GENOME 2022; 15:e20193. [PMID: 35102721 DOI: 10.1002/tpg2.20193] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 12/20/2021] [Indexed: 05/23/2023]
Abstract
Many wild-relative species are being used in prebreeding programs to increase the genetic diversity of wheat (Triticum aestivum L.). Genotyping tools such as single nucleotide polymorphism (SNP)-based arrays and molecular markers have been widely used to characterize wheat-wild relative introgression lines. However, due to the polyploid nature of the recipient wheat genome, it is difficult to develop SNP-based Kompetitive allele-specific polymerase chain reaction (KASP) markers that are codominant to track the introgressions from the wild species. Previous attempts to develop KASP markers have involved both exome- and polymerase chain reaction (PCR)-amplicon-based sequencing of the wild species. But chromosome-specific KASP assays have been hindered by homoeologous SNPs within the wheat genome. This study involved whole genome sequencing of the diploid wheat wild relative Amblyopyrum muticum (Boiss.) Eig and development of a de novo SNP discovery pipeline that generated ∼38,000 SNPs in unique wheat genome sequences. New assays were designed to increase the density of Am. muticum polymorphic KASP markers. With a goal of one marker per 60 Mbp, 335 new KASP assays were validated as diagnostic for Am. muticum in a wheat background. Together with assays validated in previous studies, 498 well distributed chromosome-specific markers were used to recharacterize previously genotyped wheat-Am. muticum doubled haploid (DH) introgression lines. The chromosome-specific nature of the KASP markers allowed clarification of which wheat chromosomes were involved with recombination events or substituted with Am. muticum chromosomes and the higher density of markers allowed detection of new small introgressions in these DH lines.
Collapse
Affiliation(s)
- Surbhi Grewal
- Nottingham BBSRC Wheat Research Centre, School of Biosciences, Univ. of Nottingham, Loughborough, UK
| | | | - Ryan Joynson
- Earlham Institute, Norwich Research Park, Norwich, UK
- Current address: Limagrain Europe, Clermont-Ferrand, France
| | - Anthony Hall
- Earlham Institute, Norwich Research Park, Norwich, UK
| | - John Fellers
- USDA-ARS, Hard Winter Wheat Genetics Research Unit, Manhattan, KS, USA
| | - Cai-Yun Yang
- Nottingham BBSRC Wheat Research Centre, School of Biosciences, Univ. of Nottingham, Loughborough, UK
| | - Duncan Scholefield
- Nottingham BBSRC Wheat Research Centre, School of Biosciences, Univ. of Nottingham, Loughborough, UK
| | - Stephen Ashling
- Nottingham BBSRC Wheat Research Centre, School of Biosciences, Univ. of Nottingham, Loughborough, UK
| | - Peter Isaac
- iDna Genetics Ltd., Norwich Research Park, Norwich, UK
| | - Ian P King
- Nottingham BBSRC Wheat Research Centre, School of Biosciences, Univ. of Nottingham, Loughborough, UK
| | - Julie King
- Nottingham BBSRC Wheat Research Centre, School of Biosciences, Univ. of Nottingham, Loughborough, UK
| |
Collapse
|
20
|
Improvement and Re-Evolution of Tetraploid Wheat for Global Environmental Challenge and Diversity Consumption Demand. Int J Mol Sci 2022; 23:ijms23042206. [PMID: 35216323 PMCID: PMC8878472 DOI: 10.3390/ijms23042206] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 01/21/2022] [Accepted: 01/24/2022] [Indexed: 02/01/2023] Open
Abstract
Allotetraploid durum wheat is the second most widely cultivated wheat, following hexaploid bread wheat, and is one of the major protein and calorie sources of the human diet. However, durum wheat is encountered with a severe grain yield bottleneck due to the erosion of genetic diversity stemming from long-term domestication and especially modern breeding programs. The improvement of yield and grain quality of durum wheat is crucial when confronted with the increasing global population, changing climate environments, and the non-ignorable increasing incidence of wheat-related disorders. This review summarized the domestication and evolution process and discussed the durum wheat re-evolution attempts performed by global researchers using diploid einkorn, tetraploid emmer wheat, hexaploid wheat (particularly the D-subgenome), etc. In addition, the re-evolution of durum wheat would be promoted by the genetic enrichment process, which could diversify allelic combinations through enhancing chromosome recombination (pentaploid hybridization or pairing of homologous chromosomes gene Ph mutant line induced homoeologous recombination) and environmental adaptability via alien introgressive genes (wide cross or distant hybridization followed by embryo rescue), and modifying target genes or traits by molecular approaches, such as CRISPR/Cas9 or RNA interference (RNAi). A brief discussion of the future perspectives for exploring germplasm for the modern improvement and re-evolution of durum wheat is included.
Collapse
|
21
|
Keilwagen J, Lehnert H, Berner T, Badaeva E, Himmelbach A, Börner A, Kilian B. Detecting major introgressions in wheat and their putative origins using coverage analysis. Sci Rep 2022; 12:1908. [PMID: 35115645 PMCID: PMC8813953 DOI: 10.1038/s41598-022-05865-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 01/12/2022] [Indexed: 12/11/2022] Open
Abstract
Introgressions from crop wild relatives (CWRs) have been used to introduce beneficial traits into cultivated plants. Introgressions have traditionally been detected using cytological methods. Recently, single nucleotide polymorphism (SNP)-based methods have been proposed to detect introgressions in crosses for which both parents are known. However, for unknown material, no method was available to detect introgressions and predict the putative donor species. Here, we present a method to detect introgressions and the putative donor species. We demonstrate the utility of this method using 10 publicly available wheat genome sequences and identify nine major introgressions. We show that the method can distinguish different introgressions at the same locus. We trace introgressions to early wheat cultivars and show that natural introgressions were utilised in early breeding history and still influence elite lines today. Finally, we provide evidence that these introgressions harbour resistance genes.
Collapse
Affiliation(s)
| | | | | | - Ekaterina Badaeva
- N.I. Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia.,The Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), Novosibirsk, Russia
| | - Axel Himmelbach
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Andreas Börner
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | | |
Collapse
|
22
|
Keilwagen J, Lehnert H, Berner T, Badaeva E, Himmelbach A, Börner A, Kilian B. Detecting major introgressions in wheat and their putative origins using coverage analysis. Sci Rep 2022; 12:1908. [PMID: 35115645 DOI: 10.21203/rs.3.rs-910879/v1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 01/12/2022] [Indexed: 05/26/2023] Open
Abstract
Introgressions from crop wild relatives (CWRs) have been used to introduce beneficial traits into cultivated plants. Introgressions have traditionally been detected using cytological methods. Recently, single nucleotide polymorphism (SNP)-based methods have been proposed to detect introgressions in crosses for which both parents are known. However, for unknown material, no method was available to detect introgressions and predict the putative donor species. Here, we present a method to detect introgressions and the putative donor species. We demonstrate the utility of this method using 10 publicly available wheat genome sequences and identify nine major introgressions. We show that the method can distinguish different introgressions at the same locus. We trace introgressions to early wheat cultivars and show that natural introgressions were utilised in early breeding history and still influence elite lines today. Finally, we provide evidence that these introgressions harbour resistance genes.
Collapse
Affiliation(s)
| | | | | | - Ekaterina Badaeva
- N.I. Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
- The Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), Novosibirsk, Russia
| | - Axel Himmelbach
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Andreas Börner
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | | |
Collapse
|
23
|
King J, Grewal S, Othmeni M, Coombes B, Yang CY, Walter N, Ashling S, Scholefield D, Walker J, Hubbart-Edwards S, Hall A, King IP. Introgression of the Triticum timopheevii Genome Into Wheat Detected by Chromosome-Specific Kompetitive Allele Specific PCR Markers. FRONTIERS IN PLANT SCIENCE 2022; 13:919519. [PMID: 35720607 PMCID: PMC9198554 DOI: 10.3389/fpls.2022.919519] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 05/12/2022] [Indexed: 05/08/2023]
Abstract
Triticum timopheevii (2n = 28, A t A t GG) is a tetraploid wild relative species with great potential to increase the genetic diversity of hexaploid wheat Triticum aestivum (2n = 42, AABBDD) for various important agronomic traits. A breeding scheme that propagated advanced backcrossed populations of wheat-T. timopheevii introgression lines through further backcrossing and self-fertilisation resulted in the generation of 99 introgression lines (ILs) that carried 309 homozygous segments from the A t and G subgenomes of T. timopheevii. These introgressions contained 89 and 74 unique segments from the A t and G subgenomes, respectively. These overlapping segments covered 98.9% of the T. timopheevii genome that has now been introgressed into bread wheat cv. Paragon including the entirety of all T. timopheevii chromosomes via varying sized segments except for chromosomes 3A t , 4G, and 6G. Homozygous ILs contained between one and eight of these introgressions with an average of three per introgression line. These homozygous introgressions were detected through the development of a set of 480 chromosome-specific Kompetitive allele specific PCR (KASP) markers that are well-distributed across the wheat genome. Of these, 149 were developed in this study based on single nucleotide polymorphisms (SNPs) discovered through whole genome sequencing of T. timopheevii. A majority of these KASP markers were also found to be T. timopheevii subgenome specific with 182 detecting A t subgenome and 275 detecting G subgenome segments. These markers showed that 98% of the A t segments had recombined with the A genome of wheat and 74% of the G genome segments had recombined with the B genome of wheat with the rest recombining with the D genome of wheat. These results were validated through multi-colour in situ hybridisation analysis. Together these homozygous wheat-T. timopheevii ILs and chromosome-specific KASP markers provide an invaluable resource to wheat breeders for trait discovery to combat biotic and abiotic stress factors affecting wheat production due to climate change.
Collapse
Affiliation(s)
- Julie King
- Nottingham BBSRC Wheat Research Centre, School of Biosciences, University of Nottingham, Loughborough, United Kingdom
- *Correspondence: Julie King,
| | - Surbhi Grewal
- Nottingham BBSRC Wheat Research Centre, School of Biosciences, University of Nottingham, Loughborough, United Kingdom
- Surbhi Grewal,
| | - Manel Othmeni
- Nottingham BBSRC Wheat Research Centre, School of Biosciences, University of Nottingham, Loughborough, United Kingdom
| | | | - Cai-yun Yang
- Nottingham BBSRC Wheat Research Centre, School of Biosciences, University of Nottingham, Loughborough, United Kingdom
| | - Nicola Walter
- Nottingham BBSRC Wheat Research Centre, School of Biosciences, University of Nottingham, Loughborough, United Kingdom
| | - Stephen Ashling
- Nottingham BBSRC Wheat Research Centre, School of Biosciences, University of Nottingham, Loughborough, United Kingdom
| | - Duncan Scholefield
- Nottingham BBSRC Wheat Research Centre, School of Biosciences, University of Nottingham, Loughborough, United Kingdom
| | - Jack Walker
- Nottingham BBSRC Wheat Research Centre, School of Biosciences, University of Nottingham, Loughborough, United Kingdom
| | - Stella Hubbart-Edwards
- Nottingham BBSRC Wheat Research Centre, School of Biosciences, University of Nottingham, Loughborough, United Kingdom
| | | | - Ian Phillip King
- Nottingham BBSRC Wheat Research Centre, School of Biosciences, University of Nottingham, Loughborough, United Kingdom
| |
Collapse
|
24
|
Tian X, Xia X, Xu D, Liu Y, Xie L, Hassan MA, Song J, Li F, Wang D, Zhang Y, Hao Y, Li G, Chu C, He Z, Cao S. Rht24b
, an ancient variation of
TaGA2ox‐A9
, reduces plant height without yield penalty in wheat. NEW PHYTOLOGIST 2022; 233:738-750. [PMID: 0 DOI: 10.1111/nph.17808] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 09/13/2021] [Indexed: 05/22/2023]
Affiliation(s)
- Xiuling Tian
- Institute of Crop Sciences National Wheat Improvement Center Chinese Academy of Agricultural Sciences (CAAS) 12 Zhongguancun South Street Beijing 100081 China
| | - Xianchun Xia
- Institute of Crop Sciences National Wheat Improvement Center Chinese Academy of Agricultural Sciences (CAAS) 12 Zhongguancun South Street Beijing 100081 China
| | - Dengan Xu
- Institute of Crop Sciences National Wheat Improvement Center Chinese Academy of Agricultural Sciences (CAAS) 12 Zhongguancun South Street Beijing 100081 China
| | - Yongqiang Liu
- State Key Laboratory of Plant Genomics Institute of Genetics and Developmental Biology The Innovative Academy for Seed Design Chinese Academy of Sciences 1 West Beichen Road Beijing 100101 China
| | - Li Xie
- Institute of Crop Sciences National Wheat Improvement Center Chinese Academy of Agricultural Sciences (CAAS) 12 Zhongguancun South Street Beijing 100081 China
| | - Muhammad Adeel Hassan
- Institute of Crop Sciences National Wheat Improvement Center Chinese Academy of Agricultural Sciences (CAAS) 12 Zhongguancun South Street Beijing 100081 China
| | - Jie Song
- Institute of Crop Sciences National Wheat Improvement Center Chinese Academy of Agricultural Sciences (CAAS) 12 Zhongguancun South Street Beijing 100081 China
| | - Faji Li
- Crop Research Institute Shandong Academy of Agricultural Sciences 202 Industry North Road Jinan 250100 China
| | - Desen Wang
- Institute of Crop Sciences National Wheat Improvement Center Chinese Academy of Agricultural Sciences (CAAS) 12 Zhongguancun South Street Beijing 100081 China
| | - Yong Zhang
- Institute of Crop Sciences National Wheat Improvement Center Chinese Academy of Agricultural Sciences (CAAS) 12 Zhongguancun South Street Beijing 100081 China
| | - Yuanfeng Hao
- Institute of Crop Sciences National Wheat Improvement Center Chinese Academy of Agricultural Sciences (CAAS) 12 Zhongguancun South Street Beijing 100081 China
| | - Genying Li
- Crop Research Institute Shandong Academy of Agricultural Sciences 202 Industry North Road Jinan 250100 China
| | - Chengcai Chu
- State Key Laboratory of Plant Genomics Institute of Genetics and Developmental Biology The Innovative Academy for Seed Design Chinese Academy of Sciences 1 West Beichen Road Beijing 100101 China
| | - Zhonghu He
- Institute of Crop Sciences National Wheat Improvement Center Chinese Academy of Agricultural Sciences (CAAS) 12 Zhongguancun South Street Beijing 100081 China
- International Maize and Wheat Improvement Center (CIMMYT) China Office c/o CAAS 12 Zhongguancun South Street Beijing 100081 China
| | - Shuanghe Cao
- Institute of Crop Sciences National Wheat Improvement Center Chinese Academy of Agricultural Sciences (CAAS) 12 Zhongguancun South Street Beijing 100081 China
| |
Collapse
|
25
|
Zhao X, Fu X, Yin C, Lu F. Wheat speciation and adaptation: perspectives from reticulate evolution. ABIOTECH 2021; 2:386-402. [PMID: 36311810 PMCID: PMC9590565 DOI: 10.1007/s42994-021-00047-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 04/27/2021] [Indexed: 12/16/2022]
Abstract
Reticulate evolution through the interchanging of genetic components across organisms can impact significantly on the fitness and adaptation of species. Bread wheat (Triticum aestivum subsp. aestivum) is one of the most important crops in the world. Allopolyploid speciation, frequent hybridization, extensive introgression, and occasional horizontal gene transfer (HGT) have been shaping a typical paradigm of reticulate evolution in bread wheat and its wild relatives, which is likely to have a substantial influence on phenotypic traits and environmental adaptability of bread wheat. In this review, we outlined the evolutionary history of bread wheat and its wild relatives with a highlight on the interspecific hybridization events, demonstrating the reticulate relationship between species/subspecies in the genera Triticum and Aegilops. Furthermore, we discussed the genetic mechanisms and evolutionary significance underlying the introgression of bread wheat and its wild relatives. An in-depth understanding of the evolutionary process of Triticum species should be beneficial to future genetic study and breeding of bread wheat.
Collapse
Affiliation(s)
- Xuebo Zhao
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiangdong Fu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Changbin Yin
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Fei Lu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| |
Collapse
|
26
|
Zhang Y, Li Z, Zhang Y, Lin K, Peng Y, Ye L, Zhuang Y, Wang M, Xie Y, Guo J, Teng W, Tong Y, Zhang W, Xue Y, Lang Z, Zhang Y. Evolutionary rewiring of the wheat transcriptional regulatory network by lineage-specific transposable elements. Genome Res 2021; 31:2276-2289. [PMID: 34503979 PMCID: PMC8647832 DOI: 10.1101/gr.275658.121] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 09/01/2021] [Indexed: 01/03/2023]
Abstract
More than 80% of the wheat genome consists of transposable elements (TEs), which act as major drivers of wheat genome evolution. However, their contributions to the regulatory evolution of wheat adaptations remain largely unclear. Here, we created genome-binding maps for 53 transcription factors (TFs) underlying environmental responses by leveraging DAP-seq in Triticum urartu, together with epigenomic profiles. Most TF binding sites (TFBSs) located distally from genes are embedded in TEs, whose functional relevance is supported by purifying selection and active epigenomic features. About 24% of the non-TE TFBSs share significantly high sequence similarity with TE-embedded TFBSs. These non-TE TFBSs have almost no homologous sequences in non-Triticeae species and are potentially derived from Triticeae-specific TEs. The expansion of TE-derived TFBS linked to wheat-specific gene responses, suggesting TEs are an important driving force for regulatory innovations. Altogether, TEs have been significantly and continuously shaping regulatory networks related to wheat genome evolution and adaptation.
Collapse
Affiliation(s)
- Yuyun Zhang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Zijuan Li
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Yu'e Zhang
- University of the Chinese Academy of Sciences, Beijing, 100049, China
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, the Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Kande Lin
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Collaborative Innovation Center for Modern Crop Production co-sponsored by Province and Ministry (CIC-MCP), Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Yuan Peng
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
- Shanghai Center for Plant Stress Biology, National Key Laboratory of Plant Molecular Genetics, Center of Excellence in Molecular Plant Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Luhuan Ye
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Yili Zhuang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Meiyue Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Yilin Xie
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Jingyu Guo
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- Henan University, School of Life Science, Kaifeng, Henan 457000, China
| | - Wan Teng
- University of the Chinese Academy of Sciences, Beijing, 100049, China
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, the Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Yiping Tong
- University of the Chinese Academy of Sciences, Beijing, 100049, China
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, the Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Wenli Zhang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Collaborative Innovation Center for Modern Crop Production co-sponsored by Province and Ministry (CIC-MCP), Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Yongbiao Xue
- University of the Chinese Academy of Sciences, Beijing, 100049, China
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, the Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
- Beijing Institute of Genomics, Chinese Academy of Sciences, and National Centre for Bioinformation, Beijing 100101 China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Zhaobo Lang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
- Shanghai Center for Plant Stress Biology, National Key Laboratory of Plant Molecular Genetics, Center of Excellence in Molecular Plant Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Yijing Zhang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
| |
Collapse
|
27
|
Palma-Guerrero J, Chancellor T, Spong J, Canning G, Hammond J, McMillan VE, Hammond-Kosack KE. Take-All Disease: New Insights into an Important Wheat Root Pathogen. TRENDS IN PLANT SCIENCE 2021; 26:836-848. [PMID: 33752966 DOI: 10.1016/j.tplants.2021.02.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 01/27/2021] [Accepted: 02/18/2021] [Indexed: 06/12/2023]
Abstract
Take-all disease, caused by the fungal root pathogen Gaeumannomyces tritici, is considered to be the most important root disease of wheat worldwide. Here we review the advances in take-all research over the last 15 years, focusing on the identification of new sources of genetic resistance in wheat relatives and the role of the microbiome in disease development. We also highlight recent breakthroughs in the molecular interactions between G. tritici and wheat, including genome and transcriptome analyses. These new findings will aid the development of novel control strategies against take-all disease. In light of this growing understanding, the G. tritici-wheat interaction could provide a model study system for root-infecting fungal pathogens of cereals.
Collapse
Affiliation(s)
- Javier Palma-Guerrero
- Department of Biointeractions and Crop Protection, Rothamsted Research, Harpenden, UK.
| | - Tania Chancellor
- Department of Biointeractions and Crop Protection, Rothamsted Research, Harpenden, UK
| | - Jess Spong
- Department of Biointeractions and Crop Protection, Rothamsted Research, Harpenden, UK
| | - Gail Canning
- Department of Biointeractions and Crop Protection, Rothamsted Research, Harpenden, UK
| | - Jess Hammond
- Department of Biointeractions and Crop Protection, Rothamsted Research, Harpenden, UK
| | - Vanessa E McMillan
- Department of Biointeractions and Crop Protection, Rothamsted Research, Harpenden, UK
| | - Kim E Hammond-Kosack
- Department of Biointeractions and Crop Protection, Rothamsted Research, Harpenden, UK.
| |
Collapse
|
28
|
Taranto F, Mangini G, Miazzi MM, Stevanato P, De Vita P. Polyphenol oxidase genes as integral part of the evolutionary history of domesticated tetraploid wheat. Genomics 2021; 113:2989-3001. [PMID: 34182080 DOI: 10.1016/j.ygeno.2021.06.030] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 04/14/2021] [Accepted: 06/23/2021] [Indexed: 01/05/2023]
Abstract
Studying and understanding the genetic basis of polyphenol oxidases (PPO)-related traits plays a crucial role in genetic improvement of crops. A tetraploid wheat collection (T. turgidum ssp., TWC) was analyzed using the 90K wheat SNP iSelect assay and phenotyped for PPO activity. A total of 21,347 polymorphic SNPs were used to perform genome-wide association analysis (GWA) in TWC and durum wheat sub-groups, detecting 23 and 85 marker-trait associations (MTA). In addition, candidate genes responsible for PPO activity were predicted. Based on the 23 MTAs detected in TWC, two haplotypes associated with low and high PPO activity were identified. Four SNPs were developed and validated providing one reliable marker (IWB75732) for marker assisted selection. The 23 MTAs were used to evaluate the genetic divergence (FST > 0.25) between the T. turgidum subspecies, providing new information important for understanding the domestication process of Triticum turgidum ssp. and in particular of ssp. carthlicum.
Collapse
Affiliation(s)
- Francesca Taranto
- National Research Council (CNR), Institute of Biosciences and Bioresources (CNR-IBBR), 80055 Portici, NA, Italy.
| | - Giacomo Mangini
- National Research Council (CNR), Institute of Biosciences and Bioresources (CNR-IBBR), 70126 Bari, BA, Italy.
| | - Monica Marilena Miazzi
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, 70126 Bari, Italy
| | | | - Pasquale De Vita
- Council for Agricultural Research and Economics (CREA), Research Centre for Cereal and Industrial Crops (CREA-CI), 71122 Foggia, Italy
| |
Collapse
|
29
|
Wang FH, Qiao K, Shen YH, Wang H, Chai TY. Characterization of the gene family encoding metal tolerance proteins in Triticum urartu: Phylogenetic, transcriptional, and functional analyses. Metallomics 2021; 13:6308381. [PMID: 34160615 DOI: 10.1093/mtomcs/mfab038] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 06/11/2021] [Accepted: 06/13/2021] [Indexed: 12/22/2022]
Abstract
Homeostasis of microelements in organisms is vital for normal metabolism. In plants, the cation diffusion facilitator (CDF) protein family, also known as metal tolerance proteins (MTPs), play critical roles in maintaining trace metal homeostasis. However, little is known about these proteins in wheat. In this study, we characterized the MTP family of Triticum urartu, the donor of 'A' genome of Triticum aestivum, and analysed their phylogenetic relationships, sequence signatures, spatial expression patterns in the diploid wheat, and their transport activity when heterologously expressed. Nine MTPs were identified in the T. urartu genome database, and were classified and designated based on their sequence similarity to Arabidopsis thaliana (Arabidopsis) and Oryza sativa MTPs. Phylogenetic and sequence analyses indicated that the triticum urartu metal tolerance protein (TuMTP)s comprise three Zn-CDFs, two Fe/Zn-CDFs, and four Mn-CDFs; and can be further classified into six subgroups. Among the TuMTPs, there are no MTP2-5 and MTP9-10 counterparts but two MTP1/8/11 orthologs in relation to AtMTPs. It was also shown that members of the same cluster share similar sequence characteristic, i.e. number of introns, predicted transmembrane domains, and motifs. When expressed in yeast, TuMTP1 and TuMTP1.1 conferred tolerance to Zn and Co but not to other metal ions; while TuMTP8, TuMTP8.1, TuMTP11, and TuMTP11.1 conferred tolerance to Mn. When expressed in Arabidopsis, TuMTP1 localized to the tonoplast and significantly enhanced Zn and Co tolerance. TuMTPs showed diverse tissue-specific expression patterns. Taken together, the closely clustered TuMTPs share structural features and metal specificity but play diverse roles in the homeostasis of microelements in plant cells.
Collapse
Affiliation(s)
- Fan-Hong Wang
- College of Life Sciences, Northwest Normal University, Lanzhou, 730070, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Kun Qiao
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030, China
| | - Yong-Hua Shen
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hong Wang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Tuan-Yao Chai
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- The Innovative Academy of Seed Design, Chinese Academy of Science, Beijing, 100049, China
| |
Collapse
|
30
|
Özbek Ö, Zencirci N. Characterization of Genetic Diversity in Cultivated Einkorn Wheat (Triticum monococcum L. ssp. monococcum) Landrace Populations from Turkey as Revealed by ISSR. RUSS J GENET+ 2021. [DOI: 10.1134/s1022795421060089] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
31
|
Nave M, Taş M, Raupp J, Tiwari VK, Ozkan H, Poland J, Hale I, Komatsuda T, Distelfeld A. The Independent Domestication of Timopheev's Wheat: Insights from Haplotype Analysis of the Brittle rachis 1 ( BTR1-A) Gene. Genes (Basel) 2021; 12:genes12030338. [PMID: 33668927 PMCID: PMC7996576 DOI: 10.3390/genes12030338] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 02/11/2021] [Accepted: 02/19/2021] [Indexed: 01/19/2023] Open
Abstract
Triticum turgidum and T. timopheevii are two tetraploid wheat species sharing T. urartu as a common ancestor, and domesticated accessions from both of these allopolyploids exhibit nonbrittle rachis (i.e., nonshattering spikes). We previously described the loss-of-function mutations in the Brittle Rachis 1 genes BTR1-A and BTR1-B in the A and B subgenomes, respectively, that are responsible for this most visible domestication trait in T. turgidum. Resequencing of a large panel of wild and domesticated T. turgidum accessions subsequently led to the identification of the two progenitor haplotypes of the btr1-A and btr1-B domesticated alleles. Here, we extended the haplotype analysis to other T. turgidum subspecies and to the BTR1 homologues in the related T. timopheevii species. Our results showed that all the domesticated wheat subspecies within T. turgidum share common BTR1-A and BTR1-B haplotypes, confirming their common origin. In T. timopheevii, however, we identified a novel loss-of-function btr1-A allele underlying a partially brittle spike phenotype. This novel recessive allele appeared fixed within the pool of domesticated Timopheev’s wheat but was also carried by one wild timopheevii accession exhibiting partial brittleness. The promoter region for BTR1-B could not be amplified in any T. timopheevii accessions with any T. turgidum primer combination, exemplifying the gene-level distance between the two species. Altogether, our results support the concept of independent domestication processes for the two polyploid, wheat-related species.
Collapse
Affiliation(s)
- Moran Nave
- Department of Evolutionary and Environmental Biology, Faculty of Natural Sciences and the Institute of Evolution, University of Haifa, Haifa 3498838, Israel;
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Mihriban Taş
- Department of Field Crops, Faculty of Agriculture, Cukurova University, Adana 01250, Turkey; (M.T.); (H.O.)
| | - John Raupp
- Wheat Genetics Resource Center, Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, USA; (J.R.); (J.P.)
| | - Vijay K. Tiwari
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD 20742, USA;
| | - Hakan Ozkan
- Department of Field Crops, Faculty of Agriculture, Cukurova University, Adana 01250, Turkey; (M.T.); (H.O.)
| | - Jesse Poland
- Wheat Genetics Resource Center, Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, USA; (J.R.); (J.P.)
| | - Iago Hale
- Department of Agriculture, Nutrition, and Food Systems, University of New Hampshire, Durham, NH 03824, USA;
| | - Takao Komatsuda
- National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8518, Japan;
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), Tsukuba 305-8518, Japan
| | - Assaf Distelfeld
- Department of Evolutionary and Environmental Biology, Faculty of Natural Sciences and the Institute of Evolution, University of Haifa, Haifa 3498838, Israel;
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv 6997801, Israel
- Correspondence: ; Tel.: +972-(0)4-8288328
| |
Collapse
|
32
|
Zhang W, Zhao J, He J, Kang L, Wang X, Zhang F, Hao C, Ma X, Chen D. Functional gene assessment of bread wheat: breeding implications in Ningxia Province. BMC PLANT BIOLOGY 2021; 21:103. [PMID: 33602134 PMCID: PMC7893757 DOI: 10.1186/s12870-021-02870-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 02/01/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND The overall genetic distribution and divergence of cloned genes among bread wheat varieties that have occurred during the breeding process over the past few decades in Ningxia Province, China, are poorly understood. Here, we report the genetic diversities of 44 important genes related to grain yield, quality, adaptation and resistance in 121 Ningxia and 86 introduced wheat cultivars and advanced lines. RESULTS The population structure indicated characteristics of genetic components of Ningxia wheat, including landraces of particular genetic resources, introduced varieties with rich genetic diversities and modern cultivars in different periods. Analysis of allele frequencies showed that the dwarfing alleles Rht-B1b at Rht-B1 and Rht-D1b at Rht-D1, 1BL/1RS translocation, Hap-1 at GW2-6B and Hap-H at Sus2-2B are very frequently present in modern Ningxia cultivars and in introduced varieties from other regions but absent in landraces. This indicates that the introduced wheat germplasm with numerous beneficial genes is vital for broadening the genetic diversity of Ningxia wheat varieties. Large population differentiation between modern cultivars and landraces has occurred in adaptation genes. Founder parents carry excellent allele combinations of important genes, with a higher number of favorable alleles than modern cultivars. Gene flow analysis showed that six founder parents have greatly contributed to breeding improvement in Ningxia Province, particularly Zhou 8425B, for yield-related genes. CONCLUSIONS Varieties introduced from other regions with rich genetic diversity and landraces with well-adapted genetic resources have been applied to improve modern cultivars. Founder parents, particularly Zhou 8425B, for yield-related genes have contributed greatly to wheat breeding improvement in Ningxia Province. These findings will greatly benefit bread wheat breeding in Ningxia Province as well as other areas with similar ecological environments.
Collapse
Affiliation(s)
- Weijun Zhang
- Crop Research Institute, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, 750002 Ningxia China
| | - Junjie Zhao
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 Henan China
| | - Jinshang He
- Crop Research Institute, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, 750002 Ningxia China
| | - Ling Kang
- Crop Research Institute, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, 750002 Ningxia China
| | - Xiaoliang Wang
- Crop Research Institute, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, 750002 Ningxia China
| | - Fuguo Zhang
- Crop Research Institute, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, 750002 Ningxia China
| | - Chenyang Hao
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs/The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Xiongfeng Ma
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 Henan China
| | - Dongsheng Chen
- Crop Research Institute, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, 750002 Ningxia China
| |
Collapse
|
33
|
Grewal S, Guwela V, Newell C, Yang CY, Ashling S, Scholefield D, Hubbart-Edwards S, Burridge A, Stride A, King IP, King J. Generation of Doubled Haploid Wheat- Triticum urartu Introgression Lines and Their Characterisation Using Chromosome-Specific KASP Markers. FRONTIERS IN PLANT SCIENCE 2021; 12:643636. [PMID: 34054892 PMCID: PMC8155260 DOI: 10.3389/fpls.2021.643636] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 04/19/2021] [Indexed: 05/07/2023]
Abstract
Wheat is one of the most important food and protein sources in the world and although, in recent years wheat breeders have achieved yield gains, they are not sufficient to meet the demands of an ever-growing population. Development of high yielding wheat varieties, resilient to abiotic and biotic stress resulting from climate change, has been limited by wheat's narrow genetic base. In contrast to wheat, the wild relatives of wheat provide a vast reservoir of genetic variation for most, if not all, agronomic traits. Previous studies by the authors have shown the transfer of genetic variation from T. urartu into bread wheat. However, before the introgression lines can be exploited for trait analysis, they are required to have stable transmission of the introgressions to the next generation. In this work, we describe the generation of 86 doubled haploid (DH) wheat-T. urartu introgression lines that carry homozygous introgressions which are stably inherited. The DH lines were characterised using the Axiom® Wheat Relative Genotyping Array and 151 KASP markers to identify 65 unique T. urartu introgressions in a bread wheat background. DH production has helped accelerate the breeding process and facilitated the early release of homozygous wheat-T. urartu introgression lines. Together with the KASP markers, this valuable resource could greatly advance identification of beneficial alleles that can be used in wheat improvement.
Collapse
Affiliation(s)
- Surbhi Grewal
- Nottingham BBSRC Wheat Research Centre, School of Biosciences, University of Nottingham, Loughborough, United Kingdom
| | - Veronica Guwela
- Nottingham BBSRC Wheat Research Centre, School of Biosciences, University of Nottingham, Loughborough, United Kingdom
| | - Claire Newell
- Limagrain UK Limited, Bury St Edmunds, United Kingdom
| | - Cai-yun Yang
- Nottingham BBSRC Wheat Research Centre, School of Biosciences, University of Nottingham, Loughborough, United Kingdom
| | - Stephen Ashling
- Nottingham BBSRC Wheat Research Centre, School of Biosciences, University of Nottingham, Loughborough, United Kingdom
| | - Duncan Scholefield
- Nottingham BBSRC Wheat Research Centre, School of Biosciences, University of Nottingham, Loughborough, United Kingdom
| | - Stella Hubbart-Edwards
- Nottingham BBSRC Wheat Research Centre, School of Biosciences, University of Nottingham, Loughborough, United Kingdom
| | - Amanda Burridge
- School of Biological Sciences, University of Bristol, United Kingdom
| | - Alex Stride
- Limagrain UK Limited, Bury St Edmunds, United Kingdom
| | - Ian P. King
- Nottingham BBSRC Wheat Research Centre, School of Biosciences, University of Nottingham, Loughborough, United Kingdom
| | - Julie King
- Nottingham BBSRC Wheat Research Centre, School of Biosciences, University of Nottingham, Loughborough, United Kingdom
- *Correspondence: Julie King,
| |
Collapse
|
34
|
Yildiz A, Hajyzadeh M, Ozbek K, Nadeem MA, Hunter D. Molecular characterisation of the oldest domesticated Turkish einkorn wheat landraces with simple sequence repeat (SSR) markers. BIOTECHNOL BIOTEC EQ 2021. [DOI: 10.1080/13102818.2021.1970023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Affiliation(s)
- Ayse Yildiz
- The National Botanical Garden of Turkey, Rebublic of Turkey Ministry of Agriculture and Forestry, Üniversiteler Mah. Dumlupınar Boulevard, Ankara, Turkey
| | - Mortaza Hajyzadeh
- Department of Field Crops, Faculty of Agriculture, Şirnak University, Şirnak, Turkey
| | - Kursad Ozbek
- The National Botanical Garden of Turkey, Rebublic of Turkey Ministry of Agriculture and Forestry, Üniversiteler Mah. Dumlupınar Boulevard, Ankara, Turkey
| | - Muhammad Azhar Nadeem
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Turkey
| | - Danny Hunter
- Alliance of Bioversity International and CIAT, Via di San Domenico, Rome, Italy
| |
Collapse
|
35
|
Raffan S, Halford NG. Cereal asparagine synthetase genes. THE ANNALS OF APPLIED BIOLOGY 2021; 178:6-22. [PMID: 33518769 PMCID: PMC7818274 DOI: 10.1111/aab.12632] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 07/14/2020] [Accepted: 07/14/2020] [Indexed: 05/12/2023]
Abstract
Asparagine synthetase catalyses the transfer of an amino group from glutamine to aspartate to form glutamate and asparagine. The accumulation of free (nonprotein) asparagine in crops has implications for food safety because free asparagine is the precursor for acrylamide, a carcinogenic contaminant that forms during high-temperature cooking and processing. Here we review publicly available genome data for asparagine synthetase genes from species of the Pooideae subfamily, including bread wheat and related wheat species (Triticum and Aegilops spp.), barley (Hordeum vulgare) and rye (Secale cereale) of the Triticeae tribe. Also from the Pooideae subfamily: brachypodium (Brachypodium dIstachyon) of the Brachypodiae tribe. More diverse species are also included, comprising sorghum (Sorghum bicolor) and maize (Zea mays) of the Panicoideae subfamily and rice (Oryza sativa) of the Ehrhartoideae subfamily. The asparagine synthetase gene families of the Triticeae species each comprise five genes per genome, with the genes assigned to four groups: 1, 2, 3 (subdivided into 3.1 and 3.2) and 4. Each species has a single gene per genome in each group, except that some bread wheat varieties (genomes AABBDD) and emmer wheat (Triticum dicoccoides; genomes AABB) lack a group 2 gene in the B genome. This raises questions about the ancestry of cultivated pasta wheat and the B genome donor of bread wheat, suggesting that the hybridisation event that gave rise to hexaploid bread wheat occurred more than once. In phylogenetic analyses, genes from the other species cluster with the Triticeae genes, but brachypodium, sorghum and maize lack a group 2 gene, while rice has only two genes, one group 3 and one group 4. This means that TaASN2, the most highly expressed asparagine synthetase gene in wheat grain, has no equivalent in maize, rice, sorghum or brachypodium. An evolutionary pathway is proposed in which a series of gene duplications gave rise to the five genes found in modern Triticeae species.
Collapse
Affiliation(s)
- Sarah Raffan
- Plant Sciences DepartmentRothamsted ResearchHarpendenUK
| | | |
Collapse
|
36
|
Domestication affects the composition, diversity, and co-occurrence of the cereal seed microbiota. J Adv Res 2020; 31:75-86. [PMID: 34194833 PMCID: PMC8240117 DOI: 10.1016/j.jare.2020.12.008] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Accepted: 12/14/2020] [Indexed: 12/15/2022] Open
Abstract
Introduction The seed-associated microbiome has a strong influence on plant ecology, fitness, and productivity. Plant microbiota could be exploited for a more responsible crop management in sustainable agriculture. However, the relationships between seed microbiota and hosts related to the changes from ancestor species to breeded crops still remain poor understood. Objectives Our aims were i) to understand the effect of cereal domestication on seed endophytes in terms of diversity, structure and co-occurrence, by comparing four cereal crops and the respective ancestor species; ii) to test the phylogenetic coherence between cereals and their seed microbiota (clue of co-evolution). Methods We investigated the seed microbiota of four cereal crops (Triticum aestivum, Triticum monococcum, Triticum durum, and Hordeum vulgare), along with their respective ancestors (Aegilops tauschii, Triticum baeoticum, Triticum dicoccoides, and Hordeum spontaneum, respectively) using 16S rRNA gene metabarcoding, Randomly Amplified Polymorphic DNA (RAPD) profiling of host plants and co-evolution analysis. Results The diversity of seed microbiota was generally higher in cultivated cereals than in wild ancestors, suggesting that domestication lead to a bacterial diversification. On the other hand, more microbe-microbe interactions were detected in wild species, indicating a better-structured, mature community. Typical human-associated taxa, such as Cutibacterium, dominated in cultivated cereals, suggesting an interkingdom transfers of microbes from human to plants during domestication. Co-evolution analysis revealed a significant phylogenetic congruence between seed endophytes and host plants, indicating clues of co-evolution between hosts and seed-associated microbes during domestication. Conclusion This study demonstrates a diversification of the seed microbiome as a consequence of domestication, and provides clues of co-evolution between cereals and their seed microbiota. This knowledge is useful to develop effective strategies of microbiome exploitation for sustainable agriculture.
Collapse
|
37
|
Production of synthetic wheat lines to exploit the genetic diversity of emmer wheat and D genome containing Aegilops species in wheat breeding. Sci Rep 2020; 10:19698. [PMID: 33184344 PMCID: PMC7661528 DOI: 10.1038/s41598-020-76475-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 10/27/2020] [Indexed: 12/12/2022] Open
Abstract
Due to the accumulation of various useful traits over evolutionary time, emmer wheat (Triticum turgidum subsp. dicoccum and dicoccoides, 2n = 4x = 28; AABB), durum wheat (T. turgidum subsp. durum, 2n = 4x = 28; AABB), T. timopheevii (2n = 4x = 28; AAGG) and D genome containing Aegilops species offer excellent sources of novel variation for the improvement of bread wheat (T. aestivum L., AABBDD). Here, we made 192 different cross combinations between diverse genotypes of wheat and Aegilops species including emmer wheat × Ae. tauschii (2n = DD or DDDD), durum wheat × Ae. tauschii, T. timopheevii × Ae. tauschii, Ae. crassa × durum wheat, Ae. cylindrica × durum wheat and Ae. ventricosa × durum wheat in the field over three successive years. We successfully recovered 56 different synthetic hexaploid and octaploid F2 lines with AABBDD, AABBDDDD, AAGGDD, D1D1XcrXcrAABB, DcDcCcCcAABB and DvDvNvNvAABB genomes via in vitro rescue of F1 embryos and spontaneous production of F2 seeds on the Fl plants. Cytogenetic analysis of F2 lines showed that the produced synthetic wheat lines were generally promising stable amphiploids. Contribution of D genome bearing Aegilops and the less-investigated emmer wheat genotypes as parents in the crosses resulted in synthetic amphiploids which are a valuable resource for bread wheat breeding.
Collapse
|
38
|
Jiang Y, Yuan Z, Hu H, Ye X, Zheng Z, Wei Y, Zheng YL, Wang YG, Liu C. Differentiating homoploid hybridization from ancestral subdivision in evaluating the origin of the D lineage in wheat. THE NEW PHYTOLOGIST 2020; 228:409-414. [PMID: 32255512 DOI: 10.1111/nph.16578] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2019] [Accepted: 03/19/2020] [Indexed: 06/11/2023]
Affiliation(s)
- Yunfeng Jiang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China
- CSIRO Agriculture and Food, St Lucia, Qld, 4067, Australia
| | - Zhongwei Yuan
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China
- CSIRO Agriculture and Food, St Lucia, Qld, 4067, Australia
| | - Haiyan Hu
- CSIRO Agriculture and Food, St Lucia, Qld, 4067, Australia
- College of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang, Henan, 453003, China
| | - Xueling Ye
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China
- CSIRO Agriculture and Food, St Lucia, Qld, 4067, Australia
| | - Zhi Zheng
- CSIRO Agriculture and Food, St Lucia, Qld, 4067, Australia
| | - Yuming Wei
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China
| | - You-Liang Zheng
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China
| | - You-Gan Wang
- Science and Engineering Facility, Queensland University of Technology, Brisbane, Qld, 4000, Australia
| | - Chunji Liu
- CSIRO Agriculture and Food, St Lucia, Qld, 4067, Australia
| |
Collapse
|
39
|
Fang T, Lei L, Li G, Powers C, Hunger RM, Carver BF, Yan L. Development and deployment of KASP markers for multiple alleles of Lr34 in wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:2183-2195. [PMID: 32281004 PMCID: PMC7311377 DOI: 10.1007/s00122-020-03589-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 03/31/2020] [Indexed: 05/03/2023]
Abstract
Heterogeneous Lr34 genes for leaf rust in winter wheat cultivar 'Duster' and KASP markers for allelic variation in exon 11 and exon 22 of Lr34. Wheat, Triticum aestivum (2n = 6x = 42, AABBDD), is a hexaploid species, and each of three homoeologous genomes A, B, and D should have one copy for a gene in its ancestral form if the gene has no duplication. Previously reported leaf rust resistance gene Lr34 has one copy on the short arm of chromosome 7D in hexaploid wheat, and allelic variation in Lr34 is in intron 4, exon 11, exon 12, or exon 22. In this study, we discovered that Oklahoma hard red winter wheat cultivar 'Duster' (PI 644,016) has two copies of the Lr34 gene, the resistance allele Lr34a and the susceptibility allele Lr34b. Both Lr34a and Lr34b were mapped in the same linkage group on chromosome 7D in a doubled-haploid population generated from a cross between Duster and a winter wheat cultivar 'Billings' which carries the susceptibility allele Lr34c. A chromosomal fragment including Lr34 and at least two neighboring genes on its proximal side but excluding genes on its distal side was duplicated in Duster. The Duster Lr34ab allele was associated with tip necrosis and increased resistance against leaf rust at adult plants in the Duster × Billings DH population tested in the field, demonstrating the function of the Duster Lr34ab allele in wheat. We have developed KASP markers for allelic variation in exon 11 and exon 22 of Lr34 in wheat. These markers can be utilized to accelerate the selection of Lr34 in wheat.
Collapse
Affiliation(s)
- Tilin Fang
- Department of Plant and Soil Sciences Department, Oklahoma State University, 368 AG Hall, Stillwater, OK, 74078, USA
| | - Lei Lei
- Department of Plant and Soil Sciences Department, Oklahoma State University, 368 AG Hall, Stillwater, OK, 74078, USA
| | - Genqiao Li
- Department of Plant and Soil Sciences Department, Oklahoma State University, 368 AG Hall, Stillwater, OK, 74078, USA
| | - Carol Powers
- Department of Plant and Soil Sciences Department, Oklahoma State University, 368 AG Hall, Stillwater, OK, 74078, USA
| | - Robert M Hunger
- Entomology and Plant Pathology Department, Oklahoma State University, Stillwater, OK, 74078, USA
| | - Brett F Carver
- Department of Plant and Soil Sciences Department, Oklahoma State University, 368 AG Hall, Stillwater, OK, 74078, USA
| | - Liuling Yan
- Department of Plant and Soil Sciences Department, Oklahoma State University, 368 AG Hall, Stillwater, OK, 74078, USA.
| |
Collapse
|
40
|
Genome-Wide Discovery of G-Quadruplexes in Wheat: Distribution and Putative Functional Roles. G3-GENES GENOMES GENETICS 2020; 10:2021-2032. [PMID: 32295768 PMCID: PMC7263691 DOI: 10.1534/g3.120.401288] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
G-quadruplexes are nucleic acid secondary structures formed by a stack of square planar G-quartets. G-quadruplexes were implicated in many biological functions including telomere maintenance, replication, transcription, and translation, in many species including humans and plants. For wheat, however, though it is one of the world's most important staple food, no G-quadruplex studies have been reported to date. Here, we computationally identify putative G4 structures (G4s) in wheat genome for the first time and compare its distribution across the genome against five other genomes (human, maize, Arabidopsis, rice, and sorghum). We identified close to 1 million G4 motifs with a density of 76 G4s/Mb across the whole genome and 93 G4s/Mb over genic regions. Remarkably, G4s were enriched around three regions, two located on the antisense and one on the sense strand at the following positions: 1) the transcription start site (TSS) (antisense), 2) the first coding domain sequence (CDS) (antisense), and 3) the start codon (sense). Functional enrichment analysis revealed that the gene models containing G4 motifs within these peaks were associated with specific gene ontology (GO) terms, such as developmental process, localization, and cellular component organization or biogenesis. We investigated genes encoding MADS-box transcription factors and showed examples of G4 motifs within critical regulatory regions in the VRN-1 genes in wheat. Furthermore, comparison with other plants showed that monocots share a similar distribution of G4s, but Arabidopsis shows a unique G4 distribution. Our study shows for the first time the prevalence and possible functional roles of G4s in wheat.
Collapse
|
41
|
Bariah I, Keidar-Friedman D, Kashkush K. Identification and characterization of large-scale genomic rearrangements during wheat evolution. PLoS One 2020; 15:e0231323. [PMID: 32287287 PMCID: PMC7156093 DOI: 10.1371/journal.pone.0231323] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 03/20/2020] [Indexed: 12/25/2022] Open
Abstract
Following allopolyploidization, nascent polyploid wheat species react with massive genomic rearrangements, including deletion of transposable element-containing sequences. While such massive rearrangements are considered to be a prominent process in wheat genome evolution and speciation, their structure, extent, and underlying mechanisms remain poorly understood. In this study, we retrieved ~3500 insertions of a specific variant of Fatima, one of the most dynamic gypsy long-terminal repeat retrotransposons in wheat from the recently available high-quality genome drafts of Triticum aestivum (bread wheat) and Triticum turgidum ssp. dicoccoides or wild emmer, the allotetraploid mother of all modern wheats. The dynamic nature of Fatima facilitated the identification of large (i.e., up to ~ 1 million bases) Fatima-containing insertions/deletions (indels) upon comparison of bread wheat and wild emmer genomes. We characterized 11 such indels using computer-assisted analysis followed by PCR validation, and found that they might have occurred via unequal intra-strand recombination or double-strand break (DSB) events. Additionally, we observed one case of introgression of novel DNA fragments from an unknown source into the wheat genome. Our data thus indicate that massive large-scale DNA rearrangements might play a prominent role in wheat speciation.
Collapse
Affiliation(s)
- Inbar Bariah
- Department of Life Sciences, Ben-Gurion University, Beer-Sheva, Israel
| | | | - Khalil Kashkush
- Department of Life Sciences, Ben-Gurion University, Beer-Sheva, Israel
- * E-mail:
| |
Collapse
|
42
|
Zhang M, Zhang W, Zhu X, Sun Q, Chao S, Yan C, Xu SS, Fiedler J, Cai X. Partitioning and physical mapping of wheat chromosome 3B and its homoeologue 3E in Thinopyrum elongatum by inducing homoeologous recombination. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:1277-1289. [PMID: 31970450 DOI: 10.1007/s00122-020-03547-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 01/14/2020] [Indexed: 06/10/2023]
Abstract
We performed homoeologous recombination-based partitioning and physical mapping of wheat chromosome 3B and Th. elongatum chromosome 3E, providing a unique physical framework of this homoeologous pair for genome studies. The wheat (Triticum aestivum, 2n = 6x = 42, AABBDD) and Thinopyrum elongatum (2n = 2x = 14, EE) genomes can be differentiated from each other by fluorescent genomic in situ hybridization (FGISH) as well as molecular markers. This has facilitated homoeologous recombination-based partitioning and engineering of their genomes for physical mapping and alien introgression. Here, we constructed a special wheat genotype, which was double monosomic for wheat chromosome 3B and Th. elongatum chromosome 3E and homozygous for the ph1b mutant, to induce 3B-3E homoeologous recombination. Totally, 81 3B-3E recombinants were recovered and detected in the primary, secondary, and tertiary homoeologous recombination cycles by FGISH. Comparing to the primary recombination, the secondary and tertiary recombination shifted toward the proximal regions due to the increase in homology between the pairing partners. The 3B-3E recombinants were genotyped by high-throughput wheat 90-K single nucleotide polymorphism (SNP) arrays and their recombination breakpoints physically mapped based on the FGISH patterns and SNP results. The 3B-3E recombination physically partitioned chromosome 3B into 38 bins, and 429 SNPs were assigned to the distinct bins. Integrative analysis of FGISH and SNP results led to the construction of a composite bin map for chromosome 3B. Additionally, we developed 22 SNP-derived semi-thermal asymmetric reverse PCR markers specific for chromosome 3E and constructed a comparative map of homoeologous chromosomes 3E, 3B, 3A, and 3D. In summary, this work provides a unique physical framework for further studies of the 3B-3E homoeologous pair and diversifies the wheat genome for wheat improvement.
Collapse
Affiliation(s)
- Mingyi Zhang
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA
| | - Wei Zhang
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA
| | - Xianwen Zhu
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA
| | - Qing Sun
- Department of Computer Science, North Dakota State University, Fargo, ND, 58108, USA
| | - Shiaoman Chao
- USDA-ARS, Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, Fargo, ND, 58102, USA
| | - Changhui Yan
- Department of Computer Science, North Dakota State University, Fargo, ND, 58108, USA
| | - Steven S Xu
- USDA-ARS, Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, Fargo, ND, 58102, USA
| | - Jason Fiedler
- USDA-ARS, Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, Fargo, ND, 58102, USA
| | - Xiwen Cai
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA.
| |
Collapse
|
43
|
Xu J, Wang L, Deal KR, Zhu T, Ramasamy RK, Luo MC, Malvick J, You FM, McGuire PE, Dvorak J. Genome-wide introgression from a bread wheat × Lophopyrum elongatum amphiploid into wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:1227-1241. [PMID: 31980837 DOI: 10.1007/s00122-020-03544-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 01/10/2020] [Indexed: 06/10/2023]
Abstract
We introgressed wheatgrass germplasm from the octoploid amphiploid Triticum aestivum× Lophopyrum elongatum into wheat by manipulating the wheat Ph1 gene and discovered and characterized 130 introgression lines harboring single or, in various combinations, complete and recombined L. elongatum chromosomes. Diploid wheatgrass Lophopyrum elongatum (genomes EE) possesses valuable traits for wheat genetics and breeding. We evaluated several strategies for introgression of this germplasm into wheat. To detect it, we developed and validated multiplexed sets of Sequenom MassARRAY single nucleotide polymorphism (SNP) markers, which differentiated disomic and monosomic L. elongatum chromosomes from wheat chromosomes. We identified 130 introgression lines (ILs), which harbored 108 complete and 89 recombined L. elongatum chromosomes. Of the latter, 59 chromosomes were recombined by one or more crossovers and 30 were involved in centromeric (Robertsonian) translocations or were telocentric. To identify wheat chromosomes substituted for or recombined with L. elongatum chromosomes, we genotyped the ILs with the wheat 90-K Infinium SNP array. We found that most of the wheat 90-K probes correctly detected their targets in the L. elongatum genome and showed that some wheat SNPs are ancient and had originated prior to the divergence of the wheat and L. elongatum lineages. Of the 130 ILs, 52% were homozygous for Ph1 deletion and thus are staged to be recombined further. We failed to detect in the L. elongatum genome the 4/5 reciprocal translocation that has been reported in Thinopyrum bessarabicum and several other Triticeae genomes.
Collapse
Affiliation(s)
- Jiale Xu
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Le Wang
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Karin R Deal
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Tingting Zhu
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Ramesh K Ramasamy
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Ming-Cheng Luo
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Julia Malvick
- Veterinary Genetics Laboratory, University of California, Davis, CA, 95616, USA
| | - Frank M You
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, K1A 0C6, Canada
| | - Patrick E McGuire
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Jan Dvorak
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA.
| |
Collapse
|
44
|
Wang H, Zou S, Li Y, Lin F, Tang D. An ankyrin-repeat and WRKY-domain-containing immune receptor confers stripe rust resistance in wheat. Nat Commun 2020; 11:1353. [PMID: 32170056 PMCID: PMC7070047 DOI: 10.1038/s41467-020-15139-6] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 02/18/2020] [Indexed: 02/08/2023] Open
Abstract
Perception of pathogenic effectors in plants often relies on nucleotide-binding domain (NBS) and leucine-rich-repeat-containing (NLR) proteins. Some NLRs contain additional domains that function as integrated decoys for pathogen effector targets and activation of immune signalling. Wheat stripe rust is one of the most devastating diseases of crop plants. Here, we report the cloning of YrU1, a stripe rust resistance gene from the diploid wheat Triticum urartu, the progenitor of the A genome of hexaploid wheat. YrU1 encodes a coiled-coil-NBS-leucine-rich repeat protein with N-terminal ankyrin-repeat and C-terminal WRKY domains, representing a unique NLR structure in plants. Database searches identify similar architecture only in wheat relatives. Transient expression of YrU1 in Nicotiana benthamiana does not induce cell death in the absence of pathogens. The ankyrin-repeat and coiled-coil domains of YrU1 self-associate, suggesting that homodimerisation is critical for YrU1 function. The identification and cloning of this disease resistance gene sheds light on NLR protein function and may facilitate breeding to control the devastating wheat stripe rust disease.
Collapse
Affiliation(s)
- Huan Wang
- State Key Laboratory of Ecological Control of Fujian-Taiwan Crop Pests, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Plant Immunity Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Development Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Shenghao Zou
- State Key Laboratory of Ecological Control of Fujian-Taiwan Crop Pests, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Plant Immunity Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yiwen Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Development Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Fanyun Lin
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Development Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Dingzhong Tang
- State Key Laboratory of Ecological Control of Fujian-Taiwan Crop Pests, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Plant Immunity Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
| |
Collapse
|
45
|
Erdayani E, Nagarajan R, Grant NP, Gill KS. Genome-wide analysis of the HSP101/CLPB gene family for heat tolerance in hexaploid wheat. Sci Rep 2020; 10:3948. [PMID: 32127546 PMCID: PMC7054433 DOI: 10.1038/s41598-020-60673-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 02/12/2020] [Indexed: 02/06/2023] Open
Abstract
Heat Shock Protein 101 (HSP101), the homolog of Caseinolytic Protease B (CLPB) proteins, has functional conservation across species to play roles in heat acclimation and plant development. In wheat, several TaHSP101/CLPB genes were identified, but have not been comprehensively characterized. Given the complexity of a polyploid genome with its phenomena of homoeologous expression bias, detailed analysis on the whole TaCLPB family members is important to understand the genetic basis of heat tolerance in hexaploid wheat. In this study, a genome-wide analysis revealed thirteen members of TaCLPB gene family and their expression patterns in various tissues, developmental stages, and stress conditions. Detailed characterization of TaCLPB gene and protein structures suggested potential variations of the sub-cellular localization and their functional regulations. We revealed homoeologous specific variations among TaCLPB gene copies that have not been reported earlier. A study of the Chromosome 1 TaCLPB in four wheat genotypes demonstrated unique patterns of the homoeologous gene expression under moderate and extreme heat treatments. The results give insight into the strategies to improve heat tolerance by targeting one or some of the TaCLPB genes in wheat.
Collapse
Affiliation(s)
- Eva Erdayani
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA., USA
- Research Center for Biotechnology, Indonesian Institute of Sciences, Cibinong, Jawa Barat, Indonesia
| | - Ragupathi Nagarajan
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA., USA
| | - Nathan P Grant
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA., USA
| | - Kulvinder S Gill
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA., USA.
| |
Collapse
|
46
|
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. FRONTIERS IN PLANT SCIENCE 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] [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.
Collapse
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,
| |
Collapse
|
47
|
Li H, Wang L, Luo MC, Nie F, Zhou Y, McGuire PE, Distelfeld A, Dai X, Song CP, Dvorak J. Recombination between homoeologous chromosomes induced in durum wheat by the Aegilops speltoides Su1-Ph1 suppressor. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:3265-3276. [PMID: 31529271 DOI: 10.1007/s00122-019-03423-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 09/06/2019] [Indexed: 05/21/2023]
Abstract
Su1-Ph1, which we previously introgressed into wheat from Aegilops speltoides, is a potent suppressor of Ph1 and a valuable tool for gene introgression in tetraploid wheat. We previously introgressed Su1-Ph1, a suppressor of the wheat Ph1 gene, from Aegilops speltoides into durum wheat cv Langdon (LDN). Here, we evaluated the utility of the introgressed suppressor for inducing introgression of alien germplasm into durum wheat. We built LDN plants heterozygous for Su1-Ph1 that simultaneously contained a single LDN chromosome 5B and a single Ae. searsii chromosome 5Sse, which targeted them for recombination. We genotyped 28 BC1F1 and 84 F2 progeny with the wheat 90-K Illumina single-nucleotide polymorphism assay and detected extensive recombination between the two chromosomes, which we confirmed by non-denaturing fluorescence in situ hybridization (ND-FISH). We constructed BC1F1 and F2 genetic maps that were 65.31 and 63.71 cM long, respectively. Recombination rates between the 5B and 5Sse chromosomes were double the expected rate computed from their meiotic pairing, which we attributed to selection against aneuploid gametes. Recombination rate between 5B and 5Sse was depressed compared to that between 5B chromosomes in the proximal region of the long arm. We integrated ND-FISH signals into the genetic map and constructed a physical map, which we used to map a 172,188,453-bp Ph1 region. Despite the location of the region in a low-recombination region of the 5B chromosome, we detected three crossovers in it. Our data show that Su1-Ph1 is a valuable tool for gene introgression and gene mapping based on recombination between homoeologous chromosomes in wheat.
Collapse
Affiliation(s)
- Hao Li
- Key Laboratory of Plant Stress Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Le Wang
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Ming-Cheng Luo
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Fang Nie
- Key Laboratory of Plant Stress Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
| | - Yun Zhou
- Key Laboratory of Plant Stress Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
| | - Patrick E McGuire
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Assaf Distelfeld
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
| | - Xiongtao Dai
- Department of Statistics, Iowa State University, Ames, IA, 50011, USA
| | - Chun-Peng Song
- Key Laboratory of Plant Stress Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
| | - Jan Dvorak
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA.
| |
Collapse
|
48
|
Genome-Wide Characterization and Expression Profiling of Squamosa Promoter Binding Protein-like (SBP) Transcription Factors in Wheat (Triticum aestivum L.). AGRONOMY-BASEL 2019. [DOI: 10.3390/agronomy9090527] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Transcription factors (TFs) play fundamental roles in the developmental processes of all living organisms. Squamosa Promoter Binding Protein-like (SBP/SBP-Box) is a major family of plant-specific TFs, which plays important roles in multiple processes involving plant growth and development. While some work has been done, there is a lot more that is yet to be discovered in the hexaploid wheat SBP (TaSBP) family. With the completion of whole genome sequencing, genome-wide analysis of SBPs in common hexaploid wheat is now possible. In this study, we used protein–protein Basic Local Alignment Search Tool (BLASTp) to hunt the newly released reference genome sequence of hexaploid wheat (Chinese spring). Seventy-four TaSBP proteins (belonging to 56 genes) were identified and clustered into five groups. Gene structure and motif analysis indicated that most TaSBPs have relatively conserved exon–intron arrangements and motif composition. Analysis of transcriptional data showed that many TaSBP genes responded to some biological and abiotic stresses with different expression patterns. Moreover, three TaSBP genes were generally expressed in the majority of tissues throughout the wheat growth and also responded to many environmental biotic and abiotic stresses. Collectively, the detailed analyses presented here will help in understanding the roles of the TaSBP and also provide a reference for the further study of its biological function in wheat.
Collapse
|
49
|
Rawale KS, Khan MA, Gill KS. The novel function of the Ph1 gene to differentiate homologs from homoeologs evolved in Triticum turgidum ssp. dicoccoides via a dramatic meiosis-specific increase in the expression of the 5B copy of the C-Ph1 gene. Chromosoma 2019; 128:561-570. [PMID: 31494715 DOI: 10.1007/s00412-019-00724-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 08/12/2019] [Accepted: 08/14/2019] [Indexed: 11/29/2022]
Abstract
The Ph1 gene is the principal regulator of homoeologous chromosome pairing control (HECP) that ensures the diploid-like meiotic chromosome pairing behavior of polyploid wheat. The HECP control was speculated to have evolved after the first event of polyploidization. With the objective to accurately understand the evolution of the HECP control, wild emmer wheat accessions previously known to differ for HECP control were characterized for the structure and expression of the candidate Ph1 gene, C-Ph1. The C-TdPh1-5A and 5B gene copies of emmer wheat showed 98 and 99% DNA sequence similarity respectively with the corresponding hexaploid wheat copies. Further, the C-TdPh1-5B carried the C-Ph1-5B specific structural changes and transcribed three splice variants as observed in the hexaploid wheat. Further, single nucleotide changes differentiating accessions varying for HECP control were identified. Analyzed by quantitative expression analysis, the wild emmer accessions with HECP control showed ~ 10,000-fold higher transcript abundance of the C-TdPh1-5B copy during prophase-I compared to accessions lacking the control. Differential transcriptional regulation of C-TdPh1-5B splice variants further revealed that C-Ph1-5Balt1 variant is mainly responsible for differential accumulation of C-Ph1-5B copy in accessions with HECP control. Taken together, these results showed that the HECP control evolved via transcriptional regulation of splice variants during meiosis.
Collapse
Affiliation(s)
- Kanwardeep S Rawale
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, USA
| | - Muhammad A Khan
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, USA
| | - Kulvinder S Gill
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, USA.
| |
Collapse
|
50
|
Liu J, Rasheed A, He Z, Imtiaz M, Arif A, Mahmood T, Ghafoor A, Siddiqui SU, Ilyas MK, Wen W, Gao F, Xie C, Xia X. Genome-wide variation patterns between landraces and cultivars uncover divergent selection during modern wheat breeding. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:2509-2523. [PMID: 31139853 DOI: 10.1007/s00122-019-03367-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 05/17/2019] [Indexed: 05/21/2023]
Abstract
Genetic diversity, population structure, LD decay, and selective sweeps in 687 wheat accessions were analyzed, providing relevant guidelines to facilitate the use of the germplasm in wheat breeding. Common wheat (Triticum aestivum L.) is one of the most widely grown crops in the world. Landraces were subjected to strong human-mediated selection in developing high-yielding, good quality, and widely adapted cultivars. To investigate the genome-wide patterns of allelic variation, population structure and patterns of selective sweeps during modern wheat breeding, we tested 687 wheat accessions, including landraces (148) and cultivars (539) mainly from China and Pakistan in a wheat 90 K single nucleotide polymorphism array. Population structure analysis revealed that cultivars and landraces from China and Pakistan comprised three relatively independent genetic clusters. Cultivars displayed lower nucleotide diversity and a wider average LD decay across whole genome, indicating allelic erosion and a diversity bottleneck due to the modern breeding. Analysis of genetic differentiation between landraces and cultivars from China and Pakistan identified allelic variants subjected to selection during modern breeding. In total, 477 unique genome regions showed signatures of selection, where 109 were identified in both China and Pakistan germplasm. The majority of genomic regions were located in the B genome (225), followed by the A genome (175), and only 77 regions were located in the D genome. EigenGWAS was further used to identify key selection loci in modern wheat cultivars from China and Pakistan by comparing with global winter wheat and spring wheat diversity panels, respectively. A few known functional genes or loci found within these genome regions corresponded to known phenotypes for disease resistance, vernalization, quality, adaptability and yield-related traits. This study uncovered molecular footprints of modern wheat breeding and explained the genetic basis of polygenic adaptation in wheat. The results will be useful for understanding targets of modern wheat breeding, and in devising future breeding strategies to target beneficial alleles currently not pursued.
Collapse
Affiliation(s)
- Jindong Liu
- Institute of Crop Science, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
- Department of Plant Genetics and Breeding/State Key Laboratory for Agrobiotechnology, China Agricultural University, 2 Yuanmingyuan West Road, Beijing, 100193, China
| | - Awais Rasheed
- Institute of Crop Science, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
- International Maize and Wheat Improvement Center (CIMMYT) China Office, c/o CAAS, 12 Zhongguancun South Street, Beijing, 100081, China
- Quaid-i-Azam University, Islamabad, Pakistan
| | - Zhonghu He
- Institute of Crop Science, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
- International Maize and Wheat Improvement Center (CIMMYT) China Office, c/o CAAS, 12 Zhongguancun South Street, Beijing, 100081, China
| | - Muhammad Imtiaz
- International Maize and Wheat Improvement Center (CIMMYT) Pakistan Office, c/o National Agriculture Research Center (NARC), Islamabad, Pakistan
| | - Anjuman Arif
- National Institute of Agriculture and Biology (NIAB), Faisalabad, Pakistan
| | | | - Abdul Ghafoor
- Bio-resources Conservation Institute (BCI), National Agriculture Research Center (NARC), Islamabad, Pakistan
| | - Sadar Uddin Siddiqui
- Bio-resources Conservation Institute (BCI), National Agriculture Research Center (NARC), Islamabad, Pakistan
| | - Muhammad Kashif Ilyas
- Bio-resources Conservation Institute (BCI), National Agriculture Research Center (NARC), Islamabad, Pakistan
| | - Weie Wen
- Institute of Crop Science, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Fengmei Gao
- Crop Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, Heilongjiang, China
| | - Chaojie Xie
- Department of Plant Genetics and Breeding/State Key Laboratory for Agrobiotechnology, China Agricultural University, 2 Yuanmingyuan West Road, Beijing, 100193, China
| | - Xianchun Xia
- Institute of Crop Science, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China.
| |
Collapse
|