1
|
Wu X, Hu Z, Zhang Y, Li M, Liao N, Dong J, Wang B, Wu J, Wu X, Wang Y, Wang J, Lu Z, Yang Y, Sun Y, Dong W, Zhang M, Li G. Differential selection of yield and quality traits has shaped genomic signatures of cowpea domestication and improvement. Nat Genet 2024; 56:992-1005. [PMID: 38649710 DOI: 10.1038/s41588-024-01722-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 03/19/2024] [Indexed: 04/25/2024]
Abstract
Cowpeas (tropical legumes) are important in ensuring food and nutritional security in developing countries, especially in sub-Saharan Africa. Herein, we report two high-quality genome assemblies of grain and vegetable cowpeas and we re-sequenced 344 accessions to characterize the genomic variations landscape. We identified 39 loci for ten important agronomic traits and more than 541 potential loci that underwent selection during cowpea domestication and improvement. In particular, the synchronous selections of the pod-shattering loci and their neighboring stress-relevant loci probably led to the enhancement of pod-shattering resistance and the compromise of stress resistance during the domestication from grain to vegetable cowpeas. Moreover, differential selections on multiple loci associated with pod length, grain number per pod, seed weight, pod and seed soluble sugars, and seed crude proteins shaped the yield and quality diversity in cowpeas. Our findings provide genomic insights into cowpea domestication and improvement footprints, enabling further genome-informed cultivar improvement of cowpeas.
Collapse
Affiliation(s)
- Xinyi Wu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, P. R. China
| | - Zhongyuan Hu
- Laboratory of Vegetable Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, P. R. China
| | - Yan Zhang
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, P. R. China
| | - Mao Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, P. R. China
- Key Laboratory of Vegetable Legumes Germplasm Enhancement and Molecular Breeding in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou, P. R. China
| | - Nanqiao Liao
- Laboratory of Vegetable Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, P. R. China
| | - Junyang Dong
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, P. R. China
- Key Laboratory of Vegetable Legumes Germplasm Enhancement and Molecular Breeding in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou, P. R. China
| | - Baogen Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, P. R. China
- Key Laboratory of Vegetable Legumes Germplasm Enhancement and Molecular Breeding in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou, P. R. China
| | - Jian Wu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, P. R. China
- Key Laboratory of Vegetable Legumes Germplasm Enhancement and Molecular Breeding in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou, P. R. China
| | - Xiaohua Wu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, P. R. China
- Key Laboratory of Vegetable Legumes Germplasm Enhancement and Molecular Breeding in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou, P. R. China
| | - Ying Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, P. R. China
- Key Laboratory of Vegetable Legumes Germplasm Enhancement and Molecular Breeding in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou, P. R. China
| | - Jian Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, P. R. China
- Key Laboratory of Vegetable Legumes Germplasm Enhancement and Molecular Breeding in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou, P. R. China
| | - Zhongfu Lu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, P. R. China
- Key Laboratory of Vegetable Legumes Germplasm Enhancement and Molecular Breeding in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou, P. R. China
| | - Yi Yang
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, P. R. China
| | - Yuyan Sun
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, P. R. China
- Key Laboratory of Vegetable Legumes Germplasm Enhancement and Molecular Breeding in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou, P. R. China
| | - Wenqi Dong
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, P. R. China
- Key Laboratory of Vegetable Legumes Germplasm Enhancement and Molecular Breeding in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou, P. R. China
| | - Mingfang Zhang
- Laboratory of Vegetable Germplasm Innovation and Molecular Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, P. R. China.
- Hainan Institute of Zhejiang University, Yazhou Bay Science and Technology City, Sanya, P. R. China.
- Key Laboratory of Horticultural Plant Growth and Development, Ministry of Agriculture and Rural Affairs, Hangzhou, P. R. China.
| | - Guojing Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, P. R. China.
- Key Laboratory of Vegetable Legumes Germplasm Enhancement and Molecular Breeding in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou, P. R. China.
| |
Collapse
|
2
|
Yuan G, Zhang N, Zou Y, Hao Y, Pan J, Liu Y, Zhang W, Li B. Genome-wide identification and expression analysis of WRKY gene family members in red clover ( Trifolium pratense L.). FRONTIERS IN PLANT SCIENCE 2023; 14:1289507. [PMID: 38130488 PMCID: PMC10733489 DOI: 10.3389/fpls.2023.1289507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 11/21/2023] [Indexed: 12/23/2023]
Abstract
Trifolium pratense is an important legume forage grass and a key component of sustainable livestock development. Serving as an essential component, the WRKY gene family, a crucial group of regulatory transcription factors in plants, holds significant importance in their response to abiotic stresses. However, there has been no systematic analysis conducted on the WRKY gene family in Trifolium pratense. This study conducted a comprehensive genomic characterization of the WRKY gene family in Trifolium pratense, utilizing the latest genomic data, resulting in the identification of 59 TpWRKY genes. Based on their structural features, phylogenetic characteristics, and conserved motif composition, the WRKY proteins were classified into three groups, with group II further subdivided into five subgroups (II-a, II-b, II-c, II-d, and II-e). The majority of the TpWRKYs in a group share a similar structure and motif composition. Intra-group syntenic analysis revealed eight pairs of duplicate segments. The expression patterns of 59 TpWRKY genes in roots, stems, leaves, and flowers were examined by analyzing RNA-seq data. The expression of 12 TpWRKY genes under drought, low-temperature (4°C), methyl jasmonate (MeJA) and abscisic acid (ABA) stresses was analyzed by RT-qPCR. The findings indicated that TpWRKY46 was highly induced by drought stress, and TpWRKY26 and TpWRKY41 were significantly induced by low temperature stress. In addition, TpWRKY29 and TpWRKY36 were greatly induced by MeJA stress treatment, and TpWRKY17 was significantly upregulated by ABA stress treatment. In this research, we identified and comprehensively analyzed the structural features of the WRKY gene family in T.pratense, along with determined the possible roles of WRKY candidate genes in abiotic stress. These discoveries deepen our understandings of how WRKY transcription factors contribute to species evolution and functional divergence, laying a solid molecular foundation for future exploration and study of stress resistance mechanisms in T.pratense.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Weiguo Zhang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Northwest University, Xi’an, China
| | - Beibei Li
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Northwest University, Xi’an, China
| |
Collapse
|
3
|
Tay Fernandez CG, Bayer PE, Petereit J, Varshney R, Batley J, Edwards D. The conservation of gene models can support genome annotation. THE PLANT GENOME 2023; 16:e20377. [PMID: 37602500 DOI: 10.1002/tpg2.20377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 07/19/2023] [Accepted: 07/24/2023] [Indexed: 08/22/2023]
Abstract
Many genome annotations include false-positive gene models, leading to errors in phylogenetic and comparative studies. Here, we propose a method to support gene model prediction based on evolutionary conservation and use it to identify potentially erroneous annotations. Using this method, we developed a set of 15,345 representative gene models from 12 legume assemblies that can be used to support genome annotations for other legumes.
Collapse
Affiliation(s)
- Cassandria G Tay Fernandez
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, Western Australia, Australia
| | - Philipp E Bayer
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, Western Australia, Australia
| | - Jakob Petereit
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, Western Australia, Australia
| | - Rajeev Varshney
- State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, Western Australia, Australia
- Centre of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Telangana, India
| | - Jacqueline Batley
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, Western Australia, Australia
| | - David Edwards
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, Western Australia, Australia
| |
Collapse
|
4
|
Kim BC, Lim I, Ha J. Metabolic profiling and expression analysis of key genetic factors in the biosynthetic pathways of antioxidant metabolites in mungbean sprouts. FRONTIERS IN PLANT SCIENCE 2023; 14:1207940. [PMID: 37396630 PMCID: PMC10313209 DOI: 10.3389/fpls.2023.1207940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 05/31/2023] [Indexed: 07/04/2023]
Abstract
Mungbeans (Vigna radiata L.), a major legume crop in Asia, contain higher amounts of functional substances than other legumes, such as catechin, chlorogenic acid, and vitexin. Germination can improve the nutritional value of legume seeds. Here, 20 functional substances were profiled in germinated mungbeans and the expression levels of the transcripts of key enzymes in targeted secondary metabolite biosynthetic pathways were identified. VC1973A, a reference mungbean elite cultivar, had the highest amount of gallic acid (99.93 ± 0.13 mg/100 g DW) but showed lower contents of most metabolites than the other genotypes. Wild mungbeans contained a large amount of isoflavones compared with cultivated genotypes, especially for daidzin, genistin and glycitin. The expression of key genes involved in biosynthetic pathways had significant positive or negative correlations with the target secondary metabolite contents. The results indicate that functional substance contents are regulated at the transcriptional level, which can be applied to improve the nutritional value of mungbean sprouts in molecular breeding or genetic engineering, and wild mungbeans are a useful resource to improve the quality of mungbean sprouts.
Collapse
Affiliation(s)
- Byeong Cheol Kim
- Department of Plant Science, Gangneung-Wonju National University, Gangneung, Republic of Korea
| | - Insu Lim
- Department of Plant Science, Gangneung-Wonju National University, Gangneung, Republic of Korea
| | - Jungmin Ha
- Department of Plant Science, Gangneung-Wonju National University, Gangneung, Republic of Korea
- Haeram Institute of Bakery Science, Gangneung-Wonju National University, Gangneung, Republic of Korea
| |
Collapse
|
5
|
Zanotto S, Ruttink T, Pégard M, Skøt L, Grieder C, Kölliker R, Ergon Å. A genome-wide association study of freezing tolerance in red clover ( Trifolium pratense L.) germplasm of European origin. FRONTIERS IN PLANT SCIENCE 2023; 14:1189662. [PMID: 37235014 PMCID: PMC10208120 DOI: 10.3389/fpls.2023.1189662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Accepted: 04/13/2023] [Indexed: 05/28/2023]
Abstract
Improvement of persistency is an important breeding goal in red clover (Trifolium pratense L.). In areas with cold winters, lack of persistency is often due to poor winter survival, of which low freezing tolerance (FT) is an important component. We conducted a genome wide association study (GWAS) to identify loci associated with freezing tolerance in a collection of 393 red clover accessions, mostly of European origin, and performed analyses of linkage disequilibrium and inbreeding. Accessions were genotyped as pools of individuals using genotyping-by-sequencing (pool-GBS), generating both single nucleotide polymorphism (SNP) and haplotype allele frequency data at accession level. Linkage disequilibrium was determined as a squared partial correlation between the allele frequencies of pairs of SNPs and found to decay at extremely short distances (< 1 kb). The level of inbreeding, inferred from the diagonal elements of a genomic relationship matrix, varied considerably between different groups of accessions, with the strongest inbreeding found among ecotypes from Iberia and Great Britain, and the least found among landraces. Considerable variation in FT was found, with LT50-values (temperature at which 50% of the plants are killed) ranging from -6.0°C to -11.5°C. SNP and haplotype-based GWAS identified eight and six loci significantly associated with FT (of which only one was shared), explaining 30% and 26% of the phenotypic variation, respectively. Ten of the loci were found within or at a short distance (<0.5 kb) from genes possibly involved in mechanisms affecting FT. These include a caffeoyl shikimate esterase, an inositol transporter, and other genes involved in signaling, transport, lignin synthesis and amino acid or carbohydrate metabolism. This study paves the way for a better understanding of the genetic control of FT and for the development of molecular tools for the improvement of this trait in red clover through genomics assisted breeding.
Collapse
Affiliation(s)
- Stefano Zanotto
- Faculty of Biosciences, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Tom Ruttink
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Melle, Belgium
| | | | - Leif Skøt
- IBERS, Aberystwyth University, Aberystwyth, United Kingdom
| | | | - Roland Kölliker
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
| | - Åshild Ergon
- Faculty of Biosciences, Norwegian University of Life Sciences (NMBU), Ås, Norway
| |
Collapse
|
6
|
Shirasawa K, Moraga R, Ghelfi A, Hirakawa H, Nagasaki H, Ghamkhar K, Barrett BA, Griffiths AG, Isobe SN. An improved reference genome for Trifolium subterraneum L. provides insight into molecular diversity and intra-specific phylogeny. FRONTIERS IN PLANT SCIENCE 2023; 14:1103857. [PMID: 36875612 PMCID: PMC9975737 DOI: 10.3389/fpls.2023.1103857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 01/30/2023] [Indexed: 06/18/2023]
Abstract
Subterranean clover (Trifolium subterraneum L., Ts) is a geocarpic, self-fertile annual forage legume with a compact diploid genome (n = x = 8, 544 Mb/1C). Its resilience and climate adaptivity have made it an economically important species in Mediterranean and temperate zones. Using the cultivar Daliak, we generated higher resolution sequence data, created a new genome assembly TSUd_3.0, and conducted molecular diversity analysis for copy number variant (CNV) and single-nucleotide polymorphism (SNP) among 36 cultivars. TSUd_3.0 substantively improves prior genome assemblies with new Hi-C and long-read sequence data, covering 531 Mb, containing 41,979 annotated genes and generating a 94.4% BUSCO score. Comparative genomic analysis among select members of the tribe Trifolieae indicated TSUd 3.0 corrects six assembly-error inversion/duplications and confirmed phylogenetic relationships. Its synteny with T. pratense, T. repens, Medicago truncatula and Lotus japonicus genomes were assessed, with the more distantly related T. repens and M. truncatula showing higher levels of co-linearity with Ts than between Ts and its close relative T. pratense. Resequencing of 36 cultivars discovered 7,789,537 SNPs subsequently used for genomic diversity assessment and sequence-based clustering. Heterozygosity estimates ranged from 1% to 21% within the 36 cultivars and may be influenced by admixture. Phylogenetic analysis supported subspecific genetic structure, although it indicates four or five groups, rather than the three recognized subspecies. Furthermore, there were incidences where cultivars characterized as belonging to a particular subspecies clustered with another subspecies when using genomic data. These outcomes suggest that further investigation of Ts sub-specific classification using molecular and morpho-physiological data is needed to clarify these relationships. This upgraded reference genome, complemented with comprehensive sequence diversity analysis of 36 cultivars, provides a platform for future gene functional analysis of key traits, and genome-based breeding strategies for climate adaptation and agronomic performance. Pangenome analysis, more in-depth intra-specific phylogenomic analysis using the Ts core collection, and functional genetic and genomic studies are needed to further augment knowledge of Trifolium genomes.
Collapse
Affiliation(s)
- Kenta Shirasawa
- Department of Frontier Research and Development, Kazusa DNA Research Institute, Kisarazu, Japan
| | - Roger Moraga
- AgResearch, Grasslands Research Centre, Palmerston North, New Zealand
- Tea Break Bioinformatics Limited, Palmerston North, New Zealand
| | - Andrea Ghelfi
- Department of Frontier Research and Development, Kazusa DNA Research Institute, Kisarazu, Japan
- Bioinformation and DDBJ Center, National Institute of Genetics, Mishima, Japan
| | - Hideki Hirakawa
- Department of Frontier Research and Development, Kazusa DNA Research Institute, Kisarazu, Japan
| | - Hideki Nagasaki
- Department of Frontier Research and Development, Kazusa DNA Research Institute, Kisarazu, Japan
| | - Kioumars Ghamkhar
- AgResearch, Grasslands Research Centre, Palmerston North, New Zealand
| | - Brent A. Barrett
- AgResearch, Grasslands Research Centre, Palmerston North, New Zealand
| | | | - Sachiko N. Isobe
- Department of Frontier Research and Development, Kazusa DNA Research Institute, Kisarazu, Japan
| |
Collapse
|
7
|
Gemeinholzer B, Rupp O, Becker A, Strickert M, Müller CM. Genotyping by sequencing and a newly developed mRNA-GBS approach to link population genetic and transcriptome analyses reveal pattern differences between sites and treatments in red clover (Trifolium pratense L.). Front Ecol Evol 2023. [DOI: 10.3389/fevo.2022.1003057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The important worldwide forage crop red clover (Trifolium pratense L.) is widely cultivated as cattle feed and for soil improvement. Wild populations and landraces have great natural diversity that could be used to improve cultivated red clover. However, to date, there is still insufficient knowledge about the natural genetic and phenotypic diversity of the species. Here, we developed a low-cost complexity reduced mRNA analysis (mRNA-GBS) and compared the results with population genetic (GBS) and previously published mRNA-Seq data, to assess whether analysis of intraspecific variation within and between populations and transcriptome responses is possible simultaneously. The mRNA-GBS approach was successful. SNP analyses from the mRNA-GBS approach revealed comparable patterns to the GBS results, but due to site-specific multifactorial influences of environmental responses as well as conceptual and methodological limitations of mRNA-GBS, it was not possible to link transcriptome analyses with reduced complexity and sequencing depth to previously published greenhouse and field expression studies. Nevertheless, the use of short sequences upstream of the poly(A) tail of mRNA to reduce complexity are promising approaches that combine population genetics and expression profiling to analyze many individuals with trait differences simultaneously and cost-effectively, even in non-model species. Nevertheless, our study design across different regions in Germany was also challenging. The use of reduced complexity differential expression analyses most likely overlays site-specific patterns due to highly complex plant responses under natural conditions.
Collapse
|
8
|
Lukjanová E, Hanulíková A, Řepková J. Investigating the Origin and Evolution of Polyploid Trifolium medium L. Karyotype by Comparative Cytogenomic Methods. PLANTS (BASEL, SWITZERLAND) 2023; 12:235. [PMID: 36678948 PMCID: PMC9866396 DOI: 10.3390/plants12020235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 12/30/2022] [Accepted: 01/03/2023] [Indexed: 06/17/2023]
Abstract
Trifolium medium L. is a wild polyploid relative of the agriculturally important red clover that possesses traits promising for breeding purposes. To date, T. medium also remains the only clover species with which agriculturally important red clover has successfully been hybridized. Even though allopolyploid origin has previously been suggested, little has in fact been known about the T. medium karyotype and its origin. We researched T. medium and related karyotypes using comparative cytogenomic methods, such as fluorescent in situ hybridization (FISH) and RepeatExplorer cluster analysis. The results indicate an exceptional karyotype diversity regarding numbers and mutual positions of 5S and 26S rDNA loci and centromeric repeats in populations of T. medium ecotypes and varieties. The observed variability among T. medium ecotypes and varieties suggests current karyotype instability that can be attributed to ever-ongoing battle between satellite DNA together with genomic changes and rearrangements enhanced by post-hybridization events. Comparative cytogenomic analyses of a T. medium hexaploid variety and diploid relatives revealed stable karyotypes with a possible case of chromosomal rearrangement. Moreover, the results provided evidence of T. medium having autopolyploid origin.
Collapse
|
9
|
Frey LA, Vleugels T, Ruttink T, Schubiger FX, Pégard M, Skøt L, Grieder C, Studer B, Roldán-Ruiz I, Kölliker R. Phenotypic variation and quantitative trait loci for resistance to southern anthracnose and clover rot in red clover. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:4337-4349. [PMID: 36153770 PMCID: PMC9734235 DOI: 10.1007/s00122-022-04223-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 09/14/2022] [Indexed: 06/02/2023]
Abstract
High variability for and candidate loci associated with resistance to southern anthracnose and clover rot in a worldwide collection of red clover provide a first basis for genomics-assisted breeding. Red clover (Trifolium pratense L.) is an important forage legume of temperate regions, particularly valued for its high yield potential and its high forage quality. Despite substantial breeding progress during the last decades, continuous improvement of cultivars is crucial to ensure yield stability in view of newly emerging diseases or changing climatic conditions. The high amount of genetic diversity present in red clover ecotypes, landraces, and cultivars provides an invaluable, but often unexploited resource for the improvement of key traits such as yield, quality, and resistance to biotic and abiotic stresses. A collection of 397 red clover accessions was genotyped using a pooled genotyping-by-sequencing approach with 200 plants per accession. Resistance to the two most pertinent diseases in red clover production, southern anthracnose caused by Colletotrichum trifolii, and clover rot caused by Sclerotinia trifoliorum, was assessed using spray inoculation. The mean survival rate for southern anthracnose was 22.9% and the mean resistance index for clover rot was 34.0%. Genome-wide association analysis revealed several loci significantly associated with resistance to southern anthracnose and clover rot. Most of these loci are in coding regions. One quantitative trait locus (QTL) on chromosome 1 explained 16.8% of the variation in resistance to southern anthracnose. For clover rot resistance we found eight QTL, explaining together 80.2% of the total phenotypic variation. The SNPs associated with these QTL provide a promising resource for marker-assisted selection in existing breeding programs, facilitating the development of novel cultivars with increased resistance against two devastating fungal diseases of red clover.
Collapse
Affiliation(s)
- Lea A Frey
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, 8092, Zurich, Switzerland
| | - Tim Vleugels
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Plant Sciences Unit, Caritasstraat 39, 9090, Melle, Belgium
| | - Tom Ruttink
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Plant Sciences Unit, Caritasstraat 39, 9090, Melle, Belgium
| | - Franz X Schubiger
- Agroscope, Plant Breeding, Reckenholzstrasse 191, 8046, Zurich, Switzerland
| | - Marie Pégard
- INRAE, Centre Nouvelle-Aquitaine-Poitiers, UR4 (UR P3F), 86600, Lusignan, France
| | - Leif Skøt
- Institute of Biological, Environmental & Rural Sciences, Aberystwyth University, Gogerddan, Aberystwyth, Ceredigion, SY23 3EE, UK
| | - Christoph Grieder
- Agroscope, Plant Breeding, Reckenholzstrasse 191, 8046, Zurich, Switzerland
| | - Bruno Studer
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, 8092, Zurich, Switzerland
| | - Isabel Roldán-Ruiz
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Plant Sciences Unit, Caritasstraat 39, 9090, Melle, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Roland Kölliker
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, 8092, Zurich, Switzerland.
| |
Collapse
|
10
|
Vlk D, Trněný O, Řepková J. Genes Associated with Biological Nitrogen Fixation Efficiency Identified Using RNA Sequencing in Red Clover ( Trifolium pratense L.). LIFE (BASEL, SWITZERLAND) 2022; 12:life12121975. [PMID: 36556339 PMCID: PMC9785344 DOI: 10.3390/life12121975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 11/22/2022] [Accepted: 11/22/2022] [Indexed: 11/29/2022]
Abstract
Commonly studied in the context of legume-rhizobia symbiosis, biological nitrogen fixation (BNF) is a key component of the nitrogen cycle in nature. Despite its potential in plant breeding and many years of research, information is still lacking as to the regulation of hundreds of genes connected with plant-bacteria interaction, nodulation, and nitrogen fixation. Here, we compared root nodule transcriptomes of red clover (Trifolium pratense L.) genotypes with contrasting nitrogen fixation efficiency, and we found 491 differentially expressed genes (DEGs) between plants with high and low BNF efficiency. The annotation of genes expressed in nodules revealed more than 800 genes not yet experimentally confirmed. Among genes mediating nodule development, four nod-ule-specific cysteine-rich (NCR) peptides were confirmed in the nodule transcriptome. Gene duplication analyses revealed that genes originating from tandem and dispersed duplication are significantly over-represented among DEGs. Weighted correlation network analysis (WGCNA) organized expression profiles of the transcripts into 16 modules linked to the analyzed traits, such as nitrogen fixation efficiency or sample-specific modules. Overall, the results obtained broaden our knowledge about transcriptomic landscapes of red clover's root nodules and shift the phenotypic description of BNF efficiency on the level of gene expression in situ.
Collapse
Affiliation(s)
- David Vlk
- Department of Experimental Biology, Faculty of Sciences, Masaryk University, 611 37 Brno, Czech Republic
| | - Oldřich Trněný
- Agricultural Research, Ltd., Zahradní 1, 664 41 Troubsko, Czech Republic
| | - Jana Řepková
- Department of Experimental Biology, Faculty of Sciences, Masaryk University, 611 37 Brno, Czech Republic
- Correspondence: ; Tel.: +420-549-49-6895
| |
Collapse
|
11
|
Singh G, Gudi S, Amandeep, Upadhyay P, Shekhawat PK, Nayak G, Goyal L, Kumar D, Kumar P, Kamboj A, Thada A, Shekhar S, Koli GK, DP M, Halladakeri P, Kaur R, Kumar S, Saini P, Singh I, Ayoubi H. Unlocking the hidden variation from wild repository for accelerating genetic gain in legumes. FRONTIERS IN PLANT SCIENCE 2022; 13:1035878. [PMID: 36438090 PMCID: PMC9682257 DOI: 10.3389/fpls.2022.1035878] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Accepted: 10/17/2022] [Indexed: 11/02/2023]
Abstract
The fluctuating climates, rising human population, and deteriorating arable lands necessitate sustainable crops to fulfil global food requirements. In the countryside, legumes with intriguing but enigmatic nitrogen-fixing abilities and thriving in harsh climatic conditions promise future food security. However, breaking the yield plateau and achieving higher genetic gain are the unsolved problems of legume improvement. Present study gives emphasis on 15 important legume crops, i.e., chickpea, pigeonpea, soybean, groundnut, lentil, common bean, faba bean, cowpea, lupin, pea, green gram, back gram, horse gram, moth bean, rice bean, and some forage legumes. We have given an overview of the world and India's area, production, and productivity trends for all legume crops from 1961 to 2020. Our review article investigates the importance of gene pools and wild relatives in broadening the genetic base of legumes through pre-breeding and alien gene introgression. We have also discussed the importance of integrating genomics, phenomics, speed breeding, genetic engineering and genome editing tools in legume improvement programmes. Overall, legume breeding may undergo a paradigm shift once genomics and conventional breeding are integrated in the near future.
Collapse
Affiliation(s)
- Gurjeet Singh
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Santosh Gudi
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Amandeep
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Priyanka Upadhyay
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Pooja Kanwar Shekhawat
- Division of Crop Improvement, Plant Breeding and Genetics, Indian Council of Agricultural Research (ICAR)-Central Soil Salinity Research Institute, Karnal, Haryana, India
- Department of Plant Breeding and Genetics, Sri Karan Narendra Agriculture University, Jobner, Rajasthan, India
| | - Gyanisha Nayak
- Department of Genetics and Plant Breeding, Indira Gandhi Krishi Vishwavidyalaya, Raipur, Chhattisgarh, India
| | - Lakshay Goyal
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Deepak Kumar
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh Haryana Agricultural University, Hisar, Haryana, India
| | - Pradeep Kumar
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Akashdeep Kamboj
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Antra Thada
- Department of Genetics and Plant Breeding, Indira Gandhi Krishi Vishwavidyalaya, Raipur, Chhattisgarh, India
| | - Shweta Shekhar
- Department of Plant Molecular Biology and Biotechnology, Indira Gandhi Krishi Vishwavidyalaya, Raipur, Chhattisgarh, India
| | - Ganesh Kumar Koli
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh Haryana Agricultural University, Hisar, Haryana, India
| | - Meghana DP
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Priyanka Halladakeri
- Department of Genetics and Plant Breeding, Anand Agricultural University, Anand, Gujarat, India
| | - Rajvir Kaur
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Sumit Kumar
- Department of Agronomy, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Pawan Saini
- CSB-Central Sericultural Research & Training Institute (CSR&TI), Ministry of Textiles, Govt. of India, Jammu- Kashmir, Pampore, India
| | - Inderjit Singh
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Habiburahman Ayoubi
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| |
Collapse
|
12
|
Dinkins RD, Hancock JA, Bickhart DM, Sullivan ML, Zhu H. Expression and Variation of the Genes Involved in Rhizobium Nodulation in Red Clover. PLANTS (BASEL, SWITZERLAND) 2022; 11:2888. [PMID: 36365339 PMCID: PMC9655500 DOI: 10.3390/plants11212888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 10/21/2022] [Accepted: 10/25/2022] [Indexed: 06/16/2023]
Abstract
Red clover (Trifolium pratense L.) is an important forage crop and serves as a major contributor of nitrogen input in pasture settings because of its ability to fix atmospheric nitrogen. During the legume-rhizobial symbiosis, the host plant undergoes a large number of gene expression changes, leading to development of root nodules that house the rhizobium bacteria as they are converted into nitrogen-fixing bacteroids. Many of the genes involved in symbiosis are conserved across legume species, while others are species-specific with little or no homology across species and likely regulate the specific plant genotype/symbiont strain interactions. Red clover has not been widely used for studying symbiotic nitrogen fixation, primarily due to its outcrossing nature, making genetic analysis rather complicated. With the addition of recent annotated genomic resources and use of RNA-seq tools, we annotated and characterized a number of genes that are expressed only in nodule forming roots. These genes include those encoding nodule-specific cysteine rich peptides (NCRs) and nodule-specific Polycystin-1, Lipoxygenase, Alpha toxic (PLAT) domain proteins (NPDs). Our results show that red clover encodes one of the highest number of NCRs and ATS3-like/NPDs, which are postulated to increase nitrogen fixation efficiency, in the Inverted-Repeat Lacking Clade (IRLC) of legumes. Knowledge of the variation and expression of these genes in red clover will provide more insights into the function of these genes in regulating legume-rhizobial symbiosis and aid in breeding of red clover genotypes with increased nitrogen fixation efficiency.
Collapse
Affiliation(s)
- Randy D. Dinkins
- Forage-Animal Production Research Unit, USDA-ARS, Lexington, KY 40506, USA
| | - Julie A. Hancock
- College of Agriculture, Food and Environment, University of Kentucky, Lexington, KY 40508, USA
| | | | | | - Hongyan Zhu
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY 40546, USA
| |
Collapse
|
13
|
Osterman J, Hammenhag C, Ortiz R, Geleta M. Discovering candidate SNPs for resilience breeding of red clover. FRONTIERS IN PLANT SCIENCE 2022; 13:997860. [PMID: 36247534 PMCID: PMC9554550 DOI: 10.3389/fpls.2022.997860] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 09/07/2022] [Indexed: 06/02/2023]
Abstract
Red clover is a highly valuable crop for the ruminant industry in the temperate regions worldwide. It also provides multiple environmental services, such as contribution to increased soil fertility and reduced soil erosion. This study used 661 single nucleotide polymorphism (SNP) markers via targeted sequencing using seqSNP, to describe genetic diversity and population structure in 382 red clover accessions. The accessions were selected from NordGen representing red clover germplasm from Norway, Sweden, Finland and Denmark as well as from Lantmännen, a Swedish seed company. Each accession was represented by 10 individuals, which was sequenced as a pool. The mean Nei's standard genetic distance between the accessions and genetic variation within accessions were 0.032 and 0.18, respectively. The majority of the accessions had negative Tajima's D, suggesting that they contain significant proportions of rare alleles. A pairwise FST revealed high genetic similarity between the different cultivated types, while the wild populations were divergent. Unlike wild populations, which exhibited genetic differentiation, there was no clear differentiation among all cultivated types. A principal coordinate analysis revealed that the first principal coordinate, distinguished most of the wild populations from the cultivated types, in agreement with the results obtained using a discriminant analysis of principal components and cluster analysis. Accessions of wild populations and landraces collected from southern and central Scandinavia showed a higher genetic similarity to Lantmännen accessios. It is therefore possible to link the diversity of the environments where wild populations were collected to the genetic diversity of the cultivated and wild gene pools. Additionally, least absolute shrinkage and selection operator (LASSO) models revealed associations between variation in temperature and precipitation and SNPs within genes controlling stomatal opening. Temperature was also related to kinase proteins, which are known to regulate plant response to temperature stress. Furthermore, the variation between wild populations and cultivars was correlated with SNPs within genes regulating root development. Overall, this study comprehensively investigated Nordic European red clover germplasm, and the results provide forage breeders with valuable information for further selection and development of red clover cultivars.
Collapse
|
14
|
Ergon Å, Milvang ØW, Skøt L, Ruttink T. Identification of loci controlling timing of stem elongation in red clover using genotyping by sequencing of pooled phenotypic extremes. Mol Genet Genomics 2022; 297:1587-1600. [PMID: 36001174 DOI: 10.1007/s00438-022-01942-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 08/07/2022] [Indexed: 10/15/2022]
Abstract
MAIN CONCLUSION Through selective genotyping of pooled phenotypic extremes, we identified a number of loci and candidate genes putatively controlling timing of stem elongation in red clover. We have identified candidate genes controlling the timing of stem elongation prior to flowering in red clover (Trifolium pratense L.). This trait is of ecological and agronomic significance, as it affects fitness, competitivity, climate adaptation, forage and seed yield, and forage quality. We genotyped replicate pools of phenotypically extreme individuals (early and late-elongating) within cultivar Lea using genotyping-by-sequencing in pools (pool-GBS). After calling and filtering SNPs and GBS locus haplotype polymorphisms, we estimated allele frequencies and searched for markers with significantly different allele frequencies in the two phenotypic groups using BayeScan, an FST-based test utilizing replicate pools, and a test based on error variance of replicate pools. Of the three methods, BayeScan was the least stringent, and the error variance-based test the most stringent. Fifteen significant markers were identified in common by all three tests. The candidate genes flanking the markers include genes with potential roles in the vernalization, autonomous, and photoperiod regulation of floral transition, hormonal regulation of stem elongation, and cell growth. These results provide a first insight into the potential genes and mechanisms controlling transition to stem elongation in a perennial legume, which lays a foundation for further functional studies of the genetic determinants regulating this important trait.
Collapse
Affiliation(s)
- Åshild Ergon
- Department of Plant Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, P.O. Box 5003, N-1432 Ås, Norway.
| | - Øystein W Milvang
- Department of Plant Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, P.O. Box 5003, N-1432 Ås, Norway
| | - Leif Skøt
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK
| | - Tom Ruttink
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Plant Sciences Unit, Caritasstraat 39, B-9090 Melle, Belgium
| |
Collapse
|
15
|
Transcriptome Analysis of Air Space-Type Variegation Formation in Trifolium pratense. Int J Mol Sci 2022; 23:ijms23147794. [PMID: 35887138 PMCID: PMC9322087 DOI: 10.3390/ijms23147794] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 07/12/2022] [Accepted: 07/13/2022] [Indexed: 02/04/2023] Open
Abstract
Air space-type variegation is the most diverse among the species of known variegated leaf plants and is caused by conspicuous intercellular spaces between the epidermal and palisade cells and among the palisade cells at non-green areas. Trifolium pratense, a species in Fabaceae with V-shaped air space-type variegation, was selected to explore the application potential of variegated leaf plants and accumulate basic data on the molecular regulatory mechanism and evolutionary history of leaf variegation. We performed comparative transcriptome analysis on young and adult leaflets of variegated and green plants and identified 43 candidate genes related to air space-type variegation formation. Most of the genes were related to cell-wall structure modification (CESA, CSL, EXP, FLA, PG, PGIP, PLL, PME, RGP, SKS, and XTH family genes), followed by photosynthesis (LHCB subfamily, RBCS, GOX, and AGT family genes), redox (2OG and GSH family genes), and nitrogen metabolism (NodGS family genes). Other genes were related to photooxidation, protein interaction, and protease degradation systems. The downregulated expression of light-responsive LHCB subfamily genes and the upregulated expression of the genes involved in cell-wall structure modification were important conditions for air space-type variegation formation in T. pratense. The upregulated expression of the ubiquitin-protein ligase enzyme (E3)-related genes in the protease degradation systems were conducive to air space-type variegation formation. Because these family genes are necessary for plant growth and development, the mechanism of the leaf variegation formation in T. pratense might be a widely existing regulation in air space-type variegation in nature.
Collapse
|
16
|
Yan Z, Sang L, Ma Y, He Y, Sun J, Ma L, Li S, Miao F, Zhang Z, Huang J, Wang Z, Yang G. A de novo assembled high-quality chromosome-scale Trifolium pratense genome and fine-scale phylogenetic analysis. BMC PLANT BIOLOGY 2022; 22:332. [PMID: 35820796 PMCID: PMC9277957 DOI: 10.1186/s12870-022-03707-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 06/20/2022] [Indexed: 05/12/2023]
Abstract
BACKGROUND Red clover (Trifolium pratense L.) is a diploid perennial temperate legume with 14 chromosomes (2n = 14) native to Europe and West Asia, with high nutritional and economic value. It is a very important forage grass and is widely grown in marine climates, such as the United States and Sweden. Genetic research and molecular breeding are limited by the lack of high-quality reference genomes. In this study, we used Illumina, PacBio HiFi, and Hi-C to obtain a high-quality chromosome-scale red clover genome and used genome annotation results to analyze evolutionary relationships among related species. RESULTS The red clover genome obtained by PacBio HiFi assembly sequencing was 423 M. The assembly quality was the highest among legume genome assemblies published to date. The contig N50 was 13 Mb, scaffold N50 was 55 Mb, and BUSCO completeness was 97.9%, accounting for 92.8% of the predicted genome. Genome annotation revealed 44,588 gene models with high confidence and 52.81% repetitive elements in red clover genome. Based on a comparison of genome annotation results, red clover was closely related to Trifolium medium and distantly related to Glycine max, Vigna radiata, Medicago truncatula, and Cicer arietinum among legumes. Analyses of gene family expansions and contractions and forward gene selection revealed gene families and genes related to environmental stress resistance and energy metabolism. CONCLUSIONS We report a high-quality de novo genome assembly for the red clover at the chromosome level, with a substantial improvement in assembly quality over those of previously published red clover genomes. These annotated gene models can provide an important resource for molecular genetic breeding and legume evolution studies. Furthermore, we analyzed the evolutionary relationships among red clover and closely related species, providing a basis for evolutionary studies of clover leaf and legumes, genomics analyses of forage grass, the improvement of agronomic traits.
Collapse
Affiliation(s)
- Zhenfei Yan
- College of Grassland Science, Qingdao Agricultural University, Qingdao, 266109, China
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, Qingdao, 266109, China
| | - Lijun Sang
- College of Grassland Science, Qingdao Agricultural University, Qingdao, 266109, China
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, Qingdao, 266109, China
| | - Yue Ma
- College of Grassland Science, Qingdao Agricultural University, Qingdao, 266109, China
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, Qingdao, 266109, China
| | - Yong He
- College of Grassland Science, Qingdao Agricultural University, Qingdao, 266109, China
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, Qingdao, 266109, China
| | - Juan Sun
- College of Grassland Science, Qingdao Agricultural University, Qingdao, 266109, China
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, Qingdao, 266109, China
| | - Lichao Ma
- College of Grassland Science, Qingdao Agricultural University, Qingdao, 266109, China
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, Qingdao, 266109, China
| | - Shuo Li
- College of Grassland Science, Qingdao Agricultural University, Qingdao, 266109, China
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, Qingdao, 266109, China
| | - Fuhong Miao
- College of Grassland Science, Qingdao Agricultural University, Qingdao, 266109, China
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, Qingdao, 266109, China
| | - Zixin Zhang
- College of Grassland Science, Qingdao Agricultural University, Qingdao, 266109, China
| | | | - Zengyu Wang
- College of Grassland Science, Qingdao Agricultural University, Qingdao, 266109, China.
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, Qingdao, 266109, China.
| | - Guofeng Yang
- College of Grassland Science, Qingdao Agricultural University, Qingdao, 266109, China.
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, Qingdao, 266109, China.
| |
Collapse
|
17
|
Pan L, Luo Y, Wang J, Li X, Tang B, Yang H, Hou X, Liu F, Zou X. Evolution and functional diversification of catalase genes in the green lineage. BMC Genomics 2022; 23:411. [PMID: 35650553 PMCID: PMC9158360 DOI: 10.1186/s12864-022-08621-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 05/09/2022] [Indexed: 11/10/2022] Open
Abstract
Background Catalases (CATs) break down hydrogen peroxide into water and oxygen to prevent cellular oxidative damage, and play key roles in the development, biotic and abiotic stresses of plants. However, the evolutionary relationships of the plant CAT gene family have not been systematically reported. Results Here, we conducted genome-wide comparative, phylogenetic, and structural analyses of CAT orthologs from 29 out of 31 representative green lineage species to characterize the evolution and functional diversity of CATs. We found that CAT genes in land plants were derived from core chlorophytes and detected a lineage-specific loss of CAT genes in Fabaceae, suggesting that the CAT genes in this group possess divergent functions. All CAT genes were split into three major groups (group α, β1, and β2) based on the phylogeny. CAT genes were transferred from bacteria to core chlorophytes and charophytes by lateral gene transfer, and this led to the independent evolution of two types of CAT genes: α and β types. Ten common motifs were detected in both α and β groups, and β CAT genes had five unique motifs, respectively. The findings of our study are inconsistent with two previous hypotheses proposing that (i) new CAT genes are acquired through intron loss and that (ii) the Cys-343 residue is highly conserved in plants. We found that new CAT genes in most higher plants were produced through intron acquisition and that the Cys-343 residue was only present in monocots, Brassicaceae and Pp_CatX7 in P. patens, which indicates the functional specificity of the CATs in these three lineages. Finally, our finding that CAT genes show high overall sequence identity but that individual CAT genes showed developmental stage and organ-specific expression patterns suggests that CAT genes have functionally diverged independently. Conclusions Overall, our analyses of the CAT gene family provide new insights into their evolution and functional diversification in green lineage species. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08621-6.
Collapse
|
18
|
Jha UC, Nayyar H, Parida SK, Bakır M, von Wettberg EJB, Siddique KHM. Progress of Genomics-Driven Approaches for Sustaining Underutilized Legume Crops in the Post-Genomic Era. Front Genet 2022; 13:831656. [PMID: 35464848 PMCID: PMC9021634 DOI: 10.3389/fgene.2022.831656] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 02/24/2022] [Indexed: 12/22/2022] Open
Abstract
Legume crops, belonging to the Fabaceae family, are of immense importance for sustaining global food security. Many legumes are profitable crops for smallholder farmers due to their unique ability to fix atmospheric nitrogen and their intrinsic ability to thrive on marginal land with minimum inputs and low cultivation costs. Recent progress in genomics shows promise for future genetic gains in major grain legumes. Still it remains limited in minor legumes/underutilized legumes, including adzuki bean, cluster bean, horse gram, lathyrus, red clover, urd bean, and winged bean. In the last decade, unprecedented progress in completing genome assemblies of various legume crops and resequencing efforts of large germplasm collections has helped to identify the underlying gene(s) for various traits of breeding importance for enhancing genetic gain and contributing to developing climate-resilient cultivars. This review discusses the progress of genomic resource development, including genome-wide molecular markers, key breakthroughs in genome sequencing, genetic linkage maps, and trait mapping for facilitating yield improvement in underutilized legumes. We focus on 1) the progress in genomic-assisted breeding, 2) the role of whole-genome resequencing, pangenomes for underpinning the novel genomic variants underlying trait gene(s), 3) how adaptive traits of wild underutilized legumes could be harnessed to develop climate-resilient cultivars, 4) the progress and status of functional genomics resources, deciphering the underlying trait candidate genes with putative function in underutilized legumes 5) and prospects of novel breeding technologies, such as speed breeding, genomic selection, and genome editing. We conclude the review by discussing the scope for genomic resources developed in underutilized legumes to enhance their production and play a critical role in achieving the "zero hunger" sustainable development goal by 2030 set by the United Nations.
Collapse
Affiliation(s)
- Uday Chand Jha
- ICAR-Indian Institute of Pulses Research (IIPR), Kanpur, India
| | | | - Swarup K Parida
- National Institute of Plant Genome Research (NIPGR), New Delhi, India
| | - Melike Bakır
- Department of Agricultural Biotechnology, Faculty of Agriculture, Erciyes University, Kayseri, Turkey
| | - Eric J. B. von Wettberg
- Plant and Soil Science and Gund Institute for the Environment, The University of Vermont, Burlington, VT, United States
- Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russia
| | | |
Collapse
|
19
|
Wu F, Duan Z, Xu P, Yan Q, Meng M, Cao M, Jones CS, Zong X, Zhou P, Wang Y, Luo K, Wang S, Yan Z, Wang P, Di H, Ouyang Z, Wang Y, Zhang J. Genome and systems biology of Melilotus albus provides insights into coumarins biosynthesis. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:592-609. [PMID: 34717292 PMCID: PMC8882801 DOI: 10.1111/pbi.13742] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 10/14/2021] [Accepted: 10/19/2021] [Indexed: 05/08/2023]
Abstract
Melilotus species are used as green manure and rotation crops worldwide and contain abundant pharmacologically active coumarins. However, there is a paucity of information on its genome and coumarin production and function. Here, we reported a chromosome-scale assembly of Melilotus albus genome with 1.04 Gb in eight chromosomes, containing 71.42% repetitive elements. Long terminal repeat retrotransposon bursts coincided with declining of population sizes during the Quaternary glaciation. Resequencing of 94 accessions enabled insights into genetic diversity, population structure, and introgression. Melilotus officinalis had relatively larger genetic diversity than that of M. albus. The introgression existed between M. officinalis group and M. albus group, and gene flows was from M. albus to M. officinalis. Selection sweep analysis identified candidate genes associated with flower colour and coumarin biosynthesis. Combining genomics, BSA, transcriptomics, metabolomics, and biochemistry, we identified a β-glucosidase (BGLU) gene cluster contributing to coumarin biosynthesis. MaBGLU1 function was verified by overexpression in M. albus, heterologous expression in Escherichia coli, and substrate feeding, revealing its role in scopoletin (coumarin derivative) production and showing that nonsynonymous variation drives BGLU enzyme activity divergence in Melilotus. Our work will accelerate the understanding of biologically active coumarins and their biosynthetic pathways, and contribute to genomics-enabled Melilotus breeding.
Collapse
Affiliation(s)
- Fan Wu
- State Key Laboratory of Grassland Agro‐ecosystemsKey Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural AffairsEngineering Research Center of Grassland Industry, Ministry of EducationCollege of Pastoral Agriculture Science and TechnologyLanzhou UniversityLanzhouChina
| | - Zhen Duan
- State Key Laboratory of Grassland Agro‐ecosystemsKey Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural AffairsEngineering Research Center of Grassland Industry, Ministry of EducationCollege of Pastoral Agriculture Science and TechnologyLanzhou UniversityLanzhouChina
| | - Pan Xu
- State Key Laboratory of Grassland Agro‐ecosystemsKey Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural AffairsEngineering Research Center of Grassland Industry, Ministry of EducationCollege of Pastoral Agriculture Science and TechnologyLanzhou UniversityLanzhouChina
| | - Qi Yan
- State Key Laboratory of Grassland Agro‐ecosystemsKey Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural AffairsEngineering Research Center of Grassland Industry, Ministry of EducationCollege of Pastoral Agriculture Science and TechnologyLanzhou UniversityLanzhouChina
| | - Minghui Meng
- State Key Laboratory of Grassland Agro‐ecosystemsKey Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural AffairsEngineering Research Center of Grassland Industry, Ministry of EducationCollege of Pastoral Agriculture Science and TechnologyLanzhou UniversityLanzhouChina
| | - Mingshu Cao
- Grasslands Research CentreAgResearch LimitedPalmerston NorthNew Zealand
| | - Chris S. Jones
- Feed and Forage DevelopmentInternational Livestock Research InstituteNairobiKenya
| | - Xifang Zong
- State Key Laboratory of Grassland Agro‐ecosystemsKey Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural AffairsEngineering Research Center of Grassland Industry, Ministry of EducationCollege of Pastoral Agriculture Science and TechnologyLanzhou UniversityLanzhouChina
| | - Pei Zhou
- State Key Laboratory of Grassland Agro‐ecosystemsKey Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural AffairsEngineering Research Center of Grassland Industry, Ministry of EducationCollege of Pastoral Agriculture Science and TechnologyLanzhou UniversityLanzhouChina
| | - Yimeng Wang
- State Key Laboratory of Grassland Agro‐ecosystemsKey Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural AffairsEngineering Research Center of Grassland Industry, Ministry of EducationCollege of Pastoral Agriculture Science and TechnologyLanzhou UniversityLanzhouChina
| | - Kai Luo
- State Key Laboratory of Grassland Agro‐ecosystemsKey Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural AffairsEngineering Research Center of Grassland Industry, Ministry of EducationCollege of Pastoral Agriculture Science and TechnologyLanzhou UniversityLanzhouChina
| | - Shengsheng Wang
- State Key Laboratory of Grassland Agro‐ecosystemsKey Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural AffairsEngineering Research Center of Grassland Industry, Ministry of EducationCollege of Pastoral Agriculture Science and TechnologyLanzhou UniversityLanzhouChina
| | - Zhuanzhuan Yan
- State Key Laboratory of Grassland Agro‐ecosystemsKey Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural AffairsEngineering Research Center of Grassland Industry, Ministry of EducationCollege of Pastoral Agriculture Science and TechnologyLanzhou UniversityLanzhouChina
| | - Penglei Wang
- State Key Laboratory of Grassland Agro‐ecosystemsKey Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural AffairsEngineering Research Center of Grassland Industry, Ministry of EducationCollege of Pastoral Agriculture Science and TechnologyLanzhou UniversityLanzhouChina
| | - Hongyan Di
- State Key Laboratory of Grassland Agro‐ecosystemsKey Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural AffairsEngineering Research Center of Grassland Industry, Ministry of EducationCollege of Pastoral Agriculture Science and TechnologyLanzhou UniversityLanzhouChina
| | - Zifeng Ouyang
- State Key Laboratory of Grassland Agro‐ecosystemsKey Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural AffairsEngineering Research Center of Grassland Industry, Ministry of EducationCollege of Pastoral Agriculture Science and TechnologyLanzhou UniversityLanzhouChina
| | - Yanrong Wang
- State Key Laboratory of Grassland Agro‐ecosystemsKey Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural AffairsEngineering Research Center of Grassland Industry, Ministry of EducationCollege of Pastoral Agriculture Science and TechnologyLanzhou UniversityLanzhouChina
| | - Jiyu Zhang
- State Key Laboratory of Grassland Agro‐ecosystemsKey Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural AffairsEngineering Research Center of Grassland Industry, Ministry of EducationCollege of Pastoral Agriculture Science and TechnologyLanzhou UniversityLanzhouChina
| |
Collapse
|
20
|
Bickhart DM, Koch LM, Smith TPL, Riday H, Sullivan ML. Chromosome-scale assembly of the highly heterozygous genome of red clover ( Trifolium pratense L.), an allogamous forage crop species. GIGABYTE 2022; 2022:gigabyte42. [PMID: 36824517 PMCID: PMC9650271 DOI: 10.46471/gigabyte.42] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 02/14/2022] [Indexed: 11/09/2022] Open
Abstract
Relative to other crops, red clover (Trifolium pratense L.) has various favorable traits making it an ideal forage crop. Conventional breeding has improved varieties, but modern genomic methods could accelerate progress and facilitate gene discovery. Existing short-read-based genome assemblies of the ∼420 megabase pair (Mbp) genome are fragmented into >135,000 contigs, with numerous order and orientation errors within scaffolds, probably associated with the plant's biology, which displays gametophytic self-incompatibility resulting in inherent high heterozygosity. Here, we present a high-quality long-read-based assembly of red clover with a more than 500-fold reduction in contigs, improved per-base quality, and increased contig N50 by three orders of magnitude. The 413.5 Mbp assembly is nearly 20% longer than the 350 Mbp short-read assembly, closer to the predicted genome size. We also present quality measures and full-length isoform RNA transcript sequences for assessing accuracy and future genome annotation. The assembly accurately represents the seven main linkage groups in an allogamous (outcrossing), highly heterozygous plant genome.
Collapse
Affiliation(s)
- Derek M. Bickhart
- US Dairy Forage Research Center, United States Department of Agriculture Agricultural Research Service (USDA-ARS), Madison, WI, USA, Corresponding authors. E-mail: ;
| | - Lisa M. Koch
- US Dairy Forage Research Center, United States Department of Agriculture Agricultural Research Service (USDA-ARS), Madison, WI, USA
| | - Timothy P. L. Smith
- US Meat Animal Research Center, United States Department of Agriculture Agricultural Research Service (USDA-ARS), Clay Center, NE, USA
| | - Heathcliffe Riday
- US Dairy Forage Research Center, United States Department of Agriculture Agricultural Research Service (USDA-ARS), Madison, WI, USA
| | - Michael L. Sullivan
- US Dairy Forage Research Center, United States Department of Agriculture Agricultural Research Service (USDA-ARS), Madison, WI, USA, Corresponding authors. E-mail: ;
| |
Collapse
|
21
|
Koudounas K, Guirimand G, Hoyos LFR, Carqueijeiro I, Cruz PL, Stander E, Kulagina N, Perrin J, Oudin A, Besseau S, Lanoue A, Atehortùa L, St-Pierre B, Giglioli-Guivarc'h N, Papon N, O'Connor SE, Courdavault V. Tonoplast and Peroxisome Targeting of γ-tocopherol N-methyltransferase Homologs Involved in the Synthesis of Monoterpene Indole Alkaloids. PLANT & CELL PHYSIOLOGY 2022; 63:200-216. [PMID: 35166361 DOI: 10.1093/pcp/pcab160] [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: 07/02/2021] [Revised: 10/08/2021] [Accepted: 11/02/2021] [Indexed: 06/14/2023]
Abstract
Many plant species from the Apocynaceae, Loganiaceae and Rubiaceae families evolved a specialized metabolism leading to the synthesis of a broad palette of monoterpene indole alkaloids (MIAs). These compounds are believed to constitute a cornerstone of the plant chemical arsenal but above all several MIAs display pharmacological properties that have been exploited for decades by humans to treat various diseases. It is established that MIAs are produced in planta due to complex biosynthetic pathways engaging a multitude of specialized enzymes but also a complex tissue and subcellular organization. In this context, N-methyltransferases (NMTs) represent an important family of enzymes indispensable for MIA biosynthesis but their characterization has always remained challenging. In particular, little is known about the subcellular localization of NMTs in MIA-producing plants. Here, we performed an extensive analysis on the subcellular localization of NMTs from four distinct medicinal plants but also experimentally validated that two putative NMTs from Catharanthus roseus exhibit NMT activity. Apart from providing unprecedented data regarding the targeting of these enzymes in planta, our results point out an additional layer of complexity to the subcellular organization of the MIA biosynthetic pathway by introducing tonoplast and peroxisome as new actors of the final steps of MIA biosynthesis.
Collapse
Affiliation(s)
- Konstantinos Koudounas
- EA2106 Biomolécules et Biotechnologies Végétales, Université de Tours, 31 Av. Monge, Tours 37200, France
| | | | - Luisa Fernanda Rojas Hoyos
- Grupo de Biotransformación-Escuela de Microbiología, Universidad de Antioquia, Calle 70 No 52-21, A.A 1226, Medellín, Colombia
| | - Ines Carqueijeiro
- EA2106 Biomolécules et Biotechnologies Végétales, Université de Tours, 31 Av. Monge, Tours 37200, France
| | - Pamela Lemos Cruz
- EA2106 Biomolécules et Biotechnologies Végétales, Université de Tours, 31 Av. Monge, Tours 37200, France
| | - Emily Stander
- EA2106 Biomolécules et Biotechnologies Végétales, Université de Tours, 31 Av. Monge, Tours 37200, France
| | - Natalja Kulagina
- EA2106 Biomolécules et Biotechnologies Végétales, Université de Tours, 31 Av. Monge, Tours 37200, France
| | - Jennifer Perrin
- EA2106 Biomolécules et Biotechnologies Végétales, Université de Tours, 31 Av. Monge, Tours 37200, France
| | - Audrey Oudin
- EA2106 Biomolécules et Biotechnologies Végétales, Université de Tours, 31 Av. Monge, Tours 37200, France
| | - Sébastien Besseau
- EA2106 Biomolécules et Biotechnologies Végétales, Université de Tours, 31 Av. Monge, Tours 37200, France
| | - Arnaud Lanoue
- EA2106 Biomolécules et Biotechnologies Végétales, Université de Tours, 31 Av. Monge, Tours 37200, France
| | - Lucia Atehortùa
- Laboratorio de Biotecnología, Sede de Investigación Universitaria, Universidad de Antioquia, Medellin 50010, Colombia
| | - Benoit St-Pierre
- EA2106 Biomolécules et Biotechnologies Végétales, Université de Tours, 31 Av. Monge, Tours 37200, France
| | | | - Nicolas Papon
- GEIHP, SFR ICAT, University of Angers, Université de Bretagne Occidentale, 4 rue de Larrey - F49933, Angers 49000, France
| | - Sarah E O'Connor
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, Jena 07745, Germany
| | - Vincent Courdavault
- EA2106 Biomolécules et Biotechnologies Végétales, Université de Tours, 31 Av. Monge, Tours 37200, France
- Graduate School of Sciences, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
| |
Collapse
|
22
|
Xi H, Nguyen V, Ward C, Liu Z, Searle IR. Chromosome-level assembly of the common vetch (Vicia sativa) reference genome. GIGABYTE 2022; 2022:gigabyte38. [PMID: 36824524 PMCID: PMC9650280 DOI: 10.46471/gigabyte.38] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Accepted: 01/26/2022] [Indexed: 11/09/2022] Open
Abstract
Vicia sativa L. (common vetch, n = 6) is an annual, herbaceous, climbing legume, originating in the Fertile Crescent of the Middle East and now widespread in the Mediterranean basin, West, Central and Eastern Asia, North and South America. V. sativa is of economic importance as a forage legume in countries such as Australia, China, and the USA, and contributes valuable nitrogen to agricultural rotation cropping systems. To accelerate precision genome breeding and genomics-based selection of this legume, we present a chromosome-level reference genome sequence for V. sativa, constructed using a combination of long-read Oxford Nanopore sequencing, short-read Illumina sequencing, and high-throughput chromosome conformation data (CHiCAGO and Hi-C) analysis. The chromosome-level assembly of six pseudo-chromosomes has a total genome length of 1.65 Gbp, with a median contig length of 684 Kbp. BUSCO analysis of the assembly demonstrated very high completeness of 98% of the dicotyledonous orthologs. RNA-seq analysis and gene modelling enabled the annotation of 53,218 protein-coding genes. This V. sativa assembly will provide insights into vetch genome evolution and be a valuable resource for genomic breeding, genetic diversity and for understanding adaption to diverse arid environments.
Collapse
Affiliation(s)
- Hangwei Xi
- School of Biological Sciences, The University of Adelaide, Adelaide, Adelaide 5005, Australia
| | - Vy Nguyen
- School of Biological Sciences, The University of Adelaide, Adelaide, Adelaide 5005, Australia
| | - Christopher Ward
- School of Biological Sciences, The University of Adelaide, Adelaide, Adelaide 5005, Australia
| | - Zhipeng Liu
- State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, No 768 Jiayuguan West Road, Chengguan District, Lanzhou 730020, China
| | - Iain R. Searle
- School of Biological Sciences, The University of Adelaide, Adelaide, Adelaide 5005, Australia
| |
Collapse
|
23
|
Di Marsico M, Paytuvi Gallart A, Sanseverino W, Aiese Cigliano R. GreeNC 2.0: a comprehensive database of plant long non-coding RNAs. Nucleic Acids Res 2022; 50:D1442-D1447. [PMID: 34723326 PMCID: PMC8728176 DOI: 10.1093/nar/gkab1014] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/08/2021] [Accepted: 10/12/2021] [Indexed: 02/04/2023] Open
Abstract
The Green Non-Coding Database (GreeNC) is one of the reference databases for the study of plant long non-coding RNAs (lncRNAs). Here we present our most recent update where 16 species have been updated, while 78 species have been added, resulting in the annotation of more than 495 000 lncRNAs. Moreover, sequence clustering was applied providing information about sequence conservation and gene families. The current version of the database is available at: http://greenc.sequentiabiotech.com/wiki2/Main_Page.
Collapse
Affiliation(s)
- Marco Di Marsico
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università degli Studi di Perugia, Borgo XX Giugno 74, 06121 Perugia, Italy
| | | | | | | |
Collapse
|
24
|
Tello-Ruiz MK, Jaiswal P, Ware D. Gramene: A Resource for Comparative Analysis of Plants Genomes and Pathways. Methods Mol Biol 2022; 2443:101-131. [PMID: 35037202 DOI: 10.1007/978-1-0716-2067-0_5] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Gramene is an integrated bioinformatics resource for accessing, visualizing, and comparing plant genomes and biological pathways. Originally targeting grasses, Gramene has grown to host annotations for over 90 plant genomes including agronomically important cereals (e.g., maize, sorghum, wheat, teff), fruits and vegetables (e.g., apple, watermelon, clementine, tomato, cassava), specialty crops (e.g., coffee, olive tree, pistachio, almond), and plants of special or emerging interest (e.g., cotton, tobacco, cannabis, or hemp). For some species, the resource includes multiple varieties of the same species, which has paved the road for the creation of species-specific pan-genome browsers. The resource also features plant research models, including Arabidopsis and C4 warm-season grasses and brassicas, as well as other species that fill phylogenetic gaps for plant evolution studies. Its strength derives from the application of a phylogenetic framework for genome comparison and the use of ontologies to integrate structural and functional annotation data. This chapter outlines system requirements for end-users and database hosting, data types and basic navigation within Gramene, and provides examples of how to (1) explore Gramene's search results, (2) explore gene-centric comparative genomics data visualizations in Gramene, and (3) explore genetic variation associated with a gene locus. This is the first publication describing in detail Gramene's integrated search interface-intended to provide a simplified entry portal for the resource's main data categories (genomic location, phylogeny, gene expression, pathways, and external references) to the most complete and up-to-date set of plant genome and pathway annotations.
Collapse
Affiliation(s)
| | - Pankaj Jaiswal
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA
| | - Doreen Ware
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.
- USDA-ARS NAA Plant, Soil & Nutrition Laboratory Research Unit, Cornell University, Ithaca, NY, USA.
| |
Collapse
|
25
|
Loera-Sánchez M, Studer B, Kölliker R. A multispecies amplicon sequencing approach for genetic diversity assessments in grassland plant species. Mol Ecol Resour 2021; 22:1725-1745. [PMID: 34918474 PMCID: PMC9305562 DOI: 10.1111/1755-0998.13577] [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: 08/02/2021] [Revised: 12/08/2021] [Accepted: 12/10/2021] [Indexed: 11/30/2022]
Abstract
Grasslands are widespread and economically relevant ecosystems at the basis of sustainable roughage production. Plant genetic diversity (PGD; i.e., within‐species diversity) is related to many beneficial effects on the ecosystem functioning of grasslands. The monitoring of PGD in temperate grasslands is complicated by the multiplicity of species present and by a shortage of methods for large‐scale assessments. However, the continuous advancement of high‐throughput DNA sequencing approaches has improved the prospects of broad, multispecies PGD monitoring. Among them, amplicon sequencing stands out as a robust and cost‐effective method. Here, we report a set of 12 multispecies primer pairs that can be used for high‐throughput PGD assessments in multiple grassland plant species. The target loci were selected and tested in two phases: a “discovery phase” based on a sequence capture assay (611 nuclear loci assessed in 16 grassland plant species), which resulted in the selection of 11 loci; and a “validation phase”, in which the selected loci were targeted and sequenced using multispecies primers in test populations of Dactylis glomerata L., Lolium perenne L., Festuca pratensis Huds., Trifolium pratense L. and T. repens L. The multispecies amplicons had nucleotide diversities per species from 5.19 × 10−3 to 1.29 × 10−2, which is in the range of flowering‐related genes but slightly lower than pathogen resistance genes. We conclude that the methodology, the DNA sequence resources, and the primer pairs reported in this study provide the basis for large‐scale, multispecies PGD monitoring in grassland plants.
Collapse
Affiliation(s)
- Miguel Loera-Sánchez
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
| | - Bruno Studer
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
| | - Roland Kölliker
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
| |
Collapse
|
26
|
Moyer TB, Brechbill AM, Hicks LM. Mass Spectrometric Identification of Antimicrobial Peptides from Medicinal Seeds. Molecules 2021; 26:molecules26237304. [PMID: 34885884 PMCID: PMC8659199 DOI: 10.3390/molecules26237304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 11/23/2021] [Accepted: 11/25/2021] [Indexed: 12/02/2022] Open
Abstract
Traditional medicinal plants contain a variety of bioactive natural products including cysteine-rich (Cys-rich) antimicrobial peptides (AMPs). Cys-rich AMPs are often crosslinked by multiple disulfide bonds which increase their resistance to chemical and enzymatic degradation. However, this class of molecules is relatively underexplored. Herein, in silico analysis predicted 80–100 Cys-rich AMPs per species from three edible traditional medicinal plants: Linum usitatissimum (flax), Trifolium pratense (red clover), and Sesamum indicum (sesame). Bottom-up proteomic analysis of seed peptide extracts revealed direct evidence for the translation of 3–10 Cys-rich AMPs per species, including lipid transfer proteins, defensins, α-hairpinins, and snakins. Negative activity revealed by antibacterial screening highlights the importance of employing a multi-pronged approach for AMP discovery. Further, this study demonstrates that flax, red clover, and sesame are promising sources for further AMP discovery and characterization.
Collapse
|
27
|
Shi K, Liu X, Pan X, Liu J, Gong W, Gong P, Cao M, Jia S, Wang Z. Unveiling the Complexity of Red Clover ( Trifolium pratense L.) Transcriptome and Transcriptional Regulation of Isoflavonoid Biosynthesis Using Integrated Long- and Short-Read RNAseq. Int J Mol Sci 2021; 22:ijms222312625. [PMID: 34884432 PMCID: PMC8658037 DOI: 10.3390/ijms222312625] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 11/17/2021] [Accepted: 11/17/2021] [Indexed: 11/16/2022] Open
Abstract
Red clover (Trifolium pratense L.) is used as forage and contains a high level of isoflavonoids. Although isoflavonoids in red clover were discovered a long time ago, the transcriptional regulation of isoflavonoid biosynthesis is virtually unknown because of the lack of accurate and comprehensive characterization of the transcriptome. Here, we used a combination of long-read (PacBio Iso-Seq) and short-read (Illumina) RNAseq sequencing to develop a more comprehensive full-length transcriptome in four tissues (root, stem, leaf, and flower) and to identify transcription factors possibly involved in isoflavonoid biosynthesis in red clover. Overall, we obtained 50,922 isoforms, including 19,860 known genes and 2817 novel isoforms based on the annotation of RefGen Tp_v2.0. We also found 1843 long non-coding RNAs, 1625 fusion genes, and 34,612 alternatively spliced events, with some transcript isoforms validated experimentally. A total of 16,734 differentially expressed genes were identified in the four tissues, including 43 isoflavonoid-biosynthesis-related genes, such as stem-specific expressed TpPAL, TpC4H, and Tp4CL and root-specific expressed TpCHS, TpCHI1, and TpIFS. Further, weighted gene co-expression network analysis and a targeted compound assay were combined to investigate the association between the isoflavonoid content and the transcription factors expression in the four tissues. Twelve transcription factors were identified as key genes for isoflavonoid biosynthesis. Among these transcription factors, the overexpression of TpMYB30 or TpRSM1-2 significantly increased the isoflavonoid content in tobacco. In particular, the glycitin was increased by 50-100 times in the plants overexpressing TpRSM1-2, in comparison to that in the WT plants. Our study provides a comprehensive and accurate annotation of the red clover transcriptome and candidate genes to improve isoflavonoid biosynthesis and accelerate research into molecular breeding in red clover or other crops.
Collapse
Affiliation(s)
- Kun Shi
- College of Grassland Science and Technology, China Agricultural University, Beijing 100193, China; (K.S.); (X.L.); (J.L.); (S.J.)
| | - Xiqiang Liu
- College of Grassland Science and Technology, China Agricultural University, Beijing 100193, China; (K.S.); (X.L.); (J.L.); (S.J.)
| | - Xinyi Pan
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China;
| | - Jia Liu
- College of Grassland Science and Technology, China Agricultural University, Beijing 100193, China; (K.S.); (X.L.); (J.L.); (S.J.)
| | - Wenlong Gong
- Pratacultural College, Gansu Agricultural University, Lanzhou 730070, China;
| | - Pan Gong
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China;
| | - Mingshu Cao
- Grasslands Research Centre, AgResearch Limited, Palmerston North 4410, New Zealand;
| | - Shangang Jia
- College of Grassland Science and Technology, China Agricultural University, Beijing 100193, China; (K.S.); (X.L.); (J.L.); (S.J.)
| | - Zan Wang
- College of Grassland Science and Technology, China Agricultural University, Beijing 100193, China; (K.S.); (X.L.); (J.L.); (S.J.)
- Correspondence:
| |
Collapse
|
28
|
Lukjanová E, Řepková J. Chromosome and Genome Diversity in the Genus Trifolium (Fabaceae). PLANTS (BASEL, SWITZERLAND) 2021; 10:2518. [PMID: 34834880 PMCID: PMC8621578 DOI: 10.3390/plants10112518] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 11/11/2021] [Accepted: 11/16/2021] [Indexed: 06/13/2023]
Abstract
Trifolium L. is an economically important genus that is characterized by variable karyotypes relating to its ploidy level and basic chromosome numbers. The advent of genomic resources combined with molecular cytogenetics provides an opportunity to develop our understanding of plant genomes in general. Here, we summarize the current state of knowledge on Trifolium genomes and chromosomes and review methodologies using molecular markers that have contributed to Trifolium research. We discuss possible future applications of cytogenetic methods in research on the Trifolium genome and chromosomes.
Collapse
Affiliation(s)
| | - Jana Řepková
- Department of Experimental Biology, Faculty of Sciences, Masaryk University, 611 37 Brno, Czech Republic;
| |
Collapse
|
29
|
Rubiales D, Annicchiarico P, Vaz Patto MC, Julier B. Legume Breeding for the Agroecological Transition of Global Agri-Food Systems: A European Perspective. FRONTIERS IN PLANT SCIENCE 2021; 12:782574. [PMID: 34868184 PMCID: PMC8637196 DOI: 10.3389/fpls.2021.782574] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 10/18/2021] [Indexed: 06/13/2023]
Abstract
Wider and more profitable legume crop cultivation is an indispensable step for the agroecological transition of global agri-food systems but represents a challenge especially in Europe. Plant breeding is pivotal in this context. Research areas of key interest are represented by innovative phenotypic and genome-based selection procedures for crop yield, tolerance to abiotic and biotic stresses enhanced by the changing climate, intercropping, and emerging crop quality traits. We see outmost priority in the exploration of genomic selection (GS) opportunities and limitations, to ease genetic gains and to limit the costs of multi-trait selection. Reducing the profitability gap of legumes relative to major cereals will not be possible in Europe without public funding devoted to crop improvement research, pre-breeding, and, in various circumstances, public breeding. While most of these activities may profit of significant public-private partnerships, all of them can provide substantial benefits to seed companies. A favorable institutional context may comprise some changes to variety registration tests and procedures.
Collapse
Affiliation(s)
- Diego Rubiales
- Institute for Sustainable Agriculture, CSIC, Córdoba, Spain
| | | | | | - Bernadette Julier
- Institut National de Recherche Pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), URP3F, Lusignan, France
| |
Collapse
|
30
|
Chromosome-length genome assemblies of six legume species provide insights into genome organization, evolution, and agronomic traits for crop improvement. J Adv Res 2021; 42:315-329. [PMID: 36513421 PMCID: PMC9788938 DOI: 10.1016/j.jare.2021.10.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 10/20/2021] [Accepted: 10/24/2021] [Indexed: 12/27/2022] Open
Abstract
INTRODUCTION Legume crops are an important source of protein and oil for human health and in fixing atmospheric N2 for soil enrichment. With an objective to accelerate much-needed genetic analyses and breeding applications, draft genome assemblies were generated in several legume crops; many of them are not high quality because they are mainly based on short reads. However, the superior quality of genome assembly is crucial for a detailed understanding of genomic architecture, genome evolution, and crop improvement. OBJECTIVES Present study was undertaken with an objective of developing improved chromosome-length genome assemblies in six different legumes followed by their systematic investigation to unravel different aspects of genome organization and legume evolution. METHODS We employed in situ Hi-C data to improve the existing draft genomes and performed different evolutionary and comparative analyses using improved genome assemblies. RESULTS We have developed chromosome-length genome assemblies in chickpea, pigeonpea, soybean, subterranean clover, and two wild progenitor species of cultivated groundnut (A. duranensis and A. ipaensis). A comprehensive comparative analysis of these genome assemblies offered improved insights into various evolutionary events that shaped the present-day legume species. We highlighted the expansion of gene families contributing to unique traits such as nodulation in legumes, gravitropism in groundnut, and oil biosynthesis in oilseed legume crops such as groundnut and soybean. As examples, we have demonstrated the utility of improved genome assemblies for enhancing the resolution of "QTL-hotspot" identification for drought tolerance in chickpea and marker-trait associations for agronomic traits in pigeonpea through genome-wide association study. Genomic resources developed in this study are publicly available through an online repository, 'Legumepedia'. CONCLUSION This study reports chromosome-length genome assemblies of six legume species and demonstrates the utility of these assemblies in crop improvement. The genomic resources developed here will have significant role in accelerating genetic improvement applications of legume crops.
Collapse
|
31
|
Contreras-Moreira B, Filippi CV, Naamati G, Girón CG, Allen JE, Flicek P. K-mer counting and curated libraries drive efficient annotation of repeats in plant genomes. THE PLANT GENOME 2021; 14:e20143. [PMID: 34562304 PMCID: PMC7614178 DOI: 10.1002/tpg2.20143] [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: 04/07/2021] [Accepted: 07/06/2021] [Indexed: 06/13/2023]
Abstract
The annotation of repetitive sequences within plant genomes can help in the interpretation of observed phenotypes. Moreover, repeat masking is required for tasks such as whole-genome alignment, promoter analysis, or pangenome exploration. Although homology-based annotation methods are computationally expensive, k-mer strategies for masking are orders of magnitude faster. Here, we benchmarked a two-step approach, where repeats were first called by k-mer counting and then annotated by comparison to curated libraries. This hybrid protocol was tested on 20 plant genomes from Ensembl, with the k-mer-based Repeat Detector (Red) and two repeat libraries (REdat, last updated in 2013, and nrTEplants, curated for this work). Custom libraries produced by RepeatModeler were also tested. We obtained repeated genome fractions that matched those reported in the literature but with shorter repeated elements than those produced directly by sequence homology. Inspection of the masked regions that overlapped genes revealed no preference for specific protein domains. Most Red-masked sequences could be successfully classified by sequence similarity, with the complete protocol taking less than 2 h on a desktop Linux box. A guide to curating your own repeat libraries and the scripts for masking and annotating plant genomes can be obtained at https://github.com/Ensembl/plant-scripts.
Collapse
Affiliation(s)
- Bruno Contreras-Moreira
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Carla V Filippi
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
- Instituto de Biotecnología, Centro de Investigaciones en Ciencias Veterinarias y Agronómicas (CICVyA), Instituto Nacional de Tecnología Agropecuaria (INTA); Instituto de Agrobiotecnología y Biología Molecular (IABIMO), INTA-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) Nicolas Repetto y Los Reseros s/n (1686), Hurlingham, Buenos Aires, Argentina
- CONICET, Av Rivadavia 1917, C1033AAJ Ciudad de Buenos Aires, Argentina
| | - Guy Naamati
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Carlos García Girón
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - James E Allen
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| |
Collapse
|
32
|
Osterman J, Hammenhag C, Ortiz R, Geleta M. Insights Into the Genetic Diversity of Nordic Red Clover ( Trifolium pratense) Revealed by SeqSNP-Based Genic Markers. FRONTIERS IN PLANT SCIENCE 2021; 12:748750. [PMID: 34759943 PMCID: PMC8574770 DOI: 10.3389/fpls.2021.748750] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 10/01/2021] [Indexed: 06/01/2023]
Abstract
Red clover (Trifolium pratense) is one of the most important fodder crops worldwide. The knowledge of genetic diversity among red clover populations, however, is under development. This study provides insights into its genetic diversity, using single nucleotide polymorphism (SNP) markers to define population structure in wild and cultivated red clover. Twenty-nine accessions representing the genetic resources available at NordGen (the Nordic gene bank) and Lantmännen (a Swedish agricultural company with a red clover breeding program) were used for this study. Genotyping was performed via SeqSNP, a targeted genotype by sequencing method that offers the capability to target specific SNP loci and enables de novo discovery of new SNPs. The SNPs were identified through a SNP mining approach based on coding sequences of red clover genes known for their involvement in development and stress responses. After filtering the genotypic data using various criteria, 623 bi-allelic SNPs, including 327 originally targeted and 296 de novo discovered SNPs were used for population genetics analyses. Seventy-one of the SNP loci were under selection considering both Hardy-Weinberg equilibrium and pairwise FST distributions. The average observed heterozygosity (H O ), within population diversity (H S ) and overall diversity (H T ) were 0.22, 0.21 and 0.22, respectively. The tetraploids had higher average H O (0.35) than diploids (0.21). The analysis of molecular variance (AMOVA) showed low but significant variation among accessions (5.4%; P < 0.001), and among diploids and tetraploids (1.08%; P = 0.02). This study revealed a low mean inbreeding coefficient (FIS = -0.04) exhibiting the strict outcrossing nature of red clover. As per cluster, principal coordinate and discriminant analyses, most wild populations were grouped together and were clearly differentiated from the cultivated types. The cultivated types of red clover had a similar level of genetic diversity, suggesting that modern red clover breeding programs did not negatively affect genetic diversity or population structure. Hence, the breeding material used by Lantmännen represents the major genetic resources in Scandinavia. This knowledge of how different types of red clover accessions relate to each other and the level of outcrossing and heterozygosity will be useful for future red clover breeding.
Collapse
|
33
|
Variation in Ribosomal DNA in the Genus Trifolium (Fabaceae). PLANTS 2021; 10:plants10091771. [PMID: 34579303 PMCID: PMC8465422 DOI: 10.3390/plants10091771] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 08/23/2021] [Indexed: 01/13/2023]
Abstract
The genus Trifolium L. is characterized by basic chromosome numbers 8, 7, 6, and 5. We conducted a genus-wide study of ribosomal DNA (rDNA) structure variability in diploids and polyploids to gain insight into evolutionary history. We used fluorescent in situ hybridization to newly investigate rDNA variation by number and position in 30 Trifolium species. Evolutionary history among species was examined using 85 available sequences of internal transcribed spacer 1 (ITS1) of 35S rDNA. In diploid species with ancestral basic chromosome number (x = 8), one pair of 5S and 26S rDNA in separate or adjacent positions on a pair of chromosomes was prevalent. Genomes of species with reduced basic chromosome numbers were characterized by increased number of signals determined on one pair of chromosomes or all chromosomes. Increased number of signals was observed also in diploids Trifolium alpestre and Trifolium microcephalum and in polyploids. Sequence alignment revealed ITS1 sequences with mostly single nucleotide polymorphisms, and ITS1 diversity was greater in diploids with reduced basic chromosome numbers compared to diploids with ancestral basic chromosome number (x = 8) and polyploids. Our results suggest the presence of one 5S rDNA site and one 26S rDNA site as an ancestral state.
Collapse
|
34
|
Wahdan SFM, Tanunchai B, Wu Y, Sansupa C, Schädler M, Dawoud TM, Buscot F, Purahong W. Deciphering Trifolium pratense L. holobiont reveals a microbiome resilient to future climate changes. Microbiologyopen 2021; 10:e1217. [PMID: 34459547 PMCID: PMC8302017 DOI: 10.1002/mbo3.1217] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 06/14/2021] [Accepted: 06/23/2021] [Indexed: 12/24/2022] Open
Abstract
The plant microbiome supports plant growth, fitness, and resistance against climate change. Trifolium pratense (red clover), an important forage legume crop, positively contributes to ecosystem sustainability. However, T. pratense is known to have limited adaptive ability toward climate change. Here, the T. pratense microbiomes (including both bacteria and fungi) of the rhizosphere and the root, shoot, and flower endospheres were comparatively examined using metabarcoding in a field located in Central Germany that mimics the climate conditions projected for the next 50-70 years in comparison with the current climate conditions. Additionally, the ecological functions and metabolic genes of the microbial communities colonizing each plant compartment were predicted using FUNGuild, FAPROTAX, and Tax4Fun annotation tools. Our results showed that the individual plant compartments were colonized by specific microbes. The bacterial and fungal community compositions of the belowground plant compartments did not vary under future climate conditions. However, future climate conditions slightly altered the relative abundances of specific fungal classes of the aboveground compartments. We predicted several microbial functional genes of the T. pratense microbiome involved in plant growth processes, such as biofertilization (nitrogen fixation, phosphorus solubilization, and siderophore biosynthesis) and biostimulation (phytohormone and auxin production). Our findings indicated that T. pratense microbiomes show a degree of resilience to future climate changes. Additionally, microbes inhabiting T. pratense may not only contribute to plant growth promotion but also to ecosystem sustainability.
Collapse
Affiliation(s)
- Sara Fareed Mohamed Wahdan
- Department of Soil EcologyUFZ‐Helmholtz Centre for Environmental ResearchHalle (Saale)Germany
- Department of BiologyLeipzig UniversityLeipzigGermany
- Botany DepartmentFaculty of ScienceSuez Canal UniversityIsmailiaEgypt
| | - Benjawan Tanunchai
- Department of Soil EcologyUFZ‐Helmholtz Centre for Environmental ResearchHalle (Saale)Germany
| | - Yu‐Ting Wu
- Department of ForestryNational Pingtung University of Science and TechnologyPingtungTaiwan
| | - Chakriya Sansupa
- Department of Soil EcologyUFZ‐Helmholtz Centre for Environmental ResearchHalle (Saale)Germany
| | - Martin Schädler
- Department of Community EcologyUFZ‐Helmholtz Centre for Environmental ResearchHalle (Saale)Germany
- German Centre for Integrative Biodiversity Research (iDiv)Halle‐Jena‐LeipzigLeipzigGermany
| | - Turki M. Dawoud
- Botany and Microbiology DepartmentCollege of ScienceKing Saud UniversityRiyadhSaudi Arabia
| | - François Buscot
- Department of Soil EcologyUFZ‐Helmholtz Centre for Environmental ResearchHalle (Saale)Germany
- German Centre for Integrative Biodiversity Research (iDiv)Halle‐Jena‐LeipzigLeipzigGermany
- Botany and Microbiology DepartmentCollege of ScienceKing Saud UniversityRiyadhSaudi Arabia
| | - Witoon Purahong
- Department of Soil EcologyUFZ‐Helmholtz Centre for Environmental ResearchHalle (Saale)Germany
| |
Collapse
|
35
|
Wang X, Liu S, Zuo H, Zheng W, Zhang S, Huang Y, Pingcuo G, Ying H, Zhao F, Li Y, Liu J, Yi TS, Zan Y, Larkin RM, Deng X, Zeng X, Xu Q. Genomic basis of high-altitude adaptation in Tibetan Prunus fruit trees. Curr Biol 2021; 31:3848-3860.e8. [PMID: 34314676 DOI: 10.1016/j.cub.2021.06.062] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 02/25/2021] [Accepted: 06/22/2021] [Indexed: 01/03/2023]
Abstract
The Great Himalayan Mountains and their foothills are believed to be the place of origin and development of many plant species. The genetic basis of adaptation to high plateaus is a fascinating topic that is poorly understood at the population level. We comprehensively collected and sequenced 377 accessions of Prunus germplasm along altitude gradients ranging from 2,067 to 4,492 m in the Himalayas. We de novo assembled three high-quality genomes of Tibetan Prunus species. A comparative analysis of Prunus genomes indicated a remarkable expansion of the SINE retrotransposons occurred in the genomes of Tibetan species. We observed genetic differentiation between Tibetan peaches from high and low altitudes and that genes associated with light stress signaling, especially UV stress signaling, were enriched in the differentiated regions. By profiling the metabolomes of Tibetan peach fruit, we determined 379 metabolites had significant genetic correlations with altitudes and that in particular phenylpropanoids were positively correlated with altitudes. We identified 62 Tibetan peach-specific SINEs that colocalized with metabolites differentially accumualted in Tibetan relative to cultivated peach. We demonstrated that two SINEs were inserted in a locus controlling the accumulation of 3-O-feruloyl quinic acid. SINE1 was specific to Tibetan peach. SINE2 was predominant in high altitudes and associated with the accumulation of 3-O-feruloyl quinic acid. These genomic and metabolic data for Prunus populations native to the Himalayan region indicate that the expansion of SINE retrotransposons helped Tibetan Prunus species adapt to the harsh environment of the Himalayan plateau by promoting the accumulation of beneficial metabolites.
Collapse
Affiliation(s)
- Xia Wang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070, China; Key Laboratory of Horticultural Crop (Fruit trees) Biology and Genetic Improvement (Ministry of Agriculture and Rural Affairs), Huazhong Agricultural University, Wuhan 430070, China
| | - Shengjun Liu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070, China; Key Laboratory of Horticultural Crop (Fruit trees) Biology and Genetic Improvement (Ministry of Agriculture and Rural Affairs), Huazhong Agricultural University, Wuhan 430070, China
| | - Hao Zuo
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070, China; Key Laboratory of Horticultural Crop (Fruit trees) Biology and Genetic Improvement (Ministry of Agriculture and Rural Affairs), Huazhong Agricultural University, Wuhan 430070, China
| | - Weikang Zheng
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070, China; Key Laboratory of Horticultural Crop (Fruit trees) Biology and Genetic Improvement (Ministry of Agriculture and Rural Affairs), Huazhong Agricultural University, Wuhan 430070, China
| | - Shanshan Zhang
- Qinghai-Tibet Plateau Fruit Trees Scientific Observation Test Station (Ministry of Agriculture and Rural Affairs), Lhasa, Tibet 850032, China; Institute of Vegetables, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet 850002, China
| | - Yue Huang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070, China; Key Laboratory of Horticultural Crop (Fruit trees) Biology and Genetic Improvement (Ministry of Agriculture and Rural Affairs), Huazhong Agricultural University, Wuhan 430070, China
| | - Gesang Pingcuo
- Qinghai-Tibet Plateau Fruit Trees Scientific Observation Test Station (Ministry of Agriculture and Rural Affairs), Lhasa, Tibet 850032, China; Institute of Vegetables, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet 850002, China
| | - Hong Ying
- Qinghai-Tibet Plateau Fruit Trees Scientific Observation Test Station (Ministry of Agriculture and Rural Affairs), Lhasa, Tibet 850032, China; Institute of Vegetables, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet 850002, China
| | - Fan Zhao
- Qinghai-Tibet Plateau Fruit Trees Scientific Observation Test Station (Ministry of Agriculture and Rural Affairs), Lhasa, Tibet 850032, China; Institute of Vegetables, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet 850002, China
| | - Yuanrong Li
- Qinghai-Tibet Plateau Fruit Trees Scientific Observation Test Station (Ministry of Agriculture and Rural Affairs), Lhasa, Tibet 850032, China; Institute of Vegetables, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet 850002, China
| | - Junwei Liu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070, China; Key Laboratory of Horticultural Crop (Fruit trees) Biology and Genetic Improvement (Ministry of Agriculture and Rural Affairs), Huazhong Agricultural University, Wuhan 430070, China
| | - Ting-Shuang Yi
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Yanjun Zan
- Department of Forestry Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå 90736, Sweden
| | - Robert M Larkin
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070, China
| | - Xiuxin Deng
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China; Key Laboratory of Horticultural Crop (Fruit trees) Biology and Genetic Improvement (Ministry of Agriculture and Rural Affairs), Huazhong Agricultural University, Wuhan 430070, China
| | - Xiuli Zeng
- Qinghai-Tibet Plateau Fruit Trees Scientific Observation Test Station (Ministry of Agriculture and Rural Affairs), Lhasa, Tibet 850032, China; Institute of Vegetables, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet 850002, China.
| | - Qiang Xu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China; Key Laboratory of Horticultural Crop (Fruit trees) Biology and Genetic Improvement (Ministry of Agriculture and Rural Affairs), Huazhong Agricultural University, Wuhan 430070, China.
| |
Collapse
|
36
|
Egan LM, Hofmann RW, Ghamkhar K, Hoyos-Villegas V. Prospects for Trifolium Improvement Through Germplasm Characterisation and Pre-breeding in New Zealand and Beyond. FRONTIERS IN PLANT SCIENCE 2021; 12:653191. [PMID: 34220882 PMCID: PMC8242581 DOI: 10.3389/fpls.2021.653191] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 05/10/2021] [Indexed: 06/13/2023]
Abstract
Trifolium is the most used pastoral legume genus in temperate grassland systems, and a common feature in meadows and open space areas in cities and parks. Breeding of Trifolium spp. for pastoral production has been going on for over a century. However, the breeding targets have changed over the decades in response to different environmental and production pressures. Relatively small gains have been made in Trifolium breeding progress. Trifolium breeding programmes aim to maintain a broad genetic base to maximise variation. New Zealand is a global hub in Trifolium breeding, utilising exotic germplasm imported by the Margot Forde Germplasm Centre. This article describes the history of Trifolium breeding in New Zealand as well as the role and past successes of utilising genebanks in forage breeding. The impact of germplasm characterisation and evaluation in breeding programmes is also discussed. The history and challenges of Trifolium breeding and its effect on genetic gain can be used to inform future pre-breeding decisions in this genus, as well as being a model for other forage legumes.
Collapse
Affiliation(s)
- Lucy M. Egan
- CSIRO Agriculture and Food, Narrabri, NSW, Australia
- Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln, New Zealand
| | - Rainer W. Hofmann
- Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln, New Zealand
| | - Kioumars Ghamkhar
- AgResearch Grasslands Research Centre, Palmerston North, New Zealand
| | - Valerio Hoyos-Villegas
- Department of Plant Science, Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, QC, Canada
| |
Collapse
|
37
|
Wang T, Ren L, Li C, Zhang D, Zhang X, Zhou G, Gao D, Chen R, Chen Y, Wang Z, Shi F, Farmer AD, Li Y, Zhou M, Young ND, Zhang WH. The genome of a wild Medicago species provides insights into the tolerant mechanisms of legume forage to environmental stress. BMC Biol 2021; 19:96. [PMID: 33957908 PMCID: PMC8103640 DOI: 10.1186/s12915-021-01033-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 04/21/2021] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND Medicago ruthenica, a wild and perennial legume forage widely distributed in semi-arid grasslands, is distinguished by its outstanding tolerance to environmental stress. It is a close relative of commonly cultivated forage of alfalfa (Medicago sativa). The high tolerance of M. ruthenica to environmental stress makes this species a valuable genetic resource for understanding and improving traits associated with tolerance to harsh environments. RESULTS We sequenced and assembled genome of M. ruthenica using an integrated approach, including PacBio, Illumina, 10×Genomics, and Hi-C. The assembled genome was 904.13 Mb with scaffold N50 of 99.39 Mb, and 50,162 protein-coding genes were annotated. Comparative genomics and transcriptomic analyses were used to elucidate mechanisms underlying its tolerance to environmental stress. The expanded FHY3/FAR1 family was identified to be involved in tolerance of M. ruthenica to drought stress. Many genes involved in tolerance to abiotic stress were retained in M. ruthenica compared to other cultivated Medicago species. Hundreds of candidate genes associated with drought tolerance were identified by analyzing variations in single nucleotide polymorphism using accessions of M. ruthenica with varying tolerance to drought. Transcriptomic data demonstrated the involvements of genes related to transcriptional regulation, stress response, and metabolic regulation in tolerance of M. ruthenica. CONCLUSIONS We present a high-quality genome assembly and identification of drought-related genes in the wild species of M. ruthenica, providing a valuable resource for genomic studies on perennial legume forages.
Collapse
Affiliation(s)
- Tianzuo Wang
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, The Chinese Academy of Sciences, Beijing, China
| | - Lifei Ren
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, The Chinese Academy of Sciences, Beijing, China
| | - Caihong Li
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, The Chinese Academy of Sciences, Beijing, China
| | - Di Zhang
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, The Chinese Academy of Sciences, Beijing, China
| | - Xiuxiu Zhang
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, The Chinese Academy of Sciences, Beijing, China
| | - Gang Zhou
- Novogene Bioinformatics Institute, Beijing, China
| | - Dan Gao
- Novogene Bioinformatics Institute, Beijing, China
| | - Rujin Chen
- School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Yuhui Chen
- School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Zhaolan Wang
- Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Huhehot, China
| | - Fengling Shi
- College of Ecology and Environmental Science, Inner Mongolia Agricultural University, Huhehot, China
| | - Andrew D Farmer
- National Centre for Genome Resources, Santa Fe, New Mexico, USA
| | - Yansu Li
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Mengyan Zhou
- Novogene Bioinformatics Institute, Beijing, China.
| | - Nevin D Young
- Departments of Plant Pathology and Plant Biology, University of Minnesota, Minnesota, USA
| | - Wen-Hao Zhang
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, The Chinese Academy of Sciences, Beijing, China.
- Inner Mongolia Research Centre for Prataculture, The Chinese Academy of Sciences, Beijing, China.
| |
Collapse
|
38
|
Zheng T, Li P, Li L, Zhang Q. Research advances in and prospects of ornamental plant genomics. HORTICULTURE RESEARCH 2021; 8:65. [PMID: 33790259 PMCID: PMC8012582 DOI: 10.1038/s41438-021-00499-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 01/04/2021] [Accepted: 01/11/2021] [Indexed: 05/14/2023]
Abstract
The term 'ornamental plant' refers to all plants with ornamental value, which generally have beautiful flowers or special plant architectures. China is rich in ornamental plant resources and known as the "mother of gardens". Genomics is the science of studying genomes and is useful for carrying out research on genome evolution, genomic variations, gene regulation, and important biological mechanisms based on detailed genome sequence information. Due to the diversity of ornamental plants and high sequencing costs, the progress of genome research on ornamental plants has been slow for a long time. With the emergence of new sequencing technologies and a reduction in costs since the whole-genome sequencing of the first ornamental plant (Prunus mume) was completed in 2012, whole-genome sequencing of more than 69 ornamental plants has been completed in <10 years. In this review, whole-genome sequencing and resequencing of ornamental plants will be discussed. We provide analysis with regard to basic data from whole-genome studies of important ornamental plants, the regulation of important ornamental traits, and application prospects.
Collapse
Affiliation(s)
- Tangchun Zheng
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China
| | - Ping Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China
| | - Lulu Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China
| | - Qixiang Zhang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China.
| |
Collapse
|
39
|
Malaviya DR, Roy AK, Kaushal P, Pathak S, Kalendar R. Phenotype study of multifoliolate leaf formation in Trifolium alexandrinum L. PeerJ 2021; 9:e10874. [PMID: 33717683 PMCID: PMC7936568 DOI: 10.7717/peerj.10874] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 01/11/2021] [Indexed: 12/02/2022] Open
Abstract
Background The genus Trifolium is characterized by typical trifoliolate leaves. Alterations in leaf formats from trifoliolate to multifoliolate, i.e., individual plants bearing trifoliolate, quadrifoliolate, pentafoliolate or more leaflets, were previously reported among many species of the genus. The study is an attempt to develop pure pentafoliolate plants of T. alexandrinum and to understand its genetic control. Methods The experimental material consisted of two populations of T. alexandrinum with multifoliolate leaf expression, i.e.,interspecific hybrid progenies of T. alexandrinum with T. apertum, and T. alexandrinum genotype Penta-1. Penetrance of the multifoliolate trait was observed among multifoliolate and trifoliolate plant progenies. In vitro culture and regeneration of plantlets from the axillary buds from different plant sources was also attempted. Results The inheritance among a large number of plant progenies together with in vitro micro-propagation results did not establish a definite pattern. The multifoliolate leaf formation was of chimeric nature, i.e., more than one leaf format appearing on individual branches. Reversal to normal trifoliolate from multifoliolate was also quite common. Penetrance and expression of multifoliolate leaf formation was higher among the plants raised from multifoliolate plants. Multifoliolate and pure pentafoliolate plants were observed in the progenies of pure trifoliolate plants and vice-versa. There was an apparent increase in the pentafoliolate leaf formation frequency over the years due to targeted selection. A few progenies of the complete pentafoliolate plants in the first year were true breeding in the second year. Frequency of plantlets with multifoliolate leaf formation was also higher in in vitro axillary bud multiplication when the explant bud was excised from the multifoliolate leaf node. Conclusion Number of leaflets being a discrete variable, occurrence of multifoliolate leaves on individual branches, reversal of leaf formats on branches and developing true breeding pentafoliolates were the factors leading to a hypothesis beyond normal Mendelian inheritance. Transposable elements (TEs) involved in leaf development in combination with epigenetics were probably responsible for alterations in the expression of leaflet number. Putative TE’s movement owing to chromosomal rearrangements possibly resulted in homozygous pentafoliolate trait with evolutionary significance. The hypothesis provides a new insight into understanding the genetic control of this trait in T. alexandrinum and may also be useful in other Trifolium species where such observations are reported.
Collapse
Affiliation(s)
- Devendra Ram Malaviya
- ICAR - Indian Institute of Sugarcane Research, Lucknow, India.,ICAR - Indian Grassland and Fodder Research Institute, Jhansi, India
| | - Ajoy Kumar Roy
- ICAR - Indian Grassland and Fodder Research Institute, Jhansi, India
| | - Pankaj Kaushal
- ICAR - Indian Grassland and Fodder Research Institute, Jhansi, India.,ICAR - National Institute of Biotic Stress Management, Raipur, India
| | - Shalini Pathak
- ICAR - Indian Grassland and Fodder Research Institute, Jhansi, India
| | - Ruslan Kalendar
- Department of Agricultural Sciences, University of Helsinki, Helsinki, Uusimaa, Finland.,National Laboratory Astana, Nazarbayev University, Nur-Sultan, Aqmola, Kazakhstan
| |
Collapse
|
40
|
Dinkins RD, Hancock J, Coe BL, May JB, Goodman JP, Bass WT, Liu J, Fan Y, Zheng Q, Zhu H. Isoflavone levels, nodulation and gene expression profiles of a CRISPR/Cas9 deletion mutant in the isoflavone synthase gene of red clover. PLANT CELL REPORTS 2021; 40:517-528. [PMID: 33389047 DOI: 10.1007/s00299-020-02647-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 12/01/2020] [Indexed: 06/12/2023]
Abstract
Isoflavones are not involved in rhizobial signaling in red clover, but likely play a role in defense in the rhizosphere. Red clover (Trifolium pratense) is a high-quality forage legume, well suited for grazing and hay production in the temperate regions of the world. Like many legumes, red clover produces a number of phenylpropanoid compounds including anthocyanidins, flavan-3-ols, flavanols, flavanones, flavones, and isoflavones. The study of isoflavone biosynthesis and accumulation in legumes has come into the forefront of biomedical and agricultural research due to potential for medicinal, antimicrobial, and environmental implications. CRISPR/Cas9 was used to knock out the function of a key enzyme in the biosynthesis of isoflavones, isoflavone synthase (IFS1). A hemizygous plant carrying a 9-bp deletion in the IFS1 gene was recovered and was intercrossed to obtain homozygous mutant plants. Levels of the isoflavones formononetin, biochanin A and genistein were significantly reduced in the mutant plants. Wild-type and mutant plants were inoculated with rhizobia to test the effect of the mutation on nodulation, but no significant differences were observed, suggesting that these isoflavones do not play important roles in nodulation. Gene expression profiling revealed an increase in expression of the upstream genes producing the precursors for IFS1, namely, phenylalanine ammonium lyase and chalcone synthase, but there were no significant differences in IFS1 gene expression or in the downstream genes in the production of specific isoflavones. Higher expression in genes involved in ethylene response was observed in the mutant plants. This response is normally associated with biotic stress, suggesting that the plants may have been responding to cues in the surrounding rhizosphere due to lower levels of isoflavones.
Collapse
Affiliation(s)
- Randy D Dinkins
- USDA-ARS, Forage-Animal Production Research Unit, Lexington, KY, USA.
| | - Julie Hancock
- College of Agriculture, Food and Environment, University of Kentucky, Lexington, KY, USA
| | - Brenda L Coe
- USDA-ARS, Forage-Animal Production Research Unit, Lexington, KY, USA
| | - John B May
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, USA
| | - Jack P Goodman
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, USA
| | - William T Bass
- USDA-ARS, Forage-Animal Production Research Unit, Lexington, KY, USA
| | - Jinge Liu
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, USA
| | - Yinglun Fan
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, USA
- College of Agriculture, Liaocheng University, Liaocheng, China
| | - Qiaolin Zheng
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, USA
- Department of Plant Pathology, University of Florida, IFAS, Fort Pierce, FL, USA
| | - Hongyan Zhu
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, USA
| |
Collapse
|
41
|
Herbert DB, Gross T, Rupp O, Becker A. Transcriptome analysis reveals major transcriptional changes during regrowth after mowing of red clover (Trifolium pratense). BMC PLANT BIOLOGY 2021; 21:95. [PMID: 33588756 PMCID: PMC7885512 DOI: 10.1186/s12870-021-02867-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 02/01/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Red clover (Trifolium pratense) is globally used as a fodder plant due its high nutritional value and soil improving qualities. In response to mowing, red clover exhibits specific morphological traits to compensate the loss of biomass. The morphological reaction is well described, but the underlying molecular mechanisms and its role for plants grown in the field are unclear. RESULTS Here, we characterize the global transcriptional response to mowing of red clover by comparing plants grown under greenhouse conditions with plants growing on agriculturally used fields. Unexpectedly, we found that biotic and abiotic stress related changes of plants grown in the field overlay their regrowth related transcriptional changes and characterized transcription related protein families involved in these processes. Further, we can show that gibberellins, among other phytohormones, also contribute to the developmental processes related to regrowth after biomass-loss. CONCLUSIONS Our findings show that massive biomass loss triggers less transcriptional changes in field grown plants than their struggle with biotic and abiotic stresses and that gibberellins also play a role in the developmental program related to regrowth after mowing in red clover. Our results provide first insights into the physiological and developmental processes of mowing on red clover and may serve as a base for red clover yield improvement.
Collapse
Affiliation(s)
- Denise Brigitte Herbert
- Justus Liebig University, Institute of Botany, Heinrich-Buff-Ring 38, D-35392, Giessen, Germany
| | - Thomas Gross
- Justus Liebig University, Institute of Botany, Heinrich-Buff-Ring 38, D-35392, Giessen, Germany
| | - Oliver Rupp
- Department of Bioinformatics and Systems Biology, Justus Liebig University, Heinrich-Buff-Ring 26-32, D-35392, Giessen, Germany
| | - Annette Becker
- Justus Liebig University, Institute of Botany, Heinrich-Buff-Ring 38, D-35392, Giessen, Germany.
| |
Collapse
|
42
|
Giraldo PA, Shinozuka H, Spangenberg GC, Smith KF, Cogan NOI. Rapid and Detailed Characterization of Transgene Insertion Sites in Genetically Modified Plants via Nanopore Sequencing. FRONTIERS IN PLANT SCIENCE 2021; 11:602313. [PMID: 33613582 PMCID: PMC7889508 DOI: 10.3389/fpls.2020.602313] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 12/24/2020] [Indexed: 05/15/2023]
Abstract
Molecular characterization of genetically modified plants can provide crucial information for the development of detection and identification methods, to comply with traceability, and labeling requirements prior to commercialization. Detailed description of the genetic modification was previously a challenging step in the safety assessment, since it required the use of laborious and time-consuming techniques. In this study an accurate, simple, and fast method was developed for molecular characterization of genetically modified (GM) plants, following a user-friendly workflow for researchers with limited bioinformatic capabilities. Three GM events from a diverse array of crop species-perennial ryegrass, white clover, and canola-were used to test the approach that exploits long-read sequencing by the MinION device, from Oxford Nanopore Technologies. The method delivered a higher degree of resolution of the transgenic events within the host genome than has previously been possible with the standard Illumina short-range sequencing strategies. The flanking sequences, copy number, and presence of backbone sequences, and overall transgene insertion structure were determined for each of the plant genomes, with the additional identification of moderate-sized secondary insertions that would have previously been missed. The proposed workflow takes only about 1 week from DNA extraction to analyzed result, and the method will complement the existing approaches for molecular characterization of GM plants, since it makes the process faster, simpler, and more cost-effective.
Collapse
Affiliation(s)
- Paula A. Giraldo
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, Australia
- Agriculture Victoria Research, AgriBio, The Centre for AgriBioscience, Bundoora, VIC, Australia
| | - Hiroshi Shinozuka
- Agriculture Victoria Research, AgriBio, The Centre for AgriBioscience, Bundoora, VIC, Australia
| | - German C. Spangenberg
- Agriculture Victoria Research, AgriBio, The Centre for AgriBioscience, Bundoora, VIC, Australia
- AgriBio, The Centre for AgriBioscience, School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
| | - Kevin F. Smith
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, Australia
- Agriculture Victoria Research, Hamilton, VIC, Australia
| | - Noel O. I. Cogan
- Agriculture Victoria Research, AgriBio, The Centre for AgriBioscience, Bundoora, VIC, Australia
- AgriBio, The Centre for AgriBioscience, School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
| |
Collapse
|
43
|
Worthington M, Perez JG, Mussurova S, Silva-Cordoba A, Castiblanco V, Cardoso Arango JA, Jones C, Fernandez-Fuentes N, Skot L, Dyer S, Tohme J, Di Palma F, Arango J, Armstead I, De Vega JJ. A new genome allows the identification of genes associated with natural variation in aluminium tolerance in Brachiaria grasses. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:302-319. [PMID: 33064149 PMCID: PMC7853602 DOI: 10.1093/jxb/eraa469] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 10/12/2020] [Indexed: 05/08/2023]
Abstract
Toxic concentrations of aluminium cations and low phosphorus availability are the main yield-limiting factors in acidic soils, which represent half of the potentially available arable land. Brachiaria grasses, which are commonly sown as forage in the tropics because of their resilience and low demand for nutrients, show greater tolerance to high concentrations of aluminium cations (Al3+) than most other grass crops. In this work, we explored the natural variation in tolerance to Al3+ between high and low tolerant Brachiaria species and characterized their transcriptional differences during stress. We identified three QTLs (quantitative trait loci) associated with root vigour during Al3+ stress in their hybrid progeny. By integrating these results with a new Brachiaria reference genome, we identified 30 genes putatively responsible for Al3+ tolerance in Brachiaria. We observed differential expression during stress of genes involved in RNA translation, response signalling, cell wall composition, and vesicle location homologous to aluminium-induced proteins involved in limiting uptake or localizing the toxin. However, there was limited regulation of malate transporters in Brachiaria, which suggests that exudation of organic acids and other external tolerance mechanisms, common in other grasses, might not be relevant in Brachiaria. The contrasting regulation of RNA translation and response signalling suggests that response timing is critical in high Al3+-tolerant Brachiaria.
Collapse
Affiliation(s)
- Margaret Worthington
- International Center for Tropical Agriculture (CIAT), Cali, Colombia
- Present address: Department of Horticulture, University of Arkansas, 306 Plant Sciences Bldg, Fayetteville, AR 72701, USA
| | | | | | | | | | | | - Charlotte Jones
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Aberystwyth, UK
| | - Narcis Fernandez-Fuentes
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Aberystwyth, UK
| | - Leif Skot
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Aberystwyth, UK
| | - Sarah Dyer
- Earlham Institute, Norwich Research Park, Norwich, UK
- Present address: NIAB, Huntingdon Road, Cambridge CB3 0LE, UK
| | - Joe Tohme
- International Center for Tropical Agriculture (CIAT), Cali, Colombia
| | | | - Jacobo Arango
- International Center for Tropical Agriculture (CIAT), Cali, Colombia
| | - Ian Armstead
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Aberystwyth, UK
| | - Jose J De Vega
- Earlham Institute, Norwich Research Park, Norwich, UK
- Correspondence:
| |
Collapse
|
44
|
Abstract
Miscanthus sacchariflorus (Maxim.) Hack. is a highly productive C4 perennial rhizomatous biofuel grass crop. M. sacchariflorus is among the most widely distributed species in the genus, particularly at cold northern latitudes, and is one of the progenitor species of the commercial M. × giganteus genotypes. We generated a 2.54 Gb whole-genome assembly of the diploid M. sacchariflorus cv. "Robustus 297" genotype, which represented ~59% of the expected total genome size. We later anchored this assembly using the chromosomes from the M. sinensis genome to generate a second assembly with improved contiguity. We annotated 86,767 and 69,049 protein-coding genes in the unanchored and anchored assemblies, respectively. We estimated our assemblies included ~85% of the M. sacchariflorus genes based on homology and core markers. The utility of the new reference for genomic studies was evidenced by a 99% alignment rate of the RNA-seq reads from the same genotype. The raw data, unanchored and anchored assemblies, and respective gene annotations are publicly available.
Collapse
Affiliation(s)
| | - Iain Donnison
- Institute of Biological, Environmental & Rural Sciences (IBERS) - Aberystwyth University, Aberystwyth, SY23 3EE, UK
| | | | - Kerrie Farrar
- Institute of Biological, Environmental & Rural Sciences (IBERS) - Aberystwyth University, Aberystwyth, SY23 3EE, UK
| |
Collapse
|
45
|
Chromosome-level genome assembly of Ophiorrhiza pumila reveals the evolution of camptothecin biosynthesis. Nat Commun 2021; 12:405. [PMID: 33452249 PMCID: PMC7810986 DOI: 10.1038/s41467-020-20508-2] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 12/07/2020] [Indexed: 01/29/2023] Open
Abstract
Plant genomes remain highly fragmented and are often characterized by hundreds to thousands of assembly gaps. Here, we report chromosome-level reference and phased genome assembly of Ophiorrhiza pumila, a camptothecin-producing medicinal plant, through an ordered multi-scaffolding and experimental validation approach. With 21 assembly gaps and a contig N50 of 18.49 Mb, Ophiorrhiza genome is one of the most complete plant genomes assembled to date. We also report 273 nitrogen-containing metabolites, including diverse monoterpene indole alkaloids (MIAs). A comparative genomics approach identifies strictosidine biogenesis as the origin of MIA evolution. The emergence of strictosidine biosynthesis-catalyzing enzymes precede downstream enzymes' evolution post γ whole-genome triplication, which occurred approximately 110 Mya in O. pumila, and before the whole-genome duplication in Camptotheca acuminata identified here. Combining comparative genome analysis, multi-omics analysis, and metabolic gene-cluster analysis, we propose a working model for MIA evolution, and a pangenome for MIA biosynthesis, which will help in establishing a sustainable supply of camptothecin.
Collapse
|
46
|
Mello B, Tao Q, Barba-Montoya J, Kumar S. Molecular dating for phylogenies containing a mix of populations and species by using Bayesian and RelTime approaches. Mol Ecol Resour 2020; 21:122-136. [PMID: 32881388 DOI: 10.1111/1755-0998.13249] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 08/14/2020] [Accepted: 08/19/2020] [Indexed: 12/11/2022]
Abstract
Simultaneous molecular dating of population and species divergences is essential in many biological investigations, including phylogeography, phylodynamics and species delimitation studies. In these investigations, multiple sequence alignments consist of both intra- and interspecies samples (mixed samples). As a result, the phylogenetic trees contain interspecies, interpopulation and within-population divergences. Bayesian relaxed clock methods are often employed in these analyses, but they assume the same tree prior for both inter- and intraspecies branching processes and require specification of a clock model for branch rates (independent vs. autocorrelated rates models). We evaluated the impact of a single tree prior on Bayesian divergence time estimates by analysing computer-simulated data sets. We also examined the effect of the assumption of independence of evolutionary rate variation among branches when the branch rates are autocorrelated. Bayesian approach with coalescent tree priors generally produced excellent molecular dates and highest posterior densities with high coverage probabilities. We also evaluated the performance of a non-Bayesian method, RelTime, which does not require the specification of a tree prior or a clock model. RelTime's performance was similar to that of the Bayesian approach, suggesting that it is also suitable to analyse data sets containing both populations and species variation when its computational efficiency is needed.
Collapse
Affiliation(s)
- Beatriz Mello
- Department of Genetics, Federal University of Rio de Janeiro, Brazil.,Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA, USA
| | - Qiqing Tao
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA, USA.,Center for Excellence in Genome Medicine and Research, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Jose Barba-Montoya
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA, USA.,Center for Excellence in Genome Medicine and Research, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Sudhir Kumar
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA, USA.,Center for Excellence in Genome Medicine and Research, King Abdulaziz University, Jeddah, Saudi Arabia
| |
Collapse
|
47
|
Abd El-Wahab MMH, Aljabri M, Sarhan MS, Osman G, Wang S, Mabrouk M, El-Shabrawi HM, Gabr AMM, Abd El-Haliem AM, O’Sullivan DM, El-Soda M. High-Density SNP-Based Association Mapping of Seed Traits in Fenugreek Reveals Homology with Clover. Genes (Basel) 2020; 11:E893. [PMID: 32764325 PMCID: PMC7464718 DOI: 10.3390/genes11080893] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Revised: 07/28/2020] [Accepted: 08/02/2020] [Indexed: 12/02/2022] Open
Abstract
Fenugreek as a self-pollinated plant is ideal for genome-wide association mapping where traits can be marked by their association with natural mutations. However, fenugreek is poorly investigated at the genomic level due to the lack of information regarding its genome. To fill this gap, we genotyped a collection of 112 genotypes with 153,881 SNPs using double digest restriction site-associated DNA sequencing. We used 38,142 polymorphic SNPs to prove the suitability of the population for association mapping. One significant SNP was associated with both seed length and seed width, and another SNP was associated with seed color. Due to the lack of a comprehensive genetic map, it is neither possible to align the newly developed markers to chromosomes nor to predict the underlying genes. Therefore, systematic targeting of those markers to homologous genomes of other legumes can overcome those problems. A BLAST search using the genomic fenugreek sequence flanking the identified SNPs showed high homology with several members of the Trifolieae tribe indicating the potential of translational approaches to improving our understanding of the fenugreek genome. Using such a comprehensively-genotyped fenugreek population is the first step towards identifying genes underlying complex traits and to underpin fenugreek marker-assisted breeding programs.
Collapse
Affiliation(s)
- Mustafa M. H. Abd El-Wahab
- Department of Agronomy, Faculty of Agriculture, Cairo University, Giza 12613, Egypt; (M.M.H.A.E.-W.); (M.M.)
| | - Maha Aljabri
- Department of Biology, Faculty of Applied Sciences, Umm Al-Qura University, Makkah 21955, Saudi Arabia; (M.A.); (G.O.)
- Research Laboratories Centre, Faculty of Applied Science, Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | - Mohamed S. Sarhan
- Environmental Studies and Research Unit, Cairo University, Giza 12613, Egypt;
| | - Gamal Osman
- Department of Biology, Faculty of Applied Sciences, Umm Al-Qura University, Makkah 21955, Saudi Arabia; (M.A.); (G.O.)
- Research Laboratories Centre, Faculty of Applied Science, Umm Al-Qura University, Makkah 21955, Saudi Arabia
- Agricultural Genetic Engineering Research Institute (AGERI), ARC, Giza 12915, Egypt
| | - Shichen Wang
- Genomics and Bioinformatics Service Texas A&M AgriLife Research, Amarillo College Station, Amarillo, TX 77845, USA;
| | - Mahmoud Mabrouk
- Department of Agronomy, Faculty of Agriculture, Cairo University, Giza 12613, Egypt; (M.M.H.A.E.-W.); (M.M.)
| | - Hattem M. El-Shabrawi
- Plant Biotechnology Department, National Research Center, Giza 12622, Egypt; (H.M.E.-S.); (A.M.M.G.)
| | - Ahmed M. M. Gabr
- Plant Biotechnology Department, National Research Center, Giza 12622, Egypt; (H.M.E.-S.); (A.M.M.G.)
| | - Ahmed M. Abd El-Haliem
- Plant Physiology, University of Amsterdam, Swammerdam Institute for Life Sciences Amsterdam, 1098 XH Amsterdam, The Netherlands;
| | - Donal M. O’Sullivan
- School of Agriculture, Policy and Development, University of Reading, Whiteknights, Reading RG6 6AR, UK;
| | - Mohamed El-Soda
- Department of Genetics, Faculty of Agriculture, Cairo University, Giza 12613, Egypt
| |
Collapse
|
48
|
Nelson MN, Jabbari JS, Turakulov R, Pradhan A, Pazos-Navarro M, Stai JS, Cannon SB, Real D. The First Genetic Map for a Psoraleoid Legume ( Bituminaria bituminosa) Reveals Highly Conserved Synteny with Phaseoloid Legumes. PLANTS (BASEL, SWITZERLAND) 2020; 9:E973. [PMID: 32752081 PMCID: PMC7463921 DOI: 10.3390/plants9080973] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 07/27/2020] [Accepted: 07/29/2020] [Indexed: 11/17/2022]
Abstract
We present the first genetic map of tedera (Bituminaria bituminosa (L.) C.H. Stirton), a drought-tolerant forage legume from the Canary Islands with useful pharmaceutical properties. It is also the first genetic map for any species in the tribe Psoraleeae (Fabaceae). The map comprises 2042 genotyping-by-sequencing (GBS) markers distributed across 10 linkage groups, consistent with the haploid chromosome count for this species (n = 10). Sequence tags from the markers were used to find homologous matches in the genome sequences of the closely related species in the Phaseoleae tribe: soybean, common bean, and cowpea. No tedera linkage groups align in their entirety to chromosomes in any of these phaseoloid species, but there are long stretches of collinearity that could be used in tedera research for gene discovery purposes using the better-resourced phaseoloid species. Using Ks analysis of a tedera transcriptome against five legume genomes provides an estimated divergence time of 17.4 million years between tedera and soybean. Genomic information and resources developed here will be invaluable for breeding tedera varieties for forage and pharmaceutical purposes.
Collapse
Affiliation(s)
- Matthew N. Nelson
- CSIRO Agriculture & Food, Floreat, WA 6014, Australia
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6009, Australia
- Royal Botanic Gardens Kew, Millennium Seed Bank, Ardingly RH17 6TN, UK
| | - Jafar S. Jabbari
- Australian Genome Research Facility, Victorian Comprehensive Cancer Centre, Melbourne, VIC 3000, Australia; (J.S.J.); (R.T.)
| | - Rust Turakulov
- Australian Genome Research Facility, Victorian Comprehensive Cancer Centre, Melbourne, VIC 3000, Australia; (J.S.J.); (R.T.)
- Research School of Biology & Centre for Biodiversity Analysis, 134 Linnaeus Way, Acton, ACT 2601, Australia
| | - Aneeta Pradhan
- School of Biological Sciences, The University of Western Australia, Perth, WA 6009, Australia;
| | - Maria Pazos-Navarro
- School of Agriculture and Environment, The University of Western Australia, Perth, WA 6009, Australia;
| | - Jacob S. Stai
- Interdepartmental Genetics and Genomics Graduate Program, Iowa State University, Ames, IA 50010, USA;
| | - Steven B. Cannon
- USDA-ARS, Corn Insects and Crop Genetics Research Unit, Ames, IA 50011, USA;
| | - Daniel Real
- Department of Primary Industries and Regional Development, South Perth, WA 6151, Australia;
| |
Collapse
|
49
|
Yadav A, Fernández-Baca D, Cannon SB. Family-Specific Gains and Losses of Protein Domains in the Legume and Grass Plant Families. Evol Bioinform Online 2020; 16:1176934320939943. [PMID: 32694909 PMCID: PMC7350399 DOI: 10.1177/1176934320939943] [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: 06/09/2020] [Accepted: 06/15/2020] [Indexed: 11/27/2022] Open
Abstract
Protein domains can be regarded as sections of protein sequences capable of folding independently and performing specific functions. In addition to amino-acid level changes, protein sequences can also evolve through domain shuffling events such as domain insertion, deletion, or duplication. The evolution of protein domains can be studied by tracking domain changes in a selected set of species with known phylogenetic relationships. Here, we conduct such an analysis by defining domains as “features” or “descriptors,” and considering the species (target + outgroup) as instances or data-points in a data matrix. We then look for features (domains) that are significantly different between the target species and the outgroup species. We study the domain changes in 2 large, distinct groups of plant species: legumes (Fabaceae) and grasses (Poaceae), with respect to selected outgroup species. We evaluate 4 types of domain feature matrices: domain content, domain duplication, domain abundance, and domain versatility. The 4 types of domain feature matrices attempt to capture different aspects of domain changes through which the protein sequences may evolve—that is, via gain or loss of domains, increase or decrease in the copy number of domains along the sequences, expansion or contraction of domains, or through changes in the number of adjacent domain partners. All the feature matrices were analyzed using feature selection techniques and statistical tests to select protein domains that have significant different feature values in legumes and grasses. We report the biological functions of the top selected domains from the analysis of all the feature matrices. In addition, we also perform domain-centric gene ontology (dcGO) enrichment analysis on all selected domains from all 4 feature matrices to study the gene ontology terms associated with the significantly evolving domains in legumes and grasses. Domain content analysis revealed a striking loss of protein domains from the Fanconi anemia (FA) pathway, the pathway responsible for the repair of interstrand DNA crosslinks. The abundance analysis of domains found in legumes revealed an increase in glutathione synthase enzyme, an antioxidant required from nitrogen fixation, and a decrease in xanthine oxidizing enzymes, a phenomenon confirmed by previous studies. In grasses, the abundance analysis showed increases in domains related to gene silencing which could be due to polyploidy or due to enhanced response to viral infection. We provide a docker container that can be used to perform this analysis workflow on any user-defined sets of species, available at https://cloud.docker.com/u/akshayayadav/repository/docker/akshayayadav/protein-domain-evolution-project.
Collapse
Affiliation(s)
- Akshay Yadav
- Bioinformatics and Computational Biology Graduate Program, Iowa State University, Ames, IA, USA
| | | | - Steven B Cannon
- Corn Insects and Crop Genetics Research Unit, USDA-Agricultural Research Service, Ames, IA, USA
| |
Collapse
|
50
|
Population structure and genetic diversity in red clover (Trifolium pratense L.) germplasm. Sci Rep 2020; 10:8364. [PMID: 32433569 PMCID: PMC7239897 DOI: 10.1038/s41598-020-64989-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 04/22/2020] [Indexed: 01/29/2023] Open
Abstract
Red clover (Trifolium pratense L.) is a highly adaptable forage crop for temperate livestock agriculture. Genetic variation can be identified, via molecular techniques, and used to assess diversity among populations that may otherwise be indistinguishable. Here we have used genotyping by sequencing (GBS) to determine the genetic variation and population structure in red clover natural populations from Europe and Asia, and varieties or synthetic populations. Cluster analysis differentiated the collection into four large regional groups: Asia, Iberia, UK, and Central Europe. The five varieties clustered with the geographical area from which they were derived. Two methods (BayeScan and Samβada) were used to search for outlier loci indicating signatures of selection. A total of 60 loci were identified by both methods, but no specific genomic region was highlighted. The rate of decay in linkage disequilibrium was fast, and no significant evidence of any bottlenecks was found. Phenotypic analysis showed that a more prostrate and spreading growth habit was predominantly found among populations from Iberia and the UK. A genome wide association study identified a single nucleotide polymorphism (SNP) located in a homologue of the VEG2 gene from pea, associated with flowering time. The identification of genetic variation within the natural populations is likely to be useful for enhancing the breeding of red clover in the future.
Collapse
|