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Masters LE, Tomaszewska P, Schwarzacher T, Hackel J, Zuntini AR, Heslop-Harrison P, Vorontsova MS. Phylogenomic analysis reveals five independently evolved African forage grass clades in the genus Urochloa. Ann Bot 2024; 133:725-742. [PMID: 38365451 PMCID: PMC11082517 DOI: 10.1093/aob/mcae022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 02/21/2024] [Indexed: 02/18/2024]
Abstract
BACKGROUND AND AIMS The grass genus Urochloa (Brachiaria) sensu lato includes forage crops that are important for beef and dairy industries in tropical and sub-tropical Africa, South America and Oceania/Australia. Economically important species include U. brizantha, U. decumbens, U. humidicola, U. mutica, U. arrecta, U. trichopus, U. mosambicensis and Megathyrsus maximus, all native to the African continent. Perennial growth habits, large, fast growing palatable leaves, intra- and interspecific morphological variability, apomictic reproductive systems and frequent polyploidy are widely shared within the genus. The combination of these traits probably favoured the selection for forage domestication and weediness, but trait emergence across Urochloa cannot be modelled, as a robust phylogenetic assessment of the genus has not been conducted. We aim to produce a phylogeny for Urochloa that includes all important forage species, and identify their closest wild relatives (crop wild relatives). Finally, we will use our phylogeny and available trait data to infer the ancestral states of important forage traits across Urochloa s.l. and model the evolution of forage syndromes across the genus. METHODS Using a target enrichment sequencing approach (Angiosperm 353), we inferred a species-level phylogeny for Urochloa s.l., encompassing 54 species (~40 % of the genus) and outgroups. Phylogenies were inferred using a multispecies coalescent model and maximum likelihood method. We determined the phylogenetic placement of agriculturally important species and identified their closest wild relatives, or crop wild relatives, based on well-supported monophyly. Further, we mapped key traits associated with Urochloa forage crops to the species tree and estimated ancestral states for forage traits along branch lengths for continuous traits and at ancestral nodes in discrete traits. KEY RESULTS Agricultural species belong to five independent clades, including U. brizantha and U. decumbens lying in a previously defined species complex. Crop wild relatives were identified for these clades supporting previous sub-generic groupings in Urochloa based on morphology. Using ancestral trait estimation models, we find that five morphological traits that correlate with forage potential (perennial growth habits, culm height, leaf size, a winged rachis and large seeds) independently evolved in forage clades. CONCLUSIONS Urochloa s.l. is a highly diverse genus that contains numerous species with agricultural potential, including crop wild relatives that are currently underexploited. All forage species and their crop wild relatives naturally occur on the African continent and their conservation across their native distributions is essential. Genomic and phenotypic diversity in forage clade species and their wild relatives need to be better assessed both to develop conservation strategies and to exploit the diversity in the genus for improved sustainability in Urochloa cultivar production.
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Affiliation(s)
- Lizo E Masters
- Department of Genetics and Genome Biology, Institute for Environmental Futures, University of Leicester, Leicester LE17RH, UK
- Accelerated Taxonomy/Trait Diversity and Function, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB, UK
| | - Paulina Tomaszewska
- Department of Genetics and Genome Biology, Institute for Environmental Futures, University of Leicester, Leicester LE17RH, UK
- Department of Genetics and Cell Physiology, University of Wroclaw, 50-328 Wroclaw, Poland
| | - Trude Schwarzacher
- Department of Genetics and Genome Biology, Institute for Environmental Futures, University of Leicester, Leicester LE17RH, UK
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization/Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Jan Hackel
- Accelerated Taxonomy/Trait Diversity and Function, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB, UK
- Department of Biology, University of Marburg, Karl-von-Frisch-Straße 8, 35043 Marburg, Germany
| | - Alexandre R Zuntini
- Accelerated Taxonomy/Trait Diversity and Function, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB, UK
| | - Pat Heslop-Harrison
- Department of Genetics and Genome Biology, Institute for Environmental Futures, University of Leicester, Leicester LE17RH, UK
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization/Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Maria S Vorontsova
- Accelerated Taxonomy/Trait Diversity and Function, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB, UK
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Higgins J, Tomaszewska P, Pellny TK, Castiblanco V, Arango J, Tohme J, Schwarzacher T, Mitchell RA, Heslop-Harrison JS, De Vega JJ. Diverged subpopulations in tropical Urochloa (Brachiaria) forage species indicate a role for facultative apomixis and varying ploidy in their population structure and evolution. Ann Bot 2022; 130:657-669. [PMID: 36112370 PMCID: PMC9670755 DOI: 10.1093/aob/mcac115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 09/13/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Urochloa (syn. Brachiaria) is a genus of tropical grasses sown as forage feedstock, particularly in marginal soils. Here we aimed to clarify the genetic diversity and population structure in Urochloa species to understand better how population evolution relates to ploidy level and occurrence of apomictic reproduction. METHODS We explored the genetic diversity of 111 accessions from the five Urochloa species used to develop commercial cultivars. These accessions were conserved from wild materials collected at their centre of origin in Africa, and they tentatively represent the complete Urochloa gene pool used in breeding programmes. We used RNA-sequencing to generate 1.1 million single nucleotide polymorphism loci. We employed genetic admixture, principal component and phylogenetic analyses to define subpopulations. RESULTS We observed three highly differentiated subpopulations in U. brizantha, which were unrelated to ploidy: one intermixed with U. decumbens, and two diverged from the former and the other species in the complex. We also observed two subpopulations in U. humidicola, unrelated to ploidy; one subpopulation had fewer accessions but included the only characterized sexual accession in the species. Our results also supported a division of U. decumbens between diploids and polyploids, and no subpopulations within U. ruziziensis and U. maxima. CONCLUSIONS Polyploid U. decumbens are more closely related to polyploid U. brizantha than to diploid U. decumbens, which supports the divergence of both polyploid groups from a common tetraploid ancestor and provides evidence for the hybridization barrier of ploidy. The three differentiated subpopulations of apomictic polyploid U. brizantha accessions constitute diverged ecotypes, which can probably be utilized in hybrid breeding. Subpopulations were not observed in non-apomictic U. ruziziensis. Sexual Urochloa polyploids were not found (U. brizantha, U. decumbens) or were limited to small subpopulations (U. humidicola). The subpopulation structure observed in the Urochloa sexual-apomictic multiploidy complexes supports geographical parthenogenesis, where the polyploid genotypes exploit the evolutionary advantage of apomixis, i.e. uniparental reproduction and clonality, to occupy extensive geographical areas.
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Affiliation(s)
- J Higgins
- Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK
| | - P Tomaszewska
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
- Department of Genetics and Cell Physiology, Faculty of Biological Sciences, University of Wroclaw, 50-328 Wroclaw, Poland
| | - T K Pellny
- Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, UK
| | - V Castiblanco
- International Center for Tropical Agriculture (CIAT), 6713 Cali, Colombia
| | - J Arango
- International Center for Tropical Agriculture (CIAT), 6713 Cali, Colombia
| | - J Tohme
- International Center for Tropical Agriculture (CIAT), 6713 Cali, Colombia
| | - T Schwarzacher
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
| | - R A Mitchell
- Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, UK
| | - J S Heslop-Harrison
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization/Guangdong Provincial, Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
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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. J Exp Bot 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] [What about the content of this article? (0)] [Affiliation(s)] [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.
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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:
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