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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. ANNALS OF BOTANY 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] [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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Ferreira RCU, da Costa Lima Moraes A, Chiari L, Simeão RM, Vigna BBZ, de Souza AP. An Overview of the Genetics and Genomics of the Urochloa Species Most Commonly Used in Pastures. FRONTIERS IN PLANT SCIENCE 2021; 12:770461. [PMID: 34966402 PMCID: PMC8710810 DOI: 10.3389/fpls.2021.770461] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 11/17/2021] [Indexed: 06/14/2023]
Abstract
Pastures based on perennial monocotyledonous plants are the principal source of nutrition for ruminant livestock in tropical and subtropical areas across the globe. The Urochloa genus comprises important species used in pastures, and these mainly include Urochloa brizantha, Urochloa decumbens, Urochloa humidicola, and Urochloa ruziziensis. Despite their economic relevance, there is an absence of genomic-level information for these species, and this lack is mainly due to genomic complexity, including polyploidy, high heterozygosity, and genomes with a high repeat content, which hinders advances in molecular approaches to genetic improvement. Next-generation sequencing techniques have enabled the recent release of reference genomes, genetic linkage maps, and transcriptome sequences, and this information helps improve our understanding of the genetic architecture and molecular mechanisms involved in relevant traits, such as the apomictic reproductive mode. However, more concerted research efforts are still needed to characterize germplasm resources and identify molecular markers and genes associated with target traits. In addition, the implementation of genomic selection and gene editing is needed to reduce the breeding time and expenditure. In this review, we highlight the importance and characteristics of the four main species of Urochloa used in pastures and discuss the current findings from genetic and genomic studies and research gaps that should be addressed in future research.
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Affiliation(s)
| | - Aline da Costa Lima Moraes
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, Brazil
| | - Lucimara Chiari
- Embrapa Gado de Corte, Brazilian Agricultural Research Corporation, Campo Grande, Brazil
| | - Rosangela Maria Simeão
- Embrapa Gado de Corte, Brazilian Agricultural Research Corporation, Campo Grande, Brazil
| | | | - Anete Pereira de Souza
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, Brazil
- Department of Plant Biology, Biology Institute, University of Campinas (UNICAMP), Campinas, Brazil
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Tegegn A, Kyalo M, Mutai C, Hanson J, Asefa G, Djikeng A, Ghimire S. Genetic diversity and population structure of Brachiaria brizantha (A.Rich.) Stapf accessions from Ethiopia. AFRICAN JOURNAL OF RANGE & FORAGE SCIENCE 2019; 36:129-133. [PMID: 0 DOI: 10.2989/10220119.2019.1573760] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 01/11/2019] [Accepted: 01/20/2019] [Indexed: 05/24/2023]
Affiliation(s)
- Asheber Tegegn
- Ethiopian Institute of Agricultural Research, Addis Ababa, Ethiopia
- Biosciences Eastern and Central Africa–International Livestock Research Institute (BecA-ILRI) Hub, Nairobi, Kenya
| | - Martina Kyalo
- Biosciences Eastern and Central Africa–International Livestock Research Institute (BecA-ILRI) Hub, Nairobi, Kenya
| | - Collins Mutai
- Biosciences Eastern and Central Africa–International Livestock Research Institute (BecA-ILRI) Hub, Nairobi, Kenya
| | - Jean Hanson
- International Livestock Research Institute, Addis Ababa, Ethiopia
| | - Getnet Asefa
- Ethiopian Institute of Agricultural Research, Addis Ababa, Ethiopia
| | - Appolinaire Djikeng
- Biosciences Eastern and Central Africa–International Livestock Research Institute (BecA-ILRI) Hub, Nairobi, Kenya
- Current address: University of Edinburgh, Edinburgh, UK
| | - Sita Ghimire
- Biosciences Eastern and Central Africa–International Livestock Research Institute (BecA-ILRI) Hub, Nairobi, Kenya
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Souza JS, Chiari L, Simeão RM, de Mendonça Vilela M, Salgado LR. Development, Validation and Characterization of Genic Microsatellite Markers in <i>Urochloa</i> Species. ACTA ACUST UNITED AC 2018. [DOI: 10.4236/ajps.2018.92023] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Pessoa-Filho M, Martins AM, Ferreira ME. Molecular dating of phylogenetic divergence between Urochloa species based on complete chloroplast genomes. BMC Genomics 2017; 18:516. [PMID: 28683832 PMCID: PMC5499013 DOI: 10.1186/s12864-017-3904-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2016] [Accepted: 06/27/2017] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Forage species of Urochloa are planted in millions of hectares of tropical and subtropical pastures in South America. Most of the planted area is covered with four species (U. ruziziensis, U. brizantha, U. decumbens and U. humidicola). Breeding programs rely on interspecific hybridizations to increase genetic diversity and introgress traits of agronomic importance. Knowledge of phylogenetic relationships is important to optimize compatible hybridizations in Urochloa, where phylogeny has been subject of some controversy. We used next-generation sequencing to assemble the chloroplast genomes of four Urochloa species to investigate their phylogenetic relationships, compute their times of divergence and identify chloroplast DNA markers (microsatellites, SNPs and InDels). RESULTS Whole plastid genome sizes were 138,765 bp in U. ruziziensis, 138,945 bp in U. decumbens, 138,946 bp in U. brizantha and 138,976 bp in U. humidicola. Each Urochloa chloroplast genome contained 130 predicted coding regions and structural features that are typical of Panicoid grasses. U. brizantha and U. decumbens chloroplast sequences are highly similar and show reduced SNP, InDel and SSR polymorphism as compared to U. ruziziensis and U. humidicola. Most of the structural and sequence polymorphisms were located in intergenic regions, and reflected phylogenetic distances between species. Divergence of U. humidicola from a common ancestor with the three other Urochloa species was estimated at 9.46 mya. U. ruziziensis, U. decumbens, and U. brizantha formed a clade where the U. ruziziensis lineage would have diverged by 5.67 mya, followed by a recent divergence event between U. decumbens and U. brizantha around 1.6 mya. CONCLUSION Low-coverage Illumina sequencing allowed the successful sequence analysis of plastid genomes in four species of Urochloa used as forages in the tropics. Pairwise sequence comparisons detected multiple microsatellite, SNP and InDel sites prone to be used as molecular markers in genetic analysis of Urochloa. Our results placed the origin of U. humidicola and U. ruziziensis divergence in the Miocene-Pliocene boundary, and the split between U. brizantha and U. decumbens in the Pleistocene.
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Affiliation(s)
- Marco Pessoa-Filho
- Embrapa Cerrados, BR 020, Km 18, Planaltina, Brasília, 73310-970 DF Brazil
| | - Alexandre Magalhães Martins
- Laboratório de Genética Vegetal, Embrapa Recursos Genéticos e Biotecnologia, CP 02372 Brasília, Parque Estação Biológica, 70770-900 DF, Brazil
| | - Márcio Elias Ferreira
- Laboratório de Genética Vegetal, Embrapa Recursos Genéticos e Biotecnologia, CP 02372 Brasília, Parque Estação Biológica, 70770-900 DF, Brazil
- Embrapa Labex USA, Agricultural Research Service, United States Department of Agriculture, Beltsville Agricultural Research Center, Bldg 006 Rm 200, 10300 Ave, Belstville, Baltimore, MD 20705 USA
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Ondabu N, Maina S, Kimani W, Njarui D, Djikeng A, Ghimire S. Molecular Characterizations of Kenyan Brachiaria Grass Ecotypes with Microsatellite (SSR) Markers. AGRONOMY-BASEL 2017; 7:8. [PMID: 33304637 PMCID: PMC7672370 DOI: 10.3390/agronomy7010008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Accepted: 01/18/2017] [Indexed: 11/16/2022]
Abstract
Brachiaria grass is an emerging forage option for livestock production in Kenya. Kenya lies within the center of diversity for Brachiaria species, thus a high genetic variation in natural populations of Brachiaria is expected. Overgrazing and clearing of natural vegetation for crop production and nonagricultural uses and climate change continue to threaten the natural biodiversity. In this study, we collected 79 Brachiaria ecotypes from different parts of Kenya and examined them for genetic variations and their relatedness with 8 commercial varieties. A total of 120 different alleles were detected by 22 markers in the 79 ecotypes. Markers were highly informative in differentiating ecotypes with average diversity and polymorphic information content of 0.623 and 0.583, respectively. Five subpopulations: International Livestock Research Institute (ILRI), Kitui, Kisii, Alupe, and Kiminini differed in sample size, number of alleles, number of private alleles, diversity index, and percentage polymorphic loci. The contribution of within-the-individual difference to total genetic variation of Kenyan ecotype population was 81%, and the fixation index (FST = 0.021) and number of migrant per generation (Nm = 11.58) showed low genetic differentiation among the populations. The genetic distance was highest between Alupe and Kisii populations (0.510) and the lowest between ILRI and Kiminini populations (0.307). The unweighted neighbor-joining (NJ) tree showed test ecotypes grouped into three major clusters: ILRI ecotypes were present in all clusters; Kisii and Alupe ecotypes and improved varieties grouped in clusters I and II; and ecotypes from Kitui and Kiminini grouped in cluster I. This study confirms higher genetic diversity in Kenyan ecotypes than eight commercial varieties (Basilisk, Humidicola, Llanero, Marandú, MG4, Mulato II, Piatá and Xaraés) that represent three species and one three-way cross-hybrid Mulato II. There is a need for further collection of local ecotypes and their morphological, agronomical, and genetic characterizations to support Brachiaria grass breeding and conservation programs.
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Affiliation(s)
- Naftali Ondabu
- Biosciences Eastern and Central Africa-International Livestock Research Institute (BecA-ILRI) Hub, P.O. Box 30709, Nairobi 00100, Kenya; (N.O.); (S.M.); (W.K.); (A.D.)
- Kenya Agricultural and Livestock Research Organization (KALRO), P.O. Box 57811, Nairobi 00200, Kenya; (D.N.)
| | - Solomon Maina
- Biosciences Eastern and Central Africa-International Livestock Research Institute (BecA-ILRI) Hub, P.O. Box 30709, Nairobi 00100, Kenya; (N.O.); (S.M.); (W.K.); (A.D.)
| | - Wilson Kimani
- Biosciences Eastern and Central Africa-International Livestock Research Institute (BecA-ILRI) Hub, P.O. Box 30709, Nairobi 00100, Kenya; (N.O.); (S.M.); (W.K.); (A.D.)
| | - Donald Njarui
- Kenya Agricultural and Livestock Research Organization (KALRO), P.O. Box 57811, Nairobi 00200, Kenya; (D.N.)
| | - Appolinaire Djikeng
- Biosciences Eastern and Central Africa-International Livestock Research Institute (BecA-ILRI) Hub, P.O. Box 30709, Nairobi 00100, Kenya; (N.O.); (S.M.); (W.K.); (A.D.)
| | - Sita Ghimire
- Biosciences Eastern and Central Africa-International Livestock Research Institute (BecA-ILRI) Hub, P.O. Box 30709, Nairobi 00100, Kenya; (N.O.); (S.M.); (W.K.); (A.D.)
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Vigna BBZ, de Oliveira FA, de Toledo-Silva G, da Silva CC, do Valle CB, de Souza AP. Leaf transcriptome of two highly divergent genotypes of Urochloa humidicola (Poaceae), a tropical polyploid forage grass adapted to acidic soils and temporary flooding areas. BMC Genomics 2016; 17:910. [PMID: 27835957 PMCID: PMC5106776 DOI: 10.1186/s12864-016-3270-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2016] [Accepted: 11/05/2016] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Urochloa humidicola (Koronivia grass) is a polyploid (6x to 9x) species that is used as forage in the tropics. Facultative apospory apomixis is present in most of the genotypes of this species, although one individual has been described as sexual. Molecular studies have been restricted to molecular marker approaches for genetic diversity estimations and linkage map construction. The objectives of the present study were to describe and compare the leaf transcriptome of two important genotypes that are highly divergent in terms of their phenotypes and reproduction modes: the sexual BH031 and the aposporous apomictic cultivar BRS Tupi. RESULTS We sequenced the leaf transcriptome of Koronivia grass using an Illumina GAIIx system, which produced 13.09 Gb of data that consisted of 163,575,526 paired-end reads between the two libraries. We de novo-assembled 76,196 transcripts with an average length of 1,152 bp and filtered 35,093 non-redundant unigenes. A similarity search against the non-redundant National Center of Biotechnology Information (NCBI) protein database returned 65 % hits. We annotated 24,133 unigenes in the Phytozome database and 14,082 unigenes in the UniProtKB/Swiss-Prot database, assigned 108,334 gene ontology terms to 17,255 unigenes and identified 5,324 unigenes in 327 known metabolic pathways. Comparisons with other grasses via a reciprocal BLAST search revealed a larger number of orthologous genes for the Panicum species. The unigenes were involved in C4 photosynthesis, lignocellulose biosynthesis and flooding stress responses. A search for functional molecular markers revealed 4,489 microsatellites and 560,298 single nucleotide polymorphisms (SNPs). A quantitative real-time PCR analysis validated the RNA-seq expression analysis and allowed for the identification of transcriptomic differences between the two evaluated genotypes. Moreover, 192 unannotated sequences were classified as containing complete open reading frames, suggesting that the new, potentially exclusive genes should be further investigated. CONCLUSION The present study represents the first whole-transcriptome sequencing of U. humidicola leaves, providing an important public information source of transcripts and functional molecular markers. The qPCR analysis indicated that the expression of certain transcripts confirmed the differential expression observed in silico, which demonstrated that RNA-seq is useful for identifying differentially expressed and unique genes. These results corroborate the findings from previous studies and suggest a hybrid origin for BH031.
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Affiliation(s)
| | - Fernanda Ancelmo de Oliveira
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, SP Brazil
| | - Guilherme de Toledo-Silva
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, SP Brazil
- Present Address: Department of Biochemistry, Center of Biological Sciences, Federal University of Santa Catarina, Florianopolis, SC Brazil
| | - Carla Cristina da Silva
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, SP Brazil
| | | | - Anete Pereira de Souza
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, SP Brazil
- Department of Plant Biology, Biology Institute, UNICAMP, Campinas, SP Brazil
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Vigna BBZ, Santos JCS, Jungmann L, do Valle CB, Mollinari M, Pastina MM, Pagliarini MS, Garcia AAF, Souza AP. Evidence of Allopolyploidy in Urochloa humidicola Based on Cytological Analysis and Genetic Linkage Mapping. PLoS One 2016; 11:e0153764. [PMID: 27104622 PMCID: PMC4841517 DOI: 10.1371/journal.pone.0153764] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 04/04/2016] [Indexed: 01/30/2023] Open
Abstract
The African species Urochloa humidicola (Rendle) Morrone & Zuloaga (syn. Brachiaria humidicola (Rendle) Schweick.) is an important perennial forage grass found throughout the tropics. This species is polyploid, ranging from tetra to nonaploid, and apomictic, which makes genetic studies challenging; therefore, the number of currently available genetic resources is limited. The genomic architecture and evolution of U. humidicola and the molecular markers linked to apomixis were investigated in a full-sib F1 population obtained by crossing the sexual accession H031 and the apomictic cultivar U. humidicola cv. BRS Tupi, both of which are hexaploid. A simple sequence repeat (SSR)-based linkage map was constructed for the species from 102 polymorphic and specific SSR markers based on simplex and double-simplex markers. The map consisted of 49 linkage groups (LGs) and had a total length of 1702.82 cM, with 89 microsatellite loci and an average map density of 10.6 cM. Eight homology groups (HGs) were formed, comprising 22 LGs, and the other LGs remained ungrouped. The locus that controls apospory (apo-locus) was mapped in LG02 and was located 19.4 cM from the locus Bh027.c.D2. In the cytological analyses of some hybrids, bi- to hexavalents at diakinesis were observed, as well as two nucleoli in some meiocytes, smaller chromosomes with preferential allocation within the first metaphase plate and asynchronous chromosome migration to the poles during anaphase. The linkage map and the meiocyte analyses confirm previous reports of hybridization and suggest an allopolyploid origin of the hexaploid U. humidicola. This is the first linkage map of an Urochloa species, and it will be useful for future quantitative trait locus (QTL) analysis after saturation of the map and for genome assembly and evolutionary studies in Urochloa spp. Moreover, the results of the apomixis mapping are consistent with previous reports and confirm the need for additional studies to search for a co-segregating marker.
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Affiliation(s)
- Bianca B. Z. Vigna
- University of Campinas (UNICAMP), Center of Molecular Biology and Genetic Engineering (CBMEG), CP 6010, CEP 13083–970, Campinas, SP, Brazil
- Embrapa Pecuária Sudeste, CP 399, CEP 13560–970, São Carlos, SP, Brazil
| | - Jean C. S. Santos
- University of Campinas (UNICAMP), Center of Molecular Biology and Genetic Engineering (CBMEG), CP 6010, CEP 13083–970, Campinas, SP, Brazil
| | - Leticia Jungmann
- Embrapa Gado de Corte, Av. Radio Maia, 830, CEP 79106–550, Campo Grande, MS, Brazil
| | - Cacilda B. do Valle
- Embrapa Gado de Corte, Av. Radio Maia, 830, CEP 79106–550, Campo Grande, MS, Brazil
| | - Marcelo Mollinari
- University of São Paulo, Escola Superior de Agricultura Luiz de Queiroz, Department of Genetics, CP 83, CEP 13400–970, Piracicaba, SP, Brazil
| | - Maria M. Pastina
- Embrapa Milho e Sorgo, Rod. MG 424, Km 65, CEP 35701–970, Sete Lagoas, MG, Brazil
| | - Maria Suely Pagliarini
- University of Maringá (UEM), Department of Genetics and Cell Biology, Av. Colombo, 5790, Zona 7, CEP 87020–900, Maringá, PR, Brazil
| | - Antonio A. F. Garcia
- University of São Paulo, Escola Superior de Agricultura Luiz de Queiroz, Department of Genetics, CP 83, CEP 13400–970, Piracicaba, SP, Brazil
| | - Anete P. Souza
- University of Campinas (UNICAMP), Center of Molecular Biology and Genetic Engineering (CBMEG), CP 6010, CEP 13083–970, Campinas, SP, Brazil
- University of Campinas (UNICAMP), Biology Institute, Department of Plant Biology, CP6109, CEP 13083–970, Campinas, SP, Brazil
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Santos JCS, Barreto MA, Oliveira FA, Vigna BBZ, Souza AP. Microsatellite markers for Urochloa humidicola (Poaceae) and their transferability to other Urochloa species. BMC Res Notes 2015; 8:83. [PMID: 25889143 PMCID: PMC4365966 DOI: 10.1186/s13104-015-1044-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Accepted: 03/03/2015] [Indexed: 11/29/2022] Open
Abstract
Background Urochloa humidicola is a warm-season grass commonly used as forage in the tropics and is recognized for its tolerance to seasonal flooding. This grass is an important forage species for the Cerrado and Amazon regions of Brazil. U. humidicola is a polyploid species with variable ploidy (6X–9X) and facultative apomixis with high phenotypic plasticity. However, this apomixis and ploidy, as well as the limited knowledge of the genetic basis of the germplasm collection, have constrained genetic breeding activities, yet microsatellite markers may enable a better understanding of the species’ genetic composition. This study aimed to develop and characterize new polymorphic microsatellite molecular markers in U. humidicola and to evaluate their transferability to other Urochloa species. Findings A set of microsatellite markers for U. humidicola was identified from two new enriched genomic DNA libraries: the first library was constructed from a single sexual genotype and the second from a pool of eight apomictic genotypes selected on the basis of previous results. Of the 114 loci developed, 72 primer pairs presented a good amplification product, and 64 were polymorphic among the 34 genotypes tested. The number of bands per simple sequence repeat (SSR) locus ranged from 1 to 29, with a mean of 9.6 bands per locus. The mean polymorphism information content (PIC) of all loci was 0.77, and the mean discrimination power (DP) was 0.87. STRUCTURE analysis revealed differences among U. humidicola accessions, hybrids, and other Urochloa accessions. The transferability of these microsatellites was evaluated in four species of the genus, U. brizantha, U. decumbens, U. ruziziensis, and U. dictyoneura, and the percentage of transferability ranged from 58.33% to 69.44% depending on the species. Conclusions This work reports new polymorphic microsatellite markers for U. humidicola that can be used for breeding programs of this and other Urochloa species, including genetic linkage mapping, quantitative trait loci identification, and marker-assisted selection.
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Affiliation(s)
- Jean C S Santos
- Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade Estadual de Campinas (UNICAMP), Cidade Universitária Zeferino Vaz, CP 6010, CEP 13083-875, Campinas, SP, Brazil.
| | - Mariana A Barreto
- Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade Estadual de Campinas (UNICAMP), Cidade Universitária Zeferino Vaz, CP 6010, CEP 13083-875, Campinas, SP, Brazil.
| | - Fernanda A Oliveira
- Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade Estadual de Campinas (UNICAMP), Cidade Universitária Zeferino Vaz, CP 6010, CEP 13083-875, Campinas, SP, Brazil.
| | - Bianca B Z Vigna
- EMBRAPA Southeast Livestock, Brazilian Agricultural Research Corporation, CP 339, São Carlos, SP, CEP 13560-970, Brazil.
| | - Anete P Souza
- Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade Estadual de Campinas (UNICAMP), Cidade Universitária Zeferino Vaz, CP 6010, CEP 13083-875, Campinas, SP, Brazil. .,Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Cidade Universitária Zeferino Vaz, CP 6109, CEP 13083-862, Campinas, SP, Brazil.
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Silva PIT, Martins AM, Gouvea EG, Pessoa-Filho M, Ferreira ME. Development and validation of microsatellite markers for Brachiaria ruziziensis obtained by partial genome assembly of Illumina single-end reads. BMC Genomics 2013; 14:17. [PMID: 23324172 PMCID: PMC3565986 DOI: 10.1186/1471-2164-14-17] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2012] [Accepted: 12/18/2012] [Indexed: 11/29/2022] Open
Abstract
Background Brachiaria ruziziensis is one of the most important forage species planted in the tropics. The application of genomic tools to aid the selection of superior genotypes can provide support to B. ruziziensis breeding programs. However, there is a complete lack of information about the B. ruziziensis genome. Also, the availability of genomic tools, such as molecular markers, to support B. ruziziensis breeding programs is rather limited. Recently, next-generation sequencing technologies have been applied to generate sequence data for the identification of microsatellite regions and primer design. In this study, we present a first validated set of SSR markers for Brachiaria ruziziensis, selected from a de novo partial genome assembly of single-end Illumina reads. Results A total of 85,567 perfect microsatellite loci were detected in contigs with a minimum 10X coverage. We selected a set of 500 microsatellite loci identified in contigs with minimum 100X coverage for primer design and synthesis, and tested a subset of 269 primer pairs, 198 of which were polymorphic on 11 representative B. ruziziensis accessions. Descriptive statistics for these primer pairs are presented, as well as estimates of marker transferability to other relevant brachiaria species. Finally, a set of 11 multiplex panels containing the 30 most informative markers was validated and proposed for B. ruziziensis genetic analysis. Conclusions We show that the detection and development of microsatellite markers from genome assembled Illumina single-end DNA sequences is highly efficient. The developed markers are readily suitable for genetic analysis and marker assisted selection of Brachiaria ruziziensis. The use of this approach for microsatellite marker development is promising for species with limited genomic information, whose breeding programs would benefit from the use of genomic tools. To our knowledge, this is the first set of microsatellite markers developed for this important species.
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Affiliation(s)
- Pedro I T Silva
- Embrapa Recursos Genéticos e Biotecnologia, Genetics Lab, PO Box 02372, Brasília, CEP 70770-917 Distrito Federal, Brazil
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Vigna BB, Alleoni GC, Jungmann L, do Valle CB, de Souza AP. New microsatellite markers developed from Urochloa humidicola (Poaceae) and cross amplification in different Urochloa species. BMC Res Notes 2011; 4:523. [PMID: 22142493 PMCID: PMC3251623 DOI: 10.1186/1756-0500-4-523] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2011] [Accepted: 12/05/2011] [Indexed: 11/16/2022] Open
Abstract
Background Urochloa humidicola is a forage grass that grows in tropical regions and is recognized for its tolerance to seasonal flooding. It is a polyploid and apomictic species with high phenotypic plasticity. As molecular tools are important in facilitating the development of new cultivars and in the classification of related species, the objectives of this study were to develop new polymorphic microsatellite markers from an enriched library constructed from U. humidicola and to evaluate their transferability to other Urochloa species. Findings Microsatellite sequences were identified from a previously constructed enriched library, and specific primers were designed for 40 loci. Isolated di-nucleotide repeat motifs were the most abundant followed by tetra-nucleotide repeats. Of the tested loci, 38 displayed polymorphism when screened across 34 polyploid Urochloa sp. genotypes, including 20 accessions and six hybrids of U. humidicola and two accessions each from U. brizantha, U. dictyoneura, U. decumbens and U. ruziziensis. The number of bands per Simple Sequence Repeat (SSR) locus ranged from one to 29 with a mean of 11.5 bands per locus. The mean Polymorphism Information Content (PIC) of all loci was 0.7136, and the mean Discrimination Power (DP) was 0.7873. Six loci amplified in all species tested. STRUCTURE analysis revealed six different allelic pools, and the genetic similarity values analyzed using Jaccard's coefficient ranged from 0.000 to 0.913. Conclusions This work reports new polymorphic microsatellite markers that will be useful for breeding programs for Urochloa humidicola and other Urochloa species as well as for genetic map development, germplasm characterization, evolutionary and taxonomic studies and marker-assisted trait selection.
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Affiliation(s)
- Bianca Bz Vigna
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas, CP 6010, Campinas, SP CEP 13083-970, Brazil.
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Jungmann L, Vigna BBZ, Boldrini KR, Sousa ACB, do Valle CB, Resende RMS, Pagliarini MS, Zucchi MI, de Souza AP. Genetic diversity and population structure analysis of the tropical pasture grass Brachiaria humidicola based on microsatellites, cytogenetics, morphological traits, and geographical origin. Genome 2011; 53:698-709. [PMID: 20924419 DOI: 10.1139/g10-055] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Brachiaria humidicola (Rendle) Schweick. is a warm-season grass commonly used as forage in the tropics. Accessions of this species were collected in eastern Africa and massively introduced into South America in the 1980s. Several of these accessions form a germplasm collection at the Brazilian Agricultural Research Corporation. However, apomixis, ploidy, and limited knowledge of the genetic basis of this germplasm collection have constrained breeding activities. The objectives of this work were to identify genetic variability in the Brazilian B. humidicola germplasm collection using microsatellite markers and to compare the results with information on the following: (1) collection sites of the accessions; (2) reproductive mode and ploidy levels; and (3) genetic diversity revealed by morphological traits. The evaluated germplasm population is highly structured into four major groups. The sole sexual accession did not group with any of the clusters. Genetic dissimilarities did not correlate with either geographic distances or genetic distances inferred from morphological descriptors. Additionally, the genetic structure identified in this collection did not correspond to differences in ploidy level. Alleles exclusive to either sexual or apomictic accessions were identified, suggesting that further evaluation of the association of these loci with apospory should be carried out.
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Affiliation(s)
- L Jungmann
- Brazilian Agricultural Research Corporation (Embrapa), Center for Beef Cattle Research, Plant Biotechnology Laboratory, CP 154, Campo Grande, MS 79002-970, Brazil
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