Complex polyploid and hybrid species in an apomictic and sexual tropical forage grass group: genomic composition and evolution in Urochloa (Brachiaria) species

AbstractBackground and AimsDiploid and polyploid Urochloa (including Brachiaria, Panicum and Megathyrsus species) C4 tropical forage grasses originating from Africa and now planted worldwide are important for food security and the environment, often being planted in marginal lands. We aimed to characterize the nature of their genomes, the repetitive DNA, and the genome composition of polyploids, leading to a model of the evolutionary pathways within the group including many apomictic species.MethodsSome 362 forage grass accessions from international germplasm collections were studied, and ploidy determined using an optimized flow cytometry method. Whole-genome survey sequencing and molecular cytogenetic analysis with in situ hybridization to chromosomes were used to identify chromosomes and genomes in Urochloa accessions belonging to the different agamic complexes.Key ResultsGenome structures are complex and variable, with multiple ploidies and genome compositions within the species, and no clear geographical patterns. Sequence analysis of nine diploid and polyploid accessions enabled identification of abundant genome-specific repetitive DNA motifs. In situ hybridization with a combination of repetitive DNA and genomic DNA probes, identified evolutionary divergence and allowed us to discriminate the different genomes present in polyploids.ConclusionsWe suggest a new coherent nomenclature for the genomes present. We develop a model of evolution at the whole-genome level in diploid and polyploid accessions showing processes of grass evolution. We support the retention of narrow species concepts for U. brizantha, U. decumbens, and U. ruziziensis. The results and model will be valuable in making rational choices of parents for new hybrids, assist in use of the germplasm for breeding and selection of Urochloa with improved sustainability and agronomic potential, and will assist in measuring and conserving biodiversity in grasslands.

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Complex polyploid and hybrid species in an apomictic and sexual tropical forage grass group: genomic composition and evolution in Urochloa (Brachiaria) species

Annals of Botany ◽

10.1093/aob/mcab147 ◽

2021 ◽

Author(s):

Paulina Tomaszewska ◽

Maria S Vorontsova ◽

Stephen A Renvoize ◽

Sarah Z Ficinski ◽

Joseph Tohme ◽

...

Keyword(s):

Repetitive Dna ◽

Single Species ◽

Evolutionary Divergence ◽

Forage Grass ◽

Whole Genome ◽

Marginal Lands ◽

Geographical Patterns ◽

Germplasm Collections ◽

Genome Survey ◽

Tropical Forage

Abstract Background and Aims Diploid and polyploid Urochloa (including Brachiaria, Panicum and Megathyrsus species) C4 tropical forage grasses originating from Africa are important for food security and the environment, often being planted in marginal lands worldwide. We aimed to characterize the nature of their genomes, the repetitive DNA, and the genome composition of polyploids, leading to a model of the evolutionary pathways within the group including many apomictic species. Methods Some 362 forage grass accessions from international germplasm collections were studied, and ploidy determined using an optimized flow cytometry method. Whole-genome survey sequencing and molecular cytogenetic analysis were used to identify chromosomes and genomes in Urochloa accessions belonging to the 'brizantha' and 'humidicola' agamic complexes and U. maxima. Key Results Genome structures are complex and variable, with multiple ploidies and genome compositions within the species, and no clear geographical patterns. Sequence analysis of nine diploid and polyploid accessions enabled identification of abundant genome-specific repetitive DNA motifs. In situ hybridization with a combination of repetitive DNA and genomic DNA probes, identified evolutionary divergence and allowed us to discriminate the different genomes present in polyploids. Conclusions We suggest a new coherent nomenclature for the genomes present. We develop a model of evolution at the whole-genome level in diploid and polyploid accessions showing processes of grass evolution. We support the retention of narrow species concepts for U. brizantha, U. decumbens, and U. ruziziensis, and do not consider diploids and polyploids of single species as cytotypes. The results and model will be valuable in making rational choices of parents for new hybrids, assist in use of the germplasm for breeding and selection of Urochloa with improved sustainability and agronomic potential, and will assist in measuring and conserving biodiversity in grasslands.

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Flow Cytometry-Based Determination of Ploidy from Dried Leaf Specimens in Genomically Complex Collections of the Tropical Forage Grass Urochloa s. l.

Genes ◽

10.3390/genes12070957 ◽

2021 ◽

Vol 12 (7) ◽

pp. 957

Author(s):

Paulina Tomaszewska ◽

Till K. Pellny ◽

Luis M. Hernández ◽

Rowan A. C. Mitchell ◽

Valheria Castiblanco ◽

...

Keyword(s):

Flow Cytometry ◽

Germplasm Collection ◽

Forage Grass ◽

Breeding Programs ◽

Robust Identification ◽

Ploidy Levels ◽

Sustainable Improvement ◽

Tropical Forage ◽

Relative Differences

Urochloa (including Brachiaria, Megathyrus and some Panicum) tropical grasses are native to Africa and are now, after selection and breeding, planted worldwide, particularly in South America, as important forages with huge potential for further sustainable improvement and conservation of grasslands. We aimed to develop an optimized approach to determine ploidy of germplasm collection of this tropical forage grass group using dried leaf material, including approaches to collect, dry and preserve plant samples for flow cytometry analysis. Our methods enable robust identification of ploidy levels (coefficient of variation of G0/G1 peaks, CV, typically <5%). Ploidy of some 348 forage grass accessions (ploidy range from 2x to 9x), from international genetic resource collections, showing variation in basic chromosome numbers and reproduction modes (apomixis and sexual), were determined using our defined standard protocol. Two major Urochloa agamic complexes are used in the current breeding programs at CIAT and EMBRAPA: the ’brizantha’ and ’humidicola’ agamic complexes are variable, with multiple ploidy levels. Some U. brizantha accessions have odd level of ploidy (5x), and the relative differences in fluorescence values of the peak positions between adjacent cytotypes is reduced, thus more precise examination of this species is required. Ploidy measurement of U. humidicola revealed aneuploidy.

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Fluorescence in situ hybridization on plant extended chromatin DNA fibers for single-copy and repetitive DNA sequences

Plant Cell Reports ◽

10.1007/s00299-011-1086-y ◽

2011 ◽

Vol 30 (9) ◽

pp. 1779-1786 ◽

Cited By ~ 5

Author(s):

Kun Yang ◽

Hecui Zhang ◽

Richard Converse ◽

Yong Wang ◽

Xiaoying Rong ◽

...

Keyword(s):

In Situ Hybridization ◽

Fluorescence In Situ Hybridization ◽

Repetitive Dna ◽

Dna Sequences ◽

Single Copy ◽

Repetitive Dna Sequences

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Localisation of repetitive DNA in mouse cells by in situ hybridization and dye binding techniques

Hereditas ◽

10.1111/j.1601-5223.1974.tb01349.x ◽

2009 ◽

Vol 76 (2) ◽

pp. 316-320 ◽

Cited By ~ 3

Author(s):

Gunnar Ahnström ◽

A. T. Natarajan

Keyword(s):

In Situ Hybridization ◽

Repetitive Dna ◽

Dye Binding ◽

Mouse Cells

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A rapid procedure for the isolation of C0t-1 DNA from plants

Genome ◽

10.1139/g97-020 ◽

1997 ◽

Vol 40 (1) ◽

pp. 138-142 ◽

Cited By ~ 137

Author(s):

Michael S. Zwick ◽

Robert E. Hanson ◽

M. Nurul Islam-Faridi ◽

David M. Stelly ◽

Rod A. Wing ◽

...

Keyword(s):

In Situ Hybridization ◽

Repetitive Dna ◽

Copy Number ◽

Genomic Dna ◽

Mammalian Species ◽

Repetitive Dnas ◽

Rapid Procedure ◽

Dna Elements ◽

Repetitive Dna Elements

In situ hybridization (ISH) for the detection of single- or low-copy sequences, particularly large DNA fragments cloned into YAC or BAC vectors, generally requires the suppression or "blocking" of highly-repetitive DNAs. C0t-1 DNA is enriched for repetitive DNA elements, high or moderate in copy number, and can therefore be used more effectively than total genomic DNA to prehybridize and competitively hybridize repetitive elements that would otherwise cause nonspecific hybridization. C0t-1 DNAs from several mammalian species are commercially available, however, none is currently available for plants to the best of our knowledge. We have developed a simple 1-day procedure to generate C0t-1 DNA without the use of specialized equipment.Key words: C0t-1 DNA, in situ hybridization, BACs, plants.

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Evolutionary conservatism will limit responses to climate change in the tropics

Biology Letters ◽

10.1098/rsbl.2021.0363 ◽

2021 ◽

Vol 17 (10) ◽

Author(s):

Ethan B. Linck ◽

Benjamin G. Freeman ◽

C. Daniel Cadena ◽

Cameron K. Ghalambor

Keyword(s):

Thermal Tolerance ◽

Species Turnover ◽

Tropical Species ◽

Evolutionary Divergence ◽

Closely Related Species ◽

Tropical Mountains ◽

Low Latitudes ◽

Parapatric Speciation ◽

The Tropics

Rapid species turnover in tropical mountains has fascinated biologists for centuries. A popular explanation for this heightened beta diversity is that climatic stability at low latitudes promotes the evolution of narrow thermal tolerance ranges, leading to local adaptation, evolutionary divergence and parapatric speciation along elevational gradients. However, an emerging consensus from research spanning phylogenetics, biogeography and behavioural ecology is that this process rarely, if ever, occurs. Instead, closely related species typically occupy a similar elevational niche, while species with divergent elevational niches tend to be more distantly related. These results suggest populations have responded to past environmental change not by adapting and diverging in place, but instead by shifting their distributions to tightly track climate over time. We argue that tropical species are likely to respond similarly to ongoing and future climate warming, an inference supported by evidence from recent range shifts. In the absence of widespread in situ adaptation to new climate regimes by tropical taxa, conservation planning should prioritize protecting large swaths of habitat to facilitate movement.

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Karyotyping Dasypyrum breviaristatum chromosomes with multiple oligonucleotide probes reveals the genomic divergence in Dasypyrum

Genome ◽

10.1139/gen-2020-0147 ◽

2021 ◽

Author(s):

Zhihui Yu ◽

Hongjin Wang ◽

Wenxi Jiang ◽

Chengzhi Jiang ◽

Weiguang Yuan ◽

...

Keyword(s):

Repetitive Sequences ◽

Wheat Breeding ◽

Evolutionary Divergence ◽

Oligonucleotide Probes ◽

Addition Lines ◽

Partial Amphiploid ◽

Standard Karyotype ◽

Molecular Marker Analysis ◽

Dasypyrum Breviaristatum

The perennial species Dasypyrum breviaristatum (genome Vb) contains many potentially valuable genes for the improvement of common wheat. Construction of a detailed karyotype of D. breviaristatum chromosomes will be useful for the detection of Dasypyrum chromatin in wheat background. We established the standard karyotype of 1Vb-7Vb chromosomes through non-denaturing fluorescence in situ hybridization (ND-FISH) technique using 28 oligonucleotide probes from the wheat-D. breviaristatum partial amphiploid TDH-2 (AABBVbVb) and newly identified wheat-D. breviaristatum disomic translocation and addition lines D2138 (6VbS.2VbL), D2547 (4Vb) and D2532 (3VbS.6VbL) by comparative molecular marker analysis. The ND-FISH with multiple oligo probes were conducted on the durum wheat-D. villosum amphiploid TDV-1 and large karyotype differences between D. breviaristatum and D. villosum was revealed. These ND-FISH probes will be valuable for screening the wheat-Dasypyrum derivative lines for chromosome identification, and newly developed wheat-D. breviaristatum addition lines may broaden the gene pool of wheat breeding. The differences between D. villosum and D. breviaristatum chromosomes revealed by ND-FISH will help us understand evolutionary divergence of repetitive sequences within the genus Dasypyrum.

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