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Genomic Composition and Evolution in Urochloa (Brachiaria) Species

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bioRxiv preprint doi: https://doi.org/10.1101/2021.02.19.431966; this version posted February 19, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 ORIGINAL ARTICLE 2 3 Complex polyploid and hybrid species in an apomictic and sexual tropical forage grass 4 group: genomic composition and evolution in Urochloa (Brachiaria) species 5 6 Paulina Tomaszewska1)*), Maria S. Vorontsova2), Stephen A. Renvoize2), Sarah Z. Ficinski2), 7 Joseph Tohme3), Trude Schwarzacher1), Valheria Castiblanco3), José J. de Vega4), Rowan A. 8 C. Mitchell5) and J. S. (Pat) Heslop-Harrison1) 9 10 1) Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, 11 United Kingdom 12 2) Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AB, United Kingdom 13 3) International Center for Tropical Agriculture (CIAT), A.A. 6713, Cali, Colombia 14 4) Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, United Kingdom 15 5) Rothamsted Research, Harpenden, Hertfordshire Al5 2JQ, United Kingdom 16 *) For correspondence. E-mail [email protected] 17 18 ORCID: 19 PT: https://orcid.org/0000-0002-9596-7219; MV: https://orcid.org/0000-0003-0899-1120; JT: 20 https://orcid.org/0000-0003-2765-7101; TS: https://orcid.org/0000-0001-8310-5489; VC: 21 https://orcid.org/0000-0003-2801-2153; JV: https://orcid.org/0000-0003-2847-5158; RM: 22 https://orcid.org/0000-0002-1412-8828; PHH: https://orcid.org/0000-0002-3105-2167 Tomaszewska et al. Urochloa genomes. Page 1 of 44. bioRxiv preprint doi: https://doi.org/10.1101/2021.02.19.431966; this version posted February 19, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 Abstract 2 Background and Aims Diploid and polyploid Urochloa (including Brachiaria, Panicum and 3 Megathyrsus species) C4 tropical forage grasses originating from Africa and now planted 4 worldwide are important for food security and the environment, often being planted in 5 marginal lands. We aimed to characterize the nature of their genomes, the repetitive DNA, 6 and the genome composition of polyploids, leading to a model of the evolutionary pathways 7 within the group including many apomictic species. 8 Methods Some 362 forage grass accessions from international germplasm collections were 9 studied, and ploidy determined using an optimized flow cytometry method. Whole-genome 10 survey sequencing and molecular cytogenetic analysis with in situ hybridization to 11 chromosomes were used to identify chromosomes and genomes in Urochloa accessions 12 belonging to the different agamic complexes. 13 Key Results Genome structures are complex and variable, with multiple ploidies and genome 14 compositions within the species, and no clear geographical patterns. Sequence analysis of 15 nine diploid and polyploid accessions enabled identification of abundant genome-specific 16 repetitive DNA motifs. In situ hybridization with a combination of repetitive DNA and 17 genomic DNA probes, identified evolutionary divergence and allowed us to discriminate the 18 different genomes present in polyploids. 19 Conclusions We suggest a new coherent nomenclature for the genomes present. We develop a 20 model of evolution at the whole-genome level in diploid and polyploid accessions showing 21 processes of grass evolution. We support the retention of narrow species concepts for U. 22 brizantha, U. decumbens, and U. ruziziensis. The results and model will be valuable in 23 making rational choices of parents for new hybrids, assist in use of the germplasm for 24 breeding and selection of Urochloa with improved sustainability and agronomic potential, and 25 will assist in measuring and conserving biodiversity in grasslands. Tomaszewska et al. Urochloa genomes. Page 2 of 44. bioRxiv preprint doi: https://doi.org/10.1101/2021.02.19.431966; this version posted February 19, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 Keywords: polyploidy, apomixis, repetitive DNA motifs, genome-specific sequences, 2 evolution, Urochloa, tropical forage grasses 3 4 Introduction 5 The evolution and domestication of most arable crops is well-understood and the 6 genetic diversity of their wild relatives is being exploited in breeding new varieties. Native 7 grasslands include high biodiversity that can be threatened by expansion of cultivated areas, 8 while forage grasses occupy half the world’s agricultural land. Genomic knowledge is being 9 increasingly applied to breeding the temperate Lolium-Festuca (ryegrass) complex 10 (Velmurugan et al., 2016), and there are a number of genetic selection and breeding 11 programmes for tropical and sub-tropical forage (e.g. Worthington and Miles, 2015) but 12 applications of omics-based technologies (Ishitani et al., 2004) remain limited. The tropical 13 forage grasses include clusters of species with various ploidies, and many reproduce through 14 apomixis. Their genomic composition and diversity in general remain poorly characterized. 15 Rational choice of parents for making crosses in breeding programmes requires knowledge of 16 genome composition and ploidy. The integration of sequencing, molecular cytogenetic and 17 bioinformatic tools allows the identification of genomes which come together in polyploids 18 (Soltis et al., 2013). Many crop species with polyploid members, including Brassica (Alix et 19 al., 2008) and the Brassicaceae (Cheng et al., 2013), Avena (Tomaszewska and Kosina, 2018; 20 Liu et al., 2019) and particularly the tribe Triticeae (Hordeae) (Linde-Laursen et al., 1997) 21 have well-established genome designations (as single letters) to describe the ancestral 22 genomes in auto- and allo-polyploids (amphiploids). Resolution of genome relationships in 23 the wheat group has assisted with extensive use of the germplasm pool in breeding (Feldman 24 and Sears, 1981; Ali et al., 2016; Rasheed et al., 2018). Tomaszewska et al. Urochloa genomes. Page 3 of 44. bioRxiv preprint doi: https://doi.org/10.1101/2021.02.19.431966; this version posted February 19, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 The pantropical grass genus Urochloa includes species previously classified under 2 Brachiaria, Megathyrsus, and some Eriochloa and Panicum (Webster, 1987; González and 3 Morton, 2005; Kellogg, 2015) and is a member of the Panicoideae tribe Paniceae, subtribe 4 Melinidinae, comprising of an estimated 150 annual and perennial grasses centred in sub- 5 Saharan Africa (Kellogg, 2015; Soreng et al., 2017). Joint missions in the early 1980s 6 conducted by CGIAR (Consultative Group on International Agricultural Research) centres, 7 CIAT (Centro Internacional de Agricultura Tropical) and ILRI (International Livestock 8 Research Institute) in several African countries collected wild species mostly as live plant 9 cuttings or ramets. These activities built a global grass collection with 700 accessions of 10 Urochloa species representing a highly diverse gene pool for breeding and systematic studies 11 (Keller-Grein et al., 1996). Valuable traits of Urochloa include biomass yield, physiological 12 tolerance to low-fertility acid soils of the tropics (Arroyave et al., 2011), digestibility and 13 energy content (Hanley et al., 2020), insect tolerance (particularly to neotropical spittlebugs; 14 Miles et al., 2006) and disease resistance (Valério et al., 2013; Alvarez et al., 2014; 15 Hernandez et al., 2017). However, undesirable traits are also present, such as allelopathy 16 (leaving bare soil; Kato-Noguchi et al., 2014), cold-susceptibility (Mulato II; Pizarro et al., 17 2013) and invasiveness (Durigan et al., 2007 in the Brazilian Cerrado; U. panicoides is on the 18 US Federal Noxious Weed List 19 https://www.aphis.usda.gov/plant_health/plant_pest_info/weeds/downloads/weedlist.pdf). 20 These Urochloa grass collections have huge potential for sustainable improvement as well as 21 conservation of grasslands, including pastures, rangelands, savannah, prairie, cerrado, and 22 roadsides and verges, with various degrees of management of grazing. Breeding or trial 23 programmes based in Colombia, Brazil, Thailand, Zimbabwe, Ethiopia, South Africa and 24 Australia have led to the development of over a dozen of cultivars (do Valle and Savidan, 25 1996; Singh et al., 2010) and Urochloa is now the most widely planted forage grass in South Tomaszewska et al. Urochloa genomes. Page 4 of 44. bioRxiv preprint doi: https://doi.org/10.1101/2021.02.19.431966; this version posted February 19, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 America occupying 60 million hectares of grasslands in the tropical savannah ecoregion of 2 Brazil (Gracindo et al., 2014). 3 Evolution of the monophyletic Urochloa lineage group remains poorly understood, but 4 it encompasses most species previously placed in the genus Brachiaria on morphological 5 grounds (Webster, 1987; Salariato et al., 2010, 2012). The species level taxonomy within 6 Urochloa established in African floras (Hutchinson and Dalziel, 1972; Clayton and Renvoize 7 1982; Clayton, 1989) has, however, not been fully maintained by recent floristic work (Sosef, 8 2016). Some Urochloa species have been arranged in agamic (apomictic) complexes: U. 9 brizantha, U. decumbens and U. ruziziensis were classified into the 'brizantha' complex, and 10 U.
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    Herbage Dynamics and Forage Quality of Texas Cupgrass (Eriochloa sericea) R.B. SHAW AND F.E. SMEINS munity of the Edwards Plateu, Texas. Dyksterhuis (1946) referred AbStnCt to this species as a secondary climax species of lowland sites on the Herbage dynamics and forage quality of Texas cupgrass (Eli- Fort Worth Prairie. Collins et al. (1975) described this species as a octi sericea) were monitored during the 1977 and 1978 growing climax dominant on the Blackland Prairies vegetation area of seasons on the Edwards Plateau, Texas. This species was dominant Texas, where it approached 25% of the herbaceous composition by on a shallow rocky range site wbicb bad been excluded from weight on some Blackland sites. Smeins et al. (1976) found Texas grazing for 30 years. Average herbage production was low (527 cupgrass had an absolute foliar cover in excess of 40% on deep soil kg/ha), and mulch constituted 85% of the total biomass. Peak live areas in grazing exclosures on the Edwards Plateau near Sonora. standing crop was only 145 kg/ha during the study. Green herbage Historical data showed that 10 years was required for Texas cup- production reflectedthe ability of this taxon to adjust phenologicai grass to become reestablished following protection from heavy stage in response to precipitation. Litterbag studies showed continuous grazing. However, it tripled in abundance during the decomposition rates of herbage held flat on the soii surface to be second IO-year period of protection (Smeins et al. 1976). twice as rapid as herbage held upright in clumps of Texas cupgrass. Taylor et al.
  • Effects of Plant Diversity on Simulated Climate–Vegetation Interaction

    Effects of Plant Diversity on Simulated Climate–Vegetation Interaction

    Effects of plant diversity on simulated climate-vegetation interaction towards the end of the African Humid Period Vivienne Pascale Groner Hamburg 2017 Berichte zur Erdsystemforschung 195 Reports on Earth System Science 2017 Hinweis Notice Die Berichte zur Erdsystemforschung werden The Reports on Earth System Science are vom Max-Planck-Institut für Meteorologie in published by the Max Planck Institute for Hamburg in unregelmäßiger Abfolge heraus- Meteorology in Hamburg. They appear in gegeben. irregular intervals. Sie enthalten wissenschaftliche und technische They contain scientific and technical contribu- Beiträge, inklusive Dissertationen. tions, including Ph. D. theses. Die Beiträge geben nicht notwendigerweise die The Reports do not necessarily reflect the Auffassung des Instituts wieder. opinion of the Institute. Die "Berichte zur Erdsystemforschung" führen The "Reports on Earth System Science" continue die vorherigen Reihen "Reports" und "Examens- the former "Reports" and "Examensarbeiten" of arbeiten" weiter. the Max Planck Institute. Anschrift / Address Layout Max-Planck-Institut für Meteorologie Bettina Diallo and Norbert P. Noreiks Bundesstrasse 53 Communication 20146 Hamburg Deutschland Copyright Tel./Phone: +49 (0)40 4 11 73 - 0 Fax: +49 (0)40 4 11 73 - 298 Photos below: ©MPI-M Photos on the back from left to right: [email protected] Christian Klepp, Jochem Marotzke, www.mpimet.mpg.de Christian Klepp, Clotilde Dubois, Christian Klepp, Katsumasa Tanaka Effects of plant diversity on simulated climate-vegetation interaction towards the end of the African Humid Period Dissertation with the aim of achieving a doctoral degree at the Faculty of Mathematics, Informatics and Natural Sciences Department of Earth Sciences of Universität Hamburg submitted by Vivienne Pascale Groner Hamburg 2017 Vivienne Pascale Groner Max-Planck-Institut für Meteorologie Bundesstrasse 53 20146 Hamburg Tag der Disputation: 06.07.2017 Folgende Gutachter empfehlen die Annahme der Dissertation: Prof.