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Muktar MS, Bizuneh T, Anderson W, Assefa Y, Negawo AT, Teshome A, Habte E, Muchugi A, Feyissa T, Jones CS. Analysis of global Napier grass (Cenchrus purpureus) collections reveals high genetic diversity among genotypes with some redundancy between collections. Sci Rep 2023; 13:14509. [PMID: 37667017 PMCID: PMC10477186 DOI: 10.1038/s41598-023-41583-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 08/29/2023] [Indexed: 09/06/2023] Open
Abstract
Genetic diversity amongst genotypes of several Napier grass collections was analyzed and compared with the diversity in a set of open pollinated progeny plants. A total of 114,881 SNP and 46,293 SilicoDArT genome-wide markers were generated on 574 Napier grass genotypes. Of these, 86% of the SNP and 66% of the SilicoDArT markers were mapped onto the fourteen chromosomes of the Napier grass genome. For genetic diversity analysis, a subset of highly polymorphic and informative SNP markers was filtered using genomic position information, a maximum of 10% missing values, a minimum minor allele frequency of 5%, and a maximum linkage-disequilibrium value of 0.5. Extensive genetic variation, with an average Nei's genetic distance value of 0.23, was identified in the material. The genotypes clustered into three major and eleven sub-clusters with high levels of genetic variation contained both within (54%) and between (46%) clusters. However, we found that there was low to moderate genetic differentiation among the collections and that some overlap and redundancy occurred between collections. The progeny plants were genetically diverse and divergent from the germplasm collections, with an average FST value of 0.08. We also reported QTL regions associated with forage biomass yield based on field phenotype data measured on a subset of the Napier grass collections. The findings of this study offer useful information for Napier grass breeding strategies, enhancement of genetic diversity, and provide a guide for the management and conservation of the collections.
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Affiliation(s)
- Meki S Muktar
- Feed and Forage Development, International Livestock Research Institute, Addis Ababa, Ethiopia
| | - Tadelech Bizuneh
- Ethiopian Institute of Agricultural Research, Holeta Agricultural Research Centre, Holeta, Ethiopia
| | - William Anderson
- Crop Genetics and Breeding Research Unit, USDA-ARS, 115 Coastal Ways, Tifton, GA, 31793, USA
| | - Yilikal Assefa
- Feed and Forage Development, International Livestock Research Institute, Addis Ababa, Ethiopia
| | - Alemayehu T Negawo
- Feed and Forage Development, International Livestock Research Institute, Addis Ababa, Ethiopia
| | - Abel Teshome
- Feed and Forage Development, International Livestock Research Institute, Addis Ababa, Ethiopia
| | - Ermias Habte
- Feed and Forage Development, International Livestock Research Institute, Addis Ababa, Ethiopia
| | - Alice Muchugi
- Feed and Forage Development, International Livestock Research Institute, Addis Ababa, Ethiopia
| | - Tileye Feyissa
- Institute of Biotechnology, College of Natural Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Chris S Jones
- Feed and Forage Development, International Livestock Research Institute, Nairobi, Kenya.
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Maybery-Reupert K, Isenegger D, Hayden M, Cogan N. Development of genomic resources for Rhodes grass ( Chloris gayana), draft genome and annotated variant discovery. FRONTIERS IN PLANT SCIENCE 2023; 14:1239290. [PMID: 37731974 PMCID: PMC10507473 DOI: 10.3389/fpls.2023.1239290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 08/18/2023] [Indexed: 09/22/2023]
Abstract
Genomic resources for grasses, especially warm-season grasses are limited despite their commercial and environmental importance. Here, we report the first annotated draft whole genome sequence for diploid Rhodes grass (Chloris gayana), a tropical C4 species. Generated using long read nanopore sequencing and assembled using the Flye software package, the assembled genome is 603 Mbp in size and comprises 5,233 fragments that were annotated using the GenSas pipeline. The annotated genome has 46,087 predicted genes corresponding to 92.0% of the expected genomic content present via BUSCO analysis. Gene ontology terms and repetitive elements are identified and discussed. An additional 94 individual plant genotypes originating from three diploid and two tetraploid Rhodes grass cultivars were short-read whole genome resequenced (WGR) to generate a single nucleotide polymorphism (SNP) resource for the species that can be used to elucidate inter- and intra-cultivar relationships across both ploidy levels. A total of 75,777 high quality SNPs were used to generate a phylogenetic tree, highlighting the diversity present within the cultivars which agreed with the known breeding history. Differentiation was observed between diploid and tetraploid cultivars. The WGR data were also used to provide insights into the nature and evolution of the tetraploid status of the species, with results largely agreeing with the published literature that the tetraploids are autotetraploid.
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Affiliation(s)
- Kellie Maybery-Reupert
- Agriculture Victoria Research, AgriBio, The Centre for AgriBioscience, Bundoora, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
| | - Daniel Isenegger
- Agriculture Victoria Research, AgriBio, The Centre for AgriBioscience, Bundoora, VIC, Australia
| | - Matthew Hayden
- Agriculture Victoria Research, AgriBio, The Centre for AgriBioscience, Bundoora, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
| | - Noel Cogan
- Agriculture Victoria Research, AgriBio, The Centre for AgriBioscience, Bundoora, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
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Negawo AT, Akinmade HO, Muktar MS, Habte E, Assefa Y, Muchugi A, Sartie AM, Jones CS. Genetic Diversity, Population Structure and Subset Development in a Sesbania sesban Collection. PLANTS (BASEL, SWITZERLAND) 2022; 12:13. [PMID: 36616142 PMCID: PMC9823922 DOI: 10.3390/plants12010013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 11/30/2022] [Accepted: 12/02/2022] [Indexed: 06/17/2023]
Abstract
Sesbania sesban (L.) Merr. is a multipurpose legume tree grown primarily for fodder and forage in the tropical and subtropical world. In this study, the Sesbania sesban collection maintained in the International Livestock Research Institute (ILRI) forage Genebank was studied using genome-wide markers generated on the DArTseq platform. Genotyping produced 84,673 and 60,626 SNP and SilicoDArT markers with a mean polymorphic information content of 0.153 and 0.123, respectively. From the generated markers, 7587 and 15,031 highly informative SNP and SilicoDArT markers, respectively, were filtered and used for genetic diversity analysis and subset development. Analysis of molecular variance (AMOVA) revealed higher variability 'within' (52.73% for SNP markers and 67.36% for SilicoDArT markers) than 'between' accessions. Hierarchical cluster analysis showed the presence of four main clusters in the collection. Mantel correlation analysis showed a lack of relationship between genetic variation of the germplasm and their geographical origin. A representative subset of 34 accessions containing germplasm from diverse origins and agro-ecologies was developed using SNP markers. The genetic diversity information generated in this study could be used for marker-assisted screening for stress tolerance, gap analysis and identification and acquisition of new distinct genotype(s) to broaden the genetic basis of the collection for future improvement programs to develop high-yielding, stress-tolerant varieties for enhancing food and environmental security in crop-livestock-based production systems.
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Affiliation(s)
- Alemayehu Teressa Negawo
- Feed and Forage Development, International Livestock Research Institute, Addis Ababa P.O. Box 5689, Ethiopia
| | - Habib Olumide Akinmade
- Feed and Forage Development, International Livestock Research Institute, Addis Ababa P.O. Box 5689, Ethiopia
- Forage Breeding and Genetics, Agronomy Department, University of Florida, Gainesville, FL 32611, USA
| | - Meki S. Muktar
- Feed and Forage Development, International Livestock Research Institute, Addis Ababa P.O. Box 5689, Ethiopia
| | - Ermias Habte
- Feed and Forage Development, International Livestock Research Institute, Addis Ababa P.O. Box 5689, Ethiopia
| | - Yilikal Assefa
- Feed and Forage Development, International Livestock Research Institute, Addis Ababa P.O. Box 5689, Ethiopia
| | - Alice Muchugi
- Feed and Forage Development, International Livestock Research Institute, Addis Ababa P.O. Box 5689, Ethiopia
| | - Alieu M. Sartie
- Feed and Forage Development, International Livestock Research Institute, Addis Ababa P.O. Box 5689, Ethiopia
- The Pacific Community (SPC), Private Mail Bag, Suva, Fiji
| | - Chris S. Jones
- Feed and Forage Development, International Livestock Research Institute, Addis Ababa P.O. Box 5689, Ethiopia
- Feed and Forage Development, International Livestock Research Institute, Nairobi 00100, Kenya
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Oi T, Clode PL, Taniguchi M, Colmer TD, Kotula L. Salt tolerance in relation to elemental concentrations in leaf cell vacuoles and chloroplasts of a C 4 monocotyledonous halophyte. PLANT, CELL & ENVIRONMENT 2022; 45:1490-1506. [PMID: 35128687 PMCID: PMC9305513 DOI: 10.1111/pce.14279] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 12/11/2021] [Accepted: 01/30/2022] [Indexed: 06/14/2023]
Abstract
Halophytes accumulate and sequester high concentrations of salt in vacuoles while maintaining lower levels of salt in the cytoplasm. The current data on cellular and subcellular partitioning of salt in halophytes are, however, limited to only a few dicotyledonous C3 species. Using cryo-scanning electron microscopy X-ray microanalysis, we assessed the concentrations of Na, Cl, K, Ca, Mg, P and S in various cell types within the leaf-blades of a monocotyledonous C4 halophyte, Rhodes grass (Chloris gayana). We also linked, for the first time, elemental concentrations in chloroplasts of mesophyll and bundle sheath cells to their ultrastructure and photosynthetic performance of plants grown in nonsaline and saline (200 mM NaCl) conditions. Na and Cl accumulated to the highest levels in xylem parenchyma and epidermal cells, but were maintained at lower concentrations in photosynthetically active mesophyll and bundle sheath cells. Concentrations of Na and Cl in chloroplasts of mesophyll and bundle sheath cells were lower than in their respective vacuoles. No ultrastructural changes were observed in either mesophyll or bundle sheath chloroplasts, and photosynthetic activity was maintained in saline conditions. Salinity tolerance in Rhodes grass is related to specific cellular Na and Cl distributions in leaf tissues, and the ability to regulate Na and Cl concentrations in chloroplasts.
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Affiliation(s)
- Takao Oi
- Graduate School of Bioagricultural SciencesNagoya UniversityNagoyaJapan
| | - Peta L Clode
- Centre for Microscopy, Characterisation and AnalysisThe University of Western AustraliaPerthWestern AustraliaAustralia
- School of Biological SciencesThe University of Western AustraliaPerthWestern AustraliaAustralia
| | | | - Timothy D Colmer
- The UWA School of Agriculture and EnvironmentThe University of Western AustraliaPerthWestern AustraliaAustralia
- The UWA Institute of AgricultureThe University of Western AustraliaPerthWestern AustraliaAustralia
| | - Lukasz Kotula
- The UWA School of Agriculture and EnvironmentThe University of Western AustraliaPerthWestern AustraliaAustralia
- The UWA Institute of AgricultureThe University of Western AustraliaPerthWestern AustraliaAustralia
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