Genotyping by sequencing provides new insights into the diversity of Napier grass (Cenchrus purpureus) and reveals variation in genome-wide LD patterns between collections

Omics-driven utilization of wild relatives for empowering pre-breeding in pearl millet

MAIN CONCLUSION

Pearl millet wild relatives harbour novel alleles which could be utilized to broaden genetic base of cultivated species. Genomics-informed pre-breeding is needed to speed up introgression from wild to cultivated gene pool in pearl millet. Rising episodes of intense biotic and abiotic stresses challenge pearl millet production globally. Wild relatives provide a wide spectrum of novel alleles which could address challenges posed by climate change. Pre-breeding holds potential to introgress novel diversity in genetically narrow cultivated Pennisetum glaucum from diverse gene pool. Practical utilization of gene pool diversity remained elusive due to genetic intricacies. Harnessing promising traits from wild pennisetum is limited by lack of information on underlying candidate genes/QTLs. Next-Generation Omics provide vast scope to speed up pre-breeding in pearl millet. Genomic resources generated out of draft genome sequence and improved genome assemblies can be employed to utilize gene bank accessions effectively. The article highlights genetic richness in pearl millet and its utilization with a focus on harnessing next-generation Omics to empower pre-breeding.

Phenotypic characterization and analysis of genetic diversity between commercial crossbred and indigenous chickens from three different agro-ecological zones using DArT-Seq technology

Indigenous and were used to study genetic diversity and population structure analyses. Polymorphism information content (PIC) values ranged from 0.0 to 0.5, with 21,285 SNP markers (35%) being in the lowest PIC value range (0 to 0.15) while 13,511 (commercial chickens have developed unique adaptations to their environments, which may include nutrition, pathogens, and thermal stress. Besides, environmental pressures and artificial selection have generated significant genome-wide divergence in chickens, as those selection pressures contribute a considerable evolutionary force to phenotypic and genotypic differentiation. Herein, we determined genomic diversity of indigenous chickens from semi-deciduous rainforest (SDR), coastal savannah (CS) and Guinea savannah (GS) agro-ecological zones (AEZs) in Ghana and commercial crossbreds (CC) reared at the Kwame Nkrumah University of Science and Technology (KNUST). We generated SNP markers from 82 chickens (62 indigenous chicken ecotypes and 26 commercial crossbred ecotype) using DArT-Seq technology. A total of 85,396 SNP markers were generated and after filtering the data, 58,353 markers 21%) were in the highest PIC value range (0.45 to 0.50). The CC were more genetically diverse than the indigenous birds, with the highest expected heterozygosity value of 0.220. Between the commercial crossbreds population and the indigenous ecotypes, pairwise FST values were estimated to be 0.105 between CS, 0.096 between SDF, and 0.133 between GS. Furthermore, PCA analysis showed that the CC, SDF and GS chickens clustered together and are genetically distant from the commercial crossbred. We herein show that chickens from the AEZs studied can be considered as one population. However, due the abundance of agro-byproducts in the SDR compared to the CS and GS, chickens from the SDR AEZ had better growth compared to their counterparts. It is suggested that the genetic diversity within the local ecotypes could form the basis for genetic improvement.

Effectiveness of DArTseq markers application in genetic diversity and population structure of indigenous chickens in Eastern Province of Rwanda

BACKGROUND

The application of biotechnologies which make use of genetic markers in chicken breeding is developing rapidly. Diversity Array Technology (DArT) is one of the current Genotyping-By-Sequencing techniques allowing the discovery of whole genome sequencing. In livestock, DArT has been applied in cattle, sheep, and horses. Currently, there is no study on the application of DArT markers in chickens. The aim was to study the effectiveness of DArTSeq markers in the genetic diversity and population structure of indigenous chickens (IC) and SASSO in the Eastern Province of Rwanda.

METHODS

In total 87 blood samples were randomly collected from 37 males and 40 females of indigenous chickens and 10 females of SASSO chickens purposively selected from 5 sites located in two districts of the Eastern Province of Rwanda. Genotyping by Sequencing (GBS) using DArTseq technology was employed. This involved the complexity reduction method through digestion of genomic DNA and ligation of barcoded adapters followed by PCR amplification of adapter-ligated fragments.

RESULTS

From 45,677 DArTseq SNPs and 25,444 SilicoDArTs generated, only 8,715 and 6,817 respectively remained for further analysis after quality control. The average call rates observed, 0.99 and 0.98 for DArTseq SNPs and SilicoDArTs respectively were quite similar. The polymorphic information content (PIC) from SilicoDArTs (0.33) was higher than that from DArTseq SNPs (0.22). DArTseq SNPs and SilicoDArTs had 34.4% and 34% of the loci respectively mapped on chromosome 1. DArTseq SNPs revealed distance averages of 0.17 and 0.15 within IC and SASSO chickens respectively while the respective averages observed with SilicoDArTs were 0.42 and 0.36. The average genetic distance between IC and SASSO chickens was moderate for SilicoDArTs (0.120) compared to that of DArTseq SNPs (0.048). The PCoA and population structure clustered the chicken samples into two subpopulations (1 and 2); 1 is composed of IC and 2 by SASSO chickens. An admixture was observed in subpopulation 2 with 12 chickens from subpopulation 1.

CONCLUSIONS

The application of DArTseq markers have been proven to be effective and efficient for genetic relationship between IC and separated IC from exotic breed used which indicate their suitability in genomic studies. However, further studies using all chicken genetic resources available and large big sample sizes are required.

Analysis of global Napier grass (Cenchrus purpureus) collections reveals high genetic diversity among genotypes with some redundancy between collections

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.

Genetic diversity and population structure of Vernonia amygdalina Del. in Uganda based on genome wide markers

Determining the extent and distribution of genetic diversity is an essential component of plant breeding. In the present study, we explored the genetic diversity and population structure of Vernonia amygdalina, a fodder, vegetable and medicinal species of Africa and some parts of Yemen. Most empirical studies demonstrate that populations that are separated by geographic or ecological factors may experience genetic differentiation resulting from restricted gene flow between populations. A total of 238 individuals were sampled from two populations: i) Lake Victoria crescent (LVC) and ii) Southern and Eastern Lake Kyoga basin (SEK) agroecological zones of Uganda and genotyped using DArT platform. Of the two populations, the overall mean observed heterozygosity (Ho) was low to medium (Ho = 0.07[silicoDArTs] and 0.2[SNPs]). Inbreeding levels were also very low (-0.04 to -0.08) suggesting the presence of random mating. Partitioning of genetic structure in the two populations indicated that SEK exhibited a higher genetic diversity than LVC. The principal coordinates analysis (PCA) showed no geographical structuring, consistent with the low genetic differentiation (Fst = 0.00) and the low Euclidean genetic distance (1.38-1.39) between the LVC and SEK populations. However, STRUCTURE analysis with admixture models revealed weak possible genetic clusters with very small genetic distance among them. Overall, the results suggest low genetic diversity and weak genetic differentiation between the two populations. One possible explanation of the results could be the presence of human assisted gene flow over long distances.

Genetic Diversity, Population Structure and Subset Development in a Sesbania sesban Collection

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.

Productivity and Feed Quality Performance of Napier Grass (Cenchrus purpureus) Genotypes Growing under Different Soil Moisture Levels

In the semi-arid and arid environments of Sub-Sharan Africa, forage availability throughout the year is insufficient and highly limited during the dry seasons due to limited precipitation. Thus, the identification of drought stress-tolerant forage cultivars is one of the main activities in forage development programs. In this study, Napier grass (Cenchrus purpureus), an important forage crop in Eastern and Central Africa that is broadly adapted to produce across tropical environments, was evaluated for its water use efficiency and production performance under field drought stress conditions. Eighty-four Napier grass genotypes were evaluated for their drought stress tolerance from 2018 to 2020 using agro-morphological and feed quality traits under two soil moisture stress regimes during the dry season, i.e., moderate (MWS) and severe (SWS) water stress conditions, and under rainfed conditions in the wet season (wet). Overall, the results indicated the existence of genotype variation for the traits studied. In general, the growth and productivity of the genotypes declined under SWS compared to MWS conditions. High biomass-yielding genotypes with enhanced WUE were consistently observed across harvests in each soil moisture stress regime. In addition, the top biomass-yielding genotypes produced the highest annual crude protein yield, indicating the possibility of developing high-feed-quality Napier grass genotypes for drought stress environments.

SilicoDArT and SNP markers for genetic diversity and population structure analysis of Trema orientalis; a fodder species

Establishing the genetic diversity and population structure of a species can guide the selection of appropriate conservation and sustainable utilization strategies. Next-generation sequencing (NGS) approaches are increasingly being used to generate multi-locus data for genetic structure determination. This study presents the genetic structure of a fodder species -Trema orientalis based on two genome-wide high-throughput diversity array technology (DArT) markers; silicoDArT and single nucleotide polymorphisms (SNPs). Genotyping of 119 individuals generated 40,650 silicoDArT and 4767 SNP markers. Both marker types had a high average scoring reproducibility (>99%). Genetic relationships explored by principal coordinates analysis (PCoA) showed that the first principal coordinate axis explained most of the variation in both the SilicoDArT (34.2%) and SNP (89.6%) marker data. The average polymorphic information content did not highly differ between silicoDArT (0.22) and SNPs (0.17) suggesting minimal differences in informativeness in the two groups of markers. The, mean observed (H_o) and expected (H_e) heterozygosity were low and differed between the silicoDArT and SNPs respectively, estimated at H_o = 0.08 and H_e = 0.05 for silicoDArT and H_o = 0.23 and H_e = 0.19 for SNPs. The population of T. orientalis was moderately differentiated (F_ST  =  0.20–0.53) and formed 2 distinct clusters based on maximum likelihood and principal coordinates analysis. Analysis of molecular variance revealed that clusters contributed more to the variation (46.3–60.8%) than individuals (32.9–31.2%). Overall, the results suggest a high relatedness of the individuals sampled and a threatened genetic potential of T. orientalis in the wild. Therefore, genetic management activities such as ex-situ germplasm management are required for the sustainability of the species. Ex-situ conservation efforts should involve core collection of individuals from different populations to capture efficient diversity. This study demonstrates the importance of silicoDArT and SNP makers in population structure and genetic diversity analysis of Trema orientalis, useful for future genome wide studies in the species.

Elephant grass supplementation in the feed of fattening pigs affects growth performance, carcass characteristics, blood profiles and intestinal microorganisms

To investigate the effects of the dietary inclusion of elephant grass on the growth performance, blood profiles, carcass characteristics, ileum and stomach microbiota of fattening pigs, pigs were fed one of seven diets including a basal diet (Control), and six treatments, where the basal diet was supplemented with 10%, 15% or 20% of elephant grass, Cenchrus purpureus cv. Guiminyin (CpGui10, CpGui15, CpGui20) or cv. Purple (CpP10, CpP15, CpP20). Results showed that supplementation of 20% CpGui in the diet significantly increased (P < 0.05) average daily gain (ADG) and gain to feed (G/F) ratio by the end of the experiment. Additionally, pigs fed the CpGui20 diet showed higher (0.01 < P < 0.05) slaughter weight and tended to have increased loin-eye area and lean meat percentage, and, decreased backfat thickness compared with control pigs. Furthermore, 16S ribosomal DNA gene amplicon profiling showed that the inclusion of elephant grass in the diet was associated with modulation of the ileum and stomach microbiota composition at the order level. Relative abundance of the Lactobacillales order in the ileum and stomach increased with different proportions of elephant grass, while that of Enterobacteriales decreased. In conclusion, these results indicate that at up to 20% inclusion in the diet of pigs, elephant grass can promote enhanced growth performance and carcass characteristics, and, modulate the ileum and stomach microbiota composition of the pigs.

Erianthus germplasm collection in Thailand: genetic structure and phylogenetic aspects of tetraploid and hexaploid accessions

BACKGROUND

The genus Erianthus, which belongs to the "Saccharum complex", includes C₄ warm-season grasses. Erianthus species are widely distributed throughout Southeast Asia, East Asia and South Asia. Erianthus arundinaceus (Retz.) Jeswiet is highly adaptable to the environment, has a high percentage of dry matter, and is highly productive. Recently, this species has attracted attention as a novel bioenergy crop and as a breeding material for sugarcane improvement. Such interest in E. arundinaceus has accelerated the collection and conservation of its genetic resources, mainly in Asian countries, and also evaluation of morphological, agricultural, and cytogenetic features in germplasm collections. In Thailand, genetic resources of E. arundinaceus have been collected over the past 20 years and their phenotypic traits have been evaluated. However, the genetic differences and relatedness of the germplasms are not fully understood.

RESULTS

A set of 41 primer pairs for nuclear simple sequence repeats (SSRs) developed from E. arundinaceus were used to assess the genetic diversity of 121 Erianthus germplasms collected in Thailand; of these primer pairs, 28 detected a total of 316 alleles. A Bayesian clustering approach with these alleles classified the accessions into four main groups, generally corresponding to the previous classification based on phenotypic analysis. The results of principal coordinate analysis and phylogenetic analysis of the 121 accessions on the basis of the SSR markers showed the same trend as Bayesian clustering, whereas sequence variations of three non-coding regions of chloroplast DNA revealed eight haplotypes among the accessions. The analysis of genetic structure and phylogenetic relationships, however, found some accessions whose classification contradicted the results of previous phenotypic classification.

CONCLUSIONS

The molecular approach used in this study characterized the genetic diversity and relatedness of Erianthus germplasms collected across Thailand. This knowledge would allow efficient maintenance and conservation of the genetic resources of this grass and would help to use Erianthus species as breeding materials for development of novel bioenergy crops and sugarcane improvement.

Insights Into the Genetic Architecture of Complex Traits in Napier Grass (Cenchrus purpureus) and QTL Regions Governing Forage Biomass Yield, Water Use Efficiency and Feed Quality Traits

Napier grass is the most important perennial tropical grass native to Sub-Saharan Africa and widely grown in tropical and subtropical regions around the world, primarily as a forage crop for animal feed, but with potential as an energy crop and in a wide range of other areas. Genomic resources have recently been developed for Napier grass that need to be deployed for genetic improvement and molecular dissection of important agro-morphological and feed quality traits. From a diverse set of Napier grass genotypes assembled from two independent collections, a subset of 84 genotypes (although a small population size, the genotypes were selected to best represent the genetic diversity of the collections) were selected and evaluated for 2 years in dry (DS) and wet (WS) seasons under three soil moisture conditions: moderate water stress in DS (DS-MWS); severe water stress in DS (DS-SWS) and, under rainfed (RF) conditions in WS (WS-RF). Data for agro-morphological and feed quality traits, adjusted for the spatial heterogeneity in the experimental blocks, were collected over a 2-year period from 2018 to 2020. A total of 135,706 molecular markers were filtered, after removing markers with missing values >10% and a minor allele frequency (MAF) <5%, from the high-density genome-wide markers generated previously using the genotyping by sequencing (GBS) method of the DArTseq platform. A genome-wide association study (GWAS), using two different mixed linear model algorithms implemented in the GAPIT R package, identified more than 35 QTL regions and markers associated with agronomic, morphological, and water-use efficiency traits. QTL regions governing purple pigmentation and feed quality traits were also identified. The identified markers will be useful in the genetic improvement of Napier grass through the application of marker-assisted selection and for further characterization and map-based cloning of the QTLs.

Genetic Diversity and Population Structure of a Rhodes Grass (Chloris gayana) Collection

Rhodes grass (Chloris gayana Kunth) is one of the most important forage grasses used throughout the tropical and subtropical regions of the world. Enhancing the conservation and use of genetic resources requires the development of knowledge and understanding about the existing global diversity of the species. In this study, 104 Rhodes grass accessions, held in trust in the ILRI forage genebank, were characterized using DArTSeq markers to evaluate the genetic diversity and population structure, and to develop representative subsets, of the collection. The genotyping produced 193,988 SNP and 142,522 SilicoDArT markers with an average polymorphic information content of 0.18 and 0.26, respectively. Hierarchical clustering using selected informative markers showed the presence of two and three main clusters using SNP and SilicoDArT markers, respectively, with a cophenetic correction coefficient of 82%. Bayesian population structure analysis also showed the presence of two main subpopulations using both marker types indicating the existence of significant genetic variation in the collection. A representative subset, containing 21 accessions from diverse origins, was developed using the SNP markers. In general, the results revealed substantial genetic diversity in the Rhodes grass collection, and the generated molecular information, together with the developed subset, should help enhance the management, use and improvement of Rhodes grass germplasm in the future.

Genomic Selection in Tropical Forage Grasses: Current Status and Future Applications

The world population is expected to be larger and wealthier over the next few decades and will require more animal products, such as milk and beef. Tropical regions have great potential to meet this growing global demand, where pasturelands play a major role in supporting increased animal production. Better forage is required in consonance with improved sustainability as the planted area should not increase and larger areas cultivated with one or a few forage species should be avoided. Although, conventional tropical forage breeding has successfully released well-adapted and high-yielding cultivars over the last few decades, genetic gains from these programs have been low in view of the growing food demand worldwide. To guarantee their future impact on livestock production, breeding programs should leverage genotyping, phenotyping, and envirotyping strategies to increase genetic gains. Genomic selection (GS) and genome-wide association studies play a primary role in this process, with the advantage of increasing genetic gain due to greater selection accuracy, reduced cycle time, and increased number of individuals that can be evaluated. This strategy provides solutions to bottlenecks faced by conventional breeding methods, including long breeding cycles and difficulties to evaluate complex traits. Initial results from implementing GS in tropical forage grasses (TFGs) are promising with notable improvements over phenotypic selection alone. However, the practical impact of GS in TFG breeding programs remains unclear. The development of appropriately sized training populations is essential for the evaluation and validation of selection markers based on estimated breeding values. Large panels of single-nucleotide polymorphism markers in different tropical forage species are required for multiple application targets at a reduced cost. In this context, this review highlights the current challenges, achievements, availability, and development of genomic resources and statistical methods for the implementation of GS in TFGs. Additionally, the prediction accuracies from recent experiments and the potential to harness diversity from genebanks are discussed. Although, GS in TFGs is still incipient, the advances in genomic tools and statistical models will speed up its implementation in the foreseeable future. All TFG breeding programs should be prepared for these changes.

The elephant grass (Cenchrus purpureus) genome provides insights into anthocyanidin accumulation and fast growth

Elephant grass (2n = 4x = 28; Cenchrus purpureus Schumach.), also known as Napier grass, is an important forage grass and potential energy crop in tropical and subtropical regions of Asia, Africa and America. However, no study has yet reported a genome assembly for elephant grass at the chromosome scale. Here, we report a high‐quality chromosome‐scale genome of elephant grass with a total size of 1.97 Gb and a 1.5% heterozygosity rate, obtained using short‐read sequencing, single‐molecule long‐read sequencing and Hi‐C chromosome conformation capture. Evolutionary analysis showed that subgenome A' of elephant grass and pearl millet may have originated from a common ancestor more than 3.22 million years ago (MYA). Further, allotetraploid formation occurred at approximately 6.61 MYA. Syntenic analyses within elephant grass and with other grass species indicated that elephant grass has experienced chromosomal rearrangements. We found that some key enzyme‐encoding gene families related to the biosynthesis of anthocyanidins and flavonoids were expanded and highly expressed in leaves, which probably drives the production of these major anthocyanidin compounds and explains why this elephant grass cultivar has a high anthocyanidin content. In addition, we found a high copy number and transcript levels of genes involved in C₄ photosynthesis and hormone signal transduction pathways that may contribute to the fast growth of elephant grass. The availability of elephant grass genome data advances our knowledge of the genetic evolution of elephant grass and will contribute to further biological research and breeding as well as for other polyploid plants in the genus Cenchrus.

Comparisons of sampling methods for assessing intra- and inter-accession genetic diversity in three rice species using genotyping by sequencing

To minimize the cost of sample preparation and genotyping, most genebank genomics studies in self-pollinating species are conducted on a single individual to represent an accession, which may be heterogeneous with larger than expected intra-accession genetic variation. Here, we compared various population genetics parameters among six DNA (leaf) sampling methods on 90 accessions representing a wild species (O. barthii), cultivated and landraces (O. glaberrima, O. sativa), and improved varieties derived through interspecific hybridizations. A total of 1,527 DNA samples were genotyped with 46,818 polymorphic single nucleotide polymorphisms (SNPs) using DArTseq. Various statistical analyses were performed on eleven datasets corresponding to 5 plants per accession individually and in a bulk (two sets), 10 plants individually and in a bulk (two sets), all 15 plants individually (one set), and a randomly sampled individual repeated six times (six sets). Overall, we arrived at broadly similar conclusions across 11 datasets in terms of SNP polymorphism, heterozygosity/heterogeneity, diversity indices, concordance among genetic dissimilarity matrices, population structure, and genetic differentiation; there were, however, a few discrepancies between some pairs of datasets. Detailed results of each sampling method, the concordance in their outputs, and the technical and cost implications of each method were discussed.

Identification of Regulatory SNPs Associated with Vicine and Convicine Content of Vicia faba Based on Genotyping by Sequencing Data Using Deep Learning

Faba bean (Vicia faba) is a grain legume, which is globally grown for both human consumption as well as feed for livestock. Despite its agro-ecological importance the usage of Vicia faba is severely hampered by its anti-nutritive seed-compounds vicine and convicine (V+C). The genes responsible for a low V+C content have not yet been identified. In this study, we aim to computationally identify regulatory SNPs (rSNPs), i.e., SNPs in promoter regions of genes that are deemed to govern the V+C content of Vicia faba. For this purpose we first trained a deep learning model with the gene annotations of seven related species of the Leguminosae family. Applying our model, we predicted putative promoters in a partial genome of Vicia faba that we assembled from genotyping-by-sequencing (GBS) data. Exploiting the synteny between Medicago truncatula and Vicia faba, we identified two rSNPs which are statistically significantly associated with V+C content. In particular, the allele substitutions regarding these rSNPs result in dramatic changes of the binding sites of the transcription factors (TFs) MYB4, MYB61, and SQUA. The knowledge about TFs and their rSNPs may enhance our understanding of the regulatory programs controlling V+C content of Vicia faba and could provide new hypotheses for future breeding programs.

Genotyping-By-Sequencing Reveals Population Structure and Genetic Diversity of a Buffelgrass (Cenchrus ciliaris L.) Collection

Buffelgrass (Cenchrus ciliaris L.) is an important forage grass widely grown across the world with many good characteristics including high biomass yield, drought tolerance, and adaptability to a wide range of soil conditions and agro-ecologies. Two hundred and five buffelgrass accessions from diverse origins, conserved as part of the in-trust collection in the ILRI genebank, were analyzed by genotyping-by-sequencing using the DArTseq platform. The genotyping generated 234,581 single nucleotide polymorphism (SNP) markers, with polymorphic information content (PIC) values ranging from 0.005 to 0.5, and the short sequences of the markers were aligned with foxtail millet (Setaria italica) as a reference genome to generate genomic map positions of the markers. One thousand informative SNP markers, representing a broad coverage of the reference genome and with an average PIC value of 0.35, were selected for population structure and diversity analyses. The population structure analysis suggested two main groups, while the hierarchical clustering showed up to eight clusters in the collection. A representative core collection containing 20% of the accessions in the collection, with germplasm from 10 African countries and Oman, was developed. In general, the study revealed the presence of considerable genetic diversity and richness in the collection and a core collection that could be used for further analysis for specific traits of interest.