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

Authors: MUKTAR, MEKI - International Livestock Research Institute Ethiopia; BIZUNEH, TADELECH - Ethiopian Institute Of Agricultural Research; Anderson, William - Bill; ASSEFA, YILIKAL - International Livestock Research Institute Ethiopia; NEGAWO, ALEMAYEHU - International Livestock Research Institute Ethiopia; ABEL TESHOME, GARI - International Livestock Research Institute Ethiopia; HAILE, ERMIAS HABTE - International Livestock Research Institute Ethiopia; MUCHUGI, ALICE - International Livestock Research Institute Ethiopia; FEYISSA, TILEYE - Addis Ababa University; JONES, CHRIS - International Livestock Research Institute (ILRI) - Kenya

Submitted to: Scientific Reports
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/29/2023
Publication Date: 9/4/2023
Citation: Muktar, M.S., Bizuneh, T., Anderson, W.F., Assefa, Y., Negawo, A.T., Abel Teshome, G., Haile, E., Muchugi, A., Feyissa, T., Jones, C.S. 2023. Analysis of global napier grass (Cenchrus purpureus) collections reveals high genetic diversity among genotypes with some redundancy between collections. Scientific Reports. 13, 14509. https://doi.org/10.1038/s41598-023-41583-7.
DOI: https://doi.org/10.1038/s41598-023-41583-7

Interpretive Summary: Napier grass (also known as elephant grass) is native to Sub-Saharan Africa and have been distributed to other tropical and subtropical regions around the world, adapting to a wide range of ecologies, from sea level to 2500m above sea level., and has been acclimatized in areas of Central and South America, tropical parts of Asia, Australia, the Middle East and the Pacific islands. Napier grass is mainly cultivated as a forage crop for animal feed due to its high palatability and feed quality, high dry matter production, but can also be used as a cellulosic feedstock for bioenergy. Genetic diversity is needed for breeding and genetic improvement for agronomically important traits, such as disease and pest resistance, drought tolerance, and to withstand the current challenges associated with climate change. Napiergrass is cross-compatible with pearl millet to produce sterile hybrids that can only be propagated by vegetative means. These hybrids are favored mainly as a forage as they combine the superior forage quality of pearl millet with the high yielding ability of napiergrass. Plants from a global napiergrass collection were compared to determine the diversity and generate information useful for designing breeding strategies in napiergrass using genome-wide markers on a total of 574 napiergrass genotypes and hybrid progeny plants. The collections and progeny plants demonstrated extensive genetic variability. The genotypes were clustered into three major and eleven sub-clusters that differed significantly from each other. Generally, the three clusters were separated by geographic location where cluster 1 was from collections from Africa and India (as well as progeny), cluster 2 from South America collections, and cluster 3 was mainly composed for genotypes from progeny and the United States collection. Even though there were 3 major clusters, there was also a significant amount of genetic overlap among the collections from around the world. This may have occurred due to sharing of plant material among the different collections over the past century. The findings of this study offer useful information for the napiergrass breeding strategy, enhancement of genetic diversity, and provide a guide for the management and conservation of the collections.

Technical Abstract: The genetic diversity from numerous global Napier grass collections were analyzed and compared with the diversity in progeny plants produced from open pollination, which generates information useful for designing breeding strategies in Napier grass. Genotyping by the GBS method of the DArTseq platform generated 114,886 SNP and 46,293 SilicoDArT genome-wide markers on a total of 574 Napier grass genotypes composed from worldwide collections from Africa, Asia, South America and North America as well as progeny plants from open pollination material at the International Livestock Research Institute (ILRI). Of these, 89% of the SNP and 76% 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 markers was filtered by applying a strong SNP filtering criteria, including a maximum of 10% missing values, a minimum of 5% minor allele frequency, a maximum of 0.5 LD (Linkage-disequilibrium) value that ensures independence between markers, and markers that were able to be mapped across the Napier grass genome. The collections and progenies demonstrated extensive genetic variability with an average Nei’s genetic distance value of 0.23. The genotypes were clustered into three major and eleven sub-clusters that differed significantly from each other and had higher levels of genetic variation both within (54%) and between (46%) clusters. However, we found that there was low to moderate genetic differentiation among collections and genotype overlap and redundancy occurred between collections. The progeny plants were genetically diverse and diverged from the germplasm collections, with an average FST value of 0.08. The findings of this study offer useful information for the Napier grass breeding strategy, enhancement of genetic diversity, and provide a guide for the management and conservation of the collections.