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Genetic integrity and diversity in Urochloa brizantha collection maintained in the ILRI forage genebank

Meki Shehabu Muktar1, Shimu Lema2, Alemayehu Teresssa Negawo1, Yilikal Asefa1, Chris S. Jones3

1International Livestock Research Institute (ILRI), Feed and Forage Development, Ethiopia
2Oromia Agricultural Research Institute (OARI), Ethiopia
3International Livestock Research Institute (ILRI), Kenya


The ILRI forage genebank maintains several different species of brachiaria grasses (Urochloa spp.) in situ at its Zwai field site, Ethiopia, for over 30 years. We studied the genetic integrity in the Urochloa brizantha (syn. Brachiaria brizantha) collection, consisting of 252 accessions, in order to determine the integrity of plants within accessions and whether contaminants had been introduced. A total of 748 plants from 252 accessions, sampling two to three plants per plot per accession, were genotyped by the genotyping-by-sequencing (GBS) method of the DArTseq platform (Diversity Array Technology). A total of 162,002 SNP and 220,603 SilicoDArT genome-wide markers were generated. Of these, 51% of the SNPs and 39% of the SilicoDArTs were mapped onto the U. ruziziensis genome. The genetic integrity of plants within accessions was assessed based on a pairwise IBD (Identity-By-Descent) analysis using the Maximum Likelihood Estimation (MLE). Of the three plants sampled within a plot (within accession), 152 accessions (60 %) were 100 % true-to-type, indicating that there was no mix-up, mislabeling, or cross-pollination from other accessions. In 33 accessions (13 %), one of the three plants was genetically different but showed a close genetic relationship (parent-offspring, full-sib, or half-sib) to the remaining two plants, indicating some level of cross-pollination had taken place in these accessions. In another 50 accessions (20%), one of the three plants was genetically distinct from the other two plants, while the three plants were unrelated to each other in another 17 accessions (7 %), indicating that a mix-up or potential contamination had been taken place in this group of accessions. Clustering analysis using the discriminant analysis of principal components (DAPC) and hierarchical clustering detected four to five major clusters, each with further subclusters. The results of this study provides useful information for the management and conservation of the collection in the ILRI forage genebank. The substantial genetic diversity observed in the collection reveals the potential of the collection for further genetic studies.

Keywords: Brachiaria, forage, genetic diversity, genetic integrity, Urochloa brizantha

Contact Address: Meki Shehabu Muktar, International Livestock Research Institute (ILRI), Feed and Forage Development, Addis Ababa, Ethiopia, e-mail: mshehabu@gmail.com

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