R.F. Veerkamp and Y. de Haas (eds) Proceedings of 12 th World Congress on Genetics Applied to Livestock Production (WCGALP) 3012 DOI: 10.3920/978-90-8686-940-4_731, © S.A. Rahmatalla et al. 2022 731. Pairwise principal component analysis of African goat breeds identifes loci involved in meat and/or milk production S.A. Rahmatalla 1,2*# , D. Arends 1# , G.M. Tarekegn 3,4 , R. Onzima 5 and G.A. Brockmann 1 1 Humboldt-Universität zu Berlin, Invalidenstraβe 42, 10115 Berlin, Germany; 2 University of Khartoum, Shambat, P.O. Box 32, Khartoum North, Sudan; 3 Bahir Dar University, P.O. Box 79, Bahir Dar, Ethiopia; 4 Scotland’s Rural College, Roslin Institute Building, Easter Bush, EH125 9RG Edinburgh, United Kingdom; 5 Muni University, P.O. Box 725, Arua; Uganda; siham.rahmatalla@hu-berlin.de; # these authors contributed equally to this work Abstract Te selection process in Africa, both environmentally and human-driven, is expected to have led to distinctive variations on the genome between milk and meat goat breeds. We used genotypic data from the caprine 50k Illumina BeadChip to assess the genetic diferentiation between nine milk-type and 12 meat- type breeds from Africa by applying a novel pairwise principal component analysis (PCA) method. Using the PCA approach, 95 comparisons contribute to the optimal dissipation on PC1 for milk-type versus meat-type breeds. We identifed nine genomic regions that highly difered between milk-type and meat- type breeds in over 25% of comparisons. Tese SNPs are located on chromosomes 2, 3, 4, 5, 7, 12, 18, and 25. In particular, near these SNPs, candidate genes that might potentially control milk and meat production traits were located. Te novel PCA approach helps the identifcation of genomic regions that contributed to the genomic variation of milk-type versus meat-type breeds. Introduction Growing human populations generate an increased demand for food, including protein-rich products from animals (Henchion et al. 2017). Goats can play an important role in meeting these demands (Aziz 2010). In Africa, goats are profoundly entrenched in almost every African culture, especially within communities that cannot aford large livestock (Peacock 2005). Goats ofer an advantage in animal production and food security as they can produce milk and meat under harsh environmental conditions by using inexpensive food resources. Terefore, costs of goat production are relatively low (Peacock 2005; Mataveia et al. 2021) and milk and meat production are essential niches in most African countries to overcome poverty and malnutrition. Research and developments to improve the relatively low level of productivity of African goats do not match their importance. As a result, many goat breeds are not sufciently phenotypically explored. To improve the productivity, a better understanding of the animal’s genomic data and its relation to phenotypes is necessary (Rexroad et al. 2019). Getting, genotypic data of African goat breeds is a challenge. Nevertheless, over the last decade, researchers were successful at collecting a signifcant amount of genotypic data. Tis study aims to identify genomic regions that diferentiate between milk and meat goats. Materials & methods Animals. Illumina Goat SNP 50K genotypes from African goat breeds were obtained from the Adaptmap project (Bertolini et al. 2018) collaborators, and previous own genotyping. Te frst step is quality control (QC) of the data: Animals where the breed designation is missing, animals that do not cluster inside their designated breed, animals classifed as cross-breed animals, and animals that show high relatedness to other animals were removed from the data set. Furthermore, per breed we require a minimum of 20 animals to be genotyped afer QC. Tis resulted in 2,044 animals belonging to 45 African breeds suitable for further https://www.wageningenacademic.com/doi/pdf/10.3920/978-90-8686-940-4_731 - Saturday, February 11, 2023 12:05:25 PM - IP Address:3.231.217.247