R.F. Veerkamp and Y. de Haas (eds) Proceedings of 12 th World Congress on Genetics Applied to Livestock Production (WCGALP) 1917 DOI: 10.3920/978-90-8686-940-4_461, © M. Walugembe et al. 2022 461. Development of a low-density SNP panel for local Ghanaian and Tanzanian chicken ecotypes M. Walugembe 1 , E.N. Amuzu-Aweh 2* , K.-S. Lim 1 , Y. Wang 3 , N. Chouicha 3 , T. Kelly 4 , A.P. Muhairwa 5 , B.B. Kayang 2 , P.L.M. Msofe 5 , A. Naazie 2 , H.R. Otsyina 6 , J.S. Mushi 5 , R.A. Gallardo 4 , H. Zhou 3 , S.J. Lamont 1 and J.C.M. Dekkers 1* 1 Department of Animal Science, Iowa State University, Ames, IA, USA; 2 Department of Animal Science, University of Ghana, Legon, Accra, Ghana; 3 Animal Science, University of California, Davis, Davis, CA, USA; 4 School of Veterinary Medicine, University of California, Davis, Davis, CA, USA; 5 Department of Veterinary Medicine and Public Health, Sokoine University, P.O. Box 3000 Chuo Kikuu, Morogoro, Tanzania, 6 School of Veterinary Medicine, University of Ghana, Legon, Accra, Ghana; jdekkers@iastate.edu Abstract Genetic selection is important in choosing animals for the next generation. Animal breeders now choose selection candidates based on DNA markers, in addition to animal performance. Tere has been increased use of high-density SNP chips to enable selection of commercial broiler and layer chickens. However, genotyping a large number of selection candidates still carries a high cost. Te aim of our study was to develop an economical 5K SNP panel for local Ghanian and Tanzanian chicken ecotypes using targeted genotyping by sequencing (GBS) for imputation to higher density. Low-density panel SNPs were selected from haplotype blocks and other important genomic regions across the chicken genome based on 600K SNP panel genotypes. A total of 188 birds were genotyped by GBS and an in-house shell script pipeline was utilized to obtain SNP calls. Our in-house pipeline was compared to a standard company pipeline and 600K SNP chip genotypes for validation. Selected SNPs were evenly distributed across the genome, with at least one SNP in each megabase region. Comparison of the two pipelines revealed a good genotype match for the 5K SNP panel. Te 5K GBS panel and SNP calling pipeline are important tools to aid selective breeding in African chicken ecotypes. Introduction In the past decade, there has been an increase in the use of commercial high-density (HD) SNP chips for genotyping in chickens (Kranis et al., 2013), which has accelerated genomic selection in broiler and layer breeding. Te availability of genomic and phenotypic information enables genomic prediction of breeding values for selection candidates. Although HD SNP chips are commonly used, the costs to genotype a large number of selection candidates remains high. To reduce costs, the use of low-density (LD) panels followed by imputation to a high density could be a feasible approach (Habier et al., 2009). Array-based genotyping platforms are commonly utilized in genotyping various livestock species. However, they include SNPs that may not be geographically representative and therefore, population diversity and estimates of recombination rates may be biased (Pérez-Enciso and Ferretti, 2010; Zhan et al., 2011). In poultry, such studies have mostly been conducted in commercial layers and broilers, with limited focus on local African chicken ecotypes. New cost-efective next generation sequencing platforms such as genotyping by sequencing (GBS) have recently been developed. GBS was originally developed for plants (He et al., 2014), and follows a simple protocol that provides high SNP coverage (Sonah et al., 2013). Te objective of this study was to develop a low-density SNP panel for Ghanaian and Tanzanian local chickens using targeted GBS. Materials & methods Experimental birds. Breeding focks were established at the University of Ghana, Legon, Accra, Ghana, and Sokoine University of Agriculture, Morogoro, Tanzania. Breeder chickens from three Tanzanian (Kuchi, Morogoro Medium, and Ching’wekwe) ecotypes and three Ghanaian (Coastal Savannah, Forest and Interior Savannah) ecotypes were obtained. https://www.wageningenacademic.com/doi/pdf/10.3920/978-90-8686-940-4_461 - Saturday, February 11, 2023 1:48:04 PM - IP Address:3.239.92.156