Definition of a SNP panel for paternity testing in ten sheep populations in Mexico

• Published in: Small ruminant research 2020-12, Vol.193, p.106262, Article 106262
• Main Authors: Domínguez-Viveros, Joel, Rodríguez-Almeida, Felipe Alonso, Jahuey-Martínez, Francisco Joel, Martínez-Quintana, José Alfredo, Aguilar-Palma, Guadalupe Nelson, Ordoñez-Baquera, Perla
• Format: Article
• Language: English
• Subjects: Hardy-Weinberg equilibrium; Minor allele frequency; Polymorphic information content; Probability of exclusion; Probability of identity
• ISSN: 0921-4488; 1879-0941
• DOI: 10.1016/j.smallrumres.2020.106262

•The efficacy and benefit of a genetic marker in paternity tests differs across breeds.•Of 84 SNPs evaluated, the number of SNPs selected by population ranged from 42 to 63.•The probability of exclusion in the selected panels fluctuated from 0.99 to 0.999999. This study aimed to edit the SNPs panel for sheep paternity testing in Mexico. The genotypes of 10,097 individuals distributed in ten breeds were analyzed: Blackbelly (459), Charollais (209), White Dorper (122), Dorper (2106), Dorset (534), Hampshire (1,298), Katahdin (3864), Pelibuey (821), Suffolk (596), and Texel (88). In all breeds the panel was comprised of 84 SNPs; the allele frequencies, the polymorphic information content (PIC), and the Hardy-Weinberg (HW) equilibrium were evaluated. Within breeds, the SNPs with HW disequilibrium (p < 0.05), a minor allele frequency (MAF) below 0.2, and a percentage of genotyped individuals (PGI) lower than 95 % were discarded. The remaining subset of SNPs was sorted in descending order by PIC, and the probability of exclusion (PE) was calculated in three modes: to exclude a parent candidate, to exclude the relationship between parent and offspring, and to exclude one or both parents. The combined probability of exclusion for each situation was: CPE = 1 - Π(1 – PEi). Two probabilities of identity (PI) were estimated: for two individuals and two full siblings with identical genotypes. The combined probability of identity was CPI = ΠPIi. The CPE, in the three modes and across the ten populations, was greater than 0.99; the CPI fluctuated from 1 × 10−9 to 9 × 10-26. On average, the number of SNPs per breed was 55, with values ranging from 42 to 64; in the process by breed, 16 SNPs were separated on average by HW, with a maximum of 25; for PGI and MAF, three and nine SNPs were discarded on average, with maximum values of 5 and 22, respectively. Due to the genetic structure of the populations, the composition of a panel to verify paternity have different dimensions.