Definition and analysis of the panel of SNPs to be used in paternity tests for three breeds of cattle
DOI:
https://doi.org/10.22319/rmcp.v12i3.5771Keywords:
Heterozygosity, Exclusion probability, Identity probability, Polymorphism, Shannon IndexAbstract
In order to define the SNP panel for paternity tests in cattle, genotypes were analyzed in three breeds (number of SNPs evaluated and individuals sampled): Hereford (HER; 202; 1317), Brangus (BRA; 217; 3431) and Limousin (LIM; 151; 8205). Within breed, SNPs with a percentage of genotyped individuals (PGI) less than 90 %, with Hardy-Weinberg disequilibrium (HW; P<0.05), with allele frequency less than 0.10 or less and with linkage disequilibrium, where the correlation between genotypic frequencies was greater than 0.25, were discarded. The levels of expected (He) and observed (Ho) heterozygosity, polymorphic information content (PIC) were estimated; as well as the Shannon index, the fixation index and effective population size (Ne). The combined exclusion probability (CEP) and identity probability (CIP) were calculated. The final panel was 121, 188 and 113 SNPs in HER, BRA and LIM, respectively; the main source of discard was HW followed by PGI. Levels of Ho and He were above 0.40; CIP was greater than 0.32 and Ne presented estimates above 181.3. The results for CEP were higher than 0.999999; for CIP, they were below 1 x 10-20.
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