SNP panels for the estimation of dairy breed proportion and parentage assignment in African crossbred dairy cattle

Abstract

Background Understanding the relationship between genetic admixture and phenotypic performance is crucial for the optimization of crossbreeding programs. The use of small sets of informative ancestry markers can be a cost-effective option for the estimation of breed composition and for parentage assignment in situations where pedigree recording is difficult. The objectives of this study were to develop small single nucleotide polymorphism (SNP) panels that can accurately estimate the total dairy proportion and assign parentage in both West and East African crossbred dairy cows. Methods Medium- and high-density SNP genotype data (Illumina BovineSNP50 and BovineHD Beadchip) for 4231 animals sampled from African crossbreds, African Bos taurus, European Bos taurus, Bos indicus, and African indigenous populations were used. For estimating breed composition, the absolute differences in allele frequency were calculated between pure ancestral breeds to identify SNPs with the highest discriminating power, and different combinations of SNPs weighted by ancestral origin were tested against estimates based on all available SNPs. For parentage assignment, informative SNPs were selected based on the highest minor allele frequency (MAF) in African crossbred populations assuming two Scenarios: (1) parents were selected among all the animals with known genotypes, and (2) parents were selected only among the animals known to be a parent of at least one progeny. Results For the medium-density genotype data, SNPs selected for the largest differences in allele frequency between West African indigenous and European Bos taurus breeds performed best for most African crossbred populations and achieved a prediction accuracy (r2) for breed composition of 0.926 to 0.961 with 200 SNPs. For the high-density dataset, a panel with 70% of the SNPs selected on their largest difference in allele frequency between African and European Bos taurus performed best or very near best across all crossbred populations with r2 ranging from 0.978 to 0.984 with 200 SNPs. In all African crossbred populations, unambiguous parentage assignment was possible with ≥ 300 SNPs for the majority of the panels for Scenario 1 and ≥ 200 SNPs for Scenario 2. Conclusions The identified low-cost SNP assays could overcome incomplete or inaccurate pedigree records in African smallholder systems and allow effective breeding decisions to produce progeny of desired breed composition.

Small SNP panels for breed proportion estimation in Indian crossbred dairy cattle

“…Previous studies have shown that 200–400 markers are sufficient to obtain accurate estimates of dairy breed proportions (Gebrehiwot et al., 2021; Strucken et al., 2017), and that only a negligible improvement in estimation accuracy was achieved with more than 500 markers. Therefore, we tested small panels of 100, 200, 300, 400 and 500 SNPs.…”

“…The distinction between B. taurus (EXO) and B. indicus (IND) can be achieved with relatively fewer markers compared to the distinction between B. taurus breeds (Gebrehiwot et al., 2021). To develop a panel that could distinguish between indicine and exotic as well as between Holstein‐Friesian and Jersey proportions, we created panels with different ratios of markers selected from both optimized panels for EXO versus IND and HF versus J.…”

“…Gebrehiwot et al. (2021) showed that more markers are required to differentiate African from European taurine breeds compared to the differentiation of B. indicus and B. taurus in a ratio of 70%:30%.…”

Development of a genomic tool for breed assignment by comparison of different classification models: Application to three local cattle breeds

“…Most likely, this is due to the fact that this statistic can be easily adapted (e.g., global vs. pairwise) to make it suitable for the selection of markers for breed assignment. Regression on allele frequencies (He et al., 2018; Kuehn et al., 2011) and absolute allele frequency differences (Ding et al., 2011; Frkonja et al., 2012; Gebrehiwot et al., 2021; Hulsegge et al., 2013; Wilkinson et al., 2011) are other common methodologies for selection of markers for breed assignment. Several studies also used principal component analysis (PCA), based on different types of data input, to select the best SNP markers for discriminating breeds (Wilkinson et al., 2011).…”

Performance of using opposing homozygotes for paternity testing in Japanese Black cattle

“…Previous studies have reported the results of paternity testing based on the number of OH, which is the exclusion-based approach, using genome-wide SNP markers genotyped by commercial chips in different cattle breeds (e.g. Calus et al, 2011;García-Ruiz et al, 2019;Gebrehiwot et al, 2021;Hayes, 2011;Purfield et al, 2016;Strucken et al, 2016Strucken et al, , 2017Wiggans et al, 2009). The likelihoodbased approach might be better in theory and therefore has greater accuracy, but computational costs are high especially when applied to large-scale data sets (Moore et al, 2019).…”