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.

Fig. 1

Boxplot of the observed allele frequencies in European Bos taurus (EUT), African Bos taurus (AFT), Bos indicus (BI), and African crossbred populations for a 38,214 SNPs b 712,775 SNPs

Fig. 2

Breed proportion of crossbred cattle using a 38 k SNPs and b 713 k SNPs

Fig. 3

Accuracy ($r^2$) of estimation of dairy breed proportion in crossbreds for panels selected from 38 k SNPs in a Kenya b Uganda c Ethiopia d Tanzania e Senegal

Fig. 4

Accuracy ($r^2$) of estimates of dairy breed proportion in crossbreds for panels selected from 713 k SNP in a Kenya b Uganda c Ethiopia d Tanzania e Senegal

Fig. 5

Separation values ($\mathit{sv}$) of parentage assignment for small SNP panels for Scenario 1 in a all African crossbreds b all East African crossbreds c Kenya-Ethiopia-Tanzania together d Ugandan e Senegal crossbreds

Fig. 6

Power of assignment ($\mathit{Pa}$) and power of exclusion ($\mathit{Pe}$) of 200 SNP (a, b), 300 SNP (c, d), and 400 SNP (e, f) panels. P1 = MAF-xbreds, P2 = MAF-Pruned-xbreds, P3 = MAF-East, P4 = MAF-Pruned-East, P5 = MAF-KenEthTan, P6 = MAF-Pruned-KenEthTan, P7 = MAF-Uganda, P8 = MAF-Pruned-Uganda, P9 = MAF-Senegal, and P10 = MAF-Pruned-Senegal

Fig. 7

Performance of a reference panel (Strucken et al. [15]) and the newly derived panels (pruned and not-pruned) for estimating dairy breed proportions in a Senegalese crossbred population