Genetic diversity and effective population sizes of thirteen Indian cattle breeds.

BACKGROUND: The genetic structure of a diverse set of 15 Indian indigenous breeds and non-descript indigenous cattle sampled from eight states was examined, based on 777 k single nucleotide polymorphism (SNP) genotypes obtained on 699 animals, with sample sizes ranging from 17 to 140 animals per breed. To date, this is the largest and most detailed assessment of the genetic diversity of Indian cattle breeds. RESULTS: Admixture analyses revealed that 109 of the indigenous animals analyzed had more than 1% Bos taurus admixture of relatively recent origin. Pure indigenous animals were defined as having more than 99% Bos indicus ancestry. Assessment of the genetic diversity within and between breeds using principal component analyses, F statistics, runs of homozygosity, the genomic relationship matrix, and maximum likelihood clustering based on allele frequencies revealed a low level of genetic diversity among the indigenous breeds compared to that of Bos taurus breeds. Correlations of SNP allele frequencies between breeds indicated that the genetic variation among the Bos indicus breeds was remarkably low. In addition, the variance in allele frequencies represented less than 1.5% between the Indian indigenous breeds compared to about 40% between Bos taurus dairy breeds. Effective population sizes (Ne) increased during a period post-domestication, notably for Ongole cattle, and then declined during the last 100 generations. Although we found that most of the identified runs of homozygosity are short in the Indian indigenous breeds, indicating no recent inbreeding, the high FROH coefficients and low FIS values point towards small population sizes. Nonetheless, the Ne of the Indian indigenous breeds is currently still larger than that of Bos taurus dairy breeds. CONCLUSIONS: The changes in the estimates of effective population size are consistent with domestication from a large native population followed by consolidation into breeds with a more limited population size. The surprisingly low genetic diversity among Indian indigenous cattle breeds might be due to their large Ne since their domestication, which started to decline only 100 generations ago, compared to approximately 250 to 500 generations for Bos taurus dairy cattle.

Inference of Ancestries and Heterozygosity Proportion and Genotype Imputation in West African Cattle Populations.

Several studies have evaluated computational methods that infer the haplotypes from population genotype data in European cattle populations. However, little is known about how well they perform in African indigenous and crossbred populations. This study investigates: (1) global and local ancestry inference; (2) heterozygosity proportion estimation; and (3) genotype imputation in West African indigenous and crossbred cattle populations. Principal component analysis (PCA), ADMIXTURE, and LAMP-LD were used to analyse a medium-density single nucleotide polymorphism (SNP) dataset from Senegalese crossbred cattle. Reference SNP data of East and West African indigenous and crossbred cattle populations were used to investigate the accuracy of imputation from low to medium-density and from medium to high-density SNP datasets using Minimac v3. The first two principal components differentiated Bos indicus from European Bos taurus and African Bos taurus from other breeds. Irrespective of assuming two or three ancestral breeds for the Senegalese crossbreds, breed proportion estimates from ADMIXTURE and LAMP-LD showed a high correlation (r ≥ 0.981). The observed ancestral origin heterozygosity proportion in putative F1 crosses was close to the expected value of 1.0, and clearly differentiated F1 from all other crosses. The imputation accuracies (estimated as correlation) between imputed and the real data in crossbred animals ranged from 0.142 to 0.717 when imputing from low to medium-density, and from 0.478 to 0.899 for imputation from medium to high-density. The imputation accuracy was generally higher when the reference data came from the same geographical region as the target population, and when crossbred reference data was used to impute crossbred genotypes. The lowest imputation accuracies were observed for indigenous breed genotypes. This study shows that ancestral origin heterozygosity can be estimated with high accuracy and will be far superior to the use of observed individual heterozygosity for estimating heterosis in African crossbred populations. It was not possible to achieve high imputation accuracy in West African crossbred or indigenous populations based on reference data sets from East Africa, and population-specific genotyping with high-density SNP assays is required to improve imputation.

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

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.