Genetic diversity and effective population sizes of thirteen Indian cattle breeds

Abstract

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.

Genetic Diversity and Population Structure for Resistance and Susceptibility to Mastitis in Braunvieh Cattle

“…The overall average for F IT was 0.017 ± 0.043 for all the traits associated with mastitis. This value is similar to those found for Sahiwal (0.013 ± 0.109), Gyr (0.013 ± 0.106), and Guernsey (0.02 ± 0.217) [47]. In contrast, the F IT for the tropical breeds Landim, Angole, and Tete [48] was 70% higher than that found in our study.…”

“…Furthermore, for Creole Colombian breeds, the average was 0.09 [44]. The first group of breeds was maintained in semi-specialized systems [47], while Landim, Angole, Tete, and the Colombian Creole are non-specialized breeds. This difference could explain why smaller breeds without adequate genetic control present higher inbreeding coefficients.…”

Detection of genomic regions that differentiate Bos indicus from Bos taurus ancestral breeds for milk yield in Indian crossbred cows

“…We were unable to differentiate different sources of Desi using SNP marker data because of the remarkably low SNP variation observed between B. indicus breeds. Approximately 1% of all SNP variation within B. indicus occurs between breeds , compared to the nearly 40% of variation within B. taurus being between B. taurus breeds ( Strucken et al, 2021 ). The GWAA for QTL segregating within B. taurus in the two-ancestor model, or within HF and Jersey in the three-ancestor model, had a power equivalent to undertaking a GWAA in approximately 3,200, 2,450 and 750 purebred cows, respectively.…”

“…After being subject to QC as described by (2021), animals genotyped with the 50K chip were imputed to high density (HD) using reference samples that had real HD genotypes. The reference population for imputation included 684 pure Jerseys, and 968 pure Holsteins from the Bovine HapMap ( Consortium et al, 2009 ), 666 pure Indian B. indicus indigenous animals from a separate BAIF project ( Strucken et al, 2021 ), and the 643 crossbred cows from the BAIF EGP. The HapMap and the Indian indigenous samples were genotyped with the Illumina 777k assay and genotypes were received post-QC.…”

Comprehensive assessment of genetic diversity, structure, and relationship in four Japanese cattle breeds by Illumina 50 K SNP array analysis

“…We also used 50 K SNP datasets of foreign cattle breeds downloaded from a database to compare the genetic diversity and survey the genetic relationship between Japanese and foreign breeds. Although the number of datasets for the foreign breeds was relatively small, we were able to assess the broad relationships as with previous studies (Alam et al, 2021; Decker et al, 2014; Strucken et al, 2021). However, the number of datasets of Devon was significantly small, and therefore, we payed attention considering the small number in assessment of the relationships between Devon and the other breeds in this study.…”