Investigating Genetic Diversity and Inbreeding in Dairy and Beef Cattle Populations Using Molecular Markers

Introduction: Alongside the enhancement of economic traits through genetic advancements, it is imperative to preserve genetic diversity within cattle populations. This diversity is essential for adapting to future environmental and economic changes, as well as for ensuring a robust response to trait selection (Barker, 2001). Genetic diversity forms the foundation of successful breeding programs and includes the genetic variations among individuals, families, or populations. The increase in inbreeding rates has become one of the most significant challenges in the dairy farming industry over the past few decades. Inbreeding negatively affects animal performance, leading to reduced longevity. Some researchers have indicated that even a 1% increase in the inbreeding coefficient can significantly decrease milk production, milk composition, and reproduction performance. The primary reason for the rising inbreeding coefficient is the frequent use of specific sperm through artificial insemination in dairy farms. Single nucleotide polymorphism (SNP) markers, indicating mutations at a single base in the genome, are extensively utilized in livestock populations. These markers play a pivotal role in assessing genetic diversity among breeds, verifying the purity of livestock products, pinpointing genes linked to significant economic traits, and estimating breeding values (Yang et al., 2013). To estimate inbreeding coefficients, various methods are available, including those based on the genomic relationship matrix (FGRM), homozygosity (FHOM), and homozygosity blocks (FROH). In studies of genetic diversity, linkage disequilibrium (LD) reflects the non-random association of alleles at different genetic locations. Monitoring changes in linkage disequilibrium serves as an indicator of selection shifts over time (De Roos et al., 2008). Furthermore, identifying linkage disequilibrium or haplotype blocks facilitates the design of association studies and the detection of genetic diversity in quantitative traits (Khatkar et al., 2007). A critical statistic for evaluating genetic diversity is the effective population size (Ne), which represents the number of individuals in an ideal population that affect gene frequency changes in subsequent generations (Gutiérrez et al., 2009). Ne is vital in population genetics due to its direct correlation with inbreeding and the decline in genetic diversity within a population. Ultimately, understanding the genetic diversity of existing populations is essential for effective selection and the implementation of breeding programs at breeding stations. This research aims to investigate genetic diversity and estimate inbreeding in various dairy and beef cattle breeds using molecular markers. The study will involve estimating the genomic inbreeding coefficient, examining linkage disequilibrium, and determining effective population size.
Materials and Methods: This study utilized genomic information from 16 cattle breeds, categorized into four groups: Dairy Breeds (Holstein, Brown Swiss, Jersey, and Guernsey), American Beef Cattle Breeds (Angus, Beef Master, Brahman, and Santa), European Beef Cattle Breeds (Hereford, Limousine, Charolais, and Ramangoula), and Beef Cattle Breeds from Other Regions (Gir, N-Dama, Nellore, and Piedmonts). Blood samples from all breeds were genotyped using a 700k SNP chip, and genomic data was extracted from the Widde database. Quality control of the genotype data was performed using Plink v1.9 (Purcell et al., 2007). Principal component analysis (PCA), based on a genomic relationship matrix, was conducted to provide a general overview of the genetic structure of the breeds, using R v.3.6.2. PCA was also employed to identify and remove outlier samples from each genetic group. Inbreeding coefficients (FGRM, FHOM, and FROH) were estimated using Plink v.1.9 (Purcell et al., 2007) within the R environment v.3.6.2. Additionally, to assess genetic diversity, linkage disequilibrium (LD) and effective population size (Ne) statistics were estimated using Plink v.1.9 (Purcell et al., 2007) and SnePv1.1 (Barbato et al., 2015).
Results and Discussion: The analysis of observed and expected heterozygosity, along with the minor allele frequency, highlighted that the Beef Master and Santa breeds displayed the highest levels of genetic diversity, while the N-Dama and Tellor breeds had the lowest. The amount of FGRM across various American, European, and other meat breeds indicated different genetic structure among studied populations, showed similar patterns in genetic diversity within these groups. Among the breeds examined, Piedmonts exhibited the highest genetic diversity, whereas Angus and Hereford showed the lowest. The distribution and frequency of the calculated FHOM aligned with the patterns observed in FGRM. In dairy breeds, genetic diversity was notably lower, especially in the Jersey breed, and the Piedmonts breed again exhibiting the highest diversity in this context. European meat breeds demonstrated greater genetic diversity compared to other meat breeds. The inbreeding estimates derived from the FROH method were higher than those obtained from the other two methods. Notably, the Jersey and Hereford breeds had the highest values of estimated FROH, while the Piedmonts and N-Dama breeds had the lowest. Linkage disequilibrium (LD) analysis revealed that LD values decreased as the distance between markers increased across all populations studied. Additionally, LD was higher in dairy breeds than in meat breeds, suggesting greater selection pressure and reduced genetic diversity within dairy cattle breeds. Among the breeds, the Brahman exhibited the highest genetic diversity, while the Guernsey had the lowest. The study also indicated that the effective population size (Ne) in dairy breeds has been lower than in meat breeds over recent generations, with similar patterns of reduction observed among meat breeds. Within the meat breeds, Piedmonts and Limousin had the highest Ne, whereas the Beef Master breed had the lowest. Among dairy cattle breeds, Holstein exhibited the highest Ne, while Brown Swiss showed the lowest.
Overall, these findings suggested that genetic diversity is greater in meat breeds compared to dairy breeds, reflecting the intense selection pressure aimed at improving milk production in dairy populations. It is crucial to establish appropriate breeding programs to enhance genetic diversity in livestock, particularly in dairy species, to reduce the risks of increasing inbreeding and the potential decline in productive traits.