Assessing genetic architecture and signatures of selection of dual purpose Gir cattle populations using genomic information

Abstract

Gir is one of the main cattle breeds raised in tropical South American countries. Strong artificial selection through its domestication resulted in increased genetic differentiation among the countries in recent years. Over the years, genomic studies in Gir have become more common. However, studies of population structure and signatures of selection in divergent Gir populations are scarce and need more attention to better understand genetic differentiation, gene flow, and genetic distance. Genotypes of 173 animals selected for growth traits and 273 animals selected for milk production were used in this study. Clear genetic differentiation between beef and dairy populations was observed. Different criteria led to genetic divergence and genetic differences in allele frequencies between the two populations. Gene segregation in each population was forced by artificial selection, promoting isolation, and increasing genetic variation between them. Results showed evidence of selective forces in different regions of the genome. A total of 282 genes were detected under selection in the test population based on the fixation index (Fst), integrated haplotype score (iHS), and cross-population extend haplotype homozygosity (XP-EHH) approaches. The QTL mapping identified 35 genes associated with reproduction, milk composition, growth, meat and carcass, health, or body conformation traits. The investigation of genes and pathways showed that quantitative traits associated to fertility, milk production, beef quality, and growth were involved in the process of differentiation of these populations. These results would support further investigations of population structure and differentiation in the Gir breed.

Linkage disequilibrium and effective population size in Gir cattle selected for yearling weight

“…The authors used different methods, one of them based on LD and reported that the region of the SLC24A4 gene was common in the two populations, providing strong evidence of selection signatures in the Gir breed. Since high LD over an extended region is likely the result of recent selection (Pérez O’Brien et al, ), the results obtained could explain the findings of Maiorano et al () in Gir cattle populations, highlighting the importance of LD on chromosome 21 for the formation of this breed.…”

“…Therefore, since the animals of this herd are part of an experimental selection programme, the pedigree file was complete, a fact that may have contributed to the good imputation accuracy. Maiorano et al (), studying the population structure of the same population, showed the formation of a single cluster for animals of this herd, with mating of related animals favouring a reduction in the genetic difference among individuals. The relationship between animals may present inbreeding levels, a factor that may influence the accuracy of imputation.…”

Genome‐wide identification of runs of homozygosity islands in the Gyr breed (Bos indicus)

“…Differences in the segments of ROH islands on the chromosomes were identified between the two populations. According to the results of principal component analysis and discriminant analysis of principal components shown in of the study of Maiorano et al (), there is a genetic difference between the Bp and Dp populations and this difference reflects the variation that exists between the populations.…”

“…According to principal component analysis of the Gyr breed (beef and dairy) depicted in Figure of the study of Maiorano et al (), PC2 shows a more compact cluster in the Bp population, possibly because the population belongs to a closed herd in which few sires are used for mating, increasing the level of kinship and permitting accurate imputation of the genotypes of this population. The Dp population exhibited a more disperse cluster based on PC2, indicating a greater genetic distance and lower kinship between individuals of the population compared with Bp.…”

“…Principal component analysis probably showed a more disperse pattern as the animals belonged to different commercial herds. Thus, 18 sires representative of each population were chosen and genotyped with the HD panel, data not included in the cited study (Maiorano et al, ). The aim of including the HD genotypes was to minimize differentiation in the populations studied and to perform genotype imputation in order to ensure greater accuracy.…”