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.

This study aimed to evaluate population parameters and to describe the genetic diversity of Quarter Horse breed (QH) in Brazil, reported for the first time in the literature. The pedigree data comprised 131,716 animals representing the total population (TP), with records of animals born between 1747 and 2008. The reference population (RP) representing the last generation was applied in this study considering 47,861 animals born between 2000 and 2008. The average generation interval was 9.6 and 10.8 years in TP and RP, respectively. The average equivalent complete generations (EG) were 5.09 (TP) and 6.24 (RP). The inbreeding coefficient (F), average relatedness (AR) and the increase in inbreeding by generation (ΔF) was 1.07%, 0.95% and 0.24%, respectively, for TP. The effective population size (N e) based on ΔF was 195 and 164 for TP and RP, respectively. The effective number of founders (f e) was 1045 and 811 for TP and RP, respectively, that of ancestors (f a) was 156 and 113, and that of founder genomes (f g) was 105 and 66. The f e /f a and f e /f g ratios in TP were 6.70 and 9.95, respectively, and an increase was observed in RP, indicated a strong bottleneck effect. The total genetic diversity of the QH breed was explained by 4780 ancestors, with 50% of diversity being explained by only 121 and 72 ancestors in TP and RP, respectively. The thoroughbred stallion Three Bars is the most influential ancestor with the largest marginal genetic contribution for TP (5.73) and RP (5.94%). The results demonstrate a large number of founders and ancestors, but a small ancestor group was responsible for the continuity of the QH breed in Brazil. These finding highlight the importance of monitoring genetic diversity, including follow-up by breeding programs, to permit control of the next generations.

This study aimed to evaluate population parameters and to describe the genetic diversity of the Lusitano breed in Brazil using pedigree data. Two populations were evaluated: total population (TP) containing 18,922 animals, and reference population (RP) composed of a part of TP containing 8,329 animals, representing the last generation. The generation interval (10.1 ± 5.1 years) was in the range for horse populations. Pedigree completeness in RP shows almost 100% filling in the three most recent generations, indicating improvement in the pedigree data and accuracy of the results, and the inbreeding coefficient (4.46%) and average relatedness (5.97%) for RP, indicating control on the part of breeders. The effective population size was 89 (TP) and 90 (RP). The effective number of founders (f e) were 33 and 29, effective number of ancestors (f a) were 30 and 26, and effective number of founder genomes (f g) were 19 and 15 for TP and RP, respectively, indicating a reduction of genetic variability in the last generations. The total number of ancestors that explains 100% of the genetic diversity in the Lusitano breed in Brazil was 427 (TP) and 341 (RP). The reproductive parameters, probabilities of gene origin showing loss of variability in the last generations, and the genetic contributions of ancestors suggest the need to monitor genetic diversity over time in breeding programs to allow control of the next generations and to increase their variability.

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