Runs of homozygosity (ROH) are continuous homozygous segments of the DNA sequence. They have been applied to quantify individual autozygosity and used as a potential inbreeding measure in livestock ...species. The aim of the present study was (i) to investigate genome-wide autozygosity to identify and characterize ROH patterns in Gyr dairy cattle genome; (ii) identify ROH islands for gene content and enrichment in segments shared by more than 50% of the samples, and (iii) compare estimates of molecular inbreeding calculated from ROH (F
), genomic relationship matrix approach (F
) and based on the observed versus expected number of homozygous genotypes (F
), and from pedigree-based coefficient (F
).
ROH were identified in all animals, with an average number of 55.12 ± 10.37 segments and a mean length of 3.17 Mb. Short segments (ROH
) were abundant through the genomes, which accounted for 60% of all segments identified, even though the proportion of the genome covered by them was relatively small. The findings obtained in this study suggest that on average 7.01% (175.28 Mb) of the genome of this population is autozygous. Overlapping ROH were evident across the genomes and 14 regions were identified with ROH frequencies exceeding 50% of the whole population. Genes associated with lactation (TRAPPC9), milk yield and composition (IRS2 and ANG), and heat adaptation (HSF1, HSPB1, and HSPE1), were identified. Inbreeding coefficients were estimated through the application of F
, F
, F
, and F
approaches. F
estimates ranged from 0.00 to 0.327 and F
from 0.001 to 0.201. Low to moderate correlations were observed between F
-F
and F
-F
, with values ranging from -0.11 to 0.51. Low to high correlations were observed between F
-F
and moderate between F
-F
and F
-F
. Correlations between F
from different lengths and F
gradually increased with ROH length.
Genes inside ROH islands suggest a strong selection for dairy traits and enrichment for Gyr cattle environmental adaptation. Furthermore, low F
F
correlations for small segments indicate that F
estimates are not the most suitable method to capture ancient inbreeding. The existence of a moderate correlation between larger ROH indicates that F
can be used as an alternative to inbreeding estimates in the absence of pedigree records.
Further characterization of genetic structural variations should strongly focus on small and endangered local breeds given their role in unraveling genes and structural variants underlying selective ...pressures and phenotype variation. A comprehensive genome‐wide assessment of copy number variations (CNVs) based on whole‐genome re‐sequencing data was performed on three Brazilian locally adapted cattle breeds (Caracu Caldeano, Crioulo Lageano, and Pantaneiro) using the ARS‐UCD1.2 genome assembly. Data from 36 individuals with an average coverage depth of 14.07× per individual was used. A total of 24 945 CNVs were identified distributed among the breeds (Caracu Caldeano = 7285, Crioulo Lageano = 7297, and Pantaneiro = 10 363). Deletion events were 1.75–2.07‐fold higher than duplications, and the total length of CNVs is composed mostly of a high number of segments between 10 and 30 kb. CNV regions (CNVRs) are not uniformly scattered throughout the genomes (n = 463), and 105 CNVRs were found overlapping among the studied breeds. Functional annotation of the CNVRs revealed variants with high consequence on protein sequence harboring relevant genes, in which we highlighted the BOLA‐DQB, BOLA‐DQA5, CD1A, β‐defensins, PRG3, and ULBP21 genes. Enrichment analysis based on the gene list retrieved from the CNVRs disclosed over‐represented terms (p < 0.01) strongly associated with immunity and cattle resilience to harsh environments. Additionally, QTL associated with body conformation and dairy‐related traits were also unveiled within the CNVRs. These results provide better understanding of the selective forces shaping the genome of such cattle breeds and identify traces of natural selection pressures by which these populations have been exposed to challenging environmental conditions.
Studying structural variants that can control complex traits is relevant for dairy cattle production, especially for animals that are tolerant to breeding conditions in the tropics, such as the Dairy ...Gir cattle. This study identified and characterized high confidence copy number variation regions (CNVR) in the Gir breed genome. A total of 38 animals were whole-genome sequenced, and 566 individuals were genotyped with a high-density SNP panel, among which 36 animals had both sequencing and SNP genotyping data available. Two sets of high confidence CNVR were established: one based on common CNV identified in the studied population (CNVR_POP), and another with CNV identified in sires with both sequence and SNP genotyping data available (CNVR_ANI). We found 10 CNVR_POP and 45 CNVR_ANI, which covered 1.05 Mb and 4.4 Mb of the bovine genome, respectively. Merging these CNV sets for functional analysis resulted in 48 unique high confidence CNVR. The overlapping genes were previously related to embryonic mortality, environmental adaptation, evolutionary process, immune response, longevity, mammary gland, resistance to gastrointestinal parasites, and stimuli recognition, among others. Our results contribute to a better understanding of the Gir breed genome. Moreover, the CNV identified in this study can potentially affect genes related to complex traits, such as production, health, and reproduction.
The goal of this study was to verify the effect of heterogeneity of variance (HV) on milk production in up to 305 days of lactation (L305) of daughters of Girolando, Gir and Holstein sires, as well ...as in the genetic evaluation of these sires and their progenies. in Brazil. The model included contemporary groups (consisting of herd, year and calving season) as a fixed effect, cow age at calving (linear and quadratic effects) and heterozygosity (linear effect) as covariates, in addition to the random effects of direct additive genetic and environmental, permanent and residual. The first analysis consisted of the single-trait animal model, with L305 records (disregarding HV). The second considered classes of standard deviations (SD): two-trait model including low and high classes (considering HV), according to the standardized means of L305 for herd-year of calving. The low SD class was composed of herds with SD equal to or less than zero and the high class with positive SD values. Estimates of (co)variance components and breeding values were obtained separately for each scenario using Bayesian inference via Gibbs sampling. Different heritability was estimated. Higher for the high DP class in the Gir (0.20) and Holstein (0.15) breeds, not occurring the same in the Girolando breed, with a lower value among the classes for the high DP (0.10). High values of genetic correlations were also found between low and high SD classes (0.88; 0.85 and 0.79) for the Girolando, Gir and Holstein breeds, respectively. Like the order correlations (Spearman) which were also high for the three breeds analyzed (equal to or above 0.92). Thus, the presence of HV had a smaller impact for L305 and did not affect the genetic evaluation of sires.
The cattle introduced by European conquerors during the Brazilian colonization period were exposed to a process of natural selection in different types of biomes throughout the country, leading to ...the development of locally adapted cattle breeds. In this study, whole-genome re-sequencing data from indicine and Brazilian locally adapted taurine cattle breeds were used to detect genomic regions under selective pressure. Within-population and cross-population statistics were combined separately in a single score using the de-correlated composite of multiple signals (DCMS) method. Putative sweep regions were revealed by assessing the top 1% of the empirical distribution generated by the DCMS statistics.
A total of 33,328,447 biallelic SNPs with an average read depth of 12.4X passed the hard filtering process and were used to access putative sweep regions. Admixture has occurred in some locally adapted taurine populations due to the introgression of exotic breeds. The genomic inbreeding coefficient based on runs of homozygosity (ROH) concurred with the populations' historical background. Signatures of selection retrieved from the DCMS statistics provided a comprehensive set of putative candidate genes and revealed QTLs disclosing cattle production traits and adaptation to the challenging environments. Additionally, several candidate regions overlapped with previous regions under selection described in the literature for other cattle breeds.
The current study reported putative sweep regions that can provide important insights to better understand the selective forces shaping the genome of the indicine and Brazilian locally adapted taurine cattle breeds. Such regions likely harbor traces of natural selection pressures by which these populations have been exposed and may elucidate footprints for adaptation to the challenging climatic conditions.
The beef cattle industry has experienced a shift driven by a market demand for healthier meat, cost efficiency and environmental sustainability in recent years. Consequently, there has been a growing ...focus on the fatty acids content and functions of meat in cattle breeding programmes. Besides, a deeper understanding of the biological mechanisms influencing the expression of different phenotypes related to fatty acid profiles is crucial. In this study, we aimed to identify Single-Nucleotide Variants (SNV) and Insertion/Deletion (InDels) DNA variants in candidate genes related to fatty acid profiles described in genomic, transcriptomic and proteomic studies conducted in beef cattle breeds. Utilizing whole-genome re-sequencing data from Brazilian locally adapted bovine breeds, namely Caracu and Pantaneiro, we identified SNVs and InDels associated with 23,947 genes. From these, we identified 318 candidate genes related to fatty acid profiles that contain variants. Subsequently, we select only genes with SNVs and InDels in their promoter, 5' UTR and coding region. Through the gene-biological process network, approximately 19 genes were highlighted. Furthermore, considering the studied trait and a literature review, we selected the main transcription factors (TF). Functional analysis via gene-TF network allowed us to identify the 30 most likely candidate genes for meat fatty acid profile in cattle. LIPE, MFSD2A and SREBF1 genes were highlighted in networks due to their biological importance. Further dissection of these genes revealed 15 new variants found in promoter regions of Caracu and Pantaneiro sequences. The gene networks facilitated a better functional understanding of genes and TF, enabling the identification of variants potentially related to the expression of candidate genes for meat fatty acid profiles in cattle.
The aim of this study was to estimate genetic parameters for cow weight at calving (CW) and cumulative 305-day milk yield (MY305) in dairy Gyr cattle by two-trait analysis. The study used 1,847 CW ...records, in which 418 females presented more than one measure, and 4,048 MY305 records, wherein 1068 females provided repeated measures, from 2,339 females belonging to three herds, which calved between 1986 and 2019. Variance components were estimated by the restricted maximum likelihood method (REML) using a two-trait animal model. The model included direct additive genetic, permanent environmental and residual effects as random effects and the fixed effects of contemporary group, formed by animals that had calved on the same farm year and season, and age of cow at calving as covariates (fitted as linear and quadratic effect). The heritability estimates for CW and MY305 were 0.21 ± 0.06 and 0.29 ± 0.04, respectively, and repeatability estimates were 0.49 ± 0.03 and 0.49 ± 0.02. The genetic correlation between CW and MY305 was positive and of low magnitude (0.33 ± 0.18), indicating that selection for MY305 will cause little genetic change in the weights of dairy Gyr animals. The genetic trends of breeding values of analyzed traits showed marked genetic gains in MY305, with little changes in CW of dairy Gyr cows over the years in the herds studied, which is an important result considering the production systems adopted in the tropics.
Our objective was to establish a SNPs panel for pedigree reconstruction using microarrays of different densities and evaluate the genomic relationship coefficient of the inferred pedigree, in ...addition to analyzing the population structure based on genomic analyses in Gir cattle. For parentage analysis and genomic relationship, 16,205 genotyped Gir animals (14,458 females and 1747 males) and 1810 common markers to the four SNP microarrays were used. For population structure analyses, including linkage disequilibrium, effective population size, and runs of homozygosity (ROH), genotypes from 21,656 animals were imputed. Likelihood ratio (LR) approach was used to reconstruct the pedigree, deepening the pedigree and showing it is well established in terms of recent information. Coefficients for each relationship category of the inferred pedigree were adequate. Linkage disequilibrium showed rapid decay. We detected a decrease in the effective population size over the last 50 generations, with the average generation interval around 9.08 years. Higher ROH-based inbreeding coefficient in a class of short ROH segments, with moderate to high values, was also detected, suggesting bottlenecks in the Gir genome. Breeding strategies to minimize inbreeding and avoid massive use of few proven sires with high genetic value are suggested to maintain genetic variability in future generations. In addition, we recommend reducing the generation interval to maximize genetic progress and increase effective population size.
•Portuguese Iberian and Brazilian Iberian-derived locally adapted breeds studied.•Genetic architecture of Portuguese iberian cattle were observed.•Portuguese breeds appear to have influenced ...Brazilian locally adapted population.•Indicine breeds also seem to have influenced Brazilian locally adapted population.•Brazilian locally adapted and Portuguese breeds as an enormous genetic reservoir.
The domestication of bovines has given rise to distinct phenotypes resulting in diverse breeds worldwide. Subsequent artificial selection has further enriched the complexity and diversity to cattle sub-species adapting them to their various purposes and evolving environment. Among these cattle sub-species, native Portuguese cattle breeds are considered a repository of biodiversity shaped by genetic and environmental effects accumulated over the years. In Brazil, taurine animals were introduced between the 16th and 17th centuries by the European conquerors to be used for food, leather, and animal traction. Through generations of casual crossings in diverse ecosystems, these animals became adapted to a wide range of environments and displaying varying levels of phenotypic variability and improved fitness to local conditions, hereafter recognized as Iberian-derived Locally Adapted breeds. Thus, we focused in assess 13 cattle breeds representing two geographic origins: Portuguese Iberian cattle and Brazilian Iberian-derived Locally Adapted breeds. The aim is to understand the genetic architecture of Brazilian Iberian-derived Locally Adapted breeds and their potential relationship with Portuguese Iberian cattle and Brazilian indicine breeds. In our study, we observed varying extents of linkage disequilibrium across the evaluated breeds, along with differences in effective population size. Runs of homozygosity analyses revealed different genes associated with common traits, even within a cluster group. For instance, genes related to immune response, such as MAVS (Mertolenga), DTX (Barrosã), ZBTB16 (Brava de Lide), DUSP22 (Pantaneiro), and IL7R (Caracu Dairy and Caracu Beef). Overall, our results highlight that both populations studied, with their specificities, are crucial sources of animal genetic resource of animal genetic resources for food and agriculture. While consanguineous matings are somehow controlled in both Portuguese Iberian and Brazilian Iberian-derived Locally Adapted breeds, our analysis of genetic variability suggests that ongoing precautions are necessary in the management of these populations.
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