Signatures of selection in Charolais beef cattle identified by genome-wide analysis

Evidence of differentiation and population structure in Charolais cattle of Mexico

Charolais is one of the most important beef cattle breeds in the world. In Mexico, it was introduced almost a century ago, and it has been suggested that particular breeding management and genetic material origin have caused a process of divergence among the current population. By a high-density SNP array genome-wide analysis, this study aimed to assess the proposed differentiation and population structure of local populations by genetic distances and structure approaches, and a European Charolais sample was included as a reference population. The differentiation statistics indicated that local populations exhibit moderate divergence, confirming a significant differentiation process between northeastern and northwestern Charolais populations (Fst≥ 0.043, D≥ 0.031). These results were strongly supported by PCA and structure analysis. Genetic isolation and low genetic flow between populations and divergent origins of introduced genetic material (i.e., semen) are likely the main drivers of the outcomes. Some implications are discussed.

The Association between Charolais Cows' Age at First Calving, Parity, Breeding Seasonality, and Calf Growing Performance

The objective of this study was to evaluate the impact of cows' calving ages and newborn calf body weight on the pre-weaning growth rates of calves under the farming conditions of a northeastern European country. The females were purebred Charolais cows that calved between 2019 and 2022. A total of 130 calves (bulls = 76; heifers = 54) were observed during the evaluation. The investigation showed that, based on gender, bulls had a 4.28% higher birth weight than heifers (p < 0.05). The gender of the calves affected their weight, indicating that newborns bulls were significantly heavier. Calf gender affected calf growing performance. Male calves' weight gain was higher than that of females in the time before weaning (210 days). The highest gain of bulls was observed from 211 days to 365 days after birth. The average daily weight of male calves during this period was 6.16% (p < 0.001) higher compared to the period up to 210 days after birth. Heifers had a higher daily weight in the period up to 210 days after birth, and the daily weight gain was 12.9% (p < 0.001) higher in this period compared to the period from 211 to 365 days after birth. We observed a higher weight gain in calves from mothers with a higher number of calvings. Being born from cows with four or more calvings had a significant effect on the weight gain of calves in the period up to 210 days (p < 0.05). In the period up to 210 days, the weight gain of calves born from cows with two calvings was the lowest and was 9.79% lower compared to calves born from cows with four and more calvings (p < 0.05). The best weights were obtained from calves born in the spring and autumn seasons. Calves born in spring, summer, and autumn differed in weight by 0.37 kg. The calves of cows that were inseminated in the autumn season had the highest gain in the period up to 210 days and also from 210 to 365 days (p < 0.05). In our study, significantly higher average birth weight of calves was detected in autumn compared to summer and winter (p < 0.05). Also, the highest gain was found from 211 to 365 days after birth in the summer season, but the difference was only 1.47% (p < 0.05).

Genetic and Genomic Characterization of a New Beef Cattle Composite Breed (Purunã) Developed for Production in Pasture-Based Systems

Purunã is a composite beef cattle breed, developed in Southern Brazil by crossing the Angus, Charolais, Canchim, and Caracu breeds. The goal of this study was to perform the first genetic characterization of the Purunã breed, based on both pedigree and genomic information. For this, 100 randomly selected animals were genotyped, and 11,205 animals born from 1997 to 2019 had pedigree information. The genetic analyses performed were principal component analysis, admixture, phylogenic tree, pedigree and genomic inbreeding, linkage disequilibrium (LD), effective population size (Ne), consistency of the gametic phase, runs of homozygosity (ROH), heterozygosity-enriched regions (HERs), and functional analyses of the ROH and HER regions identified. Our findings indicate that Purunã is more genetically related to the Charolais, Canchim, and Angus breeds than Caracu or Nellore. The levels of inbreeding were shown to be small based on all the metrics evaluated and ranged from −0.009 to 0.029. A low (−0.12–0.31) correlation of the pedigree-based inbreeding compared to all the genomic inbreeding coefficients evaluated was observed. The LD average was 0.031 (±0.0517), and the consistency of the gametic phase was shown to be low for all the breed pairs, ranging from 0.42 to 0.27 to the distance of 20 Mb. The Ne values based on pedigree and genomic information were 158 and 115, respectively. A total of 1,839 ROHs were found, and the majority of them are of small length (&lt;4 Mb). An important homozygous region was identified on BTA5 with pathways related to behavioral traits (sensory perception, detection of stimulus, and others), as well as candidate genes related to heat tolerance (MY O 1A), feed conversion rate (RDH5), and reproduction (AMDHD1). A total of 1,799 HERs were identified in the Purunã breed with 92.3% of them classified within the 0.5–1 Mb length group, and 19 HER islands were identified in the autosomal genome. These HER islands harbor genes involved in growth pathways, carcass weight (SDCBP), meat and carcass quality (MT2A), and marbling deposition (CISH). Despite the genetic relationship between Purunã and the founder breeds, a multi-breed genomic evaluation is likely not feasible due to their population structure and low consistency of the gametic phase among them.

Genome-wide association study for meat tenderness in beef cattle identifies patterns of the genetic contribution in different post-mortem stages

The beef tenderization process during the post-mortem period is one of the most important sensorial attributes and it is well-established. The aim of this study was to identify the genetic contribution pattern to meat tenderness at 7-(LMD7), 14-(LMD14), and 21-(LMD21) days post-mortem. The heritabilities for LMD7 (0.194), LMD14 (0.142) and LMD21 (0.048) are well established in the population evaluated here. However, its genetic contribution in terms of genomic candidate regions is still poorly understood. Tenderness was measured in the Longissiums thoracis using Warner-Bratzler shear force in the three post-mortem periods. A total of 4323 crossbred beef cattle were phenotyped and genotyped using the Illumina BovineSNP50K. The percentage of the total genetic variance was estimated using the weighted single-step genomic best linear unbiased prediction method. The main candidate windows for LMD7 were associated with proteolysis of myofibrillar structures and the weakening endomysium and perimysium. Candidate windows for LMD14 and LMD21 were mapped in bovine QTLs for body composition, height and growth. Results presented herein highlight, the largest contribution of proteolysis related processes before 14-days post-mortem and body composition characteristics in later stages for meat tenderness.

Signatures of selection reveal candidate genes involved in production traits in Chinese crossbred buffaloes

Identification of selection signature is important for a better understanding of genetic mechanisms that affect phenotypic differentiation in livestock. However, the genome-wide selection responses have not been investigated for the production traits of Chinese crossbred buffaloes. In this study, an SNP data set of 133 buffaloes (Chinese crossbred buffalo, n = 45; Chinese local swamp buffalo, n = 88) was collected from the Dryad Digital Repository database (https://datadryad.org/stash/). Population genetics analysis showed that these buffaloes were divided into the following 2 groups: crossbred buffalo and swamp buffalo. The crossbred group had higher genetic diversity than the swamp group. Using 3 complementary statistical methods (integrated haplotype score, cross population extended haplotype homozygosity, and composite likelihood ratio), a total of 31 candidate selection regions were identified in the Chinese crossbred population. Here, within these candidate regions, 25 genes were under the putative selection. Among them, several candidate genes were reported to be associated with production traits. In addition, we identified 13 selection regions that overlapped with bovine QTLs that were mainly involved in milk production and composition traits. These results can provide useful insights regarding the selection response for production traits of Chinese crossbred buffalo, as identified candidate genes influence production performance.

A genome-wide scan to identify signatures of selection in two Iranian indigenous chicken ecotypes

Background

Various regions of the chicken genome have been under natural and artificial selection for thousands of years. The substantial diversity that exits among chickens from different geographic regions provides an excellent opportunity to investigate the genomic regions under selection which, in turn, will increase our knowledge about the mechanisms that underlie chicken diversity and adaptation. Several statistics have been developed to detect genomic regions that are under selection. In this study, we applied approaches based on differences in allele or haplotype frequencies (F_ST and hapFLK, respectively) between populations, differences in long stretches of consecutive homozygous sequences (ROH), and differences in allele frequencies within populations (composite likelihood ratio (CLR)) to identify inter- and intra-populations traces of selection in two Iranian indigenous chicken ecotypes, the Lari fighting chicken and the Khazak or creeper (short-leg) chicken.

Results

Using whole-genome resequencing data of 32 individuals from the two chicken ecotypes, approximately 11.9 million single nucleotide polymorphisms (SNPs) were detected and used in genomic analyses after quality processing. Examination of the distribution of ROH in the two populations indicated short to long ROH, ranging from 0.3 to 5.4 Mb. We found 90 genes that were detected by at least two of the four applied methods. Gene annotation of the detected putative regions under selection revealed candidate genes associated with growth (DCN, MEOX2 and CACNB1), reproduction (ESR1 and CALCR), disease resistance (S1PR1, ALPK1 and MHC-B), behavior pattern (AGMO, GNAO1 and PSEN1), and morphological traits (IHH and NHEJ1).

Conclusions

Our findings show that these two phenotypically different indigenous chicken populations have been under selection for reproduction, immune, behavioral, and morphology traits. The results illustrate that selection can play an important role in shaping signatures of differentiation across the genomic landscape of two chicken populations.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12711-021-00664-9.