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

Jahuey‐Martínez, Francisco Joel; Parra‐Bracamonte, Gaspar Manuel; Sifuentes‐Rincón, Ana María; Moreno-Medina, Víctor Ricardo

doi:10.1111/jbg.12399

Cited by 10 publications

(6 citation statements)

References 38 publications

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“…Obtained results confirmed the tested assumption that the different production type of analysed breeds could cause an increase in the frequency of specific alleles (haplotypes) responsible for desired phenotypic traits. The strong impact of selection on the genomic region related to carcass traits in beef cattle was also reported by Moravčíková et al [88], Jahuey-Martínez et al [89] or Paim et al [90]. In dairy cattle, the most significant selection signatures were found mainly on chromosome 6 that is strongly connected to milk production and composition [91,92].…”

Section: Discussionsupporting

confidence: 61%

Food Resources Biodiversity: The Case of Local Cattle in Slovakia

et al. 2021

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This study aimed to assess the level of biodiversity in selected local cattle populations as important food resources in Slovakia. The biodiversity level was derived from the genome-wide data collected for dairy (Jersey), dual-purpose (Slovak Pinzgau, Slovak Spotted), and beef breeds (Charolais, Limousine). The commonly used indices, genomic inbreeding (FROH, FGRM, FHOM, FUNI) and effective population size (NeLD), were used to quantify the impact of relatives mating on the genome of analysed populations. Even if the low NeLD estimates signalise significant loss of genetic variability within populations, the genomic inbreeding under 1% (except Jersey) showed that the intensity of diversity loss is not so rapid and can be managed by the re-arrangement of long-term breeding strategies. The analysis of genetic differentiation degree across populations assumed that the specialisation of breeds during their grading-up led to the specific nucleotide changes, especially in genes responsible for preferred phenotypic traits. The breed-specific differences observed mainly in the genome of Charolais (carcass traits) and Jersey (milk production traits) populations resulted from the polymorphisms in CAPN1 (μ-calpain) and CSN1S2 (casein alpha s2) genes, respectively. Obtained results confirmed that the specific haplotypes are strongly associated with the genetic nature of breed depending on production type.

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Section: Discussionsupporting

confidence: 61%

Food Resources Biodiversity: The Case of Local Cattle in Slovakia

et al. 2021

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“…To decipher the genetic mechanisms that are involved in domestication and in the phenotypic differentiation of individuals belonging to the same species, detection of signatures of selection using different statistics has been performed in various species, including cattle [18,19], sheep [20,21], goats [22,23], and chickens [24][25][26]. Most of the studies that explored selective footprints in chickens have used the single-site differentiation statistic commonly known as the fixation index, F ST , and have led to the identification of a range of candidates genes that contribute to adaptation to hot climates, reproduction [27], immune response, tolerance to harsh local environments [25], fat deposition, growth, skeletal development, and energy metabolism [28].…”

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confidence: 99%

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

et al. 2021

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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 (FST 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.

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“…The rearing of Charolais beef cattle is increasing across all continents [ 18 ]. The main reasons for selecting Charolais cattle are high production rates with high weight gain rates [ 1 ] and live body weight traits [ 18 ].…”

Section: Introductionmentioning

confidence: 99%

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

Šlyžienė,

Mečionytė,

Žilaitis

et al. 2023

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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).

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

Cited by 10 publications

References 38 publications

Food Resources Biodiversity: The Case of Local Cattle in Slovakia

Food Resources Biodiversity: The Case of Local Cattle in Slovakia

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

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

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