Dataset Information

Probe-based association analysis identifies several deletions associated with average daily gain in beef cattle.

ABSTRACT: BACKGROUND:Average daily gain (ADG) is an important trait that contributes to the production efficiency and economic benefits in the beef cattle industry. The molecular mechanisms of ADG have not yet been fully explored because most recent association studies for ADG are based on SNPs or haplotypes. We reported a systematic CNV discovery and association analysis for ADG in Chinese Simmental beef cattle. RESULTS:Our study identified 4912 nonredundant CNVRs with a total length of ~?248.7?Mb, corresponding to ~?8.9% of the cattle genome. Using probe-based CNV association, we identified 24 and 12 significant SNP probes within five deletions and two duplications for ADG, respectively. Among them, we found one common deletion with 89?kb imbedded in LHFPL Tetraspan Subfamily Member 6 (LHFPL6) at 22.9?Mb on BTA12, which has high frequency (12.9%) dispersing across population. CNV selection test using VST statistic suggested this common deletion may be under positive selection in Chinese Simmental cattle. Moreover, this deletion was not overlapped with any candidate SNP for ADG compared with previous SNPs-based association studies, suggesting its important role for ADG. In addition, we identified one rare deletion near gene Growth Factor Receptor-bound Protein 10 (GRB10) at 5.1?Mb on BTA4 for ADG using both probe-based association and region-based approaches. CONCLUSIONS:Our results provided some valuable insights to elucidate the genetic basis of ADG in beef cattle, and these findings offer an alternative perspective to understand the genetic mechanism of complex traits in terms of copy number variations in farm animals.

SUBMITTER: Xu L

PROVIDER: S-EPMC6327516 | biostudies-literature | 2019 Jan

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Probe-based association analysis identifies several deletions associated with average daily gain in beef cattle.

Xu Lingyang L Yang Liu L Wang Lei L Zhu Bo B Chen Yan Y Gao Huijiang H Gao Xue X Zhang Lupei L Liu George E GE Li Junya J

BMC genomics 20190110 1

<h4>Background</h4>Average daily gain (ADG) is an important trait that contributes to the production efficiency and economic benefits in the beef cattle industry. The molecular mechanisms of ADG have not yet been fully explored because most recent association studies for ADG are based on SNPs or haplotypes. We reported a systematic CNV discovery and association analysis for ADG in Chinese Simmental beef cattle.<h4>Results</h4>Our study identified 4912 nonredundant CNVRs with a total length of ~ ...[more]

PMID: 30630414

Similar Datasets

Project description:BackgroundBackgrounding (BKG), the stage between weaning and finishing, significantly impacts feedlot performance in beef cattle; however, the contributions of the rumen microbiome to this growth stage remain unexplored. A longitudinal study was designed to assess how BKG affects rumen bacterial communities and average daily gain (ADG) in beef cattle. At weaning, 38 calves were randomly assigned to three BKG systems for 55 days (d): a high roughage diet within a dry lot (DL, n = 13); annual cover crop within a strip plot (CC, n = 13); and perennial pasture vegetation within rotational paddocks (PP, n = 12), as before weaning. After BKG, all calves were placed in a feedlot for 142 d and finished with a high energy ration. Calves were weighed periodically from weaning to finishing to determine ADG. Rumen bacterial communities were profiled by collecting fluid samples via oral probe and sequencing the V4 region of the 16S rRNA bacterial gene, at weaning, during BKG and finishing.ResultsRumen bacterial communities diverged drastically among calves once they were placed in each BKG system, including sharp decreases in alpha diversity for CC and DL calves only (P < 0.001). During BKG, DL calves showed a substantial increase of Proteobacteria (Succinivibrionaceae family) (P < 0.001), which also corresponded with greater ADG (P < 0.05). At the finishing stage, Proteobacteria bloomed for all calves, with no previous alpha or beta diversity differences being retained between groups. However, at finishing, PP calves showed a compensatory ADG, particularly greater than that in calves coming from DL BKG (P = 0.02). Microbiome network traits such as lower average shortest path length, and increased neighbor connectivity, degree, number and strength of bacterial interactions between rumen bacteria better predicted ADG during BKG and finishing than variation in specific taxonomic profiles.ConclusionsBacterial co-abundance interactions, as measured by network theory approaches, better predicted growth performance in beef cattle during BKG and finishing, than the abundance of specific taxa. These findings underscore the importance of early post weaning stages as potential targets for feeding interventions that can enhance metabolic interactions between rumen bacteria, to increase productive performance in beef cattle.

Project description:We evaluated the plasma amine/phenol- and carbonyl-metabolome and whole-blood immune gene expression profiles in beef steers with divergent average daily gain (ADG). Forty-eight Angus crossbred beef steers (21 days postweaning; 210 ± 8.5 kg of body weight) were fed the same total mixed ration ad libitum for 42 days with free access to water. After 42 days of feeding, the steers were divided into two groups of lowest (LF: n = 8) and highest ADG (HF: n = 8). Blood samples were taken from all steers. The blood samples from LF and HF steers were used for further analysis. A subsample of the whole blood was immediately transferred into RNA-protect tubes for RNA extraction and messenger RNA expressions of 84 genes involved in innate and adaptive immune responses. Another subsample of the whole blood was immediately centrifuged to harvest the plasma for subsequent metabolome analysis. The average daily dry matter intake of the steers in LF and HF was 6.08 kg ± 0.57 and 6.04 kg ± 0.42, respectively, and was similar between the two groups (P = 0.72). The ADG (1.09 kg ± 0.13) of LF was lower (P = 0.01) than that of HF (1.63 kg ± 0.20). The expressions of 10 immune-related genes were upregulated (FC ≥ 1.2; P ≤ 0.05) in HF steers; these genes were involved in viral pathogen recognition and eradication, defense against intracellular and extracellular pathogens and parasites, and immune response homeostasis. A total number of 42 carbonyl-containing metabolites and 229 amine/phenol-containing metabolites were identified in the plasma samples of both groups. No alteration in carbonyl-metabolome was detected. Ten metabolites with immunomodulatory, anti-inflammatory, and reactive oxygen-scavenging properties were greater (FDR ≤ 0.05) in HF steers, whereas eight metabolites including arginine, phenylalanine, guanidoacetic acid, and aspartyl-threonine were greater in LF steers. This study demonstrated that beef steers with divergent ADG had altered plasma amine/phenol metabolome and immune-related gene expressions in the blood. Notably, plasma metabolites and immune-related genes of great health benefits were greater in steers with high ADG.

Dataset Information

Probe-based association analysis identifies several deletions associated with average daily gain in beef cattle.

Publications

Probe-based association analysis identifies several deletions associated with average daily gain in beef cattle.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets