Genomic Heritability and Genome-Wide Association Studies of Plasma Metabolites in Crossbred Beef Cattle

Li, Jiyuan; Akanno, E. C.; Valente, Tiago da Silva; Abo-Ismail, Mohammed; Karisa, Brian K; Wang, Zhiquan; Plastow, Graham

doi:10.3389/fgene.2020.538600

Cited by 14 publications

(14 citation statements)

References 59 publications

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“…Our results showed that 31 metabolites had low to moderate heritability and two metabolites had relatively high heritability (> 0.4). In a study of beef cattle, only 11 of 33 metabolites measured (29 in common with this study) were reported to be heritable 17 . Similar heritability estimates to Li et al 17 were reported here for betaine, creatinine, pyruvic acid and citric acid.…”

Section: Metabolitementioning

confidence: 50%

“…In a study of beef cattle, only 11 of 33 metabolites measured (29 in common with this study) were reported to be heritable 17 . Similar heritability estimates to Li et al 17 were reported here for betaine, creatinine, pyruvic acid and citric acid. In our study, other metabolites, such as ketone bodies (3-hydroxybutyric acid, acetoacetate and acetone), creatine, succinate, formate, and methylhistidine, showed negligible heritability estimates, suggesting that they are primarily influenced and manipulated by environmental effects such as diet, and/or age, health status etc.…”

Section: Metabolitementioning

confidence: 50%

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Heritability and genetic correlations of plasma metabolites of pigs with production, resilience and carcass traits under natural polymicrobial disease challenge

Dervishi

Yang

Dyck

et al. 2021

Sci Rep

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Metabolites in plasma of healthy nursery pigs were quantified using nuclear magnetic resonance. Heritabilities of metabolite concentration were estimated along with their phenotypic and genetic correlations with performance, resilience, and carcass traits in growing pigs exposed to a natural polymicrobial disease challenge. Variance components were estimated by GBLUP. Heritability estimates were low to moderate (0.11 ± 0.08 to 0.19 ± 0.08) for 14 metabolites, moderate to high (0.22 ± 0.09 to 0.39 ± 0.08) for 17 metabolites, and highest for l-glutamic acid (0.41 ± 0.09) and hypoxanthine (0.42 ± 0.08). Phenotypic correlation estimates of plasma metabolites with performance and carcass traits were generally very low. Significant genetic correlation estimates with performance and carcass traits were found for several measures of growth and feed intake. Interestingly the plasma concentration of oxoglutarate was genetically negatively correlated with treatments received across the challenge nursery and finisher (− 0.49 ± 0.28; P < 0.05) and creatinine was positively correlated with mortality in the challenge nursery (0.85 ± 0.76; P < 0.05). These results suggest that some plasma metabolite phenotypes collected from healthy nursery pigs are moderately heritable and genetic correlations with measures of performance and resilience after disease challenge suggest they may be potential genetic indicators of disease resilience.

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Section: Metabolitementioning

confidence: 50%

Section: Metabolitementioning

confidence: 50%

Heritability and genetic correlations of plasma metabolites of pigs with production, resilience and carcass traits under natural polymicrobial disease challenge

Dervishi

Yang

Dyck

et al. 2021

Sci Rep

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“…The population of animals was obtained from the Phenomic Gap Project that aimed to generate phenotypes of feed efficiency, carcass and meat quality as well as genomic data for Canadian crossbred beef animals [ 38 ]. Details of animal management, the herd, and animal breeds were previously described [ 12 , 39 – 41 ]. In summary, the population used in this study consisted of 493 crossbred bulls ( n = 93), heifers ( n = 125) and steers ( n = 275) that were born between 2002 and 2011.…”

Section: Methodsmentioning

confidence: 99%

“…These blood samples were used to quantify metabolites using nuclear magnetic resonance (NMR) spectroscopy. The procedure of metabolite quantification using NMR was previously described by Li et al [ 39 ]. Thirty-one metabolites and their concentration levels (µM) were quantified from plasma.…”

Section: Methodsmentioning

confidence: 99%

Identification of candidate genes and enriched biological functions for feed efficiency traits by integrating plasma metabolites and imputed whole genome sequence variants in beef cattle

Mukiibi

Plastow

et al. 2021

BMC Genomics

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Background Feed efficiency is one of the key determinants of beef industry profitability and sustainability. However, the cellular and molecular background behind feed efficiency is largely unknown. This study combines imputed whole genome DNA variants and 31 plasma metabolites to dissect genes and biological functions/processes that are associated with residual feed intake (RFI) and its component traits including daily dry matter intake (DMI), average daily gain (ADG), and metabolic body weight (MWT) in beef cattle. Results Regression analyses between feed efficiency traits and plasma metabolites in a population of 493 crossbred beef cattle identified 5 (L-valine, lysine, L-tyrosine, L-isoleucine, and L-leucine), 4 (lysine, L-lactic acid, L-tyrosine, and choline), 1 (citric acid), and 4 (L-glutamine, glycine, citric acid, and dimethyl sulfone) plasma metabolites associated with RFI, DMI, ADG, and MWT (P-value < 0.1), respectively. Combining the results of metabolome-genome wide association studies using 10,488,742 imputed SNPs, 40, 66, 15, and 40 unique candidate genes were identified as associated with RFI, DMI, ADG, and MWT (P-value < 1 × 10−5), respectively. These candidate genes were found to be involved in some key metabolic processes including metabolism of lipids, molecular transportation, cellular function and maintenance, cell morphology and biochemistry of small molecules. Conclusions This study identified metabolites, candidate genes and enriched biological functions/processes associated with RFI and its component traits through the integrative analyses of metabolites with phenotypic traits and DNA variants. Our findings could enhance the understanding of biochemical mechanisms of feed efficiency traits and could lead to improvement of genomic prediction accuracy via incorporating metabolite data.

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“…Metabolomics is the joint to connect genotypes with phenotypes [6], so their relationships are currently interpreted by the metabolome genome-wide association study (mG-WAS) using metabolites as the metabolic phenotypes. The integrated genomic−metabolomic analysis is considered as a critical supplement to biology and physiology, as the metabolites provide the details of physiological state that can drive genetic variant-associated metabolites to display larger effect sizes, and then the quantitative trait loci (QTLs) affecting metabolite concentrations can be identified [53, [59][60][61][62][63].…”

Section: Genomics-metabolomic Analysismentioning

confidence: 99%

Overview of Metabolomic Analysis and the Integration with Multi-Omics for Economic Traits in Cattle

Hao

Bai

et al. 2021

Metabolites

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Metabolomics has been applied to measure the dynamic metabolic responses, to understand the systematic biological networks, to reveal the potential genetic architecture, etc., for human diseases and livestock traits. For example, the current published results include the detected relevant candidate metabolites, identified metabolic pathways, potential systematic networks, etc., for different cattle traits that can be applied for further metabolomic and integrated omics studies. Therefore, summarizing the applications of metabolomics for economic traits is required in cattle. We here provide a comprehensive review about metabolomic analysis and its integration with other omics in five aspects: (1) characterization of the metabolomic profile of cattle; (2) metabolomic applications in cattle; (3) integrated metabolomic analysis with other omics; (4) methods and tools in metabolomic analysis; and (5) further potentialities. The review aims to investigate the existing metabolomic studies by highlighting the results in cattle, integrated with other omics studies, to understand the metabolic mechanisms underlying the economic traits and to provide useful information for further research and practical breeding programs in cattle.

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Genomic Heritability and Genome-Wide Association Studies of Plasma Metabolites in Crossbred Beef Cattle

Cited by 14 publications

References 59 publications

Heritability and genetic correlations of plasma metabolites of pigs with production, resilience and carcass traits under natural polymicrobial disease challenge

Heritability and genetic correlations of plasma metabolites of pigs with production, resilience and carcass traits under natural polymicrobial disease challenge

Identification of candidate genes and enriched biological functions for feed efficiency traits by integrating plasma metabolites and imputed whole genome sequence variants in beef cattle

Overview of Metabolomic Analysis and the Integration with Multi-Omics for Economic Traits in Cattle

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