Meta-analysis of genome-wide association studies for loin muscle area and loin muscle depth in two Duroc pig populations

Zhuang, Zhanwei; Li, Shaoyun; Ding, Rongrong; Yang, Ming; Zheng, Enqin; Yang, Huaqiang; Gu, Tao; Xu, Zheng; Cai, Guangyan; Wu, Zhenfang; Yang, Jie

doi:10.1371/journal.pone.0218263

Cited by 33 publications

(50 citation statements)

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“…An increase in the loin eye area was reported with decreased RFI, backfat and intramuscular fat content in Duroc pigs 53 . NUDT3 was related to thiamin in Landrace TP1 and PLD2 related to choline in Duroc TP1 in our study was also found to be a candidate gene for loin muscle area and loin muscle depth in pigs 54,55 . The metabolites and the genes identified are consistent with FE related traits.…”

Section: Discussionsupporting

confidence: 70%

Metabolomic networks and pathways associated with feed efficiency and related-traits in Duroc and Landrace pigs

Carmelo

Banerjee

Diniz

et al. 2020

Sci Rep

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Improving feed efficiency (FE) is a major goal of pig breeding, reducing production costs and providing sustainability to the pig industry. Reliable predictors for fe could assist pig producers. We carried out untargeted blood metabolite profiling in uncastrated males from Danbred Duroc (n = 59) and Danbred Landrace (n = 50) pigs at the beginning and end of a FE testing phase to identify biomarkers and biological processes underlying fe and related traits. By applying linear modeling and clustering analyses coupled with WGCNA framework, we identified 102 and 73 relevant metabolites in Duroc and Landrace based on two sampling time points. Among them, choline and pyridoxamine were hub metabolites in Duroc in early testing phase, while, acetoacetate, cholesterol sulfate, xanthine, and deoxyuridine were identified in the end of testing. In Landrace, cholesterol sulfate, thiamine, L-methionine, chenodeoxycholate were identified at early testing phase, while, D-glutamate, pyridoxamine, deoxycytidine, and L-2-aminoadipate were found at the end of testing. Validation of these results in larger populations could establish fe prediction using metabolomics biomarkers. We conclude that it is possible to identify a link between blood metabolite profiles and FE. These results could lead to improved nutrient utilization, reduced production costs, and increased fe.With the expanding human population and requirement for nutrient-rich food, there is an increasing demand for improvement of meat production, but simultaneously, to decrease the input costs in terms of feed 1 . Thus, feed efficiency (FE) is the most important trait in commercial pig farming 2 as increasing the amount of meat produced per feed is beneficial both economically and environmentally. Thereby, improving FE is beneficial for producers and increases the sustainability of pork meat production. Fortunately, FE is a highly heritable trait in Danish pigs (ranging from 0.34 in Duroc to 0.40 in Landrace), thus suitable for the genetic selection of pigs with high breeding values in breeding programs aimed at improving this economically important phenotype 3 .Since FE cannot be measured directly, feed conversion ratio (FCR) and residual feed intake (RFI) have been used to evaluate the animal efficiency 4 . FCR determines the ratio of feed intake (FI) to output and found to correlate with growth rate and body weight 3,5 . RFI calculates the difference between the actual and expected FI 6 predicted based on production traits such as average daily gain (ADG) 7 . ADG is also considered important in commercial pig production as pigs with higher ADG can achieve a target market weight within a shorter period than those with lower ADG, thereby saving feeding costs 8 . Thus, selection for RFI has proved to be effective in improving the FE in pigs 3,9,10 . Selection for FCR will results in co-selection for other traits, such as body composition and ADG. In contrast, RFI selects for increased metabolic efficiency without the same side effects [11][12][13] . RFI and FCR are well c...

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Section: Discussionsupporting

confidence: 70%

Metabolomic networks and pathways associated with feed efficiency and related-traits in Duroc and Landrace pigs

Carmelo

Banerjee

Diniz

et al. 2020

Sci Rep

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“…Given that the experimental animals consisted of the two Duroc pig populations in this study, principal component analysis (PCA) was conducted to identify the potential population stratification. The PCA plot was shown in our previous paper [ 12 ]. Moreover, we added the 660 Large White pig population to compare further the differences in population structure of these two Duroc populations, and PCA was performed for the Large White and the two Duroc pig populations.…”

Section: Resultsmentioning

confidence: 99%

A meta-analysis of genome-wide association studies for average daily gain and lean meat percentage in two Duroc pig populations

et al. 2021

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Background Average daily gain (ADG) and lean meat percentage (LMP) are the main production performance indicators of pigs. Nevertheless, the genetic architecture of ADG and LMP is still elusive. Here, we conducted genome-wide association studies (GWAS) and meta-analysis for ADG and LMP in 3770 American and 2090 Canadian Duroc pigs. Results In the American Duroc pigs, one novel pleiotropic quantitative trait locus (QTL) on Sus scrofa chromosome 1 (SSC1) was identified to be associated with ADG and LMP, which spans 2.53 Mb (from 159.66 to 162.19 Mb). In the Canadian Duroc pigs, two novel QTLs on SSC1 were detected for LMP, which were situated in 3.86 Mb (from 157.99 to 161.85 Mb) and 555 kb (from 37.63 to 38.19 Mb) regions. The meta-analysis identified ten and 20 additional SNPs for ADG and LMP, respectively. Finally, four genes (PHLPP1, STC1, DYRK1B, and PIK3C2A) were detected to be associated with ADG and/or LMP. Further bioinformatics analysis showed that the candidate genes for ADG are mainly involved in bone growth and development, whereas the candidate genes for LMP mainly participated in adipose tissue and muscle tissue growth and development. Conclusions We performed GWAS and meta-analysis for ADG and LMP based on a large sample size consisting of two Duroc pig populations. One pleiotropic QTL that shared a 2.19 Mb haplotype block from 159.66 to 161.85 Mb on SSC1 was found to affect ADG and LMP in the two Duroc pig populations. Furthermore, the combination of single-population and meta-analysis of GWAS improved the efficiency of detecting additional SNPs for the analyzed traits. Our results provide new insights into the genetic architecture of ADG and LMP traits in pigs. Moreover, some significant SNPs associated with ADG and/or LMP in this study may be useful for marker-assisted selection in pig breeding.

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“…The mice without this gene resulted in a lower growth rate and metabolism and a shorter lifespan [ 49 ]. Protein–Kinase C and Casein Kinase–Substrate In Neurons 1 ( PACSIN1 ), a fourth gene located in the region of 29.34–30.94 Mb, was identified concerning the bodyweight [ 50 ] and loin muscle area [ 51 ] in pigs.…”

Section: Resultsmentioning

confidence: 99%

Weighted Single-Step GWAS Identified Candidate Genes Associated with Growth Traits in a Duroc Pig Population

Ruan

Zhuang

Ding

et al. 2021

Genes

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Growth traits are important economic traits of pigs that are controlled by several major genes and multiple minor genes. To better understand the genetic architecture of growth traits, we performed a weighted single-step genome-wide association study (wssGWAS) to identify genomic regions and candidate genes that are associated with days to 100 kg (AGE), average daily gain (ADG), backfat thickness (BF) and lean meat percentage (LMP) in a Duroc pig population. In this study, 3945 individuals with phenotypic and genealogical information, of which 2084 pigs were genotyped with a 50 K single-nucleotide polymorphism (SNP) array, were used for association analyses. We found that the most significant regions explained 2.56–3.07% of genetic variance for four traits, and the detected significant regions (>1%) explained 17.07%, 18.59%, 23.87% and 21.94% for four traits. Finally, 21 genes that have been reported to be associated with metabolism, bone growth, and fat deposition were treated as candidate genes for growth traits in pigs. Moreover, gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses implied that the identified genes took part in bone formation, the immune system, and digestion. In conclusion, such full use of phenotypic, genotypic, and genealogical information will accelerate the genetic improvement of growth traits in pigs.

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Meta-analysis of genome-wide association studies for loin muscle area and loin muscle depth in two Duroc pig populations

Cited by 33 publications

References 69 publications

Metabolomic networks and pathways associated with feed efficiency and related-traits in Duroc and Landrace pigs

Metabolomic networks and pathways associated with feed efficiency and related-traits in Duroc and Landrace pigs

A meta-analysis of genome-wide association studies for average daily gain and lean meat percentage in two Duroc pig populations

Weighted Single-Step GWAS Identified Candidate Genes Associated with Growth Traits in a Duroc Pig Population

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