Dataset Information

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

ABSTRACT:

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.

SUBMITTER: Zhou S

PROVIDER: S-EPMC7788875 | biostudies-literature | 2021 Jan

REPOSITORIES: biostudies-literature

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Publications

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

Zhou Shenping S Ding Rongrong R Meng Fanming F Wang Xingwang X Zhuang Zhanwei Z Quan Jianping J Geng Qian Q Wu Jie J Zheng Enqin E Wu Zhenfang Z Yang Jianhui J Yang Jie J

BMC genomics 20210106 1

<h4>Background</h4>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.<h4>Results</h4>In the American Duroc pigs, one novel pleiotropic quantitative trait locus (QTL) on Sus scrofa chromosome 1 (SSC1) was identified to be associa ...[more]

PMID: 33407097

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Project description:BACKGROUND:The mammalian intestinal tract harbors diverse and dynamic microbial communities that play pivotal roles in host health, metabolism, immunity, and development. Average daily gain (ADG) is an important growth trait in meat rabbit industry. The effects of gut microbiota on ADG in meat rabbits are still unknown. RESULTS:In this study, we investigated the dynamic distribution of gut microbiota in commercial Ira rabbits from weaning to finishing and uncover the relationship between the microbiota and average daily gain (ADG) via 16S rRNA gene sequencing. The results indicated that the richness and diversity of gut microbiota significantly increased with age. Gut microbial structure was less variable among finishing rabbits than among weaning rabbits. The relative abundances of the dominant phyla Firmicutes, Bacteroidetes, Verrucomicrobia and Cyanobacteria, and the 15 predominant genera significantly varied with age. Metagenomic prediction analysis showed that both KOs and KEGG pathways related to the metabolism of monosaccharides and vitamins were enriched in the weaning rabbits, while those related to the metabolism of amino acids and polysaccharides were more abundant in the finishing rabbits. We identified 34 OTUs, 125 KOs, and 25 KEGG pathways that were significantly associated with ADG. OTUs annotation suggested that butyrate producing bacteria belong to the family Ruminococcaceae and Bacteroidales_S24-7_group were positively associated with ADG. Conversely, Eubacterium_coprostanoligenes_group, Christensenellaceae_R-7_group, and opportunistic pathogens were negatively associated with ADG. Both KOs and KEGG pathways correlated with the metabolism of vitamins, basic amino acids, and short chain fatty acids (SCFAs) showed positive correlations with ADG, while those correlated with aromatic amino acids metabolism and immune response exhibited negative correlations with ADG. In addition, our results suggested that 10.42% of the variation in weaning weight could be explained by the gut microbiome. CONCLUSIONS:Our findings give a glimpse into the dynamic shifts in gut microbiota of meat rabbits and provide a theoretical basis for gut microbiota modulation to improve ADG in the meat rabbit industry.

Dataset Information

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

Background

Results

Conclusions

Publications

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

Similar Datasets

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