Dataset Information

Whole genome variants across 57 pig breeds enable comprehensive identification of genetic signatures that underlie breed features.

ABSTRACT:

Background

A large number of pig breeds are distributed around the world, their features and characteristics vary among breeds, and they are valuable resources. Understanding the underlying genetic mechanisms that explain across-breed variation can help breeders develop improved pig breeds.

Results

In this study, we performed GWAS using a standard mixed linear model with three types of genome variants (SNP, InDel, and CNV) that were identified from public, whole-genome, sequencing data sets. We used 469 pigs of 57 breeds, and we identified and analyzed approximately 19 million SNPs, 1.8 million InDels, and 18,016 CNVs. We defined six biological phenotypes by the characteristics of breed features to identify the associated genome variants and candidate genes, which included coat color, ear shape, gradient zone, body weight, body length, and body height. A total of 37 candidate genes was identified, which included 27 that were reported previously (e.g., PLAG1 for body weight), but the other 10 were newly detected candidate genes (e.g., ADAMTS9 for coat color).

Conclusion

Our study indicated that using GWAS across a modest number of breeds with high density genome variants provided efficient mapping of complex traits.

SUBMITTER: Xu J

PROVIDER: S-EPMC7713148 | biostudies-literature | 2020 Dec

REPOSITORIES: biostudies-literature

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Publications

Whole genome variants across 57 pig breeds enable comprehensive identification of genetic signatures that underlie breed features.

Xu Jingya J Fu Yuhua Y Hu Yan Y Yin Lilin L Tang Zhenshuang Z Yin Dong D Zhu Mengjin M Yu Mei M Li Xinyun X Zhou Yang Y Zhao Shuhong S Liu Xiaolei X

Journal of animal science and biotechnology 20201203 1

<h4>Background</h4>A large number of pig breeds are distributed around the world, their features and characteristics vary among breeds, and they are valuable resources. Understanding the underlying genetic mechanisms that explain across-breed variation can help breeders develop improved pig breeds.<h4>Results</h4>In this study, we performed GWAS using a standard mixed linear model with three types of genome variants (SNP, InDel, and CNV) that were identified from public, whole-genome, sequencing ...[more]

PMID: 33292532

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Project description:Abstract The detection of selection signatures can help to understand the mechanisms of artificial selection. The purpose of this work is to determine the selection signatures in Civil pig relatively Large White breed. The research was carried out on Large White of three breeding centers (LW_1_New=16, LW_2_New=12, LW_3_New=15) and Civilskay, bred in Russia on the basis of local pigs and Large White boars, (Civil=17). GeneSeek GGP Porcine HD BeadChip (San Diego, USA) was used. A heatmap plot of genomic relationship matrix (GRM) was used to evaluate genetic variability between populations. The signals of diversifying selection were detected using Fst and Smoothing Fst (R package Lokern). QTLs and genes were identified and annotated in the Ensembl genome browser (Sscrofa 11.1) (https://www.ensembl.org/index.html), Panther 15.0 (http://www.pantherdb.org/) and QTLdb (https://www.animalgenome.org/cgi-bin/QTLdb/index).Data visualization from heatmapplot (Fig.) showed that all individuals are grouped in relation to their groups. However, the groups LW_1_New, LW_3_New and CIVIL were separated from LW_2_New. We have selected LW_1_New, LW_3_New and CIVIL to identify the selection signatures. After smoothing of the data by moving average, top 0.1% of the observations were considered as pinpointing CIVIL-specific selection signals. As a result, genome regions with strong selection signals on SSC1:214634036-217738857, SSSC2:137533941-138048506, SSC4:24655041-30832595, SSC7:27386432-28655399 and SSC8:55806826-56299366 were found. In these areas, 535 QTLs have been identified, including 347 QTLs for Meat and Carcass Traits (the majority related to Backfat), 67 QTLs Production (Average daily gain or Body weight), 62 QTLs Health (Mean corpuscular volume, Actinobacillus pleuropneumoniae susceptibility et al.), 32 QTLs Reproduction (Teat number) and 27 QTLs Exterior (Leg conformation). In general, 32 genes are defined in these regions (SSC1-11; SSC2-5; SSC4-10; SSC7-3; SSC8-3) (Table). They are mainly involved in the following biological processes: metabolic (GO:0008152), cellular (GO:0009987) and biological regulation (GO:0065007). This research was supported by the Russian Scientific Foundation (RSF) within Project No. 19-16-00109.

Dataset Information

Whole genome variants across 57 pig breeds enable comprehensive identification of genetic signatures that underlie breed features.

Background

Results

Conclusion

Publications

Whole genome variants across 57 pig breeds enable comprehensive identification of genetic signatures that underlie breed features.

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