Dataset Information

Polymorphism of VRTN Gene g.20311_20312ins291 Was Associated with the Number of Ribs, Carcass Diagonal Length and Cannon Bone Circumference in Suhuai Pigs.

ABSTRACT: The vertnin (VRTN) gene g.20311_20312ins291 was reported as an important variant related to the number of ribs (RIB), and the ins/ins genotype was advantageous for improving RIB of Western pigs. The purpose of this study was to determine whether the VRTN gene g.20311_20312ins291 influences RIB, carcass traits, and body size traits, including cannon bone circumference (CBC) in Chinese Suhuai pigs. We found that the VRTN gene g.20311_20312ins291 was polymorphic in Suhuai fattening pigs and gilts. The polymorphism of g.20311_20312ins291 was significantly associated with RIB and CDL in Suhuai fattening pigs (p < 0.01), whereas this variant had no influence on carcass weight (CWT). There was a tendency of association between this variant and carcass straight length (CSL) in Suhuai fattening pigs (p = 0.06). The polymorphism of g.20311_20312ins291 was also significantly associated with CBC in Suhuai gilts (p = 0.04). Furthermore, CBC was positively genetically correlated with body length (0.22, p < 0.01) and body weight (0.15, p < 0.01). Our results indicated that the VRTN gene g.20311_20312ins291 could be used as a potential marker for improving RIB, CDL, and CBC in Suhuai pigs.

SUBMITTER: Jiang N

PROVIDER: S-EPMC7142862 | biostudies-literature | 2020 Mar

REPOSITORIES: biostudies-literature

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Polymorphism of VRTN Gene g.20311_20312ins291 Was Associated with the Number of Ribs, Carcass Diagonal Length and Cannon Bone Circumference in Suhuai Pigs.

Jiang Nengjing N Liu Chenxi C Lan Tingxu T Zhang Qian Q Cao Yang Y Pu Guang G Niu Peipei P Zhang Zongping Z Li Qiang Q Zhou Juan J Li Xiaokui X Hou Liming L Huang Ruihua R Li Pinghua P

Animals : an open access journal from MDPI 20200313 3

The vertnin (VRTN) gene g.20311_20312ins291 was reported as an important variant related to the number of ribs (RIB), and the ins/ins genotype was advantageous for improving RIB of Western pigs. The purpose of this study was to determine whether the VRTN gene g.20311_20312ins291 influences RIB, carcass traits, and body size traits, including cannon bone circumference (CBC) in Chinese Suhuai pigs. We found that the VRTN gene g.20311_20312ins291 was polymorphic in Suhuai fatte ...[more]

PMID: 32183166

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Project description:BackgroundCarcass length is very important for body size and meat production for swine, thus understanding the genetic mechanisms that underly this trait is of great significance in genetic improvement programs for pigs. Although many quantitative trait loci (QTL) have been detected in pigs, very few have been fine-mapped to the level of the causal mutations. The aim of this study was to identify potential causal single nucleotide polymorphisms (SNPs) for carcass length by integrating a genome-wide association study (GWAS) and functional assays.ResultsHere, we present a GWAS in a commercial Duroc × (Landrace × Yorkshire) (DLY) population that reveals a prominent association signal (P = 4.49E-07) on pig chromosome 17 for carcass length, which was further validated in two other DLY populations. Within the detected 1 Mb region, the BMP2 gene stood out as the most likely causal candidate because of its functions in bone growth and development. Whole-genome gene expression studies showed that the BMP2 gene was differentially expressed in the cartilage tissues of pigs with extreme carcass length. Then, we genotyped an additional 267 SNPs in 500 selected DLY pigs, followed by further whole-genome SNP imputation, combined with deep genome resequencing data on multiple pig breeds. Reassociation analyses using genotyped and imputed SNP data revealed that the rs320706814 SNP, located approximately 123 kb upstream of the BMP2 gene, was the strongest candidate causal mutation, with a large association with carcass length, with a ~ 4.2 cm difference in length across all three DLY populations (N = 1501; P = 3.66E-29). This SNP segregated in all parental lines of the DLY (Duroc, Large White and Landrace) and was also associated with a significant effect on body length in 299 pure Yorkshire pigs (P = 9.2E-4), which indicates that it has a major value for commercial breeding. Functional assays showed that this SNP is likely located within an enhancer and may affect the binding affinity of transcription factors, thereby regulating BMP2 gene expression.ConclusionsTaken together, these results suggest that the rs320706814 SNP on pig chromosome 17 is a putative causal mutation for carcass length in the widely used DLY pigs and has great value in breeding for body size in pigs.

Project description:Body length, body height, and total teat number are economically important traits in pig breeding, as these traits are usually associated with the growth, reproductivity, and longevity potential of piglets. Here, we report a genetic analysis of these traits using a population comprising 2,068 Large White pigs. A genotyping-by-sequencing (GBS) approach was used to provide high-density genome-wide SNP discovery and genotyping. Univariate and bivariate animal models were used to estimate heritability and genetic correlations. The results showed that heritability estimates for body length, body height, and total teat number were 0.25 ± 0.04, 0.11 ± 0.03, and 0.22 ± 0.04, respectively. The genetic correlation between body length and body height exhibited a strongly positive correlation (0.63 ± 0.15), while a positive but low genetic correlation was observed between total teat number and body length. Furthermore, we used two different genome-wide association study (GWAS) approaches: single-locus GWAS and weighted single-step GWAS (WssGWAS), to identify candidate genes for these traits. Single-locus GWAS detected 76, 13, and 29 significant single-nucleotide polymorphisms (SNPs) associated with body length, body height, and total teat number. Notably, the most significant SNP (S17_15781294), which is located 20 kb downstream of the BMP2 gene, explained 9.09% of the genetic variance for body length traits, and it also explained 9.57% of the genetic variance for body height traits. In addition, another significant SNP (S7_97595973), which is located in the ABCD4 gene, explained 8.92% of the genetic variance for total teat number traits. GWAS results for these traits identified some candidate genomic regions, such as SSC6: 14.96-15.02 Mb, SSC7: 97.18-98.18 Mb, SSC14: 128.29-131.15 Mb, SSC17: 15.39-17.27 Mb, and SSC17: 22.04-24.15 Mb, providing a starting point for further inheritance research. Most quantitative trait loci were detected by single-locus GWAS and WssGWAS. These findings reveal the complexity of the genetic mechanism of the three traits and provide guidance for subsequent genetic improvement through genome selection.

Dataset Information

Polymorphism of VRTN Gene g.20311_20312ins291 Was Associated with the Number of Ribs, Carcass Diagonal Length and Cannon Bone Circumference in Suhuai Pigs.

Publications

Polymorphism of <i>VRTN</i> Gene g.20311_20312ins291 Was Associated with the Number of Ribs, Carcass Diagonal Length and Cannon Bone Circumference in Suhuai Pigs.

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