Genetic mapping using 1.4M SNP array refined loci for fatty acid composition traits in Chinese Erhualian and Bamaxiang pigs

Abstract

Chinese indigenous pigs display marked genetic and phenotypic differences compared with western commercial pigs. In this study, we tested the association between 660K SNPs and longissimus muscle fatty acid composition traits in Chinese Erhualian (n = 331) and Bamaxiang (n = 315) pigs based on a customized 1.4 million SNP array. We identified a total of 64 significant associations for 20 fatty acid composition traits at the p-value threshold of 1 × 10 among which 42 associations in low linkage disequilibrium (r < .2) with previously reported loci were considered novel. We substantially improved the strength and precision of the associations at four previously detected loci near FADS2, ELOVL7, ELOVL6 and FASN genes, facilitating follow-up candidate gene studies. Moreover, we also identified loci near ABCD2, ACSBG1, ELOVL5, HPGDS, DAGT2, ACAD10 and ACSL1 genes with function relevant to metabolism of fatty acids. In this study, valuable genetic variants and candidate genes associated with fatty acid composition traits were identified in Erhualian and Bamaxiang pigs. Some identified loci could be used to improve pork nutrition in pig breeding practice. Using the SNP array with higher marker density and less ascertainment bias improved QTL detection power and precision in Chinese indigenous pigs.

Genome-wide analysis of expression QTL (eQTL) and allele-specific expression (ASE) in pig muscle identifies candidate genes for meat quality traits

“…In a previous study, we confirmed that the splicing mutation g.8283C > A is the causative mutation for the eQTL signal and that pigs that carry the mutant allele have a high risk of pale, soft, and exudative meat [30]. Other identified candidate genes that are of interest include NUDT7, which was assigned to a QTL for meat color [47][48][49], and FADS2 and DGAT2, which are involved in the regulation of lipid metabolism and fat deposition [50][51][52]. The discovery of cis-eQTL that regulate the expression of these genes further confirms that these candidate genes affect economic traits in the pig and enhance possibilities to identify the causative mutations for each gene in future studies.…”

Genome-wide association study identifies quantitative trait loci regions involved in muscle acidic profile in Large White heavy pigs

“…Interestingly, the same chromosomal region was also found significantly associated with the content of gadoleic acid stored in abdominal fat and muscle in a Duroc x Eurhalian pig population (Yang et al, 2013), thus highlighting the evidence of an important role of this locus on C20:1 synthesis. Similar results for the same SSC7 genomic sequence were reported by Pena et al (2016), Zhang et al (2016, and Zhang et al (2017) in different pig populations, demonstrating the existence of a strong association linking the SSC7 46.8-49.0 Mb region and IMF FA composition.…”

Landscape of Loci and Candidate Genes for Muscle Fatty Acid Composition in Pigs Revealed by Multiple Population Association Analysis

“…Another example is that the top associated variant (8:126831850, P = 1.11 × 10 -9 ) for C18:1n-9/C16:1n-7 on chromosome 8 found in 60K chips is less significant than, and locate approximately 6 Mb from the top SNP (8:120599982, P = 3.99 × 10 -12 ) detected hereby ( Figure 1B ). Notably, the newly identified SNP locates closer to ELOVL6 , the most functionally plausible gene in this region, and those SNPs identified in DLY and Erhualian populations (Zhang et al, 2016; Zhang et al, 2017) ( Supplementary Table 3 ). In Sutai pigs, 5:73950290 for C20:0/C18:0 ( P = 2.24 × 10 -11 ) on SSC5 identified here shows greater association significance than the one (5:70181543, 3.20 × 10 -7 ) identified based on 60 K SNP data ( Figure 1C ).…”

“…In this study, six pig populations including the White Duroc × Erhualian F 2 , Sutai, Duroc-Landrace-Yorkshire (DLY) three-way cross, Laiwu, Erhualian, and Bamaxiang pigs were investigated. The detailed information on the six populations has been described (Yang et al, 2013; Liu et al, 2015; Xiong et al, 2015; Zhang et al, 2016; Zhang et al, 2017). Briefly, the F 2 cross was generated by mating two white Duroc boars and 17 Erhualian sows to produce F 1 animals, nine F 1 boars, and 59 F 1 sows were intercrossed to produce 976 F 2 males and 945 F 2 females in six batches.…”

“…Genome-wide association studies (GWAS) based on SNP arrays have successfully identified numerous genomic regions associated with fatty acid composition traits in different pig populations (Ramayo-Caldas et al, 2012; Yang et al, 2013; Ros-Freixedes et al, 2016; Zhang et al, 2016; Zhang et al, 2017). Due to the low density of porcine SNP chips and long range linkage disequilibrium among markers, most of the identified loci have large confidence intervals, which require further fine mapping studies to pinpoint the causal variants.…”