Genome-wide association analyses reveal significant loci and strong candidate genes for growth and fatness traits in two pig populations

Qiao, Ruimin; Gao, Jinliang; Zhang, Zhiyan; Lin, Liu; Xie, Xianhua; Fan, Yinglun; Cui, Leilei; Ma, Junwu; Ai, Huashui; Ren, Jun; Huang, Lusheng

doi:10.1186/s12711-015-0089-5

Cited by 61 publications

(61 citation statements)

References 59 publications

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“…This heterogeneity may be caused by distinct mechanism of fat deposition for different types of adipose involving different microbes among abdominal adipose, leaf fat and subcutaneous adipose. This condition was similar to that in genetic dissection of porcine fatness traits, in which different genomic loci were identified for each fatness trait (Qiao et al, 2015). To the best of our knowledge, this study first evaluated the fatness-associated microbes in the cecum samples.…”

Section: Discussionmentioning

confidence: 62%

Evaluating the Contribution of Gut Microbiota to the Variation of Porcine Fatness with the Cecum and Fecal Samples

Fang

Huang

et al. 2016

Front. Microbiol.

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Microbial community in gastrointestinal tract participates in the development of the obesity as well as quite a few metabolic diseases in human. However, there are few studies about the relationship between gut microbiota and porcine fatness. Here, we used high-throughput sequencing to perform 16S rRNA gene analysis in 256 cecum luminal samples from Erhualian pigs and 244 stools from Bamaxiang pigs, and adopted a two-part model statistical method to evaluate the association of gut microbes with porcine fatness. As the results, we identified a total of 6 and 108 operational taxonomic units (OTUs), and 9 and 10 bacterial taxa which showed significant associations with fatness traits in the stool and cecum samples, respectively. Cross-validation analysis indicated that gut microbiome showed the largest effect on abdominal adipose by explaining 2.73% phenotypic variance of abdominal fat weight. Significantly more fatness-associated OTUs were identified in the cecum samples than that in the stools, suggesting that cecum luminal samples were better used for identification of fatness-associated microbes than stools. The fatness-associated OTUs were mainly annotated to Lachnospiraceae, Ruminococcaceae, Prevotella, Treponema, and Bacteroides. These microbes have been reported to produce short-chain fatty acids by fermenting dietary indigested polysaccharide and pectin. The short-chain fatty acids can regulate host body energy homeostasis, protect host from inflammation and inhibit fat mass development. Our findings suggested that the gut microbiome may be an important factor modulating fatness in pigs.

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Section: Discussionmentioning

confidence: 62%

Evaluating the Contribution of Gut Microbiota to the Variation of Porcine Fatness with the Cecum and Fecal Samples

Fang

Huang

et al. 2016

Front. Microbiol.

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“…Expression of porcine PPARD inhibits the formation of myotube and increases adipocyte differentiation in mouse myoblasts [29]. In addition, several GWAS revealed the association of PPARD with limb bone length [30] and growth and fatness traits [31] in pigs. Similarly, HMGA1 which is located in a QTL region that we identified on SSC7 in Duroc, was reported to be associated with length of limb bone in pigs [30, 32] and height and length of hip axis in humans [24].…”

Section: Discussionmentioning

confidence: 99%

“…In this study, several genes involved in the growth pathway were identified, such as IGF2BP2 , G H1 , CCND2 and MSH2 . The protein IGF2BP2 plays an important role in controlling the action of IGF [36] which are associated with growth and fatness traits in pigs [31]. Similarly, GH1 is necessary for growth promotion and energy metabolism regulation [37].…”

Section: Discussionmentioning

confidence: 99%

Genome-wide association study for conformation traits in three Danish pig breeds

Christensen

Nielsen

et al. 2017

Genet Sel Evol

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BackgroundSelection for sound conformation has been widely used as a primary approach to reduce lameness and leg weakness in pigs. Identification of genomic regions that affect conformation traits would help to improve selection accuracy for these lowly to moderately heritable traits. Our objective was to identify genetic factors that underlie leg and back conformation traits in three Danish pig breeds by performing a genome-wide association study followed by meta-analyses.MethodsData on four conformation traits (front leg, back, hind leg and overall conformation) for three Danish pig breeds (23,898 Landrace, 24,130 Yorkshire and 16,524 Duroc pigs) were used for association analyses. Estimated effects of single nucleotide polymorphisms (SNPs) from single-trait association analyses were combined in two meta-analyses: (1) a within-breed meta-analysis for multiple traits to examine if there are pleiotropic genetic variants within a breed; and (2) an across-breed meta-analysis for a single trait to examine if the same quantitative trait loci (QTL) segregate across breeds. SNP annotation was implemented through Sus scrofa Build 10.2 on Ensembl to search for candidate genes.ResultsAmong the 14, 12 and 13 QTL that were detected in the single-trait association analyses for the three breeds, the most significant SNPs explained 2, 2.3 and 11.4% of genetic variance for back quality in Landrace, overall conformation in Yorkshire and back quality in Duroc, respectively. Several candidate genes for these QTL were also identified, i.e. LRPPRC, WRAP73, VRTN and PPARD likely control conformation traits through the regulation of bone and muscle development, and IGF2BP2, GH1, CCND2 and MSH2 can have an influence through growth-related processes. Meta-analyses not only confirmed many significant SNPs from single-trait analyses with higher significance levels, but also detected several additional associated SNPs and suggested QTL with possible pleiotropic effects.ConclusionsOur results imply that conformation traits are complex and may be partly controlled by genes that are involved in bone and skeleton development, muscle and fat metabolism, and growth processes. A reliable list of QTL and candidate genes was provided that can be used in fine-mapping and marker assisted selection to improve conformation traits in pigs.Electronic supplementary materialThe online version of this article (doi:10.1186/s12711-017-0289-2) contains supplementary material, which is available to authorized users.

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“…The most prospective and actual trend in farm animal breeding is studying gene polymorphisms affecting the productive traits (3,4). Over the last decade the interest of scientists has been focused on genes encoding growth factors, hormones, receptors, transport, and regulatory proteins (5,6).…”

Section: Introductionmentioning

confidence: 99%

Effect of polymorphisms in intron 1 of the swine POU1F1gene on growth and reproductive traits

Getmantseva¹,

Kolosov²,

Леонова³

et al. 2017

Turk J Vet Anim Sci

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The most prospective and actual trend in farm animal breeding is studying gene polymorphisms affecting the productive traits. The objective of this investigation was to study the effect of polymorphisms in intron 1 of the swine POU1F1 gene on number of days to 100 kg (days to 100 kg), length of body (LB), backfat thickness (BF), and number of piglets born alive (NBA). Research was conducted on purebred pigs of Landrace (n = 80) and Duroc (n = 100) and crossbred pigs (Landrace × Large White) (n = 192). Insertions/deletions in intron 1 of the POU1F1 gene were defined by the PCR method. In Landrace the frequency of genotypes АА, АВ, and ВВ was 80.0%, 20.0%, and 0.0%; in crossbred pigs it was 63.0%, 29.0%, and 8.0%; and in Duroc it was 100.0%, 0.0%, and 0.0%, respectively. Significant effects of polymorphisms in intron 1 of the POU1F1 gene have been found in Landrace on days to 100 kg and LB and in crossbred pigs on LB and BF. The effect of the POU1F1 gene on NBA was not defined in our population. The obtained results show the possibility of using polymorphism in the 1st intron of the POU1F1 gene as a promising marker in breeding programs for improving growth and meat traits.

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Genome-wide association analyses reveal significant loci and strong candidate genes for growth and fatness traits in two pig populations

Cited by 61 publications

References 59 publications

Evaluating the Contribution of Gut Microbiota to the Variation of Porcine Fatness with the Cecum and Fecal Samples

Evaluating the Contribution of Gut Microbiota to the Variation of Porcine Fatness with the Cecum and Fecal Samples

Genome-wide association study for conformation traits in three Danish pig breeds

Effect of polymorphisms in intron 1 of the swine POU1F1gene on growth and reproductive traits

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