Identification and characterization of novel single nucleotide polymorphism markers for fat deposition in muscle tissue of pigs using amplified fragment length polymorphism.

Pantaporn Supakankul,Tanavadee Kumchoo,Supamit Mekchay

doi:10.5713/ajas.16.0200

Identification and characterization of novel single nucleotide polymorphism markers for fat deposition in muscle tissue of pigs using amplified fragment length polymorphism.

Pantaporn Supakankul, Tanavadee Kumchoo + Show 1 more

Open Access

https://doi.org/10.5713/ajas.16.0200

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Abstract

ObjectiveThis study was conducted to identify and evaluate the effective single nucleotide polymorphism (SNP) markers for fat deposition in the longissimus dorsi muscles of pigs using the amplified fragment length polymorphism (AFLP) approach.MethodsSixty-four selective primer combinations were used to identify the AFLP markers in the 20 highest- and 20 lowest-intramuscular fat (IMF) content phenotypes. Five AFLP fragments were converted into simple codominant SNP markers. These SNP markers were tested in terms of their association with IMF content and fatty acid (FA) composition traits in 620 commercially crossbred pigs.ResultsThe SSC7 g.4937240C>G marker showed an association with IMF content (p<0.05). The SSC9 g.5496647_5496662insdel marker showed a significant association with IMF content and arachidonic levels (p<0.05). The SSC10 g.71225134G>A marker revealed an association with palmitoleic and ω9 FA levels (p<0.05), while the SSC17 g.61976696G>T marker showed a significant association with IMF content and FA levels of palmitoleic, eicosenoic, arachidonic, monounsaturated fatty acids, and ω9 FA levels. However, no significant association of SSC8 g.47338181G>A was observed with any IMF and FA levels in this study.ConclusionFour SNP markers (SSC7 g.4937240C>G, SSC9 g.5496647_5496662insdel, SSC10 g.71225134G>A, and SSC17 g.61976696G>T) were found to be associated with IMF and/or FA content traits in commercially crossbred pigs. These findings provide evidence of the novel SNP markers as being potentially useful for selecting pigs with the desirable IMF content and FA composition.

Highlights

Increasing levels of intramuscular fat (IMF) content has a positive impact on the meat quality of pork [1]
The genome-wide scan for fat deposition in the muscle tissue of pigs was investigated using the amplified fragment length polymorphism (AFLP) approach
The selective markers were further elucidated to determine an association with IMF content and fatty acid (FA) levels

Summary

Introduction

Increasing levels of intramuscular fat (IMF) content has a positive impact on the meat quality of pork [1]. Fat deposition and fatty acid composition in pork are very complex traits that are likely to be controlled by a variety of genes [3]. There have been several attempts made to identify the quantitative trait loci (QTL) for IMF content and FA composition in pigs using microsatellite markers [2,4,5]. The genome wide association study approach has been carried out to detect QTLs affect on IMF and FA content in the muscle tissue of pigs [7,8,9]. Empirical evidence of identifying QTL for IMF and FA content traits have been successfully performed using F2 or crossbred experimental populations, e.g. Iberian and Land-

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