BackgroundIn recent years, Thai indigenous chickens have increasingly been bred as an alternative in Thailand poultry market. Due to their popularity, there is a clear need to improve the underlying quality and productivity of these chickens. Studying chicken genetic variation can improve the chicken meat quality as well as conserving rare chicken species. To begin with, a minimal set of molecular markers that can characterize the Thai indigenous chicken breeds is required.ResultsUsing AFLP-PCR, 30 single nucleotide polymorphisms (SNPs) from Thai indigenous chickens were obtained by DNA sequencing. From these SNPs, we genotyped 465 chickens from 7 chicken breeds, comprising four Thai indigenous chicken breeds- Pradhuhangdum (PD), Luenghangkhao (LK), Dang (DA) and Chee (CH), one wild chicken - the red jungle fowls (RJF), and two commercial chicken breeds - the brown egg layer (BL) and commercial broiler (CB). The chicken genotypes reveal unique genetic structures of the four Thai indigenous chicken breeds. The average expected heterozygosities of PD= 0.341, LK= 0.357, DA=0.349 and CH= 0.373, while the references RJF= 0.327, CB=0.324 and BL= 0.285. The FST values among Thai indigenous chicken breeds vary from 0.051 to 0.096. The FST values between the pairs of Thai indigenous chickens and RJF vary from 0.083 to 0.105 and the FST values between the Thai indigenous chickens and the two commercial chicken breeds vary from 0.116 to 0.221. A neighbour-joining tree of all individual chickens showed that the Thai indigenous chickens were clustered into four groups which were closely related to the wild RJF but far from the commercial breeds. Such commercial breeds were split into two closely groups. Using genetic admixture analysis, we observed that the Thai indigenous chicken breeds are likely to share common ancestors with the RJF, while both commercial chicken breeds share the same admixture pattern.ConclusionThese results indicated that the Thai indigenous chicken breeds may descend from the same ancestors. These indigenous chicken breeds were more closely related to red jungle fowls than those of the commercial breeds. These findings showed that the proposed SNP panel can effectively be used to characterize the four Thai indigenous chickens.

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ABSTRACT. Ubiquitin protein ligase E3C (UBE3C) is involved in the ubiquitin-proteasome pathway, and several ubiquitin protein ligases are important for fat deposition and lipid metabolism. The objective of this study was to analyze the association between a single nucleotide polymorphism (SNP) of the UBE3C gene with intramuscular fat (IMF) content and fatty acid (FA) composition in Duroc pigs. Four SNP markers (g.1586399A>G, g.1591358G>A, g.1600132G>C, and g.1600166G>A) of porcine UBE3C were genotyped using the polymerase chain reaction-restriction fragment length polymorphism method, and their associations with IMF content and FA composition were investigated in a commercial Duroc pig population. Two SNP markers (g.1586399A>G and g.1591358G>A) were segregated among the pigs. No UBE3C polymorphisms at g.1600132G>C or g.1600166G>A were observed. The UBE3C g.1586399A>G SNP was significantly associated with IMF content, while the UBE3C g.1591358G>A SNP was associated with palmitic, stearic, eicosenoic, and eicosadienoic acid levels, and saturated FA levels. These results suggest that polymorphisms in porcine UBE3C are correlated with IMF content and FA composition, and confirm the importance of porcine UBE3C as a candidate gene for fat deposition in pigs.

The interleukin-4 (IL-4) and interleukin-4 receptor (IL-4R) are cytokines that are involved in the immune and reproductive systems. This study aimed to verify the polymorphisms in the porcine IL-4 and IL-4R genes and to assess their effects on litter size traits in commercial pigs. Single nucleotide polymorphisms (SNPs) in the porcine IL-4 and IL-4R genes were genotyped by the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method. A non-coding SNP of IL-4 g.134993898T > C and a non-synonymous SNP of IL-4R c.1577A > T (amino acid change at position 526, Q526L) were found to be segregating in Landrace sows. The IL-4 g.134993898T > C polymorphism was significantly associated with the number of piglets weaned alive (NWA) trait. The IL-4R c.1577A > T polymorphism was significantly associated with the number born alive (NBA) and NWA traits. Moreover, the accumulation of favorable alleles of these two SNP markers revealed significant associations with the NBA, NWA, and mean weight of piglets at weaning (MWW) traits. These findings indicate that the porcine IL-4 and IL-4R genes may contribute to the reproductive traits of pigs and could be used as candidate genes to improve litter size traits in the pig breeding industry.

Interferon-alpha-16 (IFNA16) and tumor necrosis factor receptor superfamily member 19 (TNFRSF19) are cytokines that may play a role in adipogenesis and fatness. Single nucleotide polymorphisms (SNPs) of the porcine IFNA16 and TNFRSF19 genes were verified and their association with intramuscular fat (IMF) content and fatty acid (FA) composition were evaluated in commercial crossbred pigs. Two non-synonymous SNPs of the porcine IFNA16 c.413G > A and TNFRSF19 c.860G > C loci were detected in commercial crossbred pigs. The porcine IFNA16 c.413G >A polymorphism was significantly associated with stearic acid, total saturated FAs (SFAs), and the ratio of monounsaturated FAs (MUFAs) to SFAs (p < 0.05). Furthermore, the porcine TNFRSF19 c.860G > C polymorphism was found to be significantly associated with IMF content and arachidic acid levels (p < 0.05). The results revealed that porcine IFNA16 and TNFRSF19 polymorphisms are related to IMF content and/or FA composition and affirmed the importance of these cytokine genes as potential candidate genes for lipid deposition and FA composition in the muscle tissue of pigs.

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.

Osteopontin (OPN) is a secreted phosphoprotein that is involved in the development of skeletal muscle and fat deposition. The objectives of this study were to identify the polymorphism of the OPN gene and to analyze the association of the OPN gene with intramuscular fat (IMF) content and fatty acid (FA) composition in pigs. Longissimus thoracis (LT) muscle samples taken from the 10-11th rib were collected from a total of 328 Duroc pigs. Genomic DNA samples were extracted from LT muscle tissues using the phenol-chloroform method. IMF content was measured using the ether extraction method and FA composition was measured by gas chromatography. The porcine OPN polymorphisms were identified by DNA sequencing and were genotyped using the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method. The association analysis of the OPN gene with IMF and FA composition traits was performed using a general linear model (GLM). Two polymorphic sites (OPN g.2442-2471indel and g.3836A>G) were found in the 5´-flanking region and intron 1 of the porcine OPN gene. The OPN g.2442-2471indel polymorphism was found to be significantly associated with IMF content and ω3 FA levels (P<0.05). Moreover, OPN g.3836A>G polymorphism was significantly associated with the linolenic acid levels in the muscles of pigs (P<0.05). The results of this study indicate that the OPN gene is important to IMF content, as well as linolenic and ω3 FA levels in pigs, and could be used as a candidate gene to improve fat deposition and fatty acid composition in the muscles of pigs.