Institute of Animal Science, Animal Breeding and Husbandry Group, University of Bonn, Endenicher Allee 15, 53115, Bonn, Germany.
Mol Biol Rep. 2012 Apr;39(4):4809-21. doi: 10.1007/s11033-011-1274-4. Epub 2011 Sep 27.
The aim of this research was to screen polymorphism and to perform association study of porcine AMBP (alpha-1-microglobulin/bikunin precursor), GC (group-specific component protein) and PPP1R3B (protein phosphatase 1, regulatory (inhibitor) subunit 3B) genes with meat quality traits as well as to unravel the transcriptional regulation of these genes by expression QTL (eQTL) study. For this purpose, Duroc × Pietrain F2 resource population (DuPi; n = 313) and a commercial breed Pietrain (Pi; n = 110) were used for association and only DuPi for expression and eQTL study. A SNP was identified in the genes AMBP (g.22229C>T), GC (g.398C>T) and PPP1R3B (c.479A>G), respectively. In DuPi SNP of AMBP was associated (P < 0.05) with meat colour, pH(1L), pH(24L), pH(24H) and conductivity(24L); SNP of GC showed tendency to association (P < 0.10) with pH24H, conductivity(1L) and thawing loss, and SNP of PPP1R3B was associated (P < 0.05) with meat colour, pH(1L), pH(24L), pH(24H) and shear force. In Pi SNPs of AMBP and GC was associated with pH(24H) and PPP1R3B SNP was associated with pH(24L). The mRNA levels in Longissimus dorsi muscle tissue of these three genes were evaluated by using qRT-PCR to identify association between gene expression and meat quality traits as well as to analyse eQTL. The mRNA expression of PPP1R3B associated with pH(24L) (P < 0.05). Expression of these three genes was higher in animals with low pH of muscle. Linkage analysis using QTL Express revealed ten trans-regulated eQTL on seven porcine autosomes. Suggestive eQTL [P < 0.05, CW (chromosome-wide)] were found for PPP1R3B on SSC3 and 13. These results revealed that genetic variation and gene expression of these genes are associated with the meat quality traits. These three genes could influence meat quality and could be potential positional, physiological and functional candidate gene for meat quality traits in pigs. However, the analysis of eQTL also suggested that we need to consider additional genes encoding for transcription factors (TF), via fine-mapping underlying the eQTL peaks, in order to understand interaction among these genes.
本研究旨在筛选多态性，并对猪 AMBP（α-1-微球蛋白/ bikunin 前体）、GC（组特异性成分蛋白）和 PPP1R3B（蛋白磷酸酶 1，调节（抑制剂）亚基 3B）基因进行关联研究，以探讨这些基因与肉质性状的关系，并通过表达数量性状位点（eQTL）研究揭示这些基因的转录调控机制。为此，利用杜洛克×皮特兰 F2 资源群体（DuPi；n=313）和商业品种皮特兰（Pi；n=110）进行关联分析，仅对 DuPi 进行表达和 eQTL 研究。在 AMBP 基因（g.22229C>T）、GC 基因（g.398C>T）和 PPP1R3B 基因（c.479A>G）中分别鉴定出一个 SNP。在 DuPi 中，AMBP 的 SNP 与肉色、pH（1L）、pH（24L）、pH（24H）和电导率（24L）有关（P<0.05）；GC 的 SNP 与 pH24H、电导率（1L）和解冻损失呈关联趋势（P<0.10），PPP1R3B 的 SNP 与肉色、pH（1L）、pH（24L）、pH（24H）和剪切力有关。在 Pi 中，AMBP 和 GC 的 SNP 与 pH（24H）有关，而 PPP1R3B 的 SNP 与 pH（24L）有关。利用 qRT-PCR 评估这些基因在背最长肌组织中的 mRNA 水平，以确定基因表达与肉质性状之间的关系，并分析 eQTL。PPP1R3B 的 mRNA 表达与 pH（24L）有关（P<0.05）。在 pH 值较低的肌肉中，这些基因的表达水平较高。使用 QTL Express 进行连锁分析显示，在 7 条猪染色体上有 10 个反式调控的 eQTL。在 SSC3 和 13 上发现了 PPP1R3B 的推定 eQTL[P<0.05，CW（全染色体）]。这些结果表明，这些基因的遗传变异和表达与肉质性状有关。这三个基因可能影响肉质，并可能成为猪肉质性状的潜在位置、生理和功能候选基因。然而，eQTL 的分析也表明，我们需要通过精细映射潜在的 eQTL 峰，考虑额外的转录因子（TF）编码基因，以了解这些基因之间的相互作用。
