Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, China.
PLoS One. 2013 May 28;8(5):e64047. doi: 10.1371/journal.pone.0064047. Print 2013.
Thousands of QTLs for meat quality traits have been identified by linkage mapping studies, but most of them lack precise position or replication between populations, which hinder their application in pig breeding programs. To localize QTLs for meat quality traits to precise genomic regions, we performed a genome-wide association (GWA) study using the Illumina PorcineSNP60K Beadchip in two swine populations: 434 Sutai pigs and 933 F2 pigs from a White Duroc×Erhualian intercross. Meat quality traits, including pH, color, drip loss, moisture content, protein content and intramuscular fat content (IMF), marbling and firmness scores in the M. longissimus (LM) and M. semimembranosus (SM) muscles, were recorded on the two populations. In total, 127 chromosome-wide significant SNPs for these traits were identified. Among them, 11 SNPs reached genome-wise significance level, including 1 on SSC3 for pH, 1 on SSC3 and 3 on SSC15 for drip loss, 3 (unmapped) for color a*, and 2 for IMF each on SSC9 and SSCX. Except for 11 unmapped SNPs, 116 significant SNPs fell into 28 genomic regions of approximately 10 Mb or less. Most of these regions corresponded to previously reported QTL regions and spanned smaller intervals than before. The loci on SSC3 and SSC7 appeared to have pleiotropic effects on several related traits. Besides them, a few QTL signals were replicated between the two populations. Further, we identified thirteen new candidate genes for IMF, marbling and firmness, on the basis of their positions, functional annotations and reported expression patterns. The findings will contribute to further identification of the causal mutation underlying these QTLs and future marker-assisted selection in pigs.
通过连锁作图研究已经鉴定了数千个与肉质性状相关的 QTL，但其中大多数在群体间缺乏精确的位置或重复，这阻碍了它们在猪育种计划中的应用。为了将肉质性状的 QTL 定位到精确的基因组区域，我们在两个猪群体中进行了全基因组关联（GWA）研究：434 头 Sutai 猪和 933 头来自大白杜洛克×二花脸杂交的 F2 猪。在这两个群体中，记录了肉质性状，包括 pH 值、颜色、滴水损失、水分含量、蛋白质含量和肌内脂肪含量（IMF）、大理石花纹和嫩度评分，在 LM 和 SM 肌肉中。总共鉴定出了 127 个与这些性状相关的全染色体显著 SNP。其中，有 11 个 SNP 在全基因组水平上达到显著水平，包括 SSC3 上的 pH 值 SNP，SSC3 和 SSC15 上的滴水损失 SNP，3 个（未映射）颜色 a* SNP，以及 SSC9 和 SSCX 上的 IMF SNP 各 2 个。除了 11 个未映射的 SNP 外，116 个显著 SNP 落入了大约 10 Mb 或更小的 28 个基因组区域。这些区域中的大多数与之前报道的 QTL 区域相对应，并且跨越的区间比以前更小。SSC3 和 SSC7 上的基因座似乎对几个相关性状具有多效性效应。除此之外，两个群体之间还复制了一些 QTL 信号。此外，根据它们的位置、功能注释和报道的表达模式，我们确定了 13 个新的与 IMF、大理石花纹和嫩度相关的候选基因。这些发现将有助于进一步鉴定这些 QTL 下的因果突变，并在未来的猪中进行标记辅助选择。
