Expression data from porcine ovary tissue of sows from two prolificacy levels

Previous results from a genome scan in a F2 Iberian by Meishan intercross showed several chromosome regions associated with litter size traits. In order to identify candidate genes underlying these QTL we have performed an ovary gene expression analysis during pregnancy. F2 sows were ranked by their estimated breeding values for prolificacy, the six sows with higher EBV (HIGH prolificacy) and the six with lower EBV (LOW prolificacy) were selected. Samples were hybridized to Affymetrix porcine expression microarrays. The statistical analysis with a mixed-model approach identified 221 differentially expressed probes, representing 189 genes. These genes were functionally annotated in order to identify the genetic pathways overrepresented. Among the most represented functional groups the first one was immune system response activation against external stimulus. The second group was made up of genes which regulate the maternal homeostasis by complement and coagulation cascades. The last group was involved on lipid and fatty acid enzymes of metabolic processes, which participate in steroidogenesis pathway. In order to identify powerful candidate genes for prolificacy, the second approach of this study was merging microarray data with position information of QTL affecting litter size, previously detected in the same experimental cross. According to this, we have identified 27 differentially expressed genes co-localized with QTL for litter size traits, which fulfill the biological, positional and functional criteria. Twelve ovary samples: six high prolific sows and low prolific sows, slaughtered after 30 days of pregnancy. Each sample is the average between right and left ovary from each sow.

此前在F2代伊比利亚猪与梅山猪杂交群体中开展的全基因组扫描结果显示，存在多个与产仔数性状相关的染色体区域。为鉴定这些数量性状基因座（Quantitative Trait Locus, QTL）背后的候选基因，本研究开展了妊娠时期的卵巢基因表达分析。研究人员根据母猪繁殖力的估计育种值（Estimated Breeding Value, EBV）对F2代母猪进行排序，选取其中6头高EBV（高产仔）母猪与6头低EBV（低产仔）母猪进行实验。将采集的样本与Affymetrix猪表达基因芯片进行杂交后，采用混合模型分析法开展统计检验，共鉴定出221个差异表达探针，对应189个基因。随后对这些基因进行功能注释，以筛选富集的遗传通路。在占比最高的功能类群中，第一类为针对外界刺激的免疫系统应答激活通路；第二类为通过补体与凝血级联反应调控母体稳态的基因；第三类为参与类固醇生成途径的脂质与脂肪酸代谢相关酶编码基因。为筛选更具潜力的产仔数候选基因，本研究的第二部分分析将芯片数据与此前在同一杂交群体中鉴定到的产仔数性状QTL的位置信息进行整合，最终鉴定出27个与产仔数性状QTL共定位的差异表达基因，这些基因同时满足生物学、位置学与功能学标准。本研究共纳入12份卵巢样本，分别来自妊娠30天屠宰的6头高产仔母猪与6头低产仔母猪，每份样本为对应个体左右两侧卵巢的混合样品。