Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
Genet Sel Evol. 2023 Oct 6;55(1):69. doi: 10.1186/s12711-023-00834-x.
Heterosis is routinely exploited to improve animal performance. However, heterosis and its underlying molecular mechanism for feed intake and efficiency have been rarely explored in chickens. Feed efficiency continues to be an important breeding goal trait since feed accounts for 60 to 70% of the total production costs in poultry. Here, we profiled the mRNA-lncRNA landscape of 96 samples of the hypothalamus, liver and duodenum mucosa from White Leghorn (WL), Beijing-You chicken (YY), and their reciprocal crosses (WY and YW) to elucidate the regulatory mechanisms of heterosis.
We observed negative heterosis for both feed intake and residual feed intake (RFI) in YW during the laying period from 43 to 46 weeks of age. Analysis of the global expression pattern showed that non-additivity was a major component of the inheritance of gene expression in the three tissues for YW but not for WY. The YW-specific non-additively expressed genes (YWG) and lncRNA (YWL) dominated the total number of non-additively expressed genes and lncRNA in the hypothalamus and duodenum mucosa. Enrichment analysis of YWG showed that mitochondria components and oxidation phosphorylation (OXPHOS) pathways were shared among the three tissues. The OXPHOS pathway was enriched by target genes for YWL with non-additive inheritance of expression in the liver and duodenum mucosa. Weighted gene co-expression network analysis revealed divergent co-expression modules associated with feed intake and RFI in the three tissues from WL, YW, and YY. Among the negatively related modules, the OXPHOS pathway was enriched by hub genes in the three tissues, which supports the critical role of oxidative phosphorylation. Furthermore, protein quantification of ATP5I was highly consistent with ATP5I expression in the liver, which suggests that, in crossbred YW, non-additive gene expression is down-regulated and decreases ATP production through oxidative phosphorylation, resulting in negative heterosis for feed intake and efficiency.
Our results demonstrate that non-additively expressed genes and lncRNA involved in oxidative phosphorylation in the hypothalamus, liver, and duodenum mucosa are key regulators of the negative heterosis for feed intake and RFI in layer chickens. These findings should facilitate the rational choice of suitable parents for producing crossbred chickens.
杂种优势被广泛用于提高动物的生产性能。然而，在鸡中，杂种优势及其对采食量和效率的潜在分子机制仍鲜有探索。由于饲料占家禽总生产成本的 60%至 70%，因此饲料效率仍然是一个重要的育种目标性状。在这里，我们对来自白来航鸡（WL）、北京油鸡（YY）及其正反交（WY 和 YW）的 96 个下丘脑、肝脏和十二指肠黏膜样本的 mRNA-lncRNA 图谱进行了分析，以阐明杂种优势的调控机制。
我们观察到在 43 至 46 周龄产蛋期间，YW 的采食量和残料采食量（RFI）均表现出负杂种优势。整体表达模式分析表明，在三个组织中，YW 的基因表达遗传的非加性是一个主要组成部分，但 WY 则不是。YW 特异性非加性表达基因（YWG）和 lncRNA（YWL）在数量上占主导地位，在三个组织的非加性表达基因和 lncRNA 中占主导地位。YWG 的富集分析表明，线粒体成分和氧化磷酸化（OXPHOS）途径在三个组织中共享。在肝脏和十二指肠黏膜中，表达具有非加性遗传的 YWL 的靶基因富集了 OXPHOS 途径。加权基因共表达网络分析揭示了与 WL、YW 和 YY 三个组织中的采食量和 RFI 相关的不同共表达模块。在负相关模块中，三个组织中的 OXPHOS 途径被枢纽基因富集，这支持了氧化磷酸化的关键作用。此外，ATP5I 的蛋白定量与肝脏中 ATP5I 的表达高度一致，这表明在杂交 YW 中，非加性基因表达下调，通过氧化磷酸化降低 ATP 产生，导致采食量和效率的负杂种优势。
我们的研究结果表明，在下丘脑、肝脏和十二指肠黏膜中参与氧化磷酸化的非加性表达基因和 lncRNA 是层鸡采食量和 RFI 负杂种优势的关键调控因子。这些发现应有助于合理选择杂交鸡的合适亲本。
