Zhang Yifeng, Sun Yingchun, Wu Zhongzi, Xiong Xinwei, Zhang Junjie, Ma Junwu, Xiao Shijun, Huang Lusheng, Yang Bin
State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China.
Sci China Life Sci. 2021 Oct;64(10):1732-1746. doi: 10.1007/s11427-020-1824-7. Epub 2021 Jan 27.
Subcutaneous fat (SCF) and intramuscular fat (IMF) deposition is relevant to health in humans, as well as meat production and quality in pigs. In this study, we generated RNA sequence data for 122 SCF, 120 IMF, and 87 longissimus dorsi muscle (LDM) samples using 155 F pigs from a specially designed heterogeneous population generated by intercrossing four highly selected European commercial breeds and four indigenous Chinese pig breeds. The phenotypes including waist back fat thickness and intramuscular fat content were also measured in the 155 F pigs. We found that the genes in SCF and IMF differed largely in both expression levels and network connectivity, and highlighted network modules that exhibited strongest gain of connectivity in SCF and IMF, containing genes that were associated with the immune process and DNA double-strand repair, respectively. We identified 215 SCF genes related to kinase inhibitor activity, mitochondrial fission, and angiogenesis, and 90 IMF genes related to lipolysis and fat cell differentiation, displayed a tissue-specific association with back fat thickness and IMF content, respectively. We found that cis-expression QTL for trait-associated genes in the two adipose tissues tended to have tissue-dependent predictability for the two adipose traits. Alternative splicing of genes was also found to be associated with SCF or IMF deposition, but the association was much less extensive than that based on expression levels. This study provides a better understanding of SCF and IMF gene transcription and network organization and identified critical genes and network modules that displayed tissue-specific associations with subcutaneous and intramuscular fat deposition. These features are helpful for designing breeding programs to genetically improve the two adipose traits in a balanced way.
皮下脂肪（SCF）和肌内脂肪（IMF）沉积与人类健康以及猪的肉品生产和品质相关。在本研究中，我们使用了由四个高度选育的欧洲商业品种和四个中国本土猪品种杂交产生的155头F猪，对122个SCF样本、120个IMF样本和87个背最长肌（LDM）样本进行了RNA测序。同时还测量了这155头F猪的表型，包括腰背部脂肪厚度和肌内脂肪含量。我们发现，SCF和IMF中的基因在表达水平和网络连通性上有很大差异，并突出了在SCF和IMF中连通性增加最强的网络模块，分别包含与免疫过程和DNA双链修复相关的基因。我们鉴定出215个与激酶抑制剂活性、线粒体分裂和血管生成相关的SCF基因，以及90个与脂肪分解和脂肪细胞分化相关的IMF基因，它们分别与背膘厚度和IMF含量呈现组织特异性关联。我们发现，两个脂肪组织中与性状相关基因的顺式表达QTL对这两个脂肪性状往往具有组织依赖性的预测能力。还发现基因的可变剪接与SCF或IMF沉积有关，但这种关联的范围远小于基于表达水平所发现的关联。本研究有助于更好地理解SCF和IMF的基因转录及网络组织，并鉴定出与皮下和肌内脂肪沉积呈现组织特异性关联的关键基因和网络模块。这些特征有助于设计育种计划，以平衡的方式从基因层面改善这两个脂肪性状。
