Integration of association and computational methods reveals functional variants of LEPR gene for abdominal fat content in chickens

doi:10.1016/S2095-3119(20)63575-4

摘要/Abstract

摘要：

瘦素受体（LEPR）是瘦素的高亲和力受体，在人类和动物肥胖中起着至关重要的作用。本研究的目的是以东北农业大学肉鸡双向选择品系（NEAUHLF）为研究材料，通过关联分析和电子计算分析相结合的方法，研究LEPR外显子功能变异对鸡脂肪沉积的影响。使用5种在线生物信息学工具预测编码区单核苷酸多态性（SNPs）的功能。进一步，通过基于氨基酸残基的保守性和稳定性分析、蛋白质配体结合位点的预测、蛋白质二级结构分析、蛋白质三级结构的建模等生物信息学分析，确定了高置信度SNPs的可能结构与功能。同时，对鸡LEPR基因外显子20个非同义单核苷酸多态性（nsSNPs）与腹脂性状进行了关联分析。5种在线生物信息学工具显示，rs731962924(N867I)和rs13684622（C1002R）是最可能影响鸡腹部脂肪性状的功能性nsSNPs。氨基酸残基稳定性和保守型分析显示，大部分nsSNPs可引起蛋白质稳定性下降，rs731962924（N867I）和rs13684622（C1002R）在进化过程中相对保守。蛋白质结构分析显示rs731962924（N867I）和rs13684622（C1002R）均在可引起LEPR蛋白质结构和功能的显著变化。关联分析显示rs13684622（C1002R）与鸡腹脂重和腹脂率显著相关（P=0.0413，P=0.0260）。因此，我们认为rs13684622（C1002R）可能是一个影响鸡腹脂沉积的重要功能性SNP，有望应用于分子标记辅助选择（MAS）中培育低脂肉鸡品系。本研究的主要创新点是结合了多种生物信息学方法和nsSNPs与腹脂性状之间的关联分析进行LEPR基因功能性SNPs的筛选，为后续进行深入的功能分析提供优先研究SNP（priorization SNP）。此外，本研究用到的关联分析与计算机电子计算分析相结合的方法为鉴定农业动物重要经济性状的功能性分子标记提供了一条新的途径。

Abstract:

Leptin receptor (LEPR) plays a vital role in obesity in humans and animals. The objective of this study is to assess LEPR functional variants for chicken adipose deposition by integration of association and in-silico analysis using a unique chicken population, the Northeast Agricultural University broiler lines divergently selected for abdominal fat content (NEAUHLF). Five online bioinformatics tools were used to predict the functionality of the single nucleotide polymorphisms (SNPs) in coding region. Further, the possible structure–function relationship of high confidence SNPs was determined by bioinformatics analyses, including the conservation and stability analysis based on amino acid residues, prediction of protein ligand-binding sites, and the superposition of protein tertiary structure. Meanwhile, we analyzed the association between abdominal fat traits and 20 polymorphisms of chicken LEPR gene. The integrated results showed that rs731962924 (N867I) and rs13684622 (C1002R) could lead to striking changes in the structure and function of proteins, of which rs13684622 (C1002R) was significantly associated with abdominal fat weight (AFW, P=0.0413) and abdominal fat percentage (AFP, P=0.0260) in chickens. Therefore, we are of the opinion that rs13684622 (C1002R) may be an essential functional SNP affecting chicken abdominal fat deposition, and potentially applied to improvement of broiler abdominal fat in molecular marker-assisted selection (MAS) program. Additionally, the coupling of association with computer electronic predictive analysis provides a new avenue to identify important molecular markers for breeders.

Key words: chicken , LEPR , nsSNPs , bioinformatics tools , abdominal fat content , association analysis

. [J]. Journal of Integrative Agriculture, 2021, 20(10): 2734-2748.

LI Yu-dong, WANG Wei-jia, LI Zi-wei, WANG Ning, XIAO Fan, GAO Hai-he, GUO Huai-shun, LI Hui, WANG Shou-zhi. Integration of association and computational methods reveals functional variants of LEPR gene for abdominal fat content in chickens[J]. Journal of Integrative Agriculture, 2021, 20(10): 2734-2748.

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