全基因组关联分析鉴定12个与猪生长性状相关新遗传位点

doi:10.1016/j.jia.2023.02.040

Journal of Integrative Agriculture ›› 2024, Vol. 23 ›› Issue (1): 217-227.DOI: 10.1016/j.jia.2023.02.040

全基因组关联分析鉴定12个与猪生长性状相关新遗传位点

收稿日期:2022-11-23 接受日期:2023-01-16 出版日期:2024-01-20 发布日期:2024-01-06

Genome-wide association study identifies 12 new genetic loci associated with growth traits in pigs

Mu Zeng^{1, 2, 3}, Binhu Wang³, Lei Liu³, Yalan Yang^{2, 3#}, Zhonglin Tang^{2, 3#}

¹Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding/Key Laboratory of Animal Molecular Design and Precise Breeding of Guangdong Higher Education Institutes, School of Life Science and Engineering, Foshan University, Foshan 528231, China
²Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Foshan 528200, China
³Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture/Key Laboratory of Livestock and Poultry Multi-omics of Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China

Received:2022-11-23 Accepted:2023-01-16 Online:2024-01-20 Published:2024-01-06
About author:Mu Zeng, E-mail: zengmu0520@163.com; #Correspondence Zhonglin Tang, E-mail: tangzhonglin@caas.cn; Yalan Yang, E-mail: yangyalan@caas.cn
Supported by:

This research was supported by the National Natural Science Foundation of China (32172697, 31830090 , and 32002151), the Guangdong Provincial Natural Science Foundation, China (2021A1515011336), and the Chinese Academy of Agricultural Sciences (CAAS-ZDRW202006).

摘要/Abstract

摘要：

目的：生长性状是猪最重要的经济性状之一，其遗传机制复杂，由微效多基因调控。背膘厚、眼肌面积和达100 kg体重日龄等性状通常是用作评估生长性能的主要指标。然而，目前可用于生产性状遗传改良的分子遗传标记仍然较少。本研究旨在挖掘与猪产肉性状相关的遗传标记位点，为猪的分子育种提供新的靶标。方法：我们选取了杜洛克、长白、大白三个品种共1186头纯种猪，记录所有个体的背膘厚、眼肌面积和达100 kg体重日龄等表型信息，使用猪Neogen GGP 80K SNP芯片对这1,186头纯种猪进行全基因组基因分型。用PLINK对数据进行清洗，用Beagle填充缺失的基因型数据，GCTA用于计算三个性状的遗传力、遗传相关性和表型相关性。我们使用GAPIT的四种不同统计模型进行全基因组关联分析(Genome-wide association study, GWAS)，并筛选出至少在两种模型中被检测到的单核苷酸多态性(Single nucleotide polymorphism, SNP)位点，采用SnpEff包对候选SNPs位点进行功能注释，结合公共数据库pig QTLdb定位数量性状基因座(Quantitative trait loci, QLT)，并利用课题组的转录组数据分析候选基因在骨骼肌生长发育过程中的表达模式。结果：研究结果表明，背膘厚、眼肌面积和达100 kg日龄的遗传力分别为：0.35±0.06、0.38±0.06和0.51±0.05。通过GWAS分析鉴定12个与生长性状相关的高置信度SNPs，其中5个(2_161686082, WU_10.2_1_311973532, WU_10.2_1_312813451, WU_10.2_13_6181341, WU_10.2_7_134736770)与背膘厚显著相关，3个(WU_10.2_1_311973532, WU_10.2_1_31309038, WU_10.2_12_18057237)与眼肌面积显著相关，6个(WU_10.2_12_18057237, ALGA0072703, ASGA0040345, ASGA0098828, WU_10.2_10_735574, ASGA0080085)与达100 kg日龄显著相关。通过位点注释及QTL定位，发现6个候选基因(SKAP2, SATB1, PDE7B, PPP1R16B, WNT3, WNT9B)可能与猪的生长性状相关。转录组数据分析表明，SKAP2在出生前的骨骼肌中表达水平高于出生后，PDE7B在出生前骨骼肌中表达逐渐上调，在出生后表达水平降低，提示这些基因可能在骨骼肌生长发育中扮演重要的作用。结论与创新性：本研究通过使用四种统计模型对猪生长性状进行全基因组关联分析，鉴定到12个SNPs和6个关键候选基因与生长性状相关，并分析其表达模式和潜在功能，为猪产肉性状的遗传改良提供了新的候选位点和基因，有助于猪产肉性状的遗传解析，但是候选位点和基因的功能和调控机制仍有待进一步解析。

Abstract:

Growth traits are among the most important economic traits in pigs and are regulated by polygenes with complex regulatory mechanisms. As the major indicators of growth performance, the backfat thickness (BFT), loin eye area (LEA), and days to 100 kg (D100) traits are commonly used to the genetics improvement in pigs. However, the available genetic markers for these traits are limited. To uncover novel loci and candidate genes associated with growth performance, we collected the phenotypic information of BFT, LEA, and D100 in 1,186 pigs and genotyped all these individuals using the Neogen GGP porcine 80K BeadChip. We performed a genome-wide association study (GWAS) using 4 statistical models, including mixed linear models (MLM), fixed and random model circulating probability unification (FarmCPU), settlement of MLM under progressively exclusive relationships (SUPER), Bayesian-information and linkage-disequilibrium Iteratively nested keyway (Blink), and identified 5, 3, and 6 high-confidence single nucleotide polymorphisms (SNPs) associated with BFT, LEA, and D100, respectively. Variant annotation and quantitative trait locus (QTL) mapping analysis suggested that 6 genes (SKAP2, SATB1, PDE7B, PPP1R16B, WNT3, and WNT9B) were potentially associated with growth performance in pigs. Transcriptome analysis suggested that the expression of Src Kinase Associated Phosphoprotein 2 (SKAP2) was higher in prenatal muscles than in postnatal muscles, and the expression of Phosphodiesterase 7B (PDE7B) continuously increased during the prenatal stages and gradually decreased after birth, implying their potential roles in prenatal skeletal muscle development. Overall, this study provides new candidate loci and genes for the genetic improvement of pigs.

Key words: GWAS , pig , growth trait , QTL ma pping , skeletal muscle

. 全基因组关联分析鉴定12个与猪生长性状相关新遗传位点[J]. Journal of Integrative Agriculture, 2024, 23(1): 217-227.

Mu Zeng, Binhu Wang, Lei Liu, Yalan Yang, Zhonglin Tang. Genome-wide association study identifies 12 new genetic loci associated with growth traits in pigs[J]. Journal of Integrative Agriculture, 2024, 23(1): 217-227.

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全基因组关联分析鉴定12个与猪生长性状相关新遗传位点

Genome-wide association study identifies 12 new genetic loci associated with growth traits in pigs

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