Genome-wide identification of allele-specific expression in response to Streptococcus suis 2 infection in two differentially susceptible pig breeds.
Although allele expression imbalance has been recognized in many species, and strongly linked to diseases, no whole transcriptome allele imbalance has been detected in pigs during pathogen infections. The pathogen Streptococcus suis 2 (SS2) causes serious zoonotic disease. Different pig breeds show differential susceptibility/resistance to pathogen infection, but the biological insight is little known. Here we analyzed allele-specific expression (ASE) using the spleen transcriptome of four pigs belonging to two phenotypically different breeds after SS2 infection. The comparative analysis of allele specific SNPs between control and infected animals revealed 882 and 1096 statistically significant differentially expressed allele SNPs (criteria: ratio ≧ 2 or ≦ 0.5) in Landrace and Enshi black pig, respectively. Twenty nine allelically imbalanced SNPs were further verified by Sanger sequencing, and later six SNPs were quantified by pyrosequencing assay. The pyrosequencing results are in agreement with the RNA-seq results, except two SNPs. Looking at the role of ASE in predisposition to diseases, the discovery of causative variants by ASE analysis might help the pig industry in long term to design breeding programs for improving SS2 resistance.
Institute of Animal Science and Veterinary Medicine, Hubei Academy of Agricultural Sciences, Yaoyuan No. 1, Nanhu, Hongshan District, Wuhan, 430064, China.|Hubei Key Laboratory of Animal Embryo Engineering and Molecular Breeding, Yaoyuan No. 1, Nanhu, Hongshan District, Wuhan, 430064, China.
Huayu
H
Wu
Institute of Animal Science and Veterinary Medicine, Hubei Academy of Agricultural Sciences, Yaoyuan No. 1, Nanhu, Hongshan District, Wuhan, 430064, China.|Hubei Key Laboratory of Animal Embryo Engineering and Molecular Breeding, Yaoyuan No. 1, Nanhu, Hongshan District, Wuhan, 430064, China.
Uma
U
Gaur
Department of Animal Science, Faculty of Agriculture Chiang Mai University, Chiang Mai, 50200, Thailand.
Supamit
S
Mekchay
Institute of Animal Science and Veterinary Medicine, Hubei Academy of Agricultural Sciences, Yaoyuan No. 1, Nanhu, Hongshan District, Wuhan, 430064, China.|Hubei Key Laboratory of Animal Embryo Engineering and Molecular Breeding, Yaoyuan No. 1, Nanhu, Hongshan District, Wuhan, 430064, China.
Xianwen
X
Peng
Institute of Animal Science and Veterinary Medicine, Hubei Academy of Agricultural Sciences, Yaoyuan No. 1, Nanhu, Hongshan District, Wuhan, 430064, China.|Hubei Key Laboratory of Animal Embryo Engineering and Molecular Breeding, Yaoyuan No. 1, Nanhu, Hongshan District, Wuhan, 430064, China.
Lianghua
L
Li
Institute of Animal Science and Veterinary Medicine, Hubei Academy of Agricultural Sciences, Yaoyuan No. 1, Nanhu, Hongshan District, Wuhan, 430064, China.|Hubei Key Laboratory of Animal Embryo Engineering and Molecular Breeding, Yaoyuan No. 1, Nanhu, Hongshan District, Wuhan, 430064, China.
Hua
H
Sun
Institute of Animal Science and Veterinary Medicine, Hubei Academy of Agricultural Sciences, Yaoyuan No. 1, Nanhu, Hongshan District, Wuhan, 430064, China.
Zhongxu
Z
Song
Institute of Animal Science and Veterinary Medicine, Hubei Academy of Agricultural Sciences, Yaoyuan No. 1, Nanhu, Hongshan District, Wuhan, 430064, China.|Hubei Key Laboratory of Animal Embryo Engineering and Molecular Breeding, Yaoyuan No. 1, Nanhu, Hongshan District, Wuhan, 430064, China.
Binke
B
Dong
Institute of Animal Science and Veterinary Medicine, Hubei Academy of Agricultural Sciences, Yaoyuan No. 1, Nanhu, Hongshan District, Wuhan, 430064, China.
Mingbo
M
Li
Leibniz Institute for Farm Animals Biology (FBN), Research Unit 'Molecular Biology', Wilhelm-Stahl-Allee 2, Dummerstorf, 18196, Germany.
Klaus
K
Wimmers
Leibniz Institute for Farm Animals Biology (FBN), Research Group 'Functional Genome Analysis', Wilhelm-Stahl-Allee 2, Dummerstorf, 18196, Germany.
Siriluck
S
Ponsuksili
Beijing Institute of Animal Science and Veterinary Medicine, Chinese Academy of Agricultural Sciences, Malianwa, Haidian District, Beijing, 100193, China.
Kui
K
Li
Institute of Animal Science and Veterinary Medicine, Hubei Academy of Agricultural Sciences, Yaoyuan No. 1, Nanhu, Hongshan District, Wuhan, 430064, China.|Hubei Key Laboratory of Animal Embryo Engineering and Molecular Breeding, Yaoyuan No. 1, Nanhu, Hongshan District, Wuhan, 430064, China.
Shuqi
S
Mei
Institute of Animal Science and Veterinary Medicine, Hubei Academy of Agricultural Sciences, Yaoyuan No. 1, Nanhu, Hongshan District, Wuhan, 430064, China. guisheng_liu1964@yahoo.com.|Hubei Key Laboratory of Animal Embryo Engineering and Molecular Breeding, Yaoyuan No. 1, Nanhu, Hongshan District, Wuhan, 430064, China. guisheng_liu1964@yahoo.com.
Guisheng
G
Liu
D000483:Alleles; D000818:Animals; D001947:Breeding; D059014:High-Throughput Nucleotide Sequencing; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA; D013290:Streptococcal Infections / Q000235:genetics / Q000662:veterinary*; D017011:Streptococcus suis; D034421:Sus scrofa / Q000145:classification / Q000235:genetics* / Q000382:microbiology; D013552:Swine; D013553:Swine Diseases / Q000235:genetics* / Q000382:microbiology; D059467:Transcriptome
Allele specific expression; Disease resistance; Pig; SNP; Streptococcus suis