title: Identification of genes for controlling swine adipose deposition by integrating transcriptome, whole-genome resequencing, and quantitative trait loci data.
abstract: Backfat thickness is strongly associated with meat quality, fattening efficiency, reproductive performance, and immunity in pigs. Fat storage and fatty acid synthesis mainly occur in adipose tissue. Therefore, we used a high-throughput massively parallel sequencing approach to identify transcriptomes in adipose tissue, and whole-genome differences from three full-sibling pairs of pigs with opposite (high and low) backfat thickness phenotypes. We obtained an average of 38.69 million reads for six samples, 78.68% of which were annotated in the reference genome. Eighty-nine overlapping differentially expressed genes were identified among the three pair comparisons. Whole-genome resequencing also detected multiple genetic variations between the pools of DNA from the two groups. Compared with the animal quantitative trait loci (QTL) database, 20 differentially expressed genes were matched to the QTLs associated with fatness in pigs. Our technique of integrating transcriptome, whole-genome resequencing, and QTL database information provided a rich source of important differentially expressed genes and variations. Associate analysis between selected SNPs and backfat thickness revealed that two SNPs and one haplotype of ME1 significantly affected fat deposition in pigs. Moreover, genetic analysis confirmed that variations in the differentially expressed genes may affect fat deposition.
authors.affiliation: National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, Department of Animal Genetics and Breeding, China Agricultural University, Beijing 100193, China.
authors.forename: Kai
authors.initials: K
authors.lastname: Xing
authors.affiliation: National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, Department of Animal Genetics and Breeding, China Agricultural University, Beijing 100193, China.
authors.forename: Feng
authors.initials: F
authors.lastname: Zhu
authors.affiliation: National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, Department of Animal Genetics and Breeding, China Agricultural University, Beijing 100193, China.
authors.forename: LiWei
authors.initials: L
authors.lastname: Zhai
authors.affiliation: Beijing General Station of Animal Husbandry, Beijing 100125, China.
authors.forename: ShaoKang
authors.initials: S
authors.lastname: Chen
authors.affiliation: National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, Department of Animal Genetics and Breeding, China Agricultural University, Beijing 100193, China.
authors.forename: Zhen
authors.initials: Z
authors.lastname: Tan
authors.affiliation: National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, Department of Animal Genetics and Breeding, China Agricultural University, Beijing 100193, China.
authors.forename: YangYang
authors.initials: Y
authors.lastname: Sun
authors.affiliation: National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, Department of Animal Genetics and Breeding, China Agricultural University, Beijing 100193, China.
authors.forename: ZhuoCheng
authors.initials: Z
authors.lastname: Hou
authors.affiliation: National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, Department of Animal Genetics and Breeding, China Agricultural University, Beijing 100193, China.
authors.forename: ChuDuan
authors.initials: C
authors.lastname: Wang
mesh_terms: D050154:Adiposity / Q000235:genetics*; D000818:Animals; D005260:Female; D056726:Genetic Association Studies; D016678:Genome; D050356:Lipid Metabolism / Q000235:genetics*; D058977:Molecular Sequence Annotation; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D017422:Sequence Analysis, DNA; D050151:Subcutaneous Fat / Q000033:anatomy & histology; D034421:Sus scrofa / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism; D059467:Transcriptome