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.
Highlights
Adipose tissue is the site of de novo FA synthesis in pigs[7]
We presented the systematic transcriptome profiling of adipose tissue from three full-sib pairs of pigs with extreme backfat thickness using high-throughput RNA-seq technology
Compared with previous studies[10,11,13], using three full-sib pairs of pigs could reduce false-positive results caused by genetic background noise and the number of replicates
Summary
Adipose tissue is the site of de novo FA synthesis in pigs[7] It produces and releases adipokines such as tumour necrosis factor α , peptide hormones such as leptin, adiponectin, estrogen, and resistin, and lipid hormones (lipokines) such as palmitoleate[8]. We used RNA-seq to analyse the livers and adipose tissue of six Songliao black pigs classified in two phenotypically extreme groups for backfat thickness[16,17]. We applied RNA-seq to identify differences in adipose tissue transcriptomes from three pairs of full-sibling (full-sib) Danish Landrace sows with opposite backfat thickness phenotypes. We integrated RNA-seq, whole-genome resequencing data, and information from the animal quantitative trait loci (QTL) database to identify potential key genes and variations influencing swine adipose deposition
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