Transcriptome differences in frontal cortex between wild boar and domesticated pig

Abstract

Animal domestication is a long-term, multistage process that results in modifications of many traits, especially the less aggressive behavior in domesticated animals. In this study, we used the Illumina RNA-seq to compare the transcriptome in brain frontal cortex between wild boar and Rongchang pig, a typical indigenous domestic pig in China, and revealed that 604 genes and 639 genes were specifically detected in wild boar and domesticated pig, respectively, with distinct functional characteristics that may be related to their respective environment. In addition, we identified 60 differentially expressed genes showing an enrichment in immune response-related function. Further comparison of the results against previous studies identified seven genes that are associated with domestication. Our results provide insights for deciphering the mechanism of pig domestication in the future.

Hypothalamic transcriptome of tame and aggressive silver foxes (Vulpes vulpes) identifies gene expression differences shared across brain regions

“…Similar to our findings, the identified GO terms largely belonged to a broad spectrum of biological processes such as immunity, development, reproduction and metabolism, as well as cellular processes such as cell adhesion, cell–cell interaction, motility and signal transduction. Comparably, the immune‐related processes were enriched in the comparison of frontal cortex transcriptomes of wild boar and domestic pig in a study by Long et al and in a study of blood transcriptomes between wolves and dogs . The comparative studies of transcriptomes from thalamus/hypothalamus of wild Red Junglefowl and Red Junglefowl selected for tameness for five generations largely identified genes related to spermatogenesis and immunity, but the comparative analysis of cerebral hemisphere transcriptomes in these populations suggested an enrichment for genes associated with behavioral processes .…”

“…[53][54][55][56] However, neither OXT and AVP nor any of their splice forms were altered with RNA-seq or qPCR analyses. This could be due to the area of the hypothalamus sampled, as we did not selectively screen the para- Long et al 123 and in a study of blood transcriptomes between wolves and dogs. 124 The comparative studies of transcriptomes from thalamus/hypothalamus of wild Red Junglefowl and Red Junglefowl selected for tameness for five generations largely identified genes related to spermatogenesis and immunity, 21 but the comparative analysis of cerebral hemisphere transcriptomes in these populations suggested an enrichment for genes associated with behavioral processes.…”

Genome-wide analysis reveals molecular convergence underlying domestication in 7 bird and mammals

“…RNA splicing, in response to chicken domestication. Whereas, this pattern is ambiguous in dog and pig by additionally re-analyzing the RNA-Seq data in frontal cortex from pairs of Rongchang pigs and wild boars [43], which may be attributed to the fact that avian genomes experienced extensive shorting of introns and reduced intergenic distances compared to mammals [67] and alternative splicing might be the mostly efficient mechanism to increase proteome diversity to adapt to evolutionary transition.…”

“…Supportably, our RNA-Seq data in cerebrum and cerebellum showed that expression of genes in these families like GRIK2 and SEMA3A was significantly decreased in domesticated chickens than that in RJFs (Additional file 10: Figure S9). Re-analyzing the RNA-Seq data in frontal cortex from 3 pairs of Rongchang pigs and wild boars [43], and those in cerebellum and hypothalamus from pairs of 3 dogs and 1 wolf (personal communication), we observed a consistent decrease in gene expression of GRIK2, SEMA3A, SEMA3D and SEMA3E (declined by 0.10-0.86 fold) in any brain tissues in at least 2 domesticated animals although not all of them were significant DEGs (Additional file 10: Figure S9).…”

“…Six transcriptomes of frontal cortex from 3 pairs of Rongchang pigs and wild boars with accession numbers SRR5470021~5,470,026 [43] were downloaded and reanalyzed.…”