Transcriptional profiling during foetal skeletal muscle development of Piau and Yorkshire-Landrace cross-bred pigs

Abstract

Skeletal muscle development is a complex process involving the coordinated expression of thousands of genes. The aim of this study was to identify differentially expressed genes in longissimus dorsi (LD) muscle of pigs at 40 and 70 days (d) of gestation (developmental stages encompassing primary and secondary fibre formation) in Yorkshire-Landrace (YL) cross-bred pigs and Piau pigs (a naturalized Brazilian breed), which are two breed types that differ in muscularity. Foetuses were obtained from gilts at each gestational age (n = 3 YL; n = 4 Piau), and transcriptional profiling was performed using the Pigoligoarray microarray containing 20 400 oligonucleotides. A total of 486 oligonucleotides were differentially expressed (fold change (FC) ≥ 1.5; false discovery rate (FDR) ≤ 0.05) between 40 and 70 d gestation in either YL or Piau pigs, and a total of 1300 oligonucleotides were differentially expressed (FC ≥ 1.5; FDR ≤ 0.05) between YL and Piau pigs at either age. Gene ontology annotation and pathway analyses determined functional classifications for differentially expressed genes and revealed breed type-specific developmental expression patterns. Thirteen genes were selected for confirmation by qRT-PCR analyses, and expression patterns for most of these genes were confirmed, providing further insight into the roles of these genes in pig muscle development. This study revealed both developmental and breed type-specific patterns of gene expression in foetal pig skeletal muscle, including genes not previously associated with myogenesis. This information will contribute to future pig genetic improvement efforts.

Evaluating statistical analysis models for RNA sequencing experiments

“…The data consisted on read counts from an RNA-seq experiment based on a developmental expression study (Sollero et al, 2011). Experimental and alignment protocols are described in the supplemental material (Supplementary Figure 1).…”

Using pedigree analysis to monitor the local Piau pig breed conservation program

“…In recent decades, due to the large amount of fat in their carcasses, their low production efficiency and changes in consumer eating habits, local pig breeds have been threatened with extinction. Some public research institutions and nongovernmental organizations have tried to maintain small herds of these local breeds (Lopes et al, 2002) to preserve their genetic material (Barros et al, 2012a andBarros et al, 2012b) and for genetic studies (Serão et al, 2011;Sollero et al, 2011).…”

“…The genetics underpinnings of the large fat deposition of Piau pigs have been explored in genetic studies by the Animal Breeding and Genetics group of the Federal University of Viçosa, Minas Gerais state, Brazil. These studies include QTL mapping using divergent crosses Paixão et al, 2008;Silva et al, 2008), polymorphism analysis of candidate genes (Band et al, 2005;Carmo et al, 2005;Faria et al, 2006;Peixoto et al, 2006), phylogeny and genetic diversity analyses (Sollero et al, 2009;Souza et al, 2009) and expression patterns of candidate genes (Sousa et al, 2011;Serão et al, 2011;Sollero et al, 2011).…”

Independent Component Analysis (ICA) based-clustering of temporal RNA-seq data

“…Animals were raised at the Pig Breeding Farm from Federal University of Viçosa, Brazil. Pregnant gilts were euthanized at each day of gestation following the procedures described at [14]. For every breed, three sows were used for each time point and embryos/fetuses were collected (four library per breed).…”