Development of a porcine skeletal muscle cDNA microarray: analysis of differential transcript expression in phenotypically distinct muscles.
BACKGROUND
Microarray profiling has the potential to illuminate the molecular processes that govern the phenotypic characteristics of porcine skeletal muscles, such as hypertrophy or atrophy, and the expression of specific fibre types. This information is not only important for understanding basic muscle biology but also provides underpinning knowledge for enhancing the efficiency of livestock production.


RESULTS
We report on the de novo development of a composite skeletal muscle cDNA microarray, comprising 5500 clones from two developmentally distinct cDNA libraries (longissimus dorsi of a 50-day porcine foetus and the gastrocnemius of a 3-day-old pig). Clones selected for the microarray assembly were of low to moderate abundance, as indicated by colony hybridisation. We profiled the differential expression of genes between the psoas (red muscle) and the longissimus dorsi (white muscle), by co-hybridisation of Cy3 and Cy5 labelled cDNA derived from these two muscles. Results from seven microarray slides (replicates) correctly identified genes that were expected to be differentially expressed, as well as a number of novel candidate regulatory genes. Quantitative real-time RT-PCR on selected genes was used to confirm the results from the microarray.


CONCLUSIONS
We have developed a porcine skeletal muscle cDNA microarray and have identified a number of candidate genes that could be involved in muscle phenotype determination, including several members of the casein kinase 2 signalling pathway.
Bai
Qianfan
Q
Laboratory of Veterinary Molecular Medicine, Department of Veterinary Pathology, University of Glasgow, Bearsden Road, Glasgow G61 1QH, UK. 9912270b@student.gla.ac.uk
McGillivray
Christine
C
da Costa
Nuno
N
Dornan
Saffron
S
Evans
Gary
G
Stear
Michael James
MJ
Chang
Kin-Chow
KC
D000818:Animals; D002352:Carrier Proteins / Q000096:biosynthesis / Q000235:genetics; D047390:Casein Kinase II; D003001:Cloning, Molecular / Q000379:methods; D018076:DNA, Complementary / Q000235:genetics*; D004268:DNA-Binding Proteins / Q000096:biosynthesis / Q000235:genetics; D020869:Gene Expression Profiling / Q000379:methods*; D005786:Gene Expression Regulation / Q000235:genetics; D016147:Genes, Tumor Suppressor; D018656:Muscle Fibers, Fast-Twitch / Q000737:chemistry / Q000378:metabolism; D018482:Muscle, Skeletal / Q000737:chemistry* / Q000378:metabolism*; D009687:Nuclear Proteins / Q000096:biosynthesis / Q000235:genetics; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D010641:Phenotype; D017346:Protein Serine-Threonine Kinases / Q000096:biosynthesis / Q000235:genetics; D016658:Psoas Muscles / Q000737:chemistry / Q000378:metabolism; D020133:Reverse Transcriptase Polymerase Chain Reaction / Q000379:methods; D013552:Swine / Q000235:genetics*; D014158:Transcription, Genetic / Q000235:genetics*; D025521:Tumor Suppressor Proteins / Q000096:biosynthesis / Q000235:genetics
D002352:Carrier Proteins; D018076:DNA, Complementary; D004268:DNA-Binding Proteins; D009687:Nuclear Proteins; D025521:Tumor Suppressor Proteins; D047390:Casein Kinase II; D017346:Protein Serine-Threonine Kinases