Application and prospect of gene chip in genetic breeding of livestock and poultry.

Gene chip is a high-throughput technique for detecting specific DNA sequences by DNA or DNA-RNA complementary hybridization, among which SNP genotyping chips have been widely employed in the animal genetics and breeding, and have made great achievements in cattle (Bos taurus), pigs (Sus scrofa), sheep (Caprinae), chickens (Gallus gallus) and other livestock. However, genomic selection applied in production merely uses genomic information and cannot fully explain the molecular mechanism of complex traits genetics, which limits the accuracy of genomic selection. With the continuous progresses in epigenetic research, the development of commercial methylation chips and the application of the epigenome-wide association study (EWAS), DNA methylation has been extensively used to draw the causal connections between genetics and phenotypes.

Identification of genes for controlling swine adipose deposition by integrating transcriptome, whole-genome resequencing, and quantitative trait loci data.

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.