Analysis of allele-specific expression using RNA-seq of the Korean native pig and Landrace reciprocal cross

Abstract

Objective: We tried to analyze allele-specific expression in the pig neocortex using bioinformatic analysis of high-throughput sequencing results from the parental genomes and offspring transcriptomes from reciprocal crosses between Korean Native and Landrace pigs.

Methods: We carried out sequencing of parental genomes and offspring transcriptomes using next generation sequencing. We subsequently carried out genome scale identification of SNPs in two different ways using either individual genome mapping or joint genome mapping of the same breed parents that were used for the reciprocal crosses. Using parent-specific SNPs, allele-specifically expressed genes were analyzed.

Results: Because of the low genome coverage (~4x) of the sequencing results, most SNPs were non-informative for parental lineage determination of the expressed alleles in the offspring and were thus excluded from our analysis. Consequently, 436 SNPs covering 336 genes were applicable to measure the imbalanced expression of paternal alleles in the offspring. By calculating the read ratios of parental alleles in the offspring, we identified seven genes showing allele-biased expression (P < 0.05) including three previously reported and four newly identified genes in this study.

Conclusion: The newly identified allele-specifically expressing genes in the neocortex of pigs should contribute to improving our knowledge on genomic imprinting in pigs. To our knowledge, this is the first study of allelic imbalance using high throughput analysis of both parental genomes and offspring transcriptomes of the reciprocal cross in outbred animals. Our study also showed the effect of the number of informative animals on the genome level investigation of allele-specific expression using RNA-seq analysis in livestock species.

Keywords: Allele-specific Expression (ASE); Genomic Imprinting; Korean Native Pigs; Reciprocal Cross; Swine.

Figure 1

Study design for the evaluation of allele-specific expression from crosses between Korean native and Landrace pigs. Korean native pigs (KNP) and Landrace (Landrace) were reciprocally crossed. Total RNA from three individuals of the same sex from each cross were pooled together and used for RNA-seq.

Figure 2

Workflow of bioinformatic analysis to identify candidate single nucleotide polymorphisms for the discovery of allele-specific expression. Strategies I and II differ in mapping parental reads. DP, depth of reads mapped to the position.

Figure 3

Distribution of the identification of informative SNPs using two different mapping strategies. (A) Number of overlapped and unique SNPs identified to evaluate allele-biased expression from two different mapping strategies. (B) Distribution of informative SNPs from strategy I. SNPs, single nucleotide polymorphisms.