Abstract
Simple SummaryAlthough most genes are expected to transcribe both alleles evenly in diploid animals, some genes show monoallelic expression (MAE). The expressed allele can be determined randomly or by parental origin (known as genomic imprinting). Here, we conducted genome-wide and transcriptome-wide screening of MAE genes in Korean cattle (Hanwoo) and identified tissue-specific MAE pattens. The effects of MAE genes on phenotypic variation were evaluated by association analysis with the breeding values of five traits that were used in a Hanwoo breeding program.Hanwoo, an indigenous Korean cattle breed, has been genetically improved by selecting superior sires called Korean-proven bulls. However, cows still contribute half of the genetic stock of their offspring, and allelic-specific expressed genes have potential, as selective targets of cows, to enhance genetic gain. The aim of this study is to identify genes that have MAEs based on both the genome and transcriptome and to estimate their effects on breeding values (BVs) for economically important traits in Hanwoo. We generated resequencing data for the parents and RNA-sequencing data for the muscle, fat, and brain tissues of the offspring. A total of 3801 heterozygous single nucleotide polymorphisms (SNPs) in offspring were identified and they were located in 1569 genes. Only 14 genes showed MAE (seven expressing maternal alleles and seven expressing paternal alleles). Tissue-specific MAE was observed, and LANCL1 showed maternal allele expression across all tissues. MAE genes were enriched for the biological process of cell death and angiogenesis, which included ACKR3 and PDCL3 genes, whose SNPs were significantly associated with BVs of lean meat production-related traits, such as weight at 12 months of age, carcass weight, and loin eye area. In the current study, monoallelically expressed genes were identified in various adult tissues and these genes were associated with genetic capacity in Hanwoo.
Highlights
The effects of genomic imprinting on quantitative trait loci (QTL) for economical traits have been identified in cattle [5], pigs [6,7], and sheep [8]
We identify the enriched gene ontology (GO) terms or the Kyoto encyclopedia of genes and genomes (KEGG) pathways for monoallelic expression (MAE) genes using the database for annotation, visualization, and integrated discovery (DAVID) bioinformatics resources [25]
To determine monoallelic expressions of single nucleotide polymorphisms (SNPs) with heterozygous genotypes in offspring, whole genome resequencing for blood samples from sire and dam and RNAsequencing for six tissues from offspring were conducted
Summary
Genomic imprinting is a unique epigenetic phenomenon in which certain genes have monoallelic expression (MAE) based on allelic parental origins [1]. The maternal or paternal allele is suppressed during expression of the imprinted gene. Since the first discovery of genomic imprinting in mice in the 1980s, more than 100 imprinted genes have been reported in mice and humans [2] and are listed in the web-based imprinted 4.0/). Gene database (http://www.geneimprint.com/, accessed on 1 October 2021). For farm animals in selective breeding programs, these imprinted genes have important implications since the genetic merits of reciprocal heterozygotes at imprinted loci have different effects on phenotypes [4]. The effects of genomic imprinting on quantitative trait loci (QTL) for economical traits have been identified in cattle [5], pigs [6,7], and sheep [8]
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