Abstract
Variations in allele expressions between genetically distant populations are one of the most important factors which affects their morphological and physiological variations. These variations are caused by natural mutations accumulated in their habitats. It has been reported that allelic expression differences in the hybrids of genetically distant populations are different from parental strains. In that case, there is a possibility that allelic expression changes lead to novel phenotypes in hybrids. Based on genomic information of the genetically distant populations, quantification and comparison of allelic expression changes make importance of regulatory sequences (cis-acting factors) or upstream regulatory factors (trans-acting modulators) for these changes clearer. In this study, we focused on two Medaka inbred strains, Hd-rR and HNI, derived from genetically distant populations and their hybrids. They are highly polymorphic and we can utilize whole-genome information. To analyze allelic expression changes, we established a method to quantify and compare allele-specific expressions of 11 genes between the parental strains and their reciprocal hybrids. In intestines of reciprocal hybrids, allelic expression was either similar or different in comparison with the parental strains. Total expressions in Hd-rR and HNI were tissue-dependent in the case of HPRT1, with high up-regulation of Hd-rR allele expression in liver. The proportion of genes with differential allelic expression in Medaka hybrids seems to be the same as that in other animals, despite the high SNP rate in the genomes of the two inbred strains. It is suggested that each tissue of the strain difference in trans-acting modulators is more important than polymorphisms in cis-regulatory sequences in producing the allelic expression changes in reciprocal hybrids.
Highlights
Variations in allele expressions between genetically distant populations are one of the most important factor which affects to their morphological and physiological variations
Our results indicated that up- or down-regulation of allelespecific expression of 4 (PSMB8, MT, GAPDH and HPRT1) out of 11 genes in intestines of F1 hybrids causes the disappearance of allelic expression differences though total expression differences were observed between parental strains
When total expression is different among strains, it is thought that the mutations accumulate in the regulatory region of the gene and/or transcription factors have different activities
Summary
Variations in allele expressions between genetically distant populations are one of the most important factor which affects to their morphological and physiological variations. These variations are caused by natural mutations accumulated in their habitats. Many studies have found natural hybrid zones where distant species, subspecies and races live and genetic exchange occurs. Mixture of alleles derived from genetically distant populations can lead to different allelic expressions from their parental populations These differential allelic expressions are common in many species [2]–[][][5], and can result from mutations in its regulatory sequences (cis-acting factors) or from mutations elsewhere in the genome that alter the transcriptional factors (trans-acting modulators). It has been reported that cis-acting factors dominated in yeast [6], Drosophila [7,8] and human [9]
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