Background Maternal effects contribute to adaptive significance for shaping various phenotypes of many traits. Potential implications of maternal effects are the cause of expression diversity, but these effects on mRNA expression and alternative splicing (AS) have not been fully elucidated in hybrid animal.
Results Two reciprocal cross hybrids following hybridization of Megalobrama amblycephala (blunt snout bream, BSB) and Culter alburnus (topmouth culter, TC) were used as a model to investigate maternal effects. In a comparison of BSB and TC homoeolog expression from the two reciprocal cross hybrids, we identified 49–347 differentially expressed BSB-homoeologous genes and 54–354 TC-homoeologous genes. 2402, 2959, and 3418 AS events between the two reciprocal cross hybrids were detected in Illumina data of muscle, liver, and gonads, respectively. Moreover, 21,577 (TC-homoeologs) and 30,007 (BSB-homoeologs) AS events were found in the 20,131 homoeologous gene pairs of TB F3 based on PacBio data, while 30,561 (TC-homoeologs) and 30,305 (BSB-homoeologs) AS events were found in BT F3 homoeologous gene pairs. These results further improve AS prediction at the homoeolog level. To analyze body shape traits, bmpr2a of the bone morphogenetic protein family was selected as an AS model to investigate expression diversity.
Conclusions The distribution of differentially expressed genes and AS in BSB- and TC-subgenomes exhibited various changes between the two reciprocal cross hybrids, suggesting that maternal effects are the cause of expression diversity. These findings provide a novel insight into mRNA expression changes and AS under maternal effects in lower vertebrates.