Maternal effects shape the alternative splicing of parental alleles in reciprocal cross hybrids of Megalobrama amblycephala × Culter alburnus

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 animals. 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. By comparing the expression of BSB- and TC- homoeologous genes between the two reciprocal cross hybrids, we identified 49–348 differentially expressed BSB-homoeologous genes and 54–354 differentially expressed TC-homoeologous genes. 2402, 2959, and 3418 AS events between the two reciprocal cross hybrids were detected in Illumina data of muscle, liver, and gonad, respectively. Moreover, 21,577 (TC-homoeologs) and 30,007 (BSB-homoeologs) AS events were found in the 20,131 homoeologous gene pairs of TBF(3) based on PacBio data, while 30,561 (TC-homoeologs) and 30,305 (BSB-homoeologs) AS events were found in BTF(3). These results further improve AS prediction at the homoeolog level. The various AS patterns in bmpr2a belonging to the bone morphogenetic protein family were selected as AS models to investigate the expression diversity and its potential effects to body shape traits. 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 were the cause of expression diversity. These findings provide a novel insight into mRNA expression changes and AS under maternal effects in lower vertebrates.