The Impact Of Hybridization And Polyploidization On Alternative Splicing Revealed By Transcriptome Analysis In Rice

Hybridization plays an important role in the evolutionary history of plants,affecting ecological adaptability and has been widely used in agriculture.At the molecular level,one of the direct consequences of hybridization(F1 hybrid)is effecting gene expression levels,small RNA expression patterns and epigenetic modifications,the changes in molecular level may have an important contribution to transgressive traits when compared to the parents(heterosis)in hybrids.Polyploidization is a process that is commonly experienced in eukaryotic evolution,especially when hybridization and polyploidization co-occurrence(allopolyploidization)can induce more intense gene expression changes,known as " transcriptome shock ".Gene alternative splicing(AS)is a common and important form of gene regulation in eukaryotes,creating multiple mature splicing isoforms from one type of mRNA precursor.There are few studies on the relationship between polyploidization especially about allopolyploidization and gene alternative splicing.Rice(Oryza sativa L.)is one of the world’s three major food crops.A series of studies on the changes in gene expression caused by hybridization and polyploidization of rice have been reported,but for the alternative splicing pattern is rarely mentioned.Therefore,this study focuses on alternative splicing changes in the process of hybridization and polyploidization,can be more in-depth understanding of the complexity of transcription.In this study,rice was used as the experimental material,and the RNA-seq of embryos and endosperms of parents Nipponbare(ssp.japonica)and 9311(ssp.indica),hybrids N9 and 9N,allotetraploid NN99 and 99 NN of S9 generation to invest the effects of hybridization and polyploidization on alternative splicing pattern.The results showed that a large number of alternative splicing events occurred in the parents,hybrids and polyploids,but in general,the most was polyploids,hybrids followed and the least was parents.The number of alternative splicing events in embryo was greater than that in endosperm of the same material.According to the classification of the alternative splicing pattern of the hybrids,it was found that the transgressive type occurred most in the embryo compared with the parent,while the most was 9311 parent dominant type in the endosperm.In the homozygous section of the high generation polyploids,the majority of the alternative splicing patterns inherited from their corresponding diploid parents,only a few were from the hybrids,the other parent or new emergencing in polyploids.There were few alternative splicing events new emerging or missing in hybrids and polyploids,and most of the alternative splicing events were different in splicing levels.There were different alternative splicing regulation patterns in reciprocal hybrids,between heterologous polyploids,and in tissues.These results indicated that alternative splicing was an extremely complex regulatory process with strong specificity.The homozygous regions of the higher generation inherited the original state of its diploid parents.While the alternative splicing level in the hybrids showed more transgressive phenomena,that might be associated with heterosis.That is to say,the changes of transgressive phenomena occurring at post-transcriptional process may be one of the reasons for the formation of heterosis.