Identification Of Allele-specific Expression Of Hybrid Maize And Its Association With Heterosis

Heterosis(hybrid vigor)is an important phenomenon with both theoretical and practical value.Numerous theories and hypotheses have been published to cover this unedifying mechanism.The most widely accepted and discussed hypotheses include dominance,overdominance and epistasis.However,till now understanding of the genetic and molecular mechanisms behind heterosis is still limited.Studying the genome-wide expressions of genes and proteins has bought new insights into crop improvement.The genomic differences between the parental lines relating to the structure,presence,absence,expression,and distribution of specific genes in F1 have been observed in generating positive effects.The development of highthroughput sequencing technology has raised the study of heterosis to a new level and highlighted the importance of each omics level in the formation of heterosis.Transcription is the first step in the transmission of genetic information in the genome and the most important link in gene expression,which is directly related to the variation of many traits.However,the transcriptome variation and expression patterns of the main maize hybrids grown in China are still not very clear.This study analyzed the transcriptomes of three major Chinese maize varieties,identified the expression patterns at the transcript level of hybrids,and analyzed the possible molecular mechanism of heterosis formation,which deepened the understanding of the mechanism of heterosis in maize.The specific research flow and results are as follows:1.This research analyzed a comprehensive dataset of maize(Zea mays L.),including RNAseq data from three hybrid-parent triplets(HPTs)and acetylated protein data from one HPT.Leaf samples were taken from the MBF1 hybrid combination at the 4-leaf stage.The leaves of the other two hybrid combinations were sampled at the 7-leaf stage.2.The study found that a large number(10,913)of ASEGs were identified in the hybrids,and ASEGs,DEGs,and SPEGs were expressed in the hybrids at the mid-parent level,contributing to the increase in the number of expressed genes in hybrid lines.The parental allele of ASEG with fewer deleterious SNPs was more likely to be overexpressed in hybrid lines than the other parental allele.3.Following the layout,all the F1 hybrids showed a higher number of expressed and common genes,while the SPE genes were found more in MBF1(1388).Comparing the DEGs revealed a higher number between the parents of Xianyu335(4268)HPT as compared to the parents of Zhengdan958.4.(3533)HPT.The F1 hybrids and their parents also showed a substantial number of DEGs.These comparisons between parents and between F1 hybrids and their parents have demonstrated extensive variation in the transcriptome across different HPTs.Using the SNPs and aligned reads,60% of allele-biased genes observed in Xianyu335 were non-DEGs,thus suggesting cis-factors in F1 hybrids.Likewise,ASEGs identified in all the hybrids were mostly non-DEGs and rarely DEGs,reflecting new insights into the transcriptional changes of F1 hybrids relative to their parents.Further,GO and KEGG enrichment analysis results validate the occurrence and importance of each gene in the specific pathways.5.The molecular pathways of heterosis-associated ASEGs were conserved in different hybrid combinations.ASEGs were mainly enriched in protein biosynthesis,photosynthesis,and metabolism.In addition,ASEGs in the three hybrid combinations were involved in key photosynthetic pathways,which might enhance the photosynthetic efficiency of the hybrids.6.The enrichment of ASEGs in complementary pathways associated with acetylated proteins in F1 hybrids helps explain the molecular mechanism of maize heterosis.ASEGs represent allelic variations in hybrids relative to their parents,and the identified ASEGs are regulated by transacting factors,pointing to a role for epistatic effects on heterosis.Correlation analysis of hybrid allelic expression with its parental expression levels provides a better measure of changes in ASEGs in hybrids.The results of this study provide a possible explanation for the dominance and epistasis hypothesis of heterosis.Given the widespread use of heterosis in agriculture and its achievements,ASEG may represent an excellent gene set that can be used as a hybrid Selection target for breeding.ASEGs involved in the complementary biological pathways of maize hybrids contribute to the formation of heterosis and provide a new idea for the analysis of the molecular mechanism of heterosis.