Transcriptome Analysis Of Root Heterosis In A Super Hybrid Rice Xieyou9308by RNA-Seq

Xieyou9308was one of the super hybrid rice varieties firstly recommended by the ChineseMinistry of Agriculture. Xieyou9308processes straight plant style, vigorous root and high yieldpotential. In this study, Xieyou9308, its maternal line Xieqingzao B, its paternal line R9308, and arecombinant inbred line （RIL） population derived from Xieyou9308were used as materials to conductin-depth research on molecular mechanism of root heterosis. The main results were as follows:1. A recombinant inbred line （RIL） population with234lines derived from a super hybrid riceXieyou9308were treated with normal water condition and20%polyethylene glycol （PEG-6000）. Eightroot traits including the maximum root length （MRL）, total root length （TRL）, root surface area （RSA）,root volume （RV）, root average diameter （RAD）, number of root tip （RTN）, root fresh weight （RFW）and root/shoot ratio （RS） were measured and further used for QTL analysis. A total of21QTLs weredetected. Seven QTLs under normal water condition and14QTLs under drought stress were detected,respectively. The QTLs detected under the two water supply conditions had significant differences,which indicated that there was different genetic mechanism controlling rice root traits at the twodifferent water conditions. Two important QTL clusters on chromosome3and6for root traits weredetected, especially the QTL for seedling root traits detected between RM6283and RM7370onchromosome3had linkage relation with the QTLs for drought resistance and yield related traits. Itwould be possible to improve multiple traits using DNA makers closely linked to these QTLs. Inaddition, the results of our study may provide important information for mining the key genesassociated with root development and for further studying the genetic mechanism underlying rootheterosis.2. Using the Illumina HiSeq2000platform, the root transcriptomes of the super-hybrid rice varietyXieyou9308and its parents were analyzed at tillering and heading stages. Approximately391millionhigh-quality paired-end reads （100-bp in size） were generated and aligned against the Nipponbarereference genome. We found that38,872of42,081（92.4%） annotated transcripts were represented by atleast one sequence read. A total of829and4186transcripts that were differentially expressed betweenthe hybrid and its parents (DG_HP) were identified at tillering and heading stages, respectively. Out of theDG_HP,66.59%were down-regulated at the tillering stage and64.41%were up-regulated at the headingstage. At the heading stage, the DG_HPwere significantly enriched in pathways related to processes suchas carbohydrate metabolism and plant hormone signal transduction, with most of the key genes that areinvolved in the two pathways being up-regulated in the hybrid; several DG_HPinvolved in theabove-mentioned pathways could be mapped to quantitative trait loci （QTLs） for yield and root traits.The changes in the expression of the candidate transcripts may lay a foundation for future studies onmolecular mechanisms underlying root heterosis. An extensive transcriptome dataset was obtained byRNA-Seq, providing a useful resource for the rice research community.3. We analyzed genome-wide allele-specific gene expression （ASGE） in the super-hybrid ricevariety Xieyou9308using RNA sequencing （RNA-Seq） technology. We identified9325reliable single nucleotide polymorphisms （SNPs） distributed throughout the genome. Nearly68%of the identifiedpolymorphisms were CT and GA SNPs between R9308and Xieqingzao B, suggesting the existence ofDNA methylation, a heritable epigenetic mark, in the parents and their F₁hybrid. Of2793identifiedtranscripts with consistent allelic biases, only480（17%） showed significant allelic biases duringtillering and/or heading stages, implying that trans effects may mediate most transcriptional differencesin hybrid offspring. Approximately67%and62%of the480transcripts showed R9308allelicexpression biases at tillering and heading stages, respectively. Transcripts with higher levels of geneexpression in R9308also exhibited R9308allelic biases in the hybrid. In addition,125transcripts wereidentified with significant allelic expression biases at both stages, of which74%showed R9308allelicexpression biases. R9308alleles may tend to preserve their characteristic states of activity in the hybridand may play important roles in hybrid vigor at both stages. The allelic expression of355transcriptswas highly stage-specific, with divergent allelic expression patterns observed at different developmentalstages. Many transcripts associated with stress resistance were differently regulated in the F₁hybrid.The results of this study may provide valuable insights into molecular mechanisms of heterosis.