Transcriptome Analysis of Maize Inbred Lines Reveals Important Shifts in Gene Expression Between Parents, Hybrids, and Isonuclear Lines

Maize owes its enormous productivity to the large-scale use of hybrids. Recently, we have investigated the genetic background of 82 inbred lines from Romanian maize varieties (Șuteu et al., 2013). They were placed into heterotic groups according to international standards. Subsequently, crosses were designed between members of the heterotic groups to generate superior hybrids. Field trials performed this summer (2014) confirmed the predicted heterotic effect. Here, we investigate the transcriptome of parental lines and their progenies by means of NGS, using an Illumina HiSeq2500 platform. On average, 25 million pair-end reads per sample were generated and mapped to the B73 reference genome. Our maize lines may be quite polymorphic with regard to the reference B73 and thus the mapping of the RNA-seq reads may not be optimal. To overcome this limitation, we also have assembled the transcriptome de-novo. We complemented our NGS data with microarray data, using a custom-made chip, based on the available maize ESTs in the Gramene database. Combining both methods allowed us to have an in-depth look at the transcriptome of century-old inbred lines, originating from Romania, and their respective hybrids. Furthermore, we created several isonuclear inbred lines and probed how nuclear gene expression is modulated by the cytoplasm. In turn, this would allow us to select inbred lines having a valuable cytoplasm (non-CMS) and subsequently use them in breeding programs. To the best of our knowledge this is the first transcriptome analysis by means of NGS in the maize germplasm of SE Europe, unveiling some of its distinctive features.

Funding: 
Romanian National Authority for Scientific Research, CNDI-UEFISCDI (http://uefiscdi.gov.ro/), project number PN-II-PT-PCCA-2011-3.1-0511-103/2012 to MM
SCIEX - Scientific Exchange Programme NMS-CH, project number 13334/2014 to RB