Differential Gene Expression during Sporophytic Incompatibility in European Hazelnut (Corylus avellana L.)

European hazelnut (Corylus avellana L.) is the only economically important nut crop in the family Betulaceace.  It is native to most of Europe, Asia Minor and the Caucasus mountains.  Pollen-stigma incompatibility is of the sporophytic type and is under the control of a single locus with multiple alleles.  The stigmatic surface is the site of the incompatibility reaction, which is expressed as delayed pollen germination and pollen tubes that are distorted and fail to penetrate the stigma.  We studied systemic gene expression during compatible and incompatible pollen-stigma interactions.  Styles of ‘Jefferson’ hazelnut  (S₁S₃) were pollinated with pollen of ‘Jefferson’ and ‘Tombul Ghiaghli’ (S₄S₈), giving incompatible and compatible reactions, respectively.  RNA-Seq data was obtained from an Illumima HiSeq 2000 sequencing and RNA extracted from styles at 0hr, 1hr, 3hr and 5hrs post-pollination.  The sequences were aligned to the 'Jefferson' hazelnut reference genome using Bowtie2.  Two methods were then used for pair-wise time point comparisons to quantify differential gene expression:  1) the Cufflinks/Cuffmerge/Cuffdiff programs from the “Tuxedo” bioinformatic pipeline, using default parameters, and  2) DESeq2 to fit generalized linear models to test for differential expression in compatible and incompatible pollinations at each of the four time points.  We compared the sets of differentially-expressed genes identified by these two methods.  Here, we report these results, and their implications for experimental design and statistical modeling.