Abstract

ABSTRACT

The characterization of the caleosin gene family in Triticeae
and their role in G-protein signalling
and
Identification and characterization of rye genes silenced
in allohexaploid triticale: A bioinformatic study


Hala Badr Abdel-Sadek Khalil, Ph.D.
Concordia University, 2013
The caleosin genes encode proteins with a single conserved EF hand calcium-binding domain and comprise small gene families found in a wide range of plant species. In this study, Clo3, a member of caleosin family in hexaploid wheat (Triticum aestivum), has been shown to play an important role in signaling by both in vivo and in vitro analyses of its interaction with Gα, the alpha subunit of heterotrimetric GTP binding protein. This interaction increased the GTPase activity of Gα by approximately 25%. Eleven paralogous groups of caleosins, which comprise a total of thirty-four caleosin genes, have been assembled and identified using the T. aestivum GenBank EST database and ten gene family members were assembled from Secale cereale 454-cDNA sequences. The analysis of caleosin gene expression was assayed by RNA-Seq analysis of 454 sequence sets and members of the gene family were found to have diverse patterns of gene expression in the nine tissues that were sampled in rye and in triticale, a synthetic polyploid species derived from durum wheat (Triticum turgidum) and rye (Secale cereale).
The impact of the polyploidization event on rye genes in the triticale background was investigated using both caleosin genes and whole transcriptome comparisons. The high-throughput cDNA sequence comparison between the diploid rye and the hexaploid triticale detected suppression of expression of approximately 2% of the rye genes surveyed in the triticale. The expression of 23503 rye cDNA contigs was analyzed in 454-cDNA libraries obtained from anther, root and stem from both triticale and rye as well as in five 454-cDNA data sets created from ovary, pollen, seed, seedling shoot and stigma from triticale. Among these, 112 rye cDNA contigs were found to be totally suppressed in all triticale tissues, although their expression was relatively high in rye tissues. Suppressed rye genes were found to have strikingly low similarity to their closest BASTN matches in a current draft of the wheat genome available through the International Wheat Genome Survey Consortium, IWGSC. The comparison of rye silenced genes to wheat database revealed that 89% of rye genes silenced in triticale do not have a best match in T. aestivum with sequence identity higher than 90%, whereas 59% of random rye contigs had a best hit of 90% or higher in T. aestivum. The comparisons to the draft genomes of Triticum. urartu, and Aegilops. tausshii, the A and D genome donors to T. aestivum, respectively, support the previous observation. PCR assays found that 6 out of 10 candidate suppressed genes were deleted from the triticale genome.