ARS | Publication request: Comparison of Gene Expression in Leymus Tiller and Rhizome Meristems Using Heterologous Affymetrix Wheat and Barley Gene Chips

Submitted to: Plant and Animal Genome
Publication Type: Abstract Only
Publication Acceptance Date: October 15, 2006
Publication Date: January 15, 2007
Citation: Kaur, P., Mott, I.W., Bushman, B.S., Larson, S.R. 2007. Comparison of Gene Expression in Leymus Tiller and Rhizome Meristems Using Heterologous Affymetrix Wheat and Barley Gene Chips. Plant and Animal Genome.

Technical Abstract: Perennial Leymus wildrye tillers and rhizomes develop from similar underground axillary meristems, but display different response to gravity and perhaps other cues that govern branch angle and overall patterns of subterranean growth. Corresponding variation in growth habit is an important component of grass establishment, adaptation, perenniallity, and function. We used heterologous barley and wheat DNA microarrays and bulk segregate analysis to detect gene expression polymorphisms that may be associated with a major growth habit QTL located on homoeologous chromosome 3, using progeny of interspecific hybrids of caespitose L. cinereus and rhizomatous L. triticoides. Approximately 34% and 25% of the probe sets showed detectable signals on the barley and wheat arrays, respectively. Overall gene expression patterns of tiller and rhizomes were remarkably similar. Only 29 and 30 genes on barley and wheat gene chips respectively were found to have greater than two fold differential expression between Leymus tiller and rhizome tissues at p-value of 0.00l. Expression polymorphisms for eight of these genes, including several homologous Leymus rhizome ESTs, were validated by qRT-PCR. Three of the eight verified gene expression polymorphisms BLAST to a region on the long arm of rice chromosome 1L, which is homoeologous to the Leymus chromosome 3 rhizome QTLs. Genomic DNA STS-PCR markers derived from these gene expression polymorphisms will be used as genetic markers in fine-genetic mapping evaluations of the Leymus chromosome 3 rhizome QTL.