Submitted to: Functional and Integrative Genomics
Publication Type: Peer reviewed journal
Publication Acceptance Date: 1/31/2008
Publication Date: 4/15/2008
Publication URL: www.springerlink.com/content/cn67678u46506857/fulltext.html
Citation: Hu, P., Wise, R.P. 2008. Diversification of Lrk/Tak Kinase Gene Clusters is Associated with Subfunctionalization and Cultivar-specific Transcript Accumulation in Barley. Functional and Integrative Genomics. 8:199-209. Available: http://www.springerlink.com/content/cn67678u46506857/fulltext.html. Interpretive Summary: Gene duplication plays an important role in speciation and diversification of plants and animals. Various plant gene families have been amplified as compared with their animal counterparts. Receptor like kinase (RLK) genes are a key example of this contrast. RLKs play various roles in plant cells such as hormone signaling, meristem development, cell differentiation, pollen recognition, and pathogen defense. Lrk (Lr10 receptor-like kinase)/Tak (Triticum aestivum kinase) genes identified from wheat, barley, rice, and maize exhibit colinearity among grass species, implying that they arose from a common ancestry prior to grass speciation. In this report, we identified three high-density Lrk/Tak-like, receptor kinase clusters in barley, which were then compared with their homologs in wheat and rice. Results of this analysis suggest that tandem duplication followed by subfunctionalization are the primary mechanisms for the extensive expansion of this gene family in the Poaceae. RLK kinases are important signaling genes in development and pathogen defense. The propensity for expansion of this gene family in cereal crops predicts that emerging information on the regulation of these genes has important applications for researchers working in crop improvement.
Technical Abstract: Lrk (Lr10 receptor-like kinase) and Tak (Triticum aestivum kinase) belong to the receptor-like kinase (RLK) super-gene family in higher plants. Three Lrk/Tak gene regions spanning greater than 600 kb were identified via a genome-wide survey of barley gene-rich BAC (Bacterial Artificial Chromosome) clones. Two Lrk/Tak gene clusters are positioned on barley chromosome 3 (3H) and another is localized on chromosome 5 (1H), with each Lrk and Tak open reading frame physically positioned in a back-to-back orientation. Thirteen new Lrk/Tak-like fragments were cloned from the two clusters on 3H and the single cluster on 1H, respectively, and compared phylogenetically with other grass Lrk/Tak-like genes, including a 280 kb Lrk/Tak cluster on rice chromosome 1S. Physically clustered Lrk/Tak-like genes always form monophyletic groups; this suggests that the primary mechanism of expansion of the Lrk/Tak RLK super family was by tandem duplication, of which most members were duplicated after speciation of the Poaceae. Cultivar-dependent transcript accumulation, as revealed via Barley1 GeneChip microarray analysis, is consistent with the hypothesis of subfunctionalization of Lrk/Tak members following tandem duplication.