Abstract
Vegetative axillary meristem (AXM) activity results in the production of branches. In barley (Hordeum vulgare L.), vegetative AXM develop in the crown and give rise to modified branches, referred to as tillers. Mutations in the barley low-tillering mutant uniculm2 block vegetative AXM development and prevent tiller development. The objectives of this work were to examine gene expression in wild-type and cul2 mutant plants, fine map the CUL2 gene, and to examine synteny in the CUL2 region in barley with rice. RNA profiling experiments using two near-isogenic line pairs carrying either the cul2 mutant allele or wild-type CUL2 allele in different genetic backgrounds detected 28 unique gene transcripts exhibiting similar patterns of differential accumulation in both genetic backgrounds, indicating that we have identified key genes impacted by the CUL2 gene. Twenty-four genes had higher abundance in uniculm2 mutant tissues, and nearly half of the annotated genes likely function in stress-response or signal transduction pathways. Genetic mapping identified five co-segregating markers in 1,088 F2 individuals. These markers spanned the centromere region on chromosome 6H, and coincided with a 50-cM region on rice chromosome 2, indicating that it may be difficult to positionally clone CUL2. Taken together, the results revealed stress response and signal transduction pathways that are associated with the CUL2 gene, isolating CUL2 via positional cloning approaches that may be difficult, and the remnants of barley–rice synteny in the CUL2 region.
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Acknowledgments
We thank J. Franckowiak, Department of Plant Sciences, North Dakota State University, Fargo, ND, for generously providing us seed for Bowman cultivar, and D. Rasmusson, Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, for seed for the Morex and Steptoe cultivars. Morex-cul2 was provided to us by Steve Dofing at Washington State University, Pullman, WA; Bowman-cul2 and cul2-rob1 were obtained from the USDA–ARS National Small Grain Germplasm Research Facility, Aberdeen, ID. Maria Muñoz-Amatriaín, Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, generously provided us with the updated barley SNP map data prior to publication. The University of Minnesota Supercomputing Institute for Advanced Computational Research provided computational resources, and GeneChip hybridizations were performed at the University of Minnesota BioMedical Genomics Center. This research was supported by a grant from the United States Department of Agriculture CSREES–NRI Plant Growth and Development program grant #2004-03440 to GJM.
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Fig. S1
Hierarchical clustering analysis of transcript patterns. Abundance patterns for individual samples from the different tissue types in wild-type barley and the cul2 mutant: a Morex and Morex-cul2, b Bowman and Bowman-cul2 (JPEG 92 kb)
Fig. S2
GO analysis of transcripts up-regulated in Bowman-cul2 versus Bowman. Up-regulated GO transcript categories that were over-represented in Bowman-cul2 versus Bowman were identified using the Singular Enrichment Analysis tool at AgriGO (http://www.bioinfo.cau.edu.cn/agriGO/. This figure does not include GO categories relating to cellular localization (JPEG 56 kb)
Fig. S3
GO analysis of transcripts up-regulated in Morex-cul2 versus Morex. Up-regulated GO transcript categories that were over-represented in Morex-cul2 versus Morex were identified using the Singular Enrichment Analysis tool at AgriGO (http://www.bioinfo.cau.edu.cn/agriGO/(JPEG 57 kb)
Table 1
Markers used for mapping (DOC 80 kb)
Table 2
Correlation coefficients of transcript abundance in four tissues (DOC 62 kb)
Table 3
Transcripts with at least 2-fold accumulation differences in mutant cul2 tissue compared to wild-type in the Morex background (XLS 280 kb)
Table 4
Transcripts with at least 2-fold accumulation differences in mutant cul2 tissue compared to wild-type in the Bowman background(XLS 302 kb)
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Okagaki, R.J., Cho, S., Kruger, W.M. et al. The barley UNICULM2 gene resides in a centromeric region and may be associated with signaling and stress responses. Funct Integr Genomics 13, 33–41 (2013). https://doi.org/10.1007/s10142-012-0299-7
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DOI: https://doi.org/10.1007/s10142-012-0299-7