Natural genetic variation and gene expression patterns underlying lateral shoot (tiller) development in barley (Hordeum vulgare L)

University of Minnesota Ph.D. dissertation.December 2018. Major: Plant and Microbial Biology. Advisor: Gary Muehlbauer. 1 computer file (PDF); xxv, 239 pages + 2 zip files of supplementary tables.The main shoot and other above-ground tissues develop from the shoot apical meristem (SAM), including axillary meristems (AXM) from which lateral branches develop. In barley, lateral branches called tillers contribute directly to grain yield and define shoot architecture. Two studies were completed to gain a better understanding of the genetic control of tiller development. One focused on characterizing natural phenotypic and genetic variation in tiller number throughout development in a large, diverse germplasm collection; and the second focused on identifying meristem-specific genes and characterizing gene expression patterns that varied by meristem type (SAM or AXM) and morphological stage. Results from the first study revealed that correlations between tiller development (tillering) and factors previously shown to influence tiller development, like photoperiod response and spike row-type, varied depending on environment and genetic background. Furthermore, no major trade-offs existed between tiller number and other traits, and natural genetic variation associated with tillering largely overlapped variation associated with days to heading and spike row-type. Results of the second study revealed a set of genes upregulated in most meristems compared to non-meristem tissues, many of which have been characterized in other species and are likely important for general meristem maintenance or function. Results also suggested that gene expression was primarily differentiated by genotype, meristem type, and morphological stage; however, expression profiles of SAM and AXM were very similar at later developmental stages. A small number of genes were only expressed in SAM or AXM, and clustering based on expression across all meristems revealed genes upregulated in AXM that may be important for tiller development, as some, like UNICULME4 and INTERMEDIUM-C (TEOSINTE BRANCHED 1 ortholog) have already been implicated in tiller development. Genes that were upregulated in ligules compared to leaves were also identified, and clustering of these genes revealed some that were expressed more highly in ligules and AXM that may, as in other species, have dual functions in leaf and tiller development