WOX Gene Phylogeny in Poaceae: A Comparative Approach Addressing Leaf and Embryo Development

Abstract

The phylogeny based on the homeodomain (HD) amino acid sequence of the WOX (WUSCHEL-related homeobox gene family) was established in the 3 major radiations of the Poaceae family: Pooideae (Brachypodium distachyon), Bambusoideae (Oryza sativa), and Panicoideae (Zea mays). The genomes of all 3 grasses contain an ancient duplication in the WOX3 branch, and the cellular expression patterns in maize and rice indicate subfunctionalization of paralogues during leaf development, which may relate to the architecture of the grass leaf and the encircling of the stem. The use of maize WOX gene family members as molecular markers in maize embryo development for the first time allowed us to visualize cellular decisions in the maize proembryo, including specification of the shoot/root axis at an oblique angle to the apical-basal polarity of the zygote. All molecular marker data are compatible with the conclusion that the embryonic shoot/root axis comprises a discrete domain from early proembryo stages onward. Novel cell fates of the shoot and the root are acquired within this distinct morphogenic axis domain, which elongates and thus separates the shoot apical meristem and root apical meristem (RAM) anlagen in the maize embryo.

Ontogeny of the Maize Shoot Apical Meristem

“…Whereas WOX2 functions in the apical embryo domain, WOX5 and NUC homologs accumulate in the basal regions of developing embryos, where they eventually specify distinct root domains (Haecker et al, 2004;Levesque et al, 2006;Nardmann et al, 2007). These root-specific transcription factors were probably detected in our transition-stage samples because these microdissected domains included both the apical and basal regions of the embryo ( Figures 1N and 1T), whereas only shoot domains were isolated from later stages.…”

“…In Arabidopsis, WOX2 and WOX9 (also known as STIMPY) are also expressed before SAM initiation and specify the apical-basal axis of the embryo (Haecker et al, 2004;Wu et al, 2007;Breuninger et al, 2008). Previous reports in maize revealed that WOX2A transcripts accumulate in the apical cap of the proembryo before localizing to the germinal face of the transition-stage embryo (Nardmann et al, 2007). The accumulation of WOX2A and WOX9B transcripts in the premeristematic maize proembryo is consistent with a conserved function of these WOX putative paralogs in establishing apicalbasal domains in the maize embryo before SAM initiation.…”

“…Transcripts encoding transcription factors that are known to function during organogenesis and that are not detected in the proembryo include members of the YABBY (six), GROWTH-REGULATING FACTOR (GRF, four), and NO APICAL MERISTEM/ CUP-SHAPED COTYLEDON (four) gene families (the numbers in parentheses represent the number of transcripts in that gene family) as well as two additional WOX transcripts (Aida et al, 1999;Kim et al, 2003;Vroemen et al, 2003;Juarez et al, 2004;Zimmermann and Werr, 2005;Nardmann et al, 2007;Zhang et al, 2008;Sarojam et al, 2010;Santa-Catarina et al, 2012). Previous studies in Arabidopsis and maize demonstrated that YABBY genes are expressed in leaf and floral anlagen and in the marginal tips of leaf and floral primordia (Siegfried et al, 1999;Juarez et al, 2004).…”

“…Among these are four transcripts encoding known stem cell regulators, including three CLASS I KNOX genes and a GATA domain protein homologous to HANABA TARANU in Arabidopsis (Figures 4C and 4D; see Supplemental Data Set 8 online) Zhao et al, 2004;Mukherjee et al, 2009;reviewed in Hay and Tsiantis, 2010). Upregulated transcripts encoding proteins that function in organogenesis and cell proliferation of lateral organs include WUSHEL-RELATED HOMEOBOX3A (WOX3A), the YABBY gene DROOPING LEAF2 (DL2), the lateral organ boundary gene INDETERMINATE GA-METOPHYTE1 (IG1), and two GRF-LIKE transcripts (Kim et al, 2003;Nardmann et al, 2004;Yamaguchi et al, 2004;Evans, 2007;Nardmann et al, 2007;Zhang et al, 2007;Zhang et al, 2008). In addition to three AUXIN RESPONSE FACTOR (ARF) class transcription factors, several transcripts that encode hormone biosynthetic proteins are also upregulated in stage 14 SAMs, including seven gibberellin metabolic transcripts implicated in lateral organ growth and development.…”

“…Several transcripts encoding transcription factors implicated in apical-basal patterning of the embryo were upregulated during the transition stage, including WOX2A, WOX5B, and NUT-CRACKER (NUC; Haecker et al, 2004;Levesque et al, 2006;Nardmann et al, 2007). Whereas WOX2 functions in the apical embryo domain, WOX5 and NUC homologs accumulate in the basal regions of developing embryos, where they eventually specify distinct root domains (Haecker et al, 2004;Levesque et al, 2006;Nardmann et al, 2007).…”