Seed development in Arabidopsis thaliana undergoes an initial phase of endosperm proliferation followed by a second phase in which the embryo grows at the expense of the endosperm. As mature seed size is largely attained during the initial phase, seed size is coordinately determined by the growth of the maternal ovule, endosperm, and embryo. Here, we identify SHORT HYPOCOTYL UNDER BLUE1 (SHB1) as a positive regulator of Arabidopsis seed development that affects both cell size and cell number. shb1-D, a gain-of-function overexpression allele, increases seed size, and shb1, a loss-of-function allele, reduces seed size. SHB1 is transmitted zygotically. The increase in shb1-D seed size is associated with endosperm cellurization, chalazal endosperm enlargement, and embryo development. SHB1 is required for the proper expression of two other genes that affect endosperm development, MINISEED3 (MINI3) and HAIKU2 (IKU2), a WRKY transcription factor gene and a leucine-rich repeat receptor kinase gene. SHB1 associates with both MINI3 and IKU2 promoters in vivo. SHB1 may act with other proteins that bind to MINI3 and IKU2 promoters to promote a large seed cavity and endosperm growth in the early phase of seed development. In the second phase, SHB1 enhances embryo cell proliferation and expansion through a yet unknown IKU2-independent pathway. INTRODUCTIONIn angiosperms, double fertilization leads to the formation of a diploid embryo and a triploid endosperm, as the endosperm arises from the central cell that contains two identical haploid genomes. The endosperm constitutes the major volume of the mature seed in monocots and some dicots. In Arabidopsis thaliana and many other dicots, seed development is marked by two distinct phases (Sundaresan, 2005). In an initial phase, rapid growth and proliferation of the endosperm results in a large increase in size (Boisnard-Lorig et al., 2001). Then, embryo growth takes place at the expense of endosperm during the second phase. At maturity, the seed contains only a single layer of endosperm cells, and the maternal integument ultimately becomes the seed coat (Scott et al., 1998;Garcia et al., 2003). Seed coat formation and endosperm growth precede embryo growth in Arabidopsis, and the seed reaches almost its final size before the enlargement of the embryo. Therefore, seed size is determined by the coordinated growth of the diploid embryo, the triploid endosperm, and the diploid maternal ovule.Both maternal and nonmaternal factors are involved in seed size regulation (Garcia et al., 2005). In Arabidopsis, an increased dosage of the paternal genome in the endosperm increases seed size, whereas an increased dosage of the maternal genome reduces seed size, with delayed cellularization of the peripheral endosperm and hypertrophy of the chalazal endosperm and associated nodules (Scott et al., 1998). Mutations in DNA METHYLTRANSFERASE1 (MET1) and DECREASE IN DNA METHYLATION1 (DDM1) dramatically reduce DNA methylation and cause parent-of-origin effects on F1 seed size (Xiao et al., 2006). Poll...

The control of the location and activity of stem cells depends on spatial regulation of gene activities in the stem cell niche. Using computational and experimental approaches, we have tested and found support for a hypothesis for gene interactions that specify the apical stem cell population. The hypothesis explains how the WUSCHEL gene product, synthesized basally in the meristem, induces-expressing stem cells in the meristem apex but, paradoxically, not in the basal domain where itself is expressed. The answer involves the activity of the small family of genes, which prevent the activation of and which are expressed basally in the shoot meristem.

SUMMARYPlant stem cells in the shoot apical meristem (SAM) and root apical meristem (RAM) provide for postembryonic development of above-ground tissues and roots, respectively, while secondary vascular stem cells sustain vascular development1–4. WUSCHEL (WUS), a homeodomain transcription factor expressed in the rib meristem of the SAM, is a key regulatory factor controlling stem cell populations in the Arabidopsis SAM5–6 and is thought to establish the shoot stem cell niche via a feedback circuit with the CLAVATA3 (CLV3) peptide signaling pathway7. WUSCHEL-RELATED HOMEOBOX5 (WOX5), specifically expressed in root quiescent center (QC), defines QC identity and functions interchangeably with WUS in control of shoot and root stem cell niches8. WOX4, expressed in Arabidopsis procambial cells, defines the vascular stem cell niche9–11. WUS/WOX family proteins are evolutionarily and functionally conserved throughout the plant kingdom12 and emerge as key actors in the specification and maintenance of stem cells within all meristems13. However, the nature of the genetic regime in stem cell niches that centers on WOX gene function has been elusive, and molecular links underlying conserved WUS/WOX function in stem cell niches remain unknown. Here we demonstrate that the Arabidopsis HAIRY MERISTEM (HAM)family transcription regulators act as conserved interacting co-factors with WUS/WOX proteins. HAM and WUS share common targets in vivo and their physical interaction is important in driving downstream transcriptional programs and in promoting shoot stem cell proliferation. Differences in the overlapping expression patterns of WOX and HAM family members underlie the formation of diverse stem cell niche locations, and the HAM family is essential for all of these stem cell niches. These findings establish a new framework for the control of stem cell production during plant development.

The CLAVATA3 (CLV3)-CLAVATA1 (CLV1) ligand-receptor kinase pair negatively regulates shoot stem cell proliferation in plants. clv1 null mutants are weaker in phenotype than clv3 mutants, but the clv1 null phenotype is enhanced by mutations in the related receptor kinases BARELY ANY MERISTEM 1, 2 and 3 (BAM1, 2 and 3). The basis of this genetic redundancy is unknown. Here, we demonstrate that the apparent redundancy in the CLV1 clade is in fact due to the transcriptional repression of BAM genes by CLV1 signaling. CLV1 signaling in the rib meristem (RM) of the shoot apical meristem is necessary and sufficient for stem cell regulation. CLV3-CLV1 signaling in the RM represses BAM expression in wild-type Arabidopsis plants. In clv1 mutants, ectopic BAM expression in the RM partially complements the loss of CLV1. BAM regulation by CLV1 is distinct from CLV1 regulation of WUSCHEL, a proposed CLV1 target gene. In addition, quadruple receptor mutants are stronger in phenotype than clv3, pointing to the existence of additional CLV1/BAM ligands. These data provide an explanation for the genetic redundancy seen in the CLV1 clade and reveal a novel feedback operating in the control of plant stem cells.