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1.  And Baby Makes Three: Genomic Imprinting in Plant Embryos 
PLoS Genetics  2013;9(12):e1003981.
PMCID: PMC3854966  PMID: 24339794
2.  A role for BELLRINGER in cell wall development is supported by loss-of-function phenotypes 
BMC Plant Biology  2012;12:212.
Homeodomain transcription factors play critical roles in metazoan development. BELLRINGER (BLR), one such transcription factor, is involved in diverse developmental processes in Arabidopsis, acting in vascular differentiation, phyllotaxy, flower and fruit development. BLR also has a redundant role in meristem maintenance. Cell wall remodelling underpins many of these processes, and BLR has recently been shown to regulate expression of PECTIN METHYL-ESTERASE 5 (PME5), a cell wall modifying enzyme in control of phyllotaxy. We have further explored the role of BLR in plant development by analysing phenotypes and gene expression in a series of plants over-expressing BLR, and generating combinatorial mutants with blr, brevipedicellus (bp), a member of the KNOX1 family of transcription factors that has previously been shown to interact with blr, and the homeodomain transcription factor revoluta (rev), required for radial patterning of the stem.
Plants over-expressing BLR exhibited a wide range of phenotypes. Some were defective in cell size and demonstrated misregulation of genes predominantly affecting cell wall development. Other lines with more extreme phenotypes failed to generate lateral organs, consistent with BLR repressing transcription in the shoot apex. Cell wall dynamics are also affected in blr mutant plants, and BLR has previously been shown to regulate vascular development in conjunction with BP. We found that when bp and blr were combined with rev, a set of defects was observed that were distinct from those of bp blr lines. In these triple mutants xylem development was most strikingly affected, resulting in an almost complete lack of vessels and xylem parenchyma with secondary thickening.
Our data support a role for BLR in ordering the shoot apex and, in conjunction with BP and REV, playing a part in determining the composition and organisation of the vascular system. Microarray analysis strongly indicates that the striking vascular phenotypes of blr bp rev triple mutants and plants over-expressing BLR result from the misregulation of a suite of genes, targets of BLR in wild type plants, that determine cell size and structure in the developing vasculature.
PMCID: PMC3538058  PMID: 23148846
3.  Balance between maternal and paternal alleles sets the timing of resource accumulation in the maize endosperm 
Key aspects of seed development in flowering plants are held to be under epigenetic control and to have evolved as a result of conflict between the interests of the male and female gametes (kinship theory). Attempts to identify the genes involved have focused on imprinted sequences, although imprinting is only one mechanism by which male or female parental alleles may be exclusively expressed immediately post-fertilization. We have studied the expression of a subset of endosperm gene classes immediately following interploidy crosses in maize and show that departure from the normal 2 : 1 ratio between female and male genomes exerts a dramatic effect on the timing of expression of some, but not all, genes investigated. Paternal genomic excess prolongs the expression of early genes and delays accumulation of reserves, while maternal genomic excess foreshortens the expression period of early genes and dramatically brings forward endosperm maturation. Our data point to a striking interdependence between the phases of endosperm development, and are consonant with previous work from maize showing progression from cell proliferation to endoreduplication is regulated by the balance between maternal and paternal genomes, and from Arabidopsis suggesting that this ‘phasing’ is regulated by maternally expressed imprinted genes. Our findings are discussed in context of the kinship theory.
PMCID: PMC2842618  PMID: 19793746
endosperm; imprinting; interploidy crosses; kinship theory; maize (Zea mays); plant fertilization
4.  MicroRNA and tasiRNA diversity in mature pollen of Arabidopsis thaliana 
BMC Genomics  2009;10:643.
New generation sequencing technology has allowed investigation of the small RNA populations of flowering plants at great depth. However, little is known about small RNAs in their reproductive cells, especially in post-meiotic cells of the gametophyte generation. Pollen - the male gametophyte - is the specialised haploid structure that generates and delivers the sperm cells to the female gametes at fertilisation. Whether development and differentiation of the male gametophyte depends on the action of microRNAs and trans-acting siRNAs guiding changes in gene expression is largely unknown. Here we have used 454 sequencing to survey the various small RNA populations present in mature pollen of Arabidopsis thaliana.
In this study we detected the presence of 33 different microRNA families in mature pollen and validated the expression levels of 17 selected miRNAs by Q-RT-PCR. The majority of the selected miRNAs showed pollen-enriched expression compared with leaves. Furthermore, we report for the first time the presence of trans-acting siRNAs in pollen. In addition to describing new patterns of expression for known small RNAs in each of these classes, we identified 7 putative novel microRNAs. One of these, ath-MIR2939, targets a pollen-specific F-box transcript and we demonstrate cleavage of its target mRNA in mature pollen.
Despite the apparent simplicity of the male gametophyte, comprising just two different cell types, pollen not only utilises many miRNAs and trans-acting siRNAs expressed in the somatic tissues but also expresses novel miRNAs.
PMCID: PMC2808329  PMID: 20042113
5.  When Genomes Collide: Aberrant Seed Development Following Maize Interploidy Crosses 
Annals of Botany  2008;101(6):833-843.
Background and Aims
The results of wide- or interploidy crosses in angiosperms are unpredictable and often lead to seed abortion. The consequences of reciprocal interploidy crosses have been explored in maize in detail, focusing on alterations to tissue domains in the maize endosperm, and changes in endosperm-specific gene expression.
Following reciprocal interploidy crosses between diploid and tetraploid maize lines, development of endosperm domains was studied using GUS reporter lines, and gene expression in resulting kernels was investigated using semi-quantitative RT-PCR on endosperms isolated at different stages of development.
Key Results
Reciprocal interploidy crosses result in very small, largely infertile seeds with defective endosperms. Seeds with maternal genomic excess are smaller than those with paternal genomic excess, their endosperms cellularize earlier and they accumulate significant quantities of starch. Endosperms from the reciprocal cross undergo an extended period of cell proliferation, and accumulate little starch. Analysis of reporter lines and gene expression studies confirm that functional domains of the endosperm are severely disrupted, and are modified differently according to the direction of the interploidy cross.
Interploidy crosses affect factors which regulate the balance between cell proliferation and cell differentiation within the endosperm. In particular, unbalanced crosses in maize affect transfer cell differentiation, and lead to the temporal deregulation of the ontogenic programme of endosperm development.
PMCID: PMC2710208  PMID: 18276791
Fertilization; interploidy crosses; endosperm; maize; Zea mays; imprinting; epigenetics; gene dosage; seed development
6.  Imprinting in the endosperm: a possible role in preventing wide hybridization. 
Reproductive isolation is considered to play a key part in evolution, and plants and animals have developed a range of strategies that minimize gene flow between species. In plants, these strategies involve either pre-zygotic barriers, such as differences in floral structure and pollen-stigma recognition, or post-zygotic barriers, which are less well understood and affect aspects of seed development ranging from fertilization to maturation. In most angiosperms, a double fertilization event gives rise to a zygote and the endosperm: a triploid tissue with an unequal parental genomic contribution, which, like the placenta of mammals, provides reserves to the developing embryo. Interestingly, many aspects of endosperm development, again like the placenta, are regulated by a range of epigenetic mechanisms that are globally termed imprinting. Imprinted genes are characterized by their uniparental expression, the other parental allele being silenced. Normal development of the endosperm thus requires a highly specific balance of gene expression, from either the maternal or paternal genomes. Any alteration of this balance resulting from changes in allelic copy number, sequence or epigenetic imprints can cause endosperm failure and eventual seed abortion. In its widest sense, the endosperm thus serves as an accurate 'sensor' of compatibility between parents. A first step in understanding this important, yet complex system must clearly be the isolation and characterization of as wide a range as possible of imprinted genes.
PMCID: PMC1693205  PMID: 12831476

Results 1-6 (6)