The synthesis and degradation of starch in plant leaves is a dynamic process that follows a daily cycle. During the day (light phase) starch is synthesized from the sucrose produced by photosynthesis and during the night (dark phase) the starch is degraded and used for both metabolism and export to sink organs. In this paper, the authors investigated the role of one of the isoforms of the starch synthesis enzymes, starch branching enzyme IIa (sbe2a), on transitory starch accumulation in leaves. The transitory starch in maize leaves is a branched polymer of glucose units mainly composed of amylopectin. The synthesis of amylopectin requires the action of starch branching enzymes (SBEs), of which, maize has three: SBEIa, SBEIIa and SBEIIb that show differential accumulation in leaves and endosperm. In this work, SBEIIa was shown to be the primary SBE responsible for the production of transitory starch granules in leaves that can be efficiently degraded during the night. In sbe2a mutants, the starch polymer is improperly branched leading to the formation of irregular granules. The authors hypothesize that the abnormally shaped granules are not properly degraded leading to hyperaccumulation of starch in leaves. Either due to the increased accumulation of starch or metabolic changes associated with more starch, sbe2a mutants show premature senescence and many hallmarks of programmed cell death. Thus SBEIIa is required for proper starch granule structure allowing for efficient diurnal cycling of transitory starch in leaves.

Yandeau-Nelson M, Laurens L, Shi Z, Xia H, Smith AM, Guiltinan M (2011) Starch Branching Enzyme IIa is required for proper diurnal cycling of starch in leaves of Zea mays. Plant Physiol 156:479-490 doi: 10.1104/pp.111.174094

Several of the most important advances in genetics made use of maize kernels containing anthocyanin pigments. For example, studies of spotted kernels led to the discovery of transposons. When these mobile genetic elements jump into or out of a gene required for anthocyanin synthesis, the result is a sector of the kernel with different pigmentation than the rest of the kernel (i.e. a spot). Anthocyanins are a family of purple or red pigments that accumulate in the aleurone layer of maize kernels. The anthocyanin biosynthetic pathway has been studied extensively at the genetic and biochemical levels and is an excellent model for understanding gene regulation. Mutants are available for every step in the pathway, all of the metabolic Intermediates are known and the genes for every step in the pathway have been isolated and characterized, except one. This paper describes the isolation and characterization of the only uncharacterized gene in the anthocyanin biosynthetic pathway. The Pr1 gene encodes a flavonoid 3-hydroxylase (F3H) that catalyzes the conversion of red anthocyanins to purple ones, so kernels lacking Pr1 activity are red. The authors took advantage of the maize genome sequence to identify a putative F3H gene and characterized several mutations in this gene to establish that it is responsible for Pr1 activity. Further, this gene complements an Arabidopsis mutant lacking F3H activity and is regulated by genes known to regulate the anthocyanin biosynthetic pathway. Taken together, these experiments provide convincing evidence that the gene characterized in this paper is Pr1 and constitutes the last step to be characterized at the molecular level of this pathway.

Sharma M, Cortes-Cruz M, Ahern K, McMullen M, Brutnell TP, Chopra S (2011) Identification of the Pr1 Gene Product Completes the Anthocyanin Biosynthesis Pathway of Maize. Genetics 188:69-79

Transposable elements (TEs) can rapidly increase in copy number, generating genome size differences between individuals of the same species, prime examples of which are cotton and rice. Zea luxurians and maize separated ~140,000 years ago, prior to maize domestication. The Z. luxurians genome is ~1.5 fold larger than the maize B73 genome. To determine if this recent evolutionary size difference is due to TE activity, Tenaillon et al used paired-end Illumina sequencing to survey the composition of the maize B73 and Z. luxurians genome. They found that both genomes have roughly ~85% TEs, and the types of different TEs and their relative distribution in the genome are highly conserved. TEs account for 70% of the size difference between the two genomes, with the other 30% of size difference still unaccounted for. The similarity in TE number and distribution is surprising, as TEs are the most dynamic part of the genome and it was expected that one or several TE families would show rapid amplification responsible for the genome size polymorphism. This study demonstrates that short-read deep sequencing can be a powerful tool in accessing the genic and TE composition of a genome. This powerful approach can be used to explore the genome size and TE content changes upon domestication and inbreeding in the maize lineage. Keith Slotkin, 2011

Tenaillon M, Hufford M, Gaut BS, Ross-Ibarra J (2011) Genome Size and Transposable Element Content as Determined by High-Throughput Sequencing in Maize and Zea luxurians. Genome Biology 3:219-229

This paper adds to the growing number of genes identified in maize that are critical for axillary meristem initiation. Interestingly, several of these genes are not known from Arabidopsis mutants, including Barren stalk1 (Ba1) and Barren stalk fastigiate1 (Baf1). baf1 mutants fail to produce ears in some genetic backgrounds, and when ears are produced in permissive backgrounds they are fused to the stalk suggesting that Baf1 is involved in both axillary meristem initiation and proper boundary formation. The authors show that Baf1 encodes a protein with an AT-hook DNA binding domain. The AT-hook family is present throughout the land plants, but is poorly characterized functionally. The BAF1 protein appears to be nuclear localized and can homodimerize, suggesting that it functions as a transcription factor. Baf1 is expressed in a narrow stripe of cells adaxial to initiating meristems, in a domain that is identical to Ba1. Interestingly, Baf1 expression in this domain requires Ba1 activity, suggesting that Ba1 and Baf1 act in a common pathway required for meristem initiation. However, baf1 mutants are much less severe that ba1 mutants indicating that other redundant factors are required to promote axillary meristem initiation downstream of Ba1. That orthologous mutants are not known in Arabidopsis demonstrates the utility of maize genetics in spite of high levels of redundancy. It will be interesting to further link Baf1 and Ba1 function with what is known about auxin-mediated axilary meristem initiation.

Gallavotti A, Malcomber S, Gaines C, Stanfield S, Whipple C, Kellogg EA, Schmidt RJ (2011) BARREN STALK FASTIGIATE1 Is an AT-Hook Protein Required for the Formation of Maize Ears. Plant Cell 0:doi: 10.1105/tpc.111.084590

I think about grain tissues and proteins in these tissues a lot and I was fairly comfortable with my understanding of the roles of these tissues and proteins until I read this paper. Starchy endosperm provides nutrition to the germinating seedling by accumulating starch and seed storage proteins such as zeins. On germination, the (usually) single cell layer on the outside of the endosperm called the aleurone makes hydrolytic enzymes that degrade these storage compounds to provide energy and metabolites to the germinating seedling. The authors of this paper demonstrate that like starchy endosperm, aleurone cells accumulate seed storage proteins (although at a lower level than starchy endosperm). What are these proteins doing in there? A reasonable explanation proposed by the authors is that they serve as a source of reduced nitrogen and carbon for the synthesis of hydrolytic enzymes by aleurone cells. The cell biology resulting in accumulation of seed storage proteins in aleurone cells is particularly interesting. In starchy endosperm, seed storage proteins accumulate in endplasmic reticulum-derived protein bodies, while in aleurone they accumulate protein storage vacuoles. An elegant set of micrographic experiments involving fluorescently-tagged proteins and antibody markers to subcellular marker proteins suggests that seed storage proteins arrive at aleurone protein storage vacuoles by a novel pathway. This pathway may help explain how the storage proteins of other cereals are deposited.

Reyes F, Chung T, Holding DR, Jung R, Vierstra RD, Otegui Marisa (2011) Delivery of Prolamins to the Protein Storage Vacuole in Maize Aleurone Cells. Plant Cell 23:769-784

Plants flower in response to a combination of internal and external cues that regulate production of a mobile floral-promoting signal called florigen. Key experiments in tomato, rice and Arabidopsis in the last several years have produced convincing evidence that proteins with homology to phosphatidylethanolamine binding proteins (PEBPs) encoded by the FLOWERING LOCUS T (FT) gene in Arabidopsis and related genes in other species have florigenic activity. FT-like genes with floral-promoting activity have been identified in a growing number of plant species but, until recently, maize was not counted among them. This is no longer the case. Meng and co-authors have identified one of the 16 maize FT-like genes, called Zea mays CENTRORADIALAS (ZCN), as possessing florigenic activity using a number of experimental criteria. Their systematic approach showed ZCN8 has all the characteristics expected for a florigenic gene. Moreover, their analysis of the floral transition and ZCN8 expression in day-length sensitive tropical lines compared to insensitive temperate lines indicates the diurnal expression of ZCN8 plays a role in how flowering is controlled in response to photoperiod. An illuminating study, indeed!

Meng X, Muszynski MG, Danilevskaya O (2011) The FT-Like ZCN8 Gene Functions as a Floral Activator and Is Involved in Photoperiod Sensitivity in Maize. Plant Cell 0:doi: 10.1105/tpc.110.081406

The maize and sorghum genomes are both functionally diploid and contain ten chromosomes. However, the maize genome underwent a tetraploidy event sometime after the divergence of the maize and sorghum lineages. Many of the duplicate genes (homeologs) in maize have not been maintained. This gene loss combined with chromosomal rearrangements have created a dynamic maize genome that has winnowed the genes and chromosomes back to the ancestral chromosomal number. Interestingly, the gene loss did not occur equally among the subgenomes produced by the maize tetraploidy event. By comparison of syntenic regions of the maize and sorghum genomes, the authors of this paper show that the process of gene loss has been concentrated in one of the maize subgenomes. Furthermore, presence absence variation for genes in diverse maize and teosinte lines shows that polymorphism for gene loss appears to be more frequent in one genome suggesting that the process of gene loss in maize is ongoing. Finally, the authors show that among duplicate genes that have been maintained there are frequent expression differences among the subgenomes, with the same subgenome that frequently loses genes showing reduced expression levels. They suggest a mechanism whereby deletion rates are equal among both subgenomes, but purifying selection maintains genes from the dominant subgenome that exhibits higher expression.

Schnable J, Springer N, Freeling M (2011) Differentiation of the maize subgenomes by genome dominance and both ancient and ongoing gene loss. Proc Natl Acad Sci, USA 0:doi: 10.1073/pnas.1101368108

In this paper the authors take a radical approach to the assembly and ordering of genetic elements in a plant genome. They utilize technically diverse data types to order contigs and sequences in Barley. Flow sorting of chromosomes, next generation sequencing, SNP mapping, classical cytogenetics, and leveraging of other complete genomes in the cereals are used to provide a first pass at he order of genes in Barley. The article was startling not only for the value the research provides for genetic mapping and genome-enabled biology in Barley, but also for the implication that a similar approach (or subset of approaches) coudl be taken to improve the annotations of maize and other cereal genomes. Indeed, the approach could be used to generate a set of testable hypothesis for genome organization in any group of organisms for which multiple co-linear genomes are available. As crop genomics moves forward, the sort of genetic and bioinformatic flexibility shown in this paper may well lead to comparatively improving genome assembly and contig ordering.

Mayer KFX, Stein N (2011) Unlocking the Barley Genome by Chromosomal and Comparative Genomics. Plant Cell 0:doi: 10.1105/tpc.110.082537

The juggernaut continues in the molecular identification of maize auxin pathway genes by the Auxin EvoDevo project. The vt2 gene can now be added to the ever growing list of auxin biosynthesis or signaling genes identified that function in organogenesis in the maize shoot. Unlike Arabidopsis where many auxin pathway genes function redundantly, in maize, mutations in single genes have dramatic impacts on vegetative and reproductive development. vt2 mutants, similar to another auxin biosynthetic mutant sparse inflorescence1 (spi1), have reduced shoot growth and an almost completely barren inflorescence lacking most axillary meristems. The vt2 gene was shown to encode a co-ortholog of TRYPTOPHAN AMINOTRANSFERASE OF ARABIDOPSIS (TAA1), involved in Trp-dependent auxin biosynthesis. Double mutant analysis with spi1 indicated that, unlike previously thought, spi1 and vt2 likely function together in the same auxin biosynthesis pathway. Cloning of vt2 adds another gene to the rapidly expanding maize auxin pathway and adds to our understanding of the evolution of how auxin shapes plant development in different species. Mike Muszynski, 2011

Phillips K, Phillips K, Skirpan A, Liu X, Christensen A, Slewinski TL, Hudson C, Barazesh S, Cohen JD, Malcomber S, McSteen P, McSteen P (2011) vanishing tassel2 Encodes a Grass-Specific Tryptophan Aminotransferase Required for Vegetative and Reproductive Development in Maize. Plant Cell 0:doi: 10.1105/tpc.110.075267