Whereas Arabidopsis thaliana has been intensively investigated as a model plant, plants are so diversified to adapt various environmental conditions and also change their properties during breeding processes. Whereas molecular characterization of plant functions and molecular design of crops become more feasible with their genome data obtained by next generation sequencing (NGS) and genome editing technology, such as CRISPR-Cas9, large diversity of plants still needs new reference plants to focus on the specific plant structures and functions as reviewed in this special issue; 1) liverwort (Marchantia polymorpha) as a model to study plant biology based on its simplest genome structure (Kohchi and Nishihama), 2) Brachypodium distachyon, as a model temperate grass for wheat and barley, as well as a model for energy crops such as switchgrass and Miscanthus (Mochida et al.), 3) carnation (Dianthus caryophyllus L.), as a model of ornamental plants, whose studies are often hindered due to their high heterozygosity and polyploidy (Yagi), 4) cassava (Manihot esculenta Crantz) as a model and important tropical tuberous root crop for food security (Utsumi et al.), 5) tomato (Solanum lycoperisicum), as a model of plants that bear fleshy fruits and of plants belonging to Solanaceae family (Aoki). In this introduction, the importance of NGS in emerging model plants is also discussed in California poppy to study plant specific metabolism, such as alkaloid biosynthesis.

Marchantia polymorpha is a common species in liverwort (Marchantiophyta) that occupies the basalmost lineage of land plant evolution. M. polymorpha has a long history as a model plant, and the state-of-the-art drawings of those days were published for education in late 19th century. As the gametophyte generation (n) dominates over the sporophyte generation (2n) in the life cycle, it is simple and efficient to take genetic approaches with M. polymorpha. The genome project that is in progress in Joint Genome Institute, U.S.A., with international collaboration including Japanese laboratories. M. polymorpha has relatively a simple genome context with low genetic redundancy and with fewer repetitive sequences, but possesses most genes for genetic regulatory networks that are common to other groups of land plants. With rapid and efficient methods of Agrobacterium-mediated transformation to sporelings and thalli, various molecular approaches for functional analysis of genes, including T-DNA tagging, expression modification, homologous recombination, genome editing and conditional expression, are available for research. M. polymorpha should offer a unique experimental platform to study the evolution and logics of regulatory systems in land plants.

Brachypodium distachyon, which belongs to the subfamily Pooideae, has recently been studied extensively as a model temperate grass. Since Brachypodium possesses type II cell wall, which is a structural characteristic of Poaceae plants, and is also found in energy crops, such as switchgrass and Miscanthus, as cellulose biomass resources, it has been proposed as a model plant in grass biomass research. In addition, Brachypodium is included in the Pooideae subfamily together with wheat and barley, and therefore, it could be promising to study biological functions related to agronomically important traits, such as seed development and flowering, in Triticeae crops. Brachypodium represents tractable features as a model plant ; small plant size, healthy growth inside laboratory conditions, without any requirement of any specific instruments, short life cycle, small genome size (272 Mb), and availability of transformation. Following the completion of whole-genome sequencing in 2010, various resources for Brachypodium research have been developed world wide. In this review, we introduce the current trends in Brachypodium research as well as provide prospects and expected functionalities of the model grass.

New ornamental cultivars are commonly produced by hybridization between elite cultivars and are propagated vegetatively; therefore, the genetic background of most ornamentals is highly heterozygous, with polyploidy also observed in some species. This situation complicates detailed genetic analysis using crossing populations; consequently, the development of sophisticated breeding strategies and genomic research using the information in ornamentals has lagged behind those in other crops. However, the advent of next generation sequencing technology has changed this. Carnation (Dianthus caryophyllus L.) is one of the most popular ornamentals worldwide, along with chrysanthemum and rose. Carnation has various flower colors and flower patterns that attract consumers. Carnation has a relatively small, diploid genome, making it a suitable plant material to conduct genomic analysis compared with other ornamentals that have high ploidy levels or large genome sizes. To understand the genetic systems of carnation and to accelerate molecular breeding, we sequenced the whole genome of carnation for the first time in ornamentals. The generated information and material resources for the carnation genome should enhance both fundamental and applied studies of carnations and related plants. In this review, I will summarize the carnation genome sequencing project and provide a future prospectus for genomic study in ornamentals.

Cassava (Manihot esculenta Crantz) is one of the most important crops in tropical and subtropical area. The starch production in cassava tuberous roots is of importance for food security, feeding livestock and income generation for poor farmers in Asian and African countries. Cassava starch is also utilized for efficient source of foods and industrial materials such as modified starch, sweetness, paste and bioethanol. As there are many advantages and high-potential in cassava, cassava functional genomics platform has been developed by various researchers for the last decade. Our RIKEN group has established a cassava functional genomics platform, which includes full-length cDNAs, DNA microarrays, Agrobacterium-mediated transformation, database, and has advanced cassava molecular breeding through development of heavy-ion beam mutagenenized population and genetic transformation in collaboration with the Agricultural Genetics Institute (AGI, Vietnam), Mahidol University (Thailand) and the International Center for Tropical Agriculture (CIAT). In this review, we summarize the present status and future perspectives of our cassava functional genomics approaches towards cassava improvement.

Tomato (Solanum lycopersicum) has been regarded as a model of plants that bear fleshy fruits, and of plants belonging to Solanaceae family. Various resources have been developed to elucidate the mechanisms underlying control of fruit quality as well as quantity, and also to elucidate how genomic diversity links to phenotypic diversity. The tomato reference genome sequence published in 2012 uncovered the evolutionary history of tomato genome which conferred functional diversity to tomato genes. Availability of various tomato variety has huge potential to elucidate the correlation between DNA sequence and phenotype in high resolution by comparative genome analysis. In this mini-review, I will first overview what we have learned from the tomato genome sequencing followed by a deluge of genome resequencing. In the second part, I will briefly refer to the post-genome perspectives in tomato research, with a specific focus on the use of tomato plant in the development of New Plant Breeding Techniques.

We investigated the degrees of chlorin ring deformations of the special pair chlorophylls P_<D1>/P_<D2> in the Photosystem II (PSII) crystal structure, using a quantum mechanical/molecular mechanical approach. We found that (i) the out-of-plane distortion of the PD1 chlorin ring can be described predominantly by a large "doming mode" arising from the axial ligand D1-His198. In contrast, (ii) the deformation of PD2 was caused by a "saddling mode" arising from the D2-Trp191 side chain and the axial ligand D2-His197. However, (iii) the redox potential difference between P_<D1> and P_<D2> was predominantly determined by the PSII electrostatic environment rather than by the degree of the chlorin-ring distortion. (iv) The chlorin ring deformation appears to simply originate from the local steric protein environment of PSII.

Offspring with non-parental phenotypes is often observed from biallelic genes in diploid eukaryotic organisms. Heterosis arises from allelic interactions between parental genomes and progeny of intra- or inter-species cross exhibit greater biomass, speed of development, and stress tolerance than parental lines. Although numerous studies have been carried out to understand its genetic and/or molecular basis, the molecular mechanisms underlying heterosis and heterotic gene activity remain elusive. Recent advances in technical innovations for whole-genome/epigenome analyses have accelerated understanding of mechanisms underling heterosis. In this review, we introduce the overview of heterosis and heterotic patterns in Arabidopsis and discuss the correlation between epigenetic/genetic alteration and heterosis.

Polyamines (PAs) are aliphatic compounds with low molecular masses. The major PAs are the diamine putrescine, the triamine spermidine, and the tetraamines, spermine and thermospermine in plants. PAs play crucial roles not only in growth, development and longevity but also in adaptive responses against abiotic and biotic stresses. In the last decade information on plant PAs has been accumulated. Here I summarize the current state of knowledge, with a focus on polyamine synthesis and catabolism pathways, and introduce the evidence that putrescine and spermidine are essential for plant growth. Lastly I describe that all the Arabidopsis loss-of-function mutants which are involved in thermospermine metabolism display growth defect. Therefore I further discuss the importance of thermospermine homeostasis in this organism.

Root parasitic weeds, Striga spp., Orobanche spp. and Phelipanche spp., are one of the destructive agricultural weeds and an effective parasite control strategy is desired. We revealed that a galactosyl-sucrose trisaccharide, planteose is immediately decreased in germinating seeds of Orobanche minor, and hypothesized that this metabolism is important for germination of root parasitic weeds. Glycosidase inhibitors which affect planteose metabolism were screened and nojirimycin bisulfite (NJ) was found to selectively inhibit germination of O. minor and to interfere with planteose metabolism by inhibiting sucrose degradation. The inhibitory effect of NJ on germination was cancelled by addition of glucose. The activities of sucrose hydrolyzing enzymes, invertases were lower in the NJ-treated seeds than those in germinating seeds. We concluded that NJ inhibits the germination by blocking the supply of essential glucose from sucrose in the planteose metabolic pathway by inhibiting invertase activation. The planteose metabolic pathway could be a new target for selective control of the parasites.

Function of mixture of compounds was added to thin-layer chromatography (TLC), which is originally developed for separation of compounds. When samples are slantingly and crossly loaded on TLC, each compound is symmetrically developed at a line from the upper origin to individual Rf value and the developed line crosses each other. This cross-TLC system enables simultaneous performance of separation and orderly mixture of compounds. Copigments are colorless organic compounds that can modify coloration of anthocyanin pigments to more intense and bluer. The cross-TLC was used to easily and comprehensively detect copigment, where occurrence of copigments can be indicated by coloration change on anthocyanin develop lines. By using the cross-TLC, a structurally and functionally novel copigment was detected as well as conventional copigments.

Studies on high-temperature injury and cool-weather damage in crops, wheat, barley and rice have a long history, and have identified physiological responses including abnormal abortion of developing pollen followed by male sterility. However, a full understanding of the molecular mechanism has not been achieved. We here show that endogenous auxin levels specifically decreased in the developing anthers of barley and Arabidopsis under high temperature conditions. Similarly, endogenous gibberellin levels significantly reduced in the developing anthers of rice by decreasing temperatures. In addition, the temperature fluctuations repressed each gene expression of auxin biosynthesis genes, YUCCA yuc-2 and yuc-6, and gibberellin biosynthesis genes, GA20ox3 and GA3ox1. These set of genes are dominantly expressed in the developing anthers indicating that at least auxin and gibberellin are synthesized in the anthers. It may lead to susceptibility to male sterility in temperature stress.