禾草模式植物二穗短柄草的研究进展

二穗短柄草（Brachypodium distachyon）是近来开发的一种温带禾草模式植物。它具有与粮食作物相同的许多生物学特性,可作为研究粮食作物生物学特性的模式实验植物。不同采集地的二穗短柄草具有高度的表观变异性,可帮助研究人员对这些生物学特性从表观到遗传的深入研究。二穗短柄草与其他重要经济作物如小麦、大麦及其他潜在能源植物一样同属于早熟禾亚科,使其成为研究这些重要经济作物无可非议的模式植物。近来,由于二穗短柄草基因组序列及其相关注释的完成,功能基因组学和其他实验技术手段的不断进步,二穗短柄草可为其他禾草类植物提供序列分析、基因表达和功能研究等诸多便利。本文综述了利用二穗短柄草作为模式植物来进行比较基因组学、生物学研究、转化和T—DNA突变等方面的最新研究进展。     

Recent Progress in Model Grass Brachypodium distachyon (Poaceae)

Brachypodium distachyon, recently developed model system for temperate grasses, exhibited many traits with cereal crops and proposed to be an experimental system to access the biological approach. These traits have shown a surprised degree of phenotypic variation in many collected accessions. Like some important economical cereals, Bdistachyon also belongs to subfamily Pooideae, which make it become an unquestionable model system to research the economically important crops, such as wheat, barley and several potential biofuel plants. Recently, genome sequence and annotation of Bdistachyon has been finished. Associated with the development of the functional genomics and other experimental resources establishment, Bdistachyon will provide a key resource for improving cereal crops and facilitate the approach of sequence analyze gene expression and functional resources available for a variety of species. In this article we review and assess the current progress of Bdistachyon as a model system and then focus specifically on recent studies of comparative genomics, biological improvement, transformation and T DNA mutations.     

Did gene family expansions during the Eocene–Oligocene boundary climate cooling play a role in Pooideae adaptation to cool climates?

Adaptation to cool environments is a common feature in the core group of the grass subfamily Pooideae (Triticeae and Poeae). This suggest an ancient evolutionary origin of low temperature stress tolerance dating back prior to the initiation of taxonomic divergence of core Pooideae species. Viewing the Pooideae evolution in a palaeo‐climatic perspective reveals that taxonomic divergence of the core Pooideae group initiated shortly after a global super‐cooling period at the Eocene–Oligocene boundary (～33.5–26 Ma). This global climate cooling altered distributions of plants and animals and must have imposed selection pressure for improved low temperature stress responses. Lineage‐specific gene family expansions are known to be involved in adaptation to new environmental stresses. In Pooideae, two gene families involved in low temperature stress response, the C‐repeat binding factor (CBF) and fructosyl transferase (FT) gene families, has undergone lineage‐specific expansions. We investigated the timing of these gene family expansions by molecular dating and found that Pooideae‐specific expansion events in CBF and FT gene families took place during Eocene–Oligocene super‐cooling period. We hypothesize that the E–O super‐cooling exerted selection pressure for improved low temperature stress response and frost tolerance in a core Pooideae ancestor, and that those individuals with multiple copies of CBF and FT genes were favoured.     

Brachypodium distachyon. A New Model System for Functional Genomics in Grasses

A new model for grass functional genomics is described based on Brachypodium distachyon, which in the evolution of the Pooideae diverged just prior to the clade of "core pooid" genera that contain the majority of important temperate cereals and forage grasses. Diploid ecotypes of B. distachyon (2n = 10) have five easily distinguishable chromosomes that display high levels of chiasma formation at meiosis. The B. distachyon nuclear genome was indistinguishable in size from that of Arabidopsis, making it the simplest genome described in grasses to date. B. distachyon is a self-fertile, inbreeding annual with a life cycle of less than 4 months. These features, coupled with its small size (approximately 20 cm at maturity), lack of seed-head shatter, and undemanding growth requirements should make it amenable to high-throughput genetics and mutant screens. Immature embryos exhibited a high capacity for plant regeneration via somatic embryogenesis. Regenerated plants display very low levels of albinism and have normal fertility. A simple transformation system has been developed based on microprojectile bombardment of embryogenic callus and hygromycin selection. Selected B. distachyon ecotypes were resistant to all tested cereal-adapted Blumeria graminis species and cereal brown rusts (Puccinia reconditia). In contrast, different ecotypes displayed resistance or disease symptoms following challenge with the rice blast pathogen (Magnaporthe grisea) and wheat/barley yellow stripe rusts (Puccinia striformis). Despite its small stature, B. distachyon has large seeds that should prove useful for studies on grain filling. Such biological characteristics represent important traits for study in temperate cereals.     

Update on sumoylation: defining core components of the plant SUMO conjugation system by phylogenetic comparison

The conjugation of the small ubiquitin-related modifier, SUMO, to substrate proteins is a reversible and dynamic process, and an important response of plants to environmental challenges. Nevertheless, reliable data have so far been restricted largely to the model plant Arabidopsis thaliana. The increasing availability of genome information for other plant species offers the possibility to identify a core set of indispensable components, and to discover species-specific features of the sumoylation pathway. We analyzed the enzymes responsible for the conjugation of SUMO to substrates for their conservation between dicots and monocots. We thus assembled gene sets that relate the Arabidopsis SUMO conjugation system to that of the dicot species tomato, grapevine and poplar, and to four plant species from the monocot class: rice, Brachypodium distachyon, Sorghum bicolor and maize. We found that a core set of genes with clear assignment in Arabidopsis had highly conserved homologs in all tested plants. However, we also observed a variation in the copy number of homologous genes, and sequence variations that suggested monocot-specific variants. Generally, SUMO ligases and proteases showed the most pronounced differences. Finally, we identified potential SUMO chain-binding ubiquitin ligases, pointing to an in vivo function of SUMO chains as degradation signals in plants.     

Gene space dynamics during the evolution of Aegilops tauschii, Brachypodium distachyon, Oryza sativa, and Sorghum bicolor genomes

Nine different regions totaling 9.7 Mb of the 4.02 Gb Aegilops tauschii genome were sequenced using the Sanger sequencing technology and compared with orthologous Brachypodium distachyon, Oryza sativa (rice), and Sorghum bicolor (sorghum) genomic sequences. The ancestral gene content in these regions was inferred and used to estimate gene deletion and gene duplication rates along each branch of the phylogenetic tree relating the four species. The total gene number in the extant Ae. tauschii genome was estimated to be 36,371. The gene deletion and gene duplication rates and total gene numbers in the four genomes were used to estimate the total gene number in each node of the phylogenetic tree. The common ancestor of the Brachypodieae and Triticeae lineages was estimated to have had 28,558 genes, and the common ancestor of the Panicoideae, Ehrhartoideae, and Pooideae subfamilies was estimated to have had 27,152 or 28,350 genes, depending on the ancestral gene scenario. Relative to the Brachypodieae and Triticeae common ancestor, the gene number was reduced in B. distachyon by 3,026 genes and increased in Ae. tauschii by 7,813 genes. The sum of gene deletion and gene duplication rates, which reflects the rate of gene synteny loss, was correlated with the rate of structural chromosome rearrangements and was highest in the Ae. tauschii lineage and lowest in the rice lineage. The high rate of gene space evolution in the Ae. tauschii lineage accounts for the fact that, contrary to the expectations, the level of synteny between the phylogenetically more related Ae. tauschii and B. distachyon genomes is similar to the level of synteny between the Ae. tauschii genome and the genomes of the less related rice and sorghum. The ratio of gene duplication to gene deletion rates in these four grass species closely parallels both the total number of genes in a species and the overall genome size. Because the overall genome size is to a large extent a function of the repeated sequence content in a genome, we suggest that the amount and activity of repeated sequences are important factors determining the number of genes in a genome.     

Exploiting the Brachypodium Tool Box in cereal and grass research

It is now a decade since Brachypodium distachyon (Brachypodium) was suggested as a model species for temperate grasses and cereals. Since then transformation protocols, large expressed sequence tag (EST) databases, tools for forward and reverse genetic screens, highly refined cytogenetic probes, germplasm collections and, recently, a complete genome sequence have been generated. In this review, we will describe the current status of the Brachypodium Tool Box and how it is beginning to be applied to study a range of biological traits. Further, as genomic analysis of larger cereals and forage grasses genomes are becoming easier, we will re-evaluate Brachypodium as a model species. We suggest that there remains an urgent need to employ reverse genetic and functional genomic approaches to identify the functionality of key genetic elements, which could be employed subsequently in plant breeding programmes; and a requirement for a Pooideae reference genome to aid assembling large pooid genomes. Brachypodium is an ideal system for functional genomic studies, because of its easy growth requirements, small physical stature, and rapid life cycle, coupled with the resources offered by the Brachypodium Tool Box.     

Strong population structure characterizes weediness gene evolution in the invasive grass species Brachypodium distachyon

Mediterranean annual grasses have invaded California and have replaced vast areas of native grassland. One of these invasive grasses is Brachypodium distachyon , a new model species for the grasses with extensive genomic resources and a nearly completed genome sequence. This study shows that the level of genetic variation in invaded California grasslands is lower compared to the native range in Eurasia. The invaded regions are characterized by highly differentiated populations of B. distachyon isolated by distance, most likely as a result of founder effects and a dearth of outcrossing events. EXP6 and EXP10 encoding α-expansins responsible for rapid growth, and AGL11 and AGL13 encoding proteins involved in vegetative phase regulation, appear to be under purifying selection with no evidence for local adaptation. Our data show that B. distachyon has diverged only recently from related Brachypodium species and that tetraploidization might have been as recent as a few thousand years ago. Observed low genetic variation in EXP10 and AGL13 appears to have been present in Eurasia before tetraploidization, potentially as a result of strong selective pressures on advantageous mutations, which are most likely responsible for its fast growth and rapid completion of its life cycle.