Colinearity and gene density in grass genomes

Grasses are the single most important plant family in agriculture. In the past years, comparative genetic mapping has revealed conserved gene order (colinearity) among many grass species. Recently, the first studies at gene level have demonstrated that microcolinearity of genes is less conserved: small scale rearrangements and deletions complicate the microcolinearity between closely related species, such as sorghum and maize, but also between rice and other crop plants. In spite of these problems, rice remains the model plant for grasses as there is limited useful colinearity between Arabidopsis and grasses. However, studies in rice have to be complemented by more intensive genetic work on grass species with large genomes (maize, Triticeae). Gene-rich chromosomal regions in species with large genomes, such as wheat, have a high gene density and are ideal targets for partial genome sequencing.     

Hormonal control of grass inflorescence development

Grass inflorescences produce the grain that feeds the world. Compared to eudicots such as Arabidopsis (Arabidopsis thaliana), grasses have a complex inflorescence morphology that can be explained by differences in the activity of axillary meristems. Advances in genomics, such as the completion of the rice (Oryza sativa) and sorghum (Sorghum bicolor) genomes and the recent release of a draft sequence of the maize (Zea mays) genome, have greatly facilitated research in grasses. Here, we review recent progress in the understanding of the genetic regulation of grass inflorescence development, with a focus on maize and rice. An exciting theme is the key role of plant growth hormones in inflorescence development.     

Advances in cereal protoplast research

Beginning in 1986, plants have been regenerated from protoplasts of all of the important cereal species, including wheat, rice, maize, and barley, and grasses such as sugarcane. In addition, somatic hybrids/cybrids as well as transgenic plants with introduced useful agronomic traits have been obtained in several instances. This rapid and impressive progress in the genetic manipulation of cereals has been made possible by two critical technical advances during the past decade: the establishment of embryogenic suspension cultures as a source of totipotent protoplasts and the direct delivery of DNA into protoplasts for genetic transformation.     

Flowering and determinacy in maize

All plant organs are produced by meristems, groups of stem cells located in the tips of roots and shoots. Indeterminate meristems make an indefinite number of organs, whereas determinate meristems are consumed after making a specific number of organs. Maize is an ideal system to study the genetic control of meristem fate because of the contribution from determinate and indeterminate meristems to the overall inflorescence. Here, the latest work on meristem maintenance and organ specification in maize is reviewed. Genetic networks, such as the CLAVATA components of meristem maintenance and the ABC programme of flower development, are conserved between grasses and eudicots. Maize and rice appear to have conserved mechanisms of meristem maintenance and organ identity. Other pathways, such as sex determination, are likely to be found only in maize with its separate male and female flowers. A rich genetic history has resulted in a large collection of maize mutants. The advent of genomic tools and synteny across the grasses now permits the isolation of the genes behind inflorescence architecture and the ability to compare function across the Angiosperms.     

barren inflorescence2 Encodes a co-ortholog of the PINOID serine/threonine kinase and is required for organogenesis during inflorescence and vegetative development in maize

Organogenesis in plants is controlled by meristems. Axillary meristems, which give rise to branches and flowers, play a critical role in plant architecture and reproduction. Maize (Zea mays) and rice (Oryza sativa) have additional types of axillary meristems in the inflorescence compared to Arabidopsis (Arabidopsis thaliana) and thus provide an excellent model system to study axillary meristem initiation. Previously, we characterized the barren inflorescence2 (bif2) mutant in maize and showed that bif2 plays a key role in axillary meristem and lateral primordia initiation in the inflorescence. In this article, we cloned bif2 by transposon tagging. Isolation of bif2-like genes from seven other grasses, along with phylogenetic analysis, showed that bif2 is a co-ortholog of PINOID (PID), which regulates auxin transport in Arabidopsis. Expression analysis showed that bif2 is expressed in all axillary meristems and lateral primordia during inflorescence and vegetative development in maize and rice. Further phenotypic analysis of bif2 mutants in maize illustrates additional roles of bif2 during vegetative development. We propose that bif2/PID sequence and expression are conserved between grasses and Arabidopsis, attesting to the important role they play in development. We provide further support that bif2, and by analogy PID, is required for initiation of both axillary meristems and lateral primordia.     

Population structure of Spodoptera frugiperda maize and rice host forms in South America: are they host strains?

Determining which factors contribute to the formation and maintenance of genetic divergence to evaluate their relative importance as a cause of biological differentiation is among the major challenges in evolutionary biology. In Spodoptera frugiperda (Smith) (Lepidoptera: Noctuidae) two host strains have been recognized in the 1980s: the corn‐strain prefers maize, sorghum, and cotton, whereas the rice‐strain prefers rice and wild grasses. However, it is not clear to what extent these so‐called ‘strains’, which have also been called ‘host races’ or even ‘sibling species’, are really associated with host plants. Due to the indeterminate evolutionary status, we will use the term ‘host forms’ (sensu Funk). Here, we characterized populations collected from maize, rice, and wild grasses from three countries in South America. Using two mitochondrial cytochrome oxidase I (mtCOI) markers and 10 polymorphisms in the triose phosphate isomerase (Tpi) gene, we found various patterns of host association. Two hundred twenty‐seven nuclear amplified fragment length polymorphisms (AFLPs) markers revealed significant genetic differentiation among populations, which was generally correlated to the host from which the larvae were collected. Using a multivariate discriminant analysis and a Bayesian clustering approach, we found that individuals could be grouped into 2–5 genetically distinct clusters, depending on the method. Together, our results indicate that although host‐associated differentiation is present in this species, it does not account for all observable genetic variation and other factors must be maintaining genetic differentiation between these forms. Therefore, the term ‘host strains’ should be abandoned and ‘host forms’ should be used instead for S. frugiperda.     

Transposon tagging in maize

Through recent government- and industry-sponsored efforts, several forward and reverse genetic screening programs have emerged over the past few years to aid in the genetic dissection of gene function in maize. Despite a US maize crop valued at $18.4 billion last year (http://www.ncga.com/03world/main/US_crop_value_2000.html) and rich genetic history, maize has taken a back seat to Arabidopsis thaliana as the model genetic system for plants over the past decade. With a fully sequenced genome, short generation time and small size, studies of Arabidopsis have provided plant scientists with a molecular framework for hormonal, developmental and environmental signaling pathways in plants. As investigations into Arabidopsis continue, our capacity to engineer biochemical pathways and alter plant physiological responses will become increasingly sophisticated. Nevertheless, approximately 130 million years have passed since monocot and higher eudicot lineages diverged. Thus, our ability to engineer agronomically important monocot grasses such as maize, rice and wheat will become increasingly limited by our lack of understanding of the physiological and morphological differences that have evolved in the monocots and higher eudicots. The sophisticated transposon collections now being generated for maize are but one of several recent projects (http://www.nsf.gov/bio/pubs/awards/genome01.htm) to provide grass researchers with essential tools for genome analysis. Because grain crops are such a closely related group, it is hoped that many of the findings made in one grass will be directly applicable to understanding the biology of another. The goal of this review is to highlight the recent developments in maize transposon-based gene characterization programs and provide a critical examination of the advantages and disadvantages each system offers. Electronic Publication     

Leaf shape and anatomy as indicators of phase change in the grasses: comparison of maize, rice, and bluegrass

Leaf morphology and anatomy during vegetative phase change was compared in bluegrass, rice, and maize. Maize juvenile leaves are coated with epicuticular wax, lack specialized cells, such as trichomes and bulliform cells, and epidermal cell walls stain a uniform purple color. Adult maize leaves are pubescent, lack epicuticular waxes, and have crenulated epidermal cell walls that stain purple and blue. All bluegrass and rice blades are pubescent, coated with epicuticular waxes, and show purple and blue wall staining. In all three grasses, blade width steadily increases at each node until a threshold size is achieved several nodes before reproductive competence is acquired. Blade-to-sheath length showed a similar trend of continuous change followed by discontinuous change prior to reproduction. Analysis of leaf development demonstrated that maize primordia initiate more rapidly relative to blade and sheath growth than do either bluegrass or rice. We conclude that leaf shape, as defined by blade width and blade-to-sheath ratio, is a reliable indicator of phase, whereas anatomy is not a universal indicator of phase change in the grasses. We speculate that different growth patterns among these grasses may be attributed to changes in the timing of embryonic and postembryonic development.     

Comparative genomics of grasses tolerant to aluminum

The family Poaceae includes over 10,000 species, among which are the most economically important cereals: maize, sorghum, rice, wheat, rye, barley, and oat. These cereals are very important components of human and animal food. Although divergence of the members of this family occurred about 40 million years ago, comparative genome analyses demonstrated that gene orders among species of this family remain largely conserved, which can be very useful for understanding their roles and evolution. Even with an intricate evolutionary history in which chromosome fragments, losses and duplications have to be considered at the ploidy level, grasses present a genetic model system for comparative genomics. The availability of mapped molecular markers, rice genome sequences and BAC and EST libraries from several grass species, such as rice, wheat, sorghum, and maize, facilitates biology and phylogeny studies of this group. The value of using information from different species in modern plant genetics is unquestionable, especially in the study of traits such as tolerance to aluminum in soils, which affects plant growth and development. Comparative genomic approaches to aluminum tolerance can identify genomic regions and genes responsible for aluminum tolerance in grasses.     

Targeted mutagenesis of a conserved anther‐expressed P450 gene confers male sterility in monocots

Targeted mutagenesis using programmable DNA endonucleases has broad applications for studying gene function in planta and developing approaches to improve crop yields. Recently, a genetic method that eliminates the need to emasculate the female inbred during hybrid seed production, referred to as Seed Production Technology, has been described. The foundation of this genetic system relied on classical methods to identify genes critical to anther and pollen development. One of these genes is a P450 gene which is expressed in the tapetum of anthers. Homozygous recessive mutants in this gene render maize and rice plants male sterile. While this P450 in maize corresponds to the male fertility gene Ms26, male fertility mutants have not been isolated in other monocots such as sorghum and wheat. In this report, a custom designed homing endonuclease, Ems26+, was used to generate in planta mutations in the rice, sorghum and wheat orthologs of maize Ms26. Similar to maize, homozygous mutations in this P450 gene in rice and sorghum prevent pollen formation resulting in male sterile plants and fertility was restored in sorghum using a transformed copy of maize Ms26. In contrast, allohexaploid wheat plants that carry similar homozygous nuclear mutations in only one, but not all three, of their single genomes were male fertile. Targeted mutagenesis and subsequent characterization of male fertility genes in sorghum and wheat is an important step for capturing heterosis and improving crop yields through hybrid seed.     

是金子无论在何处都发光: 玉米和水稻驯化中的趋同选择

野生植物的驯化为人类定居与文明起源奠定了重要基础。在世界范围内不同地区生活的古人类分别对当地不同的野生植物进行了驯化, 而经过驯化的作物常常表现出相似的驯化综合性状。在基因组层面上对趋同选择规律的解析, 可为作物育种提供重要信息与遗传资源。近日, 中国农业大学杨小红/李建生和华中农业大学严建兵领衔的团队从单基因和全基因组2个层次系统解析了玉米(Zea mays)和水稻(Oryza sativa)趋同选择的遗传基础, 发现玉米KRN2与水稻OsKRN2受到了趋同选择, 并通过相似的途径调控玉米与水稻的粒数与产量。他们还发现玉米与水稻在全基因组范围内存在大量趋同选择同源基因对(gene pair), 这些基因在淀粉代谢、糖及辅酶合成等途径特异富集。该研究不仅克隆了在玉米与水稻中均具有重要育种价值的趋同选择同源基因对KRN2/OsKRN2, 而且在全基因组水平上揭示了玉米与水稻趋同选择的规律, 为进一步解析驯化综合性状形成的分子机理及其在育种中的应用奠定了重要理论基础。     

Numerous small rearrangements of gene content,order and orientation differentiate grass genomes

Comparative genetic mapping has indicated that the grass family (Poaceae) exhibits extensive chromosomal collinearity. In order to investigate microcollinearity in these genomes, several laboratories have begun to undertake comparative DNA sequence analyses of orthologous chromosome segments from various grass species. Five different regions have now been investigated in detail, with four regions sequenced for maize, rice and sorghum, plus two for wheat and one for barley. In all five of these segments, gene rearrangements were observed in at least one of the comparisons. Most of the detected rearrangements are small, involving the inversion, duplication, translocation or deletion of DNA segments that contain only 1-3 genes. Even closely related species, like barley and wheat or maize and sorghum, exhibit approximately 20% alterations in gene content or orientation. These results indicate that thousands of small genetic rearrangements have occurred in several grass lineages since their divergence from common ancestors. These rearrangements have largely been missed by genetic mapping and will both complicate and enrich the use of comparative genetics in the grasses.     

Comparative genomics in the grass family: molecular characterization of grass genome structure and evolution

The genomes of grasses are very different in terms of size, ploidy level and chromosome number. Despite these significant differences, it was found by comparative mapping that the linear order (colinearity) of genetic markers and genes is very well conserved between different grass genomes. The potential of such conservation has been exploited in several directions, e.g. in defining rice as a model genome for grasses and in designing better strategies for positional cloning in large genomes. Recently, the development of large insert libraries in species such as maize, rice, barley and diploid wheat has allowed the study of large stretches of DNA sequence and has provided insight into gene organization in grasses. It was found that genes are not distributed randomly along the chromosomes and that there are clusters of high gene density in species with large genomes. Comparative analysis performed at the DNA sequence level has demonstrated that colinearity between the grass genomes is retained at the molecular level (microcolinearity) in most cases. However, detailed analysis has also revealed a number of exceptions to microcolinearity, which have given insight into mechanisms that are involved in grass-genome evolution. In some cases, the use of rice as a model to support gene isolation from other grass genomes will be complicated by local rearrangements. In this Botanical Briefing, we present recent progress and future prospects of comparative genomics in grasses.     

云南省作物种质资源的研究现状及利用前景

云南是中国作物种质资源最为丰富的省份之一,已收集保存各类作物种质资源2万余份,并在水稻、小麦、玉米、甘蔗、茶叶、油料、花卉等资源的利用方面开展了一系列的研究,取得了丰硕的成果。本文将在分析云南作物种质资源利用研究的基础上,论述云南作物种质资源在育种、科研、国际交流等方面的利用途径与发展前景。     

玉米籽粒淀粉含量遗传基础与调控机制*

玉米是世界上种植面积最大、总产量最高的粮食作物,其籽粒重量的70%来自于淀粉。淀粉不仅是人类及其他动物的主要能量来源,同时也是化工等行业的重要原料。利用拟南芥、水稻等模式植物,淀粉合成相关基因克隆与功能研究已取得较多进展。近年来,随着玉米淀粉含量相关遗传学研究的深入开展,通过数量性状位点(quantitative trait locus mapping,QTL)定位、全基因组关联分析(genome-wide association study, GWAS)及各种组学分析方法,发现了较多新的与淀粉含量相关的遗传位点及候选基因,但是尚缺乏归纳总结。综述了玉米籽粒淀粉合成与调控研究进展,对玉米籽粒淀粉含量相关的QTL和基因进行汇总和分析,通过构建一致性物理图谱,提炼玉米籽粒淀粉含量遗传定位热点区间,这为进一步解析玉米籽粒淀粉合成与代谢相关基因的功能提供参考,并为分子标记辅助育种提供遗传资源。