Information Botany

Oryza Sativa (Rice)

2010-11-14T08:58:00.000-08:00

Rice is the pre-eminent monocot theory and is distinctively both a theory and a crop within its own right. The particular importance of this duality lies within the much greater © 2007 via Taylor & Francis Group, LLC Genomic Models for Large-Crop Plant Genomes 5 potential that this lets for shifting phenotype, as well as genotype, from model to crop. Rice is a tropical species and hence many necessarily towards share pathogens and/or abiotic stresses with its tropical crop cousins such as the millets (and, towards a lesser extent, maize and sorghum) than with its meaningful temperate small-grain and pasture-grass cousins (wheat, barley, rye, oat, and ryegrass). Nevertheless, shared morphology and crop architecture among everybody cereal species do allow a lot phenotypic connections towards be made. The dicot theories, within contrast, are far swept within a crop morphology, making such shifts much less predictable.

The grasses belong towards the Poaceae, which evolved from a ordinary ancestor some 50 towards 60 MYA; together, they provide an evaluated 60% of international human calorific intake. The relations incorporates at lowest 10,000 species, classified into 650 genera. The crop species within the relations dip into the three subfamilies: Pooideae (which incorporates the temperate cereals and ryegrass), Panicoideae (maize, sorghum, millets, sugar cane), and Bambusoideae (rice). Until the industry of generic DNA technology, primarily within the 1990s, genetic innovation within each grass crop was conducted within isolation from that within the others. Before this moment there was none secure way of verifying what had already been alleged for a number of time: that because these species were related via (albeit distant) decline, they were necessarily towards share genetic content and, at lowest at a plain grade, genetic mechanisms.

The former presentation of what is already mentioned towards as “comparative genetics” was conducted within the Solanaceae, whereas ordinary RFLP linkage correlations in tomato and potato were exposed consuming DNA probes grew from a tomato template. The notion transmit hastily towards the Poaceae, and several crossspecies comparisons began towards appear within the literature during the morning towards mid-1990s. These ruled towards the construction of partial consensus maps linking maize with sorghum and wheat with barley and rye . A synthesis of these maps was generated via relating them everybody towards that of the rice genome. The notion of “synteny” elaborated via these cross-species comparisons of gene order reflects conservation again evolutionary moment at the macroscale. Whether this was extendable to the microscale was questionable, granted the wide variation within genome dimensions between individual Poaceae species.

The event of sequence-based comparisons within selective syntenic regions is that although gene flesh and sequence are extremely well potted between taxa, intergenic regions are greatly contrary, even at the grade of genotypes within a taxon. Much of this intra- and interspecific difference is produced via retroelement activity and, detailed, helitron-like transposons calm of multiple genederived fragments. In contribution, the increasing body of evidence produced from large-scale sequence comparisons between related taxa illustrates how synteny is also interrupted via the presence of species-specific localized duplications and other forms of genome reorganization.

By the end of the 1990s, with the Arabidopsis genome project already well under way, rice became an increasingly attractive candidate for complete genome sequencing in the confidential and social sectors. These efforts were jointly towards produce almost full genomic sequences of japonica and indica subspecies, along with a nearcomplete compendium of full-length cDNA sequence. The ceased sequence currently envelopes approximately 95% of the genome, incorporating most euchromatic regions and © 2007 via Taylor & Francis Group, LLC 6 Model Plants and Crop Improvement 2 (out of 12) finalise centromeres. Mirroring the situation within Arabidopsis, the genome sequence has revealed a history of polyploidization within the evolution of modern day rice, with approximately halves of the gene content duplicated as paralogs.

Populus Trichocarpa (Poplar or Black Cottonwood)

2010-09-19T04:22:00.000-07:00

Conventional genetic approaches in trees are limited by the large size, long generation interval, and outcrossing mating system of most species. The need for a tree model reflects the importance of many traits that are not shared by an herbaceous annual plant such as Arabidopsis. Important among these are wood formation, longevity, seasonal growth, and hardiness. The genus Populus consists of 30 to 40 species, 4 of which have significant commercial importance. Selection and hybridization programs in poplars began in North America in the 1960s, and the most commonly exploited crosses have involved P. trichocarpa, P. deltoides, P. nigra, P. grandidentata, P. alba, P. tremuloides, and P. tremula.

Because the genomic resources of P. trichocarpa were the most developed at the time that genome sequencing was proposed, this species became the accepted tree model. It was chosen as the first tree for genome sequencing largely because of its modest genome size (0.6 pg)—about 40 times smaller than that of pine, the most important of all forestry species. It also has a number of other advantages over potential alternative tree species specifically related to its rapid juvenile growth, which allows for phenotypic assessments to be made relatively quickly; its wellestablished transformation and regeneration protocols; and the pre-existence of a body of genetic mapping, which includes placement and tagging of a number of quantitative trait loci (QTL). The final draft sequence was scheduled for release in early 2005, but is still awaited at the time of writing.

Lotus Japonicus (Trefoil) and Medicago Truncatula (Barrel Medic)

2010-08-20T10:55:00.000-07:00

The Fabaceae, one of the largest families of flowering plants with 650 genera and over 18,000 species, is distinguished from other dicot families by its symbiotic relationship with nitrogen-fixing Rhizobium. The economic and nutritional importance of nitrogen fixation has been sufficient to justify targeting a model representative, and two competitive species are currently being pursued. Medicago truncatula © 2007 by Taylor & Francis Group, LLC 4 Model Plants and Crop Improvement has some importance in its own right as a forage crop in Australia. It has a small diploid genome and a rapid generation time, is self-fertile, transformable, and is a prolific seed producer. Lotus japonicus is a short-life-cycle, perennial wild legume that also has a small genome size.

The genomes of both species are currently being sequenced (see, respectively, medicago.org and kazusa.or.jp/lotus/index.html). The two sequences show a high degree of similarity to one another. Collinearity between M. truncatula and pea at the level of coarse genetic maps appears to be encouragingly high, although there is significant sequence divergence between those of Lotus and the major legume crop species soybean. In a computational approach, Lotus, Medicago, and Glycine unigenes were BLASTed against non-legume unigene sets and the rice genome sequence to define legume-specific gene motifs; this delivered some 2500 such contigs, of which less than 3% showed any homology to any previously identified legume genes. Such results underline the utility of a model legume to define sequences specific to this group of agriculturally important crop species.

Arabidopsis thaliana (Thale Cress)

2010-08-20T10:08:00.000-07:00

Arabidopsis is by far the most well developed of the crop plant models. In addition to its completed genome sequence, it is easily transformable and enjoys a huge range of genetic (mutants, mapping populations, ecotypes) and genomic (cloned genes, libraries, arrays, markers, etc.) resources and an ever expanding database relating phenotype to genotype. The closest crop relatives to Arabidopsis are the three diploid Brassica species rapa, nigra, and oleracea that carry, respectively, the A, B, and C genomes as described in Reference 8. Although all of these represent rather minor crop species, the major contributor of Brassica spp. to agriculture is B. napus (oilseed rape or canola), which is an AC allotetraploid formed from the combination B. oleracea B. rapa.

The lineages of Arabidopsis and Brassica are thought to have diverged from one another between 14 and 20 MYA ; this divergence has included a number of distinct polyploidization events because the present-day diploid Brassica spp. carry multiple paralogous copies of chromosomal segments collinear with the Arabidopsis genome. This copy number is most commonly three, so the inference is that the diploids must have evolved from a hexaploid ancestor. Copy number is frequently less than three, varying in 4B. napus from four to seven. Within the triplicated paralogs, a common pattern of interspersed gene loss is emerging, with the result that each paralog typically carries a slightly different spectrum of the full gene set presumably present on the progenitor segment.

A further complication is that Arabidopsis, as revealed from its genome sequence, is a cryptic polyploid, carrying a sufficient number of large segmental duplications for an evolutionary history of at least four different large-scale duplication events to have been proposed. Overall, an estimated 74 translocations, fusions, deletions, or inversions separate the genomes of Arabidopsis and B. napus, of which about one half are common to A and C genomes in present-day oilseed rape.

Introduction to Botany

2010-07-14T10:33:00.000-07:00

Plant genomes vary enormously in size. A part of this variation is generated by polyploidy, which is ubiquitous in the plant kingdom; however, even between closely related, ostensibly diploid species, it can still vary by an order of magnitude. A notable, but not atypical example is the contrast between rice (1 C DNA content of 0.50 pg, equivalent to 450 Mbp) and barley (5.55 pg, 5300 Mbp). The gene content of these two species is thought to be rather similar, numbering something under 40,000, depending on the gene prediction program employed [1]. Thus, much of the difference in DNA content is made up of nongenic DNA—in particular, retrotransposons. When large-scale genome sequencing became possible in the 1990s, the large size of the majority of the leading crop genomes was technically and financially prohibitive. This prompted the plant research community to identify species (in © 2007 by Taylor & Francis Group, LLC

2 Model Plants and Crop Improvement particular Arabidopsis thaliana) with more tractably sized genomes as genomic models. Technical improvements in the efficiency of sequencing achieved the finishing of the Arabidopsis genome by 2000 (4 years ahead of schedule) and the sequence was released with some fanfare in Nature [2].

At the time, Arabidopsis represented one of the first eukaryotes to be sequenced fully (along with Saccharomyces cerevisiae, human, and Caenorhabditis elegans). Its protein-encoding gene content has been estimated to be about 25,000 [2]. In the meantime, the genome sequence of Arabidopsis has been joined by those of a bewildering and ever-growing list of eukaryotic and prokaryotic organisms numbering over 300 as of December 2005 (http://www.genomesonline.org). Of the 40 fully sequenced eukaryotic genomes, 25 belong to simple organisms (protozoans and fungi), 7 are vertebrates, 3 are insects, 2 are nematodes, and 3 are plants (of which 2 are the indica and japonica subspecies of rice).

The divergence of the monocot from the dicot clade is an ancient event, currently dated using molecular clock methods applied to the chloroplast genome at 140 to 150 MYA during the late Jurassic to early Cretaceous periods [3]. Independent estimates based on mitochondrial sequences have placed it somewhat earlier, at 170 to 235 MYA [4]. Dating of the time of speciation within each clade has been attempted by applying molecular clock methodology to repetitive sequences such as retrotransposons, but sequence homology in this class of element between clades is insufficient to use this method to date the monocot–dicot divergence. Thus, it was recognized at an early stage that the Arabidopsis genome sequence would probably be of only partial relevance to monocot genomes. With a genome size about three times larger than that of Arabidopsis, rice was rapidly identified as the donor of a suitable model monocot genome. Before completion of the rice genome sequence, it became apparent that only a poor level of commonality in gene order existed between Arabidopsis and rice [5], thereby justifying post hoc the need for a separate model for the two major plant clades.

Nevertheless, the two genomes do retain some similarity as a result of common descent. Although some 85% of predicted Arabidopsis proteins were found to share significant homology with those of rice, about a tenth of them show a strong level of conservation [6]; in addition, most monocot–dicot homologs maintain exon order as expected. Perhaps most surprisingly, in many homologs, intron number, position, and even relative size show a remarkable level of conservation [7]. Despite the apparent disparity in gene number between the two models (25,000 vs. 40,000), it has recently been claimed that only a few hundred, or at most a few thousand, rice genes appear to lack close homologs in Arabidopsis [1].

The infrastructure and efficiency of whole genome sequencing is now at a point at which it has become much more realistic to undertake on a large scale. Current crop species targets include oat, Brassica spp., orange, coffee, barley, soybean, cotton, ryegrass, alfalfa, tomato, banana, bean, poplar, castor oil, sorghum, and maize. A growing number of other species has been targeted for sequencing of the gene space (ESTs or similar). If these trends continue, it is likely that within 10 years, most of the major crop genomes will have been fully sequenced. In the meantime, species that are nodal in crop phylogenies may be chosen to serve to © 2007 by Taylor & Francis Group, LLC Genomic Models for Large-Crop Plant Genomes 3 generate a network of submodels; a particular example of this lies behind the current proposal to sequence the grass Brachypodium distachyon. This chapter attempts to take stock of model genomes’ contribution to understanding of the genomes of crop species to date. Perhaps other contributors to this volume will show the lasting value that model species biology has made to crop improvement.

What is Botany

2010-04-25T00:18:00.000-07:00

Botany ( botany ), Pitologia ( phytology ) or Pitobiologia ( phytobiology ) it is a branch of scientific life that investigates world that grows. The botany deals in all the aspects of lives of the plants, between them structure, development, growth, reproduction, substitution of the substances and from occur.

The fields of the study that are general in the botany include sorting of world that grows, morphology of plants, that it is a field that deals in the documentation and depiction of the plants, that deals in the research of the dispersal of the plants over the earth.

In the past investigated the botanists every forms of life that they not animals, a but/auditorium during the years and with progress of the biology was understood that forms of life are different that they not animals, like viruses, fungi and bacteria, are not relation never the flora and there is not them included under the botany.