Analisis Kestabilan Lereng Gambut Pesisir Utara Bengkalis

Peat soil slope stability is influenced by soil properties, the depth of the water table and the effect of loading or surcharges. Land conversion on areas can cause changes in peatland hydrological balance that led to a decrease in ground water level and causing slope failure. This study analyzes slope stability modeling based on the limit equilibrium principle by Morgenstern-Price method. The current peat slope collapse in the Bengkalis Island North Coast continue to occur by progressive despite to the decline in groundwater levels provide increasing peat slope safety factors

Morpho-physiological and anatomical character changes of rice under waterlogged and water-saturated acidic and high Fe content soil

Waterlogging is one of the limiting factors in crop cultivation. Moreover, high iron (Fe) content in acidic soils could also disturb plant growth. However, there is limited scientific information of morpho-physiological and anatomical responses of rice grown in waterlogged acidic soils with high Fe. Therefore, the objective of the research was to investigate the morpho-physiological and anatomical responses of rice to waterlogged and water-saturated soil condition in acidic soil with high Fe. Morpho-physiological and anatomical characters of rice were evaluated. The results showed that the waterlogging in acidic and high Fe content soil disturbed the rice growth as indicated by the change of morpho-physiological and anatomical characters. The water-saturated soil showed better condition for rice cultivation than that of waterlogging. The plant biomass, root anatomical, lipid peroxidation level, Fe absorption, and leaf gas exchange parameter could be evidences of changes in rice under both conditions. Based on the waterlogging tolerance coefficient (WTC), we proposed shoot and root dry weight, cortex thickness, and Fe content in shoot as screening tools for waterlogging tolerance of rice in acidic and high Fe content soil. The finding offers insight about waterlogged condition in acidic and high Fe soil could be restored in crop cultivation

PeanutMap: an online genome database for comparative molecular maps of peanut

BACKGROUND: Molecular maps have been developed for many species, and are of particular importance for varietal development and comparative genomics. However, despite the existence of multiple sets of linkage maps, databases of these data are lacking for many species, including peanut. DESCRIPTION: PeanutMap provides a web-based interface for viewing specific linkage groups of a map set. PeanutMap can display and compare multiple maps of a set based upon marker or trait correspondences, which is particularly important as cultivated peanut is a disomic tetraploid. The database can also compare linkage groups among multiple map sets, allowing identification of corresponding linkage groups from results of different research projects. Data from the two published peanut genome map sets, and also from three maps sets of phenotypic traits are present in the database. Data from PeanutMap have been incorporated into the Legume Information System website to allow peanut map data to be used for cross-species comparisons. CONCLUSION: The utility of the database is expected to increase as several SSR-based maps are being developed currently, and expanded efforts for comparative mapping of legumes are underway. Optimal use of these data will benefit from the development of tools to facilitate comparative analysis

Chromosome Bin Map of Expressed Sequence Tags in Homoeologous Group 1 of Hexaploid Wheat and Homoeology With Rice and Arabidopsis

A total of 944 expressed sequence tags (ESTs) generated 2212 EST loci mapped to homoeologous group 1 chromosomes in hexaploid wheat (Triticum aestivum L.). EST deletion maps and the consensus map of group 1 chromosomes were constructed to show EST distribution. EST loci were unevenly distributed among chromosomes 1A, 1B, and 1D with 660, 826, and 726, respectively. The number of EST loci was greater on the long arms than on the short arms for all three chromosomes. The distribution of ESTs along chromosome arms was nonrandom with EST clusters occurring in the distal regions of short arms and middle regions of long arms. Duplications of group 1 ESTs in other homoeologous groups occurred at a rate of 35.5%. Seventy-five percent of wheat chromosome 1 ESTs had significant matches with rice sequences (E ≤ e(−10)), where large regions of conservation occurred between wheat consensus chromosome 1 and rice chromosome 5 and between the proximal portion of the long arm of wheat consensus chromosome 1 and rice chromosome 10. Only 9.5% of group 1 ESTs showed significant matches to Arabidopsis genome sequences. The results presented are useful for gene mapping and evolutionary and comparative genomics of grasses

Construction of a rye cv. Blanco BAC library, and progress towards cloning the rye Alt3 aluminium [aluminum] tolerance gene

In addition to being an important cereal crop, rye (Secale cereale L.) provides valuable traits for other crops, as a parent of the amphidiploid triticale, and as a donor of translocated chromosome segments in wheat. Rye possesses excellent tolerance to many biotic and abiotic stresses that could potentially be transferred to wheat, and as a genetic system benefits from being highly variable, diploid and closely related to the more extensively characterized species wheat and barley. To provide a resource to assist the characterization and isolation of genes and gene complexes from rye, a large-insert genomic (BAC) library of rye cv. Blanco has been constructed, which to our knowledge, is the first such library made of this species. The library is comprised of 373,632 clones with an average insert size of 130 kb, representing a little over a 6-fold coverage of the 8,110 Mbp genome. Copies of the library will be kept at the University of Missouri, the Australian Centre of Plant Functional Genomics (Adelaide), and IPK Gatersleben, and will be available to researchers for unrestricted use. Of all the cultivated cereals, rye is the most tolerant to aluminum toxicity in acid soils, a stress that is a serious constraint to cereal cultivation worldwide. We have mapped the A1 tolerance locus Alt3 in rye to high resolution using gene co-linearity with rice. Progress towards cloning and characterization of this gene using the Blanco BAC library and other resources will be presented. This rye BAC library will have a significant impact on the world's ability to analyze the rye genome and in gene cloning in the rye genus.http://trove.nla.gov.au/work/3060002

Gene and repetitive sequence annotation in the Triticeae

The Triticeae tribe contains some of the world’s most important agricultural crops (wheat, barley and rye) and is perhaps, one of the most challenging for genome annotation because Triticeae genomes are primarily composed of repetitive sequences. Further complicating the challenge is the polyploidy found in wheat and particularly in the hexaploid bread wheat genome. Genomic sequence data are available for the Triticeae in the form of large collections of Expressed Sequence Tags (>1.5 million) and an increasing number of bacterial artificial chromosome clone sequences. Given that high repetitive sequence content in the Triticeae confounds annotation of protein-coding genes, repetitive sequences have been identified, annotated, and collated into public databases. Protein coding genes in the Triticeae are structurally annotated using a combination of ab initio gene finders and experimental evidence. Functional annotation of protein coding genes involves assessment of sequence similarity to known proteins, expression evidence, and the presence of domain and motifs. Annotation methods and tools for Triticeae genomic sequences have been adapted from existing plant genome annotation projects and were designed to allow for flexibility of single sequence annotation while allowing a whole community annotation effort to be developed. With the availability of an increasing number of annotated grass genomes, comparative genomics can be exploited to accelerate and enhance the quality of Triticeae sequences annotation. This chapter provides a brief overview of the Triticeae genomes features that are challenging for genome annotation and describes the resources and methods available for sequence annotation with a particular emphasis on problems caused by the repetitive fraction of these genomes

Development of an Expressed Sequence Tag (EST) Resource for Wheat (\u3ci\u3eTriticum aestivum\u3c/i\u3e L.): EST Generation, Unigene Analysis, Probe Selection and Bioinformatics for a 16,000-Locus Bin-Delineated Map

This report describes the rationale, approaches, organization, and resource development leading to a large-scale deletion bin map of the hexaploid (2n = 6x = 42) wheat genome (Triticum aestivum L.). Accompanying reports in this issue detail results from chromosome bin-mapping of expressed sequence tags (ESTs) representing genes onto the seven homoeologous chromosome groups and a global analysis of the entire mapped wheat EST data set. Among the resources developed were the first extensive public wheat EST collection (113,220 ESTs). Described are protocols for sequencing, sequence processing, EST nomenclature, and the assembly of ESTs into contigs. These contigs plus singletons (unassembled ESTs) were used for selection of distinct sequence motif unigenes. Selected ESTs were rearrayed, validated by 5’ and 3’ sequencing, and amplified for probing a series of wheat aneuploid and deletion stocks. Images and data for all Southern hybridizations were deposited in databases and were used by the coordinators for each of the seven homoeologous chromosome groups to validate the mapping results. Results from this project have established the foundation for future developments in wheat genomics