Dataset Information

GrainGenes, the genome database for small-grain crops.

ABSTRACT: GrainGenes, http://www.graingenes.org, is the international database for the wheat, barley, rye and oat genomes. For these species it is the primary repository for information about genetic maps, mapping probes and primers, genes, alleles and QTLs. Documentation includes such data as primer sequences, polymorphism descriptions, genotype and trait scoring data, experimental protocols used, and photographs of marker polymorphisms, disease symptoms and mutant phenotypes. These data, curated with the help of many members of the research community, are integrated with sequence and bibliographic records selected from external databases and results of BLAST searches of the ESTs. Records are linked to corresponding records in other important databases, e.g. Gramene's EST homologies to rice BAC/PACs, TIGR's Gene Indices and GenBank. In addition to this information within the GrainGenes database itself, the GrainGenes homepage at http://wheat.pw.usda.gov provides many other community resources including publications (the annual newsletters for wheat, barley and oat, monographs and articles), individual datasets (mapping and QTL studies, polymorphism surveys, variety performance evaluations), specialized databases (Triticeae repeat sequences, EST unigene sets) and pages to facilitate coordination of cooperative research efforts in specific areas such as SNP development, EST-SSRs and taxonomy. The goal is to serve as a central point for obtaining and contributing information about the genetics and biology of these cereal crops.

SUBMITTER: Matthews DE

PROVIDER: S-EPMC165505 | biostudies-literature | 2003 Jan

REPOSITORIES: biostudies-literature

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GrainGenes, the genome database for small-grain crops.

Matthews David E DE Carollo Victoria L VL Lazo Gerard R GR Anderson Olin D OD

Nucleic acids research 20030101 1

GrainGenes, http://www.graingenes.org, is the international database for the wheat, barley, rye and oat genomes. For these species it is the primary repository for information about genetic maps, mapping probes and primers, genes, alleles and QTLs. Documentation includes such data as primer sequences, polymorphism descriptions, genotype and trait scoring data, experimental protocols used, and photographs of marker polymorphisms, disease symptoms and mutant phenotypes. These data, curated with th ...[more]

PMID: 12519977

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Project description:BackgroundStalk lodging (breakage of plant stems prior to harvest) is a major problem for both farmers and plant breeders. A limiting factor in addressing this problem is the lack of a reliable method for phenotyping stalk strength. Previous methods of phenotyping stalk strength induce failure patterns different from those observed in natural lodging events. This paper describes a new device for field-based phenotyping of stalk strength called "DARLING" (device for assessing resistance to lodging in grains). The DARLING apparatus consists of a vertical arm which is connected to a horizontal footplate by a hinge. The operator places the device next to a stalk, aligns the stalk with a force sensor, steps on the footplate, and then pushes the vertical arm forward until the stalk breaks. Force and rotation are continuously recorded during the test and these quantities are used to calculate two quantities: stalk flexural stiffness and stalk bending strength.ResultsField testing of DARLING was performed at multiple sites. Validation was based upon several factors. First, the device induces the characteristic "crease" or Brazier buckling failure patterns observed in naturally lodged stalks. Second, in agreement with prior research, flexural rigidity values attained using the DARLING apparatus are strongly correlated with bending strength measurements. Third, flexural stiffness and bending strength values obtained with DARLING are in agreement with laboratory-based stiffness and strength values for corn stalks. Finally, a paired specimen experimental design was used to determine that the flexural data obtained with DARLING is in agreement with laboratory-based flexural testing results of the same specimens. DARLING was also deployed in the field to assess phenotyping throughput (# of stalks phenotyped per hour). Over approximately 5000 tests, the average testing rate was found to be 210 stalks/h.ConclusionsThe DARLING apparatus provides a quantitative assessment of stalk strength in a field setting. It induces the same failure patterns observed in natural lodging events. DARLING can also be used to perform non-destructive flexural tests. This technology has many applications, including breeding, genetic studies on stalk strength, longitudinal studies of stalk flexural stiffness, and risk assessment of lodging propensity.

Project description:The origins of agriculture, 10 000 years ago, led to profound changes in the biology of plants exploited as grain crops, through the process of domestication. This special case of evolution under cultivation led to domesticated cereals and pulses requiring humans for their dispersal, but the accompanying mechanisms causing higher productivity in these plants remain unknown. The classical view of crop domestication is narrow, focusing on reproductive and seed traits including the dispersal, dormancy and size of seeds, without considering whole-plant characteristics. However, the effects of initial domestication events can be inferred from consistent differences between traditional landraces and their wild progenitors.We studied how domestication increased the yields of Fertile Crescent cereals and pulses using a greenhouse experiment to compare landraces with wild progenitors. We grew eight crops: barley, einkorn and emmer wheat, oat, rye, chickpea, lentil and pea. In each case, comparison of multiple landraces with their wild progenitors enabled us to quantify the effects of domestication rather than subsequent crop diversification. To reveal the mechanisms underpinning domestication-linked yield increases, we measured traits beyond those classically associated with domestication, including the rate and duration of growth, reproductive allocation, plant size and also seed mass and number.Cereal and pulse crops had on average 50% higher yields than their wild progenitors, resulting from a 40% greater final plant size, 90% greater individual seed mass and 38% less chaff or pod material, although this varied between species. Cereal crops also had a higher seed number per spike compared with their wild ancestors. However, there were no differences in growth rate, total seed number, proportion of reproductive biomass or the duration of growth.The domestication of Fertile Crescent crops resulted in larger seed size leading to a larger plant size, and also a reduction in chaff, with no decrease in seed number per individual, which proved a powerful package of traits for increasing yield. We propose that the important steps in the domestication process should be reconsidered, and the domestication syndrome broadened to include a wider range of traits.

Dataset Information

GrainGenes, the genome database for small-grain crops.

Publications

GrainGenes, the genome database for small-grain crops.

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