The groundnut improvement network for Africa (GINA) germplasm collection: a unique genetic resource for breeding and gene discovery.

Cultivated peanut or groundnut (Arachis hypogaea L.) is a grain legume grown in many developing countries by smallholder farmers for food, feed, and/or income. The speciation of the cultivated species, that involved polyploidization followed by domestication, greatly reduced its variability at the DNA level.

Genome-wide association studies reveal novel loci for resistance to groundnut rosette disease in the African core groundnut collection.

We identified markers associated with GRD resistance after screening an Africa-wide core collection across three seasons in Uganda Groundnut is cultivated in several African countries where it is a major source of food, feed and income. One of the major constraints to groundnut production in Africa is groundnut rosette disease (GRD), which is caused by a complex of three agents: groundnut rosette assistor luteovirus, groundnut rosette umbravirus and its satellite RNA. Despite several years of breeding for GRD resistance, the genetics of the disease is not fully understood.

RGB-image method enables indirect selection for leaf spot resistance and yield estimation in a groundnut breeding program in Western Africa.

Early Leaf Spot (ELS) caused by the fungus Passalora arachidicola and Late Leaf Spot (LLS) also caused by the fungus Nothopassalora personata, are the two major groundnut ( L.) destructive diseases in Ghana. Accurate phenotyping and genotyping to develop groundnut genotypes resistant to Leaf Spot Diseases (LSD) and to increase groundnut production is critically important in Western Africa.

Genetic fingerprinting and aflatoxin production of Aspergillus section Flavi associated with groundnut in eastern Ethiopia.

Background: Aspergillus species cause aflatoxin contamination in groundnut kernels, being a health threat in agricultural products and leading to commodity rejection by domestic and international markets. Presence of Aspergillus flavus and A. parasiticus colonizing groundnut in eastern Ethiopia, as well as presence of aflatoxins have been reported, though in this region, no genetic studies have been done of these species in relation to their aflatoxin production.

Peanut Consumption in Malawi: An Opportunity for Innovation.

Peanuts are a valuable source of nutrients, but peanut consumption patterns, consumption frequencies, and the factors influencing peanut consumption in Malawi are not known. This study surveyed consumers to fill this knowledge gap and to assess Malawian consumers' readiness to try new food products. Out of the 489 respondents surveyed, all but three consumed peanuts (in any form).

Aspergillus and aflatoxin in groundnut (Arachis hypogaea L.) and groundnut cake in Eastern Ethiopia.

This study was conducted to assess major Aspergillus species and aflatoxins associated with groundnut seeds and cake in Eastern Ethiopia and evaluate growers' management practices. A total of 160 groundnut seed samples from farmers' stores and 50 groundnut cake samples from cafe and restaurants were collected. Fungal isolation was done from groundnut seed samples.

Genetic relationships among seven sections of genus Arachis studied by using SSR markers.

Background: The genus Arachis, originated in South America, is divided into nine taxonomical sections comprising of 80 species. Most of the Arachis species are diploids (2n = 2x = 20) and the tetraploid species (2n = 2x = 40) are found in sections Arachis, Extranervosae and Rhizomatosae. Diploid species have great potential to be used as resistance sources for agronomic traits like pests and diseases, drought related traits and different life cycle spans.

A comprehensive resource of drought- and salinity- responsive ESTs for gene discovery and marker development in chickpea (Cicer arietinum L.).

Background: Chickpea (Cicer arietinum L.), an important grain legume crop of the world is seriously challenged by terminal drought and salinity stresses. However, very limited number of molecular markers and candidate genes are available for undertaking molecular breeding in chickpea to tackle these stresses.

AFLP-based molecular characterization of an elite germplasm collection of Jatropha curcas L., a biofuel plant.

Amplified fragment length polymorphism (AFLP) was employed to assess the diversity in the elite germplasm collection of Jatropha curcas, which has gained tremendous significance as a biofuel plant in India and many other countries recently. Forty-eight accessions, collected from six different states of India, were used with seven AFLP primer combinations that generated a total of 770 fragments with an average of 110 fragments per primer combination. A total of 680 (88%) fragments showed polymorphism in the germplasm analyzed, of which 59 (8.

Orphan legume crops enter the genomics era!

Many of the world's most important food legumes are grown in arid and semi-arid regions of Africa and Asia, where crop productivity is hampered by biotic and abiotic stresses. Until recently, these crops have also suffered from a dearth of genomic and molecular-genetic resources and thus were 'orphans' of the genome revolution. However, the community of legume researchers has begun a concerted effort to change this situation.

Genetic structure, diversity, and allelic richness in composite collection and reference set in chickpea (Cicer arietinum L.).

Background: Plant genetic resources (PGR) are the basic raw materials for future genetic progress and an insurance against unforeseen threats to agricultural production. An extensive characterization of PGR provides an opportunity to dissect structure, mine allelic variations, and identify diverse accessions for crop improvement. The Generation Challenge Program http://www.

An integrated pipeline of open source software adapted for multi-CPU architectures: use in the large-scale identification of single nucleotide polymorphisms.

The large amounts of EST sequence data available from a single species of an organism as well as for several species within a genus provide an easy source of identification of intra- and interspecies single nucleotide polymorphisms (SNPs). In the case of model organisms, the data available are numerous, given the degree of redundancy in the deposited EST data. There are several available bioinformatics tools that can be used to mine this data; however, using them requires a certain level of expertise: the tools have to be used sequentially with accompanying format conversion and steps like clustering and assembly of sequences become time-intensive jobs even for moderately sized datasets.

A database of annotated tentative orthologs from crop abiotic stress transcripts.

A minimal requirement to initiate a comparative genomics study on plant responses to abiotic stresses is a dataset of orthologous sequences. The availability of a large amount of sequence information, including those derived from stress cDNA libraries allow for the identification of stress related genes and orthologs associated with the stress response. Orthologous sequences serve as tools to explore genes and their relationships across species.

A database of simple sequence repeats from cereal and legume expressed sequence tags mined in silico: survey and evaluation.

Simple sequence repeats (SSRs) or microsatellites are an important class of molecular markers for genome analysis and plant breeding applications. In this paper, the SSR distributions within ESTs from the legumes soybean (Glycine max, representing 135.86 Mb), medicago (Medicago truncatula, 121.

Advances in cereal genomics and applications in crop breeding.

Recent advances in cereal genomics have made it possible to analyse the architecture of cereal genomes and their expressed components, leading to an increase in our knowledge of the genes that are linked to key agronomically important traits. These studies have used molecular genetic mapping of quantitative trait loci (QTL) of several complex traits that are important in breeding. The identification and molecular cloning of genes underlying QTLs offers the possibility to examine the naturally occurring allelic variation for respective complex traits.

Laboratory Information Management Software for genotyping workflows: applications in high throughput crop genotyping.

Background: With the advances in DNA sequencer-based technologies, it has become possible to automate several steps of the genotyping process leading to increased throughput. To efficiently handle the large amounts of genotypic data generated and help with quality control, there is a strong need for a software system that can help with the tracking of samples and capture and management of data at different steps of the process. Such systems, while serving to manage the workflow precisely, also encourage good laboratory practice by standardizing protocols, recording and annotating data from every step of the workflow.

Opportunities for nutritionally enhanced maize and wheat varieties to combat protein and micronutrient malnutrition.

Naturally occurring variation detected in the germplasm of maize and wheat, two of the top three cereal crops in the world, provides options for incorporating higher levels of iron, zinc, and beta-carotene into these grains. In addition, quality protein maize (QPM) has been developed from naturally occurring variation; its seed contains enhanced levels of lysine and tryptophan, two essential amino acids lacking in cereals. The International Maize and Wheat Improvement Center, along with its many partners, has identified several maize and wheat varieties with 25% to 30% higher grain iron and zinc concentrations.

A new intervarietal linkage map and its application for quantitative trait locus analysis of "gigas" features in bread wheat.

A doubled-haploid (DH) population from an intervarietal cross between the Japanese cultivar 'Fukuho-komugi' and the Israeli wheat line 'Oligoculm' was produced by means of wheat x maize crosses. One hundred seven DH lines were genotyped to construct a simple sequence repeat (SSR) based linkage map with RFLP, RAPD, and inter-simple sequence repeat markers. Out of 570 loci genotyped, 330 were chosen based on their positions on the linkage map to create a "framework" map for quantitative trait locus (QTL) analysis.

Competition of Bacillus thuringiensis Cry1 toxins for midgut binding sites: a basis for the development and management of transgenic tropical maize resistant to several stemborers.

Binding and competition of five Bacillus thuringiensis toxins--Cry1Ab, Cry1Ac, Cry1Ba, Cry1Ca, and Cry1Ea--for midgut binding sites from three pests, Spodoptera frugiperda, Diatraea saccharalis, and Diatraea grandiosella, were investigated as part of a strategy to develop tropical transgenic maize resistant to several stemborers. On S. frugiperda, Cry1Ab and Cry1Ac compete for the same binding site; Cry1Ba and Cry1Ca compete for a second binding site.

Stress-induced expression in wheat of the Arabidopsis thaliana DREB1A gene delays water stress symptoms under greenhouse conditions.

One of the major environmental factors limiting plant productivity is lack of water. This is especially true for the major cereals maize, rice, and wheat, which demonstrate a range of susceptibility to moisture deficit. Although conventional breeding and marker-assisted selection are being used to develop varieties more tolerant to water stress, these methods are time and resource consuming and germplasm dependent.