- Research article
- Open Access
ESTs from a wild Arachis species for gene discovery and marker development
© Proite et al; licensee BioMed Central Ltd. 2007
- Received: 07 December 2006
- Accepted: 15 February 2007
- Published: 15 February 2007
Due to its origin, peanut has a very narrow genetic background. Wild relatives can be a source of genetic variability for cultivated peanut. In this study, the transcriptome of the wild species Arachis stenosperma accession V10309 was analyzed.
ESTs were produced from four cDNA libraries of RNAs extracted from leaves and roots of A. stenosperma. Randomly selected cDNA clones were sequenced to generate 8,785 ESTs, of which 6,264 (71.3%) had high quality, with 3,500 clusters: 963 contigs and 2537 singlets. Only 55.9% matched homologous sequences of known genes. ESTs were classified into 23 different categories according to putative protein functions. Numerous sequences related to disease resistance, drought tolerance and human health were identified. Two hundred and six microsatellites were found and markers have been developed for 188 of these. The microsatellite profile was analyzed and compared to other transcribed and genomic sequence data.
This is, to date, the first report on the analysis of transcriptome of a wild relative of peanut. The ESTs produced in this study are a valuable resource for gene discovery, the characterization of new wild alleles, and for marker development. The ESTs were released in the [GenBank:EH041934 to EH048197].
- Genome Survey Sequence
- Late Leaf Spot
- Wild Allele
Peanut or groundnut (Arachis hypogaea L.) is the fourth most important oil seed in the world, cultivated mainly in tropical, subtropical and warm temperate climates . It is an important crop for both human and animal food. Its yields are reduced around the world by diseases including fungal leaf-spots caused by Cercospora arachidicola [Hori] and Phaseoisariopsis personata [Berk. & MA Curtis], the rust Puccinia arachidis [Speg.], groundnut rosette disease, and root-knot nematodes (Meloidogyne ssp.), the later causing losses of up to 12% in United States and India . High salinity and drought are also important reducers of yield in many parts of the world.
Wild relatives are an important source of genes for resistances to biotic and abiotic stresses that affect crop species. The genus Arachis arose in South America and its approximately 80 species have adapted to a wide range of environments. The cultigen A. hypogaea probably arose from a single or few events of hybridization involving AA and BB genome species. The hybrid underwent spontaneous duplication of chromosomes to produce the allotetraploid A. hypogaea with genome type AABB . This difference in ploidy rendered peanut sexually isolated, giving this species a very narrow genetic basis [4, 5].
Due to this sexual isolation, the introgression of wild genes is only possible through complex crosses or genetic transformation. To date, there is only one case of successful introgression of genes from wild species into A. hypogaea to produce commercial cultivars of peanut . This was through the use of a synthetic allotetraploid (also called a synthetic amphidiploid, or amphiploid), created by crosses between wild Arachis species. Although the wild species used were non-ancestral, the crosses, in some ways, approximate a re-synthesis of the species A. hypogaea. Genetic transformation of peanut, although difficult, has also been accomplished by a number of techniques [6–10].
For improvement of the peanut crop, there is a need to both identify novel genes with potential agronomic interest and to either develop molecular markers associated with such genes for use in marker assisted selection, or to use genes in genetic transformation. EST sequencing projects have been contributing to gene discovery and marker development as well as shedding light on the complexities of gene expression patterns and functions of transcripts [11–13].
A few projects on the generation of ESTs from A. hypogaea have recently been accomplished, using different tissues and conditions: plants subjected to Aspergillus parasiticus infection and drought stress , late leaf spot  and unstressed tissues . However, at present a total of roughly 25,000 Arachis ESTs are available in Genbank, all derived from cultivated peanut A. hypogaea and none from wild species of Arachis.
Arachis stenosperma is a wild diploid species which presents a number of disease resistances. Plants of this species form fertile hybrids with A. duranensis  (the AA genome donor of peanut [18, 19], and is therefore a potential AA genome donor for synthetic allotetraploids. It is also a parent for the population from which was derived the only SSR-based map of Arachis .
Here we report the partial sequences, database comparisons and functional categorization of 8,785 randomly collected cDNA clones of A. stenosperma and their use for the development of 107 microsatellite markers. These data will be useful for those searching for novel genes from wild Arachis.
cDNA libraries construction, sequencing and ESTs analysis
Summary of the Arachis stenosperma V10309 EST libraries
Total number of reads: 8785 clones
Number of clusters
Number of contigs
Number of singletons
Homology (% of ESTs) to known sequences
Homologies of the most abundantly expressed RNAs as determined by ESTs redundancy
# of reads
Genbank Accession number
auxin-repressed protein-like protein (Manihot esculenta)
Ara h 8 allergen (Arachis hypogaea)
type 2 metallothionein (Vigna angularis)
PR10 protein (Arachis hypogaea)
cytokinin oxidase-like protein (Arabidopsis thaliana)
alcohol dehydrogenase 1; ADH1 (Lotus corniculatus)
metallothionein-like protein (Arachis hypogaea)
proline-rich protein precursor (Phaseolus vulgaris)
ripening related protein (Glycine max)
hypothetical protein (Nicotiana tabacum)
Protein sequences derived from hypothetical translations of the 3,500 unique sequences are homologous to many classes of proteins. Automatic classification revealed, the main groups of ESTs are related to: cellular processes and signaling, especially those related to post-translational modifications, protein turnover and chaperones (30.6% of all reads); information storage and processing, including various protein kinases (29.3%), and metabolism and energy conversion and sugar, water and ion transporters (21.5%). One drawback of functional classification is the crude approach since the assignments are based on several sets of known proteins and a large percentage of ESTs (7.8%) remained unclassified.
More specifically, sequences of agronomical and medical interest were also found. Sequence contigs related to stress induced genes were numerous and included resistance gene-analogues (RGAs, 35 contigs), pathogenesis-related (PR) proteins (26 contigs), lectins (20 contigs), drought-induced proteins (13 contigs), heat-shock proteins (11 contigs) and aluminium-induced proteins (eight contigs). In addition, there are ESTs whose derived proteins are of potential importance to human health. For instance, homologs to genes encoding allergenicity-related proteins (32 contigs), enzymes involved in the synthesis of isoflavonoids: phenylalanine ammonia-lyase (two contigs), resveratrol synthase and stilbene synthase (15 contigs); oxysterol-binding protein (one contig) and tumor suppressor protein (three) were found. Other sequences of interest were related to nodulation (30 contigs) and homologous to retroelements (nine contigs).
The most frequent clones sequenced had BLASTx hits to: auxin-repressed protein-like protein (115 reads), Arah8 allergen (69 reads), type 2 metallothionein (60 reads), PR10 protein (56 reads) and cytokinin oxidase-like protein (44 reads) (Table 2).
Analysis of microsatellites and development of markers
From the EST data described in this work, a total of 188 microsatellite markers have been developed and characterized for polymorphism, 81 of these were already published in Moretzsohn et al. . From the 107 new ones published here, 84 have been characterized, of these 21 were polymorphic for the AA population, and four for cultivated peanut. Primer sequences, microsatellite types, polymorphism, homologies and linkage groups assigned to the markers are available in Additional File 1.
The most significant stresses of the peanut crop are pathogens and drought. Together with food safety (low levels of aflatoxins and allergenic compounds) they represent the most important targets for crop improvement. Because of the low genetic diversity in the peanut crop, wild relatives are an important source of novel genes. Geographically, A. stenosperma is the most widely spread Arachis species and, in consequence, has been selected in diverse environments ranging from savannah to coastal dunes. It is sexually compatible with the most probable AA genome donor of cultivated peanut (A. duranensis), and therefore is an excellent genome donor candidate for gene introgression. In addition, the species shows signs that it has itself been subject to selection for cultivation traits by South American natives . Therefore, it is a very promising source of new genes for improving cultivated peanut. More specifically, the accession A. stenosperma V10309 is very resistant to root-knot nematode, leaf spots and rust fungi (data not shown). For these reasons, A. stenosperma V10309 was chosen as the model for this EST project. In this work, a number of clones of agronomic and medical importance were found, and new microsatellite markers were developed and characterized.
Resveratrol-synthase and stilbene synthase are two enzymes involved in the production of resveratrol, a naturally occurring plant compound associated with defense mechanisms against biotic and abiotic stresses . Results from various research studies on edible peanuts have shown that, in humans, resveratrol may protect against atherosclerosis by preventing the oxidation (or breakdown) of the LDL cholesterol in the blood and thus the deposition of cholesterol in the walls of arteries leading to heart disease . It has also been shown to be linked to the suppression of the development of carcinoma cell lines . Chalcone synthase and phenylalanine ammonia-lyase are two key related enzymes involved in the biosyntheses of phytoalexin isoflavonoids in legumes . Isoflavonoids are a class of flavonoids that have estrogen-like activity and which lower serum LDL cholesterol and raise HDL cholesterol, thus having important implications in human health . Oxysterol-binding proteins comprise a large conserved family of cytosolic proteins in eukaryotes. They have been proposed to have a receptor-like role in regulating cholesterol synthesis, being therefore important in the cholesterol metabolism of the human body .
In contrast to the potential health benefits of resveratrol and stilbene synthases, allergens in peanut seeds are a major problem. Unexpectedly, the allergen AraH 8 was the second most abundant EST, with 69 occurrences. So far, nine potentially important allergens of peanut have been identified (AraH1 to AraH8 and peanut oleosin) . AraH8 has been described relatively recently; it was deposited in the NCBI in February 2005 from A. hypogaea, with a single entry. AraH8 has sequence homology to several pathogenesis-related proteins and may itself be a PR protein. Studies show that allergy to this protein is heavily correlated to allergy to birch pollen . Interestingly, this seemed to be the only allergen expressed abundantly in the roots of A. stenosperma.
Stress and Defense-related genes
Although the plants were kept in the greenhouse, in near-optimum conditions, sequences with hits to genes responsive to biotic and abiotic stresses were found in all four libraries. Similarly, defense-related sequences were previously found in a number of other EST projects with non-inoculated tissue of different species [28, 29].
One mechanism of plant defense, mediated by specific resistance genes, involves the recognition of pathogens by the plant. Among the cellular events that characterize this type of resistance are oxidative burst, cell wall strengthening, induction of defense gene expression, and rapid cell death at the site of the infection . Resistance genes are often organized in clusters, and consequently RGAs have been shown to be genetically linked to known R-genes, or indeed to be fragments of the known R-genes themselves [31–34].
The first published study on RGAs of Arachis was by Bertioli et al.  who isolated 78 complete contigs from A. hypogaea and four wild relatives, including A. stenosperma V10309, used here. Recently, Yuksel et al.  isolated 234 RGAs from A. hypogaea. In the ESTs produced in this study 35 non-redundant sequences had significant homology to A. thaliana NBS containing genes.
The plant hormone auxin regulates various growth and developmental processes including lateral root formation, apical dominance, tropism and differentiation of vascular tissue . A number of genes have been classified as auxin-response genes, with their expression levels increasing within minutes of auxin application, independent on the de novo protein synthesis [38, 39]. However, to date, auxin-repressed protein (ARP) genes and their role in plant growth and development are relatively understudied. So far, three orthologs of ARP have been isolated and described: SAR5 – isolated from strawberry receptacles and positively correlated with fruit maturation, PsDRM1- dormancy related protein from pea and RpARP- isolated from the legume tree Robinia pseudoacacia (black locust) which is negatively related to hypocotyl elongation . Although its biological function has not yet been clarified, RpARP was found to be expressed in various developmental stages and tissues and to play an important role in biological processes that are characteristic under non-growing or stress conditions . In this study, a clone encoding an amino acid sequence with homology to the auxin repressed protein domain (pfam05564.4) was the most expressed sequence in A. stenosperma roots (Table 2). The clone's top BLASTx hit was to an auxin repressed protein homolog from Manihot esculenta.
The third most abundant transcript found here had homology to type 2 metallothionein of Vigna angularis. Metallothioneins are low molecular (6–7 kD), Cys-rich, metal-binding proteins that have a role in protection against the effects of reactive oxygen species (ROS) by acting as antioxidants as they are potent scavengers of hydroxyl radicals [41, 42]. Reactive oxygen species (ROS) may accumulate after the hypersensitive response occurs due to the specific recognition of a pathogen by a plant disease resistance gene and is associated with rapid ion fluxes and protein phosphorylation. ROS may directly repel invading pathogens or serve as signaling molecules that activate defense response . However, ROS resulting from biotic and abiotic stresses can cause cellular damage and need to be detoxified by complex enzymatic and non-enzymatic mechanisms .
The reaction between the pathogen elicitor and the R-gene is the first step for an oxidative burst and Systemic Acquired Resistance (SAR). SAR, by its turn, activates gene expression mediated by the master regulator proteinNPR1 (Nonexpressor of pathogenesis-related (PR) genes). NPR1 not only directly induces the PR genes but also prepares the cell for secretion of the PR proteins by first making more secretory machinery components . PR (pathogenesis-related) proteins are soluble proteins encoded by a plant host when under attack by a pathogen. They were first described for tobacco  and are classified from PR1 to PR10 according to their mobility upon electrophoresis gel. In this work the fourth most found sequences had homology to a PR10 from peanut (Table 2).
Cytokinin oxidase-like protein
The fifth most abundant transcripts found here, with 44 clones, had homology to Arabidopsis thaliana cytokinin oxidase (Table 2). Cytokinins are essential hormones for plant growth and development. The modulation of cytokinin levels is performed by the irreversible degradation of cytokinins catalyzed by cytokinin-oxydase, . Cytokinin oxydase gene expression has been found to be induced in maize under drought and heat stresses in order to control plant growth under these conditions .
Nitrogen assimilation is an important process controlling plant growth and development. The assimilation of inorganic nitrogen into carbon skeletons has marked effects on plant productivity, biomass, and crop yield. Inorganic nitrogen is assimilated into the amino acids glutamine, glutamate, asparagine, and aspartate, which serve as important nitrogen carriers in plants. The enzymes involved in the biosynthesis of these nitrogen-carrying aminoacids are glutamine synthetase (GS), glutamate synthase (GOGAT), glutamate dehydrogenase (GDH), aspartate aminotransferase (AAT), and asparagine synthetase (AS) . Each of these enzymes is encoded by a gene family wherein individual members encode distinct isoenzymes that are differentially regulated by environmental stimuli, metabolic control, developmental control, and tissue/cell-type specificity . ESTs with homologies to all of these enzymes were found in this study. In addition, homologues to symbiosis specific genes such as ENOD40, Nodulin 35, Nodulin MtN21 and nodulation receptor kinases were also found.
Molecular markers are useful for genetic map construction, marker-assisted selection in breeding programs, studies of crop evolution, phylogenetic relationships and cultivar protection. For peanut, little variation has been observed with molecular markers, in spite of its considerable phenotypic variability (reviewed by Dwivedi et al., 49.). Microsatellite markers have been useful markers in plant genetic research, but they are expensive and labour-intensive to produce. Data-mining microsatellite markers from EST data can be a cost effective option. In the EST sequences published here, 206 microsatellites were found, from which 164 microsatellite markers have been developed and characterized. Almost all microsatellites had low repeat number of di- and tri-nucleotide motifs. Of the di-nucleotide repeats, by far the most common were TC and AT repeats.
In Arachis, certain microsatellite types are more polymorphic than others. Dinucleotide repeats are more polymorphic than trinucleotide repeats, AG/TC repeats are more polymorphic than AC/TG repeats, and, for cultivated germplasm, longer microsatellites (15 or more motif repeats) are more polymorphic . The vast majority of microsatellites in ESTs are low repeat number, and accordingly the microsatellite markers developed from these ESTs have low polymorphism in cultivated germplasm (see Additional File 1). Our analysis of microsatellites present in the ESTs and in GSSs shows that longer TC repeats are very rare in both transcribed and non-transcribed DNA, being present in c. 0.1% of ESTs, and c. 0.2% of genome survey sequences (Figure 2A and 2B). This leads us to believe that unless very large numbers of sequences are produced, the use of microsatellite enrichment strategies [17, 50, 51] will be the most productive way for cultivated germplasm marker development. In contrast, for wild germplasm the EST microsatellite markers had good levels of polymorphism and have the advantage of being genic. As previously observed, EST microsatellite markers have much potential for work with wild alleles, and for the construction of gene-rich maps .
EST databases provide a great deal of information on the complexities of gene expression patterns, the functions of transcripts and are useful for the development of molecular markers. In this study, EST analysis of the wild relative of peanut, A. stenosperma showed that this species has a considerable number of genes related to human health, plant defense, hormone response, all which could be potentially useful for introgression in the cultivated species. To conclude, ESTs produced in this study are a valuable resource for gene discovery, the characterization of new wild alleles, and for marker development.
cDNA libraries construction
Arachis stenosperma seeds were germinated in sterile soil. Materials for RNA extraction were collected from three-month old plants: healthy leaves, healthy roots, roots inoculated with 2 mL of a suspension of 108 cells of Bradyrhizobium japonicus, and roots inoculated with 10.000 juveniles (J2) Meloidogyne arenaria (Neal) Chitwood race 1. Collected materials were immediately frozen in liquid nitrogen for RNA extraction.
Total RNA was isolated from plant materials using Trizol Reagent (Invitrogen, Carlsbad, CA, USA), according to the manufacture's instructions. The quantity and quality of total RNA was evaluated by spectrophotometry (OD260/280) and formaldehyde-1% agarose gel electrophoresis. Poly (A)+ RNA was extracted from 1 mg of total RNA using the Oligotex Spin Column (Qiagen Inc., Valencia, CA, USA) according to the manufacture's protocol.
Full-length cDNA libraries were constructed using the SMART cDNA synthesis kit in ëTriplEx2 (Clontech, Palo Alto, CA, USA). The resulting cDNA was packed into ë phages using the Gigapack III Gold packaging kit (Stratagene, La Jolla, CA, USA). The pTriplEx2 phagemid clones in Escherichia coli were obtained using the mass in-vivo excision protocol according to the manufacture's instructions (Clontech, USA). The white clones grown on screening LB medium (Amp/IPTG/X-Gal) were recovered by random colony selection.
Sequencing and ESTs analysis
Plasmid DNA was isolated from the selected colonies using the alkaline-lysis method and the cDNA inserts sequenced from the 5'-end using specifically designed primer PT2F2 5'-GCGCCATTGTGTTGGTACCC-3'. Sequencing reactions were performed with Big-Dye Terminator Cycle Sequencing Kit, version 3.1 (Applied Biosystems, CA, USA) or DYEnamic ET Terminator Cycle Sequencing Kit (Amersham Pharmacia Biotech) using the Applied Biosystems automated DNA sequencers 3100 and 377.
Base calling and quality assignment of individual bases were done through the use of Phred . Ribosomal, poly(A) tails, low-quality sequences and vector and adapter regions were removed as described by Telles and da Silva  with minor adaptations. The resulting sets of cleaned sequences were assembled into clusters of overlapping sequences using the CAP3 assembler , with individual base quality and default parameters. Assembled sequences were submitted for comparison against the GenBank database using BLASTx  available from the NCBI (National Center for Biotechnology Information) . Putative functions of the ESTs were classified according to the Clusters of Orthologous Groups of proteins – KOG . Resistance Gene Analogues (RGAs) were identified in the EST bank by using a BLASTx search against a local database of Arabidopsis NBS encoding genes .
Analysis of microsatellites and development of markers
Microsatellite primers were developed using the module of softwares described by Martins et al. . For the analysis, we considered microsatellites with di-, tri-, tetra-, penta- and hexa- nucleotide motifs with six or more motif repetitions. For comparison, microsatellites were also analyzed from clustered A. hypogaea transcripts, and A. duranensis genome survey sequences (GSSs) submitted by Steven J Knapp to Genbank.
Polymorphism was screened for in the progenitors of a diploid mapping population by PCR. The progenitors of this population are A. duranensis K7988 and A. stenosperma V10309 , both deposited in the Embrapa Genetic Resources and Biotechnology Germplasm Bank. Markers polymorphic for the diploid population were genotyped and map positions determined. For screening for polymorphism in the cultivated peanut, 16 accessions with representatives from all the six botanical varieties were used.
The authors gratefully acknowledge European Union INCO-DEV Programme (ARAMAP reference: ICA4-2001-10072), The World Bank and Embrapa (Prodetab Project 004/2001), Generation Challenge Program, CNPq and host institutions for funding this research. The authors also wish to thank Dr. José Valls for providing seeds and for useful discussions, Dr. Regina Carneiro for providing nematodes, Drs. Wellington Martins and Roberto Togawa for bioinformatics support.
- FAO Statistical Yearbook 2004. [http://www.fao.org/statistics/yearbook/vol_1_1/site_en.asp?page=production]
- Bailey JE: Peanut Disease Management. 2002 peanut information. North Carolina Coop Ext Serv. Raleigh, NC, 2002:71-86.Google Scholar
- Simpson CE: Use of wild Arachis species/introgression of genes into Arachis hypogaea L. Peanut Sci. 2001, 28: 114-116.View ArticleGoogle Scholar
- Stalker HT, Simpson CE: Germplasm resources in Arachis. Advances in Peanut Science. Edited by: Pattee HE, Stalker HT. Stilwater: APRES, 1995:14-53.Google Scholar
- Raina SN, Rani V, Kojima T, Ogihara Y, Singh KP, Devarumath RM: RAPD and ISSR fingerprints as useful genetic markers for analysis of genetic diversity, varietal identification, and phylogenetic relationships in peanut (Arachis hypogaea) cultivars and wild species. Genome. 2001, 44: 763-772. 10.1139/gen-44-5-763.PubMedView ArticleGoogle Scholar
- Mansur EA, Lacorte C, Freitas VG, Oliveira DE, Timmerman B, Cordeiro AR: Regulation of transformation efficiency of peanut (Arachis hypogaea L.) explants by Agrobacterium tumefaciens. Plant Sci. 1993, 89: 93-99. 10.1016/0168-9452(93)90174-X.View ArticleGoogle Scholar
- Sharma KK, Anjaiah V: An efficient method for the production of transgenic plants of peanut (Arachis hypogaea L.) through Agrobacterium tumefasciens-mediated genetic transformation. Plant Sci. 2000, 159: 7-19. 10.1016/S0168-9452(00)00294-6.PubMedView ArticleGoogle Scholar
- Ozias-Akins P, Gill R: Progress in the development of tissue culture and transformation methods applicable to the production of transgenic peanut. Peanut Sci. 2001, 28: 123-131.View ArticleGoogle Scholar
- Yang HY, Nairn J, Ozias-Akins P: Transformation of peanut using a modified bacterial mercuric ion reductase gene driven by an actin promoter from Arabidopsis thaliana. J Plant Physiol. 2003, 160: 945-952. 10.1078/0176-1617-01087.PubMedView ArticleGoogle Scholar
- Joshi M, Niu C, Fleming G, Hazra S, Chu Y, Nairn CJ, Yang H, Ozias-Akins P: Use of green fluorescent protein as a non-destructive marker for peanut genetic transformation. In vitro cellular and development Biology – Plant. 2005, 41: 437-445. 10.1079/IVP2005676.View ArticleGoogle Scholar
- Houde M, Belcaid M, Ouellet F, Danyluk J, Monroy AF, Dryanova A, Gulick P, Bergeron A, Laroche A, Links MG, MacCarthy L, Crosby WL, Sarhan F: Wheat EST resources for functional genomics of abiotic stress. BMC Genomics. 2006, 7: 149-10.1186/1471-2164-7-149.PubMedPubMed CentralView ArticleGoogle Scholar
- Nelson RT, Shoemaker R: Identification and analysis of gene families from the duplicated genome of soybean using EST sequences. BMC Genomics. 2006, 7: 204-10.1186/1471-2164-7-204.PubMedPubMed CentralView ArticleGoogle Scholar
- Han Z, Wang C, Song X, Guo W, Gou J, Li C, Chen X, Zhang T: Characteristics, development and mapping of Gossypium hirsutum derived EST-SSRs in allotetraploid cotton. Theor Appl Genet. 2006, 112: 430-439. 10.1007/s00122-005-0142-9.PubMedView ArticleGoogle Scholar
- Luo M, Liang XQ, Dang P, Holbrook CC, Bausher MG, Lee RD, Guo BZ: Microarray-based screening of differentially expressed genes in peanut in response to Aspergillus parasiticus infection and drought stress. Plant Sci. 2005, 169: 695-703 (c). 10.1016/j.plantsci.2005.05.020.View ArticleGoogle Scholar
- Luo M, Dang P, Bausher MG, Holbrook CC, Lee RD, Lynch RE, Guo BZ: Identification of transcripts involved in resistance responses to leaf spot disease caused by Cercosporidium personatum in peanut (Arachis hypogaea). Phytopathol. 2005, 95: 381-387 (a).View ArticleGoogle Scholar
- Luo M, Dang P, Guo BZ, He G, Holbrook C, Bausher MG, Lee RD: Generation of Expressed Sequenced tags (ESTs) for gene discovery and marker development in cultivated peanut. Crop Sci. 2005, 45: 346-353 (b).View ArticleGoogle Scholar
- Moretzsohn MC, Leoi L, Proite K, Guimarães PM, Leal-Bertioli SCM, Gimenes MA, Martins WS, Grattapaglia D, Bertioli DJ: Development and mapping of microsatellite markers in Arachis (Fabaceae). Theor Appl Genet. 2005, 111: 1432-2242. 10.1007/s00122-005-0028-x.View ArticleGoogle Scholar
- Kochert G, Stalker HT, Gimenes M, Galgaro L, Lopes CR, Moore K: RFLP and cytogenetic evidence on the origin and evolution of allotetraploid domesticated peanut, Arachis hypogaea (Leguminosae). Am J Bot. 1993, 83: 1282-1291. 10.2307/2446112.View ArticleGoogle Scholar
- Seijo GJ, Lavia GI, Fernandez A, Krapovickas A, Ducasse E, Moscone DEA: Physical mapping of the 5s and 18s–25s rRNA genes by fish as evidence that Arachis duranensis and A. ipaënsis are the wild diploid progenitors of A. hypogaea (leguminosa). Am J Bot. 2004, 91: 1294-1303.PubMedView ArticleGoogle Scholar
- Chung IM, Park MR, Rehman S, Yun SJ: Tissue specific and inducible expression of resveratrol synthase gene in peanut plants. Mol Cells. 2001, 12: 353-359.PubMedGoogle Scholar
- Sanders TH, McMichael RW, Hendrix KW: Occurrence of resveratrol in edible peanuts. J Agric Food Chem. 2000, 48: 1243-1246. 10.1021/jf990737b.PubMedView ArticleGoogle Scholar
- Ulrich S, Wolter F, Stein JM: Molecular mechanisms of the chemopreventive effects of resveratrol and its analogs in carcinogenesis. Mol Nutr Food Res. 2005, 49: 452-61. 10.1002/mnfr.200400081.PubMedView ArticleGoogle Scholar
- Ellis JS, Jennings AC, Edwards LA, Mehrdad M, Lamb CJ, Dixon RA: Defense gene expression in elicitor-treated cell suspension cultures of French bean cv. Imuna. Plant cell rep. 1989, 8: 504-507. 10.1007/BF00269060.PubMedView ArticleGoogle Scholar
- Newnham HH: Oestrogens and the atherosclerotic vascular disease – lipid factors. Baillieres Clin Endocrinol Metab. 1993, 7: 61-93. 10.1016/S0950-351X(05)80271-X.PubMedView ArticleGoogle Scholar
- Patel NT, Thompson EB: Human oxysterol-binding protein. I. Identification and characterization in liver. J Clin Endocrinol Metabo. 1990, 71: 1637-1645.View ArticleGoogle Scholar
- Communicating about food allergies. [http://foodallergens.ifr.ac.uk]
- Mittag D, Akkerdaas J, Ballmer-Weber BK, Vogel L, Wensing M, Becker WM, Koppelman SJ, Knulst AC, Helbling A, Hefle SL, Van Ree R, Vieths S: Ara h 8, a Bet v 1-homologous allergen from peanut, is a major allergen in patients with combined birch pollen and peanut allergy. J Allergy Clin Immunol. 2004, 114: 1410-1417. 10.1016/j.jaci.2004.09.014.PubMedView ArticleGoogle Scholar
- Lee CM, Lee YJ, Lee MH, Nam HG, Cho TJ, Hahn TR, Cho MJ, Sohn U: Large-scale analysis of expressed genes from the leaf of oilseed rape (Brassica napus L.). Plant Cell Rep. 1998, 17: 930-936. 10.1007/s002990050512.View ArticleGoogle Scholar
- Sasaki T, Song J, Koga-Ban Y, Matsui E, Fang F, Higo H, Nagasaki H, Hori M, Miya M, Murayama-Kayano E, Takiguchi T, Takasuga A, Niki T, Ishimaru K, Ikeda H, Yamamoto Y, Mukai T, Ohta I, Miyadera N, Havukkala I, Minobe Y: Toward cataloguing all rice genes: large scale sequencing of randomly chosen rice cDNAs from a callus cDNA library. Plant J. 1994, 6: 615-624. 10.1046/j.1365-313X.1994.6040615.x.PubMedView ArticleGoogle Scholar
- Pan Q, Wendel J, Fluhr R: Divergent evolution of plant NBS-LRR resistance gene homologues in dicot and cereal genomes. J Mol Evol. 2000, 50: 203-213.PubMedGoogle Scholar
- Collins NC, Park R, Spielmeyer W, Ellis J, Pryor T: Resistance gene analogs in barley and their relationships to rust resistance genes. Genome. 2001, 44: 375-381. 10.1139/gen-44-3-375.PubMedView ArticleGoogle Scholar
- Peñuela S, Danesh D, Young ND: Targeted isolation, sequence analysis, and physical mapping of nonTIR NBS-LRR genes in soybean. Theor Appl Genet. 2002, 104: 261-272. 10.1007/s00122-001-0785-0.PubMedView ArticleGoogle Scholar
- Zhang LP, Khan A, Niño-Liu D, Foolad MR: A molecular linkage map of tomato displaying chromosomal locations of resistance gene analogs based on a Lycopersicon esculentum x Lycopersicon hirsutum cross. Genome. 2002, 45: 133-146. 10.1139/g01-124.PubMedView ArticleGoogle Scholar
- Madsen LH, Collins NC, Rakwalska M, Backes G, Sandal N, Krusell L, Jensen J, Waterman EH, Jahoor A, Ayliffe M, Pryor AJ, Langridge P, Schulze-Lefert P, Stougaard J: Barley disease resistance gene analogs of the NBS-LRR class: identification and mapping. Mol Genet Genomics. 2003, 269: 150-161.PubMedGoogle Scholar
- Bertioli DJ, Leal-Bertioli SC, Lion MB, Santos VL, Pappas G, Cannon SB, Guimarães PM: A large scale analysis of resistance gene homologues in Arachis. Mol Genet Genomics. 2003, 270: 34-45. 10.1007/s00438-003-0893-4.PubMedView ArticleGoogle Scholar
- Yuksel B, Estill JC, Schulze SR, Paterson AH: Organization and evolution of resistance gene analogs in peanut. Mol Genet Genomics. 2005, 274: 248-263. 10.1007/s00438-005-0022-7.PubMedView ArticleGoogle Scholar
- Muday GK: Auxin and Tropisms. J Plant Growth Regul. 2001, 20: 226-243. 10.1007/s003440010027.PubMedView ArticleGoogle Scholar
- Guilfoyle T, Hagen G, Ulmasov T, Murfett J: How Does Auxin Turn On Genes?. Plant Physiol. 1998, 118: 341-347. 10.1104/pp.118.2.341.PubMedPubMed CentralView ArticleGoogle Scholar
- Walker L, Estelle M: Molecular mechanisms of auxin action. Curr Opin Plant Biol. 1998, 1: 434-439. 10.1016/S1369-5266(98)80269-0.PubMedView ArticleGoogle Scholar
- Park S, Han KH: An auxin-repressed gene (RpARP) from black locust (Robinia pseudoacacia) is posttranscriptionally regulated and negatively associated with shoot elongation. Tree Physiol. 2003, 23: 815-23.PubMedView ArticleGoogle Scholar
- Chubatsu L, Meneghini R: Metallothionein protects DNA from oxidative damage. Biochem J. 1993, 291: 193-198.PubMedPubMed CentralView ArticleGoogle Scholar
- Muira T, Muraoga S, Ogiso T: Antioxidant activity of metallothionein compared with reduced glutathione. Life Sci. 1997, 60: PL 301-309. 10.1016/S0024-3205(97)00156-2.View ArticleGoogle Scholar
- Hammond-Kosack KE, Jones JDG: Inducible plant defence mechanisms and resistance gene function. Plant Cell. 1996, 8: 1773-1791. 10.1105/tpc.8.10.1773.PubMedPubMed CentralView ArticleGoogle Scholar
- Mittler R: Oxidative stress, antioxidants and stress tolerance. Trends Plant Sci. 2002, 7: 405-410. 10.1016/S1360-1385(02)02312-9.PubMedView ArticleGoogle Scholar
- Wang D, Weaver ND, Kesarwani M, Dong X: Induction of protein secretory pathway is required for systemic aquired resistance. Science. 2005, 308: 1036-1040. 10.1126/science.1108791.PubMedView ArticleGoogle Scholar
- Legrand M, Kauffmann S, Geoffroy P, Fritig B: Biological function of pathogenesis-related proteins: four tobacco pathogenesis-related proteins are chitinases. Proc Natl Acad Sci USA. 1987, 84: 6750-6754. 10.1073/pnas.84.19.6750.PubMedPubMed CentralView ArticleGoogle Scholar
- Brugière N, Jiao S, Hantke S, Zinselmeier C, Roessler JA, Niu X, Jones RJ, Habben JE: Cytokinin Oxidase Gene Expression in Maize Is Localized to the Vasculature, and Is Induced by Cytokinins, Abscisic Acid, and Abiotic Stress. Plant Physiol. 2003, 132: 1228-1240. 10.1104/pp.102.017707.PubMedPubMed CentralView ArticleGoogle Scholar
- Lam HM, Coschigano KT, Oliveira IC, Melo-Oliveira R, Coruzzi GM: The molecular genetics of nitrogen assimilation into amino acids in higher plants. Annu Rev Plant Physiol Plant Mol Biol. 1996, 47: 569-593. 10.1146/annurev.arplant.47.1.569.PubMedView ArticleGoogle Scholar
- Dwivedi Sl, Bertioli DJ, Crouch JH, Valls JFM, Upadhyaya HD, Fávero AP, Moretzsohn MC, Paterson AH: Peanut Genetics and Genomics: Toward Marker-assisted Genetic Enhancement in Peanut (Arachis hypogaea L). Oilseeds Series: Genome Mapping and Molecular Breeding in Plants. Edited by: Kole C. 2006, Springer; Oilseeds, 2: 115-151.View ArticleGoogle Scholar
- Rafalski JA, Vogel JM, Morgante M, Powell W, Andre C, Tingey SV: Generating and using DNA markers in plants. Analysis of non-mammalian genomes – a practical guide. Edited by: Birren B, Lai E. 1996, New York: Academic Press, 75-134.Google Scholar
- Ferguson ME, Burow MD, Schulze SR, Bramel PJ, Paterson AH, Kresovich S, Mitchell S: Microsatellite identification and characterization in peanut (A. hypogaea L.). Theor Appl Genet. 2004, 108: 1064-1070. 10.1007/s00122-003-1535-2.PubMedView ArticleGoogle Scholar
- Ewing B, Hillier L, Wendl M, Green P: Base-Calling of Automated Sequencer Traces Using Phred I Accuracy Assessment. Genome Res. 1998, 8: 175-185.PubMedView ArticleGoogle Scholar
- Telles GP, da Silva FL: Trimming and clustering sugarcane ESTs. Genet Mol Biol. 2001, 24: 17-23.View ArticleGoogle Scholar
- Huang X, Madan A: Cap3: a DNA sequence assembly program. Genome Res. 1999, 9: 868-877. 10.1101/gr.9.9.868.PubMedPubMed CentralView ArticleGoogle Scholar
- Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997, 25: 3389-3402. 10.1093/nar/25.17.3389.PubMedPubMed CentralView ArticleGoogle Scholar
- National Center for Biotechnology Information. 1997, [http://ncbi.nlm.nih.gov]
- Clusters of Orthologous Groups. [http://www.ncbi.nih.gov/COG/new/shokog.cgi]
- Functional and Comparative Genomics of Disease Resistance Gene Homologs. [http://niblrrs.ucdavis.edu]
- Martins W, de Sousa D, Proite K, Guimarães P, Moretzsohn M, Bertioli DJ: New softwares for automated microsatellite marker development. Nucleic Acids Res. 2006, E31-10.1093/nar/gnj030. 34 Web ServerGoogle Scholar
This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.