The legume family is the second most important crop family as a human food source after cereals and in addition provides scores of other products including fodder and feedstock, valuable timber, vegetable oil, bio-fuels, important medicines and even poisons . Legumes are unequalled for stabilization and reforestation of degraded land due to their ability to fix nitrogen, compete with other plants, repel herbivory and grow on acid soils in a range of environments . Many legumes are major elements of international trade because they are high value and a source of protein, calories and oil. Within the legume family, common bean (Phaseolus vulgaris) is the most important crop for direct human consumption and is third in overall production after soybean (Glycine max L.) and peanuts (Arachis hypogea L.). However, unlike these species, beans are primarily grown on small- to medium-scale farms and are not used for industrial processing .
Expressed sequence tags (ESTs) are partial sequences of transcribed genes and represent gene expression in different tissues and often different genotypes depending on the plant treatment and development stage at which the mRNA was extracted . ESTs are known to be derived from transcribed mRNA which is cloned into cDNA libraries which are then sequence en masse. Therefore, a large effort has gone into constructing many different cDNA libraries for major legume crops such as soybean  and model legume species such as Lotus japonicus  and barrel medic, Medicago truncatula .
The number of ESTs found for all plant species now is over 21 million sequences. For the legumes a total of over 3 million sequences have been generated with the largest numbers in soybean (1.5 million) and the model legumes barrel medic (280,000) and lotus (242,000). This compares to over 6 million sequences in the Gramineae and nearly 3 million in the Brassicaceae.
Comprehensive libraries have been made for rice and Arabidopsis thaliana for example . Among the legumes, relatively fewer ESTs are found for the crop legumes than in the model legumes and soybean. Among the more minor legume crops, only a recent effort in cowpea (Vigna unguiculata) by Muchero et al.  nears the threshold of 200,000 total ESTs while common bean has about half that.
In common bean, there have been very few large scale efforts at cDNA cloning or EST sequencing and the current number of ESTs is 114,139 as of December 2010. Preparation of ESTs for common bean began with moderate numbers of GenBank entries by groups from CIAT, UNESP and UNAM [10–12] organizations in Colombia, Brazil and Mexico, respectively, showing the importance of this crop to Latin America.
Additional ESTs have been sequenced or analyzed in US universities such as Univ. of Minnesota  and Univ. of Missouri . Among these studies the first medium sized collections by Melotto et al.  and Ramírez et al.  consisted of 5,243 and 15,333 ESTs or unigenes, respectively. However, these represented EST sequencing of three and five different cDNA libraries, respectively.
The tissues sampled in common bean have represented mainly disease-infected seedling tissue for the set of libraries from Melotto et al.  and then a range of tissues from nodules and nodulated roots to leaves and pods for Ramírez et al. . Since then there has been the publication of one large scale EST collection of 37,919 un-trimmed ESTs by Thibivilliers et al.  from beans infected with rust (Uromyces appendiculatus) and one additional set of ESTs from two root libraries . In addition, a large number 391,150 ESTs have been developed for the suspensor cells of the related species P. coccineus by UCLA. Finally, a Canadian group at the Univ. of Saskatchewan has sequenced 10,272 ESTs from P. angustissimus, another relative of common bean.
Among other tropical legumes, pigeonpea (Cajanus cajan L.), has had an EST project of around 10,000 sequences  which are of interest due to the close relationship with common bean and its adaptation to the same dry to sub-humid conditions beans face. Cultivated peanut, Arachis hypogea, with 86,935 ESTs plus two ancestral species of peanut with around 32,000 ESTs each are the only other tropical legumes that have been emphasized.
Of these EST collections, only one collection from Ramírez et al.  and another rom Blair et al.  has represented tolerance to abiotic stresses so far with both research groups emphasizing genes expressed under low phosphorus conditions in roots However, some efforts have been made to evaluate metabolic pathways and clone transcription factors  or to sequence differentially expressed cDNAs from drought-treated tissues [18, 19]. Therefore, there is a need for additional EST sequencing in common bean and other tropical legumes especially for tissues affected by the drought and soil or weather stresses that are very important issues for productivity of these crops .
Among the legumes and for common beans in particular, one aspect of transcriptome analysis and EST sequencing that has been missing is the cloning of full-length cDNA clones. This technology, as first described by Seki et al.  and Carnici et al. , consists in capture of mRNA through their 5' caps and stabilization of the full transcript during ligation into an appropriate vector and during reverse transcription from the poly A tail . Full-length cDNA libraries have been made for a large range of arabidopsis tissues [24, 25] and for several starch-rich crops [26, 27] but fewer for legumes, except for soybean .
Full length cDNA libraries are extremely useful for analysis of the transcriptome and for comparative genomics and genome sequence validation given that they represent entire transcription units rather than partial gene sequences like most other cDNA libraries . They are especially valuable in that they uncover the transcriptional start site for most genes and EST sequencing of their 5'ends uncovers the un-translated region and methionine-encoding, ATG codon, translational start signal. They can then be used along with non-full length cDNA sequenced clones to cover entire gene sequences allowing scientists to determine where the open reading frame starts and ends and anchoring all this information to genomic sequences.
These characteristics give full-length cDNA sequences essential roles in discovering alternative splicing patterns and promoter regions . In some cases, full length cDNA clones have been used to construct microarrays to characterize the binding of transcription factors to promoter elements within the 5' UTRs of genes . Full length cDNAs also have utility in functional and physical analysis of protein activity and structure through their use as expression vectors as reviewed in . Several examples exist of 3D crystal structure being determined through the use of these clones [29–32].
In addition, full length cDNA clones have a role in characterizing gene structure in different species. For example their 5' and 3'sequences can be used to compare GC content and folding capacity in 5'UTR (un-translated regions) versus ORF (open reading frames) and 3'UTR regions .
Finally, as with other sorts of ESTs, full-length cDNA clone sequencing can be used to develop many types of genetic markers including simple sequence repeats (SSRs) which tend to be in greater supply in 5'UTR sequences, single nucleotide polymorphisms (SNPs) especially for different parts of ORFs [33, 34]. It is important to use standard genotypes such as those from genome sequencing efforts in the construction of full length cDNA libraries as the genome to gene comparisons become more straightforward when this occurs. In summary, full length cDNA technology can be very important for gene annotation, for sequencing of the transcriptome and for comparative genomics
The objectives of this research, therefore, were to make full-length cDNA libraries that would be useful for gene discovery in common bean, genome annotation of the sequenced genotypes and for an understanding of abiotic stress tolerance in the crop. Multiple treatments were sampled including unstressed, drought, low phosphorus and aluminum stressed plants so as to enhance the activation of the transcriptome machinery and naturally normalize the sampling of mRNAs. Furthermore, two genotypes were used in this initial fl-cDNA library construction, one known to be drought tolerant (BAT477) and the other which is the subject of full-length genomic sequencing (G19833). A total of nearly 10,000 ESTs were generated from the second library to show the utility of this technique in determining gene structure.
This EST sequencing project was performed as part of a breeding project to discover molecular markers in common beans for marginal areas of Sub-Saharan Africa and the process of marker discovery from full-length cDNA sequences is discussed. We also aimed to compare the ESTs from the full-length cDNA library to two previous large EST sets for common bean and show the advantages this technology has for genomic tool development in this less-well studied species.