Single nucleotide polymorphism (SNP) discovery in common bean

Authors: DE SOUZA, THIAGO - Universidade Federal De Vicosa; DE BARROS, EVERALDO - Universidade Federal De Vicosa; Bellato, Claudia; Fickus, Edward; Cregan, Perry; Pastor Corrales, Marcial - Talo

Submitted to: Molecular Breeding
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/1/2011
Publication Date: 9/30/2011
Citation: De Souza, T., De Barros, E.G., Bellato, C.M., Fickus, E.W., Cregan, P.B., Pastor Corrales, M.A. 2011. Single nucleotide polymorphism (SNP) discovery in common bean. Molecular Breeding. 30:419-428.

Interpretive Summary: DNA markers serve as genetic landmarks and are interspersed among the genes throughout the genome of higher organisms including common bean. If a marker is located near a gene of interest, the marker can be used as a surrogate to select for the desired form of the gene. For example, a common bean breeder can use a DNA marker to identify plants that carry the form of the gene that gives resistance to a disease rather than the form that leads to susceptibility. Single nucleotide polymorphisms or SNPs are a common type of DNA marker. The objective of the research reported here was to identify SNP DNA markers in common bean via the comparison of the DNA sequence of genes in a small set of common bean varieties. Differences in the DNA sequence of the different common bean varieties define the existence and position of the SNP DNA marker. A total of 555 SNP DNA markers were discovered via the comparison of the DNA sequence of the six common bean varieties. The SNPs identified are a resource to common bean geneticists for use in the discovery of genes that control important traits and in marker-assisted selection for the development of new common bean varieties.

Technical Abstract: Single nucleotide polymorphisms (SNPs) were discovered in common bean (Phaseolus vulgaris L.) via resequencing of sequence-tagged sites (STSs) developed by PCR primers designed to soybean shotgun and BAC-end sequences, to common bean genes and microsatellite flanking regions. DNA fragments harboring SNPs were identified in single amplicons from six contrasting P. vulgaris genotypes of the Andean (‘Jalo EEP 558’, ‘G 19833’, and ‘AND 277’) and Mesoamerican (‘BAT 93’, ‘DOR 364’, and ‘Rudá’) gene pools. These genotypes are the parents of three common bean RIL mapping populations. From an initial set of 1,880 PCR primer pairs tested, 265 robust STSs were obtained, amplified and sequenced in each one of the six common bean genotypes. In the resulting 131,120 bp of aligned sequence, a total of 677 SNPs were identified, including 555 single-base changes (295 transitions and 260 transversions) and 122 small nucleotide insertions/deletions (indels). The frequency of SNPs was 5.16 SNPs/Kb and the mean nucleotide diversity expressed as Halushka’s theta was 0.00226. This work represents one of the pioneering efforts aimed at the detection of SNPs in P. vulgaris. The SNPs identified are an important resource to common bean geneticists for quantitative trait loci (QTLs) discovery, marker-assisted selection, and for map-based cloning. These SNPS will be also useful for diversity analysis and microsynteny studies among legume species.