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Single strand conformation polymorphism based SNP and Indel markers for genetic mapping and synteny analysis of common bean (Phaseolus vulgaris L.). 2009

Carlos H Galeano, and Andrea C Fernández, and Marcela Gómez, and Matthew W Blair
Centro Internacional de Agricultura Tropical (CIAT), Apartado Aéreo 6713, Cali, Colombia. c.h.galeano@cgiar.org

BACKGROUND Expressed sequence tags (ESTs) are an important source of gene-based markers such as those based on insertion-deletions (Indels) or single-nucleotide polymorphisms (SNPs). Several gel based methods have been reported for the detection of sequence variants, however they have not been widely exploited in common bean, an important legume crop of the developing world. The objectives of this project were to develop and map EST based markers using analysis of single strand conformation polymorphisms (SSCPs), to create a transcript map for common bean and to compare synteny of the common bean map with sequenced chromosomes of other legumes. RESULTS A set of 418 EST based amplicons were evaluated for parental polymorphisms using the SSCP technique and 26% of these presented a clear conformational or size polymorphism between Andean and Mesoamerican genotypes. The amplicon based markers were then used for genetic mapping with segregation analysis performed in the DOR364 x G19833 recombinant inbred line (RIL) population. A total of 118 new marker loci were placed into an integrated molecular map for common bean consisting of 288 markers. Of these, 218 were used for synteny analysis and 186 presented homology with segments of the soybean genome with an e-value lower than 7 x 10-12. The synteny analysis with soybean showed a mosaic pattern of syntenic blocks with most segments of any one common bean linkage group associated with two soybean chromosomes. The analysis with Medicago truncatula and Lotus japonicus presented fewer syntenic regions consistent with the more distant phylogenetic relationship between the galegoid and phaseoloid legumes. CONCLUSIONS The SSCP technique is a useful and inexpensive alternative to other SNP or Indel detection techniques for saturating the common bean genetic map with functional markers that may be useful in marker assisted selection. In addition, the genetic markers based on ESTs allowed the construction of a transcript map and given their high conservation between species allowed synteny comparisons to be made to sequenced genomes. This synteny analysis may support positional cloning of target genes in common bean through the use of genomic information from these other legumes.

UI MeSH Term Description Entries
D002874 Chromosome Mapping Any method used for determining the location of and relative distances between genes on a chromosome. Gene Mapping,Linkage Mapping,Genome Mapping,Chromosome Mappings,Gene Mappings,Genome Mappings,Linkage Mappings,Mapping, Chromosome,Mapping, Gene,Mapping, Genome,Mapping, Linkage,Mappings, Chromosome,Mappings, Gene,Mappings, Genome,Mappings, Linkage
D005819 Genetic Markers A phenotypically recognizable genetic trait which can be used to identify a genetic locus, a linkage group, or a recombination event. Chromosome Markers,DNA Markers,Markers, DNA,Markers, Genetic,Genetic Marker,Marker, Genetic,Chromosome Marker,DNA Marker,Marker, Chromosome,Marker, DNA,Markers, Chromosome
D017422 Sequence Analysis, DNA A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis. DNA Sequence Analysis,Sequence Determination, DNA,Analysis, DNA Sequence,DNA Sequence Determination,DNA Sequence Determinations,DNA Sequencing,Determination, DNA Sequence,Determinations, DNA Sequence,Sequence Determinations, DNA,Analyses, DNA Sequence,DNA Sequence Analyses,Sequence Analyses, DNA,Sequencing, DNA
D054643 INDEL Mutation A mutation named with the blend of insertion and deletion. It refers to a length difference between two ALLELES where it is unknowable if the difference was originally caused by a SEQUENCE INSERTION or by a SEQUENCE DELETION. If the number of nucleotides in the insertion/deletion is not divisible by three, and it occurs in a protein coding region, it is also a FRAMESHIFT MUTATION. INDELs Mutation,Insertions-Deletions Mutation,Insertion-Deletion Mutation,INDEL Mutations,INDELs Mutations,Insertion Deletion Mutation,Insertion-Deletion Mutations,Insertions Deletions Mutation,Insertions-Deletions Mutations,Mutation, INDEL,Mutation, INDELs,Mutation, Insertion-Deletion,Mutation, Insertions-Deletions
D018744 DNA, Plant Deoxyribonucleic acid that makes up the genetic material of plants. Plant DNA
D018807 Polymorphism, Single-Stranded Conformational Variation in a population's DNA sequence that is detected by determining alterations in the conformation of denatured DNA fragments. Denatured DNA fragments are allowed to renature under conditions that prevent the formation of double-stranded DNA and allow secondary structure to form in single stranded fragments. These fragments are then run through polyacrylamide gels to detect variations in the secondary structure that is manifested as an alteration in migration through the gels. SSCP,Single-Stranded Conformational Polymorphism,Conformational Polymorphism, Single-Stranded,Conformational Polymorphisms, Single-Stranded,Polymorphism, Single Stranded Conformational,Polymorphisms, Single-Stranded Conformational,Single Stranded Conformational Polymorphism,Single-Stranded Conformational Polymorphisms
D020224 Expressed Sequence Tags Partial cDNA (DNA, COMPLEMENTARY) sequences that are unique to the cDNAs from which they were derived. ESTs,Expressed Sequence Tag,Sequence Tag, Expressed,Sequence Tags, Expressed,Tag, Expressed Sequence,Tags, Expressed Sequence
D020641 Polymorphism, Single Nucleotide A single nucleotide variation in a genetic sequence that occurs at appreciable frequency in the population. SNPs,Single Nucleotide Polymorphism,Nucleotide Polymorphism, Single,Nucleotide Polymorphisms, Single,Polymorphisms, Single Nucleotide,Single Nucleotide Polymorphisms
D026801 Synteny The presence of two or more genetic loci on the same chromosome. Extensions of this original definition refer to the similarity in content and organization between chromosomes, of different species for example. Chromosomal Colinearity,Colinearity, Chromosomal,Conserved Synteny,Syntenic Conservation,Syntenic Homology,Chromosomal Colinearities,Colinearities, Chromosomal,Conservation, Syntenic,Conservations, Syntenic,Conserved Syntenies,Homologies, Syntenic,Homology, Syntenic,Syntenic Conservations,Syntenic Homologies,Syntenies,Syntenies, Conserved,Synteny, Conserved
D027805 Phaseolus A plant genus in the family FABACEAE which is the source of edible beans and the lectin PHYTOHEMAGGLUTININS. Bean, Kidney,Bean, Tepary,Kidney Bean,Tepary Bean,Common Bean Plant,French Bean Plant,Phaseolus acutifolius,Phaseolus vulgaris,Bean Plant, Common,Bean Plant, French,Bean Plants, Common,Bean Plants, French,Beans, Kidney,Beans, Tepary,Common Bean Plants,French Bean Plants,Kidney Beans,Phaseolus vulgari,Plant, Common Bean,Plant, French Bean,Plants, Common Bean,Plants, French Bean,Tepary Beans,vulgaris, Phaseolus

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