Genome Sequencing of 15 Phaseolus vulgaris Genotypes in the African Bean Consortium Disease Resistance Breeding Program

The African Bean Consortium, funded by the Kirkhouse Trust, seeks to pyramid resistance genes for five major diseases that drive yield reduction in common bean grown in East Africa. In order to compare the nucleotide diversity and polymorphism of disease resistance loci relative to other loci and infer the evolutionary pressure driving genome diversity at disease resistance regions, genome sequencing of 15 parental lines used in the breeding programs was performed. In a first stage, genome sequences for the parents will be used to compare the frequency of Single Nucleotide Polymorphisms and Simple Sequence Repeat polymorphisms throughout the genome in order to both determine genome diversity in resistance loci, as well as access the distribution and overall usefulness of different markers for marker-assisted breeding. Paired-end 100 bp Illumina sequencing has been performed on disease resistance donor parents and preferred varieties that have seed and growth traits desirable to farmers and consumers in Uganda, Tanzania, Ethiopia, Rwanda and Kenya. Sequencing returned an average coverage per genotype of 13.09X. Variant analysis is underway using a pipeline that utilizes Burrows Wheeler Alignment to the G19833 Phaseolus vulgaris reference genome, Mpileup to call SNPs, and SSRIT, SSR Finder, and QDD to detect Simple Sequence Repeat motifs. These data will be hosted on the PhaseolusGenes database and genome browser (http://phaseolusgenes.bioinformatics.ucdavis.edu/), a molecular marker and genome database for common bean, which will facilitate marker use in future breeding programs.