Submitted to: Frontiers in Plant Genetics and Genomics
Publication Type: Peer reviewed journal
Publication Acceptance Date: 6/21/2013
Publication Date: 7/31/2013
Citation: Mafi_Moghaddam, S., Song, Q., Mamidi, S., Schmutz, J., Lee, R., Cregan, P.B., Osorno, J.M., Mcclean, P.E. 2013. Developing market class specific InDel markers from next generation sequence data in Phaseolus vulgaris L.. Frontiers in Plant Genetics and Genomics. DOI:10.3389/fpls.2013.00251. Interpretive Summary: DNA markers serve as genetic landmarks and are interspersed among the genes throughout the genomes of higher organisms including the common bean. If a marker is located near a gene of interest, the marker can be used 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. This avoids the often expensive and time consuming process of screening each breeding line for disease resistance to identify those that carry resistance. In order to develop a useful set of DNA markers for common bean, DNA sequence was obtained from fourteen common bean varieties from different common bean market classes (pinto, black, navy, and light and dark red kidney). Based upon differences in the DNA sequence among the varieties within each market class, DNA markers, referred to as InDel markers, were developed that can be used by plant breeders and geneticists who are working to develop new varieties within each market class. The DNA markers can be used to identify breeding lines that carry genes of interest thereby reducing the time and cost associated with breeding more disease resistance and higher quality common bean varieties.
Technical Abstract: Next generation sequence data provides valuable information and tools for genetics and genomics research and offers new insights useful for marker development. These data are useful for design of accurate and user-friendly molecular tools. Common bean (Phaseolus vulgaris L.) is a diverse crop in which separate domestication events in each gene pool followed by race and market class diversification has resulted in different morphological characteristics in each commercial market class. This has led to essentially independent breeding programs within each market class which in turn have resulted in limited within market class sequence variation. Sequence data from selected genotypes of five bean market classes (pinto, black, navy, and light and dark red kidney) were used to develop InDel-based markers specific to each market class. Design of these markers was conducted through a combination of assembly, alignment and primer design software using 1.64x to 5.19x coverage of Illumina GAII sequence data for each of the selected genotypes. The procedure we developed for primer design is fast, accurate, and less error prone with a higher throughput than when they are designed manually. All InDel markers are easy to run and score with no need for PCR optimization. A total of 2,687 InDel markers distributed across the genome were developed. To highlight their usefulness, they were employed to construct a phylogenetic tree and a genetic map, showing that InDel markers are reliable, simple, and accurate.