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Abstract
Next generation sequence data provides valuable information and tools for genetic and genomic research and offers new insights useful for marker development. This data is useful for the design of accurate and user-friendly molecular tools. Common bean (Phaseolus vulgaris L.) is a diverse crop in which separate domestication events happened in each gene pool followed by race and market class diversification that 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 has 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 the InDel markers was conducted through a combination of assembly, alignment and primer design software using 1.6× to 5.1× coverage of Illumina GAII sequence data for each of the selected genotypes. The procedure we developed for primer design is fast, accurate, less error prone, and 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 2687 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.
Highlights
Plant breeding embraces both art and science for crop improvement
Genotypes were chosen based on their divergence in a neighbor joining (NJ) tree that was created for 192 genotypes from nine different market classes using 1159 high quality SNP markers (Hyten et al, 2010)
Using three genotypes within a market class, InDels were discovered by aligning contigs from one genotype as the query against a database consisting of the contigs of the two other genotypes
Summary
Plant breeding embraces both art and science for crop improvement. Marker assisted selection (MAS) can boost the efficiency of breeding when markers linked to genes of interest are discovered (Yang et al, 2012). Using MAS to improve a trait of interest in a self-pollinating species like common bean is becoming more challenging today in the United States because of the narrow genetic diversity of this species (McClean et al, 1993; Sonnante et al, 1994). According to Singh et al (1991), the Middle American gene pool with the center of domestication in Central and North America consist of three races, Durango, Jalisco, and Mesoamerican. The Andean gene pool with its center of domestication in South America includes three races: Nueva Granada, Peru, and Chile. The commercial market classes of this gene pool in the United States are light red kidney (LRK), dark red kidney (DRK), white kidney, and cranberry beans which are all from the Nueva Granada race (Mensack et al, 2010)
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