title: Developing market class specific InDel markers from next generation sequence data in Phaseolus vulgaris L.
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.
authors.affiliation: Genomics and Bioinformatics Program, North Dakota State University Fargo, ND, USA ; Department of Plant Sciences, North Dakota State University Fargo, ND, USA.
authors.forename: Samira Mafi
authors.initials: SM
authors.lastname: Moghaddam
authors.affiliation: Soybean Genomics and Improvement Laboratory, United States Department of Agriculture, Agricultural Research Service Beltsville, MD, USA.
authors.forename: Qijian
authors.initials: Q
authors.lastname: Song
authors.affiliation: Genomics and Bioinformatics Program, North Dakota State University Fargo, ND, USA ; Department of Plant Sciences, North Dakota State University Fargo, ND, USA.
authors.forename: Sujan
authors.initials: S
authors.lastname: Mamidi
authors.affiliation: HudsonAlpha Institute Huntsville, AL, USA.
authors.forename: Jeremy
authors.initials: J
authors.lastname: Schmutz
authors.affiliation: Department of Plant Sciences, North Dakota State University Fargo, ND, USA.
authors.forename: Rian
authors.initials: R
authors.lastname: Lee
authors.affiliation: Soybean Genomics and Improvement Laboratory, United States Department of Agriculture, Agricultural Research Service Beltsville, MD, USA.
authors.forename: Perry
authors.initials: P
authors.lastname: Cregan
authors.affiliation: Department of Plant Sciences, North Dakota State University Fargo, ND, USA.
authors.forename: Juan M
authors.initials: JM
authors.lastname: Osorno
authors.affiliation: Genomics and Bioinformatics Program, North Dakota State University Fargo, ND, USA ; Department of Plant Sciences, North Dakota State University Fargo, ND, USA.
authors.forename: Phillip E
authors.initials: PE
authors.lastname: McClean
keywords: InDel marker; common bean; genetic map; market class; next generation sequencing; phylogenetics