title: Genotyping-by-Sequencing to Predict Resistance to Lima Bean Downy Mildew in a Diversity Panel.
abstract: Lima bean is affected by severe downy mildew epidemics caused by the oomycete Phytophthora phaseoli. There are six documented races of P. phaseoli (A to F). Race F is currently predominant in the mid-Atlantic region, creating the need for resistant lima bean cultivars with desirable agronomic characteristics. In order to develop markers for detecting race F resistance, bulked segregant analysis (BSA) using genotyping-by-sequencing (GBS) was used on a biparental F2population comprised of 216 lima bean progeny segregating for a dominant race F resistance phenotype. Data were analyzed using a custom bioinformatic analysis pipeline (redrep). Kompetitive allele-specific polymerase chain reaction assays were developed using 12 GBS markers associated with the race F resistance phenotype. Using these assays, the F2population was used to map the race F resistance locus. Seven markers were in linkage and significantly associated with race F resistance that mapped between two markers located approximately 4.88 centimorgan (cM) apart. These assays were successfully used to genotype a newly acquired lima bean diversity panel consisting of 256 landraces, cultivars, and wild germplasm, and a haplotype consisting of two of the seven linked markers was demonstrated to accurately predict race F resistance. This confirmed the ability of our customized methods to accurately predict phenotypes in diverse lines of lima bean.
authors.affiliation: First, third, fourth, fifth, sixth, seventh, and ninth authors: Department of Plant and Soil Sciences, University of Delaware, Newark; second author: University of Delaware Research and Education Center, Georgetown; and eighth author: Center for Bioinformatics and Computational Biology, University of Delaware, Newark.
authors.forename: T T
authors.initials: TT
authors.lastname: Mhora
authors.affiliation: First, third, fourth, fifth, sixth, seventh, and ninth authors: Department of Plant and Soil Sciences, University of Delaware, Newark; second author: University of Delaware Research and Education Center, Georgetown; and eighth author: Center for Bioinformatics and Computational Biology, University of Delaware, Newark.
authors.forename: E G
authors.initials: EG
authors.lastname: Ernest
authors.affiliation: First, third, fourth, fifth, sixth, seventh, and ninth authors: Department of Plant and Soil Sciences, University of Delaware, Newark; second author: University of Delaware Research and Education Center, Georgetown; and eighth author: Center for Bioinformatics and Computational Biology, University of Delaware, Newark.
authors.forename: R J
authors.initials: RJ
authors.lastname: Wisser
authors.affiliation: First, third, fourth, fifth, sixth, seventh, and ninth authors: Department of Plant and Soil Sciences, University of Delaware, Newark; second author: University of Delaware Research and Education Center, Georgetown; and eighth author: Center for Bioinformatics and Computational Biology, University of Delaware, Newark.
authors.forename: T A
authors.initials: TA
authors.lastname: Evans
authors.affiliation: First, third, fourth, fifth, sixth, seventh, and ninth authors: Department of Plant and Soil Sciences, University of Delaware, Newark; second author: University of Delaware Research and Education Center, Georgetown; and eighth author: Center for Bioinformatics and Computational Biology, University of Delaware, Newark.
authors.forename: M E
authors.initials: ME
authors.lastname: Patzoldt
authors.affiliation: First, third, fourth, fifth, sixth, seventh, and ninth authors: Department of Plant and Soil Sciences, University of Delaware, Newark; second author: University of Delaware Research and Education Center, Georgetown; and eighth author: Center for Bioinformatics and Computational Biology, University of Delaware, Newark.
authors.forename: N F
authors.initials: NF
authors.lastname: Gregory
authors.affiliation: First, third, fourth, fifth, sixth, seventh, and ninth authors: Department of Plant and Soil Sciences, University of Delaware, Newark; second author: University of Delaware Research and Education Center, Georgetown; and eighth author: Center for Bioinformatics and Computational Biology, University of Delaware, Newark.
authors.forename: S E
authors.initials: SE
authors.lastname: Westhafer
authors.affiliation: First, third, fourth, fifth, sixth, seventh, and ninth authors: Department of Plant and Soil Sciences, University of Delaware, Newark; second author: University of Delaware Research and Education Center, Georgetown; and eighth author: Center for Bioinformatics and Computational Biology, University of Delaware, Newark.
authors.forename: S W
authors.initials: SW
authors.lastname: Polson
authors.affiliation: First, third, fourth, fifth, sixth, seventh, and ninth authors: Department of Plant and Soil Sciences, University of Delaware, Newark; second author: University of Delaware Research and Education Center, Georgetown; and eighth author: Center for Bioinformatics and Computational Biology, University of Delaware, Newark.
authors.forename: N M
authors.initials: NM
authors.lastname: Donofrio
mesh_terms: D000483:Alleles; D019295:Computational Biology; D008040:Genetic Linkage; D005819:Genetic Markers / Q000235:genetics; D005838:Genotype; D060005:Genotyping Techniques / Q000379:methods*; D006239:Haplotypes; D027805:Phaseolus / Q000235:genetics* / Q000276:immunology / Q000469:parasitology; D010641:Phenotype; D010838:Phytophthora / Q000502:physiology*; D010935:Plant Diseases / Q000276:immunology* / Q000469:parasitology; D036226:Seedlings / Q000235:genetics / Q000276:immunology / Q000469:parasitology; D017422:Sequence Analysis, DNA
chemical_list: D005819:Genetic Markers