title: Shared Genomic Regions Between Derivatives of a Large Segregating Population of Maize Identified Using Bulked Segregant Analysis Sequencing and Traditional Linkage Analysis.
abstract: Delayed transition from the vegetative stage to the reproductive stage of development and increased plant height have been shown to increase biomass productivity in grasses. The goal of this project was to detect quantitative trait loci using extremes from a large synthetic population, as well as a related recombinant inbred line mapping population for these two traits. Ten thousand individuals from a B73 × Mo17 noninbred population intermated for 14 generations (IBM Syn14) were grown at a density of approximately 16,500 plants ha(-1). Flowering time and plant height were measured within this population. DNA was pooled from the 46 most extreme individuals from each distributional tail for each of the traits measured and used in bulk segregant analysis (BSA) sequencing. Allelic divergence at each of the ∼1.1 million SNP loci was estimated as the difference in allele frequencies between the selected extremes. Additionally, 224 intermated B73 × Mo17 recombinant inbred lines were concomitantly grown at a similar density adjacent to the large synthetic population and were assessed for flowering time and plant height. Using the BSA sequencing method, 14 and 13 genomic regions were identified for flowering time and plant height, respectively. Linkage mapping with the RIL population identified eight and three regions for flowering time and plant height, respectively. Of the regions identified, three colocalized between the two populations for flowering time and two colocalized for plant height. This study demonstrates the utility of using BSA sequencing for the dissection of complex quantitative traits important for production of lignocellulosic ethanol.
authors.affiliation: Department of Agronomy, University of Wisconsin-Madison, Madison, Wisconsin 53706.
authors.forename: Nicholas J
authors.initials: NJ
authors.lastname: Haase
authors.affiliation: Department of Plant Sciences, University of California Davis, Davis, California 95616.
authors.forename: Timothy
authors.initials: T
authors.lastname: Beissinger
authors.affiliation: Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, Minnesota 55108.
authors.forename: Candice N
authors.initials: CN
authors.lastname: Hirsch
authors.affiliation: Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824 Department of Energy Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, Michigan 48824.
authors.forename: Brieanne
authors.initials: B
authors.lastname: Vaillancourt
authors.affiliation: Department of Energy, Joint Genome Institute, Walnut Creek, California 94598.
authors.forename: Shweta
authors.initials: S
authors.lastname: Deshpande
authors.affiliation: Department of Energy, Joint Genome Institute, Walnut Creek, California 94598.
authors.forename: Kerrie
authors.initials: K
authors.lastname: Barry
authors.affiliation: Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824 Department of Energy Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, Michigan 48824.
authors.forename: C Robin
authors.initials: CR
authors.lastname: Buell
authors.affiliation: Department of Agronomy, University of Wisconsin-Madison, Madison, Wisconsin 53706 Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin- Madison, Madison, Wisconsin 53706.
authors.forename: Shawn M
authors.initials: SM
authors.lastname: Kaeppler
authors.affiliation: Department of Agronomy, University of Wisconsin-Madison, Madison, Wisconsin 53706 Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin- Madison, Madison, Wisconsin 53706 ndeleongatti@wisc.edu.
authors.forename: Natalia
authors.initials: N
authors.lastname: de Leon
mesh_terms: D000483:Alleles; D002874:Chromosome Mapping; D032461:Chromosomes, Plant; D018744:DNA, Plant / Q000737:chemistry / Q000378:metabolism; D035264:Flowers / Q000378:metabolism; D005787:Gene Frequency; D008040:Genetic Linkage; D018745:Genome, Plant / Q000187:drug effects*; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D017422:Sequence Analysis, DNA; D003313:Zea mays / Q000235:genetics* / Q000254:growth & development
chemical_list: D018744:DNA, Plant
keywords: biomass; genetic mapping; maize; quantitative trait analysis; whole genome sequencing