title: A roadmap for functional structural variants in the soybean genome.
abstract: Gene structural variation (SV) has recently emerged as a key genetic mechanism underlying several important phenotypic traits in crop species. We screened a panel of 41 soybean (Glycine max) accessions serving as parents in a soybean nested association mapping population for deletions and duplications in more than 53,000 gene models. Array hybridization and whole genome resequencing methods were used as complementary technologies to identify SV in 1528 genes, or approximately 2.8%, of the soybean gene models. Although SV occurs throughout the genome, SV enrichment was noted in families of biotic defense response genes. Among accessions, SV was nearly eightfold less frequent for gene models that have retained paralogs since the last whole genome duplication event, compared with genes that have not retained paralogs. Increases in gene copy number, similar to that described at the Rhg1 resistance locus, account for approximately one-fourth of the genic SV events. This assessment of soybean SV occurrence presents a target list of genes potentially responsible for rapidly evolving and/or adaptive traits.
authors.affiliation: Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108.
authors.forename: Justin E
authors.initials: JE
authors.lastname: Anderson
authors.affiliation: Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108 Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada, V6T 1Z4.
authors.forename: Michael B
authors.initials: MB
authors.lastname: Kantar
authors.affiliation: Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108.
authors.forename: Thomas Y
authors.initials: TY
authors.lastname: Kono
authors.affiliation: Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108.
authors.forename: Fengli
authors.initials: F
authors.lastname: Fu
authors.affiliation: Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108.
authors.forename: Adrian O
authors.initials: AO
authors.lastname: Stec
authors.affiliation: United States Department of Agriculture, Agricultural Research Service, Soybean Genomics and Improvement Lab, Beltsville, Maryland 20705.
authors.forename: Qijian
authors.initials: Q
authors.lastname: Song
authors.affiliation: United States Department of Agriculture, Agricultural Research Service, Soybean Genomics and Improvement Lab, Beltsville, Maryland 20705.
authors.forename: Perry B
authors.initials: PB
authors.lastname: Cregan
authors.affiliation: Agronomy and Horticulture Department, University of Nebraska, Lincoln, Nebraska 68583.
authors.forename: James E
authors.initials: JE
authors.lastname: Specht
authors.affiliation: Department of Crop Sciences, University of Illinois, Urbana, Illinois 61801.
authors.forename: Brian W
authors.initials: BW
authors.lastname: Diers
authors.affiliation: United States Department of Agriculture, Agricultural Research Service, Corn Insects and Crop Genetics Research Unit, Ames, Iowa 50011.
authors.forename: Steven B
authors.initials: SB
authors.lastname: Cannon
authors.affiliation: Department of Horticulture and Crop Science, The Ohio State University, Columbus, Ohio 43210.
authors.forename: Leah K
authors.initials: LK
authors.lastname: McHale
authors.affiliation: Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108 rstupar@umn.edu.
authors.forename: Robert M
authors.initials: RM
authors.lastname: Stupar
mesh_terms: D055028:Comparative Genomic Hybridization; D018628:Gene Dosage; D018745:Genome, Plant; D059014:High-Throughput Nucleotide Sequencing; D010940:Plant Proteins / Q000235:genetics; D017422:Sequence Analysis, DNA; D013025:Glycine max / Q000235:genetics*
chemical_list: D010940:Plant Proteins
keywords: CNV; Glycine max; nested association mapping; soybean; structural variation