title: Genome-wide association studies identifies seven major regions responsible for iron deficiency chlorosis in soybean (Glycine max).
abstract: Iron deficiency chlorosis (IDC) is a yield limiting problem in soybean (Glycine max (L.) Merr) production regions with calcareous soils. Genome-wide association study (GWAS) was performed using a high density SNP map to discover significant markers, QTL and candidate genes associated with IDC trait variation. A stepwise regression model included eight markers after considering LD between markers, and identified seven major effect QTL on seven chromosomes. Twelve candidate genes known to be associated with iron metabolism mapped near these QTL supporting the polygenic nature of IDC. A non-synonymous substitution with the highest significance in a major QTL region suggests soybean orthologs of FRE1 on Gm03 is a major gene responsible for trait variation. NAS3, a gene that encodes the enzyme nicotianamine synthase which synthesizes the iron chelator nicotianamine also maps to the same QTL region. Disease resistant genes also map to the major QTL, supporting the hypothesis that pathogens compete with the plant for Fe and increase iron deficiency. The markers and the allelic combinations identified here can be further used for marker assisted selection.
authors.affiliation: Genomics and Bioinformatics Program, North Dakota State University, Fargo, North Dakota, United States of America; Department of Plant Sciences, North Dakota State University, Fargo, North Dakota, United States of America.
authors.forename: Sujan
authors.initials: S
authors.lastname: Mamidi
authors.affiliation: Genomics and Bioinformatics Program, North Dakota State University, Fargo, North Dakota, United States of America; Department of Plant Sciences, North Dakota State University, Fargo, North Dakota, United States of America.
authors.forename: Rian K
authors.initials: RK
authors.lastname: Lee
authors.affiliation: Department of Soil Science, North Dakota State University, Fargo, North Dakota, United States of America.
authors.forename: Jay R
authors.initials: JR
authors.lastname: Goos
authors.affiliation: Genomics and Bioinformatics Program, North Dakota State University, Fargo, North Dakota, United States of America; Department of Plant Sciences, North Dakota State University, Fargo, North Dakota, United States of America.
authors.forename: Phillip E
authors.initials: PE
authors.lastname: McClean
mesh_terms: D000483:Alleles; D002874:Chromosome Mapping; D060467:Disease Resistance / Q000235:genetics; D004843:Epistasis, Genetic; D017343:Genes, Plant; D056726:Genetic Association Studies; D020022:Genetic Predisposition to Disease; D055106:Genome-Wide Association Study; D005838:Genotype; D000090463:Iron Deficiencies; D015810:Linkage Disequilibrium; D058977:Molecular Sequence Annotation; D010641:Phenotype; D010935:Plant Diseases / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D013025:Glycine max / Q000235:genetics* / Q000378:metabolism*