title: Integration of Experiments across Diverse Environments Identifies the Genetic Determinants of Variation in Sorghum bicolor Seed Element Composition.
abstract: Seedling establishment and seed nutritional quality require the sequestration of sufficient element nutrients. The identification of genes and alleles that modify element content in the grains of cereals, including sorghum (Sorghum bicolor), is fundamental to developing breeding and selection methods aimed at increasing bioavailable element content and improving crop growth. We have developed a high-throughput work flow for the simultaneous measurement of multiple elements in sorghum seeds. We measured seed element levels in the genotyped Sorghum Association Panel, representing all major cultivated sorghum races from diverse geographic and climatic regions, and mapped alleles contributing to seed element variation across three environments by genome-wide association. We observed significant phenotypic and genetic correlation between several elements across multiple years and diverse environments. The power of combining high-precision measurements with genome-wide association was demonstrated by implementing rank transformation and a multilocus mixed model to map alleles controlling 20 element traits, identifying 255 loci affecting the sorghum seed ionome. Sequence similarity to genes characterized in previous studies identified likely causative genes for the accumulation of zinc, manganese, nickel, calcium, and cadmium in sorghum seeds. In addition to strong candidates for these five elements, we provide a list of candidate loci for several other elements. Our approach enabled the identification of single-nucleotide polymorphisms in strong linkage disequilibrium with causative polymorphisms that can be evaluated in targeted selection strategies for plant breeding and improvement.
authors.affiliation: Donald Danforth Plant Science Center, St. Louis, Missouri 63132 (N.S.);United States Department of Agriculture-Agricultural Research Service, Donald Danforth Plant Science Center, St. Louis, Missouri 63132 (G.Z., I.B.);Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907 (B.P.D.);Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina 29631 (Z.B., R.B., S.K.); andDepartment of Biological Sciences, University of South Carolina, Columbia, South Carolina 29208 (E.L.C.).
authors.forename: Nadia
authors.identifier: 0000-0002-2035-7117
authors.initials: N
authors.lastname: Shakoor
authors.affiliation: Donald Danforth Plant Science Center, St. Louis, Missouri 63132 (N.S.);United States Department of Agriculture-Agricultural Research Service, Donald Danforth Plant Science Center, St. Louis, Missouri 63132 (G.Z., I.B.);Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907 (B.P.D.);Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina 29631 (Z.B., R.B., S.K.); andDepartment of Biological Sciences, University of South Carolina, Columbia, South Carolina 29208 (E.L.C.).
authors.forename: Greg
authors.identifier: 0000-0001-6455-7148
authors.initials: G
authors.lastname: Ziegler
authors.affiliation: Donald Danforth Plant Science Center, St. Louis, Missouri 63132 (N.S.);United States Department of Agriculture-Agricultural Research Service, Donald Danforth Plant Science Center, St. Louis, Missouri 63132 (G.Z., I.B.);Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907 (B.P.D.);Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina 29631 (Z.B., R.B., S.K.); andDepartment of Biological Sciences, University of South Carolina, Columbia, South Carolina 29208 (E.L.C.).
authors.forename: Brian P
authors.identifier: 0000-0003-2799-954X
authors.initials: BP
authors.lastname: Dilkes
authors.affiliation: Donald Danforth Plant Science Center, St. Louis, Missouri 63132 (N.S.);United States Department of Agriculture-Agricultural Research Service, Donald Danforth Plant Science Center, St. Louis, Missouri 63132 (G.Z., I.B.);Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907 (B.P.D.);Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina 29631 (Z.B., R.B., S.K.); andDepartment of Biological Sciences, University of South Carolina, Columbia, South Carolina 29208 (E.L.C.).
authors.forename: Zachary
authors.identifier: 0000-0002-6543-4817
authors.initials: Z
authors.lastname: Brenton
authors.affiliation: Donald Danforth Plant Science Center, St. Louis, Missouri 63132 (N.S.);United States Department of Agriculture-Agricultural Research Service, Donald Danforth Plant Science Center, St. Louis, Missouri 63132 (G.Z., I.B.);Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907 (B.P.D.);Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina 29631 (Z.B., R.B., S.K.); andDepartment of Biological Sciences, University of South Carolina, Columbia, South Carolina 29208 (E.L.C.).
authors.forename: Richard
authors.identifier: 0000-0003-1366-7659
authors.initials: R
authors.lastname: Boyles
authors.affiliation: Donald Danforth Plant Science Center, St. Louis, Missouri 63132 (N.S.);United States Department of Agriculture-Agricultural Research Service, Donald Danforth Plant Science Center, St. Louis, Missouri 63132 (G.Z., I.B.);Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907 (B.P.D.);Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina 29631 (Z.B., R.B., S.K.); andDepartment of Biological Sciences, University of South Carolina, Columbia, South Carolina 29208 (E.L.C.).
authors.forename: Erin L
authors.initials: EL
authors.lastname: Connolly
authors.affiliation: Donald Danforth Plant Science Center, St. Louis, Missouri 63132 (N.S.);United States Department of Agriculture-Agricultural Research Service, Donald Danforth Plant Science Center, St. Louis, Missouri 63132 (G.Z., I.B.);Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907 (B.P.D.);Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina 29631 (Z.B., R.B., S.K.); andDepartment of Biological Sciences, University of South Carolina, Columbia, South Carolina 29208 (E.L.C.).
authors.forename: Stephen
authors.identifier: 0000-0001-9995-2375
authors.initials: S
authors.lastname: Kresovich
authors.affiliation: Donald Danforth Plant Science Center, St. Louis, Missouri 63132 (N.S.);United States Department of Agriculture-Agricultural Research Service, Donald Danforth Plant Science Center, St. Louis, Missouri 63132 (G.Z., I.B.);Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907 (B.P.D.);Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina 29631 (Z.B., R.B., S.K.); andDepartment of Biological Sciences, University of South Carolina, Columbia, South Carolina 29208 (E.L.C.) ivan.baxter@ars.usda.gov.
authors.forename: Ivan
authors.identifier: 0000-0001-6680-1722
authors.initials: I
authors.lastname: Baxter
mesh_terms: D004777:Environment; D014644:Genetic Variation; D055106:Genome-Wide Association Study; D040582:Inheritance Patterns / Q000235:genetics; D008954:Models, Biological; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D019655:Quantitative Trait, Heritable; D012639:Seeds / Q000235:genetics*; D045868:Sorghum / Q000235:genetics*