Environmental association analyses identify candidates for abiotic stress tolerance in 1 Glycine soja , the wild progenitor of cultivated soybeans 2

Environmental association analyses identify candidates for abiotic stress tolerance in 1 Glycine soja, the wild progenitor of cultivated soybeans 2 Justin E. Anderson *, , Thomas J. Y. Kono , Robert M. Stupar, Michael B. Kantar §, , Peter 3 L. Morrell ‡ 4 Department of Agronomy and Plant Genetics, University of Minnesota, 411 Borlaug Hall, 1991 5 Upper Buford Circle, St. Paul, MN 55108 6 Biodiversity Research Centre and Department of Botany, University of British Columbia, 35297 6270 University Boulevard, Vancouver, British Columbia V6T 1Z4, Canada 8 Contributed equally to this work 9 To whom correspondence should be addressed 10

[1]  Daniel R. Schrider,et al.  High mutational rates of large-scale duplication and deletion in Daphnia pulex , 2016, Genome research.

[2]  Jason G. Bragg,et al.  Genomic variation across landscapes: insights and applications. , 2015, The New phytologist.

[3]  P. Cregan,et al.  Fingerprinting Soybean Germplasm and Its Utility in Genomic Research , 2015, G3: Genes, Genomes, Genetics.

[4]  Peter J Bradbury,et al.  From association to prediction: statistical methods for the dissection and selection of complex traits in plants. , 2015, Current opinion in plant biology.

[5]  T. Giraud,et al.  Anthropogenic and natural drivers of gene flow in a temperate wild fruit tree: a basis for conservation and breeding programs in apples , 2015, Evolutionary applications.

[6]  Hui Xiang,et al.  Resequencing 302 wild and cultivated accessions identifies genes related to domestication and improvement in soybean , 2015, Nature Biotechnology.

[7]  P. Tiffin,et al.  Advances and limits of using population genetics to understand local adaptation. , 2014, Trends in ecology & evolution.

[8]  G. Heuvelink,et al.  SoilGrids1km — Global Soil Information Based on Automated Mapping , 2014, PloS one.

[9]  Rajeev K. Varshney,et al.  Structural variations in plant genomes , 2014, Briefings in functional genomics.

[10]  Justin E. Anderson,et al.  A Roadmap for Functional Structural Variants in the Soybean Genome , 2014, G3: Genes, Genomes, Genetics.

[11]  Stephen D. Turner,et al.  qqman: an R package for visualizing GWAS results using Q-Q and manhattan plots , 2014, bioRxiv.

[12]  Kevin P. Smith,et al.  Two Genomic Regions Contribute Disproportionately to Geographic Differentiation in Wild Barley , 2014, G3: Genes, Genomes, Genetics.

[13]  N. Young,et al.  Genomic Signature of Adaptation to Climate in Medicago truncatula , 2014, Genetics.

[14]  Y. Fujiki,et al.  Mitochondrial phosphatidylethanolamine level modulates Cyt c oxidase activity to maintain respiration capacity in Arabidopsis thaliana rosette leaves. , 2013, Plant & cell physiology.

[15]  H. Bohnert,et al.  Overexpression of Arabidopsis YUCCA6 in potato results in high-auxin developmental phenotypes and enhanced resistance to water deficit. , 2013, Molecular plant.

[16]  Randall L. Nelson,et al.  Development and Evaluation of SoySNP50K, a High-Density Genotyping Array for Soybean , 2013, PloS one.

[17]  David Levine,et al.  A high-performance computing toolset for relatedness and principal component analysis of SNP data , 2012, Bioinform..

[18]  Y. Wang,et al.  Population structure of the wild soybean (Glycine soja) in China: implications from microsatellite analyses. , 2012, Annals of botany.

[19]  M. Hufford,et al.  Complex Patterns of Local Adaptation in Teosinte , 2012, Genome biology and evolution.

[20]  Eran Halperin,et al.  A model-based approach for analysis of spatial structure in genetic data , 2012, Nature Genetics.

[21]  Steven L Salzberg,et al.  Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.

[22]  M. Nordborg,et al.  A Map of Local Adaptation in Arabidopsis thaliana , 2011, Science.

[23]  Erich Grotewold,et al.  Role of the stomatal development regulators FLP/MYB88 in abiotic stress responses. , 2010, The Plant journal : for cell and molecular biology.

[24]  Wei Li,et al.  Genetic diversity in domesticated soybean (Glycine max) and its wild progenitor (Glycine soja) for simple sequence repeat and single-nucleotide polymorphism loci. , 2010, The New phytologist.

[25]  G. Turesson The Genotypical Response of the Plant Species to the Habitat , 2010 .

[26]  D. Neale,et al.  Patterns of Population Structure and Environmental Associations to Aridity Across the Range of Loblolly Pine (Pinus taeda L., Pinaceae) , 2010, Genetics.

[27]  Zhiwu Zhang,et al.  Mixed linear model approach adapted for genome-wide association studies , 2010, Nature Genetics.

[28]  Steven B. Cannon,et al.  SoyBase, the USDA-ARS soybean genetics and genomics database , 2009, Nucleic Acids Res..

[29]  Noah A. Rosenberg,et al.  ADZE: a rarefaction approach for counting alleles private to combinations of populations , 2008, Bioinform..

[30]  Edward S. Buckler,et al.  TASSEL: software for association mapping of complex traits in diverse samples , 2007, Bioinform..

[31]  R. Hajjar,et al.  The use of wild relatives in crop improvement: a survey of developments over the last 20 years , 2007, Euphytica.

[32]  N. Tomooka,et al.  Population genetic structure of Japanese wild soybean (Glycine soja) based on microsatellite variation , 2006, Molecular ecology.

[33]  S. Thomine,et al.  Mobilization of vacuolar iron by AtNRAMP3 and AtNRAMP4 is essential for seed germination on low iron , 2005, The EMBO journal.

[34]  J. L. Parra,et al.  Very high resolution interpolated climate surfaces for global land areas , 2005 .

[35]  H. D. Bradshaw,et al.  Evolutionary Ecology of Plant Adaptation to Serpentine Soils , 2005 .

[36]  H. Scheller,et al.  A previously found thylakoid membrane protein of 14 kDa (TMP14) is a novel subunit of plant photosystem I and is designated PSI‐P , 2005, FEBS letters.

[37]  M. Beaumont Adaptation and speciation: what can F(st) tell us? , 2005, Trends in ecology & evolution.

[38]  G. Evanno,et al.  Detecting the number of clusters of individuals using the software structure: a simulation study , 2005, Molecular ecology.

[39]  J. Goudet HIERFSTAT , a package for R to compute and test hierarchical F -statistics , 2005 .

[40]  D. Balding,et al.  Identifying adaptive genetic divergence among populations from genome scans , 2004, Molecular ecology.

[41]  Noel Thompson,et al.  On the Tendency of Varieties to Depart Indefinitely from the Original Type , 2004 .

[42]  Jeffrey S Strock,et al.  Iron Deficiency of Soybean in the Upper Midwest and Associated Soil Properties , 2003 .

[43]  H. Yamaguchi,et al.  Natural hybridization in wild soybean (Glycine max ssp. soja) by pollen flow from cultivated soybean (Glycine max ssp. max) in a designed population , 2002 .

[44]  K. Roeder,et al.  Genomic Control for Association Studies , 1999, Biometrics.

[45]  Eva B Vedel Jensen,et al.  The model-based approach , 1998 .

[46]  B. Charlesworth,et al.  The effect of deleterious mutations on neutral molecular variation. , 1993, Genetics.

[47]  B. Weir,et al.  ESTIMATING F‐STATISTICS FOR THE ANALYSIS OF POPULATION STRUCTURE , 1984, Evolution; international journal of organic evolution.

[48]  E. E. Hartwig,et al.  Characterization of Flowering Response to Photoperiod in Diverse Soybean Genotypes 1 , 1984 .

[49]  J. Harlan,et al.  COMPARATIVE EVOLUTION OF CEREALS , 1973, Evolution; international journal of organic evolution.

[50]  R. Lewontin,et al.  Distribution of gene frequency as a test of the theory of the selective neutrality of polymorphisms. , 1973, Genetics.

[51]  R. Lewontin The Interaction of Selection and Linkage. I. General Considerations; Heterotic Models. , 1964, Genetics.

[52]  S WRIGHT,et al.  Genetical Structure of Populations , 1950, British medical journal.

[53]  R Core Team,et al.  R: A language and environment for statistical computing. , 2014 .

[54]  Simon Fraser,et al.  LDheatmap: An R Function for Graphical Display of Pairwise Linkage Disequilibria Between Single Nucleotide Polymorphisms , 2006 .

[55]  L R Cardon,et al.  Extent and distribution of linkage disequilibrium in three genomic regions. , 2001, American journal of human genetics.