Genome-wide association mapping of iron homeostasis in the maize association population

BackgroundIron (Fe) deficiency in plants is the result of low Fe soil availability affecting 30% of cultivated soils worldwide. To improve our understanding on Fe-efficiency this study aimed to (i) evaluate the influence of two different Fe regimes on morphological and physiological trait formation, (ii) identify polymorphisms statistically associated with morphological and physiological traits, and (iii) dissect the correlation between morphological and physiological traits using an association mapping population.ResultsThe fine-mapping analyses on quantitative trait loci (QTL) confidence intervals of the intermated B73 × Mo17 (IBM) population provided a total of 13 and 2 single nucleotide polymorphisms (SNPs) under limited and adequate Fe regimes, respectively, which were significantly (FDR = 0.05) associated with cytochrome P450 94A1, invertase beta-fructofuranosidase insoluble isoenzyme 6, and a low-temperature-induced 65 kDa protein. The genome-wide association (GWA) analyses under limited and adequate Fe regimes provided in total 18 and 17 significant SNPs, respectively.ConclusionsSignificantly associated SNPs on a genome-wide level under both Fe regimes for the traits leaf necrosis (NEC), root weight (RW), shoot dry weight (SDW), water (H 2O), and SPAD value of leaf 3 (SP3) were located in genes or recognition sites of transcriptional regulators, which indicates a direct impact on the phenotype. SNPs which were significantly associated on a genome-wide level under both Fe regimes with the traits NEC, RW, SDW, H 2O, and SP3 might be attractive targets for marker assisted selection as well as interesting objects for future functional analyses.

[1]  Y. Benjamini,et al.  Controlling the false discovery rate: a practical and powerful approach to multiple testing , 1995 .

[2]  E S Buckler,et al.  Structure of linkage disequilibrium and phenotypic associations in the maize genome , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[3]  R. Reinhardt,et al.  Ups and downs of a transcriptional landscape shape iron deficiency associated chlorosis of the maize inbreds B73 and Mo17 , 2013, BMC Plant Biology.

[4]  M. Guerinot.  It's elementary: Enhancing Fe3+ reduction improves rice yields , 2007, Proceedings of the National Academy of Sciences.

[5]  M. Guerinot,et al.  Activation of rice Yellow Stripe1-Like 16 (OsYSL16) enhances iron efficiency , 2012, Molecules and cells.

[6]  S. Dellaporta,et al.  Maize yellow stripe1 encodes a membrane protein directly involved in Fe(III) uptake , 2001, Nature.

[7]  J. Salaün,et al.  Functional expression in yeast and characterization of a clofibrate-inducible plant cytochrome P-450 (CYP94A1) involved in cutin monomers synthesis. , 1998, The Biochemical journal.

[8]  E. T. Palva,et al.  Differential expression of two related, low-temperature-induced genes in Arabidopsis thaliana (L.) Heynh , 1993, Plant Molecular Biology.

[9]  N. von Wirén,et al.  Roots of Iron-Efficient Maize also Absorb Phytosiderophore-Chelated Zinc , 1996, Plant physiology.

[10]  D. Grant,et al.  Expanding the genetic map of maize with the intermated B73 × Mo17 (IBM) population , 2002, Plant Molecular Biology.

[11]  M. Guerinot,et al.  The Essential Basic Helix-Loop-Helix Protein FIT1 Is Required for the Iron Deficiency Response , 2004, The Plant Cell Online.

[12]  Rongli Shi,et al.  The genetic basis of natural variation for iron homeostasis in the maize IBM population , 2014, BMC Plant Biology.

[13]  S. Thomine,et al.  Iron Transport and Signaling in Plants , 2011 .

[14]  D. V. D. Helm,et al.  Iron Transport in Microbes, Plants and Animals , 1987 .

[15]  V. Römheld.  Different strategies for iron acquisition in higher plants , 1987 .

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

[17]  S. Mori,et al.  Iron acquisition by plants. , 1999, Current opinion in plant biology.

[18]  D. Heckerman,et al.  Efficient Control of Population Structure in Model Organism Association Mapping , 2008, Genetics.

[19]  C. Curie,et al.  IRT1, an Arabidopsis Transporter Essential for Iron Uptake from the Soil and for Plant Growth Article, publication date, and citation information can be found at www.plantcell.org/cgi/doi/10.1105/tpc.001388. , 2002, The Plant Cell Online.

[20]  G. An,et al.  Molecular cloning and expression analysis of the cell-wall invertase gene family in rice (Oryza sativa L.) , 2005, Plant Cell Reports.

[21]  John Doebley,et al.  Maize association population: a high-resolution platform for quantitative trait locus dissection. , 2005, The Plant journal : for cell and molecular biology.

[22]  Michael A Grusak,et al.  Microarray analysis of iron deficiency chlorosis in near-isogenic soybean lines , 2007, BMC Genomics.

[23]  S Rozen,et al.  Primer3 on the WWW for general users and for biologist programmers. , 2000, Methods in molecular biology.

[24]  B. Stich,et al.  An analysis of selection on candidate genes for regulation, mobilization, uptake, and transport of iron in maize. , 2011, Genome.

[25]  A. Melchinger,et al.  Genome-wide association mapping of flowering time and northern corn leaf blight (Setosphaeria turcica) resistance in a vast commercial maize germplasm set , 2012, BMC Plant Biology.

[26]  E. Buckler,et al.  Lessons from Dwarf8 on the Strengths and Weaknesses of Structured Association Mapping , 2013, PLoS genetics.

[27]  Wolfgang Busch,et al.  The bHLH Transcription Factor POPEYE Regulates Response to Iron Deficiency in Arabidopsis Roots[W][OA] , 2010, Plant Cell.

[28]  H. Marschner.  Mineral Nutrition of Higher Plants, Second Edition , 1995 .

[29]  H. Piepho,et al.  Variation explained in mixed-model association mapping , 2010, Heredity.

[30]  D. Hincha,et al.  LEA (Late Embryogenesis Abundant) proteins and their encoding genes in Arabidopsis thaliana , 2008, BMC Genomics.

[31]  Takanori Kobayashi,et al.  Iron uptake, translocation, and regulation in higher plants. , 2012, Annual review of plant biology.

[32]  R. Visser,et al.  Identification of quantitative trait loci for ion homeostasis and salt tolerance in barley (Hordeum vulgare L.) , 2012, Molecular Breeding.

[33]  Hans-Peter Piepho,et al.  Comparison of Mixed-Model Approaches for Association Mapping , 2008, Genetics.

[34]  D. Ohta,et al.  cytochrome p450 superfamily in Arabidopsis thaliana: isolation of cDNAs, Differential Expression, and RFLP mapping of multiple cytochromes P450 , 1998, Plant Molecular Biology.

[35]  I. Chakravarti,et al.  Handbook of Methods of Applied Statistics:@@@Volume I: Techniques of Computation, Descriptive Methods, and Statistical Inference@@@Volume II: Planning of Surveys and Experiments. , 1968 .

[36]  Thomas Lübberstedt,et al.  Functional markers in plants. , 2003, Trends in plant science.

[37]  D. Brillinger,et al.  Handbook of methods of applied statistics , 1967 .