title: Genetic and molecular characterization of submergence response identifies Subtol6 as a major submergence tolerance locus in maize.
abstract: Maize is highly sensitive to short term flooding and submergence. Early season flooding reduces germination, survival and growth rate of maize seedlings. We aimed to discover genetic variation for submergence tolerance in maize and elucidate the genetic basis of submergence tolerance through transcriptional profiling and linkage analysis of contrasting genotypes. A diverse set of maize nested association mapping (NAM) founder lines were screened, and two highly tolerant (Mo18W and M162W) and sensitive (B97 and B73) genotypes were identified. Tolerant lines exhibited delayed senescence and lower oxidative stress levels compared to sensitive lines. Transcriptome analysis was performed on these inbreds to provide genome level insights into the molecular responses to submergence. Tolerant lines had higher transcript abundance of several fermentation-related genes and an unannotated Pyrophosphate-Dependent Fructose-6-Phosphate 1-Phosphotransferase gene during submergence. A coexpression network enriched for CBF (C-REPEAT/DRE BINDING FACTOR: C-REPEAT/DRE BINDING FACTOR) genes, was induced by submergence in all four inbreds, but was more activated in the tolerant Mo18W. A recombinant inbred line (RIL) population derived from Mo18W and B73 was screened for submergence tolerance. A major QTL named Subtol6 was mapped to chromosome 6 that explains 22% of the phenotypic variation within the RIL population. We identified two candidate genes (HEMOGLOBIN2 and RAV1) underlying Subtol6 based on contrasting expression patterns observed in B73 and Mo18W. Sources of tolerance identified in this study (Subtol6) can be useful to increase survival rate during flooding events that are predicted to increase in frequency with climate change.
authors: University of Nebraska-Lincoln, Department of Agronomy and Horticulture, Lincoln, Nebraska, United States of America.
authors: Malachy T
authors: MT
authors: Campbell
authors: University of Nebraska-Lincoln, Department of Agronomy and Horticulture, Lincoln, Nebraska, United States of America.
authors: Christopher A
authors: CA
authors: Proctor
authors: University of Nebraska-Lincoln, School of Biological Sciences, Lincoln, Nebraska, United States of America.
authors: Yongchao
authors: Y
authors: Dou
authors: University of Nebraska-Lincoln, Department of Agronomy and Horticulture, Lincoln, Nebraska, United States of America.
authors: Aaron J
authors: AJ
authors: Schmitz
authors: University of Nebraska-Lincoln, Department of Agronomy and Horticulture, Lincoln, Nebraska, United States of America; Nakhon Phanom University, Muang District, Thailand.
authors: Piyaporn
authors: P
authors: Phansak
authors: University of Nebraska-Lincoln, Department of Agronomy and Horticulture, Lincoln, Nebraska, United States of America.
authors: Greg R
authors: GR
authors: Kruger
authors: University of Nebraska-Lincoln, School of Biological Sciences, Lincoln, Nebraska, United States of America.
authors: Chi
authors: C
authors: Zhang
authors: University of Nebraska-Lincoln, Department of Agronomy and Horticulture, Lincoln, Nebraska, United States of America.
authors: Harkamal
authors: H
authors: Walia
mesh_terms: D000222:Adaptation, Physiological / Q000235:genetics*; D002874:Chromosome Mapping / Q000379:methods; D057231:Climate Change; D055868:Floods; D020869:Gene Expression Profiling / Q000379:methods; D018506:Gene Expression Regulation, Plant / Q000235:genetics*; D008040:Genetic Linkage / Q000235:genetics; D005838:Genotype; D018384:Oxidative Stress / Q000235:genetics; D010641:Phenotype; D010940:Plant Proteins / Q000235:genetics*; D040641:Quantitative Trait Loci / Q000235:genetics*; D036226:Seedlings / Q000235:genetics; D003313:Zea mays / Q000235:genetics*
chemical_list: D010940:Plant Proteins