title: Joint genetic and network analyses identify loci associated with root growth under NaCl stress in Arabidopsis thaliana.
abstract: Plants have evolved a series of tolerance mechanisms to saline stress, which perturbs physiological processes throughout the plant. To identify genetic mechanisms associated with salinity tolerance, we performed linkage analysis and genome-wide association study (GWAS) on maintenance of root growth of Arabidopsis thaliana in hydroponic culture with weak and severe NaCl toxicity. The top 200 single-nucleotide polymorphisms (SNPs) determined by GWAS could cumulatively explain approximately 70% of the variation observed at each stress level. The most significant SNPs were linked to the genes of ATP-binding cassette B10 and vacuolar proton ATPase A2. Several known salinity tolerance genes such as potassium channel KAT1 and calcium sensor SOS3 were also linked to SNPs in the top 200. In parallel, we constructed a gene co-expression network to independently verify that particular groups of genes work together to a common purpose. We identify molecular mechanisms to confer salt tolerance from both predictable and novel physiological sources and validate the utility of combined genetic and network analysis. Additionally, our study indicates that the genetic architecture of salt tolerance is responsive to the severity of stress. These gene datasets are a significant information resource for a following exploration of gene function.
authors.affiliation: Faculty of Applied Biological Sciences, Gifu University, Gifu, 501-1193, Japan.
authors.forename: Yuriko
authors.initials: Y
authors.lastname: Kobayashi
authors.affiliation: Faculty of Applied Biological Sciences, Gifu University, Gifu, 501-1193, Japan.|Department of Biotechnology, Indian Institute of Technology Guwahati, Guwahati, Assam, 781039, India.
authors.forename: Ayan
authors.initials: A
authors.lastname: Sadhukhan
authors.affiliation: Faculty of Applied Biological Sciences, Gifu University, Gifu, 501-1193, Japan.
authors.forename: Tanveer
authors.initials: T
authors.lastname: Tazib
authors.affiliation: Faculty of Applied Biological Sciences, Gifu University, Gifu, 501-1193, Japan.
authors.forename: Yuki
authors.initials: Y
authors.lastname: Nakano
authors.affiliation: Faculty of Applied Biological Sciences, Gifu University, Gifu, 501-1193, Japan.
authors.forename: Kazutaka
authors.initials: K
authors.lastname: Kusunoki
authors.affiliation: Faculty of Applied Biological Sciences, Gifu University, Gifu, 501-1193, Japan.|Agronomy Department, Faculty of Agriculture, Kafrelsheikh University, Kafr el-Sheikh, 33516, Egypt.
authors.forename: Mohamed
authors.initials: M
authors.lastname: Kamara
authors.affiliation: Faculty of Applied Biological Sciences, Gifu University, Gifu, 501-1193, Japan.|Laboratory of Biotechnology and Bio-Geo Resources Valorization, Higher Institute of Biotechnology, University of Manouba BiotechPole, Sidi Thabet, Ariana, 2020, Tunisia.
authors.forename: Radhouane
authors.initials: R
authors.lastname: Chaffai
authors.affiliation: Experimental Plant Division, RIKEN BioResource Center, Tsukuba, Ibaraki, 305-0074, Japan.
authors.forename: Satoshi
authors.initials: S
authors.lastname: Iuchi
authors.affiliation: Department of Biotechnology, Indian Institute of Technology Guwahati, Guwahati, Assam, 781039, India.
authors.forename: Lingaraj
authors.initials: L
authors.lastname: Sahoo
authors.affiliation: Experimental Plant Division, RIKEN BioResource Center, Tsukuba, Ibaraki, 305-0074, Japan.
authors.forename: Masatomo
authors.initials: M
authors.lastname: Kobayashi
authors.affiliation: Ithaca, New York, USA.
authors.forename: Owen A
authors.initials: OA
authors.lastname: Hoekenga
authors.affiliation: Faculty of Applied Biological Sciences, Gifu University, Gifu, 501-1193, Japan.
authors.forename: Hiroyuki
authors.initials: H
authors.lastname: Koyama
mesh_terms: D017360:Arabidopsis / Q000187:drug effects / Q000235:genetics* / Q000254:growth & development; D018506:Gene Expression Regulation, Plant / Q000187:drug effects; D063990:Gene Ontology; D053263:Gene Regulatory Networks / Q000187:drug effects*; D017343:Genes, Plant; D008040:Genetic Linkage; D056426:Genetic Loci; D014644:Genetic Variation / Q000187:drug effects; D055106:Genome-Wide Association Study; D007178:Inbreeding; D018517:Plant Roots / Q000187:drug effects / Q000235:genetics* / Q000254:growth & development*; D030821:Plants, Genetically Modified; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D040641:Quantitative Trait Loci / Q000235:genetics; D011995:Recombination, Genetic / Q000235:genetics; D012965:Sodium Chloride / Q000494:pharmacology*; D013312:Stress, Physiological / Q000187:drug effects* / Q000235:genetics; D059467:Transcriptome / Q000235:genetics
chemical_list: D012965:Sodium Chloride
keywords: GWAS; QTL; WGCNA; apoplast; genetic network; natural variation; salinity; salt tolerance; symplast