Abstract
Two hub genes GRMZM2G075104 and GRMZM2G333183 involved in salt tolerance were identified by GWAS and WGCNA. Furthermore, they were verified to affect salt tolerance by candidate gene association analysis. Salt stress influences maize growth and development. To decode the genetic basis and hub genes controlling salt tolerance is a meaningful exploration for cultivating salt-tolerant maize varieties. Herein, we used an association panel consisting of 305 lines to identify the genetic loci responsible for Na+- and K+-related traits in maize seedlings. Under the salt stress, seven significant single nucleotide polymorphisms were identified using a genome-wide association study, and 120 genes were obtained by scanning the linkage disequilibrium regions of these loci. According to the transcriptome data of the above 120 genes under salinity treatment, we conducted a weighted gene co-expression network analysis. Combined the gene annotations, two SNaC/SKC (shoot Na+ content/shoot K+ content)-associated genes GRMZM2G075104 and GRMZM2G333183 were finally identified as the hub genes involved in salt tolerance. Subsequently, these two genes were verified to affect salt tolerance of maize seedlings by candidate gene association analysis. Haplotypes TTGTCCG-CT and CTT were determined as favorable/salt-tolerance haplotypes for GRMZM2G075104 and GRMZM2G333183, respectively. These findings provide novel insights into genetic architectures underlying maize salt tolerance and contribute to the cultivation of salt-tolerant varieties in maize.
Highlights
Salinity is a major abiotic stress affecting crop growth, development, and yield (Cui et al 2015; Zhu 2001)
Under stiff stalk (SS) conditions, shoot Na+ content (SNaC), root Na+ content (RNaC), SNaC/shoot K+ content (SKC), RNaC/root K+ content (RKC), and KTC were obviously enhanced with the increased folds ranged from 0.54 to 18.32, whereas SKC, RKC, and NaTC were greatly lowered with the decreased folds ranged from 0.26 to 0.52 in comparison to their corresponding phenotypes under NT condition (Fig. 1; Table S1)
Under SS condition, the highest positive correlation was observed between NaTC and SNaC, with r = 0.80, and the highest negative correlation was observed between SNaC and SNaC/SKC, with r = -0.63 (Table S2)
Summary
Salinity is a major abiotic stress affecting crop growth, development, and yield (Cui et al 2015; Zhu 2001). Maize is sensitive to salt stress, at the seedling stage (Cui et al 2015). Two important mechanisms underlying the response of salinity stress have been widely veri ed in plants, namely SOS (salt overly sensitive) and HKT (high-a nity K+ transporter) pathways (Hamamoto et al 2015; Zhu 2002). In SOS pathway, three genes SOS1, SOS2, and SOS3 jointly participate in the plant metabolism under salt stress (Zhu 2002). SOS1 transports Na+ out of cells via H+ electrochemical potential (Shi et al 2002). Ca2+ activates SOS2 and causes the formation of SOS2-SOS3 complex, which activates the C-terminal region of SOS1 by phosphorylation (Quintero et al 2011)
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