Summary: Soil salinity is one of several major abiotic stresses that constrain maize productivity worldwide. An improved understanding of salt‐tolerance mechanisms will thus enhance the breeding of salt‐tolerant maize and boost productivity. Previous studies have indicated that the maintenance of leaf Na⁺ concentration is essential for maize salt tolerance, and the difference in leaf Na⁺ exclusion has previously been associated with variation in salt tolerance between maize varieties. Here, we report the identification and functional characterization of a maize salt‐tolerance quantitative trait locus (QTL), Zea mays Na⁺ Content1 (ZmNC1), which encodes an HKT‐type transporter (designated as ZmHKT1). We show that a natural ZmHKT1 loss‐of‐function allele containing a retrotransposon insertion confers increased accumulation of Na⁺ in leaves, and salt hypersensitivity. We next show that ZmHKT1 encodes a plasma membrane‐localized Na⁺‐selective transporter, and is preferentially expressed in root stele (including the parenchyma cells surrounding the xylem vessels). We also show that loss of ZmHKT1 function increases xylem sap Na⁺ concentration and causes increased root‐to‐shoot Na⁺ delivery, indicating that ZmHKT1 promotes leaf Na⁺ exclusion and salt tolerance by withdrawing Na⁺ from the xylem sap. We conclude that ZmHKT1 is a major salt‐tolerance QTL and identifies an important new gene target in breeding for improved maize salt tolerance.

Evolution is fueled by phenotypic diversity, which is in turn due to underlying heritable genetic (and potentially epigenetic) variation. While environmental factors are well known to influence the accumulation of novel variation in microorganisms and human cancer cells, the extent to which the natural environment influences the accumulation of novel variation in plants is relatively unknown. Here we use whole-genome and whole-methylome sequencing to test if a specific environmental stress (high-salinity soil) changes the frequency and molecular profile of accumulated mutations and epimutations (changes in cytosine methylation status) in mutation accumulation (MA) lineages ofArabidopsis thaliana. We first show that stressed lineages accumulate ∼100% more mutations, and that these mutations exhibit a distinctive molecular mutational spectrum (specific increases in relative frequency of transversion and insertion/deletion [indel] mutations). We next show that stressed lineages accumulate ∼45% more differentially methylated cytosine positions (DMPs) at CG sites (CG-DMPs) than controls, and also show that while many (∼75%) of these CG-DMPs are inherited, some can be lost in subsequent generations. Finally, we show that stress-associated CG-DMPs arise more frequently in genic than in nongenic regions of the genome. We suggest that commonly encountered natural environmental stresses can accelerate the accumulation and change the profiles of novel inherited variants in plants. Our findings are significant because stress exposure is common among plants in the wild, and they suggest that environmental factors may significantly alter the rates and patterns of incidence of the inherited novel variants that fuel plant evolution.

Sodium (Na⁺) toxicity is one of the major damages imposed on crops by saline-alkaline stress. Here we show that natural maize inbred lines display substantial variations in shoot Na⁺ contents and saline-alkaline (NaHCO₃) tolerance, and reveal that ZmNSA1 (Na⁺Content under Saline-Alkaline Condition) confers shoot Na⁺ variations under NaHCO₃ condition by a genome-wide association study. Lacking of ZmNSA1 promotes shoot Na⁺ homeostasis by increasing root Na⁺ efflux. A naturally occurred 4-bp deletion decreases the translation efficiency of ZmNSA1 mRNA, thus promotes Na⁺ homeostasis. We further show that, under saline-alkaline condition, Ca²⁺ binds to the EF-hand domain of ZmNSA1 then triggers its degradation via 26S proteasome, which in turn increases the transcripts levels of PM-H⁺-ATPases (MHA2 and MHA4), and consequently enhances SOS1 Na⁺/H⁺ antiporter-mediated root Na⁺ efflux. Our studies reveal the mechanism of Ca²⁺-triggered saline-alkaline tolerance and provide an important gene target for breeding saline-alkaline tolerant maize varieties.