Genetic analysis and candidate gene identification of salt tolerance-related traits in maize

Soil salinization poses a threat to maize production worldwide. The genetic mechanism of salt tolerance in maize is not well understood. Therefore, identification of the genetic components underlying salt tolerance in maize is of importance. In the current study, a teosinte-maize BC2F7 population was used to investigate the genetic basis of 21 salt tolerance-related traits. In total, 125 QTLs were detected by using a high-density genetic bin map, with 1 to 5 QTLs explaining 6.05-32.02% of the phenotypic variation for each trait. The total phenotypic variation explained (PVE) by all detected QTLs ranged from 6.84 to 63.88% for each trait. Of all 125 QTLs, only three were major QTLs distributed in 2 genomic regions on chromosome 6, which were involved in 3 salt tolerance-related traits. In addition, 10 pairs of epistatic QTLs with additive effects were detected for 8 traits, explaining 0.9 to 4.44% of the phenotypic variation. Furthermore, 18 QTL hotspots affecting 3-7 traits were identified. In one hotspot (L5), a gene cluster consisting of 4 genes (ZmNSA1, SAG6, ZmCLCg, and ZmHKT1;2) was found, suggesting the involvement of multiple pleiotropic genes. Finally, two important candidate genes, Zm00001d002090 and Zm00001d002391, were verified to be associated with salt tolerance-related traits by a combination of linkage and marker-trait association analysis. Zm00001d002090 encodes a calcium-dependent lipid-binding (CaLB domain) family protein, which may function as a Ca2+ sensor for transmitting the salt stress signal downstream, while Zm00001d002391 encodes a ubiquitin-specific protease belonging to the C19-related subfamily. Our findings provide valuable insights into the genetic basis of salt tolerance-related traits and a theoretical foundation for breeders to enhance salt-tolerant maize varieties.