GWAS and WGCNA uncover hub genes controlling salt tolerance in maize (Zea mays L.) seedlings

Langlang Ma, Minyan Zhang, Jie Chen, Chunyan Qing, Shijiang He, Chaoying Zou, Guangsheng Yuan, Cong Yang, Hua Peng, Guangtang Pan, Thomas Lübberstedt & Yaou Shen.



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 genesGRMZM2G075104andGRMZM2G333183were 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 forGRMZM2G075104andGRMZM2G333183, respectively. These findings provide novel insights into genetic architectures underlying maize salt tolerance and contribute to the cultivation of salt-tolerant varieties in maize.

Keymessage:Two hub genes GRMZM2G075104 and GRMZM2G333183 involved in salt tolerance were identifed by GWAS and WGCNA. Furthermore, they were verifed to afect salt tolerance by candidate gene association analysis.