GWAS and RNA-seq analysis uncover candidate genes associated with alkaline stress tolerance in maize (Zea mays L.) seedlings

Abstract

Soil salt-alkalization is a common yet critical environmental stress factor for plant growth and development. Discovering and exploiting genes associated with alkaline tolerance in maize (Zea mays L.) is helpful for improving alkaline resistance. Here, an association panel consisting of 200 maize lines was used to identify the genetic loci responsible for alkaline tolerance-related traits in maize seedlings. A total of nine single-nucleotide polymorphisms (SNPs) and their associated candidate genes were found to be significantly associated with alkaline tolerance using a genome-wide association study (GWAS). An additional 200 genes were identified when the screen was extended to include a linkage disequilibrium (LD) decay distance of r2 ≥ 0.2 from the SNPs. RNA-sequencing (RNA-seq) analysis was then conducted to confirm the linkage between the candidate genes and alkali tolerance. From these data, a total of five differentially expressed genes (DEGs; |log2FC| ≥ 0.585, p < 0.05) were verified as the hub genes involved in alkaline tolerance. Subsequently, two candidate genes, Zm00001d038250 and Zm00001d001960, were verified to affect the alkaline tolerance of maize seedlings by qRT-PCR analysis. These genes were putatively involved protein binding and “flavonoid biosynthesis process,” respectively, based on Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) enrichment analyses. Gene promoter region contains elements related to stress and metabolism. The results of this study will help further elucidate the mechanisms of alkaline tolerance in maize, which will provide the groundwork for future breeding projects.

The Transcription Factor ZmNAC89 Gene Is Involved in Salt Tolerance in Maize (Zea mays L.)

“…The NAC transcription factor is involved in abiotic stress responses in plants, including those to salinity, drought and low temperatures. Based on previous transcriptome data [36], we found that the ZmNAC89 gene was significantly induced by alkaline-salt Na 2 CO 3 stress. In this study, we identified ZmNAC89 as a transcription factor with transcriptional activation activity and localization in the nucleus.…”

“…Previously, we analyzed differentially expressed genes in the maize transcriptome under alkaline-salt Na 2 CO 3 stress using second-generation high-throughput sequencing RNA-Seq technology [36]. We found that the ZmNAC89 gene significantly increased expression levels under stress conditions.…”

Integration of GWAS and RNA-Seq Analysis to Identify SNPs and Candidate Genes Associated with Alkali Stress Tolerance at the Germination Stage in Mung Bean

“…At the seedling stage, three and four significant QTLs were detected for the survival rate 10 days and 15 days after a salt treatment (100 mM NaCl), respectively, and the candidate gene VrFRO8 could lower the SOD content by influencing the Fe 2+ /Fe 3+ ratio under salt stress [ 20 ]. However, several hub genes related to the alkali response in other crops, such as LOC_Os03g26210 [ 21 ], LOC_Os11g37300 , LOC_Os11g37320 , LOC_Os11g37390 [ 22 ], LOC_Os09g25060 [ 4 ], Zm00001d038250 , and Zm00001d001960 [ 23 ], have not been reported in mung bean using the GWAS. Therefore, this limits us in the characterization of the genetic basis and molecular mechanism of alkali tolerance in mung beans.…”