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

生物 候选基因 基因 遗传学 小桶 全基因组关联研究 连锁不平衡 数量性状位点 单核苷酸多态性 基因组 分子育种 转录组 基因表达 基因型
作者
Chunxiang Li,Yue Jia,Runyu Zhou,Liwei Liu,Mengna Cao,Yu Zhou,Zhenhua Wang,Hong Di
出处
期刊:Frontiers in Plant Science [Frontiers Media SA]
卷期号:13 被引量:5
标识
DOI:10.3389/fpls.2022.963874
摘要

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.
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