Joint GWAS and WGCNA uncover the genetic control of calcium accumulation under salt treatment in maize seedlings

Abstract

Soil salinization is an important factor threatening the yield and quality of maize. Ca2+ plays a considerable role in regulating plant growth under salt stress. Herein, we examined the shoot Ca2+ concentrations, root Ca2+ concentrations, and transport coefficients of seedlings in an association panel composed of 305 maize inbred lines under normal and salt conditions. A genome‐wide association study was conducted by using the investigated phenotypes and 46,408 single‐nucleotide polymorphisms of the panel. As a result, 53 significant SNPs were specifically detected under salt treatment, and 544 genes were identified in the linkage disequilibrium regions of these SNPs. According to the expression data of the 544 genes, we carried out a weighted coexpression network analysis. Combining the enrichment analyses and functional annotations, four hub genes (GRMZM2G051032, GRMZM2G004314, GRMZM2G421669, and GRMZM2G123314) were finally determined, which were then used to evaluate the genetic variation effects by gene‐based association analysis. Only GRMZM2G123314, which encodes a pentatricopeptide repeat protein, was significantly associated with Ca2+ transport and the haplotype G‐CT was identified as the superior haplotype. Our study brings novel insights into the genetic and molecular mechanisms of salt stress response and contributes to the development of salt‐tolerant varieties in maize.

Genome-Wide Association Study (GWAS) and genome prediction of seedling salt tolerance in bread wheat (Triticum aestivum L.)

“…Similar to our observations, previous reports have also shown that salinity negatively affects seedling-related traits [ 29 – 32 ]. In a conclusion, salt stress remarkably limits wheat seedling growth, as previously reported by Liang et al [ 9 ].…”

“…In-depth phenotyping is a key part of a GWAS procedure [ 29 ]. Herein, a total of 25 seedling-linked traits were evaluated that have been previously employed for QTL mapping of salinity tolerance at the seedling stage in cotton, rice, and maize [ 7 , 9 , 10 ]. Similar to our observations, previous reports have also shown that salinity negatively affects seedling-related traits [ 29 – 32 ].…”

Genome-Wide Association Study Reveals the Genetic Basis of Kernel and Cob Moisture Changes in Maize at Physiological Maturity Stage

“…Descriptive statistical analysis was performed using SPSS25 software. The broad-sense heritability ( H 2 ) was calculated as follows [ 39 ]: H 2 = σ G 2 /σ P 2 , σ G 2 = (MSG-MSE)/rep, σ P 2 = (MSG-MSE)/rep + MSE. Herein, σ G 2 , σ P 2 , MSG, MSE, and rep represent genotypic variance, phenotypic variance, mean square of genotype, mean square of error, and number of replicates, respectively.…”

A Combination of a Genome-Wide Association Study and a Transcriptome Analysis Reveals circRNAs as New Regulators Involved in the Response to Salt Stress in Maize

“…It is based on the linkage disequilibrium (LD) of molecular markers. Using a GWAS, 544 initial candidate genes affecting Ca 2+ concentrations were detected in maize seedlings under salt stress [ 4 ]. Luo et al identified 57 loci significantly associated with maize salt tolerance using a GWAS.…”