Combined linkage mapping and association analysis reveals genetic control of maize kernel moisture content

Abstract

The free moisture in crop kernels after being naturally dried is referred to as kernel moisture content (KMC). Maize KMC reflects grain quality and influences transportation and storage of seeds. We used an IBM Syn10 DH maize population consisting of 249 lines and an association panel comprising 310 maize inbred lines to identify the genetic loci affecting maize KMC in three environments. Using the IBM population detected 13 QTL on seven chromosomes, which were clustered into nine common QTL. Genome-wide association analysis (GWAS) identified 16 significant SNPs across the 3 environments, which were linked to 158 genes across the three environments. Combined QTL mapping and GWAS found two SNPs that were located in two of the mapped QTL, respectively. Twenty-three genes were linked with the loci co-localized in both populations. Of these 181 genes, five have previously been reported to be associated with KMC or to regulate seed development. These associations were verified by candidate gene association analysis. Two superior alleles and one favorable haplotype for Zm00001d007774 and Zm00001d047868 were found to influence KMC. These findings provide insights into molecular mechanisms underlying maize KMC and contribute to the use of markerassisted selection for breeding low-KMC maize.

Genome-wide association study uncovers new genetic loci and candidate genes underlying seed chilling-germination in maize

“…High heritability and abundant phenotypic variations were both necessary to detect the genetic architecture of target traits ( Liu et al, 2020 ; Zhang et al, 2020b ; Zhang et al, 2020c ). According to the population structure, the association panel was classified into tropical group, stiff stalk (SS) group and non-stiff stalk (NSS) group.…”

Association mapping uncovers maize ZmbZIP107 regulating root system architecture and lead absorption under lead stress

“…In detail, the genomic DNA of the 77 lines were used as the templates to amplify the gene body and its 2000 bp upstream for each gene by PCR. The B73 genome sequence (RefGen V4) was used as the reference sequence to align the amplified sequences, and the DNAMAN software (v. 5.2.2, Lynnon Bio-soft, Canada) was employed to detect insertions/deletions (InDels) and SNPs ( Zhang et al., 2020b ). The associations between these genetic variants and BSH-LTC were calculated based on the general linear model (GLM) in TASSEL v. 5.0 ( Zhang et al., 2021 ).…”

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

“…The simpleM program in R Studio ver.4.0.3 (Allaire, Boston, MA, USA) [ 42 ] was applied to calculate the effective marker number of independent tests (M eff_G = 27,507) [ 42 , 43 , 44 ]. The significance threshold was calculated as p = 0.05/M eff_G = 1.82 × 10 −6 [ 26 ]. In addition, the gene models that were located in the linkage disequilibrium (LD) region of each SNP were considered the candidate genes.…”

“…Combined with genetic population analysis, transcriptome analysis, and gene editing, two key genes Zm00001d020929 and Zm00001d046583 were shown to negatively regulate the MC. A total of 16 SNPs significantly associated with MC were detected by GWAS among a natural panel consisting of 310 maize inbred lines at the harvest stage [ 26 ]. Using GWAS, Li et al [ 27 ] identified 27 SNPs related to kernel water content (KWC) and kernel dehydration rate (KDR) in maize.…”