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

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...

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Bibliographic Details
Published in:Physiologia plantarum 2020-12, Vol.170 (4), p.508-518
Main Authors: Zhang, Yinchao, Hu, Yu, Guan, Zhongrong, Liu, Peng, He, Yongcong, Zou, Chaoying, Li, Peng, Gao, Shibin, Peng, Hua, Yang, Cong, Pan, Guangtang, Shen, Yaou, Ma, Langlang
Format: Article
Language:English
Subjects:
Association analysis
Chromosomes
Gene mapping
Genes
Genetic analysis
Genetic control
Genomes
Haplotypes
Inbreeding
Kernels
Linkage analysis
Mapping
Moisture content
Molecular modelling
Plant breeding
Quantitative trait loci
Seeds
Single-nucleotide polymorphism
Water content
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Summary: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 marker‐assisted selection for breeding low‐KMC maize.
ISSN:0031-9317
1399-3054
DOI:10.1111/ppl.13180