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. 2024 Jan 2;25(1):19.
doi: 10.1186/s12864-023-09917-x.

Genome-wide association study for stalk lodging resistance related traits in maize (Zea mays L.)

Bangtai Wang #  1   2 , Meili Yang #  1 , Hua Guo  1   2 , Jing Wang  1   2 , Zhihong Wang  1   2 , Hongwei Lu  1 , Guiwen Qin  3 , Jiafa Chen  4
Affiliations

Genome-wide association study for stalk lodging resistance related traits in maize (Zea mays L.)

Bangtai Wang et al. BMC Genomics. .

Abstract

Background: The stalk traits stalk diameter, stalk length, rind penetrometer resistance and dry matter content are important indicators for measuring lodging resistance.

Results: In this study, 377 inbred lines were used as the basic materials, and four stalk-related traits including stalk diameter, stalk length, rind penetrometer resistance and dry matter content of the third segment of maize, were investigated at the tasseling, grain filling, and maturity stages. 461,053 high-quality SNPs which were obtained by whole genome resequencing were used for genome-wide association study. As a result of mixed linear model analysis (P < 9.77 × 10-6), 29 significant SNPs related to traits were detected, accounting for 7.19% -15.03% of phenotypic variation, among which 4, 1, 4 and 20 SNPs were found related to rind penetrometer resistance, stalk diameter, stalk length, and dry matter content respectively. Most candidate genes are related to plant element structure, signal transduction mechanisms, inorganic ion transport and metabolism, nucleotide transport and metabolism, and transporter enzyme families. Comparing mixed linear model with generalized linear model, a total of 12 candidate genes were detected repeatedly, during which the candidate gene Zm00001d014449 were detected 5 times, with a phenotypic variation interpretation rate of 9.95% -10.84%. This gene is mainly expressed in cells with active cell division and tissue differentiation, and is involved in the formation of stalk vascular bundles and the synthesis of cell walls. Another candidate gene, Zm00001d005300, encodes the transcription factor MYB44, which regulates the dependence of salt stress signal phosphorylation, can effectively inhibit the accumulation of destructive reactive oxygen species, and has a certain resistance to non-biotic stress. In addition, this study also found that 10 unknown functional genes can be further Functional verification.

Conclusions: This study helps to deepen the understanding of the genetic basis of traits related to maize stalk lodging resistance, and provides theoretical guidance for future maize lodging resistance breeding.

Keywords: Dry matter content; Genome-wide association study; Lodging resistance; Maize; Stalk traits.

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Conflict of interest statement

The authors declare no competing interests.

Figures

Fig. 1
Fig. 1
Frequency distribution map of lodging resistance related traits in maize stalk
Fig. 2
Fig. 2
Genome-wide association study of stalk lodging resistance under GLM model Manhattan map and QQ map. From the inside to the outside, the SNP sites identified in the RPR, DMC, SD and SL of maize in different years are represented respectively; The red highlights represent the significant SNP loci of each trait at 0.01 levels, respectively; Figure b shows the QQ chart of stalk related traits of maize in different years
Fig. 3
Fig. 3
Genome-wide association study of stalk lodging resistance under MLM model Manhattan map and QQ map. Note in the figure is shown in Fig. 2
Fig. 4
Fig. 4
Chromosome density map containing 461,053 SNP markers
See this image and copyright information in PMC

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