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. 2022 Nov 1;23(1):76.
doi: 10.1186/s12863-022-01091-5.

Identification of quantitative trait loci for related traits of stalk lodging resistance using genome-wide association studies in maize (Zea mays L.)

Lifen Wu #  1 , Yunxiao Zheng #  1 , Fuchao Jiao #  2 , Ming Wang #  2 , Jing Zhang  1 , Zhongqin Zhang  1 , Yaqun Huang  1 , Xiaoyan Jia  1 , Liying Zhu  1 , Yongfeng Zhao  1 , Jinjie Guo  3 , Jingtang Chen  4   5
Affiliations

Identification of quantitative trait loci for related traits of stalk lodging resistance using genome-wide association studies in maize (Zea mays L.)

Lifen Wu et al. BMC Genom Data. .

Abstract

Background: Stalk lodging is one of the main factors affecting maize (Zea mays L.) yield and limiting mechanized harvesting. Developing maize varieties with high stalk lodging resistance requires exploring the genetic basis of lodging resistance-associated agronomic traits. Stalk strength is an important indicator to evaluate maize lodging and can be evaluated by measuring stalk rind penetrometer resistance (RPR) and stalk buckling strength (SBS). Along with morphological traits of the stalk for the third internodes length (TIL), fourth internode length (FIL), third internode diameter (TID), and the fourth internode diameter (FID) traits are associated with stalk lodging resistance.

Results: In this study, a natural population containing 248 diverse maize inbred lines genotyped with 83,057 single nucleotide polymorphism (SNP) markers was used for genome-wide association study (GWAS) for six stalk lodging resistance-related traits. The heritability of all traits ranged from 0.59 to 0.72 in the association mapping panel. A total of 85 significant SNPs were identified for the association mapping panel using best linear unbiased prediction (BLUP) values of all traits. Additionally, five candidate genes were associated with stalk strength traits, which were either directly or indirectly associated with cell wall components.

Conclusions: These findings contribute to our understanding of the genetic basis of maize stalk lodging and provide valuable theoretical guidance for lodging resistance in maize breeding in the future.

Keywords: Candidate gene; Genome-wide association study; Maize; Quantitative trait nucleotides; Stalk lodging resistance.

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Conflict of interest statement

The authors declare no competing interests.

The authors declare that they have no conflicts of interest.

Figures

Fig. 1
Fig. 1
Correlation analysis of lodging resistance-related traits under two plant densities in the association mapping panel. A and B stand for low plant density and high plant density, respectively. * Significant at P < 0.05. ** Significant at P < 0.01
Fig. 2
Fig. 2
Stable SNPs were repeatedly detected in the two planting densities and the BLUP model, which were associated with six stalk lodging resistance-related traits. The significance threshold is –log10 (P-value) = 4.0. LD represent low plant density, HD represent high plant density, respectively. Purple represents third internodes length, Red represents fourth internode length, Blue represents third internode diameter, Orange represents fourth internode diameter, Yellow represents rind penetrometer resistance and Green represents stalk buckling strength, respectively
Fig. 3
Fig. 3
Manhattan plots and QQ plots for the six traits at the low plant density. A Rind penetrometer strength. B Stalk bending strength. C Third internode length. D Third internode diameter. E Fourth internode length. F Fourth internode diameter
Fig. 4
Fig. 4
Manhattan plots and QQ plots for the six traits at the high plant density. A Rind penetrometer strength. B Stalk bending strength. C Third internode length. D Third internode diameter. E Fourth internode length. F Fourth internode diameter
Fig. 5
Fig. 5
GO-second class of candidate gene
Fig. 6
Fig. 6
Analysis of KEGG pathway based on candidate genes (The figure was created by R version 3.6.1 based on KEGG pathway database www. kegg. jp/ kegg/ kegg1. html)
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