Abstract
Key message
Combined linkage and association analysis revealed five co-localized genetic loci across multiple environments. The key gene Zm00001d026491 was further verified to influence leaf length by candidate gene association analysis.
Abstract
Leaf morphology and number determine the canopy structure and thus affect crop yield. Herein, the genetic basis and key genes for 25 leaf-related traits, including leaf lengths (LL), leaf widths (LW), and leaf areas (LA) of eight continuous leaves under the tassel, and the number of leaves above the primary ear (LAE), were dissected by using an association panel and a biparental population. Using an intermated B73 × Mo17 (IBM) Syn10 doubled haploid (DH) population, 290 quantitative trait loci (QTL) controlling these traits were detected across different locations, among which 115 QTL were individually repeatedly identified in at least two environments. Using the association panel, 165 unique significant single-nucleotide polymorphisms (SNPs) were associated with target traits (P < 2.15E-06), of which 35 were separately detected across multiple environments. In total, 42 pleiotropic QTL/SNPs (pQTL/SNPs) were responsible for at least two of the LL, LW, LA, and LAE traits across multiple environments. Combining the QTL mapping and association study, five unique SNPs were located within the confidence intervals of seven QTL, and 77 genes were identified based on the linkage disequilibrium regions of co-localized SNP loci. Gene-based association studies verified that the intragenic variants in the candidate gene Zm00001d026491 influenced LL of the third leaf counted from the top node. These findings will provide vital information to understanding the genetic basis of leaf-related traits and help to cultivate maize varieties with ideal plant architecture.
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Data from this study can be provided by the corresponding authors, upon request.
Change history
23 March 2023
A Correction to this paper has been published: https://doi.org/10.1007/s00122-023-04323-z
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Acknowledgements
This work is supported by the National Key Research and Development Program of China (2021YFF1000303) and the Sichuan Science and Technology Program (2021JDTD0004 and 2021YJ0476).
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Funding was provided by National Key Research and Development Program of China (Grant no. 2021YFF1000303) and the Sichuan Science and Technology Program (Grant nos. 2021JDTD0004 and 2021YJ0476).
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YS and LM designed the experiment. WD, HY, KL, XC, YJ, CZ, NX, HL, CX, CZ, and MZ collected the phenotypes and performed the data analysis. Collections of all plant materials were performed by SG and GP. WD wrote the initial manuscript. YS and LM edited this draft. All authors have read and approved the manuscript.
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Dai, W., Yu, H., Liu, K. et al. Combined linkage mapping and association analysis uncovers candidate genes for 25 leaf-related traits across three environments in maize. Theor Appl Genet 136, 12 (2023). https://doi.org/10.1007/s00122-023-04285-2
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DOI: https://doi.org/10.1007/s00122-023-04285-2