Appropriate root system architecture (RSA) can improve maize yields in densely planted fields, but little is known about its genetic basis in maize. Here we performed root phenotyping of 14,301 field-grown plants from an association mapping panel to study the genetic architecture of maize RSA. A genome-wide association study identified 81 high-confidence RSA-associated candidate genes and revealed that 28 (24.3%) of known root-related genes were selected during maize domestication and improvement. We found that modern maize breeding has selected for a steeply angled root system. Favourable alleles related to steep root system angle have continuously accumulated over the course of modern breeding, and our data pinpoint the root-related genes that have been selected in different breeding eras. We confirm that two auxin-related genes, ZmRSA3.1 and ZmRSA3.2, contribute to the regulation of root angle and depth in maize. Our genome-wide identification of RSA-associated genes provides new strategies and genetic resources for breeding maize suitable for high-density planting.
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Data supporting the findings of this work are available within the paper and its Supplementary Information. The genotype set, population structure and kinship data can be downloaded from the Maizego website (http://www.maizego.org/Resources.html). All root phenotype data for the 380 inbred maize lines are included in Supplementary Table 25. The RNA-sequencing reads used to construct the co-expression network and the root transcriptome sequencing reads were deposited in the NCBI Sequence Read Archive (https://www.ncbi.nlm.nih.gov/) under accession codes PRJNA694491 and PRJNA693427, respectively. Source data are provided with this paper.
All scripts for GWAS, co-expression network analysis, selective sweep detection for domestication and improvement, and obtaining aligned sequences of high-priority candidate genes and known root-related genes (https://doi.org/10.5281/zenodo.7112683) are available on Zenodo.
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This study was financially supported by the National Key Research and Development Program of China (grant nos. 2021YFF1000500 (Q.P.), 2021YFD1200700 (F.C.) and 2016YFD0100700 (L.Y.)), the National Natural Science Foundation of China (grant nos. 31972485 (F.C.) and 31971948 (Q.P.)), the Hainan Natural Science Foundation Innovation Research Team Project (grant no. 321CXTD443 (F.C.)), the Hainan Provincial Science and Technology Plan Sanya Yazhou Bay Science and Technology City Joint Project (grant no. 320LH011 (Q.P.)) and the China Postdoctoral Science Foundation (grant no. 2021M693431 (W.R.)). The transgenic maize seeds were produced by the Center for Crop Functional Genomics and Molecular Breeding of China Agricultural University.
The authors declare no competing interests.
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The red lines represent positive correlations, and the green lines represent negative correlations. The line width represents the strength of the correlation. Yellow lines indicate that the correlation coefficient was close to zero.
The red ellipse indicates the area-related traits; the yellow ellipse indicates the width-related traits; and the green ellipse indicates the angle-related traits.
(a) Cluster analysis of 380 inbred lines based on ROA, RMEW, and AREA. (b) Representative inbred lines from the three clusters (groups 1–3). (c) Comparison of eight root traits among groups 1–3. (d) Comparison of eight root traits among four subpopulations. (e) Proportion of lines from each of four subgroups in the three cluster groups. The four subgroups (Mixed, SS, NSS, and TST) are based on genetic relationships among the different inbred lines. Mixed, mixed group; SS, stiff stalk group; NSS, non-stiff stalk group; TST, tropical and subtropical group.
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Ren, W., Zhao, L., Liang, J. et al. Genome-wide dissection of changes in maize root system architecture during modern breeding. Nat. Plants (2022). https://doi.org/10.1038/s41477-022-01274-z