Genome-wide association study of maize plant architecture using F1 populations
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Genome-wide association study of maize plant architecture using F1 populations can better dissect various genetic effects that can provide precise guidance for genetic improvement in maize breeding.
Maize grain yield has increased at least eightfold during the past decades. Plant architecture, including plant height, leaf angle, leaf length, and leaf width, has been changed significantly to adapt to higher planting density. Although the genetic architecture of these traits has been dissected using different populations, the genetic basis remains unclear in the F1 population. In this work, we perform a genome-wide association study of the four traits using 573 F1 hybrids with a mixed linear model approach and QTXNetwork mapping software. A total of 36 highly significant associated quantitative trait SNPs were identified for these traits, which explained 51.86–79.92% of the phenotypic variation and were contributed mainly by additive, dominance, and environment-specific effects. Heritability as a result of environmental interaction was more important for leaf angle and leaf length, while major effects (a, aa, and d) were more important for leaf width and plant height. The potential breeding values of the superior lines and superior hybrids were also predicted, and these values can be applied in maize breeding by direct selection of superior genotypes for the associated quantitative trait SNPs. A total of 108 candidate genes were identified for the four traits, and further analysis was performed to screen the potential genes involved in the development of maize plant architecture. Our results provide new insights into the genetic architecture of the four traits, and will be helpful in marker-assisted breeding for maize plant architecture.
KeywordsMaize GWAS QTSs Plant architecture F1 population
Genome-wide association study
Quantitative trait SNPs
Single nucleotide polymorphism
Genotype × environment interaction
We would like to thank Yunbi Xu and Chuanxiao Xie for their assistance in providing the genotype data of the 87 inbred lines.
JBC, JZ and YZ conceived and designed the experiments; HSW, CB, WD and RHC performed the experiments; JZ, YZ and LJG analyzed the data; QM and HYJ participated in the design of the study; YZ and JZ prepared the manuscript.
This research was supported by grants from the National Natural Science Foundation of China (91435110), the National Key Research and Development Program of China (2017YFD01012054) and the Science and Technology Major Project of Anhui Province (15czz03119).
Compliance with ethical standards
Conflict of interest
The authors declare that they have no competing interests.
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