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Dynamic patterns of circular and linear RNAs in maize hybrid and parental lines

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Abstract

Hybrid vigor, also known as heterosis, has been widely utilized in agronomic production of maize (Zea mays L.) and other crops. However, the molecular mechanisms underlying heterosis are still not fully understood. To provide a more complete understanding of the transcriptomic dynamics associated with heterosis, we collected a comprehensive set of sequence data on linear mRNA transcripts and circular RNAs (circRNAs) from seedling leaves of two widely used maize inbred lines and their F1 hybrid at the V4 growth stage. We detected over 25,000 expressed genes with more than 1200 circRNAs that showed dramatic and distinct variations in expression level across the three genotypes. Although most linear and circular transcripts exhibited additive expression in the hybrid, the expression of circRNAs was more likely to be nonadditive. Interestingly, the levels of linear transcripts and their corresponding circRNAs from the same loci showed a significant relationship and coordinated expression mode across all three genotypes. Notably, in the hybrid, allele-specific expression of linear transcripts was significantly associated with the expression of circRNAs from the same locus, suggesting potential regulatory cross talk between linear and circular transcripts. Our study provides a deeper understanding of dynamic variations for both the linear and circular transcriptome in a classical hybrid triplet of maize.

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Acknowledgements

This research was supported by the National Key Research and Development Program of China (2016YFD0100800), the National Natural Science Foundation of China (31771798), the Fundamental Research Funds for the Central Universities (2662016PY096), and Huazhong Agricultural University Scientific & Technological Self-Innovation Foundation (2015RC016).We are grateful to all the partners who shared their materials and the original scientists who generated these widely used inbreds.

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  1. Zi Luo and Jia Qian have contributed equally to this work.

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  1. National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China

    Zi Luo, Jia Qian, Sijia Chen & Lin Li

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  1. Zi Luo
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  2. Jia Qian
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  4. Lin Li
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Contributions

LL designed and supervised this study. ZL and JQ collected all the data. ZL, JQ, and SC performed the data analysis. LL and ZL prepared the manuscript.

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Correspondence to Lin Li.

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Communicated by Mingliang Xu.

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Luo, Z., Qian, J., Chen, S. et al. Dynamic patterns of circular and linear RNAs in maize hybrid and parental lines. Theor Appl Genet 133, 593–604 (2020). https://doi.org/10.1007/s00122-019-03489-9

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