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bioRxiv · 10.1101/2023.08.09.552713

Comprehensive analyses of 1771 transcriptome from seven tissues enhance genetic and biological interpretations of maize complex traits

Lei, M.·Si, H.·Zhu, M.·Han, Y.·Liu, W.·Dai, Y.·Ji, Y.·Liu, Z.·Hao, F.·Hao, R.·Zhao, J.·Ye, G.·Zan, Y.
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Abstract

By analyzing 1771 RNA-seq datasets from seven tissues in a maize diversity panel, we explored the landscape of multi-tissue transcriptome variation and evolution patterns of tissue-specific genes, and built a comprehensive multi-tissue gene regulation atlas to understand the genetic regulation of maize complex trait. Using transcriptome-wide association analysis, we linked tissue-specific expression variation of 45 genes to variation of 11 agronomic traits. Through integrative analyses of tissue-specific gene regulatory variation with genome-wide association studies, we detected relevant tissue types and candidate genes for a number of agronomic traits, including leaf during the day for anthesis-silking interval (GRMZM2G093210), leaf during the day for kernel Zeinoxanthin level (GRMZM2G143202), and root for ear height (GRMZM2G700665), highlighting the contribution from tissue-specific gene expression to variation of agronomic trait. Our findings provide novel insights into the genetic and biological mechanisms underlying complex traits in maize, and the multi-tissue regulatory atlas serves as a primary source for biological interpretation, functional validation, and genomic improvement of maize.

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Lei, M., Si, H., Zhu, M., Han, Y., Liu, W., Dai, Y., Ji, Y., Liu, Z., Hao, F., Hao, R., Zhao, J., Ye, G., Zan, Y.. 2023-08-13. Comprehensive analyses of 1771 transcriptome from seven tissues enhance genetic and biological interpretations of maize complex traits. https://doi.org/10.1101/2023.08.09.552713

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