ArticleG3 (Bethesda, Md.)2025
Comprehensive analysis of 1,771 transcriptomes from 7 tissues enhance genetic and biological interpretations of maize complex traits.
Article in G3 (Bethesda, Md.), 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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Abstract
By reanalyzing 1,771 RNA-seq datasets from 7 tissues in a maize diversity panel, we explored the landscape of multi-tissue transcriptome variation, evolution patterns of tissue-specific genes, and built a comprehensive multi-tissue gene regulation atlas to understand the genetic regulation of maize complex traits. Through an integrative analysis of tissue-specific gene regulatory variation with genome-wide association studies, we detected relevant tissue types and several candidate genes for a number of agronomic traits, including leaf during the day for the anthesis-silking interval, leaf during the day for kernel Zeinoxanthin level, and root for ear height, highlighting the potential contribution of tissue-specific gene expression to variation in agronomic traits. Using transcriptome-wide association and colocalization analysis, we associated tissue-specific expression variation of 74 genes to agronomic traits variation. Our findings provide novel insights into the genetic and biological mechanisms underlying maize complex traits, 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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