biostudies-literatureMing LNatural Science Foundation of Hubei ProvinceNational Natural Science Foundation of ChinaNatural Science Foundation of Hubei Province (Hubei Provincial Natural Science Foundation)National Natural Science Foundation of China (National Science Foundation of China)7501https://www.ebi.ac.uk/biostudies/studies/S-EPMC10657423biostudies-literatureUnknown14(1)Panicle architecture is a key determinant of rice grain yield and is mainly determined at the 1-2 mm young panicle stage. Here, we investigated the transcriptome of the 1-2 mm young panicles from 275 rice varieties and identified thousands of genes whose expression levels were associated with panicle traits. Multimodel association studies suggested that many small-effect genetic loci determine spikelet per panicle (SPP) by regulating the expression of genes associated with panicle traits. We found that alleles at cis-expression quantitative trait loci of SPP-associated genes underwent positive selection, with a strong preference for alleles increasing SPP. We further developed a method that integrates the associations of cis- and trans-expression components of genes with traits to identifyNature communicationsTranscriptome-wide association analyses reveal the impact of regulatory variants on rice panicle architecture and causal gene regulatory networks.PMC106574233163005431821005322611434662023AFA043319220652022CFA024Ming LYu QWu CXiong XMao JWang LWu ZLiu YLiao KXia CWei JZhao HChai WWu XLi GZheng YXie WYang LZhou RLi MLi XFu DLi SXu TXu XfalseTranscriptome-wide association analyses reveal the impact of regulatory variants on rice panicle architecture and causal gene regulatory networks.Panicle architecture is a key determinant of rice grain yield and is mainly determined at the 1-2 mm young panicle stage. Here, we investigated the transcriptome of the 1-2 mm young panicles from 275 rice varieties and identified thousands of genes whose expression levels were associated with panicle traits. Multimodel association studies suggested that many small-effect genetic loci determine spikelet per panicle (SPP) by regulating the expression of genes associated with panicle traits. We found that alleles at cis-expression quantitative trait loci of SPP-associated genes underwent positive selection, with a strong preference for alleles increasing SPP. We further developed a method that integrates the associations of cis- and trans-expression components of genes with traits to identify2023-01-01T00:00:00Z2023 Nov2025-04-22T09:27:13.427Z2025-04-05T23:04:27.468ZS-EPMC106574233798034610.1038/s41467-023-43077-6