Liu, Z. et al. Zinc application after low temperature stress promoted rice tillers recovery: aspects of nutrient absorption and plant hormone regulation. Plant Sci. 314, 111104 (2022).
Liu, Z. et al. Nitrogen application after low-temperature exposure alleviates tiller decrease in rice. Environ. Exp. Bot. 158, 205–214 (2019).
Zhu, Z. L. & Chen, D. L. Nitrogen fertilizer use in China – contributions to food production, impacts on the environment and best management strategies. Nutr. Cycl. Agroecosyst. 63, 117–127 (2002).
Shi, Z. et al. The fates of 15N fertilizer in relation to root distributions of winter wheat under different N splits. Eur. J. Agron. 40, 86–93 (2012).
Cameron, K. C., Di, H. J. & Moir, J. L. Nitrogen losses from the soil/plant system: a review. Ann. Appl. Biol. 162, 145–173 (2013).
Wang, S., Luo, S., Yue, S., Shen, Y. & Li, S. Fate of 15N fertilizer under different nitrogen split applications to plastic mulched maize in semiarid farmland. Nutr. Cycl. Agroecosyst. 105, 129–140 (2016).
Davidson, E. A. The contribution of manure and fertilizer nitrogen to atmospheric nitrous oxide since 1860. Nat. Geosci. 2, 659–662 (2009).
Li, C. et al. Identification of cold tolerance QTLs at the bud burst stage in 211 rice landraces by GWAS. BMC Plant Biol. 21, 542 (2021).
Lesk, C., Rowhani, P. & Ramankutty, N. Influence of extreme weather disasters on global crop production. Nature 529, 84–87 (2016).
Guo, W. et al. An assessment of the relationship between spring frost indicators and global crop yield losses. Sci. Total Environ. 954, 176560 (2024).
Wang, P., Liu, H., Wu, W., Kong, F. & Hu, T. Future projections of rice exposure to cold stress in China throughout the 21st century. Eur. J. Agron. 135, 126473 (2022).
Asim, M. et al. Nitrate signaling, functions, and regulation of root system architecture: insights from Arabidopsis thaliana. Genes 11, 633 (2020).
Kiba, T. et al. The Arabidopsis nitrate transporter NRT2.4 plays a double role in roots and shoots of nitrogen-starved plants. Plant Cell 24, 245–258 (2012).
Liu, Y. et al. Genomic basis of geographical adaptation to soil nitrogen in rice. Nature 590, 600–605 (2021).
Li, J., Han, G., Sun, C. & Sui, N. Research advances of MYB transcription factors in plant stress resistance and breeding. Plant Signal. Behav. 14, 1613131 (2019).
Zhang, H., Zhu, J., Gong, Z. & Zhu, J.-K. Abiotic stress responses in plants. Nat. Rev. Genet. 23, 104–119 (2022).
Chen, Y.-S. et al. Two MYB-related transcription factors play opposite roles in sugar signaling in Arabidopsis. Plant Mol. Biol. 93, 299–311 (2017).
Lu, C.-A., Ho, T. D., Ho, S.-L. & Yu, S.-M. Three novel MYB proteins with one DNA binding repeat mediate sugar and hormone regulation of α-amylase gene expression. Plant Cell 14, 1963–1980 (2002).
Hong, Y.-F. et al. Convergent starvation signals and hormone crosstalk in regulating nutrient mobilization upon germination in cereals. Plant Cell 24, 2857–2873 (2012).
Li, W. et al. A natural allele of a transcription factor in rice confers broad-spectrum blast resistance. Cell 170, 114–126.e115 (2017).
Frangedakis, E. et al. MYB-related transcription factors control chloroplast biogenesis. Cell 187, 4859–4876.e22 (2024).
Li, Z. et al. Natural variation of codon repeats in COLD11 endows rice with chilling resilience. Sci. Adv. 9, eabq5506 (2023).
Ma, Y. et al. COLD1 confers chilling tolerance in rice. Cell 160, 1209–1221 (2015).
Zhang, J. et al. Nitrogen effects on yield, quality and physiological characteristics of giant rice. Agronomy 10, 1816 (2020).
Souza, A. F. F. et al. Knockdown of OsNRT2.4 modulates root morphology and alters nitrogen metabolism in response to low nitrate availability in rice. Mol. Breed. 42, 5 (2022).
Wei, J. et al. OsNRT2.4 encodes a dual-affinity nitrate transporter and functions in nitrate-regulated root growth and nitrate distribution in rice. J. Exp. Bot. 69, 1095–1107 (2018).
Sakai, H. et al. Rice Annotation Project Database (RAP-DB): an integrative and interactive database for rice genomics. Plant Cell Physiol. 54, e6 (2013).
Guo, D. et al. A pangenome reference of wild and cultivated rice. Nature 642, 662–671 (2025).
Jing, C.-Y. et al. Multiple domestications of Asian rice. Nat. Plants 9, 1221–1235 (2023).
Zhao, H. et al. RiceVarMap: a comprehensive database of rice genomic variations. Nucleic Acids Res. 43, D1018–D1022 (2015).
Jia, M. et al. Chilling-induced phosphorylation of IPA1 by OsSAPK6 activates chilling tolerance responses in rice. Cell Discov. 8, 71 (2022).
Chen, L. et al. OsMADS57 together with OsTB1 coordinates transcription of its target OsWRKY94 and D14 to switch its organogenesis to defense for cold adaptation in rice. New Phytol. 218, 219–231 (2018).
Li, S. et al. Modulating plant growth–metabolism coordination for sustainable agriculture. Nature 560, 595–600 (2018).
Ta, T. C. & Ohira, K. Effects of various environmental and medium conditions on the response of Indica and Japonica rice plants to ammonium and nitrate nitrogen. Soil Sci. Plant Nutr. 27, 347–355 (1981).
Yoshida, M. & Horinouchi, S. Trichostatin and leptomycin: inhibition of histone deacetylation and signal-dependent nuclear export. Ann. N. Y. Acad. Sci. 886, 23–35 (1999).
Li, L., Ng, N. K. L., Koon, A. C. & Chan, H. Y. E. Expanded polyalanine tracts function as nuclear export signals and promote protein mislocalization via eEF1A1 factor. J. Biol. Chem. 292, 5784–5800 (2017).
Chang, S.-H., Chang, W.-L., Lu, C.-C. & Tarn, W.-Y. Alanine repeats influence protein localization in splicing speckles and paraspeckles. Nucleic Acids Res. 42, 13788–13798 (2014).
Caburet, S. et al. A recurrent polyalanine expansion in the transcription factor FOXL2 induces extensive nuclear and cytoplasmic protein aggregation. J. Med. Genet. 41, 932–936 (2004).
Zhang, Y.-W., Wen, Y.-J., Dunwell, J. M. & Zhang, Y.-M. QTL.gCIMapping.GUI v2.0: an R software for detecting small-effect and linked QTLs for quantitative traits in bi-parental segregation populations. Comput. Struct. Biotechnol. J. 18, 59–65 (2020).
Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 550 (2014).
Luo, W. et al. COLD6-OSM1 module senses chilling for cold tolerance via 2’,3’-cAMP signaling in rice. Mol. Cell 84, 4224–4238.e9 (2024).
Sun, S. et al. Domestication-selected COG4-OsbZIP23 module regulates chilling tolerance in rice. Cell Rep. 43, 114965 (2024).
Wu, K. et al. Enhanced sustainable green revolution yield via nitrogen-responsive chromatin modulation in rice. Science 367, eaaz2046 (2020).
Šimkovic, M. & Träuble, B. Robustness of statistical methods when measure is affected by ceiling and/or floor effect. PLoS ONE 14, e0220889 (2019).
Krejcie, T. C. Using a microcomputer to convert percent response values to probits. J. Clin. Monit. Comput. 8, 19–23 (1991).
Tallarida, R. J. & Murray, R. B. Manual of Pharmacologic Calculations: with Computer Programs 26–31 (Springer, 1987).
Zhang, C., Dong, S.-S., Xu, J.-Y., He, W.-M. & Yang, T.-L. PopLDdecay: a fast and effective tool for linkage disequilibrium decay analysis based on variant call format files. Bioinformatics 35, 1786–1788 (2019).
Dong, S.-S. et al. LDBlockShow: a fast and convenient tool for visualizing linkage disequilibrium and haplotype blocks based on variant call format files. Brief. Bioinform. 22, bbaa227 (2021).
Kawahara, Y. et al. Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data. Rice 6, 4 (2013).
Kim, D., Paggi, J. M., Park, C., Bennett, C. & Salzberg, S. L. Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nat. Biotechnol. 37, 907–915 (2019).
Liao, Y., Smyth, G. K. & Shi, W. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics 30, 923–930 (2014).
Yu, G., Wang, L.-G., Han, Y. & He, Q.-Y. clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS 16, 284–287 (2012).
Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357–359 (2012).
Zhang, Y. et al. Model-based analysis of ChIP-Seq (MACS). Genome Biol 9, R137 (2008).
Yu, G., Wang, L.-G. & He, Q.-Y. ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization. Bioinformatics 31, 2382–2383 (2015).
Moll, R. H., Kamprath, E. J. & Jackson, W. A. Analysis and interpretation of factors which contribute to efficiency of nitrogen utilization. Agron. J. 74, 562–564 (1982).
Humphreys, I. R. et al. Computed structures of core eukaryotic protein complexes. Science 374, eabm4805 (2021).
Tamura, K., Stecher, G. & Kumar, S. MEGA11: Molecular Evolutionary Genetics Analysis version 11. Mol. Biol. Evol. 38, 3022–3027 (2021).

