If you are citing a reference for the first time in these legends, please include all new references in the Online Methods References section, and carry on the numbering from the main References section of the paper. Extended DataFig. 1 Alternative splicing site of the PHYC gene in xiaomi a, RNA-Seq reads of Jingu21. xiaomi genome sequences were used as reference genome. The blue vertical line shows the G-T mutation site. b, RNA-seq reads of xiaomi. The wrong splicing site was marked by a red arrow. Extended Data Fig. 2 Phenotypic and molecular characterization of the xiaomi-2 mutant a, Forty-day-old plants of Jingu21 (wild type, left) and xiaomi-2 (right) plants grown under natural long-day conditions. b, Heading date of Jingu21and xiaomi-2 under natural field conditions. The heading date of ≥ 20 plants was measured for each replicate (n = 3 biologically independent replicates, ≥ 102 in total). The bottom and top of boxes represent the first and third quartile, respectively. The middle line is the median and the whiskers represent the maximum and minimum values. Statistical analysis was performed using two-tailed Wilcoxon rank-sum test. c, A mature small-sized xiaomi-2 plant (right) compared to Jingu21 (left), at the 68th day in field. d, Plant height of Jingu21 and xiaomi-2 under natural field conditions. The plant height of ≥ 23 plants was measured for each replicate (n = 3 biologically independent replicates, ≥ 83 in total). e, Molecular charicterization of xiaomi-2. Exons and introns are denoted by filled boxes and lines, respectively. P2F and P2R represent a pair of primers used to amplify the fragments harboring the mutation site from the segregating M3 individuals (Primer sequences are listed in SupplementaryTable 3). c, Structure of PHYC and its mutation version deduced according to mutations in xiaomi-2. Scale bars, 10 cm in a and c. Extended Data Fig. 3 Sequence alignment of the GAF domain of PHYC in foxtail millet and its homologs software. Red box indicates the conserved residue Leu across all listed species that is substituted with His in xiaomi-2, demonstrating its functional importance for PHYC. Accession numbers for the aligned sequences: Arabidopsis thaliana NP_198433, Brachypodium distachyon XP_003559446, Brassica napus XP_013680236, Ipomoea nil XP_019162785, Oryza sativa AAF66603, Panicum miliaceum, RLN42126, Solanum lycopersicum NP_001307446, Sorghum bicolor XP_002466441, Triticum aestivum AAU06208, Vitis vinifera ACC6096 and Zea mays XP_008665426. PHYC protein in Jingu21 is presented as for Setaria italica (Si9G09200).Extended Data Fig. 4 Hi-C interaction matrices show the pairwise correlations between ordered scaffolds along the 9 pseudomolecules correlation. in T1 transgenic seeds as visualized for GFP expression or multiple (c) T-DNA insertions were scanned with a dissection microscope equipped with UV light. All experiments were performed for eight independent biological repeats, and similar results were obtained. Scale bars, 2 mm. Extended Data Fig. 6 PCR confirmation of the site-specif...

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The original article was inadvertently published with an inaccurate application rate of the composted pig manure. The correct application rate is shown here: N, P, K and organic manure were applied in the form of urea (120