| [1] |
Schmutz J, Cannon SB, Schlueter J, Ma J, Mitros T, et al. 2010. Genome sequence of the palaeopolyploid soybean. |
| [2] |
Dong L, Fang C, Cheng Q, Su T, Kou K, et al. 2021. Genetic basis and adaptation trajectory of soybean from its temperate origin to tropics. |
| [3] |
Kotilainen T, Aphalo P, Brelsford C, Böök H, Devraj S, et al. 2020. Patterns in the spectral composition of sunlight and biologically meaningful spectral photon ratios as affected by atmospheric factors. |
| [4] |
Chiang C, Olsen JE, Basler D, Bånkestad D, Hoch G. 2019. Latitude and weather influences on sun light quality and the relationship to tree growth. |
| [5] |
Fang C, Sun Z, Li S, Su T, Wang L, et al. 2024. Subfunctionalisation and self-repression of duplicated E1 homologues finetunes soybean flowering and adaptation. |
| [6] |
Zhai H, Wan Z, Jiao S, Zhou J, Xu K, et al. 2022. GmMDE genes bridge the maturity gene E1 and florigens in photoperiodic regulation of flowering in soybean. |
| [7] |
Sun J, Zheng Y, Guo J, Zhang Y, Liu Y, et al. 2023. GmGAMYB-BINDING PROTEIN 1 promotes small auxin-up RNA gene transcription to modulate soybean maturity and height. |
| [8] |
Liu H, Lin R, Deng XW. 2020. Photobiology: light signal transduction and photomorphogenesis. |
| [9] |
Ballaré CL, Pierik R. 2017. The shade-avoidance syndrome: multiple signals and ecological consequences. |
| [10] |
Lyu X, Cheng Q, Qin C, Li Y, Xu X, et al. 2021. GmCRY1s modulate gibberellin metabolism to regulate soybean shade avoidance in response to reduced blue light. |
| [11] |
Fang L, Ma Z, Wang Q, Nian H, Ma Q, et al. 2021. Plant growth and photosynthetic characteristics of soybean seedlings under different LED lighting quality conditions. |
| [12] |
Liu Y, Du H, Li P, Shen Y, Peng H, et al. 2020. Pan-genome of wild and cultivated soybeans. |
| [13] |
Wang J, Hu Z, Liao X, Wang Z, Li W, et al. 2022. Whole-genome resequencing reveals signature of local adaptation and divergence in wild soybean. |
| [14] |
Yang W, Wang Y, Li X. 2026. Soybean's evolutionary roadmap to breeding. |
| [15] |
Zhu Z, Wang Y, Liu S, Wang S, Li J, et al. 2025. Genomic atlas of 8, 105 accessions reveals stepwise domestication, global dissemination, and improvement trajectories in soybean. |
| [16] |
Bhartiya A, Aditya J, Pal RS, Chandra N, Kant L, et al. 2020. A traditional legume with high nutritional and nutraceutical properties from NW himalayan region of India. |
| [17] |
Li H, Durbin R. 2009. Fast and accurate short read alignment with Burrows-Wheeler transform. |
| [18] |
Kosugi S, Terao C. 2024. Comparative evaluation of SNVs, indels, and structural variations detected with short- and long-read sequencing data. |
| [19] |
Pertea M, Kim D, Pertea GM, Leek JT, Salzberg SL. 2016. Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown. |
| [20] |
Xu G, Liang S, Hu G, Zhao W, Li Y, et al. 2025. HDAC2 as a therapeutic target in bladder cancer: insights into the altered epigenetic regulation and lysine lactylation. |
| [21] |
Garrido-Auñón F, Puente-Moreno J, García-Pastor ME, Zapata PJ, Martínez-Romero D, et al. 2025. Brassinosteroid preharvest treatments as a useful tool to increase crop yield and red colour in blood orange fruits. |
| [22] |
Thennakoon M, Khanna RR, Singh S, Rashotte AM. 2026. cis-Zeatin is an active cytokinin that mediates gene expression and delays leaf senescence in tomato under salt stress. |
| [23] |
Peng Q, Wang H, Tong J, Kabir MH, Huang Z, et al. 2013. Effects of indole-3-acetic acid and auxin transport inhibitor on auxin distribution and development of peanut at pegging stage. |
| [24] |
Mosquna A, Peterson FC, Park SY, Lozano-Juste J, Volkman BF, et al. 2011. Potent and selective activation of abscisic acid receptors in vivo by mutational stabilization of their agonist-bound conformation. |
| [25] |
Gul N, Masoodi KZ, Ramazan S, Mir JI, Aslam S. 2023. Study on the impact of exogenously applied methyl jasmonate concentrations on Solanum lycopersicum under low temperature stress. |
| [26] |
Yue P, Jiang Z, Sun Q, Wei R, Yin Y, et al. 2023. Jasmonate activates a CsMPK6-CsMYC2 module that regulates the expression of β-citraurin biosynthetic genes and fruit coloration in orange (Citrus sinensis). |
| [27] |
Lamers J, Zhang Y, van Zelm E, Leong CK, Meyer AJ, et al. 2025. Abscisic acid signaling gates salt- induced responses of plant roots. |
| [28] |
Hayat Q, Hayat S, Alyemeni MN, Ahmad A. 2012. Salicylic acid mediated changes in growth, photosynthesis, nitrogen metabolism and antioxidant defense system in Cicer arietinum L. |
| [29] |
Cataldo DA, Maroon M, Schrader LE, Youngs VL. 1975. Rapid colorimetric determination of nitrate in plant-tissue by nitration of salicylic-acid. |
| [30] |
Toyomasu T, Shenton MR, Okada K. 2020. Evolution of labdane-related diterpene synthases in cereals. |
| [31] |
Cazzonelli CI. 2011. Carotenoids in nature: insights from plants and beyond. |
| [32] |
Liechti R, Farmer EE. 2002. The jasmonate pathway. |
| [33] |
Xu Y, Wang C, Zhang R, Ma C, Dong S, et al. 2021. The relationship between internode elongation of soybean stems and spectral distribution of light in the canopy under different plant densities. |
| [34] |
Wang C, Huang S, Zhang X, Shan F, Fan J, et al. 2025. Red and blue light differentially regulate carbon metabolism and stem elongation in soybean cultivars with contrasting lodging resistance under shade: a multi-omics perspective. |
| [35] |
Zhu B, Zhang Y, Gao R, Wu Z, Zhang W, et al. 2025. Complete biosynthesis of salicylic acid from phenylalanine in plants. |
| [36] |
Guo F, Huang Y, Qi P, Lian G, Hu X, et al. 2021. Functional analysis of auxin receptor OsTIR1/OsAFB family members in rice grain yield, tillering, plant height, root system, germination, and auxinic herbicide resistance. |
| [37] |
Vlot AC, Dempsey DA, Klessig DF. 2009. Salicylic acid, a multifaceted hormone to combat disease. |
| [38] |
Wang Z, Huang Y, Bi X, Wang T, Zhang Y, et al. 2025. HEADLESS represses a CYP735 monooxygenase gene and promotes iP-type cytokinin accumulation in the Medicago truncatula shoot apex. |
| [39] |
Zhou J, Pang R, Han Y, Guo Y, Wang Y, et al. 2025. CRISPR-Cas9-mediated knockout of OsKCS11 in rice reveals potential crosstalk between very-long-chain fatty acids and cytokinin. |
| [40] |
Werner S, Bartrina I, Schmülling T. 2021. Cytokinin regulates vegetative phase change in Arabidopsis thaliana through the miR172/TOE1-TOE2 module. |
| [41] |
Zhao M, Wang J, Hao X, Jin J, Tang J, et al. 2025. Natural variation of CsUGT71A60 determines growth and cold tolerance via regulating cytokinin glycosylation in Camellia sinensis. |
| [42] |
Neff MM, Nguyen SM, Malancharuvil EJ, Fujioka S, Noguchi T, et al. 1999. BAS1: a gene regulating brassinosteroid levels and light responsiveness in Arabidopsis. |
| [43] |
Chory J, Nagpal P, Peto CA. 1991. Phenotypic and genetic analysis of det2, a new mutant that affects light-regulated seedling development in Arabidopsis. |
| [44] |
Kang JG, Yun J, Kim DH, Chung KS, Fujioka S, et al. 2001. Light and brassinosteroid signals are integrated via a dark-induced small G protein in etiolated seedling growth. |
| [45] |
Li Z, Tu Q, Lyu X, Cheng Q, Ji R, et al. 2024. GmSTF accumulation mediated by DELLA protein GmRGAs contributes to coordinating light and gibberellin signaling to reduce plant height in soybean. |
| [46] |
Gomi K, Sasaki A, Itoh H, Ueguchi-Tanaka M, Ashikari M, et al. 2004. GID2, an F-box subunit of the SCF E3 complex, specifically interacts with phosphorylated SLR1 protein and regulates the gibberellin-dependent degradation of SLR1 in rice. |
| [47] |
Zhou Y, Zhao C, Du T, Li A, Qin Z, et al. 2023. Overexpression of 9-cis-epoxycarotenoid dioxygenase gene, IbNCED1, negatively regulates plant height in transgenic sweet potato. |
| [48] |
Li S, Wang M, Du X, Wang Y, Pan Y, et al. 2025. The GmPRL1b-GmST2-GmAOC3/4 module confers salt tolerance and botrytis cinerea resistance by inducing jasmonic acid biosynthesis in soybean. |
| [49] |
Liu X, Hu B, Chu C. 2022. Nitrogen assimilation in plants: current status and future prospects. |
| [50] |
Zhang S, Huang Y, Ji Z, Fang Y, Tian Y, et al. 2025. Discovery of SOD5 as a novel regulator of nitrogen-use efficiency and grain yield via altering auxin level. |
| [51] |
Jiang B, Huang Y, Zhang S, Yu Y, Li S, et al. 2026. OsSIZ1 regulates rice nitrogen-use efficiency and grain yield by modulating auxin levels. |
| [52] |
Xu H, Huang S, Wang J, Wang T, Han Q, et al. 2026. Soybean auxin transporter PIN3 regulates nitrate acquisition to improve nitrogen use and seed traits. |
| [53] |
Li S, Tian Y, Wu K, Ye Y, Yu J, et al. 2018. Modulating plant growth–metabolism coordination for sustainable agriculture. |
| [54] |
Li QF, Gao Q, Yu JW, Liu QQ. 2023. Brassinosteroid, a prime contributor to the next Green Revolution. |
| [55] |
Yadav RK, Analin B, Panda MK, Ranjan A, Singh AP. 2023. Brassinosteroids-regulated nitrogen metabolism fine-tunes growth physiology and low nitrogen response in tomato. |
| [56] |
Janicka M, Reda M, Mroczko E, Wdowikowska A, Kabała K. 2023. Jasmonic acid effect on Cucumis sativus L. growth is related to inhibition of plasma membrane proton pump and the uptake and assimilation of nitrates. |
| [57] |
Bellegarde F, Tjahjono O, Yoshino-Kida M, Kiba T, Shibutani M, et al. 2025. Fluctuations in nitrate availability impact cytokinin biosynthesis through histone modifications of IPT3 in Arabidopsis roots for growth acclimation. |
| [58] |
Nazar R, Iqbal N, Syeed S, Khan NA. 2011. Salicylic acid alleviates decreases in photosynthesis under salt stress by enhancing nitrogen and sulfur assimilation and antioxidant metabolism differentially in two mungbean cultivars. |