A wild soybean MADS-box gene <i>GsAGL62</i> improves seed weight by enhancing cytokinin signaling and cell proliferation

Fei Wu; Wei Li; Dezhou Hu; Zhongyi Yang; Zhen Wang; Zhiyu Wang; Xiaoyue Su; Yifei Yang; Shupeng Dong; Cui Xuan; Yu Zhang; Qinxin Song; Deyue Yu; Fang Huang

doi:10.1016/j.jgg.2026.09.005

Turn off MathJax

Article Contents

Article Navigation > Journal of Genetics and Genomics > 2026 > Accepted Manuscript

PDF( 0 KB)

A wild soybean MADS-box gene GsAGL62 improves seed weight by enhancing cytokinin signaling and cell proliferation

doi: 10.1016/j.jgg.2026.09.005

a. Key Laboratory of Biology and Genetics Improvement of Soybean, Ministry of Agriculture, Zhongshan Bio-Logical Breeding Laboratory (ZSBBL), National Innovation Platform for Soybean Breeding and Industry-Education Integration, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China;
b. Crop Tillage and Cultivation Institute, Heilongjiang Academy of Agricultural Science, Harbin 150086, China;
c. College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China

Funds:

This study was supported in part by the National Natural Science Foundation of China (32372174, 32501932), The China Postdoctoral Science Foundation (2023M741757), The Jiangsu Funding Program for Excellent Postdoctoral Talent (2024ZB343, 2023ZB605) and the Bioinformatics Center of Nanjing Agricultural University.

Received Date: 2026-04-10
Accepted Date: 2026-09-09
Rev Recd Date: 2026-09-08

Available Online: 2026-09-20

Abstract

Abstract

Soybean seed weight is a key yield determinant, but the transcriptional mechanisms connecting hormone signaling to seed growth are poorly understood. Here, we identify GsAGL62, a wild soybean MADS-box transcription factor located within a previously mapped hundred-seed weight (HSW) locus and a domestication-associated selective sweep. Functional analyses show that overexpression of GsAGL62 in cultivated soybean significantly increases HSW, whereas ethyl methanesulfonate (EMS)-induced gmagl62 mutants reduce it. Integrated transcriptomic and metabolomic analyses reveal that GsAGL62 enhances cytokinin accumulation and signaling cytokinin-associated responses, accompanied by increased expression of genes involved in cell proliferation. Mechanistically, GsAGL62 directly binds to the promoter of the conserved growth inhibitor GmATPK2 and represses its transcription. Consistently, independent EMS-induced gmatpk2 mutants exhibit increased seed weight, supporting GmATPK2 as a downstream negative regulator of seed growth. Population genetic analyses further reveal strong differentiation of GsAGL62 promoter haplotypes during soybean domestication and improvement. These haplotypes show differential promoter activities and are associated with distinct agronomic performance, suggesting that cis-regulatory variation at GsAGL62 contributes to its selection during soybean improvement. Collectively, our findings establish a regulatory module linking GsAGL62 to cytokinin-associated responses, cell proliferation, and seed growth, and highlight GsAGL62 as a potential target for soybean yield improvement.
- GsAGL62,
- Soybean,
- Hundred-seed weight,
- Cytokinin,
- Cell proliferation,
- Domestication

FullText(HTML)

References(72)

References

Alam, I., Batool, K., Huang, Y., Liu, J., Ge, L., 2022. Developing genetic engineering techniques for control of seed size and yield. Int. J. Mol. Sci. 23, 13256.

Bachlava, E., Dewey, R.E., Burton, J.W., Cardinal, A.J., 2009. Mapping and comparison of quantitative trait loci for oleic acid seed content in two segregating soybean populations. Crop Sci. 49, 433-442.

Bandelt, H.J., Forster, P., Rohl, A., 1999. Median-joining networks for inferring intraspecific phylogenies. Mol. Biol. Evol. 16, 37-48.

Barrada, A., Djendli, M., Desnos, T., Mercier, R., Robaglia, C., Montane, M., Menand, B., 2019. A TOR-YAK1 signaling axis controls cell cycle, meristem activity and plant growth in Arabidopsis. Development 146, dev171298.

Bihmidine, S., Hunter, C.T., III, Johns, C.E., Koch, K.E., Braun, D.M., 2013. Regulation of assimilate import into sink organs: Update on molecular drivers of sink strength. Front. Plant Sci. 4, 177.

Chen, S., Zhou, Y., Chen, Y., Gu, J., 2018. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 34, i884-i890.

Chen, X., Liu, C., Guo, P., Hao, X., Pan, Y., Zhang, K., Liu, W., Zhao, L., Luo, W., He, J., et al., 2023. Differential SW16.1 allelic effects and genetic backgrounds contributed to increased seed weight after soybean domestication. J. Integr. Plant Biol. 65, 1734-1752.

Chiluwal, A., Kawashima, T., Salmeron, M., 2022. Soybean seed weight responds to increases in assimilate supply during late seed-fill phase. J. Crop Improv. 36, 222-238.

Deprost, D., Yao, L., Sormani, R., Moreau, M., Leterreux, G., Nicolai, M., Bedu, M., Robaglia, C., Meyer, C., 2007. The Arabidopsis TOR kinase links plant growth, yield, stress resistance and mRNA translation. EMBO Rep. 8, 864-870.

Doebley, J.F., Gaut, B.S., Smith, B.D., 2006. The molecular genetics of crop domestication. Cell 127, 1309-1321.

Figueiredo, D.D., Batista, R.A., Roszak, P.J., Hennig, L., Kohler, C., 2016. Auxin production in the endosperm drives seed coat development in Arabidopsis. eLife 5, e20542.

Goettel, W., Zhang, H., Li, Y., Qiao, Z., Jiang, H., Hou, D., Song, Q., Pantalone, V.R., Song, B., Yu, D., et al., 2022. POWR1 is a domestication gene pleiotropically regulating seed quality and yield in soybean. Nat. Commun. 13, 3051.

Gramzow, L., Theissen, G., 2010. A hitchhiker's guide to the MADS world of plants. Genome Biol. 11, 214.

Gu, Y., Li, W., Jiang, H., Wang, Y., Gao, H., Liu, M., Chen, Q., Lai, Y., He, C., 2017. Differential expression of a WRKY gene between wild and cultivated soybeans correlates to seed size. J. Exp. Bot. 68, 2717-2729.

Guo, J., Liu, Y., Wang, Y., Chen, J., Li, Y., Huang, H., Qiu, L., Wang, Y., 2012. Population structure of the wild soybean (Glycine soja) in China: implications from microsatellite analyses. Ann. Bot. 110, 777-785.

Guo, L., Luo, X., Li, M., Joldersma, D., Plunkert, M., Liu, Z., 2022. Mechanism of fertilization-induced auxin synthesis in the endosperm for seed and fruit development. Nat. Commun. 13, 3985.

Hammond-Kosack, M.C.U., King, R., Kanyuka, K., Hammond-Kosack, K.E., 2021. Exploring the diversity of promoter and 5′UTR sequences in ancestral, historic and modern wheat. Plant Biotechnol. J. 19, 2469-2487.

Hehenberger, E., Kradolfer, D., Kohler, C., 2012. Endosperm cellularization defines an important developmental transition for embryo development. Development 139, 2031-2039.

Henriques, R., Magyar, Z., Monardes, A., Khan, S., Zalejski, C., Orellana, J., Szabados, L., de la Torre, C., Koncz, C., Bogre, L., 2010. Arabidopsis S6 kinase mutants display chromosome instability and altered RBR1-E2F pathway activity. EMBO J. 29, 2979-2993.

Henriques, R., Magyar, Z., Bogre, L., 2013. S6K1 and E2FB are in mutually antagonistic regulatory links controlling cell growth and proliferation in Arabidopsis. Plant Signal. Behav. 8, e24367.

Hou, X., Ding, L., Yu, H., 2013. Crosstalk between GA and JA signaling mediates plant growth and defense. Plant Cell Rep. 32, 1067-1074.

Hu, D., Li, X., Yang, Z., Liu, S., Hao, D., Chao, M., Zhang, J., Yang, H., Su, X., Jiang, M., et al, 2022. Downregulation of a gibberellin 3beta-hydroxylase enhances photosynthesis and increases seed yield in soybean. New Phytol. 235, 502-517.

Hu, Y., Liu, Y., Tao, J., Lu, L., Jiang, Z., Wei, J., Wu, C., Yin, C., Li, W., Bi, Y., et al, 2023. GmJAZ3 interacts with GmRR18a and GmMYC2a to regulate seed traits in soybean. J. Integr. Plant Biol. 65, 1983-2000.

Hu, Y., Liu, Y., Wei, J., Zhang, W., Chen, S., Zhang, J., 2023. Regulation of seed traits in soybean. aBIOTECH 4, 372-385.

Hyten, D.L., Song, Q., Zhu, Y., Choi, I., Nelson, R.L., Costa, J.M., Specht, J.E., Shoemaker, R.C., Cregan, P.B., 2006. Impacts of genetic bottlenecks on soybean genome diversity. Proc. Natl. Acad. Sci. U. S. A. 103, 16666-16671.

Inze, D., De Veylder, L., 2006. Cell cycle regulation in plant development. Annu. Rev. Genet. 40, 77-105.

Jameson, P.E., Song, J., 2016. Cytokinin: a key driver of seed yield. J. Exp. Bot. 67, 593-606.

Joldersma, D., Guo, L., Alger, E.I., Ippoliti, C., Luo, X., Platts, A.E., Edger, P.P., Liu, Z., 2024. Identification and analysis of imprinted genes in wild strawberry uncover a regulatory pathway in endosperm development. Plant Physiol. 196, 2599-2613.

Jumrani, K., Bhatia, V.S., 2018. Impact of combined stress of high temperature and water deficit on growth and seed yield of soybean. Physiol. Mol. Biol. Plants 24, 37-50.

Jun, T., Van, K., Kim, M.Y., Lee, S., Walker, D.R., 2008. Association analysis using SSR markers to find QTL for seed protein content in soybean. Euphytica 162, 179-191.

Kang, I., Steffen, J.G., Portereiko, M.F., Lloyd, A., Drews, G.N., 2008. The AGL62 MADS domain protein regulates cellularization during endosperm development in Arabidopsis. Plant Cell 20, 635-647.

Kastoori Ramamurthy, R., Jedlicka, J., Graef, G.L., Waters, B.M., 2014. Identification of new QTLs for seed mineral, cysteine, and methionine concentrations in soybean. Mol. Breed. 34, 431-445.

Kato, S., Sayama, T., Fujii, K., Yumoto, S., Kono, Y., Hwang, T., Kikuchi, A., Takada, Y., Tanaka, Y., Shiraiwa, T., et al, 2014. A major and stable QTL associated with seed weight in soybean across multiple environments and genetic backgrounds. Theor. Appl. Genet. 127, 1365-1374.

Khalil, M.I., Helal, M., El-Sayed, A.F., El Hajj, R., Holail, J., Houssein, M., Waraky, A., Pardo, O.E., 2024. S6K2 in focus: signaling pathways, post-translational modifications, and computational analysis. Int. J. Mol. Sci. 26, 176.

Kour, J., Kohli, S.K., Khanna, K., Bakshi, P., Sharma, P., Singh, A.D., Ibrahim, M., Devi, K., Sharma, N., Ohri, P., et al, 2021. Brassinosteroid signaling, crosstalk and, physiological functions in plants under heavy metal stress. Front. Plant Sci. 12, 608061.

Kumar, S., Stecher, G., Li, M., Knyaz, C., Tamura, K., 2018. MEGA X: Molecular Evolutionary Genetics Analysis across computing platforms. Mol. Biol. Evol. 35, 1547-1549.

Letunic, I., Bork, P., 2021. Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation. Nucleic Acids Res. 49, W293-W296.

Li, B., Dewey, C.N., 2011. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics 12, 323.

Li, H., Du, H., He, M., Wang, J., Wang, F., Yuan, W., Huang, Z., Cheng, Q., Gou, C., Chen, Z., et al., 2023. Natural variation of FKF1 controls flowering and adaptation during soybean domestication and improvement. New Phytol. 238, 1671-1684.

Li, N., Xu, R., Duan, P., Li, Y., 2018. Control of grain size in rice. Plant Reprod. 31, 237-251.

Li, N., Xu, R., Li, Y., 2019. Molecular networks of seed size control in plants. Annu. Rev. Plant Biol. 70, 435-463.

Li, X., Chen, Z., Li, H., Yue, L., Tan, C., Liu, H., Hu, Y., Yang, Y., Yao, X., Kong, L., et al, 2024. Dt1 inhibits SWEET-mediated sucrose transport to regulate photoperiod-dependent seed weight in soybean. Mol. Plant 17, 496-508.

Li, X., Schmitz, R.J., 2025. Cis-regulatory dynamics in plant domestication. Trends Genet. 41, 984-994.

Liu, Y., Du, H., Li, P., Shen, Y., Peng, H., Liu, S., Zhou, G., Zhang, H., Liu, Z., Shi, M., et al, 2020. Pan-genome of wild and cultivated soybeans. Cell 182, 162-176.

Lu, X., Xiong, Q., Cheng, T., Li, Q., Liu, X., Bi, Y., Li, W., Zhang, W., Ma, B., Lai, Y., et al, 2017. A PP2C-1 allele underlying a quantitative trait locus enhances soybean 100-seed weight. Mol. Plant 10, 670-684.

Mao, T., Jiang, Z., Han, Y., Teng, W., Zhao, X., Li, W., 2013. Identification of quantitative trait loci underlying seed protein and oil contents of soybean across multi-genetic backgrounds and environments. Plant Breed. 132, 630-641.

Maskova, T., Herben, T., 2018. Root:shoot ratio in developing seedlings: how seedlings change their allocation in response to seed mass and ambient nutrient supply. Ecol. Evol. 8, 7143-7150.

Moles, A.T., Ackerly, D.D., Webb, C.O., Tweddle, J.C., Dickie, J.B., Westoby, M., 2005a. A brief history of seed size. Science 307, 576-580.

Moles, A.T., Ackerly, D.D., Webb, C.O., Tweddle, J.C., Dickie, J.B., Pitman, A.J., Westoby, M., 2005b. Factors that shape seed mass evolution. Proc. Natl. Acad. Sci. U. S. A. 102, 10540-10544.

Obomighie, I., Lapenas, K., Murphy, B.E., Bowles, A.M.C., Bechtold, U., Prischi, F., 2021. The role of ribosomal protein S6 kinases in plant homeostasis. Front. Mol. Biosci. 8, 636560.

Panthee, D.R., Pantalone, V.R., West, D.R., Saxton, A.M., Sams, C.E., 2005. Quantitative trait loci for seed protein and oil concentration, and seed size in soybean. Crop Sci. 45, 2015-2022.

Rotundo, J.L., Borras, L., Westgate, M.E., 2011. Linking assimilate supply and seed developmental processes that determine soybean seed composition. Eur. J. Agron. 35, 184-191.

Schaller, G.E., Street, I.H., Kieber, J.J., 2014. Cytokinin and the cell cycle. Curr. Opin. Plant Biol. 21, 7-15.

Simura, J., Antoniadi, I., Siroka, J., Tarkowska, D., Strnad, M., Ljung, K., Novak, O., 2018. Plant hormonomics: multiple phytohormone profiling by targeted metabolomics. Plant Physiol. 177, 476-489.

Szklarczyk, D., Franceschini, A., Wyder, S., Forslund, K., Heller, D., Huerta-Cepas, J., Simonovic, M., Roth, A., Santos, A., Tsafou, K.P., et al., 2015. STRING v10: protein-protein interaction networks, integrated over the tree of life. Nucleic Acids Res. 43, D447-D452.

Wang, S., Liu, S., Wang, J., Yokosho, K., Zhou, B., Yu, Y., Liu, Z., Frommer, W.B., Ma, J.F., Chen, L., et al, 2020. Simultaneous changes in seed size, oil content and protein content driven by selection of SWEET homologues during soybean domestication. Natl. Sci. Rev. 7, 1776-1786.

Wang, X., Li, Y., Zhang, H., Sun, G., Zhang, W., Qiu, L., 2015. Evolution and association analysis of GmCYP78A10 gene with seed size/weight and pod number in soybean. Mol. Biol. Rep. 42, 489-496.

Wu, T., Hu, E., Xu, S., Chen, M., Guo, P., Dai, Z., Feng, T., Zhou, L., Tang, W., Zhan, L., et al., 2021. clusterProfiler 4.0: a universal enrichment tool for interpreting omics data. Innovation 2, 100141.

Yang, C., Li, B., Yu, H., Wang, Y., An, Z., Chen, M., He, C., 2025a. GmCDC7 is involved in coordinating seed size and quality in soybean. Theor. Appl. Genet. 138, 253.

Yang, J., Zhang, J., Huang, Z., Wang, Z., Zhu, Q., Liu, L., 2002. Correlation of cytokinin levels in the endosperms and roots with cell number and cell division activity during endosperm development in rice. Ann. Bot. 90, 369-377.

Yang, W., Cortijo, S., Korsbo, N., Roszak, P.J., Schiessl, K., Gurzadyan, A., Wightman, R., Jonsson, H., Meyerowitz, E., 2021. Molecular mechanism of cytokinin-activated cell division in Arabidopsis. Science 371, 1350-1355.

Yang, Z., Lu, S., Li, W., Wang, Z., Hu, D., Su, X., Wu, F., Dong, S., Cui, X., Zhang, Y., et al, 2025b. A major latex protein, GsMLP328, modulates seed traits in soybean. J. Integr. Plant Biol. 67, 2790-2792.

Ye, R., Wang, M., Du, H., Chhajed, S., Koh, J., Liu, K., Shin, J., Wu, Y., Shi, L., Xu, L., et al, 2022. Glucose-driven TOR-FIE-PRC2 signalling controls plant development. Nature 609, 986-993.

Yu, C., Qu, Z., Zhang, Y., Zhang, X., Lan, T., Adelson, D.L., Wang, D., Zhu, Y., 2017. Seed weight differences between wild and domesticated soybeans are associated with specific changes in gene expression. Plant Cell Rep. 36, 1417-1426.

Yuan, X., Jiang, X., Zhang, M., Wang, L., Jiao, W., Chen, H., Mao, J., Ye, W., Song, Q., 2024. Integrative omics analysis elucidates the genetic basis underlying seed weight and oil content in soybean. Plant Cell 36, 2160-2175.

Zdarska, M., Dobisova, T., Gelova, Z., Pernisova, M., Dabravolski, S., Hejatko, J., 2015. Illuminating light, cytokinin, and ethylene signalling crosstalk in plant development. J. Exp. Bot. 66, 4913-4931.

Zhang, H., Jiang, H., Hu, Z., Song, Q., An, Y.C., 2022. Development of a versatile resource for post-genomic research through consolidating and characterizing 1500 diverse wild and cultivated soybean genomes. BMC Genomics 23, 250.

Zhang, J., Zhang, Z., Zhang, R., Yang, C., Zhang, X., Chang, S., Chen, Q., Rossi, V., Zhao, L., Xiao, J., et al, 2024. Type I MADS-box transcription factor TaMADS-GS regulates grain size by stabilizing cytokinin signalling during endosperm cellularization in wheat. Plant Biotechnol. J. 22, 200-215.

Zhang, W., Xu, W., Zhang, H., Liu, X., Cui, X., Li, S., Song, L., Zhu, Y., Chen, X., Chen, H., 2021. Comparative selective signature analysis and high-resolution GWAS reveal a new candidate gene controlling seed weight in soybean. Theor. Appl. Genet. 134, 1329-1341.

Zhao, D., Zheng, H., Li, J., Wan, M., Shu, K., Wang, W., Hu, X., Hu, Y., Qiu, L., Wang, X., 2024. Natural variation in the promoter of GmSPL9d affects branch number in soybean. Int. J. Mol. Sci. 25, 5991.

Zhou, Z., Jiang, Y., Wang, Z., Gou, Z., Lyu, J., Li, W., Yu, Y., Shu, L., Zhao, Y., Ma, Y., et al, 2015. Resequencing 302 wild and cultivated accessions identifies genes related to domestication and improvement in soybean. Nat. Biotechnol. 33, 408-414.

Zhu, X., Zhang, B., Yang, L., Huang, J., Huang, F., Zhang, H., Song, Q., Huang, J., 2025. A machine learning-based tool for predicting transcription factor-target gene interactions in soybean. Plant Physiol. 198, kiaf318.

Relative Articles

Supplements(0)

Cited By

Proportional views