doi:10.48130/seedbio-0024-0021

[1]

Caldwell BE, Howell RW. 1973. Soybeans: Improvement, Production, and Uses. Madison, WI: American Society of Agronomy.

[2]

Wang D, Su M, Hao JH, Li ZD, Dong S, et al. 2023. Dynamic transcriptome landscape of foxtail millet grain development. Seed Biology 2:19

doi: 10.48130/seedbio-2023-0019

[3]

Zhang Z, Zhang R, Meng F, Chen Y, Wang W, et al. 2023. A comprehensive atlas of long non-coding RNAs provides insight into grain development in wheat. Seed Biology 2:12

doi: 10.48130/seedbio-2023-0012

[4]

Fu Y, Li S, Xu L, Ji C, Xiao Q, et al. 2023. RNA sequencing of cleanly isolated early endosperms reveals coenocyte-to-cellularization transition features in maize. Seed Biology 2:8

doi: 10.48130/seedbio-2023-0008

[5]

Kovacik M, Nowicka A, Zwyrtková J, Strejčková B, Vardanega I, et al. 2024. The transcriptome landscape of developing barley seeds. The Plant Cell 36(7):2512−30

doi: 10.1093/plcell/koae095

[6]

Yi F, Gu W, Chen J, Song N, Gao X, et al. 2019. High temporal-resolution transcriptome landscape of early maize seed development. The Plant Cell 31(5):974−92

doi: 10.1105/tpc.18.00961

[7]

Verma S, Attuluri VPS, Robert HS. 2022. Transcriptional control of Arobidopsis seed development. Planta 255(4):90

doi: 10.1007/s00425-022-03870-x

[8]

Gao P, Xiang D, Quilichini TD, Venglat P, Pandey PK, et al. 2019. Gene expression atlas of embryo development in Arabidopsis. Plant Reproduction 32(1):93−104

doi: 10.1007/s00497-019-00364-x

[9]

Hofman F, Schon MA, Nodine MD. 2019. The embryonic transcriptome of Arabidopsis thaliana. Plant Reproduction 32(1):77−91

doi: 10.1007/s00497-018-00357-2

[10]

Zhou X, Liu Z, Shen K, Zhao P, Sun MX. 2020. Cell lineage-specific transcriptome analysis for interpreting cell fate specification of proembryos. Nature Communications 11:1366

doi: 10.1038/s41467-020-15189-w

[11]

Zhao P, Zhou X, Shen K, Liu Z, Cheng T, et al. 2019. Two-step maternal-to-zygotic transition with two-phase parental genome contributions. Developmental Cell 49(6):882−893.E3

doi: 10.1016/j.devcel.2019.04.016

[12]

Gao P, Quilichini TD, Yang H, Li Q, Nilsen KT, et al. 2022. Evolutionary divergence in embryo and seed coat development of U's Triangle Brassica species illustrated by a spatiotemporal transcriptome atlas. New Phytologist 233(1):30−51

doi: 10.1111/nph.17759

[13]

Zhang H, Hu Z, Yang Y, Liu X, Lv H, Song BH, An YQC, Li Z, Zhang D. 2021. Transcriptome profiling reveals the spatial-temporal dynamics of gene expression essential for soybean seed development. BMC Genomics 22:453

doi: 10.1186/s12864-021-07783-z

[14]

Sun S, Yi C, Ma J, Wang S, Peirats-Llobet M, et al. 2020. Analysis od spatio-temporal transcriptome profiles of soybean (Glycine max) tissues during early seed development. International Journal of Molecular Sciences 21(20):7603

doi: 10.3390/ijms21207603

[15]

Lin JY, Le BH, Chen M, Henry KF, Hur J, et al. 2017. Similarity between soybean and Arabidopsis seed methylomes and loss of non-CG methylation does not affect seed development. Proceedings of the National Academy of Sciences of the United States of America 114(45):E9730−E9739

doi: 10.1073/pnas.1716758114

[16]

Orozco-Arroyo G, Paolo D, Ezquer I, Colombo L. 2015. Networks controlling seed size in Arobidopsis. Plant Reproduction 28:17−32

doi: 10.1007/s00497-015-0255-5

[17]

Hu Y, Liu Y, Wei JJ, Zhang WK, Chen SY, et al. 2023. Regulation of seed traits in soybean. aBIOTECH 4(4):372−85

doi: 10.1007/s42994-023-00122-8

[18]

Nguyen QT, Kisiala A, Andreas P, Neil Emery RJ, Narine S. 2016. Soybean seed development: fatty acid and phytohormone metabolism and their interactions. Current Genomics 17(3):241−60

doi: 10.2174/1389202917666160202220238

[19]

Gupta M, Bhaskar PB, Sriram S, Wang PH. 2017. Integration of omics approaches to understand oil/protein content during seed development in oilseed crops. Plant Cell Reports 36(5):637−52

doi: 10.1007/s00299-016-2064-1

[20]

Du Y, Zhao Q, Chen L, Yao X, Zhang H, et al. 2020. Effect of drought stress during soybean R2-R6 growth stages on sucrose metabolism in leaf and seed. International Journal of Molecular Sciences 21(2):618

doi: 10.3390/ijms21020618

[21]

Poudel S, Vennam RR, Shrestha A, Reddy KR, Wijewardane NK, et al. 2023. Resilience of soybean cultivars to drought stress during flowering and early-seed setting stages. Science Report 13(1):1277

doi: 10.1038/s41598-023-28354-0

[22]

Jedličková V, Hejret V, Demko M, Jedlička P, Štefková M, et al. 2023. Transcriptome analysis of thermomorphogenesis in ovules and during early seed development in Brassica napus. BMC Genomics 24:236

doi: 10.1186/s12864-023-09316-2

[23]

Kotak S, Vierling E, Bäumlein H, von Koskull-Döring P. 2007. A novel transcriptional cascade regulating expression of heat stress proteins during seed development of Arabidopsis. The Plant Cell 19:182−95

doi: 10.1105/tpc.106.048165

[24]

Sedivy EJ, Wu F, Hanzawa Y. 2017. Soybean domestication: the origin, genetic architecture and molecular bases. New Phytologist 214(2):539−53

doi: 10.1111/nph.14418

[25]

Liu Y, Du H, Li P, Shen Y, Peng H, et al. 2020. Pan-genome of wild and cultivated soybeans. Cell 182(1):162−76

doi: 10.1016/j.cell.2020.05.023

[26]

Zhuang Y, Wang X, Li X, Hu J, Fan L, et al. 2022. Phylogenomics of the genus Glycine sheds light on polyploid evolution and life-strategy transition. Nature Plants 8:233−44

doi: 10.1038/s41477-022-01102-4

[27]

Tan Z, Peng Y, Xiong Y, Xiong F, Zhang Y, et al. 2022. Comprehensive transcriptional variability analysis reveals gene networks regulating seed oil content of Brassica napus. Genome Biology 23:233

doi: 10.1186/s13059-022-02801-z

[28]

Li L, Tian Z, Chen J, Tan Z, Zhang Y, et al. 2023. Characterization of novel loci controlling seed oil content in Brassica napus by marker matebolite-based multi-omics analysis. Genome Biology 24:141

doi: 10.1186/s13059-023-02984-z

[29]

Yu L, Liu D, Yin F, Yu P, Lu S, et al. 2023. Interaction between phenylpropane metabolism and oil accumulation in the developing seed of Brassica napus revealed by high temporal-resolution transcriptomes. BMC Biology 21(1):202

doi: 10.1186/s12915-023-01705-z

[30]

Yuan X, Jiang X, Zhang M, Wang L, Jiao W, et al. 2024. Integrative omics analysis elucidates the genetic basis underlying seed weight and oil content in soybean. The Plant Cell 36(6):2160−75

doi: 10.1093/plcell/koae062

[31]

Yang S, Miao L, He J, Zhang K, Li Y, et al. 2019. Dynamic transcriptome changes related to oil accumulation in developing soybean seeds. International Journal of Molecular Sciences 20(9):2202

doi: 10.3390/ijms20092202

[32]

Yao Y, Xiong E, Qu X, Li J, Liu H, et al. 2023. WGCNA and transcriptome profiling reveal hub genes for key development stage seed size/oil content between wild and cultivated soybean. BMC Genomics 24:494

doi: 10.1186/s12864-023-09617-6

[33]

Wang L, Jia G, Jiang X, Cao S, Chen ZJ, et al. 2021. Altered chromatin architecture and gene expression during polyploidization and domestication of soybean. The Plant Cell 33(5):1430−46

doi: 10.1093/plcell/koab081

[34]

Chen M, Lin JY, Wu X, Apuya NR, Henry KF, et al. 2021. Comparative analysis of embryo proper and suspensor transcriptomes in plant embryos with different morphologies. Proceedings of the National Academy of Sciences of the United States of America 118(6):e2024704118

doi: 10.1073/pnas.2024704118

[35]

Pelletier JM, Kwong RW, Park S, Le BH, Baden R, et al. 2017. LEC1 sequentially regulates the transcription of genes involved in diverse developmental processes during seed development. Proceedings of the National Academy of Sciences of the United States of America 114(32):E6710−E6719

doi: 10.1073/pnas.1707957114

[36]

Khan D, Ziegler D, Kalichuk JL, Hoi V, Huynh N, et al. 2022. Gene expression profiling reveals transcription factor networks and subgenome bias during Brassica napus seed development. The Plant Journal 109(3):477−89

doi: 10.1111/tpj.15587

[37]

Khanday I, Skinner D, Yang B, Mercier R, Sundaresan V. 2019. A male-expressed rice embryogenic trigger redirected for asexual propagation through seeds. Nature 565:91−95

doi: 10.1038/s41586-018-0785-8

[38]

Wang C, Liu Q, Shen Y, Hua Y, Wang J, et al. 2019. Clonal seeds from hybrid rice by simultaneous genome engineering of meiosis and fertilization genes. Nature Biotechnology 37(3):283−86

doi: 10.1038/s41587-018-0003-0

[39]

Cao X, Du Q, Guo Y, Wang Y, Jiao Y. 2023. Condensation of STM is critical for shoot meristem maintenance and salt tolerance in Arabidopsis. Molecular Plant 16(9):1445−1459

doi: 10.1016/j.molp.2023.09.005

[40]

Wan Q, Zhai N, Xie D, Liu W, Xu L. 2023. WOX11: the founder of plant organ regeneration. Cell Regeneration 12:1

doi: 10.1186/s13619-022-00140-9

[41]

Liao J, Deng B, Cai X, Yang Q, Hu B, et al. 2023. Time-course transcriptome analysis reveals regulation of Arabidopsis seed dormancy by the transcription factor WOX11/12. Journal of Experimental Botany 74(3):1090−106

doi: 10.1093/jxb/erac457

[42]

Stahle MI, Kuehlich J, Staron L, von Arnim AG, Golz JF. 2009. YABBYs and the transcriptional corerepressors LEUNIG and LEUNIG_HOMOLOG maintain leaf polarity and meristem activity in Arabidopsis. The Plant Cell 21(10):3105−18

doi: 10.1105/tpc.109.070458

[43]

Wang Y, Wang N, Lan J, Pan Y, Jiang Y, et al. 2024. Arabidopsis transcription factor TCP4 controls the identity of the apical gynoecium. The Plant Cell 36(7):2668−88

doi: 10.1093/plcell/koae107

[44]

Lan J, Wang N, Wang Y, Jiang Y, Yu H, et al. 2023. Arabidopsis TCP4 transcription factor inhibits high temperature-induced homeotic conversion of ovules. Nature Communications 14:5673

doi: 10.1038/s41467-023-41416-1

[45]

Zhao B, Dai A, Wei H, Yang S, Wang B, et al. 2016. Arobidopsis KLU homologue GmCYP78A72 regulates seed size in soybean. Plant Molecular Biology 90:33−47

doi: 10.1007/s11103-015-0392-0

[46]

Li Y, Yu Y, Liu X, Zhang X, Su Y. 2021. The arabidopsis MATERNAL EFFECT EMBRYO ARREST45 protein modulates maternal auxin biosynthesis and controls seed size by inducing AINTEGUMENTA. The Plant Cell 33(6):1907−26

doi: 10.1093/plcell/koab084

[47]

Fang C, Yang M, Tang Y, Zhang L, Zhao H, et al. 2023. Dynamics of cis-regulatory sequences and transcriptional divergence of duplicated genes in soybean. Proceedings of the National Academy of Sciences of the United States of America 120(44):e2303836120

doi: 10.1073/pnas.2303836120

[48]

Yu TF, Hou ZH, Wang HL, Chang SY, Song XY, et al. 2024. Soybean steroids improve crop abiotic stress tolerance and increase yield. Plant Biotechnology Journal 22(8):2333−47

doi: 10.1111/pbi.14349

[49]

Yuan F, Chen Y, Chen X, Zhu P, Jiang S, et al. 2023. Preliminary identification of the changes of physiological characteristics and transcripts in rice after-ripened seeds. Seed Biology 2:5

doi: 10.48130/seedbio-2023-0005

[50]

Smolikova G, Leonova T, Vashurina N, Frolov A, Medvedev S. 2020. Desiccation tolerance as the basis of long-term seed viability. International Journal of Molecular Sciences 22(1):101

doi: 10.3390/ijms22010101

[51]

Li C, Chen Y, Hu Q, Yang X, Zhao Y, et al. 2024. PSEUDO-RESPONSE REGULATOR 3b and transcription factor ABF3 modelate abscisic acid-dependent drought stress response in soybean. Plant Physiology 195(4):3053−71

doi: 10.1093/plphys/kiae269

[52]

Sun Z, Li S, Chen W, Zhang J, Zhang L, et al. 2021. Plant dehydrins: expression, regulatory networks, and protective roles in plants challenged by abiotic stress. International Journal of Molecular Sciences 22(23):12619

doi: 10.3390/ijms222312619

[53]

Leprince O, Pellizzaro A, Berriri S, Buitink J. 2017. Late seed maturation: drying without dying. Journal of Experimental Botany 68(4):827−41

doi: 10.1093/jxb/erw363

[54]

Jia J, Lu W, Liu B, Fang H, Yu Y, et al. 2022. An atlas of plant full-length RNA reveals tissue-specific and monocots-dicots conserved regulation of poly(A) tail length. Nature Plants 8(9):1118−26

doi: 10.1038/s41477-022-01224-9

[55]

Liang W, Dong H, Guo X, Rodríguez V, Cheng M, et al. 2023. Identification of long-lived and stable mRNAs in the aged seeds of wheat. Seed Biology 2:14

doi: 10.48130/seedbio-2023-0014

[56]

Liu Y, Zhang Y, Liu X, Shen Y, Tian D, et al. 2023. SoyOmics: A deeply integrated database on soybean multi-omics. Molecular Plant 16(5):794−97

doi: 10.1016/j.molp.2023.03.011

[57]

Yang Z, Luo C, Pei X, Wang S, Huang Y, et al. 2024. SoyMD: a platform combining multi-omics data with various tools for soybean research and breeding. Nucleic Acids Research 52(D1):D1639−D1650

doi: 10.1093/nar/gkad786