| [1] |
Fuller DQ, Qin L, Zheng Y, Zhao Z, Chen X, et al. 2009. The domestication process and domestication rate in rice: spikelet bases from the Lower Yangtze. |
| [2] |
Anand A, Subramanian M, Kar D. 2023. Breeding techniques to dispense higher genetic gains. |
| [3] |
Huang X, Zhao P, Peng X, Sun MX. 2023. Seed development in Arabidopsis: what we have learnt in the past 30 years. |
| [4] |
Liu K. 1997. Chemistry and nutritional value of soybean components. In Soybeans. Boston, MA: Springer. pp. 25–113 doi: 10.1007/978-1-4615-1763-4_2 |
| [5] |
Goettel W, Zhang H, Li Y, Qiao Z, Jiang H, et al. 2022. POWR1 is a domestication gene pleiotropically regulating seed quality and yield in soybean. |
| [6] |
Sedivy EJ, Wu F, Hanzawa Y. 2017. Soybean domestication: the origin, genetic architecture and molecular bases. |
| [7] |
Zhou Z, Jiang Y, Wang Z, Gou Z, Lyu J, et al. 2015. Resequencing 302 wild and cultivated accessions identifies genes related to domestication and improvement in soybean. |
| [8] |
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. |
| [9] |
Zhuang Y, Li X, Hu J, Xu R, Zhang D. 2022. Expanding the gene pool for soybean improvement with its wild relatives. |
| [10] |
Wang L, Jiang X, Jiao W, Mao J, Ye W, et al. 2025. Pangenome analysis provides insights into legume evolution and breeding. |
| [11] |
Schmutz J, Cannon SB, Schlueter J, Ma J, Mitros T, et al. 2010. Genome sequence of the palaeopolyploid soybean. |
| [12] |
Kim MY, Lee S, Van K, Kim TH, Jeong SC, et al. 2010. Whole-genome sequencing and intensive analysis of the undomesticated soybean (Glycine soja Sieb. and Zucc.) genome. |
| [13] |
Li YH, Zhou G, Ma J, Jiang W, Jin LG, et al. 2014. De novo assembly of soybean wild relatives for pan-genome analysis of diversity and agronomic traits. |
| [14] |
Kim MS, Lozano R, Kim JH, Bae DN, Kim ST, et al. 2021. The patterns of deleterious mutations during the domestication of soybean. |
| [15] |
Han Y, Zhao X, Liu D, Li Y, Lightfoot DA, et al. 2016. Domestication footprints anchor genomic regions of agronomic importance in soybeans. |
| [16] |
Zuo JF, Ikram M, Liu JY, Han CY, Niu Y, et al. 2022. Domestication and improvement genes reveal the differences of seed size- and oil-related traits in soybean domestication and improvement. |
| [17] |
Duan Z, Zhang M, Zhang Z, Liang S, Fan L, et al. 2022. Natural allelic variation of GmST05 controlling seed size and quality in soybean. |
| [18] |
Miao L, Yang S, Zhang K, He J, Wu C, et al. 2020. Natural variation and selection in GmSWEET39 affect soybean seed oil content. |
| [19] |
Zhang H, Goettel W, Song Q, Jiang H, Hu Z, et al. 2020. Selection of GmSWEET39 for oil and protein improvement in soybean. |
| [20] |
Liang S, Duan Z, He X, Yang X, Yuan Y, Liang Q, et al. 2024. Natural variation in GmSW17 controls seed size in soybean. |
| [21] |
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. |
| [22] |
Xu G, Zhang X. 2023. Mechanisms controlling seed size by early endosperm development. |
| [23] |
Chen Y, Nelson RL. 2004. Genetic variation and relationships among cultivated, wild, and semiwild soybean. |
| [24] |
Xing Y, Zhang Q. 2010. Genetic and molecular bases of rice yield. |
| [25] |
Cui B, Chen L, Yang Y, Liao H. 2020. Genetic analysis and map-based delimitation of a major locus qSS3 for seed size in soybean. |
| [26] |
Xie FT, Niu Y, Zhang J, Bu SH, Zhang HZ, et al. 2014. Fine mapping of quantitative trait loci for seed size traits in soybean. |
| [27] |
Xu Y, Li HN, Li GJ, Wang X, Cheng LG, et al. 2011. Mapping quantitative trait loci for seed size traits in soybean (Glycine max L. Merr.). |
| [28] |
Kumawat G, Xu D. 2021. A major and stable quantitative trait locus qSS2 for seed size and shape traits in a soybean RIL population. |
| [29] |
Li J, Zhang Y, Ma R, Huang W, Hou J, et al. 2022. Identification of ST1 reveals a selection involving hitchhiking of seed morphology and oil content during soybean domestication. |
| [30] |
Zhang J, Wang X, Lu Y, Bhusal SJ, Song Q, et al. 2018. Genome-wide scan for seed composition provides insights into soybean quality improvement and the impacts of domestication and breeding. |
| [31] |
Yan L, Di R, Wu C, Liu Q, Wei Y, et al. 2019. Haplotype analysis of a major and stable QTL underlying soybean (Glycine max) seed oil content reveals footprint of artificial selection. |
| [32] |
Wang Z, Zhou Z, Liu Y, Liu T, Li Q, et al. 2015. Functional evolution of phosphatidylethanolamine binding proteins in soybean and Arabidopsis. |
| [33] |
Zhang C, Li W, Tan C, Huang M, Wu H, et al. 2025. Natural allelic variation in SW14 determines seed weight and quality in soybean. |
| [34] |
Wang W, He Q, Yang H, Xiang S, Xing G, et al. 2014. Identification of QTL/segments related to seed-quality traits in G. soja using chromosome segment substitution lines. |
| [35] |
Chen X, Liu C, Guo P, Hao X, Pan Y, et al. 2023. Differential SW16.1 allelic effects and genetic backgrounds contributed to increased seed weight after soybean domestication. |
| [36] |
Lu X, Xiong Q, Cheng T, Li QT, Liu XL, et al. 2017. A PP2C-1 allele underlying a quantitative trait locus enhances soybean 100-seed weight. |
| [37] |
Zhang H, Yang L, Guo S, Tian Y, Yang C, et al. 2024. A natural allelic variant of GmSW17.1 confers high 100-seed weight in soybean. |
| [38] |
Pfab A, Bruckmann A, Nazet J, Merkl R, Grasser KD. 2018. The adaptor protein ENY2 is a component of the deubiquitination module of the Arabidopsis SAGA transcriptional co-activator complex but not of the TREX-2 complex. |
| [39] |
Zhang Y, Yang X, Bhat JA, Zhang Y, Bu M, et al. 2024. Identification of superior haplotypes and candidate gene for seed size-related traits in soybean (Glycine max L.). |
| [40] |
Zhu W, Yang C, Yong B, Wang Y, Li B, et al. 2022. An enhancing effect attributed to a nonsynonymous mutation in SOYBEAN SEED SIZE 1, a SPINDLY-like gene, is exploited in soybean domestication and improvement. |
| [41] |
Li Z, Jiang L, Ma Y, Wei Z, Hong H, et al. 2017. Development and utilization of a new chemically‐induced soybean library with a high mutation density. |
| [42] |
Yang Z, Lu S, Li W, Wang Z, Hu D, et al. 2025. A major latex protein, GsMLP328, modulates seed traits in soybean. |
| [43] |
Lu X, Li QT, Xiong Q, Li W, Bi YD, et al. 2016. The transcriptomic signature of developing soybean seeds reveals the genetic basis of seed trait adaptation during domestication. |
| [44] |
Hu Y, Liu Y, Tao JJ, Lu L, Jiang ZH, et al. 2023. GmJAZ3 interacts with GmRR18a and GmMYC2a to regulate seed traits in soybean. |
| [45] |
Gu Y, Li W, Jiang H, Wang Y, Gao H, et al. 2017. Differential expression of a WRKY gene between wild and cultivated soybeans correlates to seed size. |
| [46] |
Hu Y, Liu Y, Lu L, Tao JJ, Cheng T, et al. 2023. Global analysis of seed transcriptomes reveals a novel PLATZ regulator for seed size and weight control in soybean. |
| [47] |
Patil G, Vuong TD, Kale S, Valliyodan B, Deshmukh R, et al. 2018. Dissecting genomic hotspots underlying seed protein, oil, and sucrose content in an interspecific mapping population of soybean using high-density linkage mapping. |
| [48] |
Yao Y, You Q, Duan G, Ren J, Chu S, et al. 2020. Quantitative trait loci analysis of seed oil content and composition of wild and cultivated soybean. |
| [49] |
Huang J, Ma Q, Cai Z, Xia Q, Li S, et al. 2020. Identification and mapping of stable QTLs for seed oil and protein content in soybean [Glycine max (L.) Merr.]. |
| [50] |
Cai Z, Xian P, Cheng Y, Zhong Y, Yang Y, et al. 2023. MOTHER-OF-FT-AND-TFL1 regulates the seed oil and protein content in soybean. |
| [51] |
Li QT, Lu X, Song QX, Chen HW, Wei W, et al. 2017. Selection for a zinc-finger protein contributes to seed oil increase during soybean domestication. |
| [52] |
Andre C, Froehlich JE, Moll MR, Benning C. 2007. A heteromeric plastidic pyruvate kinase complex involved in seed oil biosynthesis in Arabidopsis. |
| [53] |
Wei W, Wang LF, Tao JJ, Zhang WK, Chen SY, et al. 2025. The comprehensive regulatory network in seed oil biosynthesis. |
| [54] |
Lu L, Wei W, Li QT, Bian XH, Lu X, et al. 2021. A transcriptional regulatory module controls lipid accumulation in soybean. |
| [55] |
Liu Y, Hu Y, Wei JJ, Jiang ZH, Han JQ, et al. 2025. Transcription factor GmERFA interacts with GmNFYA and acts as a negative regulator of seed fatty acid accumulation in soybean. |
| [56] |
Yang H, Wang W, He Q, Xiang S, Tian D, et al. 2019. Identifying a wild allele conferring small seed size, high protein content and low oil content using chromosome segment substitution lines in soybean. |
| [57] |
Wang S, Liu S, Wang J, Yokosho K, Zhou B, et al. 2020. Simultaneous changes in seed size, oil content and protein content driven by selection of SWEET homologues during soybean domestication. |
| [58] |
Sun J, Li W, Wei X, Shou H, Tran LP, et al. 2025. Mechanistic roles of GmSWEET10a/b and GmSUT1 in the oil–protein balance in soybean mature seeds at transcriptional and metabolic levels. |
| [59] |
Zhang D, Zhang H, Hu Z, Chu S, Yu K, et al. 2019. Artificial selection on GmOLEO1 contributes to the increase in seed oil during soybean domestication. |
| [60] |
Mariamenatu AH, Abdu EM. 2021. Overconsumption of omega-6 polyunsaturated fatty acids (PUFAs) versus deficiency of omega-3 PUFAs in modern-day diets: the disturbing factor for their "balanced antagonistic metabolic functions" in the human body. |
| [61] |
Asekova S, Chae JH, Ha BK, Dhakal KH, Chung G, et al. 2014. Stability of elevated α-linolenic acid derived from wild soybean (Glycine soja Sieb. & Zucc.) across environments. |
| [62] |
Ha BK, Kim HJ, Velusamy V, Vuong TD, Nguyen HT, et al. 2014. Identification of quantitative trait loci controlling linolenic acid concentration in PI483463 (Glycine soja). |
| [63] |
Pantalone VR, Rebetzke GJ, Burton JW, Wilson RF. 1997. Genetic regulation of linolenic acid concentration in wild soybean Glycine soja accessions. |
| [64] |
Gishini MFS, Kachroo P, Hildebrand D. 2025. Fatty acid desaturase 3-mediated α-linolenic acid biosynthesis in plants. |
| [65] |
Derbyshire MC, Marsh J, Tirnaz S, Nguyen HT, Batley J, et al. 2023. Diversity of fatty acid biosynthesis genes across the soybean pangenome. |
| [66] |
Li B, Fan S, Yu F, Chen Y, Zhang S, et al. 2017. High-resolution mapping of QTL for fatty acid composition in soybean using specific-locus amplified fragment sequencing. |
| [67] |
Cai Z, Xian P, Cheng Y, Yang Y, Zhang Y, et al. 2023. Natural variation of GmFATA1B regulates seed oil content and composition in soybean. |
| [68] |
Qi Z, Guo C, Li H, Qiu H, Li H, et al. 2024. Natural variation in Fatty Acid 9 is a determinant of fatty acid and protein content. |
| [69] |
Boschin G, Arnoldi A. 2011. Legumes are valuable sources of tocopherols. |
| [70] |
Azzi A. 2007. Molecular mechanism of α-tocopherol action. |
| [71] |
Kamal-Eldin, A. 2006. Effect of fatty acids and tocopherols on the oxidative stability of vegetable oils. |
| [72] |
Méjean M, Brunelle A, Touboul D. 2015. Quantification of tocopherols and tocotrienols in soybean oil by supercritical-fluid chromatography coupled to high-resolution mass spectrometry. |
| [73] |
Carrera CS, Seguin P. 2016. Factors affecting tocopherol concentrations in soybean seeds. |
| [74] |
Park C, Dwiyanti MS, Nagano AJ, Liu B, Yamada T, et al. 2019. Identification of quantitative trait loci for increased α-tocopherol biosynthesis in wild soybean using a high-density genetic map. |
| [75] |
Ghosh S, Zhang S, Azam M, Agyenim-Boateng KG, Qi J, et al. 2022. Identification of genomic loci and candidate genes related to seed tocopherol content in soybean. |
| [76] |
Chu D, Zhang Z, Hu Y, Fang C, Xu X, et al. 2023. Genome-wide scan for oil quality reveals a coregulation mechanism of tocopherols and fatty acids in soybean seeds. |
| [77] |
Dwiyanti MS, Yamada T, Sato M, Abe J, Kitamura K. 2011. Genetic variation of γ-tocopherol methyltransferase gene contributes to elevated α-tocopherol content in soybean seeds. |
| [78] |
Dwiyanti MS, Maruyama S, Hirono M, Sato M, Park E, et al. 2016. Natural diversity of seed α-tocopherol ratio in wild soybean (Glycine soja) germplasm collection. |
| [79] |
Zhang C, Shao Z, Kong Y, Du H, Li W, et al. 2024. High-quality genome of a modern soybean cultivar and resequencing of 547 accessions provide insights into the role of structural variation. |
| [80] |
Lu S, Fang C, Abe J, Kong F, Liu B. 2022. Current overview on the genetic basis of key genes involved in soybean domestication. |
| [81] |
Kim WJ, Kang BH, Kang S, Shin S, Chowdhury S, et al. 2023. A genome-wide association study of protein, oil, and amino acid content in wild soybean (Glycine soja). |
| [82] |
Brummer EC, Graef GL, Orf J, Wilcox JR, Shoemaker RC. 1997. Mapping QTL for seed protein and oil content in eight soybean populations. |
| [83] |
Diers BW, Keim P, Fehr WR, Shoemaker RC. 1992. RFLP analysis of soybean seed protein and oil content. |
| [84] |
Zheng H, Feng X, Wang L, Shao W, Guo S, et al. 2025. GmSop20 functions as a key coordinator of the oil-to-protein ratio in soybean seeds. |
| [85] |
Clemente TE, Cahoon EB. 2009. Soybean oil: genetic approaches for modification of functionality and total content. |
| [86] |
Krishnan HB. 2000. Biochemistry and molecular biology of soybean seed storage proteins. |
| [87] |
Krishnan HB, Kim WS, Jang S, Kerley MS. 2009. All three subunits of soybean β-conglycinin are potential food allergens. |
| [88] |
Yang R, Ma Y, Yang Z, Pu Y, Liu M, et al. 2024. Knockdown of β-conglycinin α' and α subunits alters seed protein composition and improves salt tolerance in soybean. |
| [89] |
Tian H, Yin Y, Li X, Zhang Z, Feng S, et al. 2025. Identification of HSSP1 as a regulator of soybean protein content through QTL analysis and Soy-SPCC network. |
| [90] |
Yang Y, Zhang L, Zuo H, Yang Y, Hu D, et al. 2025. GmGASA12 coordinates hormonal dynamics to enhance soybean water-soluble protein accumulation and seed size. |
| [91] |
Padhy AK, Singh A, Chaurasia S, Parida SK, Tripathi K, et al. 2025. Key determinants of seed size for enhancing genetic gain in legumes. |
| [92] |
Yu LA, Sussman H, Khmelnitsky O, Rahmati Ishka M, Srinivasan A, et al. 2024. Development of a mobile, high-throughput, and low-cost image-based plant growth phenotyping system. |
| [93] |
Dwivedi SL, Spillane C, Lopez F, Ayele BT, Ortiz R. 2021. First the seed: Genomic advances in seed science for improved crop productivity and food security. |
| [94] |
Shi R, Zhang H, Wang C, Zhou Y, Kang K, et al. 2025. Data fusion-driven hyperspectral imaging for non-destructive detection of single maize seed vigor. |
| [95] |
Xue H, Xu X, Yang Y, Hu D, Niu G. 2024. Rapid and non-destructive prediction of moisture content in maize seeds using hyperspectral imaging. |
| [96] |
Jiang W, Wang J, Lin R, Chen R, Chen W, et al. 2024. Machine learning-based non-destructive terahertz detection of seed quality in peanut. |
| [97] |
Chen Z, Wei Y, Hou J, Huang J, Zhu X, et al. 2024. Transcriptional atlas for embryo development in soybean. |
| [98] |
Lin P, Wang K, Wang Y, Hu Z, Yan C, et al. 2022. The genome of oil-Camellia and population genomics analysis provide insights into seed oil domestication. |
| [99] |
Šimková H, Câmara AS, Mascher M. 2024. Hi-C techniques: from genome assemblies to transcription regulation. |
| [100] |
Zhang X, Luo Z, Marand AP, Yan H, Jang H, et al. 2025. A spatially resolved multi-omic single-cell atlas of soybean development. |
| [101] |
Zhang M, Kong D, Wang H. 2023. Genomic landscape of maize domestication and breeding improvement. |
| [102] |
Lam HM, Xu X, Liu X, Chen W, Yang G, et al. 2010. Resequencing of 31 wild and cultivated soybean genomes identifies patterns of genetic diversity and selection. |
| [103] |
Bai M, Zhang J, Lin W, Zhou Y, Jiang M, et al. 2026. A flanking-nicks prime editor (FLICK-PE) system to boost prime editing in dicots. |
| [104] |
Cao X, Xie H, Wang Z, Guo R, Jing F, et al. 2026. An efficient tissue-culture-free soybean genetic transformation technology using the extremely simple cut-dip-budding strategy. |
| [105] |
Lin W, Li C, Li M, Guan Y. 2025. Emerging nucleases in crop genome editing: towards intellectual property independence and technical flexibility. |
| [106] |
Zhong X, Wang J, Shi X, Bai M, Yuan C, et al. 2024. Genetically optimizing soybean nodulation improves yield and protein content. Nature. |
| [107] |
Tang X, Su T, Han M, Wei L, Wang W, et al. 2017. Suppression of extracellular invertase inhibitor gene expression improves seed weight in soybean (Glycine max). |
| [108] |
Wang J, Zhang L, Wang S, Wang X, Li S, et al. 2025. AlphaFold-guided bespoke gene editing enhances field-grown soybean oil contents. |