Molecular Regulatory Networks of Seed Size in Soybean: History
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Contributor:
Ye Zhang
,
Javaid Akhter Bhat
,
Yaohua Zhang
,
Suxin Yang

Soybean being a major cash crop provides half of the vegetable oil and a quarter of the plant proteins to the global population. Seed size traits are the most important agronomic traits determining the soybean yield. These are complex traits governed by polygenes with low heritability as well as are highly influenced by the environment as well as by genotype x environment interactions. Extensive efforts have been made to unravel the genetic basis and molecular mechanism of seed size in soybean. 

  • soybean
  • seed size
  • regulatory mechanism
  • genes
  • yield

1. Introduction

Soybean [Glycine max (Linn.) Merr.] is an important oilseed crop that supplies half of the world’s vegetable oil and a quarter of the plant protein to the world population [1]. Throughout the history of crop breeding, substantial yield increases have been achieved for major grain crops such as rice, wheat, and maize; however, the yield gains of other important crops such as soybean have remained relatively stable or experienced slow growth. For example, in the highest soybean-consuming countries such as China, the past five decades have seen that soybean yield improvement efforts have been almost stagnant [2]. Hence, there is a great need for these countries as well as the world to increase domestic production to make self-sufficiency in soybean production. Breeders target different yield-related traits to increase soybean production. In this regard, seed size traits are an important trait that is directly related to the yield of soybeans [3]. Nitrogen fixation is vital for plant growth and yield, especially in legumes (such as soybeans) with their unique biological nitrogen-fixing ability [4]. Current research indicates that soybeans, through symbiosis with rhizobia, convert atmospheric nitrogen into ammonium [5], which crucially influences seed size and crop yield [6][7]. Optimizing this symbiotic advantage presents a promising avenue for agricultural yield improvement. Overall, the above results highlight the urgent need for the efficient and effective enhancement of soybean productivity [8].

2. The Seed Size Diversity of Soybean Makes It an Ideal Model Plant for Study

Besides the importance of genetic diversity for trait improvement in plant breeding, it also has great significance for the study of genetic evolution as well as the molecular regulatory mechanism. Hence, species possessing larger genetic diversity are serving as the model species in the study of crop evolution and genetic mechanisms. Among the flowering plants, leguminous plants constitute one of the largest and most diverse plant families, with approximately 20,000 species. The Fabaceae family is the largest subfamily within legumes and it encompasses a majority of model species such as soybean [9]. The soybean plants possess a unique advantage in the study of seed morphology. They exhibit a diverse range of seed sizes [10], and their embryos display diverse morphological forms (Figure 1).
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Figure 1. Seed size variation across the soybean germplasm. Soybeans exhibit abundant genetic diversity, often displaying significant variations in seed size and shape among different cultivars. This makes them an ideal material for investigating seed traits. Scale bar = 1 cm.
As early as around 5000 BC mankind started to cultivate soybeans, and conserved as well as managed the rich source of soybean germplasm resources. The abundance of genetic diversity allows soybean breeders and researchers to conduct genetic analysis as well as functional studies using different soybean varieties and mutants. By using recent genetic and omics techniques combined with artificial intelligence (AI) based models such as machine learning (ML) and deep learning (DL) the soybean researchers will be able to unravel regulatory molecular mechanisms that influence seed size. Moreover, soybean exhibits extensive genetic variation in traits such as seed size (Figure 1). The seed size differences among different soybean varieties can exceed fivefold, hence it makes the soybean an ideal model plant for studying seed size.

3. Molecular Regulatory Network Underlying Seed Size in Soybean

The molecular regulatory network controlling seed size in soybeans is a complex system involving interactions at multiple levels, such as gene regulation, hormone regulation, nutrient regulation, and signal transduction pathways (Table 1). These regulatory factors collectively modulate the development of the embryo and endosperm, ultimately influencing seed size traits. Furthermore, previous studies on seed size regulatory mechanisms have mostly focused on internal factors, neglecting the profound impact of environmental factors on soybean seed development. For instance, soybean is highly sensitive to photoperiod, and the duration as well as intensity of light exposure can affect the process of seed development. In recent years, the influence of environmental factors on soybean seed development has gained widespread attention among researchers [11][12].
Table 1. Genes associated with the development of soybean seed size/weight.
Position Protein Name Protein Category Accession Number Positive/Negative Molecular Mechanism Reference
Transcriptional regulators BBM AP2 family transcription factors Glyma.09G248200 positive Positively regulates the process of seed embryogenesis and development and plays a decisive role in seed maturation Ouakfaoui, 2010 [13]
GmAP2-1 AP2 family transcription factors Glyma.01G188400 positive All three together regulate seed size and grain weight by affecting seed length, width, and area Jiang, 2020 [14]
GmAP2-4 AP2 family transcription factors Glyma.13G329700 positive Jiang, 2020 [14]
GmAP2-6 AP2 family transcription factors Glyma.08G279000 positive Jiang, 2020 [14]
PP2C-1 Phosphatase 2C-1 Glyma.17G221100 positive Increases bead cell size and activates seed development-related genes; interacts with GmBZR1 Lu, 2017 [15]
GmBS1 Tify domain Glyma.10G244400 negative Negative regulation of primary cell proliferation by suppressing the expression of GIF1 and GRF5 Ge,2016 [16]
GmBS2 Glyma.20G150000 negative
GmCYP78A5 cytochrome P450 family protein CYP78A10 Glyma.05G00220 positive Prediction by RNA-seq data analysis may correlate with seed size Du, 2017 [17]
CYP78A10 Cytochrome P450 Glyma.05G019200 positive Predicted by evolutionary correlation analysis to be extremely correlated with seed size, but leads to lower pod numbers Wang, 2015 [18]
CYP78A72 Cytochrome P450 Glyma.19G240800 positive Overexpression increases seed size and is functionally redundant with two other homologous genes Zhao, 2016 [19]
GmWRKY15a WRKY family transcription factor Glyma.05G096500 positive Differential expression in soybean pods is significantly associated with CT repeat variation during soybean domestication Gu, 2017 [20]
Phytohormone signalling and homeostasis GmBZR1 transcription factor of the BR signalling pathway Glyma.17G248900 positive Conserved regulation by BR signalling promotes phosphorylation/dephosphorylation ratios Zhang, 2016 [21]
GmGA20OX gibberellin biosynthetic enzymes Glyma.07G081700 positive Highly selected during domestication to increase the rate of GA biosynthesis Lu, 2016 [22]
GmJAZ3 protein TIFY 6a-related Glyma.09G123600 positive Promotes seed size/weight and other organ sizes in stable transgenic soybean plants by increasing cell proliferation Hu, 2023 [23]
SGF14f protein SGF14f Glyma.02G115900 unknown May regulate the balance of GA and ABA signalling and determine embryogenesis and seed germination Schooheim, 2009 [24]
GmFAD3 microsomal omega-3 fatty acid desaturase Glyma.18G062000 negative Associated with fatty acid synthesis, which inhibits jasmonic acid accumulation, and silencing leads to greater seed Singh, 2020 [25]
unnamed ethylene-response factor C3 Glyma.19G163900 positive AHP can promote cytokinin signaling with multiple functionally redundant genes Claire, 2019 [26]
unnamed Hpt domain Glyma.19G151900 positive Possible involvement in cytokinin-mediated seed size and weight regulatory networks Assefa1, 2019 [27]
GmPSKγ1 PSK-like peptide Glyma.02G126200 positive Novel peptide hormone whose tyrosine is sulfated induces embryonic cell expansion for seed growth Yu, 2019 [28]
Metabolic pathway GmST01 UDP-galactose4-epimerase; domain 1 Glyma.08G109100 positive Regulation of cell division and amplification patterns in soybean to determine seed shape Li, 2022 [29]
GmST05 Phosphatidylethanolamine-binding Protein Glyma.05G244100 positive regulates seed size and affects oil and protein content, which may affect the transcription of GmSWEET10a Duan, 2022 [30]
GmSWEET10a sugar efflux transporter SWEET39 Glyma.15G049200 positive The former is strongly selected in domestication and the latter is being selected, both contribute to the sugar distribution from the seed coat to the embryo by transporting sucrose and hexose, thus increasing oil content and seed size Wang, 2020 [31]
GmSWEET10b sugar efflux transporter SWEET24 Glyma.08G183500 positive
CIF1 Cell wall invertase inhibitors Glyma.17G036300 negative Coordination of seed maturation by post-translational fine-tuning of sucrose metabolism and library strength by CWI Tang, 2017 [32]
GmDREBL Caskin/Ankyrin repeat-containing protein Glyma.12G11150 positive Involved in the regulation of fatty acid accumulation by controlling the expression of WRI1 and its downstream genes Zhang, 2016 [33]
GmNSS PEPTIDASE-C1 DOMAIN-CONTAINING PROTEIN Glyma.08G309000 positive Regulation of the size of the outer bead cover cell Zhang, 2023 [34]
Other regulators GmDof4 DOF ZINC FINGER PROTEIN DOF1.1-RELATED Glyma.17G081800 positive Increasing lipid content in soybean seeds by upregulating genes related to fatty acid biosynthesis and direct binding downregulation of the storage protein gene CRA1 by the cis-DNA element in its promoter region Wang, 2007 [35]
GmDof11 DOF ZINC FINGER PROTEIN DOF1.1-RELATED Glyma.13G329000 positive
unnamed RING FINGER AND CHY ZINC FINGER DOMAIN-CONTAINING PROTEIN 1 Glyma.17G202700 unknown Prediction by GWAS analysis may correlate with seed size Assefa1, 2019 [27]
GmSSS1 tetratricopeptide repeat protein, TPR Glyma.19G196000 positive Exerts a positive impact on cell expansion and cell division, thus regulating the ultimate size of soybean seeds Zhu, 2022 [36]

3.1. The Ubiquitin-Proteasome Pathway

Protein ubiquitination controls many aspects of cellular processes by affecting protein stability, activity, and localization [37]. The ubiquitination process involves a series of specialized enzymes such as ubiquitin-activating enzymes (E1s), ubiquitin-conjugating enzymes (E2s), and ubiquitin ligases (E3s) [38]. Ubiquitin or ubiquitin chains can be removed by deubiquitinating enzymes. Recent studies have revealed the important role of the ubiquitin-proteasome pathway in the regulation of seed size. For example, DA1 is a ubiquitin receptor in A. thaliana that contains two ubiquitin-interacting motif (UIM) domains viz., a LIM domain and a C-terminal peptidase domain [39]. DA1 negatively regulates seed and organ growth by modulating cell proliferation in the ovule integument [40]. Additionally, DA1 can interact with its closest homolog, DAR, to control seed size.
In soybean, a gene encoding an E3 ligase zinc finger protein (Glyma.17G202700) is highly expressed in the seed coat of large seeds. Additionally, a gene encoding an E2 conjugating enzyme phosphatase 2 (Glyma.07G196500) is expressed at seven-fold higher levels in the seed coat of large seeds compared to small seeds. These findings suggest the key role of the ubiquitin-mediated protein degradation pathway in the regulation of seed size in soybean [17].

3.2. Plant Hormone Signaling Pathways

Plant hormones have been documented to play a crucial role in the regulation of seed development. Different hormones exert their specific effects on various aspects of seed development, including seed size, embryo development, endosperm development, and seed dormancy.

3.3. Regulation of Seed Size by Transcription Factors

Transcriptional regulation is crucial for plant growth and development, and several transcription factors have been identified as the key regulators of seed size. These transcription factors, along with transcriptional co-activators and regulators involved in chromatin modification, play important roles in determining seed size in plants.
In soybeans, several transcription factors have been reported to be involved in seed size regulation. This includes important gene families such as WRKY and CP450 [17]. These transcription factors likely control seed size by regulating the expression of genes that are involved in cell proliferation, cell expansion, and other processes during seed development. Their precise mechanisms of action and specific target genes are still being investigated to gain a better understanding of their roles in the regulation of seed size in soybeans.

3.4. Photoperiod Regulation of Soybean Seed Size

The photoperiod i.e., the duration of light and dark periods in a day, can have an impact on seed size in plants [41]. Different plant species showed varied responses to photoperiod, and it can influence different aspects of seed development and growth. Plants have developed effective strategies to adapt to environmental changes throughout their evolution. For instance, plants perceive variations in daylight duration, allowing them to undergo the transition to flowering during seasons most conducive to successful reproduction [42]. Flowering time is a critical trait in domestication, and increased knowledge of flowering regarding its genetic basis and molecular mechanism will greatly enhance crop plants’ adaptation to the environment [43].
CONSTANS (CO) acts as a central regulator in the photoperiodic flowering pathway, and CO orthologs have been identified in various plant species [44][45][46][47]. Yu et al. [43] discovered that under favourable conditions of reproductive growth, plants tend to suppress the transcription of APETALA2 (AP2) through CO, thereby regulating the proliferation of seed coat epidermal cells and promoting larger seed production [48]. Under conditions favouring vegetative growth, CO protein becomes unstable, leading the plants to prioritize nutrient acquisition and generate smaller seeds by attenuating the inhibitory effect of CO on AP2. When CO is mutated, the seed size of the plant becomes unresponsive to photoperiod. Thus providing the first insight into the core regulatory module governing seed size in response to photoperiodic cues.

3.5. Other Regulatory Pathways of Soybean Seed Size

Nguyen et al. [49] reported and characterized the GmKIX8-1, a gene that encodes a nuclear protein regulating organ size in soybeans. GmKIX8-1 encodes a conserved KIX domain protein that is homologous to AtKIX8 in A. thaliana, which limits organ growth by modulating cell proliferation in meristematic tissues [49]. Previous studies have revealed that the KIX-PPD-MYC-GIF1 module controls seed size in A. thaliana by inhibiting cell proliferation in the outer integument during the development of embryo sac and early seed [50], this regulatory mechanism may also exist during seed development in soybean.
Flavonoids viz., anthocyanins, proanthocyanidins, flavonols, and isoflavones, are the most important components affecting seed coat colour [51]. Zhang et al. [34] identified a novel gene, Glyma.08G309000, from the mutant S006, which was named Novel Seed Size (NSS) [34]. This gene is associated with brown and small-seeded phenotypes. This study indicated a significant increase in anthocyanin accumulation in the S006 mutant leading to pigmentation in the seed coat. Moreover, the outer integument cell area was significantly reduced in the S006 mutant, thus negatively impacting seed size in soybeans. This study provides evidence that the brown seed coat colour might be attributed to elevated expression of chalcone synthase 7/8 genes, while decreased expression of NSS contributes to reduced seed size. These findings suggest that the NSS gene represents a novel regulator of seed development. The NSS gene encodes a protein of unknown function, but it contains a peptidase-c1 domain resembling a potential DNA helicase RuvA subunit, indicating a possible involvement in apoptosis.
The plant cell wall is a highly complex structure composed of structural proteins, enzymes, and various polysaccharides as well as pectin [52], which plays a crucial role in the primary cell wall of plants [53]. Li et al. [29] reported a semi-dominant locus named ST1 (Seed Thickness 1) [29] and successfully identified the underlying major functional gene of ST1 as Glyma.08G109100. This gene was documented to regulate soybean seed thickness and encodes a UDP-D-glucuronic acid 4-epimerase, which regulates the production of UDP-rhamnose and promotes pectin biosynthesis. Thus, it may determine seed shape by modulating cell division and expansion patterns in soybeans. Interestingly, this morphological variation simultaneously increases seed oil content. Together with the upregulation of sugar metabolism regulated by ST1, soybean has become a major oilseed crop, suggesting a strong selection for this gene during domestication. Additionally, Tang et al. [32] discovered that the soybean transformation inhibitor GmCIF1 participates in controlling seed maturation by specifically inhibiting the activity of cell wall invertase (CWI) [32]. Silencing of GmCIF1 expression elevates the CWI post-translational levels to finely tune sucrose metabolism and sink strength, thereby coordinating the process of seed maturation and increasing seed weight, as well as accumulating hexoses, starch, and proteins in mature seeds.
The 100-seed weight is considered one of the pivotal domestication traits that greatly influences soybean yield. Nevertheless, its elusive genetic foundation remains enigmatic. Zhu et al. [36] elucidated a soybean seed size 1 (sss1) mutant with enlarged seeds in comparison to its wild-type counterpart [36]. These authors showed that candidate gene GmSSS1 (SOYBEAN SEED SIZE 1) encodes a SPINDLY homolog that resides within a well-defined quantitative trait locus (QTL) hotspot on chromosome 19, which underwent intense selection during the cultivation of soybeans. Deletion of GmSSS1 causes reduced seed size, while its overexpression results the larger seeds, subsequently augmenting the 100-seed weight of a soybean. Further investigations indicate that GmSSS1 exerts a positive effect on cell expansion and cell division, thus regulating the ultimate size of soybean seeds (Figure 2).
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Figure 2. The major signalling pathways involved in soybean seed size control. The size of seeds is regulated through a complex network of signals, involving genes, hormones, transcription factors, and other intricate mechanisms. Dashed lines represent uncertain genetic relationships. Modulators that regulate seed size by influencing cell proliferation, cell expansion, and other regulatory processes are depicted in red, blue, and green, respectively. Abbreviations: BS, big seed; NIJIA, novel interactors of JAZ; NSS, novel seed size; SSS, soybean seed size; CWI, cell wall invertase; ST, seed thickness.

This entry is adapted from the peer-reviewed paper 10.3390/ijms25031441

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