Soybean (
The legumes are major source of edible proteins in the vegetarian diets, and accommodate the need of protein supplement to the world. Among the legumes, soybean [
In plants, most miRNAs bind and cleave to either the coding regions or the mRNA targets in the 5’ and 3’ UTR region, contributing to translational inhibition of the target mRNA. Plant miRNAs are known to regulate numerous biological functions as main regulators, including growth, organ recognition, metabolism, stress response, and physiological processes [
Subramanian et al. [
129 miRNAs were identified from four small RNA libraries from root, seed, flower, and nodules in soybean; out of these, 42 miRNAs matched with known miRNAs in soybean or other species, while 87 novel miRNAs were identified and putative target were predicted [
Throughout its life cycle, soybean is exposed to many abiotic and biotic stresses. Drought, salinity, cold and heavy metals are the main abiotic stresses. Biotic stresses include infections caused by nematodes and insect pests caused by bacteria, viruses, fungi, and infestations. These stresses ultimately affect the crop yield. Exploration of miRNAs in soybean revealed many miRNAs with regulatory roles in different biological processes modulating stress responses, crop yield and nutritional quality [
miRNAs | Target genes/Expression | Regulation status under stress/Improved Character/Phenotype | References | |
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miR169 | NFYA3 | Drought Tolerance | [ |
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miR397ab, miR166-5p, miR1513c, miR169f-3p | Predicted calmodulin-binding protein, LRR-containing protein, |
Downregulated (tolerant genotype); Upregulated (sensitive genotype) | [ |
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miR2111, miR1512, miR408, miR3522, miR4403, miR1535, miR397, miR4411, miR4385, miR167, miR4344 | – | Upregulated | [ |
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miR398, miR394, miR4391, miR4397-3, miR5037, miR1536, miR2119, miR5370, miR171, miR5559, miR530, miR4408, miR403 | – | Downregulated | ||
miR159b, miR319a, b, miR319a, amiR1520c, miR319b, miR169c, miR1517, miR1523, miR169b, miR4416b, miR5037e, miR5559, miR160, miR159c | MYB-Like, NF-YA) Subunit B, Triacylglycerol Lipase, ARF, Serine-Threonine Protein Kinase, LRR Protein | Downregulated | [ |
|
miR4416d, miR4416d, miR171p, miR482, miR395c, miR1520b, miR166a, miR1510a, miR166b, miR408c, miR395b, miR2111, miR171, miR390a-3p, miR171p, miR4416c miR399i, miR399k, miR399j, miR408a | GRAS, Kelch-Related Proteins, Helix-Loop-Helix Dna-Binding, Cation efflux family protein, Lipase |
Upregulated | ||
miR4380a, miR2118, miR4374b, miR1510a-5p, miR4378a, miR4342, miR1520, miR4405, miR4385, miR395a, miR4407, miR4387b, miR4366, miR4397, miR4401, miR4404, miR4349, miR4406, miR169d, miR4409, miR4411, miR4371c, miR4359b, miR4369, miR482, miR482b, miR4351, miR4344 | YA3, CCAAT-binding TF WHAP12, NFY-A3, Zinc finger CCCH, MADS box (AGL1, SEP3), WRKY, Ras, CDC2, GTPase, AP2, | Upregulated | [ |
|
mIR4411, mIR156k, |
SAM, EF-Tu, PP2C, | Upregulated | [ |
|
mIR172c, mIR172d, mIR172e, |
CBS, ETR, ABS Transporter, | Downregulated | ||
miR403b, miR164k, miR4996, miR1507a, miR4380b, PN-miR477, miR390gmiR396c, PNmiR156f, miR159d, miR398c, miR162c, miR5373, miR166k, miR169r, miR1529n, miR166O, miR396k, miR166u, miR171-5p, PN-miR168a, miR159f-3p, miR5786, miR3522, miR1507c-3p, miR5037c, miR1512b, miR4403, miR5037a, miR5678, miR482a-3p, miR5044 | NBS-LRR, |
Differentially expressed Aluminum | [ |
|
miR160, gso-miR2109, PN-miR1514, PN-miR159, |
ARF, WRC, SBP, TCP, SPT6, AP2 and CCAAT type TF | Differentially expressed Aluminum | [ |
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-miR3522, a b, miR397a, miR408-3p, miR408, miR408b-5p, miR4996, miR396a-3p, miR398 | Laccase, plantacyanin, CDPK, copper/zinc SOD, Isopentenyltransferase, CYS, MET, PRO, and GLY, GRF, MYB, HCO3, | Upregulated in response to Cadmium | [ |
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miR166u, miR171p, miR397a, | Multicopper oxidase, bZIP TF, Homeobox-leucine zipper, GRAS | Upregulated | [ |
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miR5559, miR319a/b, mi159b, mi169c | MYB, TCP TF, Mediator complex subunit 28 | Downregulated | ||
miR1508a | PPR, XTH, SAUR, SUB | Cold tolerance | [ |
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miR166, miR393 | ARF, LRR, Transcription factor HEX, | Upregulated | [ |
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miR169-3p, miR397ab, miR166a-5p, miR166f, | – | Downregulated (Sensitive) | [ |
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miR482bd | – | High to low expression (Resistant) | ||
miR1513 | F-box domain-containing protein | Down-regulated (Resistant) | ||
miR4415b | – | Downregulated (Sensitive), High expression (Resistant) | ||
miRseq07 | – | Downregulated (Sensitive/ Resistant) | ||
miRseq-15 | – | Downregulated (Sensitive), Upregulated (Resistant) | ||
miRNA1507 | – | Downregulated | [ |
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miR2118, miR171c, miR1510, miRNA1507c, miR319, miR169, miR390b, miR5372, miR862 | TCP, Plasma membrane intrinsic protein, HSP, HAP2, R1, | Upregulated | ||
miR156q, miR166u, miR166b, miR166j-3p, miR319d, miR394a-3p, miR396e | Upregulated | [ |
||
miR396e | GRF3 and GRF5 | Resistance against bean pyralid larvae infestation | [ |
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miR394, miR1510, miR530, miR160, miR169, miR166, miR408, miR399, miR168, miR172, miR393, miR159, miR403, | MYB, Glycosyl hydrolase, ARF, Homeobox-leucine zipper, NFY, ARF-GAP, AP2, NYC, LRR-F box, |
Upregulated | [ |
|
miR167, miR390, miR156, miR162, miR482-5p, miR164 | SBP, NAC, ARF, Pectin Lyase, Plant invertase, TIR-NBS-LRR class protein | Downregulated | [ |
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miR168 | Stabilizer of iron transporter SufD / Polynucleotidyl transferase | Upregulated | ||
miR394, miR168, miR396 | – | Upregulated (Susceptible) | [ |
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miR398, miR160, miR393, miR162, miR169, miR167 | – | Downregulated (Susceptible) | ||
miR394, miR398, miR169 | – | Upregulated (Resistant) | ||
miR162, miR168, miR160, miR393, miR167, miR396 | – | Downregulated (Resistant) | ||
miR408 | – | Upregulated Roots in long-term N starvation | [ |
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miR160 |
TCP | Downregulated roots in short-term N deprivation | ||
miR397, |
Laccases |
Downregulated shoot in long-term low N | ||
miR398c-5p | – | Downregulated shoot in short-term low N | ||
miR159 | MYB/ TCP TF | Upregulated in N deprivation | ||
miR169 |
HAP2 TF |
Downregulated in N deprivation | ||
miR169c | GmNFYA-C | Upregulated by high N and its overexpression inhibited nodulation | [ |
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miR159 | MYB/ TCP TF | Under Pi limiting conditions in shoot | [ |
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miR319 | TCP transcription factors | Under Pi limiting conditions in root | [ |
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miR169q, miR396j, miR399e, and miR4416a | – | In Pi limiting conditions in leaves | [ |
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miR408c-3p, miR408a-3p, miR408b-3p, miR408d, miR398c, miR398d, miR5786, miR2118a-3p, miR2118b-3p, miR894 | – | In Pi limiting conditions in roots | [ |
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miR160 | – | root growth, hypersensitivity to Auxin and decreased nodulation | [ |
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miR1530 | ARF, Transketolase | Root and seed development | [ |
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miR167 | Soybean roots | Higher lateral root number and length, with reduced auxin sensitivity | [ |
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miR156, |
SBP TF |
highly abundant in primary root tips | [ |
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miR167c, miR319l, miR1510b-3p, |
ARF, Zn Finger, TCP TF | Root developmental plasticity | [ |
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miR164 | NAC transcription factor | Leaf and SAM development | [ |
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miR156 and miR172 | – | Juvenile to adult phase transition | [ |
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miR156b | SPL2a, SPL9a, SPL9d | regulator of shoot branching | [ |
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MIR156b | SPL AP1, FULs, LFY, LFY2, SOCs, FT5a | reproductive stage transformation in the vegetative tissue, | [ |
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miR156b | SPL9 |
flower bud development | [ |
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and MIR172 | AP2 TF | role in a diurnal rhythm and produced early flowering | [ |
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miR4393a and miR5667 |
LBD22, LBD36, AGL30 and AGL104 | flower bud development | [ |
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miR156, 159, 160, 164, 166, and 167 | – | Expressed in seed coats and cotyledons | [ |
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miR156, miR164, miR172, miR160, miR166, miR136, | SGS3, ARF transcription factor | Expressed during development of seed | [ |
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miR1508, miR1510, miR156, miR159, miR166, miR319, miR164, miR167, miR482, and miR3522 | ARF and TCP TFs | Highly expressed in seed development stages | [ |
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miR166v, miR166w miR166x |
HD-ZIP III, Phytoene Synthase (psy), Ammonium Transporter 2-like APRR2 | role at late stages of seed |
[ |
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miR1521a, b |
ADP-glucose pyrophosphorylase |
Storage regulatory genes during seed development | [ |
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miR156 | SPL1, SPL2 | Key control point for soybean nodule formation. And controls Level of nodulation | [ |
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miR160 | ARF10/16/17 | Soybean nodule development | [ |
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miR167 | ARF8 | Soybean nodule development, lateral root development | [ |
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miR172 | AP2-2 | Level of nodulation | [ |
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miR165/166 | HD-ZIP III | Nodule development | [ |
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miR393j-3p | ENOD93 | reduced the nodule formation | [ |
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miR482, miR1511 miR1512, and miR1515 | Resistance (R) gene receptor kinases), Copine I-like calmodulin-binding protein, Protein phosphatase 2C and | over-expression increased nodule numbers | [ |
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miR167, miR172, miR396, miR399, | Symbiotic nitrogen fixation | regulation of nodule maturation and nitrogen fixation | [ |
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miR2606b |
Mannosyl-oligosaccharide 1,2-alpha-mannosidase |
Expressed in root hairs during nodulation | [ |
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miR393j | ENOD93 | Nodule development in the crop legume | [ |
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MiR172c | AP2 Transcription Factor NNC1 and ENOD4 (early nodulin gene) | Regulate Nodule Initiation | [ |
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miR1507, miR1508, miR1509, and miR1510 families | ARF, nitrate transporters, Defense-related proteins, proteins related to development processes. | Nodule maturation and nitrogen fixation. | [ |
Abiotic stresses like drought stress, cold stress, heat stress, salt stress, and stresses laid upon by heavy metals are the major challenges to enhance the crop productivity in many crops [
Drought, characterized by the water deficit, is considered one of the important environmental constraints affecting overall growth and development in many crops. The effects caused due to drought are apparent at all the stages of growth and development of plants and could be evident from morphological to molecular level [
Like drought, salinity has also a profound effect on growth and yield of many crop plants, including the soybean. About 6% of the agricultural land over the world is exposed to excessive salinity stress [
Another study revealed miR172c as a salt responsive miRNA. Increased sensitivity to salinity stress was observed in a transgenic plant over-expressing the miR172c whereas reduced sensitivity to salt stress was observed when the miR172c was knocked down. The miR172c target gene, Nodule Number Control 1 (NNC1), was also downregulated in response to salt stress [
(miR169c, miR159b, miR319a/b, miR5559) was significantly downregulated. Similarly, 51 cold responsiveness miRNAs with 898 mRNAs target transcripts have also been identified in vegetable soybean. The mRNAs target transcripts were associated with redox chemical reactions and different signaling pathways [
Heavy metal stress is another major environmental stress which is increasing due to heavy industrial activities which affects normal plant growth and productivity in plants. These include aluminium, arsenic, cadmium, lead, and mercury. Treatment of 50 μM AlCl3; among two soybean genotypes, BX10 (Al-tolerant) and BD2 (Al-sensitive), led to differential expression of 32 miRNAs. miRNAs, associated with root elongation, such as GMA-miR166k/o, GMA-miR390g, and gma-miR396c/k, DE in BX10 can help in Al tolerance in BX10 compared to BD2 [
In addition to abiotic stresses, soybean is also affected by various biotic stresses such as insect-pests, and diseases caused by bacteria, virus, fungi, and nematodes [
The
In addition to cyst nematode, fungal infection also severely damages the soybean crop. A major fungal pathogen of soybean,
Soybean mosaic virus (SMV) infection is also another devastating viral infection causes major productivity loss in soybean. During the early stages of infection, some strains of SMV causes downregulation of numerous defensive genes [
Involvement of Gma-miR156q, Gma-miR166u, Gma-miR166b, Gma-miR166j-3p, Gma-miR319d, Gma-miR394a-3p and Gma-miR396e have been predicted to contribute resistance against soybean pyralid larvae. Gma-miR396e mainly target the GRF genes; GRF3 and GRF5 to enhance the resistance against bean pyralid larvae infestation [
Plant growth and development require optimal amount of macro and micronutrients from the soil to drive several metabolic processes. These nutrients serve both structural and catalytic roles, either by acting as structural component of several proteins and enzymes or catalyzing of plant metabolism. These nutrients play crucial role in the vital processes of plant system, such as photosynthesis, cellular respiration, growth and differentiation, etc. [
miRNAs are involved in organizing the nutrient signal, physiological processes that help plants adapt to nutrient stresses and toxicity and survive. Studies have shown that plants have developed advanced mechanisms for detecting their nutrient levels and responding to changes in nutrient availability [
Nitrogen (N) is an important plant macronutrient, which greatly influences seed development and nutrition in plants [
Phosphorus (Pi), an essential plant macronutrient plays a vital role in plant growth and productivity. In soybean nodule under Pi-deficiency miRNAs were detected to be responsive in Pi-deficiency. Few miRNAs have been reported in soybean to response to the Pi deficiency using Microarray and Next-Generation Sequencing [
Roots are responsible for providing support to aerial part of the plant and are responsible for water uptake, nutrients translocation, hormone signaling, secondary metabolites biosynthesis, and protection of plant against stress. Root development occurs at embryonic and postembryonic stages with the formation of plant root system from primary and lateral roots [
Role of miRNAs has been observed in the root apical meristem of control as well as water deficit conditions. Five miRNA families namely miR156, miR166, miR1507, miR1509 and miR1510 were found to be highly abundant in primary root tips of which miR1507 is the most abundant miRNA [
The shoot apical meristem (SAM) is a region that contains stem cells that give rise to the above-ground organs of the plants, such as leaves and stem. A microarray study in soybean reported 31 and 42 miRNAs expressed in the SAM or leaf, respectively, and six of them were found to be legume specific miRNAs, suggesting their crucial roles in mediating SAM development. The higher number of miRNAs expression in the leaf than SAM can be related to the structural complexity, metabolic and developmental networks in leaves. The identified potential miRNAs can be key regulators and help understand miRNAs’ regulatory role in the soybean SAM during shoot development [
miR159 expression was observed in the primordial SAM and leaf and its pattern of expression is close to that recorded in Arabidopsis for miR159 [
The expression of miR156 was high in the two-leaf stage and decreased moderately in the third leaf, which down-regulated in stages of fourth to sixth leaves that decreased the expression of miR156 expression with development. In case of miR172 inverse expression pattern, low in first and second leaves; increase in the third and fourth leaves and ultimately reached to highest in fifth and sixth leaves. This antagonistic expression pattern of miR156 and miR172 genes is associated with juvenile-adult transition and suggest miR156 and miR172 role in vegetative phase transition in soybean [
Two SPL13 genes (SPL13Ba and SPL13Bb) were predicted as target of miR156b at translational level; the rest of the SPL mRNAs are likely cleaved by miR156b. In the shoot apex and axillary buds of miR156bOE-5 plants, SPL2a, SPL9a and (particularly) SPL9d were significantly down-regulated, while the expression of other target genes was marginally down-regulated or not altered. Number of branches were found to increase in soybean miR15*6b overexpressing plants, which supports miR156 as a regulator of shoot branching [
The transformation from vegetative to reproductive stages is known as floral transformation, which comprises of vast changes during a plant’s life cycle. The conversion of shoot meristem into the reproductive organ is due to the interplay of several miRNAs and their target genes. MIR156 and MIR172 facilitate reproductive stage transformation in the vegetative tissue, caused by age or environmental signals. miR156b can negatively target SPL orthologs SPLs, and thus delays flowering. miR156b down-regulates flower time regulators like AP1, FULs, LFY, LFY2, SOCs, FT5a, and miR172 [
A total of 200 mature miRNAs were identified by Kulcheski et al. [
In soybean seeds, during growth, a lot of nutritional compounds are accumulated. Soybean is the world’s most significant legume, commercially and essential double-purpose crop with seeds enriched with proteins and oils that provide food for livestock and human consumption. Soybean cotyledons have formed as complex sink tissue for protein and oil accumulation that directly affects the yield and quality of soybean seeds. The storage of proteins and oil in soybean cotyledons directly affects the yield and consistency of soybean seeds. Too little is known about soybean cotyledon miRNAs and their regulatory networks. Discovery of novel miRNA involved in soybean seed development will facilitate understanding of miRNA regulatory network in improving soybean seed quality. miRNA family members miR156, 159, 160, 164, 166, and 167 were reported from seed coats and cotyledons [
Shamimuzzaman et al. [
A total of one hundred and fourty five genes were identified as miRNA targets and twenty-five as target for novel miRNAs [
Soybean oil flavor and stability can be improved by reducing the content of alpha-linolenic acid (18:3). To down-regulate omega-3 fatty acid desaturase (enzyme catalyze linoleic acid (18:2) to alpha-linolenic acid (18:3), Flores et al. [
Legume plants in association with nitrogen-fixing soil bacteria, form a specialized organ, the nodule. The molecular mechanisms of signaling that regulate the formation of nodules have been extensively characterized, and microRNAs (miRNAs) have been reported in different legumes nodulation processes [
Symbiotic relationship with nitrogen-fixing bacteria (Rhizobia) to receive nitrogen during nodulation of plant roots [
miR171o and miR171q expression are negatively associated with that of their target genes. These miRNAs in transgenic hairy roots resulted in a substantial decrease in nodule formation targeting GRAS TFs members. GRAS TFs SCL-6 and NSP2 are known to influence expression of the genes Nodule Inception (NIN), Early Nodulin 40 (ENOD40) and Ethylene Response Factor Required for Nodulation (ERN) during the process of
Soybean is a legume crop model that is used to explain plant morphology, adaptation, and domestication in practical genomics. A selection of data sets, such as the abundance of mRNA transcripts, small RNA communities and methylation status, offer unprecedented insight into gene regulation during developmental and environmental responses. There are also undefined and little-known features of many miRNAs as well as their operating mechanisms. miRNAs preserved in broad families include representatives with anonymous functions; exploring the involvement of different family members in relation to tissue/organ-specific tasks is of great importance. High-performance techniques of sequencing have assisted researchers with miRNA genome-wide identification and characterization supported by different computational tools and public web services. This has allowed the effective and quick identification of defining the targets of miRNAs in degradome sequencing with some limitations. A reliable method for improving crops is the ability of miRNA modification, but unintentional side effects may also be recorded since adverse improvements in plant growth and morphology may be seen separately from favorable and beneficial ones [
By modifying the target miRNA that controls the number of plant genetic traits [
This will allow researchers and breeders to understand the function of miRNA in improving plants by incorporating modern biotechnological techniques. With the combined efforts of various omics technologies and post-genomics resources, expanding awareness of miRNA regulatory roles will provide better molecular breeding options to speed up the selection process, and significantly shorten the time necessary for improved variety development. This modification of miRNA genes and miRNA tolerant target genes will help to enhance the engineering of desirable features in agricultural products.