Name: Author Spotlight: Soybean Hairy Root Transformation for the Analysis of Gene Function
Uploaded: 2023-05-05T14:40:00
Description: Watch this Scientific Journal Video about Soybean Hairy Root Transformation for the Analysis of Gene Function at JoVE.com

This research was funded by the Natural Sciences and Engineering Research Council of Canada (NSERC) grant number RGPIN-2020-06111 and by a generous donation from Brad Lace. We would like to thank Wayne Parrott (University of Georgia) for the K599 Agrobacterium and the preliminary protocol, and the Nakagawa &#38; Hachiya lab (Shimane University) for the pGWB2, pGWB6, and pANDA35HK empty vectors.

NOTE: It is recommended that all of the proceeding steps be conducted under sterile conditions.
1. Soybean seed sterilization
<ol>
	<li>In a biosafety cabinet, place 16-20 round Williams 82 soybean seeds in pristine condition (i.e., no cracks or blemishes) in a 50 mL centrifuge tube.</li>
	<li>Add 30 mL of 70% isopropyl alcohol, gently shake for 30 s, and then decant the alcohol.</li>
	<li>Gently shake the seeds with 30 mL of 10% bleach for 10 s and allow the seeds to sit in...

High-Efficiency Production of Transgenic Soybean Hairy Roots

<ol>
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M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Agrobacterium-mediated+plant+transformation:+biology+and+applications.">Agrobacterium-mediated plant transformation: biology and applications.</a> The Arabidopsis Book. 15, e0186 (2017).</li><li>Gutierrez-Valdes, N., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Hairy+root+cultures-a+versatile+tool+with+multiple+applications.">Hairy root cultures-a versatile tool with multiple applications.</a> Frontiers in Plant Science. 11, 33 (2020).</li><li>Ono, N. N., Tian, L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+multiplicity+of+hairy+root+cultures:+prolific+possibilities.">The multiplicity of hairy root cultures: prolific possibilities.</a> Plant Science. 180 (3), 439-446 (2011).</li><li>Kereszt, A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Agrobacterium+rhizogenes-mediated+transformation+of+soybean+to+study+root+biology.">Agrobacterium rhizogenes-mediated transformation of soybean to study root biology.</a> Nature Protocols. 2 (4), 948-952 (2007).</li><li>Chen, L., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Soybean+hairy+roots+produced+in+vitro+by+Agrobacterium+rhizogenes-mediated+transformation.">Soybean hairy roots produced in vitro by Agrobacterium rhizogenes-mediated transformation.</a> The Crop Journal. 6 (2), 162-171 (2018).</li><li>Song, J., T&#243;th, K., Montes-Luz, B., Stacey, G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Soybean+hairy+root+transformation:+a+rapid+and+highly+efficient+method.">Soybean hairy root transformation: a rapid and highly efficient method.</a> Current Protocols. 1 (7), e195 (2021).</li><li>Fattahi, F., Shojaeiyan, A., Palazon, J., Moyano, E., Torras-Claveria, L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Methyl-&#946;-cyclodextrin+and+coronatine+as+new+elicitors+of+tropane+alkaloid+biosynthesis+in+Atropa+acuminata+and+Atropa+belladonna+hairy+root+cultures.">Methyl-&#946;-cyclodextrin and coronatine as new elicitors of tropane alkaloid biosynthesis in Atropa acuminata and Atropa belladonna hairy root cultures.</a> Physiologia Plantarum. 172 (4), 2098-2111 (2021).</li><li>Farrell, K., Jahan, M., Kovinich, N. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Distinct+mechanisms+of+biotic+and+chemical+elicitors+enable+additive+elicitation+of+the+anticancer+Phytoalexin+Glyceollin+I.">Distinct mechanisms of biotic and chemical elicitors enable additive elicitation of the anticancer Phytoalexin Glyceollin I.</a> Molecules. 22 (8), 1261 (2017).</li><li>Cheng, Y., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Highly+efficient+Agrobacterium+rhizogenes-mediated+hairy+root+transformation+for+gene+functional+and+gene+editing+analysis+in+soybean.">Highly efficient Agrobacterium rhizogenes-mediated hairy root transformation for gene functional and gene editing analysis in soybean.</a> Plant Methods. 17 (1), 73 (2021).</li><li>Arora, D., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Establishment+of+proximity-dependent+biotinylation+approaches+in+different+plant+model+systems.">Establishment of proximity-dependent biotinylation approaches in different plant model systems.</a> Plant Cell. 32 (11), 3388-3407 (2020).</li><li>Gomes, C., Dupas, A., Pagano, A., Grima-Pettenati, J., Paiva, J. A. P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Hairy+root+transformation:+a+useful+tool+to+explore+gene+function+and+expression+in+Salix+spp.+recalcitrant+to+transformation.">Hairy root transformation: a useful tool to explore gene function and expression in Salix spp. recalcitrant to transformation.</a> Frontiers in Plant Science. 10, 1427 (2019).</li><li>Ahmed, S., Kovinich, N. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Regulation+of+phytoalexin+biosynthesis+for+agriculture+and+human+health.">Regulation of phytoalexin biosynthesis for agriculture and human health.</a> Phytochemistry Reviews. 20, 483-505 (2021).</li><li>Walker, R. R., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Glyceollins+trigger+anti-proliferative+effects+in+hormone-dependent+aromatase-inhibitor-resistant+breast+cancer+cells+through+the+induction+of+apoptosis.">Glyceollins trigger anti-proliferative effects in hormone-dependent aromatase-inhibitor-resistant breast cancer cells through the induction of apoptosis.</a> International Journal of Molecular Sciences. 23 (5), 2887 (2022).</li><li>Tong, X., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+complete+genome+sequence+of+cucumopine-type+Agrobacterium+rhizogenes+strain+K599+(NCPPB2659),+a+nature's+genetic+engineer+inducing+hairy+roots.">The complete genome sequence of cucumopine-type Agrobacterium rhizogenes strain K599 (NCPPB2659), a nature's genetic engineer inducing hairy roots.</a> International Journal of Agriculture Biology. 20 (5), 1167-1174 (2018).</li><li>Lin, J., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=RNA-Seq+dissects+incomplete+activation+of+phytoalexin+biosynthesis+by+the+soybean+transcription+factors+GmMYB29A2+and+GmNAC42-1.">RNA-Seq dissects incomplete activation of phytoalexin biosynthesis by the soybean transcription factors GmMYB29A2 and GmNAC42-1.</a> Plants. 12 (3), 545 (2023).</li><li>Jahan, M. A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Glyceollin+transcription+factor+GmMYB29A2+regulates+soybean+resistance+to+Phytophthora+sojae.">Glyceollin transcription factor GmMYB29A2 regulates soybean resistance to Phytophthora sojae.</a> Plant Physiology. 183 (2), 530-546 (2020).</li><li>Jahan, M. A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+NAC+family+transcription+factor+GmNAC42-1+regulates+biosynthesis+of+the+anticancer+and+neuroprotective+glyceollins+in+soybean.">The NAC family transcription factor GmNAC42-1 regulates biosynthesis of the anticancer and neuroprotective glyceollins in soybean.</a> BMC Genomics. 20, 149 (2019).</li><li>Nguyen, C. X., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Critical+role+for+uricase+and+xanthine+dehydrogenase+in+soybean+nitrogen+fixation+and+nodule+development.">Critical role for uricase and xanthine dehydrogenase in soybean nitrogen fixation and nodule development.</a> The Plant Genome. , e20171 (2021).</li><li>Brear, E. M., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=GmVTL1a+is+an+iron+transporter+on+the+symbiosome+membrane+of+soybean+with+an+important+role+in+nitrogen+fixation.">GmVTL1a is an iron transporter on the symbiosome membrane of soybean with an important role in nitrogen fixation.</a> New Phytologist. 228 (2), 667-681 (2020).</li><li>Chen, Z., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Overexpression+of+transcription+factor+GmTGA15+enhances+drought+tolerance+in+transgenic+soybean+hairy+roots+and+Arabidopsis+plants.">Overexpression of transcription factor GmTGA15 enhances drought tolerance in transgenic soybean hairy roots and Arabidopsis plants.</a> Agronomy. 11 (1), 170 (2021).</li><li>Savka, M., Ravillion, B., Noel, G., Farrand, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Induction+of+hairy+roots+on+cultivated+soybean+genotypes+and+their+use+to+propagate+the+soybean+cyst+nematode.">Induction of hairy roots on cultivated soybean genotypes and their use to propagate the soybean cyst nematode.</a> Phytopathology. 80 (5), 503-508 (1990).</li><li>Subramanian, S., Graham, M. Y., Yu, O., Graham, T. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=RNA+interference+of+soybean+isoflavone+synthase+genes+leads+to+silencing+in+tissues+distal+to+the+transformation+site+and+to+enhanced+susceptibility+to+Phytophthora+sojae.">RNA interference of soybean isoflavone synthase genes leads to silencing in tissues distal to the transformation site and to enhanced susceptibility to Phytophthora sojae.</a> Plant Physiology. 137 (4), 1345-1353 (2005).</li><li>Sharma, A. R., Gajurel, G., Ahmed, I., Roedel, K., Medina-Bolivar, F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Induction+of+the+prenylated+stilbenoids+arachidin-1+and+arachidin-3+and+their+semi-preparative+separation+and+purification+from+hairy+root+cultures+of+peanut+(Arachis+hypogaea+l.).">Induction of the prenylated stilbenoids arachidin-1 and arachidin-3 and their semi-preparative separation and purification from hairy root cultures of peanut (Arachis hypogaea l.).</a> Molecules. 27 (18), 6118 (2022).</li><li>Lozovaya, V. 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During the past decade, the soybean HR method has been developed as a powerful tool to study genes involved in nitrogen fixation22,23, biotic and abiotic stress tolerance24,25, and metabolite biosynthetic pathways26,27. The knowledge of how plants produce metabolites has a plethora of benefits for agricultural production and the pharmaceutical ind...

Soybean (Glycine max) is among the most valuable crops in agriculture. It has thousands of commercial and industrial uses, such as food, animal feed, oil, and as a source of raw materials for manufacturing1. Its ability to form a symbiotic relationship with nitrogen-fixing soil microorganisms, namely rhizobia, further elevates the importance of studying soybean genetics2. For instance, fine-tuning nitrogen fixation properties in soybean roots can lead to the reduction of carbon emissions and greatly reduce requirements for nitrogen fertilizer3. Thus, understanding the genetics that controls aspects of soybean root biology, in particular, has wide applications in agriculture and industry. Considering these benefits, it is important to have a reliable protocol to analyze the function of soybean genes.
Agrobacterium tumefaciens is perhaps the most commonly used tool for plant genetic transformation as it has the capability of integrating transfer DNA (T-DNA) into the nuclear genome of many plant species. When Agrobacterium infects a plant, it transfers the tumor-inducing (Ti) plasmid into the host chromosome, leading to the formation of a tumor at the infection site. The Agrobacterium-mediated transformation has been widely used for decades for gene functional analysis and in order to modify crop traits4. Although any gene of interest can be readily transferred into host plant cells through A. tumefaciens-mediated transformation, this method has several drawbacks; it is time-consuming, expensive, and requires extensive expertise for many plant species, such as soybean. Although a few varieties of soybean can be transformed by the cotyledonary node approach using A. tumefaciens, the inefficiency of this approach necessitates the need for an alternative genetic transformation technology that is rapid and highly efficient4,5. Even a non-expert can use this Agrobacterium rhizogenes-mediated hairy root (HR) transformation method to overcome these disadvantages.
HR transformation is a relatively fast tool, not only for analyzing gene function, but also for biotechnological applications, such as the production of specialized metabolites and fine chemicals, and complex bioactive glycoproteins6. The production of soybean HRs does not require extensive expertise, as they can be generated by wounding the surfaces of cotyledons, followed by inoculation with Agrobacterium rhizogenes7. A. rhizogenes expresses virulence (Vir) genes encoded by its Ti plasmid that transfer, carry, and integrate its T-DNA segment into the genome of plant cells while simultaneously stimulating ectopic root growth8.
Compared to other soybean gene&#160;expression systems, such as biolistics or A. tumefaciens-based transformation of tissue, cell, and organ culture, the HR expression system exhibits several advantages. Firstly, HRs are genetically stable and produced quickly on hormone-free media1,9,10. Additionally, HRs can produce specialized metabolites in amounts equivalent to or greater than native roots11,12. These advantages make HRs a desirable biotechnological tool for plant species that are incompatible with A. tumefaciens or that require special tissue culture conditions to form compatible tissues. The HR method is an efficient approach for analyzing protein-protein interactions, protein subcellular localization, recombinant protein production, phytoremediation, mutagenesis, and genome wide effects using RNA sequencing13,14,15. It can also be used to study the production of specialized metabolites that have value in the industry, including glyceollins, which medicate soybean&#39;s defense against the important microbial pathogen Phytophthora sojae and have impressive anticancer and neuroprotective activities in humans16,17.
This report demonstrates an easy, efficient protocol to produce soybean HRs. Compared to previous HR transformation methods, this protocol provides a significant (33%-50%) improvement in the rate of HR formation by prescreening A. rhizogenes transformants for the presence of the Ti plasmid prior to inoculating soybean cotyledons. We demonstrate the applicability of this protocol by transforming several binary vectors that overexpress or silence soybean transcription factor genes.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>Acetosyringone</td>
			<td>Cayman</td>
			<td>23224</td>
			<td></td>
		</tr>
		<tr>
			<td>Bleach</td>
			<td>lavo</td>
			<td>21124</td>
			<td></td>
		</tr>
		<tr>
			<td>DMSO</td>
			<td>Fisher bioreagents</td>
			<td>195679</td>
			<td></td>
		</tr>
		<tr>
			<td>Gelzan</td>
			<td>Phytotech</td>
			<td>HYY3251089A</td>
			<td></td>
		</tr>
		<tr>
			<td>Hygromycin</td>
			<td>Phytotech</td>
			<td>HHA0397050B</td>
			<td></td>
		</tr>
		<tr>
			<td>Isopropyl alcohol</td>
			<td>Fisher chemical</td>
			<td>206462</td>
			<td></td>
		</tr>
		<tr>
			<td>Kanamycin</td>
			<td>Phytotech</td>
			<td>SQS0378007G</td>
			<td></td>
		</tr>
		<tr>
			<td>LB powder</td>
			<td>Fisher bioreagents</td>
			<td>200318</td>
			<td></td>
		</tr>
		<tr>
			<td>MS powder</td>
			<td>Caisson labs</td>
			<td>2210001</td>
			<td></td>
		</tr>
		<tr>
			<td>Na2HPO4</td>
			<td>Fisher bioreagents</td>
			<td>194171</td>
			<td></td>
		</tr>
		<tr>
			<td>NaCl</td>
			<td>Fisher chemical</td>
			<td>192946</td>
			<td></td>
		</tr>
		<tr>
			<td>Petri dishes</td>
			<td>Fisherbrand</td>
			<td>08-757-11</td>
			<td>100 mm x 25 mm</td>
		</tr>
		<tr>
			<td>Phosphinothricin</td>
			<td>Cedarlane</td>
			<td>P034-250MG</td>
			<td></td>
		</tr>
		<tr>
			<td>REDExtract-N-Amp PCR Kit</td>
			<td>Sigma</td>
			<td>R4775</td>
			<td></td>
		</tr>
		<tr>
			<td>Sucrose</td>
			<td>Bioshop</td>
			<td>2D76475</td>
			<td></td>
		</tr>
		<tr>
			<td>Timentin</td>
			<td>Caisson labs</td>
			<td>12222002</td>
			<td></td>
		</tr>
		<tr>
			<td>Vitamins</td>
			<td>Caisson labs</td>
			<td>2211010</td>
			<td></td>
		</tr>
	</tbody>
</table>

soybean hairy root transformation for the analysis of gene function

Soybean (Glycine max) is a valuable crop in agriculture that has thousands of industrial uses. Soybean roots are the primary site of interaction with soil-borne microbes that form symbiosis to fix nitrogen and pathogens, which makes research involving soybean root genetics of prime importance to improve its agricultural production. The genetic transformation of soybean hairy roots (HRs) is mediated by the Agrobacterium rhizogenes strain NCPPB2659 (K599) and is an efficient tool for studying gene function in soybean roots, taking only 2 months from start to finish. Here, we provide a detailed protocol that outlines the method for overexpressing and silencing a gene of interest in soybean HRs. This methodology includes soybean seed sterilization, infection of cotyledons with K599, and the selection and harvesting of genetically transformed HRs for RNA isolation and, if warranted, metabolite analyses. The throughput of the approach is sufficient to simultaneously study several genes or networks and could determine the optimal engineering strategies prior to committing to long-term stable transformation approaches.

Author Spotlight: Soybean Hairy Root Transformation for the Analysis of Gene Function  

Soybean Hairy Root Transformation for the Analysis of Gene Function

Our soybean hairy root transformation method is sufficient to simultaneously study the functions of several genes or networks, and could determine the optimal engineering strategies prior to committing to long-term stable transformation approaches. Soybean hairy root transformation is a useful tool for the analysis of gene function in soybean plants. The technology that are currently used, include CRISPR-Cas9 genome editing, RNA interference, transcriptomics and proteomics, and imaging technologies.The major challenge in the model era of functional genomics is sufficient analyzing the function of numerous genes. Most genes are polygenic, being achieved by the interaction of many genes. Our hairy root protocol will facilitate gene function analysis with sufficient throughput, so that polygenic networks can begin to be understood.We have established the importance of the Ti plasmid in agrobacterium rhizogene strains. We found that without screening for the Ti plasmid, it increased the risk for the transformed soybean cotyledon, to fail to produce any colors. As a result, screening for the plasmid became a vital step before the transformation.Compared to other gene expression techniques, our hair root expression system is easy to handle, less time consuming, and cost effective. Also, our new protocol has improved hairy root transformation rate up to 50%by checking for the Ti plasmid and agrobacterium prior to cotyledon transformation. By characterizing the function of more than a dozen transcription factor genes, our recent results have paved the way for multi-gene engineering studies, aimed at unlocking the biosynthesis of valuable phytoalexin metabolites in plants.In the future, we will use this hairy root transformation method to dissect the transcription factor gene networks that regulate the biosynthesis of phytoalexins. The approach could be used to enhance the production of these specialized metabolites for pharmaceutical and agricultural industries.

The representative results are from the published data19,20. The colony PCR (cPCR) results of the transformed K599 Agrobacterium are shown in Figure 1. As indicated by the positive colonies in Figure 1, the gene of interest was detected by cPCR (Figure 1A). However, one-third to one-half of the colonies were negative for the VirD2 gene screening (<strong cl...

Watch this Scientific Journal Video about Soybean Hairy Root Transformation for the Analysis of Gene Function at JoVE.com

Here, we present a protocol for the high-efficiency production of transgenic soybean hairy roots.

Soybean (Glycine max) is a valuable crop in agriculture that has thousands of industrial uses. Soybean roots are the primary site of interaction with ...