Abstract
All lateral organ development in plants, such as nodulation in legumes, requires the temporal and spatial regulation of genes and gene networks. A total mRNA profiling approach using RNA-seq to target the specific soybean (Glycine max) root tissues responding to compatible rhizobia [i.e. the Zone Of Nodulation (ZON)] revealed a large number of novel, often transient, mRNA changes occurring during the early stages of nodulation. Focusing on the ZON enabled us to discard the majority of root tissues and their developmentally diverse gene transcripts, thereby highlighting the lowly and transiently expressed nodulation-specific genes. It also enabled us to concentrate on a precise moment in early nodule development at each sampling time. We focused on discovering genes regulated specifically by the Bradyrhizobium-produced Nod factor signal, by inoculating roots with either a competent wild-type or incompetent mutant (nodC(-) ) strain of Bradyrhizobium japonicum. Collectively, 2915 genes were identified as being differentially expressed, including many known soybean nodulation genes. A number of unknown nodulation gene candidates and soybean orthologues of nodulation genes previously reported in other legume species were also identified. The differential expression of several candidates was confirmed and further characterized via inoculation time-course studies and qRT-PCR. The expression of many genes, including an endo-1,4-β-glucanase, a cytochrome P450 and a TIR-LRR-NBS receptor kinase, was transient, peaking quickly during the initiation of nodule ontogeny. Additional genes were found to be down-regulated. Significantly, a set of differentially regulated genes acting in the gibberellic acid (GA) biosynthesis pathway was discovered, suggesting a novel role of GAs in nodulation.
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Claims 10
Claim · model-written summary
RNA-seq identified many novel, often transient mRNA changes early in soybean nodulation.
- Taxon
- soybean (Glycine max)
Glycine maxe0 - Organ / stage
- root tissuese0
- Interactor
- rhizobiae0symbiont
- Outcome
- mRNA changese0
- Value
- a large numbere0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“A total mRNA profiling approach using RNA-seq to target the specific soybean (Glycine max) root tissues responding to compatible rhizobia [i.e. the Zone Of Nodulation (ZON)] revealed a large number of novel, often transient, mRNA changes occurring during the early stages of nodulation”
Claim · model-written summary
Focusing on ZON highlighted lowly and transiently expressed nodulation genes.
- Organ / stage
- root tissuese0
- Outcome
- lowly and transiently expressed nodulation-specific genese0
- Value
- the majoritye0
Not reportedTaxon
Verbatim
e0“Focusing on the ZON enabled us to discard the majority of root tissues and their developmentally diverse gene transcripts, thereby highlighting the lowly and transiently expressed nodulation-specific genes”
Claim · model-written summary
The comparison identified 2915 differentially expressed genes, including known soybean nodulation genes.
- Taxon
- soybeanGlycine maxe0
- Outcome
- genes were identified as being differentially expressede0
- Value
- 2915 genese0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Collectively, 2915 genes were identified as being differentially expressed, including many known soybean nodulation genes”
Claim · model-written summary
Unknown nodulation candidates and soybean orthologues of known legume nodulation genes were identified.
- Taxon
- soybeanGlycine maxe0
- Outcome
- unknown nodulation gene candidates and soybean orthologues of nodulation genese0
Not reportedDirection
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“A number of unknown nodulation gene candidates and soybean orthologues of nodulation genes previously reported in other legume species were also identified”
Claim · model-written summary
Several candidate genes had their differential expression confirmed by time course and qRT-PCR.
- Taxon
- soybeanGlycine maxt0
- Outcome
- differential expression of several candidatese0
- Value
- several candidatese0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“The differential expression of several candidates was confirmed and further characterized via inoculation time-course studies and qRT-PCR”
t0“soybean (Glycine max [L.] Merr.)”
Claim · model-written summary
An endo-1,4-β-glucanase showed transient expression peaking early in nodule development.
- Taxon
- soybeanGlycine maxt0
- Organ / stage
- nodulee0
- Gene
- endo-1,4-β-glucanasee0
- Outcome
- expressione0
- Direction
- peaking quicklye0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“The expression of many genes, including an endo-1,4-β-glucanase, a cytochrome P450 and a TIR-LRR-NBS receptor kinase, was transient, peaking quickly during the initiation of nodule ontogeny”
t0“soybean (Glycine max [L.] Merr.)”
Claim · model-written summary
A cytochrome P450 showed transient expression peaking early in nodule development.
- Taxon
- soybeanGlycine maxt0
- Organ / stage
- nodulee0
- Gene
- cytochrome P450e0
- Outcome
- expressione0
- Direction
- peaking quicklye0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“The expression of many genes, including an endo-1,4-β-glucanase, a cytochrome P450 and a TIR-LRR-NBS receptor kinase, was transient, peaking quickly during the initiation of nodule ontogeny”
t0“soybean (Glycine max [L.] Merr.)”
Claim · model-written summary
A TIR-LRR-NBS receptor kinase showed transient expression peaking early in nodule development.
- Taxon
- soybeanGlycine maxt0
- Organ / stage
- nodulee0
- Gene
- TIR-LRR-NBS receptor kinasee0
- Outcome
- expressione0
- Direction
- peaking quicklye0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“The expression of many genes, including an endo-1,4-β-glucanase, a cytochrome P450 and a TIR-LRR-NBS receptor kinase, was transient, peaking quickly during the initiation of nodule ontogeny”
t0“soybean (Glycine max [L.] Merr.)”
Claim · model-written summary
Additional nodulation genes were down-regulated.
- Taxon
- soybeanGlycine maxt0
- Outcome
- genese0
- Direction
- down-regulatede0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Additional genes were found to be down-regulated”
t0“soybean (Glycine max [L.] Merr.)”
Claim · model-written summary
Differentially regulated GA biosynthesis genes suggested a role of GAs in nodulation.
- Taxon
- soybeanGlycine maxt0
- Gene
- genes acting in the gibberellic acid (GA) biosynthesis pathwaye0
- Outcome
- novel role of GAs in nodulatione0
Not reportedDirection
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“a set of differentially regulated genes acting in the gibberellic acid (GA) biosynthesis pathway was discovered, suggesting a novel role of GAs in nodulation”
t0“soybean (Glycine max [L.] Merr.)”