Abstract
BACKGROUND: Iron is one of fourteen mineral elements required for proper plant growth and development of soybean (Glycine max L. Merr.). Soybeans grown on calcareous soils, which are prevalent in the upper Midwest of the United States, often exhibit symptoms indicative of iron deficiency chlorosis (IDC). Yield loss has a positive linear correlation with increasing severity of chlorotic symptoms. As soybean is an important agronomic crop, it is essential to understand the genetics and physiology of traits affecting plant yield. Soybean cultivars vary greatly in their ability to respond successfully to iron deficiency stress. Microarray analyses permit the identification of genes and physiological processes involved in soybean's response to iron stress. RESULTS: RNA isolated from the roots of two near isogenic lines, which differ in iron efficiency, PI 548533 (Clark; iron efficient) and PI 547430 (IsoClark; iron inefficient), were compared on a spotted microarray slide containing 9,728 cDNAs from root specific EST libraries. A comparison of RNA transcripts isolated from plants grown under iron limiting hydroponic conditions for two weeks revealed 43 genes as differentially expressed. A single linkage clustering analysis of these 43 genes showed 57% of them possessed high sequence similarity to known stress induced genes. A control experiment comparing plants grown under adequate iron hydroponic conditions showed no differences in gene expression between the two near isogenic lines. Expression levels of a subset of the differentially expressed genes were also compared by real time reverse transcriptase PCR (RT-PCR). The RT-PCR experiments confirmed differential expression between the iron efficient and iron inefficient plants for 9 of 10 randomly chosen genes examined. To gain further insight into the iron physiological status of the plants, the root iron reductase activity was measured in both iron efficient and inefficient genotypes for plants grown under iron sufficient and iron limited conditions. Iron inefficient plants failed to respond to decreased iron availability with increased activity of Fe reductase. CONCLUSION: These experiments have identified genes involved in the soybean iron deficiency chlorosis response under iron deficient conditions. Single linkage cluster analysis suggests iron limited soybeans mount a general stress response as well as a specialized iron deficiency stress response. Root membrane bound reductase capacity is often correlated with iron efficiency. Under iron-limited conditions, the iron efficient plant had high root bound membrane reductase capacity while the iron inefficient plants reductase levels remained low, further limiting iron uptake through the root. Many of the genes up-regulated in the iron inefficient NIL are involved in known stress induced pathways. The most striking response of the iron inefficient genotype to iron deficiency stress was the induction of a profusion of signaling and regulatory genes, presumably in an attempt to establish and maintain cellular homeostasis. Genes were up-regulated that point toward an increased transport of molecules through membranes. Genes associated with reactive oxidative species and an ROS-defensive enzyme were also induced. The up-regulation of genes involved in DNA repair and RNA stability reflect the inhospitable cellular environment resulting from iron deficiency stress. Other genes were induced that are involved in protein and lipid catabolism; perhaps as an effort to maintain carbon flow and scavenge energy. The under-expression of a key glycolitic gene may result in the iron-inefficient genotype being energetically challenged to maintain a stable cellular environment. These experiments have identified candidate genes and processes for further experimentation to increase our understanding of soybeans' response to iron deficiency stress.
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Claims 16
Claim · model-written summary
Under iron limiting hydroponic conditions for two weeks, 43 soybean genes were differentially expressed between near-isogenic lines.
- Taxon
- soybean
Glycine maxt0 - Treatment
- iron limiting hydroponic conditionse1
- Outcome
- genes as differentially expressede1
- Value
- 43 genese1
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“Microarray analysis of iron deficiency chlorosis in near-isogenic soybean lines”
e1“A comparison of RNA transcripts isolated from plants grown under iron limiting hydroponic conditions for two weeks revealed 43 genes as differentially expressed”
Claim · model-written summary
Of the 43 differentially expressed soybean genes, 57% showed high sequence similarity to known stress induced genes.
- Taxon
- soybeanGlycine maxt0
- Outcome
- sequence similarity to known stress induced genese2
- Value
- 57%e2
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“Microarray analysis of iron deficiency chlorosis in near-isogenic soybean lines”
e2“A single linkage clustering analysis of these 43 genes showed 57% of them possessed high sequence similarity to known stress induced genes”
Claim · model-written summary
Under adequate iron hydroponic conditions, the two near-isogenic soybean lines showed no differences in gene expression.
- Taxon
- soybeanGlycine maxt0
- Material
- two near isogenic linese3
- Treatment
- adequate iron hydroponic conditionse3
- Outcome
- gene expressione3
- Direction
- no differencese3
- Comparator
- near isogenic linese3
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“Microarray analysis of iron deficiency chlorosis in near-isogenic soybean lines”
e3“A control experiment comparing plants grown under adequate iron hydroponic conditions showed no differences in gene expression between the two near isogenic lines”
Claim · model-written summary
RT-PCR confirmed differential expression between iron efficient and iron inefficient soybean plants for 9 of 10 randomly chosen genes.
- Taxon
- soybeanGlycine maxt0
- Material
- iron efficient and iron inefficient plantse4
- Outcome
- differential expressione4
- Value
- 9 of 10e4
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“Microarray analysis of iron deficiency chlorosis in near-isogenic soybean lines”
e4“The RT-PCR experiments confirmed differential expression between the iron efficient and iron inefficient plants for 9 of 10 randomly chosen genes examined”
Claim · model-written summary
Iron inefficient soybean plants failed to respond to decreased iron availability with increased Fe reductase activity.
- Taxon
- soybeanGlycine maxt0
- Material
- Iron inefficient plantse5
- Treatment
- decreased iron availabilitye5
- Outcome
- activity of Fe reductasee5
- Direction
- failed to responde5
Not reportedComparator
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“Microarray analysis of iron deficiency chlorosis in near-isogenic soybean lines”
e5“Iron inefficient plants failed to respond to decreased iron availability with increased activity of Fe reductase”
Claim · model-written summary
Under iron-limited conditions, the iron efficient soybean plant had high root membrane-bound reductase capacity.
- Taxon
- soybeanGlycine maxt0
- Material
- iron efficient plante6
- Treatment
- Under iron-limited conditionse6
- Outcome
- root bound membrane reductase capacitye6
- Direction
- highe6
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“Microarray analysis of iron deficiency chlorosis in near-isogenic soybean lines”
e6“Under iron-limited conditions, the iron efficient plant had high root bound membrane reductase capacity”
Claim · model-written summary
Under iron-limited conditions, root reductase levels remained low in the iron inefficient soybean plants.
- Taxon
- soybeanGlycine maxt0
- Material
- iron inefficient plantse6
- Outcome
- reductase levelse6
- Direction
- remained lowe6
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“Microarray analysis of iron deficiency chlorosis in near-isogenic soybean lines”
e6“while the iron inefficient plants reductase levels remained low, further limiting iron uptake through the root”
Claim · model-written summary
Low root reductase levels in iron inefficient soybean plants may further limit iron uptake through the root.
- Taxon
- soybeanGlycine maxt0
- Organ / stage
- roote6
- Outcome
- iron uptakee6
- Qualifier
- reductase levels remained lowe6
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“Microarray analysis of iron deficiency chlorosis in near-isogenic soybean lines”
e6“while the iron inefficient plants reductase levels remained low, further limiting iron uptake through the root”
Claim · model-written summary
Many genes up-regulated in the iron inefficient soybean NIL are involved in known stress induced pathways.
- Taxon
- soybeanGlycine maxt0
- Material
- iron inefficient NILe7
- Outcome
- involved in known stress induced pathwayse7
- Direction
- up-regulatede7
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“Microarray analysis of iron deficiency chlorosis in near-isogenic soybean lines”
e7“Many of the genes up-regulated in the iron inefficient NIL are involved in known stress induced pathways”
Claim · model-written summary
The most striking response of the iron inefficient soybean genotype to iron deficiency stress was induction of signaling and regulatory genes.
- Taxon
- soybeanGlycine maxt0
- Material
- iron inefficient genotypee1
- Treatment
- iron deficiency stresse1
- Outcome
- signaling and regulatory genese1
- Direction
- inductione1
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“Microarray analysis of iron deficiency chlorosis in near-isogenic soybean lines”
e1“The most striking response of the iron inefficient genotype to iron deficiency stress was the induction of a profusion of signaling and regulatory genes”
Claim · model-written summary
Genes for increased transport of molecules through membranes were up-regulated in soybean.
- Taxon
- soybeanGlycine maxt0
- Outcome
- transport of molecules through membranese1
- Direction
- increasede1
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“Microarray analysis of iron deficiency chlorosis in near-isogenic soybean lines”
e1“Genes were up-regulated that point toward an increased transport of molecules through membranes”
Claim · model-written summary
Genes associated with reactive oxygen species and an ROS-defensive enzyme were induced in soybean under iron deficiency.
- Taxon
- soybeanGlycine maxt0
- Gene
- ROS-defensive enzymee1
- Outcome
- Genes associated with reactive oxidative speciese1
- Direction
- inducede1
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“Microarray analysis of iron deficiency chlorosis in near-isogenic soybean lines”
e1“Genes associated with reactive oxidative species and an ROS-defensive enzyme were also induced”
Claim · model-written summary
Genes involved in DNA repair and RNA stability were up-regulated in soybean under iron deficiency stress.
- Taxon
- soybeanGlycine maxt0
- Treatment
- iron deficiency stresse1
- Outcome
- genes involved in DNA repair and RNA stabilitye1
- Direction
- up-regulatione1
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“Microarray analysis of iron deficiency chlorosis in near-isogenic soybean lines”
e1“The up-regulation of genes involved in DNA repair and RNA stability reflect the inhospitable cellular environment resulting from iron deficiency stress”
Claim · model-written summary
Genes involved in protein and lipid catabolism were induced in soybean.
- Taxon
- soybeanGlycine maxt0
- Outcome
- protein and lipid catabolisme1
- Direction
- inducede1
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“Microarray analysis of iron deficiency chlorosis in near-isogenic soybean lines”
e1“Other genes were induced that are involved in protein and lipid catabolism”
Claim · model-written summary
A key glycolytic gene was under-expressed in the iron inefficient soybean genotype.
- Taxon
- soybeanGlycine maxt0
- Material
- iron-inefficient genotypee1
- Gene
- key glycolitic genee1
- Outcome
- expressione1
- Direction
- under-expressione1
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“Microarray analysis of iron deficiency chlorosis in near-isogenic soybean lines”
e1“The under-expression of a key glycolitic gene may result in the iron-inefficient genotype being energetically challenged”
Claim · model-written summary
Iron limited soybeans mount a general stress response as well as a specialized iron deficiency stress response.
- Taxon
- soybeansGlycine maxe1
- Treatment
- iron limitede1
- Outcome
- general stress responsee1
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“Microarray analysis of iron deficiency chlorosis in near-isogenic soybean lines”
e1“Single linkage cluster analysis suggests iron limited soybeans mount a general stress response as well as a specialized iron deficiency stress response”
The same questions in other papers
iron atom · nutrient: content · Glycine max (soybean)Positive and negative results
24 papers in the same direction as this paper · 13 in the opposite direction
This paper is about lacking the nutrient, so it counts the other way round here.
- no effect
- no effect
- negative
34 papers more in this group
See all 38 papers →Claims are grouped by organism, treatment and what was measured or targeted. A paper counts as positive when any of its claims in the group is positive.