Abstract
Zinc (Zn) is an essential micronutrient for plant growth and development, which plays important roles in DNA binding, metabolic, catalytic and transcriptional regulator activities. However, Zn deficiency is a worldwide problem due to its limited bioavailability in soils in many agricultural areas, often as a result of high CaCO3 content and high pH. In addition, phytic acid is able to strongly chelate cations, such as Zn2+, Fe2+, Ca2+ and Mg2+ to form the phytate salts. Phytate cannot be digested by human beings or other monogastric animals due to lack of phytase, an enzyme that can hydrolyze phytate. Therefore, Zn bioavailability in seeds (or grains) is restricted by phytate. Moreover, seed Zn concentration is also reduced by elevated CO2, especially in C3 plants, such as wheat, rice and soybean. Regarding to the crucial roles but limited bioavailability of Zn, here I present a comprehensive analysis on roots, leaves (and flowering) and seeds in response to Zn deficiency in the model plant Arabidopsis thaliana via three experiments. First, I investigated the transcriptional response and whole-genome DNA methylation profile upon Zn deficiency in roots using next-generation sequencing. Ionome analysis on shoots showed that Zn concentration was strongly reduced in Zn deficiency, whereas other nutrients were not affected. Microarray Analysis identified several known Zn-deficiency responsive genes, confirming the effectiveness of Zn deficiency in this work. However, bisulfite sequencing results revealed that DNA methylation was eliminated by Zn deficiency in transposable elements and slightly in gene bodies as well. The DNA demethylation response to nutrient stress was a novel finding, as reversed to previous reports about phosphate stress which accumulated methylation. Surprisingly, further analysis suggested that DNA methylation occurred independent of gene transcription. Nevertheless, non-CpG methylation has a potential impact on flower development in response to Zn deficiency. The second experiment investigated the relationship between rosette size and flowering, and how rosette size and flowering time were regulated by Zn deficiency. Using natural variation population (168 Arabidopsis accessions), I found that flowering time was positively correlated with rosette size in early-flowering accessions but not in late-flowering accessions. Intriguingly, the flowering time was delayed by Zn deficiency in these early-flowering plants and resulting in promotion of vegetative biomass. However, Zn-regulated flowering time was independent of previously reported flowering pathways. Then genome-wide association study identified the underlying candidate gene was FLOWERING LOCUS T (FT) which was strongly inhibited by Zn deficiency in all accessions. Detailed genetic analysis confirmed this result as well. Furthermore, the promotion of leaf size in Zn deficiency was found being contributed by cell proliferation (cell number) but not cell size. Lastly, in the third experiment I was interested in the natural genetic variation in seed Zn concentration, together with iron (Fe) and manganese (Mn), in response to Zn deficiency. Across around 100 accessions, average seed Zn concentration decreased from 47.4 µg g-1 to 31.3 µg g-1 due to Zn deficiency. To identify candidate genes affecting seed Zn, Fe and Mn concentrations, genome-wide association mapping was performed. A candidate gene, inositol 1,3,4-trisphosphate 5/6-kinase 3 gene (ITPK3), was associated which is involved in phytate synthesis pathways. However, loss of this gene in itpk3-1 did neither affect phytate seed levels nor seed Zn, Fe and Mn. Nevertheless, large natural variance of micronutrient seed levels was identified in the population and several accessions maintained high seed Zn despite growth in Zn-deficient conditions. Altogether, this study presents comprehensive analyses in how Arabidopsis adapts to Zn deficiency in regard of root transcription and DNA methylation, flowering and leaf regulation, and seed mineral accumulation. I provided new possibilities of correlation between DNA methylation and gene transcription, which is much more complex than previously reported. I also opened a novel insight into flowering regulation on leaf size, resulting in promotion of vegetative biomass in nutrient deficiency. Substantial natural variation of seed experiment indicated that the evolution process was involved in seed mineral accumulation in Arabidopsis, especially those accessions maintaining Zn concentration in Zn-deficient soils are valuable for further investigations. I believe these findings in Arabidopsis also provide precious knowledge for plant breeders and agronomists who work on crops.
Abstract from the paper’s OpenAlex record; open copy licensed cc-by. Read at the source ↗
The text the model read, with the source record’s inline markup (italics, sub- and superscripts) rendered and its character entities decoded; quote offsets refer to the raw text.
Claims 20
Claim · model-written summary
Shoot Zn concentration was strongly reduced under Zn deficiency.
- Taxon
- Arabidopsis thaliana
Arabidopsis thalianat0 - Organ / stage
- shootse0
- Treatment
- Zn deficiencye0
- Outcome
- Zn concentratione0
- Direction
- reducede0
- Comparator
- other nutrientse0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Ionome analysis on shoots showed that Zn concentration was strongly reduced in Zn deficiency, whereas other nutrients were not affected.”
t0“Arabidopsis thaliana”
Claim · model-written summary
Other shoot nutrients were not affected by Zn deficiency.
- Taxon
- Arabidopsis thalianaArabidopsis thalianat0
- Organ / stage
- shootse0
- Treatment
- Zn deficiencye0
- Outcome
- other nutrientse0
- Direction
- not affectede0
- Comparator
- Zn concentratione0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Ionome analysis on shoots showed that Zn concentration was strongly reduced in Zn deficiency, whereas other nutrients were not affected.”
t0“Arabidopsis thaliana”
Claim · model-written summary
Microarray analysis identified known Zn deficiency responsive genes.
- Taxon
- Arabidopsis thalianaArabidopsis thalianat0
- Gene
- Zn-deficiency responsive genese0
- Outcome
- known Zn-deficiency responsive genese0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Microarray Analysis identified several known Zn-deficiency responsive genes, confirming the effectiveness of Zn deficiency in this work.”
t0“Arabidopsis thaliana”
Claim · model-written summary
Zn deficiency eliminated DNA methylation in transposable elements and reduced it slightly in gene bodies.
- Taxon
- Arabidopsis thalianaArabidopsis thalianat0
- Organ / stage
- transposable elementse0
- Treatment
- Zn deficiencye0
- Outcome
- DNA methylatione0
- Direction
- eliminatede0
- Comparator
- gene bodiese0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“However, bisulfite sequencing results revealed that DNA methylation was eliminated by Zn deficiency in transposable elements and slightly in gene bodies as well.”
t0“Arabidopsis thaliana”
Claim · model-written summary
DNA methylation appeared independent of gene transcription.
- Taxon
- Arabidopsis thalianaArabidopsis thalianat0
- Gene
- gene transcriptione0
- Outcome
- DNA methylatione0
Not reportedDirection
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Surprisingly, further analysis suggested that DNA methylation occurred independent of gene transcription.”
t0“Arabidopsis thaliana”
Claim · model-written summary
Non-CpG methylation may affect flower development under Zn deficiency.
- Taxon
- Arabidopsis thalianaArabidopsis thalianat0
- Treatment
- Zn deficiencye0
- Gene
- non-CpG methylatione0
- Outcome
- flower developmente0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Nevertheless, non-CpG methylation has a potential impact on flower development in response to Zn deficiency.”
t0“Arabidopsis thaliana”
Claim · model-written summary
Flowering time correlated positively with rosette size in early flowering accessions.
- Taxon
- Arabidopsis thalianaArabidopsis thalianat0
- Material
- early-flowering accessionse0
- Organ / stage
- rosettee0
- Outcome
- flowering timee0
- Direction
- positively correlatede0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“I found that flowering time was positively correlated with rosette size in early-flowering accessions but not in late-flowering accessions.”
t0“Arabidopsis thaliana”
Claim · model-written summary
The flowering time and rosette size correlation was absent in late flowering accessions.
- Taxon
- Arabidopsis thalianaArabidopsis thalianat0
- Material
- late-flowering accessionse0
- Organ / stage
- rosettee0
- Outcome
- flowering timee0
- Direction
- note0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“I found that flowering time was positively correlated with rosette size in early-flowering accessions but not in late-flowering accessions.”
t0“Arabidopsis thaliana”
Claim · model-written summary
Zn deficiency delayed flowering in early flowering plants.
- Taxon
- Arabidopsis thalianaArabidopsis thalianat0
- Material
- early-flowering plantse0
- Treatment
- Zn deficiencye0
- Outcome
- flowering timee0
- Direction
- delayede0
Not reportedComparator
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Intriguingly, the flowering time was delayed by Zn deficiency in these early-flowering plants and resulting in promotion of vegetative biomass.”
t0“Arabidopsis thaliana”
Claim · model-written summary
Zn deficiency promoted vegetative biomass in early flowering plants.
- Taxon
- Arabidopsis thalianaArabidopsis thalianat0
- Material
- early-flowering plantse0
- Treatment
- Zn deficiencye0
- Outcome
- vegetative biomasse0
- Direction
- promotione0
Not reportedComparator
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Intriguingly, the flowering time was delayed by Zn deficiency in these early-flowering plants and resulting in promotion of vegetative biomass.”
t0“Arabidopsis thaliana”
Claim · model-written summary
Zn regulation of flowering time was independent of previously reported flowering pathways.
- Taxon
- Arabidopsis thalianaArabidopsis thalianat0
- Outcome
- Zn-regulated flowering timee0
- Qualifier
- independent of previously reported flowering pathwayse0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“However, Zn-regulated flowering time was independent of previously reported flowering pathways.”
t0“Arabidopsis thaliana”
Claim · model-written summary
The association study identified FLOWERING LOCUS T as a flowering candidate gene.
- Taxon
- Arabidopsis thalianaArabidopsis thalianat0
- Gene
- FLOWERING LOCUS T (FT)e0
- Outcome
- underlying candidate genee0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Then genome-wide association study identified the underlying candidate gene was FLOWERING LOCUS T (FT) which was strongly inhibited by Zn deficiency in all accessions.”
t0“Arabidopsis thaliana”
Claim · model-written summary
Zn deficiency strongly inhibited FLOWERING LOCUS T in all accessions.
- Taxon
- Arabidopsis thalianaArabidopsis thalianat0
- Material
- all accessionse0
- Treatment
- Zn deficiencye0
- Gene
- FLOWERING LOCUS T (FT)e0
- Outcome
- FLOWERING LOCUS T (FT)e0
- Direction
- inhibitede0
Not reportedComparator
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Then genome-wide association study identified the underlying candidate gene was FLOWERING LOCUS T (FT) which was strongly inhibited by Zn deficiency in all accessions.”
t0“Arabidopsis thaliana”
Claim · model-written summary
Leaf size promotion under Zn deficiency was attributed to cell proliferation rather than cell size.
- Taxon
- Arabidopsis thalianaArabidopsis thalianat0
- Treatment
- Zn deficiencye0
- Outcome
- promotion of leaf sizee0
- Qualifier
- cell proliferation (cell number) but not cell sizee0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Furthermore, the promotion of leaf size in Zn deficiency was found being contributed by cell proliferation (cell number) but not cell size.”
t0“Arabidopsis thaliana”
Claim · model-written summary
Average seed Zn concentration decreased from 47.4 to 31.3 µg g-1 under Zn deficiency.
- Taxon
- Arabidopsis thalianaArabidopsis thalianat0
- Material
- accessionse0
- Organ / stage
- seede0
- Treatment
- Zn deficiencye0
- Outcome
- seed Zn concentratione0
- Direction
- decreasede0
- Value
- 31.3 µg g-1e0
Not reportedComparator
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Across around 100 accessions, average seed Zn concentration decreased from 47.4 µg g-1 to 31.3 µg g-1 due to Zn deficiency.”
t0“Arabidopsis thaliana”
Claim · model-written summary
ITPK3 was identified as a candidate gene associated with seed mineral concentrations.
- Taxon
- Arabidopsis thalianaArabidopsis thalianat0
- Gene
- inositol 1,3,4-trisphosphate 5/6-kinase 3 gene (ITPK3)e0
- Outcome
- phytate synthesis pathwayse0
Not reportedDirection
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“A candidate gene, inositol 1,3,4-trisphosphate 5/6-kinase 3 gene (ITPK3), was associated which is involved in phytate synthesis pathways.”
t0“Arabidopsis thaliana”
Claim · model-written summary
ITPK3 loss did not affect seed phytate levels.
- Taxon
- Arabidopsis thalianaArabidopsis thalianat0
- Material
- itpk3-1e0
- Treatment
- loss of this genee0
- Outcome
- phytate seed levelse0
- Direction
- neither affecte0
Not reportedComparator
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“However, loss of this gene in itpk3-1 did neither affect phytate seed levels nor seed Zn, Fe and Mn.”
t0“Arabidopsis thaliana”
Claim · model-written summary
ITPK3 loss did not affect seed Zn, Fe and Mn concentrations.
- Taxon
- Arabidopsis thalianaArabidopsis thalianat0
- Material
- itpk3-1e0
- Treatment
- loss of this genee0
- Outcome
- seed Zn, Fe and Mne0
- Direction
- neither affecte0
Not reportedComparator
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“However, loss of this gene in itpk3-1 did neither affect phytate seed levels nor seed Zn, Fe and Mn.”
t0“Arabidopsis thaliana”
Claim · model-written summary
Seed micronutrient levels varied substantially across the population.
- Taxon
- Arabidopsis thalianaArabidopsis thalianat0
- Material
- populatione0
- Outcome
- large natural variance of micronutrient seed levelse0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Nevertheless, large natural variance of micronutrient seed levels was identified in the population and several accessions maintained high seed Zn despite growth in Zn-deficient conditions.”
t0“Arabidopsis thaliana”
Claim · model-written summary
Several accessions maintained high seed Zn in deficient conditions.
- Taxon
- Arabidopsis thalianaArabidopsis thalianat0
- Material
- several accessionse0
- Outcome
- high seed Zne0
- Qualifier
- Zn-deficient conditionse0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Nevertheless, large natural variance of micronutrient seed levels was identified in the population and several accessions maintained high seed Zn despite growth in Zn-deficient conditions.”
t0“Arabidopsis thaliana”
The same questions in other papers
zinc atom · nutrient: content · Arabidopsis thaliana (thale cress)Positive and negative results
1 paper in the same direction as this paper · 1 in the opposite direction
This paper is about lacking the nutrient, so it counts the other way round here.
- negative
- positive
zinc atom · molecular: expression · Arabidopsis thaliana (thale cress)Positive and negative results
1 paper in the same direction as this paper · 4 in the opposite direction
This paper is about lacking the nutrient, so it counts the other way round here.
- no effect
- no effect
- no effect
2 papers more in this group
See all 6 papers →zinc atom · growth · Arabidopsis thaliana (thale cress)Positive and negative results
5 papers in the same direction as this paper · 1 in the opposite direction
This paper is about lacking the nutrient, so it counts the other way round here.
- positive
- negative
- negative
3 papers more in this group
See all 7 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.