Abstract
Molecular links between miRNA: target modules regulating downstream genes for crop maturation/yield are poorly understood. Here, we report that elevated miR169d expression and concomitant reduced NF-YA2 (Nuclear Factor-Y subunit-A) target levels positively regulate vegetative growth and yield in Arabidopsis along with a shorter life cycle. In agreement, increased NF-YA2 levels in (1) NF-YA2-OE (overexpression) lines, (2) miR169d-target-mimicry lines (in which miR169d is chelated), and (3) miR169d-non-cleavable NF-YA2 resistant target lines show the opposite phenotype. Further, we find increased auxin levels in MIR169d-OE and nf-ya2 mutant lines, supporting the enrichment of 'auxin terms' in MIR169-OE transcriptome data. We show that ARGOS (auxin-regulated gene involved in organ size) is upregulated in MIR169d-OE due to reduced NF-YA2 repressor levels and that NF-YA2 directly binds the ARGOS promoter. Genetic screens of this module show that neither overexpressing miR169d in an argos mutant background nor the nf-ya2:argos double mutants rescue the argos mutant phenotype, suggesting a parallel pathway of ARGOS regulation via the MIR169:NF-YA2 node, independent of auxin. To assess the translational potential of this module in a crop, we show that Sly-MIR169-OE lines in tomato, having reduced target Sly-NF-YA10 levels, also regulate Sly-ARGOS resulting in early flowering, larger sized fruits, more fruit fresh weight, higher fruit set, early fruiting, and better shelf life than wild-type plants. In contrast, Sly-STTM169 plants inhibited for Sly-miR169 action and having increased levels of Sly-NF-YA10 have a longer life cycle with reduced biomass, decreased fruit set, and an overall reduction in yield. Thus, our findings show a conserved MIR169:NF-YA:ARGOS module which can be applied to crops for addressing future food demands.
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Claims 17
Claim · model-written summary
Elevated miR169d expression with reduced NF-YA2 target levels positively regulates vegetative growth and yield in Arabidopsis.
- Taxon
- Arabidopsis
Arabidopsise1 - Treatment
- elevated miR169d expressione1
- Gene
- NF-YA2e1
- Outcome
- vegetative growth and yielde1
- Direction
- positively regulatee1
- Qualifier
- shorter life cyclee1
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e1“elevated miR169d expression and concomitant reduced NF-YA2 (Nuclear Factor-Y subunit-A) target levels positively regulate vegetative growth and yield in Arabidopsis along with a shorter life cycle”
Claim · model-written summary
Lines with increased NF-YA2 levels show the opposite phenotype to miR169d-overexpressing lines.
- Taxon
- ArabidopsisArabidopsise1
- Material
- NF-YA2-OE (overexpression) linese2
- Treatment
- increased NF-YA2 levelse2
- Gene
- NF-YA2e2
- Outcome
- phenotypee2
- Direction
- oppositee2
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e1“elevated miR169d expression and concomitant reduced NF-YA2 (Nuclear Factor-Y subunit-A) target levels positively regulate vegetative growth and yield in Arabidopsis along with a shorter life cycle”
e2“In agreement, increased NF-YA2 levels in (1) NF-YA2-OE (overexpression) lines, (2) miR169d-target-mimicry lines (in which miR169d is chelated), and (3) miR169d-non-cleavable NF-YA2 resistant target lines show the opposite phenotype”
Claim · model-written summary
Auxin levels are increased in MIR169d-OE and nf-ya2 mutant lines.
- Taxon
- ArabidopsisArabidopsise1
- Material
- MIR169d-OEe3
- Compound
- auxine3
- Outcome
- auxin levelse3
- Direction
- increasede3
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e1“elevated miR169d expression and concomitant reduced NF-YA2 (Nuclear Factor-Y subunit-A) target levels positively regulate vegetative growth and yield in Arabidopsis along with a shorter life cycle”
e3“we find increased auxin levels in MIR169d-OE and nf-ya2 mutant lines”
Claim · model-written summary
ARGOS is upregulated in MIR169d-OE lines due to reduced NF-YA2 repressor levels.
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e1“elevated miR169d expression and concomitant reduced NF-YA2 (Nuclear Factor-Y subunit-A) target levels positively regulate vegetative growth and yield in Arabidopsis along with a shorter life cycle”
e4“ARGOS (auxin-regulated gene involved in organ size) is upregulated in MIR169d-OE due to reduced NF-YA2 repressor levels”
Claim · model-written summary
NF-YA2 directly binds the ARGOS promoter.
- Taxon
- ArabidopsisArabidopsise1
- Gene
- NF-YA2e5
- Outcome
- directly binds the ARGOS promotere5
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e1“elevated miR169d expression and concomitant reduced NF-YA2 (Nuclear Factor-Y subunit-A) target levels positively regulate vegetative growth and yield in Arabidopsis along with a shorter life cycle”
e5“NF-YA2 directly binds the ARGOS promoter”
Claim · model-written summary
Overexpressing miR169d in an argos mutant background does not rescue the argos mutant phenotype, and nf-ya2:argos double mutants do not either.
- Taxon
- ArabidopsisArabidopsise1
- Treatment
- overexpressing miR169d in an argos mutant backgrounde6
- Gene
- nf-ya2:argose6
- Outcome
- argos mutant phenotypee6
- Direction
- rescuee6
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e1“elevated miR169d expression and concomitant reduced NF-YA2 (Nuclear Factor-Y subunit-A) target levels positively regulate vegetative growth and yield in Arabidopsis along with a shorter life cycle”
e6“neither overexpressing miR169d in an argos mutant background nor the nf-ya2:argos double mutants rescue the argos mutant phenotype”
Claim · model-written summary
The data suggest a parallel, auxin-independent pathway of ARGOS regulation via the MIR169:NF-YA2 node.
- Taxon
- ArabidopsisArabidopsise1
- Gene
- MIR169:NF-YA2e7
- Outcome
- parallel pathway of ARGOS regulatione7
- Qualifier
- independent of auxine7
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e1“elevated miR169d expression and concomitant reduced NF-YA2 (Nuclear Factor-Y subunit-A) target levels positively regulate vegetative growth and yield in Arabidopsis along with a shorter life cycle”
e7“suggesting a parallel pathway of ARGOS regulation via the MIR169:NF-YA2 node, independent of auxin”
Claim · model-written summary
Sly-MIR169-OE tomato lines flower early.
- Taxon
- tomato
Solanum lycopersicume1 - Material
- Sly-MIR169-OE linese1
- Treatment
- reduced target Sly-NF-YA10 levelse1
- Gene
- Sly-ARGOSe1
- Outcome
- floweringe1
- Direction
- earlye1
- Comparator
- wild-type plantse1
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e1“Sly-MIR169-OE lines in tomato, having reduced target Sly-NF-YA10 levels, also regulate Sly-ARGOS resulting in early flowering, larger sized fruits, more fruit fresh weight, higher fruit set, early fruiting, and better shelf life than wild-type plants”
Claim · model-written summary
Sly-MIR169-OE tomato lines fruit early.
- Taxon
- tomatoSolanum lycopersicume1
- Material
- Sly-MIR169-OE linese1
- Treatment
- reduced target Sly-NF-YA10 levelse1
- Gene
- Sly-ARGOSe1
- Outcome
- fruitinge1
- Direction
- earlye1
- Comparator
- wild-type plantse1
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e1“Sly-MIR169-OE lines in tomato, having reduced target Sly-NF-YA10 levels, also regulate Sly-ARGOS resulting in early flowering, larger sized fruits, more fruit fresh weight, higher fruit set, early fruiting, and better shelf life than wild-type plants”
Claim · model-written summary
Sly-MIR169-OE tomato lines have more fruit fresh weight than wild-type plants.
- Taxon
- tomatoSolanum lycopersicume1
- Material
- Sly-MIR169-OE linese1
- Treatment
- reduced target Sly-NF-YA10 levelse1
- Gene
- Sly-ARGOSe1
- Outcome
- fruit fresh weighte1
- Direction
- moree1
- Comparator
- wild-type plantse1
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e1“Sly-MIR169-OE lines in tomato, having reduced target Sly-NF-YA10 levels, also regulate Sly-ARGOS resulting in early flowering, larger sized fruits, more fruit fresh weight, higher fruit set, early fruiting, and better shelf life than wild-type plants”
Claim · model-written summary
Sly-MIR169-OE tomato lines produce larger sized fruits than wild-type plants.
- Taxon
- tomatoSolanum lycopersicume1
- Material
- Sly-MIR169-OE linese1
- Treatment
- reduced target Sly-NF-YA10 levelse1
- Gene
- Sly-ARGOSe1
- Outcome
- larger sized fruitse1
- Direction
- larger sizede1
- Comparator
- wild-type plantse1
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e1“Sly-MIR169-OE lines in tomato, having reduced target Sly-NF-YA10 levels, also regulate Sly-ARGOS resulting in early flowering, larger sized fruits, more fruit fresh weight, higher fruit set, early fruiting, and better shelf life than wild-type plants”
Claim · model-written summary
Sly-MIR169-OE tomato lines have higher fruit set than wild-type plants.
- Taxon
- tomatoSolanum lycopersicume1
- Material
- Sly-MIR169-OE linese1
- Treatment
- reduced target Sly-NF-YA10 levelse1
- Gene
- Sly-ARGOSe1
- Outcome
- fruit sete1
- Direction
- highere1
- Comparator
- wild-type plantse1
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e1“Sly-MIR169-OE lines in tomato, having reduced target Sly-NF-YA10 levels, also regulate Sly-ARGOS resulting in early flowering, larger sized fruits, more fruit fresh weight, higher fruit set, early fruiting, and better shelf life than wild-type plants”
Claim · model-written summary
Sly-MIR169-OE tomato lines have better shelf life than wild-type plants.
- Taxon
- tomatoSolanum lycopersicume1
- Material
- Sly-MIR169-OE linese1
- Treatment
- reduced target Sly-NF-YA10 levelse1
- Gene
- Sly-ARGOSe1
- Outcome
- shelf lifee1
- Direction
- bettere1
- Comparator
- wild-type plantse1
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e1“Sly-MIR169-OE lines in tomato, having reduced target Sly-NF-YA10 levels, also regulate Sly-ARGOS resulting in early flowering, larger sized fruits, more fruit fresh weight, higher fruit set, early fruiting, and better shelf life than wild-type plants”
Claim · model-written summary
Sly-STTM169 tomato plants with increased Sly-NF-YA10 have a longer life cycle.
- Taxon
- tomatoSolanum lycopersicume1
- Material
- Sly-STTM169 plantse2
- Treatment
- increased levels of Sly-NF-YA10e2
- Outcome
- life cyclee2
- Direction
- longere2
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e1“Sly-MIR169-OE lines in tomato, having reduced target Sly-NF-YA10 levels, also regulate Sly-ARGOS resulting in early flowering, larger sized fruits, more fruit fresh weight, higher fruit set, early fruiting, and better shelf life than wild-type plants”
e2“In contrast, Sly-STTM169 plants inhibited for Sly-miR169 action and having increased levels of Sly-NF-YA10 have a longer life cycle with reduced biomass, decreased fruit set, and an overall reduction in yield”
Claim · model-written summary
Sly-STTM169 tomato plants have reduced biomass.
- Taxon
- tomatoSolanum lycopersicume1
- Material
- Sly-STTM169 plantse2
- Treatment
- increased levels of Sly-NF-YA10e2
- Outcome
- biomasse2
- Direction
- reducede2
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e1“Sly-MIR169-OE lines in tomato, having reduced target Sly-NF-YA10 levels, also regulate Sly-ARGOS resulting in early flowering, larger sized fruits, more fruit fresh weight, higher fruit set, early fruiting, and better shelf life than wild-type plants”
e2“In contrast, Sly-STTM169 plants inhibited for Sly-miR169 action and having increased levels of Sly-NF-YA10 have a longer life cycle with reduced biomass, decreased fruit set, and an overall reduction in yield”
Claim · model-written summary
Sly-STTM169 tomato plants have decreased fruit set.
- Taxon
- tomatoSolanum lycopersicume1
- Material
- Sly-STTM169 plantse2
- Treatment
- increased levels of Sly-NF-YA10e2
- Outcome
- fruit sete2
- Direction
- decreasede2
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e1“Sly-MIR169-OE lines in tomato, having reduced target Sly-NF-YA10 levels, also regulate Sly-ARGOS resulting in early flowering, larger sized fruits, more fruit fresh weight, higher fruit set, early fruiting, and better shelf life than wild-type plants”
e2“In contrast, Sly-STTM169 plants inhibited for Sly-miR169 action and having increased levels of Sly-NF-YA10 have a longer life cycle with reduced biomass, decreased fruit set, and an overall reduction in yield”
Claim · model-written summary
Sly-STTM169 tomato plants show an overall reduction in yield.
- Taxon
- tomatoSolanum lycopersicume1
- Material
- Sly-STTM169 plantse2
- Treatment
- increased levels of Sly-NF-YA10e2
- Outcome
- yielde2
- Direction
- reductione2
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e1“Sly-MIR169-OE lines in tomato, having reduced target Sly-NF-YA10 levels, also regulate Sly-ARGOS resulting in early flowering, larger sized fruits, more fruit fresh weight, higher fruit set, early fruiting, and better shelf life than wild-type plants”
e2“In contrast, Sly-STTM169 plants inhibited for Sly-miR169 action and having increased levels of Sly-NF-YA10 have a longer life cycle with reduced biomass, decreased fruit set, and an overall reduction in yield”