Abstract
Despite advances in genetic engineering for cotton improvement, salt stress severely impacts cotton productivity. Photosynthesis is critical for cotton yield, but this decline is often exacerbated by the growth-defence trade-off under salt stress. Therefore, exploring semi-wild cotton relatives is a promising approach to understand such a trade-off. Here, we examined the growth-defence dilemma in semi-wild cotton genotypes by integrating multi-omics and machine learning (ML)-assisted phenotyping. The ML-assisted physiological screening distinguished 204 as a salt-sensitive genotype and TM-1 as a salt-tolerant genotype, based on leaf gas exchange, biomass production, and whole-plant responses to salt stress. The integrated microRNA-transcriptomics analysis indicated that TM-1 exhibited significant enriched miRNAs and differentially expressed genes (DEGs) in the transcriptional regulation of photosynthesis and carbon fixation, whereas 204 showed a more generalised response to salt stress. Weighted Gene Co-expression Network Analysis (WGCNA) identified three core modules associated with photosynthetic traits, with enriched hub genes in the Calvin cycle ( RUBISCO , FBPase , PGK ) and redox homeostasis ( POD , CYP450 ). Notably, the downregulation of ghr-miR156b, ghr-miR160, ghr-miR164, and ghr-miR166b in TM-1 was consistent with the upregulation of their target genes. However, 204 showed less coordinated regulation with reduced expression of growth-related genes under salt stress. In agreement with these findings, both TM-1 and 204 showed higher antioxidant activities under salt stress, except for the activation of photosynthetic enzymes, which was higher in TM-1 only. Our study indicates a putative regulatory module of hub genes and miRNAs for biotechnological optimisation by potentially reducing growth-defence trade-offs in cotton.
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Claims 12
Claim · model-written summary
TM-1 was classed as a salt-tolerant cotton genotype.
- Taxon
- cotton
Gossypium hirsutumt0 - Material
- TM-1e0
- Outcome
- salt-tolerant genotypee0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“in cotton”
e0“The ML-assisted physiological screening distinguished 204 as a salt-sensitive genotype and TM-1 as a salt-tolerant genotype”
Claim · model-written summary
204 was classed as a salt-sensitive cotton genotype.
- Taxon
- cottonGossypium hirsutumt0
- Material
- 204e0
- Outcome
- salt-sensitive genotypee0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“in cotton”
e0“The ML-assisted physiological screening distinguished 204 as a salt-sensitive genotype and TM-1 as a salt-tolerant genotype”
Claim · model-written summary
TM-1 showed significantly enriched miRNAs and DEGs in the transcriptional regulation of photosynthesis and carbon fixation.
- Taxon
- cottonGossypium hirsutumt0
- Material
- TM-1e1
- Outcome
- transcriptional regulation of photosynthesis and carbon fixatione1
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“in cotton”
e1“TM-1 exhibited significant enriched miRNAs and differentially expressed genes (DEGs) in the transcriptional regulation of photosynthesis and carbon fixation”
Claim · model-written summary
204 showed a more generalised response to salt stress.
- Taxon
- cottonGossypium hirsutumt0
- Material
- 204e2
- Outcome
- generalised response to salt stresse2
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“in cotton”
e2“204 showed a more generalised response to salt stress”
Claim · model-written summary
Three core WGCNA modules were associated with photosynthetic traits in cotton.
- Taxon
- cottonGossypium hirsutumt0
- Gene
- RUBISCOe4
- Outcome
- photosynthetic traitse3
Not reportedDirection
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“in cotton”
e3“identified three core modules associated with photosynthetic traits”
e4“enriched hub genes in the Calvin cycle ( RUBISCO , FBPase , PGK ) and redox homeostasis ( POD , CYP450 )”
Claim · model-written summary
Hub genes RUBISCO, FBPase and PGK were enriched in the Calvin cycle in cotton.
- Taxon
- cottonGossypium hirsutumt0
- Gene
- RUBISCO, FBPase, PGKe4
- Outcome
- enriched hub genes in the Calvin cyclee4
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“in cotton”
e4“enriched hub genes in the Calvin cycle ( RUBISCO , FBPase , PGK ) and redox homeostasis ( POD , CYP450 )”
Claim · model-written summary
Hub genes POD and CYP450 were enriched in redox homeostasis in cotton.
- Taxon
- cottonGossypium hirsutumt0
- Gene
- POD, CYP450e4
- Outcome
- redox homeostasise4
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“in cotton”
e4“enriched hub genes in the Calvin cycle ( RUBISCO , FBPase , PGK ) and redox homeostasis ( POD , CYP450 )”
Claim · model-written summary
In TM-1 the miRNAs ghr-miR156b, ghr-miR160, ghr-miR164 and ghr-miR166b were downregulated, consistent with upregulation of their target genes.
- Taxon
- cottonGossypium hirsutumt0
- Material
- TM-1e6
- Gene
- ghr-miR156b, ghr-miR160, ghr-miR164, and ghr-miR166be6
- Outcome
- target genese6
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“in cotton”
e6“the downregulation of ghr-miR156b, ghr-miR160, ghr-miR164, and ghr-miR166b in TM-1 was consistent with the upregulation of their target genes”
Claim · model-written summary
204 showed reduced expression of growth-related genes under salt stress.
- Taxon
- cottonGossypium hirsutumt0
- Material
- 204e7
- Treatment
- salt stresse7
- Outcome
- expression of growth-related genese7
- Direction
- reducede7
Not reportedComparator
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“in cotton”
e7“204 showed less coordinated regulation with reduced expression of growth-related genes under salt stress”
Claim · model-written summary
TM-1 had higher antioxidant activities under salt stress.
- Taxon
- cottonGossypium hirsutumt0
- Material
- TM-1e7
- Treatment
- salt stresse7
- Outcome
- antioxidant activitiese7
- Direction
- highere7
Not reportedComparator
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“in cotton”
e7“both TM-1 and 204 showed higher antioxidant activities under salt stress”
Claim · model-written summary
204 had higher antioxidant activities under salt stress.
- Taxon
- cottonGossypium hirsutumt0
- Material
- 204e7
- Treatment
- salt stresse7
- Outcome
- antioxidant activitiese7
- Direction
- highere7
Not reportedComparator
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“in cotton”
e7“both TM-1 and 204 showed higher antioxidant activities under salt stress”
Claim · model-written summary
Activation of photosynthetic enzymes was higher in TM-1 than in 204 under salt stress.
- Taxon
- cottonGossypium hirsutumt0
- Material
- TM-1e7
- Treatment
- salt stresse6
- Outcome
- activation of photosynthetic enzymese7
- Direction
- highere7
- Comparator
- 204e6
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“in cotton”
e6“both TM-1 and 204 showed higher antioxidant activities under salt stress”
e7“except for the activation of photosynthetic enzymes, which was higher in TM-1 only”
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See all 20 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.