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Abstract Rice, an important food resource, is highly sensitive to salt stress, which is directly related to food security. Although many studies have identified physiological mechanisms that confer tolerance to the osmotic effects of salinity, the link between rice genotype and salt tolerance is not very clear yet. Association of gene co‐expression network and rice phenotypic data under stress has penitential to identify stress‐responsive genes, but there is no standard method to associate stress phenotype with gene co‐expression network. A novel method for integration of gene co‐expression network and stress phenotype data was developed to conduct a system analysis to link genotype to phenotype. We applied aLASSO‐based method to the gene co‐expression network of rice with salt stress to discover key genes and their interactions for salt tolerance‐related phenotypes. Submodules in gene modules identified from the co‐expression network were selected by theLASSOregression, which establishes a linear relationship between gene expression profiles and physiological responses, that is, sodium/potassium condenses under salt stress. Genes in these submodules have functions related to ion transport, osmotic adjustment, and oxidative tolerance. We argued that these genes in submodules are biologically meaningful and useful for studies on rice salt tolerance. This method can be applied to other studies to efficiently and reliably integrate co‐expression network and phenotypic data.
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This content will become publicly available on June 1, 2026
Constitutive Differences in Immune Gene Expression Are Correlated With Wood Frog Populations From Contrasting Winter Environments
ABSTRACT Many terrestrial ectotherms have gone to great evolutionary lengths to adapt to long cold winters; some have even evolved the ability to tolerate the freezing of most of the extracellular fluid in the body. Now, however, high‐elevation and high‐latitude winters are experiencing an accelerated period of warming. Specialised winter adaptations that promoted fitness in a seasonally frozen environment may soon be superfluous or even maladaptive. We ask whether winter adaptations include changes in immune functions, and whether changing winter conditions could exert disparate effects on populations of a wide‐ranging terrestrial ectotherm, the wood frog (Lithobates sylvaticus). By rearing wood frogs from ancestral winter environments that vary in length and temperature in a common garden, and reciprocally exposing post‐metamorphic frogs to unfrozen and frozen artificial winter conditions in the lab, we were able to decompose transcriptomic differences in ventral skin gene expression into those that were environmentally induced (responsive to temperature) and genetically determined and those that varied as an interaction between the genotype and environment. We found that frogs from harsh ancestral winter environments constitutively upregulated immune processes, including cellular immunity, inflammatory processes and adaptive immune processes, as compared to frogs from mild ancestral winter environments. Further, we saw that the expression of several genes varied in an interaction between the genotype and artificial winter. We suggest that just as winter climates likely served as the selective force resulting in remarkable winter adaptations such as freeze tolerance, they may have also induced constitutive changes in immune gene expression.
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- PAR ID:
- 10646993
- Publisher / Repository:
- Molecular Ecology
- Date Published:
- Journal Name:
- Molecular Ecology
- Volume:
- 34
- Issue:
- 12
- ISSN:
- 0962-1083
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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