Universität zu Köln

Khan, Abdul Saboor ORCID: 0000-0001-7924-7986 (2025). Comparative analysis of abiotic stress responses in closely related Arabis species. PhD thesis, Universität zu Köln.

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Abstract

Abiotic stresses, such as submergence and drought, present major challenges to plant survival in extreme environments. This study examines the physiological and molecular responses of floodplain species Arabis nemorensis and Arabis sagittata to water-related stresses, aiming to identify key mechanisms underlying resilience and adaptation. Drought stress imposes severe constraints on plant survival, necessitating adaptive strategies for water conservation and stress tolerance. In a controlled dry-down experiment, A. sagittata exhibited higher recovery rates (90% vs. 50%) at a soil water content of 5% compared to A. nemorensis. Gene expression analysis revealed 2825 upregulated and 2746 downregulated genes in A. nemorensis, and 3236 upregulated and 3123 downregulated genes in A. sagittata in drought stress. A. sagittata had a stronger transcriptional response, with significantly stronger upregulation of genes related to water deprivation, cellular response to hypoxia, red/far red light, and other stress-responsive signaling functions. A. sagittata showed stronger response with significant upregulation of starch metabolism in recovery. In contrast, A. nemorensis prioritized translation, ribosomal biogenesis, and chloroplast organization in stress and cytoplasmic translation in recovery. Using machine-learning based methods to identify the sequence motifs that effectively predict gene expression level, we identify 307 sequence motifs specific from each species and/or stress conditions. The distribution of these motifs not only reveal that the two species activate a network of different responses, but also identifies an array of candidate regulatory factors whose targets are enriched among genes that respond differentially to drought stress in each species. Unlike drought stress, under submergence stress both Arabis species exhibited marked resilience, with an 85% mean survival rate after six weeks of submergence, in contrast to A. thaliana, which dies in less than two weeks under similar conditions. A comparative molecular analysis of A. nemorensis, A. sagittata, contrasted with A. thaliana following a one-week submergence revealed 4775 upregulated and 4637 downregulated genes in A. nemorensis, 4788 up and 4518 down in A. sagittata, and 5079 up and 4373 down in A. thaliana. We first showed that both A. sagittata and A. nemorensis shared common molecular response to submergence stress with activation of protein ubiquitination, cellular response to oxygen-containing compound, hormone-mediated signaling pathway, reflecting processes involved in cellular reorganization and reproductive development. Compared to A. sagittata, the genes up-regulated in response to submergence in A. thaliana were enriched in ethylene-activated signaling and transport. In contrast, A. sagittata activated genes in starch biosynthetic process, mRNA cis splicing and embyo developments, supporting energy maintenance, developmemt and detoxification. Compared to A. nemorensis, A. thaliana upregulated genes associated with defense response, and transport, while A. nemorensis showed strong transcriptional activity in mRNA splicing, and chloroplast processing. miRNA analysis highlighted significant differential expression of miR408, a known regulator of oxidative stress and ABA signaling, in A. sagittata during drought stress and in A. thaliana during submergence stress. Notably, a 6 kb insertion upstream of miR408 in A. nemorensis was identified, potentially influencing its expression. Further genotyping of an F4 Arabis population revealed that miR408 is linked to a segregation distortion region on chromosome 4, suggesting that genetic hitchhiking might be driving its fixation in populations where the two species hybridize. All in all, our findings reveal divergent survival strategies in these closely related species, with A. sagittata exhibiting stronger drought tolerance through transcriptional and metabolic flexibility, while both Arabis species show superior post-submergence recovery. The association of miR408 with segregation distortion highlights its potential evolutionary significance in shaping adaptive traits in these species that are known to hybridize naturally. These new understandings enhance our knowledge of plant survival strategies in fluctuating floodplain environments and establish the Arabis genus as a valuable non-model plant for studying drought and submergence tolerance.

Item Type:	Thesis (PhD thesis)
Creators:	Creators Email ORCID ORCID Put Code Khan, Abdul Saboor abdul.suboor123@yahoo.com orcid.org/0000-0001-7924-7986 UNSPECIFIED
URN:	urn:nbn:de:hbz:38-787322
Date:	2025
Language:	English
Faculty:	Faculty of Mathematics and Natural Sciences
Divisions:	Faculty of Mathematics and Natural Sciences > Department of Biology > Botanical Institute
Subjects:	Natural sciences and mathematics
Uncontrolled Keywords:	Keywords Language drought stress, submergence stress, Arabis sagittata, Arabis nemorensis, gene expression, miRNA408, structural equation modeling, recovery, segregation distortion English
Date of oral exam:	26 June 2025
Referee:	Name Academic Title de Meaux, Juliette Professor
Refereed:	Yes
URI:	http://kups.ub.uni-koeln.de/id/eprint/78732