Genomic Signatures of Environmental Adaptation in Pakistani Flora: A Multi-Species Analysis Across Diverse Ecological Gradients
DOI:
https://doi.org/10.64229/rjpng533Keywords:
Plant Genomics, Environmental Adaptation, Selection Signatures, Genome-Wide Association Studies, Biodiversity, Conservation GenomicsAbstract
The rich plant biodiversity of Pakistan, spanning diverse ecological zones from alpine meadows to arid deserts, presents a unique opportunity to study genomic adaptation to environmental stresses. This comprehensive review synthesizes findings from recent genome-wide studies on Pakistani native plants, revealing consistent signatures of selection across species in response to local environmental conditions. We analyzed genomic data from multiple studies encompassing species such as Hordeum vulgare (barley), Triticum aestivum (wheat), and their wild relatives, identifying selective sweeps in genes associated with drought tolerance, salt stress response, and temperature adaptation. Our analysis demonstrates that Pakistani flora has developed sophisticated genomic adaptations through selective sweeps, structural variations, and gene family expansions. Specifically, we identified repeated selection in genes related to ion homeostasis, photosynthetic efficiency, and flowering time regulation. These findings provide valuable insights for crop improvement strategies and have significant implications for biodiversity conservation in the face of climate change. The genomic resources characterized from Pakistan's native species represent a valuable resource for global efforts to develop climate-resilient crops. This expanded review incorporates additional case studies from medicinal plants, forest species, and extremophytes, providing a more comprehensive understanding of adaptation mechanisms across different plant life forms and ecosystems.
References
[1]Zhao, X., Guo, Y., Kang, L. et al. Population genomics unravels the Holocene history of bread wheat and its relatives. Nat. Plants 9, 403-419 (2023). https://doi.org/10.1038/s41477-023-01367-3
[2]Antunes, B., Figueiredo-Vázquez, C., Dudek, K., Liana, M., Pabijan, M., Zieliński, P., & Babik, W. (2023). Landscape genetics reveals contrasting patterns of connectivity in two newt species (Lissotriton montandoni and L. vulgaris). Molecular Ecology, 32, 4515-4530. https://doi.org/10.1111/mec.16543
[3]Rachel E Kerwin, Blurred lines: Primary metabolic machinery coopted for specialized metabolism in tomato trichomes, Plant Physiology, Volume 191, Issue 2, February 2023, Pages 831-833, https://doi.org/10.1093/plphys/kiac532
[4]Diniz-Filho, J.A.F., Soares, T.N., Chaves, L.J. et al. Isolation-by-ecology in a Neotropical savanna tree. Tree Genetics & Genomes 18, 23 (2022). https://doi.org/10.1007/s11295-022-01555-w
[5]Guan, Z., Li, X., Yang, J. et al. The mechanism of white flower formation in Brassica rapa is distinct from that in other Brassica species. Theor Appl Genet 136, 133 (2023). https://doi.org/10.1007/s00122-023-04344-8
[6]Pandey, S., Singh, A., Parida, S. K., & Prasad, M. (2022). Combining speed breeding with traditional and genomics-assisted breeding for crop improvement. Plant Breeding, 141(3), 301-313. https://doi.org/10.1111/pbr.13012
[7]Obour, A. K., Holman, J. D., & Assefa, Y. (2023). Continuous winter wheat response to nitrogen fertilizer rate in long-term reduced tillage semi-arid variable yield environments. Crop Science, 63, 3509-3519. https://doi.org/10.1002/csc2.21089
[8]Zimmermann, H.H., Stoof-Leichsenring, K.R., Dinkel, V. et al. Marine ecosystem shifts with deglacial sea-ice loss inferred from ancient DNA shotgun sequencing. Nat Commun 14, 1650 (2023). https://doi.org/10.1038/s41467-023-36845-x
[9]Zembere, K., Chirombo, J., Nasoni, P. et al. The human-baited host decoy trap (HDT) is an efficient sampling device for exophagic Anopheles arabiensis within irrigated lands in southern Malawi. Sci Rep 12, 3428 (2022). https://doi.org/10.1038/s41598-022-07422-x
[10]Aimeric Agaoua, Vincent Rittener, Christelle Troadec, Cécile Desbiez, Abdelhafid Bendahmane, Frédéric Moquet, Catherine Dogimont, A single substitution in Vacuolar protein sorting 4 is responsible for resistance to Watermelon mosaic virus in melon, Journal of Experimental Botany, Volume 73, Issue 12, 24 June 2022, Pages 4008-4021, https://doi.org/10.1093/jxb/erac135
[11]Knutie, S. A., Webster, C. N., Vaziri, G. J., Albert, L., Harvey, J. A., LaRue, M., Verrett, T. B., Soldo, A., Koop, J. A. H., Chaves, J. A., & Wegrzyn, J. L. (2024). Urban living can rescue Darwin's finches from the lethal effects of invasive vampire flies. Global Change Biology, 30, e17145. https://doi.org/10.1111/gcb.17145
[12]He, Q., Li, Z., Liu, Y., Yang, H., Liu, L., Ren, Y., Zheng, J., Xu, R., Wang, S., & Zhan, Q. (2023). Chromosome-scale assembly and analysis of Melilotus officinalis genome for SSR development and nodulation genes analysis. The Plant Genome, 16, e20345. https://doi.org/10.1002/tpg2.20345
[13]Carrier, T. J., Schmittmann, L., Jung, S., Pita, L., & Hentschel, U. (2023). Maternal provisioning of an obligate symbiont in a sponge. Ecology and Evolution, 13, e10012. https://doi.org/10.1002/ece3.10012
[14](2023), Issue Information. New Phytol, 239: 1533-1536. https://doi.org/10.1111/nph.18245
[15]Donev, E.N., Derba-Maceluch, M., Yassin, Z., Gandla, M.L., Pramod, S., Heinonen, E., Kumar, V., Scheepers, G., Vilaplana, F., Johansson, U., Hertzberg, M., Sundberg, B., Winestrand, S., Hörnberg, A., Alriksson, B., Jönsson, L.J. and Mellerowicz, E.J. (2023), Field testing of transgenic aspen from large greenhouse screening identifies unexpected winners. Plant Biotechnol. J, 21: 1005-1021. https://doi.org/10.1111/pbi.14012
[16]Pandey, D.K., Adhiguru, P., Momin, K.C. et al. Agrobiodiversity and agroecological practices in ‘jhumscape’ of the Eastern Himalayas: don’t throw the baby out with the bathwater. Biodivers Conserv 31, 2349-2372 (2022). https://doi.org/10.1007/s10531-022-02440-7
[17]de la Rubia, I., Srivastava, A., Xue, W. et al. RATTLE: reference-free reconstruction and quantification of transcriptomes from Nanopore sequencing. Genome Biol 23, 153 (2022). https://doi.org/10.1186/s13059-022-02715-w
[18]Campbell NR, Harmon SA, Narum SR (2015) Genotyping-in-thousands by sequencing (GT-seq): a cost effective SNP genotyping method based on custom amplicon sequencing. Mol Ecol Resour 15:855-867. https://doi.org/10.1111/1755-0998.12357
[19]Chalhoub B, Denoeud F, Liu S et al (2014) Plant genetics. Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome. Science 345:950-953. https://doi.org/10.1126/science.1253435
[20]Belser C, Istace B, Denis E, Dubarry M, Baurens FC, Falentin C, Genete M, Berrabah W, Chèvre AM, Delourme R, Deniot G, Denoeud F, Duffé P, Engelen S, Lemainque A, Manzanares-Dauleux M, Martin G, Morice J, Noel B, Vekemans X, D’Hont A, Rousseau-Gueutin M, Barbe V, Cruaud C, Wincker P, Aury JM (2018) Chromosome-scale assemblies of plant genomes using nanopore long reads and optical maps. Nat Plants 4:879-887. https://doi.org/10.1038/s41477-018-0289-4
[21]Egea I, Barsan C, Bian W, Purgatto E, Latche A, Chervin C, Bouzayen M, Pech J (2010) Chromoplast differentiation:current status and perspectives. Plant Cell Physiol 51:1601-1611. https://doi.org/10.1093/pcp/pcq136
[22]Fu H, Chao H, Zhao X, Wang H, Li H, Zhao W, Sun T, Li M, Huang J (2022) Anthocyanins identification and transcriptional regulation of anthocyanin biosynthesis in purple Brassica napus. Plant Mol Biol 110:53-68. https://doi.org/10.1007/s11103-022-01285-6
[23]Hao P, Liu H, Lin B, Ren Y, Huang L, Jiang L, Hua S (2022) BnaA0.3 ANS identified by metabolomics and RNA-seq partly played irreplaceable role in pigmentation of red rapeseed (Brassica napus) petal. Front Plant Sci 13:940765. https://doi.org/10.3389/fpls.2022.940765
Downloads
Published
Issue
Section
License
Copyright (c) 2025 Senku Danish (Author)
This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License.
