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Transcriptomic analysis of differentially expressed genes in leaves and roots of two alfalfa (Medicago sativa L.) cultivars with different salt tolerance.
BMC Plant Biol. 2021 Oct 05; 21(1):446.BP

Abstract

BACKGROUND

Alfalfa (Medicago sativa L.) production decreases under salt stress. Identification of genes associated with salt tolerance in alfalfa is essential for the development of molecular markers used for breeding and genetic improvement.

RESULT

An RNA-Seq technique was applied to identify the differentially expressed genes (DEGs) associated with salt stress in two alfalfa cultivars: salt tolerant 'Halo' and salt intolerant 'Vernal'. Leaf and root tissues were sampled for RNA extraction at 0 h, 3 h, and 27 h under 12 dS m- 1 salt stress maintained by NaCl. The sequencing generated a total of 381 million clean sequence reads and 84.8% were mapped on to the alfalfa reference genome. A total of 237 DEGs were identified in leaves and 295 DEGs in roots of the two alfalfa cultivars. In leaf tissue, the two cultivars had a similar number of DEGs at 3 h and 27 h of salt stress, with 31 and 49 DEGs for 'Halo', 34 and 50 for 'Vernal', respectively. In root tissue, 'Halo' maintained 55 and 56 DEGs at 3 h and 27 h, respectively, while the number of DEGs decreased from 42 to 10 for 'Vernal'. This differential expression pattern highlights different genetic responses of the two cultivars to salt stress at different time points. Interestingly, 28 (leaf) and 31 (root) salt responsive candidate genes were highly expressed in 'Halo' compared to 'Vernal' under salt stress, of which 13 candidate genes were common for leaf and root tissues. About 60% of DEGs were assigned to known gene ontology (GO) categories. The genes were involved in transmembrane protein function, photosynthesis, carbohydrate metabolism, defense against oxidative damage, cell wall modification and protection against lipid peroxidation. Ion binding was found to be a key molecular activity for salt tolerance in alfalfa under salt stress.

CONCLUSION

The identified DEGs are significant for understanding the genetic basis of salt tolerance in alfalfa. The generated genomic information is useful for molecular marker development for alfalfa genetic improvement for salt tolerance.

Authors+Show Affiliations

Department of Plant Sciences, College of Agriculture and Bioresources, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK, S7N 5A8, Canada.Plant Gene Resources of Canada, Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, S7N 0X2, Canada.Department of Plant Sciences, College of Agriculture and Bioresources, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK, S7N 5A8, Canada.Department of Plant Sciences, College of Agriculture and Bioresources, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK, S7N 5A8, Canada.Canadian Light Source, 44 Innovation Boulevard, Saskatoon, SK, S7N 2V3, Canada.Department of Plant Sciences, College of Agriculture and Bioresources, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK, S7N 5A8, Canada. bill.biligetu@usask.ca.

Pub Type(s)

Comparative Study
Journal Article

Language

eng

PubMed ID

34610811

Citation

Bhattarai, Surendra, et al. "Transcriptomic Analysis of Differentially Expressed Genes in Leaves and Roots of Two Alfalfa (Medicago Sativa L.) Cultivars With Different Salt Tolerance." BMC Plant Biology, vol. 21, no. 1, 2021, p. 446.
Bhattarai S, Fu YB, Coulman B, et al. Transcriptomic analysis of differentially expressed genes in leaves and roots of two alfalfa (Medicago sativa L.) cultivars with different salt tolerance. BMC Plant Biol. 2021;21(1):446.
Bhattarai, S., Fu, Y. B., Coulman, B., Tanino, K., Karunakaran, C., & Biligetu, B. (2021). Transcriptomic analysis of differentially expressed genes in leaves and roots of two alfalfa (Medicago sativa L.) cultivars with different salt tolerance. BMC Plant Biology, 21(1), 446. https://doi.org/10.1186/s12870-021-03201-4
Bhattarai S, et al. Transcriptomic Analysis of Differentially Expressed Genes in Leaves and Roots of Two Alfalfa (Medicago Sativa L.) Cultivars With Different Salt Tolerance. BMC Plant Biol. 2021 Oct 5;21(1):446. PubMed PMID: 34610811.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Transcriptomic analysis of differentially expressed genes in leaves and roots of two alfalfa (Medicago sativa L.) cultivars with different salt tolerance. AU - Bhattarai,Surendra, AU - Fu,Yong-Bi, AU - Coulman,Bruce, AU - Tanino,Karen, AU - Karunakaran,Chithra, AU - Biligetu,Bill, Y1 - 2021/10/05/ PY - 2021/03/18/received PY - 2021/08/31/accepted PY - 2021/10/6/entrez PY - 2021/10/7/pubmed PY - 2021/11/23/medline KW - Alfalfa KW - Differentially expressed genes KW - Salt stress KW - Transcriptome SP - 446 EP - 446 JF - BMC plant biology JO - BMC Plant Biol VL - 21 IS - 1 N2 - BACKGROUND: Alfalfa (Medicago sativa L.) production decreases under salt stress. Identification of genes associated with salt tolerance in alfalfa is essential for the development of molecular markers used for breeding and genetic improvement. RESULT: An RNA-Seq technique was applied to identify the differentially expressed genes (DEGs) associated with salt stress in two alfalfa cultivars: salt tolerant 'Halo' and salt intolerant 'Vernal'. Leaf and root tissues were sampled for RNA extraction at 0 h, 3 h, and 27 h under 12 dS m- 1 salt stress maintained by NaCl. The sequencing generated a total of 381 million clean sequence reads and 84.8% were mapped on to the alfalfa reference genome. A total of 237 DEGs were identified in leaves and 295 DEGs in roots of the two alfalfa cultivars. In leaf tissue, the two cultivars had a similar number of DEGs at 3 h and 27 h of salt stress, with 31 and 49 DEGs for 'Halo', 34 and 50 for 'Vernal', respectively. In root tissue, 'Halo' maintained 55 and 56 DEGs at 3 h and 27 h, respectively, while the number of DEGs decreased from 42 to 10 for 'Vernal'. This differential expression pattern highlights different genetic responses of the two cultivars to salt stress at different time points. Interestingly, 28 (leaf) and 31 (root) salt responsive candidate genes were highly expressed in 'Halo' compared to 'Vernal' under salt stress, of which 13 candidate genes were common for leaf and root tissues. About 60% of DEGs were assigned to known gene ontology (GO) categories. The genes were involved in transmembrane protein function, photosynthesis, carbohydrate metabolism, defense against oxidative damage, cell wall modification and protection against lipid peroxidation. Ion binding was found to be a key molecular activity for salt tolerance in alfalfa under salt stress. CONCLUSION: The identified DEGs are significant for understanding the genetic basis of salt tolerance in alfalfa. The generated genomic information is useful for molecular marker development for alfalfa genetic improvement for salt tolerance. SN - 1471-2229 UR - https://www.unboundmedicine.com/medline/citation/34610811/Transcriptomic_analysis_of_differentially_expressed_genes_in_leaves_and_roots_of_two_alfalfa__Medicago_sativa_L___cultivars_with_different_salt_tolerance_ DB - PRIME DP - Unbound Medicine ER -