Identification and Functional Prediction of Salt/Alkali-Responsive lncRNAs during Alfalfa Germination

Yajiao Liu, Lei Xu, Tiejun Zhang, Bilig Sod, Yanchao Xu, Mingna Li, Junmei Kang, Qingchuan Yang, Xiao Li () and Ruicai Long ()
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Yajiao Liu: School of Grassland Science, Beijing Forestry University, Beijing 100083, China
Lei Xu: Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
Tiejun Zhang: School of Grassland Science, Beijing Forestry University, Beijing 100083, China
Bilig Sod: Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
Yanchao Xu: Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
Mingna Li: Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
Junmei Kang: Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
Qingchuan Yang: Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
Xiao Li: School of Grassland Science, Beijing Forestry University, Beijing 100083, China
Ruicai Long: Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China

Agriculture, 2024, vol. 14, issue 6, 1-18

Abstract: Long non-coding RNAs (lncRNAs) are pivotal regulators of the abiotic stress responses in plants, yet their specific involvement in salt/alkali stress during alfalfa germination remains incompletely understood. Here, we subjected Zhongmu No.1 alfalfa ( Medicago sativa L.) seeds to salt stress (20 mM NaCl and 20 mM Na 2 SO 4 solutions) or alkali stress (5 mM NaHCO 3 and 5 mM Na 2 CO 3 solutions) treatments for 3 days, followed by total RNA extraction and RNA-seq analysis to delineate stress-responsive alfalfa lncRNAs. We identified 17,473 novel alfalfa lncRNAs, among which 101 and 123 were differentially expressed lncRNAs (DElncRNAs) under salt and alkali stress, respectively, compared to the control. Furthermore, we predicted 16 and 237 differentially expressed target genes regulated by DElncRNAs through cis / trans -regulatory mechanisms under salt or alkali stress, respectively. A functional enrichment analysis of DElncRNA target genes indicated that lncRNAs were implicated in the fatty acid metabolism pathway under salt stress, while they played a significant role in the phenylpropanoid and flavonoid biosynthesis pathway under alkali stress. Notably, lncRNAs were found to participate in the plant hormone signal transduction pathway, a common regulatory mechanism in both salt and alkali stress responses. These findings contribute to a deeper understanding of the mechanisms underlying alfalfa’s response to salt and alkali stresses.

Keywords: alkali stress; long non-coding RNA; Medicago sativa; regulatory mechanism; salt stress; target genes (search for similar items in EconPapers)
JEL-codes: Q1 Q10 Q11 Q12 Q13 Q14 Q15 Q16 Q17 Q18 (search for similar items in EconPapers)
Date: 2024
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