Comparative transcriptome analysis to identify the important mRNA and lncRNA associated with salinity tolerance in alfalfa.

Salinity represents a fatal factor affecting the productivity of alfalfa. But the regulation of salinity tolerance via lncRNAs and mRNAs remains largely unclear within alfalfa. For evaluating salinity stress resistance-related lncRNAs and mRNAs within alfalfa, we analyzed root transcriptomics in two alfalfa varieties, GN5 (salinity-tolerant) and GN3 (salinity-sensitive), after treatments with NaCl at 0 and 150 mM. There were altogether 117,677 lncRNAs and 172,986 mRNAs detected, including 1,466 lncRNAs and 2,288 mRNAs with significant differential expression in GN5 ₁₅₀ /GN5 ₀ , GN3 ₁₅₀ /GN3 ₀ , GN5 ₀ /GN3 ₀ , and GN5 ₁₅₀ /GN3 ₁₅₀ . As revealed by GO as well as KEGG enrichment, some ionic and osmotic stress-associated genes, such as HPCA1-LRR , PP2C60 , PP2C71 , CRK1 , APX3 , HXK2 , BAG6 , and ARF1 , had up-regulated levels in GN5 compared with in GN3. In addition, NaCl treatment markedly decreased CNGC1 expression in GN5. According to co-expressed network analyses, six lncRNAs (TCONS_00113549, TCONS_00399794, TCONS_00297228, TCONS_00004647, TCONS_00033214 and TCONS_00285177) modulated 66 genes including ARF1 , BAG6 , PP2C71 , and CNGC1 in alfalfa roots, suggesting that these nine genes and six lncRNAs probably facilitated the different salinity resistance in GN5 vs . GN3. These results shed more lights on molecular mechanisms underlying genotype difference in salinity tolerance among alfalfas.
Competing Interests: The authors declare that they have no competing interests.
(© 2024 Yang et al.)