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 <i>via</i> 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 GN5₁₅₀/GN5₀, GN3₁₅₀/GN3₀, GN5₀/GN3₀, and GN5₁₅₀/GN3₁₅₀. As revealed by GO as well as KEGG enrichment, some ionic and osmotic stress-associated genes, such as <i>HPCA1-LRR</i>, <i>PP2C60</i>, <i>PP2C71</i>, <i>CRK1</i>, <i>APX3</i>, <i>HXK2</i>, <i>BAG6</i>, and <i>ARF1</i>, had up-regulated levels in GN5 compared with in GN3. In addition, NaCl treatment markedly decreased <i>CNGC1</i> 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 <i>ARF1</i>, <i>BAG6</i>, <i>PP2C71</i>, and <i>CNGC1</i> in alfalfa roots, suggesting that these nine genes and six lncRNAs probably facilitated the different salinity resistance in GN5 <i>vs</i>. GN3. These results shed more lights on molecular mechanisms underlying genotype difference in salinity tolerance among alfalfas.