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 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/GN5, GN3/GN3, GN5/GN3, and GN5/GN3. As revealed by GO as well as KEGG enrichment, some ionic and osmotic stress-associated genes, such as , , , , , , , and , had up-regulated levels in GN5 compared with in GN3. In addition, NaCl treatment markedly decreased 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 , , , and in alfalfa roots, suggesting that these nine genes and six lncRNAs probably facilitated the different salinity resistance in GN5 . GN3. These results shed more lights on molecular mechanisms underlying genotype difference in salinity tolerance among alfalfas.