Identification and expression analysis of lncRNAs in rice roots (Oryza sativa L.) under elevated CO2 concentration and/or cadmium stress

The gradual rise of CO₂ is one of the global climate changes, Cd stress is also a major abiotic stress factor that affects rice (Oryza sativa L.). The rice seedlings were treated under two CO₂ concentrations and two CdCl₂ concentrations for 7 days (treatments names: 400 ± 20 μmol mol^-1 CO₂ and 0 μmol L^-1 CdCl₂ concentrations, AC; 400 ± 20 μmol mol^-1 CO₂ and 150 μmol L^-1 CdCl₂ concentrations, Cd; 800 ± 20 μmol mol^-1 CO₂ and 0 μmol L^-1 CdCl₂ concentrations, EC; 800 ± 20 μmol mol^-1 CO₂ and 150 μmol L^-1 CdCl₂ concentrations, EC + Cd). The lncRNAs informations were analyzed and excavated using high-throughput sequencing, target genes annotation, and qRT-PCR analysis techniques so as to reveal the regulatory mechanism of lncRNAs in rice roots under high CO₂ concentrations and/or Cd stress. The results show that: (1) 326 (AC vs Cd), 331 (AC vs EC), 343 (AC vs EC + Cd), 112 (Cd vs EC + Cd) DE-lncRNAs were identified. (2) MAPK signaling pathway-plant (relevant genes Os04g0534166, Os05g0399800 regulated by MSTRG.18576.11, MSTRG.20864.1) and diterpenoid biosynthesis (relevant genes Os12g0491800, Os02g0570400 regulated by MSTRG.8965.1, MSTRG.11509.1) were annotated in AC vs Cd; Under EC relative to AC, DE-lncRNAs were annotated significantly to the flavonoid biosynthesis (relevant genes Os10g0196100, Os10g0320100, Os11g0116300, Os03g0819600 regulated by MSTRG.4612.1, MSTRG.4668.1, MSTRG.6051.1, MSTRG.16669.1); Under composite treatments, relative to AC, DE-lncRNAs were mainly annotated in the plant hormone signal transduction pathway (relevant genes Os03g0180800, Os03g0180900, Os03g0181100 regulated by MSTRG.13776.1). Under combined treatment, elevated CO₂ alleviates Cd stress damage by regulating phenylpropanoid biosynthesis through DE-lncRNAs (relevant genes Os09g0419200 regulated by MSTRG. 29,573.1).