Transcriptomic and genome-wide association study reveal long noncoding RNAs responding to nitrogen deficiency in maize

BMC Plant Biology

Xiao Zhang¹  Duojiang Gao¹  Haiying Zhang¹  Ling Wu¹  Xuan He¹  Shiqiang Gao¹  Peng Ma¹  Bowen Luo¹  Dan Liu¹  Zhen Chen¹  Binyang Li¹  Suzhi Zhang¹  Shibin Gao² 

[1] Maize Research Institute, Sichuan Agricultural University, 611130, Chengdu, Sichuan, China;Maize Research Institute, Sichuan Agricultural University, 611130, Chengdu, Sichuan, China;State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, 611130, Chengdu, Sichuan, China;

关键词: Maize;    Nitrogen use efficiency;    RNA-Seq;    Genome-wide association study;     LncRNA;    Co-expression;   

DOI  :  10.1186/s12870-021-02847-4

来源: Springer

【 摘 要 】

BackgroundLong noncoding RNAs (lncRNAs) play important roles in essential biological processes. However, our understanding of lncRNAs as competing endogenous RNAs (ceRNAs) and their responses to nitrogen stress is still limited.ResultsHere, we surveyed the lncRNAs and miRNAs in maize inbred line P178 leaves and roots at the seedling stage under high-nitrogen (HN) and low-nitrogen (LN) conditions using lncRNA-Seq and small RNA-Seq. A total of 894 differentially expressed lncRNAs and 38 different miRNAs were identified. Co-expression analysis found that two lncRNAs and four lncRNA-targets could competitively combine with ZmmiR159 and ZmmiR164, respectively. To dissect the genetic regulatory by which lncRNAs might enable adaptation to limited nitrogen availability, an association mapping panel containing a high-density single–nucleotide polymorphism (SNP) array (56,110 SNPs) combined with variable LN tolerant-related phenotypes obtained from hydroponics was used for a genome-wide association study (GWAS). By combining GWAS and RNA-Seq, 170 differently expressed lncRNAs within the range of significant markers were screened. Moreover, 40 consistently LN-responsive genes including those involved in glutamine biosynthesis and nitrogen acquisition in root were identified. Transient expression assays in Nicotiana benthamiana demonstrated that LNC_002923 could inhabit ZmmiR159-guided cleavage of Zm00001d015521.ConclusionsThese lncRNAs containing trait-associated significant SNPs could consider to be related to root development and nutrient utilization. Taken together, the results of our study can provide new insights into the potential regulatory roles of lncRNAs in response to LN stress, and give valuable information for further screening of candidates as well as the improvement of maize resistance to LN stress.

【 授权许可】

CC BY