Genome-wide identification and integrated analysis of lncRNAs in rice backcross introgression lines (BC2F12)

Abstract

Background: Distant hybridization is an important way to create interspecific genetic variation and breed new varieties in rice. A lot of backcross introgression lines (BILs) had been constructed for the scientific issues in rice. However, studies on the critical regulatory factor lncRNA in cultivated rice, wild rice and their BIL progenies were poorly reported. Results: Here, high-throughput RNA sequencing technology was used to explore the functional characteristics and differences of lncRNAs in O. sativa, O. longistaminata and their three BC 2 F 12 progenies. A total of 1254 lncRNAs were screened out, and the number of differentially expressed lncRNAs between progenies and O. sativa were significantly less than that between progenies and O. longistaminata. Some lncRNAs regulated more than one mRNA, and 89.5% of lncRNAs regulated the expression of target genes through cis-acting. A total of 78 lncRNAs and 271 mRNAs were targeted by 280 miRNAs, and 22 lncRNAs were predicted to be the precursor of 20 microRNAs. Some miRNAs were found to target their own potential precursor lncRNAs. Over 50% of lncRNAs showed parental expression level dominance (ELD) in all three progenies, and most lncRNAs showed ELD-O. sativa rather than ELD-O. longistaminata. Further analysis showed that lncRNAs might regulate the expression of plant hormone-related genes and the adaptability of O. sativa, O. longistaminata and their progenies. Conclusions: Taken together, the above results provided valuable clues for elucidating the functional features and expression differences of lncRNAs between O. sativa, O. longistaminata and their BIL progenies, and expanded our understanding about the biological functions of lncRNAs in rice.

Non-coding RNA expression analysis revealed the molecular mechanism of flag leaf heterosis in inter-subspecific hybrid rice

“…In recent years, studies on plant ncRNAs have mainly focused on lncRNAs, circRNAs and miRNAs ( Dou et al, 2017 ; Wang et al, 2018 , 2021c ; Li et al, 2020 ; You et al, 2021 ; Zhou et al, 2021 ). Due to the differences in the sources and functions of these three types of ncRNAs, they play a role in various plant growth and development processes ( Voinnet, 2009 ; Tang and Chu, 2017 ; Zhai et al, 2020 ; Chand Jha et al, 2021 ).…”

“…The overexpression of lncRNA LAIR increases rice grain yield and upregulates some neighboring gene expression ( Wang et al, 2018 ). Parental expression level dominance lncRNAs were identified in rice backcross introgression lines ( Li et al, 2020 ), but lncRNA expression profile and the important role of lncRNA in heterosis formation of inter-subspecific hybrid rice need to be studied.…”

RNA-Seq with a novel glabrous-ZM24fl reveals some key lncRNAs and the associated targets in fiber initiation of cotton

“…NcRNA includes microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and so on, which have emerged as key regulators of gene expression through their direct and indirect actions on chromatin [23][24][25]. In Oryza sativa, 1,254 differentially expressed lncRNAs (DELs) were identified from BIL progenies [26]. Another RNA-Seq showed that 328 of 444 DELs were associated with meiosis and the low fertility in autotetraploid rice [27].…”

Genome-Wide Identification and Characterization of Potato Long Non-coding RNAs Associated With Phytophthora infestans Resistance

“…Based on their genomic location, lncRNAs are classified into three major categories, including long intergenic non-coding RNA (lincRNA), long non-coding natural antisense transcripts, and long intronic non-coding RNA ( Cui et al, 2017 ). The functional roles of lncRNAs in plants are increasingly being unraveled, and a number of various reports associated with identification of lncRNAs in multiple plant species ( Wang and Chekanova, 2017 ), including Zea mays ( Li et al, 2014 ; Kim et al, 2019 ), Solanum lycopersicum ( Cui et al, 2020 ), Arachis hypogaea ( Zhao et al, 2019 ; Tian et al, 2020 ), Oryza sativa ( Li et al, 2020 ), Populus ( Ma et al, 2019 ), and Arabidopsis thaliana ( Zhao et al, 2018 ), have been published. However, most experimental proofs focus on the functions of lncRNAs associated with plant development and abiotic stress responses, such as fruit ripening ( Li et al, 2018 ; Yu et al, 2019 ), growth ( Meng et al, 2018 ; Wang Y. et al, 2018 ), nutritional stimulation ( Wang et al, 2017 ), and salt and drought stresses ( Qin et al, 2017 ).…”