Abstract
Background
Long-intergenic non-coding RNAs (lincRNAs) originate from intergenic regions and have no coding potential. LincRNAs have emerged as key players in the regulation of various biological processes in plant development. Cytoplasmic male-sterility (CMS) in association with restorer-of-fertility (Rf) systems makes it a highly reliable tool for exploring heterosis for producing commercial hybrid seeds. To date, there have been no reports of lincRNAs during pollen development in CMS and fertility restorer lines in pigeon pea.
Objective
Identification of lincRNAs in the floral buds of cytoplasmic male-sterile (AKCMS11) and fertility restorer (AKPR303) pigeon pea lines.
Methods
We employed a computational approach to identify lincRNAs in the floral buds of cytoplasmic male-sterile (AKCMS11) and fertility restorer (AKPR303) pigeon pea lines using RNA-Seq data.
Results
We predicted a total of 2145 potential lincRNAs of which 966 were observed to be differentially expressed between the sterile and fertile pollen. We identified, 927 cis-regulated and 383 trans-regulated target genes of the lincRNAs. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of the target genes revealed that these genes were specifically enriched in pathways like pollen and pollen tube development, oxidative phosphorylation, etc. We detected 23 lincRNAs that were co-expressed with 17 pollen-related genes with known functions. Fifty-nine lincRNAs were predicted to be endogenous target mimics (eTMs) for 25 miRNAs, and found to be associated with pollen development. The, lincRNA regulatory networks revealed that different lincRNA-miRNA-mRNA networks might be associated with CMS and fertility restoration.
Conclusion
Thus, this study provides valuable information by highlighting the functions of lincRNAs as regulators during pollen development in pigeon pea and utilization in hybrid seed production.
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Data availability
Publically available datasets were analyzed in this study. This data can be found here: National Centre for Biotechnology Information (NCBI) SRA database (SRX3740150, SRX3740151, SRX3740153 and SRX3740152). Following is the reviewer’s link as generated by NCBI http://www.ncbi.nlm.nih.gov/sra/SRX3740153[accn]; http://www.ncbi.nlm.nih.gov/sra/SRX3740152[accn]; http://www.ncbi.nlm.nih.gov/sra/SRX3740151[accn]; http://www.ncbi.nlm.nih.gov/sra/SRX3740150[accn].
Abbreviations
- AL:
-
ALFIN-LIKE
- ARF:
-
Auxin responsive factor
- BG:
-
β-Glucosidase
- bp:
-
Base pair
- cDNA:
-
Complementary DNA
- CMS:
-
Cytoplasmic male-sterility
- CNCI:
-
Coding non-coding index
- COG:
-
Clusters of Orthologous Groups
- COLDAIR:
-
Cold assisted intronic noncoding RNA
- COOLAIR:
-
Cold induced long antisense intragenic RNA
- CPC:
-
Coding potential calculator
- DE:
-
Differentially expressed
- EMS:
-
Excess microsporocytes
- ERF:
-
Ethylene-responsive factor
- eTMs:
-
Endogenous target mimics
- FC:
-
Fold change
- FDR:
-
False discovery rate
- FLC:
-
Flowering locus C
- FPKM:
-
Fragments per kilo base per million
- GMS:
-
Genic male-sterility
- GNL1:
-
GNOM-LIKE1
- GNL2:
-
GNOM-LIKE2
- GO:
-
Gene Ontology
- GST:
-
Glutathione S-transferase
- IPS1:
-
Induced by phosphate starvation
- KEGG:
-
Kyoto encyclopedia of genes and genomes
- LDMAR:
-
Long day specific male fertility associated RNA
- lincRNA:
-
Long-intergenic non-coding RNAs
- lncRNAs:
-
Long non-coding RNAs
- LRR-RPK:
-
Leucine-rich repeat receptor protein kinase
- miRNAs:
-
MicroRNAs
- NCBI:
-
National centre for biotechnology information
- ncRNAs:
-
Non-coding RNAs
- Nr:
-
NCBI non-redundant protein
- nt:
-
Nucleotide(s)
- ORF:
-
Open reading frame
- PCR:
-
Polymerase chain reaction
- PHD:
-
Plant HomeoDomain
- pol II:
-
RNA polymerase II
- pol III:
-
RNA polymerase III
- pol IV:
-
RNA polymerase IV
- pol V:
-
RNA polymerase V
- PPR:
-
Pentatricopeptide-repeat protein
- qRT-PCR:
-
Quantitative real-time PCR
- Rbohs:
-
Respiratory burst oxidase homologs
- Rf:
-
Restorer-of-fertility
- ROS:
-
Reactive oxygen species
- rRNAs:
-
Ribosomal RNAs
- siRNAs:
-
Small interfering RNAs
- sncRNAs:
-
Small non-coding RNAs
- snoRNAs:
-
Small nucleolar RNAs
- SPL:
-
Squamosa promoter-binding-like
- TF's:
-
Transcription factors
- tRNAs:
-
Transfer RNAs
- UBC:
-
Ubiquitin-conjugating enzyme
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The authors are grateful to the Director, ICAR- National Institute for Plant Biotechnology (NIPB), New Delhi, India for providing the facilities. The authors also thank the other members of our research groups and collaborators for technical assistance and discussions.
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This work was supported by grants from Department of Science & Technology (DST), New Delhi, India under Women Scientist Scheme-A (WOS-A) and ICAR-National Institute for Plant Biotechnology, New Delhi, India.
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SS: methodology, formal analysis, investigation, fund acquisition and writing (original draft). AD: methodology, software, formal analysis, reviewing and editing. TK: reviewing and editing. GR: resources. SS: reviewing and editing. KG: conceptualization, methodology, funding acquisition and supervision. All authors read and approved the final manuscript.
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Saxena, S., Das, A., Kaila, T. et al. Genomic survey of high-throughput RNA-Seq data implicates involvement of long intergenic non-coding RNAs (lincRNAs) in cytoplasmic male-sterility and fertility restoration in pigeon pea. Genes Genom 45, 783–811 (2023). https://doi.org/10.1007/s13258-023-01383-9
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DOI: https://doi.org/10.1007/s13258-023-01383-9