Genome-Wide Identification and Posttranscriptional Regulation Analyses Elucidate Roles of Key Argonautes and Their miRNA Triggers in Regulating Complex Yield Traits in Rapeseed
Abstract
:1. Introduction
2. Results
2.1. Genome-Wide Prediction, Phylogenetic Analysis, and Nomenclature of AGO Genes
2.2. Protein Profiles, Gene Structure and Conserved Motif Analysis of the 24 BnaAGOs
2.3. Differential Expression of 24 BnaAGOs among Differently Yielding B. napus Cultivars
2.4. MiRNA-Mediated Posttranscriptional Regulation of the BnaAGOs
2.5. miRNA-Seq and mRNA-Seq Analysis of miR168a–AGO1s and miR403–AGO2s in Differentially Yielding B. napus Materials
3. Discussion
3.1. Genome-Wide Identification, Phylogenetic Analysis of AGOs, and Their miRNA Triggers
3.2. Diversity and Conservation of the 24 BnaAGOs
3.3. Posttranscriptional Regulation by the B. napus miRNA–AGOs and the Future Regulation of Yield-Related Traits
4. Materials and Methods
4.1. Genome-Wide Prediction of AGOs and Their miRNA Triggers
4.2. Chromosomal Location, Gene Structure and Protein Properties
4.3. Identification of B. napus miRNAs with Perfect Complementarity to the BnaAGOs
4.4. Plant Materials
4.5. miRNA-Seq and mRNA-Seq Analysis among Multiple Yield-Related Materials
4.6. RNA Extraction and qRT-PCR Verification
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Gene Name | A. thaliana | B. rapa | B. naus (A) | B. oleracea | B. naus (C) |
---|---|---|---|---|---|
Zero-copy in B. napus | |||||
AGO3 | 1 | 0 | 0 | 0 | 0 |
AGO8 | 1 | 0 | 0 | 0 | 0 |
Two-copy in B. napus | |||||
AGO5 | 1 | 1 | 1 | 1 | 1 |
AGO10 | 1 | 1 | 1 | 1 | 1 |
AGO6 | 1 | 1 | 1 | 1 | 1 |
Three-copy in B. napus | |||||
AGO7 | 1 | 1 | 1 | 2 | 2 |
AGO9 | 1 | 2 | 2 | 2 | 1 |
Four-copy in B. napus | |||||
AGO1 | 1 | 2 | 2 | 2 | 2 |
AGO2 | 1 | 2 | 2 | 2 | 2 |
AGO4 | 1 | 1 | 2 | 2 | 2 |
Gene Name | Transcript Name | gDNA Size (bp) | CDS Size (nts) | Protein | No. of Introns | Genomic Location | ||
---|---|---|---|---|---|---|---|---|
Length (aa) | Mw (kDa) | pI | ||||||
BnaAGO1-1 | BnaC08g46720D | 5291 | 3159 | 1052 | 116.78 | 9.45 | 20 | chrC08_random:953598-958888 |
BnaAGO1-2 | BnaA08g03260D | 5847 | 3135 | 1044 | 115.85 | 9.4 | 22 | chrA08:2681072-2686918 |
BnaAGO1-3 | BnaC05g25730D | 5910 | 2943 | 980 | 100.15 | 9.17 | 22 | chrC05:21116236-21122145 |
BnaAGO1-4 | BnaA05g17460D | 6740 | 3261 | 1086 | 120.33 | 9.38 | 22 | chrA05:12290150-12296889 |
BnaAGO2-1 | BnaA05g14760D | 3501 | 3033 | 1010 | 112.74 | 9.51 | 1 | chrA05:9228612-9232112 |
BnaAGO2-2 | BnaC06g41790D | 3340 | 3108 | 1035 | 114.35 | 9.54 | 1 | chrC06_random:1066401-1069740 |
BnaAGO2-3 | BnaCnng68320D | 3169 | 2664 | 887 | 100.7 | 9.44 | 2 | chrCnn_random:67905947-67909115 |
BnaAGO2-4 | BnaA09g25290D | 3712 | 3072 | 1023 | 113.91 | 9.66 | 3 | chrA09:18324937-18328648 |
BnaAGO4-1 | BnaC04g54830D | 5652 | 2772 | 923 | 103.36 | 8.87 | 21 | chrC04_random:2230442-2236093 |
BnaAGO4-2 | BnaA07g13010D | 5716 | 2772 | 923 | 103.36 | 8.82 | 21 | chrA07:11653377-11659092 |
BnaAGO4-3 | BnaA04g15560D | 5887 | 2769 | 922 | 103.06 | 8.91 | 21 | chrA04:12884285-12890171 |
BnaAGO4-4 | BnaC04g38560D | 5890 | 2769 | 922 | 103.11 | 8.87 | 21 | chrC04:39739228-39745117 |
BnaAGO5-1 | BnaA07g13430D | 4997 | 2874 | 957 | 106.71 | 9.52 | 19 | chrA07:11907998-11912994 |
BnaAGO5-2 | BnaC04g16450D | 5220 | 2859 | 952 | 106.03 | 9.62 | 20 | chrC04:14487678-14492897 |
BnaAGO6-1 | BnaA03g15180D | 4948 | 2604 | 867 | 97.2 | 9.03 | 21 | chrA03:7005357-7010304 |
BnaAGO6-2 | BnaC03g18310D | 4736 | 2604 | 867 | 97.37 | 8.99 | 21 | chrC03:9391663-9396398 |
BnaAGO7-1 | BnaA07g24280D | 3461 | 2955 | 984 | 112.47 | 9.37 | 2 | chrA07:18160385-18163845 |
BnaAGO7-2 | BnaC06g43420D | 3447 | 2700 | 899 | 102.67 | 9.38 | 5 | chrC06_random:2865213-2868659 |
BnaAGO7-3 | BnaC02g19190D | 3334 | 2931 | 976 | 111.58 | 9.32 | 2 | chrC02:15451981-15455314 |
BnaAGO9-1 | BnaCnng35060D | 4647 | 2721 | 906 | 102.57 | 9.42 | 21 | chrCnn_random:33265084-33269730 |
BnaAGO9-2 | BnaA10g14450D | 4627 | 2715 | 904 | 102.04 | 9.31 | 21 | chrA10:11492941-11497567 |
BnaAGO9-3 | BnaA02g05290D | 5571 | 2721 | 906 | 101.34 | 9.31 | 20 | chrA02:2403187-2408757 |
BnaAGO10-1 | BnaA06g36540D | 4921 | 2928 | 975 | 109.27 | 9.38 | 16 | chrA06:23915363-23920283 |
BnaAGO10-2 | BnaC07g17330D | 5667 | 2946 | 981 | 109.75 | 9.38 | 16 | chrC07:23533982-23539648 |
miRNA_ID | Target_Name | Expection | miRNA_aligned_fragment | Target_aligned_fragment | Alignment | Inhibition |
---|---|---|---|---|---|---|
bna-miR403 | BnaAGO2-4 | 0 | UUAGAUUCACGCACAAACUCG | GGAGUUUGUGCGUGAAUCUAA | :::::::::::::::::::: | Cleavage |
bna-miR403 | BnaAGO2-1 | 0 | UUAGAUUCACGCACAAACUCG | GGAGUUUGUGCGUGAAUCUAA | :::::::::::::::::::: | Cleavage |
bna-miR403 | BnaAGO2-3 | 0 | UUAGAUUCACGCACAAACUCG | GGAGUUUGUGCGUGAAUCUAA | :::::::::::::::::::: | Cleavage |
bna-miR168a | BnaAGO1-2 | 3 | UCGCUUGGUGCAGGUCGGGAA | UUCCCGAGCUGCAUCAAGCUA | ::::::: :::::.::::: : | Cleavage |
bna-miR168a | BnaAGO1-1 | 3 | UCGCUUGGUGCAGGUCGGGAA | UUCCCGAGCUGCAUCAAGCUA | ::::::: :::::.::::: : | Cleavage |
bna-miR168a | BnaAGO1-4 | 3 | UCGCUUGGUGCAGGUCGGGAA | UUCCCGAGCUGCAUCAAGCUA | ::::::: :::::.::::: : | Cleavage |
bna-miR168a | BnaAGO1-3 | 3 | UCGCUUGGUGCAGGUCGGGAA | UUCCCGAGCUGCAUCAAGCUA | ::::::: :::::.::::: : | Cleavage |
Trait | Material | 2016 | 2017 | 2018 | 2019 | 2021 | 2022 | Mean Value | SEM | p_Value |
---|---|---|---|---|---|---|---|---|---|---|
Thousand Seed Weight/g (TSW) | LTSW | - | 4.27 | 3.54 | 4.08 | 3.15 | 2.78 | 3.56 | 0.56 | |
HTSW | - | 6.03 | 6.15 | 7.58 | 6.55 | 6.99 | 6.66 | 0.57 | 0.000 | |
Seed number Per Silique (SPS) | LSPS-1 | - | 13.47 | 14.74 | 14.99 | - | 21.50 | 16.17 | 3.13 | |
LSPS-2 | - | 15.30 | 13.97 | 8.98 | 15.59 | 11.50 | 13.07 | 2.51 | ||
HSPS-1 | - | 31.43 | 33.53 | 25.23 | 34.60 | 31.00 | 31.16 | 3.25 | 0.00 | |
HSPS-2 | - | 29.40 | 29.40 | - | 24.36 | 29.70 | 28.22 | 2.23 | ||
Initial embryonic number (IEN) | LIEN-1 | - | - | - | - | 25.67 | 24.33 | 25.00 | 0.67 | |
LIEN-2 | - | - | - | - | 24.00 | 23.00 | 23.50 | 0.50 | ||
HIEN-1 | - | - | - | - | 38.33 | 34.33 | 36.33 | 2.00 | 0.00 | |
HIEN-2 | - | - | - | - | 35.67 | 33.00 | 34.34 | 1.34 |
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Zhang, L.; Yang, B.; Zhang, C.; Chen, H.; Xu, J.; Qu, C.; Lu, K.; Li, J. Genome-Wide Identification and Posttranscriptional Regulation Analyses Elucidate Roles of Key Argonautes and Their miRNA Triggers in Regulating Complex Yield Traits in Rapeseed. Int. J. Mol. Sci. 2023, 24, 2543. https://doi.org/10.3390/ijms24032543
Zhang L, Yang B, Zhang C, Chen H, Xu J, Qu C, Lu K, Li J. Genome-Wide Identification and Posttranscriptional Regulation Analyses Elucidate Roles of Key Argonautes and Their miRNA Triggers in Regulating Complex Yield Traits in Rapeseed. International Journal of Molecular Sciences. 2023; 24(3):2543. https://doi.org/10.3390/ijms24032543
Chicago/Turabian StyleZhang, Liyuan, Bo Yang, Chao Zhang, Huan Chen, Jinxiong Xu, Cunmin Qu, Kun Lu, and Jiana Li. 2023. "Genome-Wide Identification and Posttranscriptional Regulation Analyses Elucidate Roles of Key Argonautes and Their miRNA Triggers in Regulating Complex Yield Traits in Rapeseed" International Journal of Molecular Sciences 24, no. 3: 2543. https://doi.org/10.3390/ijms24032543