Abstract
The adaptation to aerobic environments enables upland rice to produce a sustainable grain yield under suboptimal conditions. In order to understand the molecular mechanisms involved in providing the adaptation of upland rice to aerobic environments, we previously developed introgression lines (ILs) with the irrigated rice variety Minghui63 (MH63) as the recipient parent and the upland rice variety Luyin46 (LY46) as the donor parent for subsequent identification of the relevant genes. In this study, IL-U135 was analyzed in detail because of its adaptation to aerobic conditions. Transcriptome profiling revealed 20 and 8 differentially expressed genes (DEGs) between IL-U135 and MH63 under anaerobic and aerobic conditions, respectively. In contrast, 306 and 188 DEGs were identified between LY46 and MH63 under anaerobic and aerobic conditions, respectively. Gene ontology (GO) analysis indicated that the adaptation of upland rice to aerobic environments is intimately associated with CLV3/ESR-related (CLE) signal transduction pathways, CLAVATA1 kinase activity, and salicylic acid related metabolism biosynthetic pathways. The IL-U135, LY46 and MH63 genomes were resequenced to map the genes responsible for adaptations to aerobic conditions. One the basis of an integrated analysis of the transcriptomic and genomic profiles, we propose that genes encoding an NBS-LRR protein (LOC_Os11g10570) and an ATP-binding protein (LOC_Os11g31480) may contribute to the adaptation of upland rice to aerobic environments. Our results may provide new insights into the molecular mechanism underlying the adaptation of rice to aerobic conditions.
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Abbreviations
- MH 63:
-
Minghui63
- LY 46:
-
Luyin46
- DEGs:
-
Differentially expressed genes
- QTL:
-
Quantitative trait loci
- RNA-Seq:
-
RNA sequencing
- SA:
-
Salicylic acid
- SLs:
-
Segments derived from LY46
- GO:
-
Gene ontology
- BP:
-
Biological process
- CC:
-
Cellular component
- MF:
-
Molecular function
- JA:
-
Jasmonic acid
- IAA:
-
Auxin
- EA:
-
Ethylene
- GA:
-
Gibberellic acid
- CTK:
-
Cytokinin
- BR:
-
Brassinosteroid
- ABA:
-
Abscisic acid
- SNPs:
-
Single nucleotide polymorphisms
- InDels:
-
Insertion/deletions
- RT-qPCR:
-
Quantitative reverse transcription pcr
- KEGG:
-
Kyoto Encyclopedia of Genes and Genomes
- CDS:
-
Coding regions
- UTR:
-
Untranslated region
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Acknowledgements
We thank Public Technology Service Center, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences for technical support. We are grateful for the critical comments from Dr. Qingjun Xie (South China Agricultural University) for this paper.
Funding
This work was supported by grants from the National Natural Science Foundation of China (31360330) to P.X, “One-Three-Five” Strategic Planning of Chinese Academy of Sciences (2017XTBG-T02) and Strategic Leading Science & Technology Programme (XDA08020203).
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DQY designed the experiments, JW and PX provided the materials, JY and PX performed the experiments and analyzed the RNA-Seq and wrote the manuscript, FW gave a support for experiment. All authors have discussed the results and contributed to the drafting of the manuscript. All authors read and approved the final manuscript.
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10725_2020_606_MOESM1_ESM.tif
Supplementary file1 (TIF 586 kb) Supplementary Figure. 1 Chromosome structure of IL-U135. Red rectangle indicates the introgression fragments from LuYin 46 into Ming Hui 63. The details of introgression fragments position were in the Supplementary Table S4.
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Supplementary file2 (TIF 820 kb) Supplementary Figure. 2 Validation of RNA-seq by quantitative reverse transcription PCR (RT-qPCR) assays. The correlation coefficient (R2) between the two datasets is 0.977. a. The RT-qPCR results with the RNA-seq for 10 randomly selected introgressed genes. b. The RT-qPCR results with the RNA-seq for two introgressed genes LOC_Os11g31480 and LOC_Os11g10570.
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Supplementary file4 (XLS 25 kb) Supplementary Table S2: Mapping results for RNA-seq reads of Minghui63, Luyin46, and IL-U135 under anaerobic and aerobic conditions.
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Supplementary file5 (XLSX 11 kb) Supplementary Table S3: Mapping results of the genome resequencing reads of Minghui63, Luyin46, and IL-U135.
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Supplementary file6 (XLSX 13 kb) Supplementary Table S4: The schematic diagram of introgression fragments’ position. Red indicates the details of introgression fragments’ position from LuYin 46 into Ming Hui 63.
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Supplementary file7 (XLSX 12583 kb) Supplementary Table S5: The details of SNPs for Introgressed region from LY 46 to MH 63.
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Supplementary file8 (XLSX 3294 kb) Supplementary Table S6: The details of InDels for Introgressed region from LY 46 to MH 63.
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Supplementary file9 (XLSX 207 kb) Supplementary Table S7: Details of SNPs of introgression and differential expressed genes between MH63 and LY46, MH63 and IL-U135.
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Supplementary file10 (XLSX 43 kb) Supplementary Table S8: Details of InDels of introgression and differential expressed genes between MH63 and LY46, MH63 and IL-U135.
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Yang, J., Wang, F., Tao, D. et al. Characterization of genes responsive to aerobic conditions by transcriptomic and genomic analyses of upland rice. Plant Growth Regul 91, 289–303 (2020). https://doi.org/10.1007/s10725-020-00606-3
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DOI: https://doi.org/10.1007/s10725-020-00606-3