Conserved Imprinted Genes between Intra-Subspecies and Inter-Subspecies Are Involved in Energy Metabolism and Seed Development in Rice
Abstract
:1. Introduction
2. Results
2.1. The Number of Genes Expressed in Embryo and Endosperm
2.2. The Number of Parental Polymorphic Genes Expressed in Embryo and Endosperm of Hybrids
2.3. Identification of Imprinted Gene from Three Sets of Reciprocal Crosses
2.4. Preference Expression of Imprinted Genes in Endosperm
2.5. Confirmation of Maternally Expressed Genes
2.6. Mini Cluster of Imprinted Genes
2.7. Conservation of Imprinted Genes between Subspecies in Rice
2.8. Two Imprinting Genes Verified for Grain Filling
2.9. MEGs Involved in Carbohydrate Metabolism while PEGs Involved in Signal Transduction
2.10. Subcellular Location of Proteins Encoded by Imprinted Genes
2.11. KEGG (Kyoto Encyclopedia of Genes and Genomes) Pathway Enrichment Analysis
3. Discussion
4. Materials and Methods
4.1. Plant Materials
4.2. Identification of Hybrids and RNA Extraction
4.3. Construction of RNA and DNA Sequencing Library
4.4. Construction of Pseudo Genomes of ZH11 and ZS97
4.5. Identification of Cultivar Specific Reads
4.6. Identification of Imprinted Genes
4.7. Transferring 9311 Gene ID and MSU (Michigan State University) Gene ID to RAP-DB Gene ID
4.8. Validation of Imprinted Genes
4.9. Identification of Conserved Imprinted Genes among Species
4.10. Calculation of Abundance of Gene Expression
4.11. Gene Ontology (GO) Analysis, Subcellular Location, and KEGG Pathway Analysis
4.12. Generation of Knockout Mutants of Two Imprinted Genes
4.13. Measurement of Grain Filling
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
Abbreviations
R9N | Reciprocal crosses between 9311 and Nipponbare |
R9Z | Reciprocal crosses between 9311 and Zhenshan97 |
RZN | Reciprocal crosses between Zhonghua 11 and Nipponbare |
SNP InDel | Single Nucleotide Polymorphism Insertion and Deletion |
DAF | Days after flowering |
DAP | Days after pollination |
PEGs | Paternally expressed genes |
MEGs | Maternally expressed genes |
FPKM | fragments per kilobase of exon model per million |
RAP-DB | Rice Annotation Project Database |
WT | wild type |
CRISPR/Cas9 | Clustered Regularly-Interspaced Short Palindromic Repeats/CRISPR associated protein 9 |
GO | Gene Ontology |
KEGG | Kyoto Encyclopedia of Genes and Genomes |
CTAB | hexadecyl trimethyl ammonium bromide |
RID | rice InDels marker |
BWA | Burrows-Wheeler Aligner |
MSU | Michigan State University |
BLAT | BLAST-like alignment tool |
BLASTP | basic local alignment search tool for proteins |
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Sample Name | SNP Number | InDel Number | Expressed Genes 1 | SNP Genes 2 | InDel Genes 3 |
---|---|---|---|---|---|
N9 endosperm | 168,864 | 21,180 | 23,512 | 21,638 | 11,539 |
N9 embryo | 202,828 | 26,279 | 23,092 | 22,850 | 9991 |
9N endospermrep1 | 67,783 | 6688 | 22,624 | 16,380 | 4370 |
9N embryo rep1 | 93,470 | 9588 | 24,265 | 18,022 | 5953 |
9Nendosperm rep2 | 56,332 | 4681 | 22,933 | 15,332 | 3089 |
9N embryo rep2 | 75,491 | 6478 | 24,801 | 16,792 | 4228 |
Total 4 | 229,065/189,303 | 34,809/28,026 | 26,346/24,558 | 24,598/24,558 | 12,499/10,864 |
9Z endosperm | 36,319 | 2329 | 18,096 | 5484 | 799 |
9Zembryo | 46,725 | 3210 | 19,484 | 5700 | 283 |
Z9 endosperm | 29,136 | 1822 | 18,587 | 5220 | 681 |
Z9 embryo | 52,875 | 3687 | 19,964 | 6151 | 1452 |
Total | 59,941/41,470 | 4517/2825 | 25,528/25,021 | 8330/7180 | 1795/986 |
ZN endosperm | 9279 | 341 | 23,573 | 2138 | 262 |
ZN embryo | 14,735 | 523 | 24,477 | 2373 | 403 |
NZ endosperm | 8842 | 279 | 23,320 | 1956 | 228 |
NZ embryo | 12,758 | 491 | 23,464 | 2138 | 375 |
Total | 16,776/11,870 | 689/421 | 25,256/24,866 | 2891/2462 | 492/307 |
Hybrids | Endosperm | Embryo | ||||
---|---|---|---|---|---|---|
Total 1 | MEG | PEG | Total 1 | MEG | PEG | |
R9N 2 | 546 | 482 | 64 | 0 | 0 | 0 |
R9Z 3 | 286 | 234 | 52 | 1 | 0 | 1 |
RZN 4 | 211 | 195 | 16 | 3 | 3 | 0 |
Gene Classification | R9N | R9Z | RZN |
---|---|---|---|
imprinted gene | 546 | 286 | 211 |
Non-significant 1 | 260 | 21 | 23 |
no SNP 2 | 48 | 544 | 676 |
no ASR 3 | 60 | 62 | 4 |
Gene ID | Imprinting Type | Annotation |
---|---|---|
Os01g0151700 | MEG | Similar to Short-chain dehydrogenase Tic32. |
Os07g0103100 | MEG | Similar to Glutamate receptor 3.4 precursor (Ligand-gated ion channel 3.4) (AtGLR4). Splice isoform 2. |
Os10g0340600 | MEG | Similar to Beta-galactosidase. |
Os11g0679700 | MEG | Glycerol-3-phosphate acyltransferase, Anther development, Pollen formation. |
Os12g0632800 | MEG | Protein kinase, catalytic domain containing protein. |
Cross Combination | Direct Cross | Reciprocal Cross |
---|---|---|
R9N 1 | 9311 × Nip 2 | Nip × 9311 |
R9Z | 9311 × ZS97 | ZS97 × 9311 |
RZN | ZH11 × Nip | Nip × ZH11 |
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Yang, L.; Xing, F.; He, Q.; Tahir ul Qamar, M.; Chen, L.-L.; Xing, Y. Conserved Imprinted Genes between Intra-Subspecies and Inter-Subspecies Are Involved in Energy Metabolism and Seed Development in Rice. Int. J. Mol. Sci. 2020, 21, 9618. https://doi.org/10.3390/ijms21249618
Yang L, Xing F, He Q, Tahir ul Qamar M, Chen L-L, Xing Y. Conserved Imprinted Genes between Intra-Subspecies and Inter-Subspecies Are Involved in Energy Metabolism and Seed Development in Rice. International Journal of Molecular Sciences. 2020; 21(24):9618. https://doi.org/10.3390/ijms21249618
Chicago/Turabian StyleYang, Lin, Feng Xing, Qin He, Muhammad Tahir ul Qamar, Ling-Ling Chen, and Yongzhong Xing. 2020. "Conserved Imprinted Genes between Intra-Subspecies and Inter-Subspecies Are Involved in Energy Metabolism and Seed Development in Rice" International Journal of Molecular Sciences 21, no. 24: 9618. https://doi.org/10.3390/ijms21249618