Genome-Wide Identification of MDH Family Genes and Their Association with Salt Tolerance in Rice
Abstract
:1. Introduction
2. Results
2.1. Identification and Characterization of MDH Genes in Rice
2.2. Phylogenetic Analysis of MDH Proteins
2.3. Putative Cis-Regulatory Elements Analysis in the Promoter of OsMDH Genes
2.4. Expression Pattern of MDH Genes in Rice
2.5. Gene-Based Association and Haplotype Analysis of OsMDH Genes
3. Discussion
4. Materials and Methods
4.1. Identification of the MDH Gene Family in Rice
4.2. Construction of Phylogenetic Tree of the MDH Gene Family
4.3. Structure and Motif Analysis of the MDH Gene Family in Rice
4.4. Duplication Analysis of OsMDH
4.5. Plant Materials and Salt Stress Treatment
4.6. Transcriptomic Analysis, RNA Extraction and qRT-PCR Analysis
4.7. Association Analysis of Candidate OsMDH Genes
4.8. Haplotype Analysis of Candidate Genes
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Gene ID | Gene Name | Chr | Start | End | Genomic Sequence Length (bp) | CDS (bp) | Protein Length (aa) | MW (kDa) | Isoelectric Point (PI) | Subcellular Localization |
---|---|---|---|---|---|---|---|---|---|---|
LOC_Os01g61380 | OsMDH1 [12] | 1 | 35499017 | 35501765 | 2749 | 1191 | 396 | 41.79 | 7.90 | cytoplasmic |
LOC_Os01g46070 | OsMDH1.2 | 1 | 26190752 | 26194517 | 3766 | 1023 | 340 | 35.46 | 8.74 | cytoplasmic |
LOC_Os02g01510 | OsMDH2.1 | 2 | 295302 | 299174 | 3873 | 1179 | 392 | 42.72 | 7.29 | endoplasmic reticulum |
LOC_Os03g56280 | OsMDH3.1 | 3 | 32086001 | 32089685 | 3685 | 1065 | 354 | 37.02 | 8.06 | cytoplasmic |
LOC_Os04g46560 | OsMDH4.1 | 4 | 27605166 | 27608347 | 3182 | 1059 | 352 | 38.30 | 7.22 | endoplasmic reticulum |
LOC_Os05g49880 | OsMDH5.1 | 5 | 28617595 | 28621585 | 3991 | 1023 | 340 | 35.44 | 8.30 | nuclear |
LOC_Os06g01590 | OsMDH6.1 | 6 | 346985 | 348516 | 1532 | 1083 | 360 | 38.72 | 8.46 | nuclear |
LOC_Os07g43700 | OsMDH7.1 | 7 | 26153825 | 26156006 | 2182 | 1215 | 404 | 42.22 | 9.03 | nuclear |
LOC_Os08g33720 | OsMDH8.1 | 8 | 21054659 | 21057561 | 2903 | 1194 | 397 | 41.54 | 7.54 | cytoplasmic |
LOC_Os08g44810 | OsMDH8.2 | 8 | 28141042 | 28146270 | 5229 | 1302 | 433 | 47.01 | 7.34 | endoplasmic reticulum |
LOC_Os10g33800 | OsMDH10.1(FLO16) [9] | 10 | 17913818 | 17917850 | 4033 | 999 | 332 | 35.57 | 5.97 | endoplasmic reticulum |
LOC_Os12g43630 | OsMDH12.1 | 12 | 27094647 | 27099351 | 4705 | 1071 | 356 | 37.39 | 7.99 | cytoplasmic |
Gene ID | Gene Name | Polymorphic Number | GLM (p ≤ 0.01) | GLM (p ≤ 0.001) | CMLM (p ≤ 0.01) | CMLM (p ≤ 0.001) |
---|---|---|---|---|---|---|
LOC_Os01g61380 | OsMDH1 | 9 | 0 | 0 | 0 | 0 |
LOC_Os01g46070 | OsMDH1.2 | 9 | 0 | 0 | 0 | 0 |
LOC_Os02g01510 | OsMDH2.1 | 19 | 0 | 0 | 0 | 0 |
LOC_Os03g56280 | OsMDH3.1 | 40 | 0 | 0 | 0 | 0 |
LOC_Os04g46560 | OsMDH4.1 | 63 | 6 | 0 | 0 | 0 |
LOC_Os05g49880 | OsMDH5.1 | 29 | 0 | 0 | 0 | 0 |
LOC_Os06g01590 | OsMDH6.1 | 49 | 14 | 0 | 0 | 0 |
LOC_Os07g43700 | OsMDH7.1 | 33 | 0 | 0 | 0 | 0 |
LOC_Os08g33720 | OsMDH8.1 | 56 | 6 | 4 | 2 | 0 |
LOC_Os08g44810 | OsMDH8.2 | 35 | 4 | 0 | 0 | 0 |
LOC_Os10g33800 | OsMDH10.1 | 56 | 0 | 0 | 0 | 0 |
LOC_Os12g43630 | OsMDH12.1 | 159 | 134 | 3 | 0 | 0 |
Gene ID | Primer Name | Sequence of Forward Primer | Sequence of Reverse Primer | Annotation |
---|---|---|---|---|
LOC_Os01g61380 | OsMDH1 | CGAAAGCTGGTGCTGGATCTG | CACGGAGGGATGACTCAACA | OsMDH1 [12] |
LOC_Os01g46070 | OsMDH1.2 | AACGCCGGCATCGTTAAGAAC | GGGTTGCTGATCATGTTGACAAG | lactate/malate dehydrogenase |
LOC_Os02g01510 | OsMDH2.1 | CGGCACCAACCTCGACTC | CGTGCTCTCCCACCATGTAC | lactate/malate dehydrogenase |
LOC_Os03g56280 | OsMDH3.1 | TGGCGTTGTGGAATGTTCA | GGCTCCAGCACGACCTAAC | lactate/malate dehydrogenase |
LOC_Os04g46560 | OsMDH4.1 | CGAGGCTGAGGCGTTCAAG | GCAGAGGCCTGGGATTTGTAG | lactate/malate dehydrogenase |
LOC_Os05g49880 | OsMDH5.1 | GCCAGCTTTCCGAGTTTGAGAAG | GTTCGCGTGAGCAAACTTGATG | lactate/malate dehydrogenase |
LOC_Os06g01590 | OsMDH6.1 | AGCGCGTACGAGGTGATCAAG | GATGCTGGCGACGGAGTAG | lactate/malate dehydrogenase |
LOC_Os07g43700 | OsMDH7.1 | GCGCTGCACCTGTACGAC | CGTGTTGCAGTGTCCAAGATC | lactate/malate dehydrogenase |
LOC_Os08g44810 | OsMDH8.1 | GCAGAGGACATCGTGTTCAGTA | CGTCCATTGCCACATCTTTAACTAG | lactate/malate dehydrogenase |
LOC_Os08g33720 | OsMDH8.2 | GCTGACCTTGAGGGAGTGA | TCGATGCCCTTCTCGATACTG | lactate/malate dehydrogenase |
LOC_Os10g33800 | OsMDH10.1 | AGCAAACACCAACGCTCTCATC | TGCCCTGTTGTGGTCAAGA | FLO16 [9] |
LOC_Os12g436301 | OsMDH12.1 | GCCAGCCACAGTTGGAAA | CCCAGGCTTACGAGGAACA | lactate/malate dehydrogenase |
LOC_Os03g13170 | Ubi | AACCAGCTGAGGCCCAAGA | ACGATTGATTTAACCAGTCCATGA | Ubq (ubiquitin fusion protein) [60] |
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Zhang, Y.; Wang, Y.; Sun, X.; Yuan, J.; Zhao, Z.; Gao, J.; Wen, X.; Tang, F.; Kang, M.; Abliz, B.; et al. Genome-Wide Identification of MDH Family Genes and Their Association with Salt Tolerance in Rice. Plants 2022, 11, 1498. https://doi.org/10.3390/plants11111498
Zhang Y, Wang Y, Sun X, Yuan J, Zhao Z, Gao J, Wen X, Tang F, Kang M, Abliz B, et al. Genome-Wide Identification of MDH Family Genes and Their Association with Salt Tolerance in Rice. Plants. 2022; 11(11):1498. https://doi.org/10.3390/plants11111498
Chicago/Turabian StyleZhang, Yanhong, Yulong Wang, Xingming Sun, Jie Yuan, Zhiqiang Zhao, Jie Gao, Xiaorong Wen, Fusen Tang, Mintai Kang, Buhaliqem Abliz, and et al. 2022. "Genome-Wide Identification of MDH Family Genes and Their Association with Salt Tolerance in Rice" Plants 11, no. 11: 1498. https://doi.org/10.3390/plants11111498