Genome-Wide Identification and Expression Profiling of Cytokinin Oxidase/Dehydrogenase (CKX) Genes Reveal Likely Roles in Pod Development and Stress Responses in Oilseed Rape (Brassica napus L.)
Abstract
:1. Introduction
2. Materials and Methods
2.1 Identification of CKXs in B. napus, B. rapa, and B. oleracea
2.2. Multiple Sequence Alignment and Phylogenetic Analysis
2.3. Chromosomal Locations, Gene Structures and Protein Profiles of BnCKXs
2.4. Sequence Analysis of the BnCKXs Promoters
2.5. Plant Materials, Growth Conditions, and Treatments
2.6. RNA-seq Analysis
2.7. RNA Isolation and qRT-PCR Analysis
3. Results
3.1. Identification and Phylogenetic Analysis of BnCKXs
3.2. Chromosomal Localization
3.3. Gene Structures and Protein Profiles of BnCKXs
3.4. Cis-Acting Elements in the BnCKXs
3.5. RNA-Seq Analysis
3.6. qRT-PCR Measurement of BnCKXs Gene Expression in Specific Tissues and at Different Developmental Stages
3.7. Expression of Selected BnCKX Genes in Different Plant Materials and in Response to IAA and 6-BA Treatment
4. Discussion
Supplementary Materials
Acknowledgments
Author Contributions
Conflicts of Interest
References
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Gene Name | Locus Name | Chr. | Location | ORF Length (bp) | Protein | Subcellular Location | ||
---|---|---|---|---|---|---|---|---|
Length (aa) | Mw (Da) | pI | ||||||
BnCKX1-1 | BnaA04g23980D | A04 | 17680020…17682356 | 1611 | 536 | 60,681.24 | 8.58 | chlo: 6, extr: 3, vacu: 2, nucl: 1, plas: 1 |
BnCKX1-2 | BnaA05g02240D | A05 | 1254144...1259378 | 1602 | 533 | 60,411.94 | 8.72 | mito: 7, chlo_mito: 6.33333, chlo: 4.5, cyto_mito: 4.33333 |
BnCKX1-3 | BnaC04g01930D | C04 | 1500877…1503073 | 1791 | 596 | 68,227.7 | 8.53 | nucl: 4, vacu: 4, chlo: 3, plas: 1, extr: 1 |
BnCKX1-4 | BnaC04g47740D | C04 | 46681907…46684463 | 1641 | 546 | 61,665.39 | 9.2 | mito: 7.5, cyto_mito: 4.5, chlo: 3, nucl: 2 |
BnCKX1-5 | BnaA03g19500D | A03 | 9235344...9237387 | 1638 | 545 | 61,439.11 | 8.72 | mito:4,chlo: 4, cyto: 3, nucl: 2 |
BnCKX1-6 | BnaC03g23380D | C03 | 13022610...13024649 | 1599 | 532 | 60,320.83 | 8.8 | mito: 5, chlo: 4, nucl: 2, cyto: 2 |
BnCKX2-1 | BnaA07g35940D | A07_random | 5099…13485 | 2307 | 768 | 87,023.55 | 5.86 | nucl: 7, cyto: 4, chlo: 2 |
BnCKX2-2 | BnaC07g01710D | C07 | 2422452...2425861 | 1011 | 336 | 38,171.83 | 5.83 | chlo: 4, cyto: 2, extr: 2, vacu: 2, mito: 1.5, mito_plas: 1.5, nucl: 1 |
BnCKX2-3 | BnaA09g52930D | A09_random | 753807...758243 | 1455 | 484 | 53,519.55 | 5.96 | vacu: 4, chlo: 3, extr: 3, plas: 2, cyto: 1 |
BnCKX3-1 | BnaA02g08420D | A02 | 4,079,790…4,082,972 | 1554 | 517 | 58,722.84 | 5.7 | vacu: 6, mito: 2, extr: 2, golg: 2, plas: 1 |
BnCKX3-2 | BnaA10g28940D | A10_random | 1464876…1467891 | 1437 | 478 | 54,173.56 | 5.93 | vacu: 5, extr: 3, mito: 2, plas: 2, chlo: 1 |
BnCKX3-3 | BnaC09g33450D | C09 | 36760027…36762978 | 1437 | 478 | 54,183.47 | 5.78 | vacu: 7, extr: 4, cyto: 1, mito: 1 |
BnCKX3-4 | BnaCnng41060D | Cnn_random | 39653407…39656550 | 1557 | 518 | 58,855.91 | 5.83 | vacu: 6, extr: 3, golg: 2, mito: 1, plas: 1 |
BnCKX4-1 | BnaA03g49660D | A03 | 25641300…25644280 | 1551 | 516 | 57,072.39 | 5.51 | chlo: 5, cyto: 2, mito: 2, vacu: 2, E.R.: 2 |
BnCKX4-2 | BnaC07g50850D | C07_random | 2732541…2736266 | 1551 | 516 | 57,301.75 | 5.62 | vacu: 4, chlo: 2, mito: 2, extr: 2, golg: 2, cyto: 1 |
BnCKX5-1 | BnaAnng09190D | Ann_random | 9695112...9698437 | 1596 | 531 | 59,613.56 | 5.62 | extr: 5, chlo: 3, vacu: 3, cyto: 1, mito: 1 |
BnCKX5-2 | BnaC06g36220D | C06 | 34801906…34804721 | 1608 | 535 | 60,144.10 | 5.53 | vacu: 8, extr: 3, cyto: 1, mito: 1 |
BnCKX6-1 | BnaA09g40400D | A09 | 28427957...28430033 | 1350 | 449 | 50,468.31 | 7.3 | mito: 7, nucl: 4, chlo: 2 |
BnCKX6-2 | BnaC08g32840D | C08 | 31616324...31618400 | 1602 | 533 | 60,109.91 | 8.55 | mito: 7, chlo: 1, nucl: 1, cyto: 1, plas: 1, extr: 1, E.R.: 1 |
BnCKX7-1 | BnaA02g05340D | A02 | 2433263…2436786 | 1554 | 517 | 57,559.29 | 5.2 | cyto: 6, nucl: 3, cysk: 2, chlo: 1, plas: 1 |
BnCKX7-2 | BnaA10g14370D | A10 | 11435086…11438436 | 1578 | 525 | 57,864.41 | 4.92 | cyto: 11, chlo: 1, plas: 1 |
BnCKX7-3 | BnaA10g24380D | A10 | 15919508...15923282 | 1704 | 567 | 61,909.23 | 7.93 | chlo: 7.5, chlo_mito: 7, mito: 5.5 |
BnCKX7-4 | BnaC09g36710D | C09 | 40060399…40063686 | 1395 | 464 | 51,901.91 | 5.45 | chlo: 8, cyto: 4, nucl: 1 |
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Liu, P.; Zhang, C.; Ma, J.-Q.; Zhang, L.-Y.; Yang, B.; Tang, X.-Y.; Huang, L.; Zhou, X.-T.; Lu, K.; Li, J.-N. Genome-Wide Identification and Expression Profiling of Cytokinin Oxidase/Dehydrogenase (CKX) Genes Reveal Likely Roles in Pod Development and Stress Responses in Oilseed Rape (Brassica napus L.). Genes 2018, 9, 168. https://doi.org/10.3390/genes9030168
Liu P, Zhang C, Ma J-Q, Zhang L-Y, Yang B, Tang X-Y, Huang L, Zhou X-T, Lu K, Li J-N. Genome-Wide Identification and Expression Profiling of Cytokinin Oxidase/Dehydrogenase (CKX) Genes Reveal Likely Roles in Pod Development and Stress Responses in Oilseed Rape (Brassica napus L.). Genes. 2018; 9(3):168. https://doi.org/10.3390/genes9030168
Chicago/Turabian StyleLiu, Pu, Chao Zhang, Jin-Qi Ma, Li-Yuan Zhang, Bo Yang, Xin-Yu Tang, Ling Huang, Xin-Tong Zhou, Kun Lu, and Jia-Na Li. 2018. "Genome-Wide Identification and Expression Profiling of Cytokinin Oxidase/Dehydrogenase (CKX) Genes Reveal Likely Roles in Pod Development and Stress Responses in Oilseed Rape (Brassica napus L.)" Genes 9, no. 3: 168. https://doi.org/10.3390/genes9030168
APA StyleLiu, P., Zhang, C., Ma, J.-Q., Zhang, L.-Y., Yang, B., Tang, X.-Y., Huang, L., Zhou, X.-T., Lu, K., & Li, J.-N. (2018). Genome-Wide Identification and Expression Profiling of Cytokinin Oxidase/Dehydrogenase (CKX) Genes Reveal Likely Roles in Pod Development and Stress Responses in Oilseed Rape (Brassica napus L.). Genes, 9(3), 168. https://doi.org/10.3390/genes9030168