|
1
|
Wang F, Li P, Liu Q, Nie G, Zhu Y, Zhang X. Selection and Validation of Reference Genes in Sudan Grass ( Sorghum sudanense (Piper) Stapf) under Various Abiotic Stresses by qRT-PCR. Genes (Basel) 2024; 15:210. [PMID: 38397200 PMCID: PMC10887928 DOI: 10.3390/genes15020210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 01/28/2024] [Accepted: 02/03/2024] [Indexed: 02/25/2024] Open
Abstract
Quantitative reverse transcription PCR (qRT-PCR) can screen applicable reference genes of species, and reference genes can be used to reduce experimental errors. Sudan grass (Sorghum sudanense (Piper) Stapf) is a high-yield, abiotic-tolerant annual high-quality forage with a wide range of uses. However, no studies have reported reference genes suitable for Sudan grass. Therefore, we found eight candidate reference genes, including UBQ10, HIS3, UBQ9, Isoform0012931, PP2A, ACP2, eIF4α, and Actin, under salt stress (NaCl), drought stress (DR), acid aluminum stress (AlCl3), and methyl jasmonate treatment (MeJA). By using geNorm, NormFinder, BestKeeper, and RefFinder, we ranked eight reference genes on the basis of their expression stabilities. The results indicated that the best reference gene was PP2A under all treatments. eIF4α can be used in CK, MeJA, NaCl, and DR. HIS3 can serve as the best reference gene in AlCl3. Two target genes (Isoform0007606 and Isoform0002387) belong to drought-stress-response genes, and they are highly expressed in Sudan grass according to transcriptome data. They were used to verify eight candidate reference genes under drought stress. The expression trends of the two most stable reference genes were similar, but the trend in expression for Actin showed a significant difference. The reference genes we screened provided valuable guidance for future research on Sudan grass.
Collapse
Affiliation(s)
- Fangyan Wang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (F.W.); (P.L.); (G.N.)
| | - Peng Li
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (F.W.); (P.L.); (G.N.)
| | - Qiuxu Liu
- Institute of Agricultural Resources and Environment, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China;
| | - Gang Nie
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (F.W.); (P.L.); (G.N.)
| | - Yongqun Zhu
- Institute of Agricultural Resources and Environment, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China;
| | - Xinquan Zhang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (F.W.); (P.L.); (G.N.)
| |
Collapse
|
|
2
|
Wang X, Shu X, Su X, Xiong Y, Xiong Y, Chen M, Tong Q, Ma X, Zhang J, Zhao J. Selection of Suitable Reference Genes for RT-qPCR Gene Expression Analysis in Centipedegrass under Different Abiotic Stress. Genes (Basel) 2023; 14:1874. [PMID: 37895223 PMCID: PMC10606319 DOI: 10.3390/genes14101874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Revised: 09/21/2023] [Accepted: 09/25/2023] [Indexed: 10/29/2023] Open
Abstract
As a C4 warm-season turfgrass, centipedegrass (Eremochloa ophiuroides (Munro) Hack.) is known for its exceptional resilience to intensive maintenance practices. In this research, the most stably expressed reference genes in the leaves of centipedegrass under different stress treatments, including salt, cold, drought, aluminum (Al), and herbicide, were screened by the quantitative real-time PCR (RT-qPCR) technique. The stability of 13 candidate reference genes was evaluated by software GeNorm V3.4, NormFinder V20, BestKeeper V1.0, and ReFinder V1.0. The results of this experiment demonstrated that the expression of the UBC (ubiquitin-conjugating enzyme) remained the most stable under cold and Al stress conditions. On the other hand, the MD (malate dehydrogenase) gene exhibited the best performance in leaf tissues subjected to salt and drought stresses. Under herbicide stress, the expression level of the RIP (60S ribosomal protein L2) gene ranked the highest. The expression levels of abiotic stress-associated genes such as PIP1, PAL, COR413, ALMT9, and BAR were assessed to validate the reliability of the selected reference genes. This study provides valuable information and reference points for gene expression under abiotic stress conditions in centipedegrass.
Collapse
Affiliation(s)
- Xiaoyun Wang
- College of Grassland Science and Technology, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China
| | - Xin Shu
- College of Grassland Science and Technology, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China
| | - Xiaoli Su
- College of Grassland Science and Technology, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China
| | - Yanli Xiong
- College of Grassland Science and Technology, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China
| | - Yi Xiong
- College of Grassland Science and Technology, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China
| | - Minli Chen
- Sichuan Academy of Grassland Sciences, Pidu, Chengdu 611731, China
| | - Qi Tong
- Sichuan Academy of Grassland Sciences, Pidu, Chengdu 611731, China
| | - Xiao Ma
- College of Grassland Science and Technology, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China
| | - Jianbo Zhang
- Sichuan Academy of Grassland Sciences, Pidu, Chengdu 611731, China
| | - Junming Zhao
- College of Grassland Science and Technology, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China
| |
Collapse
|
|
3
|
Yi S, Lu H, Tian C, Xu T, Song C, Wang W, Wei P, Gu F, Liu D, Cai Y, Han B. Selection of Suitable Reference Genes for Gene Expression Normalization Studies in Dendrobium huoshanense. Genes (Basel) 2022; 13:genes13081486. [PMID: 36011396 PMCID: PMC9408602 DOI: 10.3390/genes13081486] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 08/15/2022] [Accepted: 08/17/2022] [Indexed: 11/16/2022] Open
Abstract
Dendrobium huoshanense is a kind of precious herb with important medicinal and edible value in China, which is widely used in traditional Chinese medicine for various diseases. Recent studies have paid close attention to the genetic expression of the biosynthetic pathway of the main active components (polysaccharides, alkaloids, and flavonoids), and real-time polymerase chain reaction (qPCR) is one of the most widely used methods for doing so. However, so far, no reference gene selections have been reported in D. huoshanense. In this study, 15 reference gene candidates (GAPDH, eIF, EF-1α, PP2A, UBCE, RPL5, TBP, APT1, MDH, PTBP3, PEPC, CYP71, NCBP2, TIP41, and F-box) were selected and evaluated for their expression stability in D. huoshanense under various experimental conditions, including in different tissues (root, stem, and leaf), abiotic stresses (oxidative, drought, cold, and UV), and hormone treatment (methyl jasmonate) using three statistical programs (geNorm, NormFinder, and BestKeeper). Then, the RefFinder program was employed to comprehensively validate the stability of the selected reference genes. Finally, the expression profiles of the CESA and GMPP genes were further analyzed, and these results indicated that TBP, NCBP2, and CYP71 were the top three most stable reference genes after comprehensive comparison, which could be used as stable reference genes for normalizing the genes expression in D. huoshanense. This study described here provides the first data regarding on reference gene selection in D. huoshanense, which will be extremely beneficial for future research on the gene expression normalization in D. huoshanense.
Collapse
Affiliation(s)
- Shanyong Yi
- Department of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an 237012, China
- Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, West Anhui University, Lu’an 237061, China
| | - Haibo Lu
- Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, West Anhui University, Lu’an 237061, China
| | - Chuanjun Tian
- Department of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an 237012, China
| | - Tao Xu
- Department of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an 237012, China
- Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, West Anhui University, Lu’an 237061, China
| | - Cheng Song
- Department of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an 237012, China
- Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, West Anhui University, Lu’an 237061, China
| | - Wei Wang
- Department of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an 237012, China
- Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, West Anhui University, Lu’an 237061, China
| | - Peipei Wei
- Department of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an 237012, China
- Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, West Anhui University, Lu’an 237061, China
| | - Fangli Gu
- Department of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an 237012, China
- Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, West Anhui University, Lu’an 237061, China
| | - Dong Liu
- Department of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an 237012, China
- Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, West Anhui University, Lu’an 237061, China
| | - Yongping Cai
- College of Life Sciences, Anhui Agricultural University, Hefei 230036, China
- Correspondence: (Y.C.); (B.H.); Tel.: +86-564-3307060 (B.H.)
| | - Bangxing Han
- Department of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an 237012, China
- Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, West Anhui University, Lu’an 237061, China
- Correspondence: (Y.C.); (B.H.); Tel.: +86-564-3307060 (B.H.)
| |
Collapse
|