Transcriptome sequencing analysis of maize embryonic callus during early redifferentiation
Abstract Background Maize is one of the primary crops of genetic manipulation, which provides an excellent means of promoting stress resistance and increasing yield. However, the differences in induction and regeneration capacity of embryonic callus (EC) among various genotypes result in genotypic d...
| Main Authors: | , , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BMC
2019-02-01
|
| Series: | BMC Genomics |
| Subjects: | |
| Online Access: | http://link.springer.com/article/10.1186/s12864-019-5506-7 |
| _version_ | 1811287104813006848 |
|---|---|
| author | Xiaoling Zhang Yanli Wang Yuanyuan Yan Hua Peng Yun Long Yinchao Zhang Zhou Jiang Peng Liu Chaoying Zou Huanwei Peng Guangtang Pan Yaou Shen |
| author_facet | Xiaoling Zhang Yanli Wang Yuanyuan Yan Hua Peng Yun Long Yinchao Zhang Zhou Jiang Peng Liu Chaoying Zou Huanwei Peng Guangtang Pan Yaou Shen |
| author_sort | Xiaoling Zhang |
| collection | DOAJ |
| description | Abstract Background Maize is one of the primary crops of genetic manipulation, which provides an excellent means of promoting stress resistance and increasing yield. However, the differences in induction and regeneration capacity of embryonic callus (EC) among various genotypes result in genotypic dependence in genetic transformation. Results In this study, embryonic calli of two maize inbred lines with strong redifferentiation capacity and two lines with weak redifferentiation capability were separately subjected to transcriptome sequencing analysis during the early redifferentiation stages (stage I, 1–3 d; stage II, 4–6 d; stage III, 7–9 d) along with their corresponding controls. A total of ~ 654.72 million cDNA clean reads were yielded, and 62.64%~ 69.21% clean reads were mapped to the reference genome for each library. In comparison with the control, the numbers of differentially expressed genes (DEGs) for the four inbred lines identified in the three stages ranged from 1694 to 7193. By analyzing the common and specific DEGs of the four materials, we found that there were 321 upregulated genes and 386 downregulated genes identified in the high-regeneration lines (141 and DH40), whereas 611 upregulated genes and 500 downregulated genes were specifically expressed in the low-regeneration lines (ZYDH381–1 and DH3732). Analysis of the DEG expression patterns indicated a sharp change at stage I in both the high- and low-regeneration lines, which suggested that stage I constitutes a crucial period for EC regeneration. Notably, the specific common DEGs of 141 and DH40 were mainly associated with photosynthesis, porphyrin and chlorophyll metabolism, ribosomes, and plant hormone signal transduction. In contrast, the DEGs in ZYDH381–1 and DH3732 were mainly related to taurine and hypotaurine metabolism, nitrogen metabolism, fatty acid elongation, starch and sucrose metabolism, phenylpropanoid biosynthesis, and plant circadian rhythm. More importantly, WOX genes, which have an ancestral role in embryo development in seed plants and promote the regeneration of transformed calli, were specifically upregulated in the two high-regeneration lines. Conclusions Our research contributes to the elucidation of molecular regulation during early redifferentiation in the maize embryonic callus. |
| first_indexed | 2024-04-13T03:13:05Z |
| format | Article |
| id | doaj.art-47341bde08b347c58f0ea94eac7b826b |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-04-13T03:13:05Z |
| publishDate | 2019-02-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-47341bde08b347c58f0ea94eac7b826b2022-12-22T03:04:59ZengBMCBMC Genomics1471-21642019-02-0120112210.1186/s12864-019-5506-7Transcriptome sequencing analysis of maize embryonic callus during early redifferentiationXiaoling Zhang0Yanli Wang1Yuanyuan Yan2Hua Peng3Yun Long4Yinchao Zhang5Zhou Jiang6Peng Liu7Chaoying Zou8Huanwei Peng9Guangtang Pan10Yaou Shen11Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural UniversityKey Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural UniversityKey Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural UniversitySichuan Tourism CollegeKey Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural UniversityKey Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural UniversityKey Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural UniversityKey Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural UniversityKey Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural UniversityInstitute of Animal Nutrition, Sichuan Agricultural UniversityKey Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural UniversityKey Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural UniversityAbstract Background Maize is one of the primary crops of genetic manipulation, which provides an excellent means of promoting stress resistance and increasing yield. However, the differences in induction and regeneration capacity of embryonic callus (EC) among various genotypes result in genotypic dependence in genetic transformation. Results In this study, embryonic calli of two maize inbred lines with strong redifferentiation capacity and two lines with weak redifferentiation capability were separately subjected to transcriptome sequencing analysis during the early redifferentiation stages (stage I, 1–3 d; stage II, 4–6 d; stage III, 7–9 d) along with their corresponding controls. A total of ~ 654.72 million cDNA clean reads were yielded, and 62.64%~ 69.21% clean reads were mapped to the reference genome for each library. In comparison with the control, the numbers of differentially expressed genes (DEGs) for the four inbred lines identified in the three stages ranged from 1694 to 7193. By analyzing the common and specific DEGs of the four materials, we found that there were 321 upregulated genes and 386 downregulated genes identified in the high-regeneration lines (141 and DH40), whereas 611 upregulated genes and 500 downregulated genes were specifically expressed in the low-regeneration lines (ZYDH381–1 and DH3732). Analysis of the DEG expression patterns indicated a sharp change at stage I in both the high- and low-regeneration lines, which suggested that stage I constitutes a crucial period for EC regeneration. Notably, the specific common DEGs of 141 and DH40 were mainly associated with photosynthesis, porphyrin and chlorophyll metabolism, ribosomes, and plant hormone signal transduction. In contrast, the DEGs in ZYDH381–1 and DH3732 were mainly related to taurine and hypotaurine metabolism, nitrogen metabolism, fatty acid elongation, starch and sucrose metabolism, phenylpropanoid biosynthesis, and plant circadian rhythm. More importantly, WOX genes, which have an ancestral role in embryo development in seed plants and promote the regeneration of transformed calli, were specifically upregulated in the two high-regeneration lines. Conclusions Our research contributes to the elucidation of molecular regulation during early redifferentiation in the maize embryonic callus.http://link.springer.com/article/10.1186/s12864-019-5506-7MaizeEmbryonic callusRedifferentiationRNA-Seq |
| spellingShingle | Xiaoling Zhang Yanli Wang Yuanyuan Yan Hua Peng Yun Long Yinchao Zhang Zhou Jiang Peng Liu Chaoying Zou Huanwei Peng Guangtang Pan Yaou Shen Transcriptome sequencing analysis of maize embryonic callus during early redifferentiation BMC Genomics Maize Embryonic callus Redifferentiation RNA-Seq |
| title | Transcriptome sequencing analysis of maize embryonic callus during early redifferentiation |
| title_full | Transcriptome sequencing analysis of maize embryonic callus during early redifferentiation |
| title_fullStr | Transcriptome sequencing analysis of maize embryonic callus during early redifferentiation |
| title_full_unstemmed | Transcriptome sequencing analysis of maize embryonic callus during early redifferentiation |
| title_short | Transcriptome sequencing analysis of maize embryonic callus during early redifferentiation |
| title_sort | transcriptome sequencing analysis of maize embryonic callus during early redifferentiation |
| topic | Maize Embryonic callus Redifferentiation RNA-Seq |
| url | http://link.springer.com/article/10.1186/s12864-019-5506-7 |
| work_keys_str_mv | AT xiaolingzhang transcriptomesequencinganalysisofmaizeembryoniccallusduringearlyredifferentiation AT yanliwang transcriptomesequencinganalysisofmaizeembryoniccallusduringearlyredifferentiation AT yuanyuanyan transcriptomesequencinganalysisofmaizeembryoniccallusduringearlyredifferentiation AT huapeng transcriptomesequencinganalysisofmaizeembryoniccallusduringearlyredifferentiation AT yunlong transcriptomesequencinganalysisofmaizeembryoniccallusduringearlyredifferentiation AT yinchaozhang transcriptomesequencinganalysisofmaizeembryoniccallusduringearlyredifferentiation AT zhoujiang transcriptomesequencinganalysisofmaizeembryoniccallusduringearlyredifferentiation AT pengliu transcriptomesequencinganalysisofmaizeembryoniccallusduringearlyredifferentiation AT chaoyingzou transcriptomesequencinganalysisofmaizeembryoniccallusduringearlyredifferentiation AT huanweipeng transcriptomesequencinganalysisofmaizeembryoniccallusduringearlyredifferentiation AT guangtangpan transcriptomesequencinganalysisofmaizeembryoniccallusduringearlyredifferentiation AT yaoushen transcriptomesequencinganalysisofmaizeembryoniccallusduringearlyredifferentiation |