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Zhang P, Chen S, Chen S, Zhu Y, Lin Y, Xu X, Liu Z, Zou S. Selection and Validation of qRT-PCR Internal Reference Genes to Study Flower Color Formation in Camellia impressinervis. Int J Mol Sci 2024; 25:3029. [PMID: 38474274 DOI: 10.3390/ijms25053029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 02/26/2024] [Accepted: 02/27/2024] [Indexed: 03/14/2024] Open
Abstract
Real-time quantitative PCR (qRT-PCR) is a pivotal technique for gene expression analysis. To ensure reliable and accurate results, the internal reference genes must exhibit stable expression across varied experimental conditions. Currently, no internal reference genes for Camellia impressinervis have been established. This study aimed to identify stable internal reference genes from eight candidates derived from different developmental stages of C. impressinervis flowers. We employed geNorm, NormFinder, and BestKeeper to evaluate the expression stability of these candidates, which was followed by a comprehensive stability analysis. The results indicated that CiTUB, a tubulin gene, exhibited the most stable expression among the eight reference gene candidates in the petals. Subsequently, CiTUB was utilized as an internal reference for the qRT-PCR analysis of six genes implicated in the petal pigment synthesis pathway of C. impressinervis. The qRT-PCR results were corroborated by transcriptome sequencing data, affirming the stability and suitability of CiTUB as a reference gene. This study marks the first identification of stable internal reference genes within the entire genome of C. impressinervis, establishing a foundation for future gene expression and functional studies. Identifying such stable reference genes is crucial for advancing molecular research on C. impressinervis.
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Affiliation(s)
- Peilan Zhang
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Shuying Chen
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Siyu Chen
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yuanming Zhu
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yuqing Lin
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xinyu Xu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zhongjian Liu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Shuangquan Zou
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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Zhang D, Tan Y, Dong F, Zhang Y, Huang Y, Zhou Y, Zhao Z, Yin Q, Xie X, Gao X, Zhang C, Tu N. The Expression of IbMYB1 Is Essential to Maintain the Purple Color of Leaf and Storage Root in Sweet Potato [ Ipomoea batatas (L.) Lam]. FRONTIERS IN PLANT SCIENCE 2021; 12:688707. [PMID: 34630449 PMCID: PMC8495246 DOI: 10.3389/fpls.2021.688707] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 08/16/2021] [Indexed: 05/14/2023]
Abstract
IbMYB1 was one of the major anthocyanin biosynthesis regulatory genes that has been identified and utilized in purple-fleshed sweet potato breeding. At least three members of this gene, namely, IbMYB1-1, -2a, and -2b, have been reported. We found that IbMYB1-2a and -2b are not necessary for anthocyanin accumulation in a variety of cultivated species (hexaploid) with purple shoots or purplish rings/spots of flesh. Transcriptomic and quantitative reverse transcription PCR (RT-qPCR) analyses revealed that persistent and vigorous expression of IbMYB1 is essential to maintain the purple color of leaves and storage roots in this type of cultivated species, which did not contain IbMYB1-2 gene members. Compared with IbbHLH2, IbMYB1 is an early response gene of anthocyanin biosynthesis in sweet potato. It cannot exclude the possibility that other MYBs participate in this gene regulation networks. Twenty-two MYB-like genes were identified from 156 MYBs to be highly positively or negatively correlated with the anthocyanin content in leaves or flesh. Even so, the IbMYB1 was most coordinately expressed with anthocyanin biosynthesis genes. Differences in flanking and coding sequences confirm that IbMYB2s, the highest similarity genes of IbMYB1, are not the members of IbMYB1. This phenomenon indicates that there may be more members of IbMYB1 in sweet potato, and the genetic complementation of these members is involved in the regulation of anthocyanin biosynthesis. The 3' flanking sequence of IbMYB1-1 is homologous to the retrotransposon sequence of TNT1-94. Transposon movement is involved in the formation of multiple members of IbMYB1. This study provides critical insights into the expression patterns of IbMYB1, which are involved in the regulation of anthocyanin biosynthesis in the leaf and storage root. Notably, our study also emphasized the presence of a multiple member of IbMYB1 for genetic improvement.
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Affiliation(s)
- Daowei Zhang
- College of Agronomy, Hunan Agricultural University, Changsha, China
- Crop Research Institute, Hunan Academy of Agricultural Sciences, Changsha, China
- *Correspondence: Daowei Zhang,
| | - Yongjun Tan
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Fang Dong
- Crop Research Institute, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Ya Zhang
- Crop Research Institute, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Yanlan Huang
- Crop Research Institute, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Yizhou Zhou
- Crop Research Institute, Hunan Academy of Agricultural Sciences, Changsha, China
| | - ZhiJian Zhao
- Dryland Crop Research Institute, Shao Yang Academy of Agriculture Science, Shaoyang, China
| | - Qin Yin
- Crop Research Institute, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Xuehua Xie
- Crop Research Institute, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Xiewang Gao
- Crop Research Institute, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Chaofan Zhang
- Crop Research Institute, Hunan Academy of Agricultural Sciences, Changsha, China
- Chaofan Zhang,
| | - Naimei Tu
- College of Agronomy, Hunan Agricultural University, Changsha, China
- Naimei Tu,
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Comparative transcriptome analysis implied a ZEP paralog was a key gene involved in carotenoid accumulation in yellow-fleshed sweetpotato. Sci Rep 2020; 10:20607. [PMID: 33244002 PMCID: PMC7693279 DOI: 10.1038/s41598-020-77293-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 11/09/2020] [Indexed: 12/29/2022] Open
Abstract
The mechanisms of carotenoid accumulation in yellow-fleshed sweetpotato cultivars are unclear. In this study, we compared the transcriptome profiles of a yellow-fleshed cultivar, Beniharuka (BH) and two of its spontaneous white-fleshed mutants (WH2 and WH3) to reveal the genes involved in yellow flesh. As a result of RNA sequencing, a total of 185 differentially expressed genes (DEGs) were commonly detected in WH2 and WH3 compared to BH. Of these genes, 85 DEGs and 100 DEGs were commonly upregulated and downregulated in WH2 and WH3 compared to BH, respectively. g1103.t1, a paralog of zeaxanthin epoxidase (ZEP), was only DEG common to WH2 and WH3 among 38 genes considered to be involved in carotenoid biosynthesis in storage roots. The expression level of g1103.t1 was also considerably lower in five white-fleshed cultivars than in five yellow-fleshed cultivars. Analysis of carotenoid composition in the storage roots showed that the epoxidised carotenoids were drastically reduced in both WH2 and WH3. Therefore, we propose that the ZEP paralog, g1103.t1, may be involved in carotenoid accumulation through the epoxidation of β-carotene and β-cryptoxanthin in sweetpotato.
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Qin Z, Hou F, Li A, Dong S, Huang C, Wang Q, Zhang L. Comparative analysis of full-length transcriptomes based on hybrid population reveals regulatory mechanisms of anthocyanin biosynthesis in sweet potato (Ipomoea batatas (L.) Lam). BMC PLANT BIOLOGY 2020; 20:299. [PMID: 32600332 PMCID: PMC7325064 DOI: 10.1186/s12870-020-02513-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 06/22/2020] [Indexed: 05/27/2023]
Abstract
BACKGROUND Sweet potato (Ipomoea batatas (L.) Lam.) is a highly heterozygous autohexaploid crop with high yield and high anthocyanin content. Purple sweet potato is the main source of anthocyanins, and the mechanism of anthocyanin biosynthesis in storage roots has not been fully revealed. RESULTS In order to reveal the mechanism of anthocyanin biosynthesis and identify new homologous genes involved in anthocyanin biosynthesis in the storage roots of sweet potato, we used Ningzishu 1 and Jizishu 2 as parents to construct a F1 hybrid population. Seven anthocyanin-containing lines and three anthocyanin-free lines were selected for full-length and second-generation transcriptome analyses. A total of 598,375 circular consensus sequencing reads were identified from full-length transcriptome sequencing. After analysis and correction of second-generation transcriptome data, 41,356 transcripts and 18,176 unigenes were obtained. Through a comparative analysis between anthocyanin-containing and anthocyanin-free groups 2329 unigenes were found to be significantly differentially expressed, of which 1235 were significantly up-regulated and 1094 were significantly down-regulated. GO enrichment analysis showed that the differentially expressed unigenes were significantly enriched in molecular function and biological process. KEGG enrichment analysis showed that the up-regulated unigenes were significantly enriched in the flavonoid biosynthesis and phenylpropanoid biosynthesis pathways, and the down-regulated unigenes were significantly enriched in the plant hormone signal transduction pathway. Weighted gene co-expression network analysis of differentially expressed unigenes revealed that anthocyanin biosynthesis genes were co-expressed with transcription factors such as MYB, bHLH and WRKY at the transcription level. CONCLUSIONS Our study will shed light on the regulatory mechanism of anthocyanin biosynthesis in sweet potato storage roots at the transcriptome level.
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Affiliation(s)
- Zhen Qin
- Crop Research Institute, Shandong Academy of Agricultural Sciences, No. 202 Industry North Road, Jinan City, 250100, Shandong Province, China
- Scientific Observing and Experimental Station of Tuber and Root Crops in Huang-Huai-Hai Region, Ministry of Agriculture, Jinan Shandong, China
| | - Fuyun Hou
- Crop Research Institute, Shandong Academy of Agricultural Sciences, No. 202 Industry North Road, Jinan City, 250100, Shandong Province, China
- Scientific Observing and Experimental Station of Tuber and Root Crops in Huang-Huai-Hai Region, Ministry of Agriculture, Jinan Shandong, China
| | - Aixian Li
- Crop Research Institute, Shandong Academy of Agricultural Sciences, No. 202 Industry North Road, Jinan City, 250100, Shandong Province, China
- Scientific Observing and Experimental Station of Tuber and Root Crops in Huang-Huai-Hai Region, Ministry of Agriculture, Jinan Shandong, China
| | - Shuxu Dong
- Crop Research Institute, Shandong Academy of Agricultural Sciences, No. 202 Industry North Road, Jinan City, 250100, Shandong Province, China
- Scientific Observing and Experimental Station of Tuber and Root Crops in Huang-Huai-Hai Region, Ministry of Agriculture, Jinan Shandong, China
| | - Chengxing Huang
- Jining Academy of Agricultural Sciences, Jining, Shandong, China
| | - Qingmei Wang
- Crop Research Institute, Shandong Academy of Agricultural Sciences, No. 202 Industry North Road, Jinan City, 250100, Shandong Province, China.
- Scientific Observing and Experimental Station of Tuber and Root Crops in Huang-Huai-Hai Region, Ministry of Agriculture, Jinan Shandong, China.
| | - Liming Zhang
- Crop Research Institute, Shandong Academy of Agricultural Sciences, No. 202 Industry North Road, Jinan City, 250100, Shandong Province, China.
- Scientific Observing and Experimental Station of Tuber and Root Crops in Huang-Huai-Hai Region, Ministry of Agriculture, Jinan Shandong, China.
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Arisha MH, Aboelnasr H, Ahmad MQ, Liu Y, Tang W, Gao R, Yan H, Kou M, Wang X, Zhang Y, Li Q. Transcriptome sequencing and whole genome expression profiling of hexaploid sweetpotato under salt stress. BMC Genomics 2020; 21:197. [PMID: 32131729 PMCID: PMC7057664 DOI: 10.1186/s12864-020-6524-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 01/21/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Purple-fleshed sweetpotato (PFSP) is one of the most important crops in the word which helps to bridge the food gap and contribute to solve the malnutrition problem especially in developing countries. Salt stress is seriously limiting its production and distribution. Due to lacking of reference genome, transcriptome sequencing is offering a rapid approach for crop improvement with promising agronomic traits and stress adaptability. RESULTS Five cDNA libraries were prepared from the third true leaf of hexaploid sweetpotato at seedlings stage (Xuzi-8 cultivar) treated with 200 mM NaCl for 0, 1, 6, 12, 48 h. Using second and third generation technology, Illumina sequencing generated 170,344,392 clean high-quality long reads that were assembled into 15,998 unigenes with an average length 2178 base pair and 96.55% of these unigenes were functionally annotated in the NR protein database. A number of 537 unigenes failed to hit any homologs which may be considered as novel genes. The current results indicated that sweetpotato plants behavior during the first hour of salt stress was different than the other three time points. Furthermore, expression profiling analysis identified 4, 479, 281, 508 significantly expressed unigenes in salt stress treated samples at the different time points including 1, 6, 12, 48 h, respectively as compared to control. In addition, there were 4, 1202, 764 and 2195 transcription factors differentially regulated DEGs by salt stress at different time points including 1, 6, 12, 48 h of salt stress. Validation experiment was done using 6 randomly selected unigenes and the results was in agree with the DEG results. Protein kinases include many genes which were found to play a vital role in phosphorylation process and act as a signal transductor/ receptor proteins in membranes. These findings suggest that salt stress tolerance in hexaploid sweetpotato plants may be mainly affected by TFs, PKs, Protein Detox and hormones related genes which contribute to enhance salt tolerance. CONCLUSION These transcriptome sequencing data of hexaploid sweetpotato under salt stress conditions can provide a valuable resource for sweetpotato breeding research and focus on novel insights into hexaploid sweetpotato responses to salt stress. In addition, it offers new candidate genes or markers that can be used as a guide to the future studies attempting to breed salt tolerance sweetpotato cultivars.
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Affiliation(s)
- Mohamed Hamed Arisha
- Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District / Key Laboratory of Biology and Genetic Improvement of Sweetpotato, Ministry of Agriculture / Sweetpotato Research Institute, CAAS, Xuzhou, 221131, Jiangsu, China
- Department of Horticulture, Faculty of Agriculture, Zagazig University, Zagazig, Sharkia, 44511, Egypt
| | - Hesham Aboelnasr
- Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District / Key Laboratory of Biology and Genetic Improvement of Sweetpotato, Ministry of Agriculture / Sweetpotato Research Institute, CAAS, Xuzhou, 221131, Jiangsu, China
- Plant pathology department, Agriculture and Biology research division, National research center, Giza, Egypt
| | - Muhammad Qadir Ahmad
- Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District / Key Laboratory of Biology and Genetic Improvement of Sweetpotato, Ministry of Agriculture / Sweetpotato Research Institute, CAAS, Xuzhou, 221131, Jiangsu, China
- Department of Plant Breeding and Genetics, Bahauddin Zakariya University, Multan, 60000, Pakistan
| | - Yaju Liu
- Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District / Key Laboratory of Biology and Genetic Improvement of Sweetpotato, Ministry of Agriculture / Sweetpotato Research Institute, CAAS, Xuzhou, 221131, Jiangsu, China
| | - Wei Tang
- Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District / Key Laboratory of Biology and Genetic Improvement of Sweetpotato, Ministry of Agriculture / Sweetpotato Research Institute, CAAS, Xuzhou, 221131, Jiangsu, China
| | - Runfei Gao
- Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District / Key Laboratory of Biology and Genetic Improvement of Sweetpotato, Ministry of Agriculture / Sweetpotato Research Institute, CAAS, Xuzhou, 221131, Jiangsu, China
| | - Hui Yan
- Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District / Key Laboratory of Biology and Genetic Improvement of Sweetpotato, Ministry of Agriculture / Sweetpotato Research Institute, CAAS, Xuzhou, 221131, Jiangsu, China
| | - Meng Kou
- Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District / Key Laboratory of Biology and Genetic Improvement of Sweetpotato, Ministry of Agriculture / Sweetpotato Research Institute, CAAS, Xuzhou, 221131, Jiangsu, China
| | - Xin Wang
- Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District / Key Laboratory of Biology and Genetic Improvement of Sweetpotato, Ministry of Agriculture / Sweetpotato Research Institute, CAAS, Xuzhou, 221131, Jiangsu, China
| | - Yungang Zhang
- Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District / Key Laboratory of Biology and Genetic Improvement of Sweetpotato, Ministry of Agriculture / Sweetpotato Research Institute, CAAS, Xuzhou, 221131, Jiangsu, China
| | - Qiang Li
- Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District / Key Laboratory of Biology and Genetic Improvement of Sweetpotato, Ministry of Agriculture / Sweetpotato Research Institute, CAAS, Xuzhou, 221131, Jiangsu, China.
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Yang Y, Shi D, Wang Y, Zhang L, Chen X, Yang X, Xiong H, Bhattarai G, Ravelombola W, Olaoye D, Yang G, Shi A. Transcript profiling for regulation of sweet potato skin color in Sushu8 and its mutant Zhengshu20. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2020; 148:1-9. [PMID: 31923733 DOI: 10.1016/j.plaphy.2019.12.035] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Revised: 12/24/2019] [Accepted: 12/26/2019] [Indexed: 06/10/2023]
Abstract
Sweet potato [Ipomoea batatas (L.) Lam.] (2n = 6x = 90) is an economic important autopolyploid species and its varieties differ regarding storage root skin and flesh colors. Two sweet potato genetic lines, Sushu8 (with red skin) and its mutant Zhengshu20, which produced different colored storage roots, were used in this study. The total flavonoid, carotenoid, and anthocyanin contents of the two lines were analyzed and revealed that anthocyanin was primarily responsible for the skin color difference. In addition, the early storage root expanding stage was the key period for anthocyanin accumulation in Sushu8. A total of 24 samples, including the skins of the fibrous root and the storage root at the early and middle expanding stages as well as the flesh of the storage root at the middle expanding stage, were analyzed based on differentially expressed genes identified by transcriptome sequencing and a weighted gene co-expression network analysis. Two gene modules highly related with the regulation of sweet potato skin color through stress responses as well as starch synthesis and glucose metabolism were identified. Furthermore, the WRKY75 transcription factor gene, fructose-bisphosphate aldolase 2 gene, and other DEGs highly related to the regulation of anthocyanin metabolism were enriched in the brown and green modules.
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Affiliation(s)
- Yufeng Yang
- Cereal Crop Institute, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China; Department of Horticulture, University of Arkansas, Fayetteville, AR72701, USA.
| | - Dianyi Shi
- College of Life Sciences, Neijiang Normal University, Neijiang, 641100, China.
| | - Yannan Wang
- Cereal Crop Institute, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China.
| | - Li Zhang
- Cereal Crop Institute, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China.
| | - Xiangong Chen
- Cereal Crop Institute, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China.
| | - Xiaoping Yang
- Cereal Crop Institute, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China.
| | - Haizheng Xiong
- Department of Horticulture, University of Arkansas, Fayetteville, AR72701, USA.
| | - Gehendra Bhattarai
- Department of Horticulture, University of Arkansas, Fayetteville, AR72701, USA.
| | - Waltram Ravelombola
- Department of Horticulture, University of Arkansas, Fayetteville, AR72701, USA.
| | - Dotun Olaoye
- Department of Horticulture, University of Arkansas, Fayetteville, AR72701, USA.
| | - Guohong Yang
- Cereal Crop Institute, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China.
| | - Ainong Shi
- Department of Horticulture, University of Arkansas, Fayetteville, AR72701, USA.
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Xie Z, Zhou Z, Li H, Yu J, Jiang J, Tang Z, Ma D, Zhang B, Han Y, Li Z. High throughput sequencing identifies chilling responsive genes in sweetpotato (Ipomoea batatas Lam.) during storage. Genomics 2019; 111:1006-1017. [DOI: 10.1016/j.ygeno.2018.05.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 05/13/2018] [Accepted: 05/18/2018] [Indexed: 01/20/2023]
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De novo transcriptome sequencing and gene expression profiling of sweet potato leaves during low temperature stress and recovery. Gene 2019; 700:23-30. [DOI: 10.1016/j.gene.2019.02.097] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 02/07/2019] [Accepted: 02/23/2019] [Indexed: 01/19/2023]
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Kou M, Liu YJ, Li ZY, Zhang YG, Tang W, Yan H, Wang X, Chen XG, Su ZX, Arisha MH, Li Q, Ma DF. A novel glutathione S-transferase gene from sweetpotato, IbGSTF4, is involved in anthocyanin sequestration. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2019; 135:395-403. [PMID: 30634134 DOI: 10.1016/j.plaphy.2018.12.028] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 12/26/2018] [Accepted: 12/30/2018] [Indexed: 05/11/2023]
Abstract
Anthocyanins are synthesized by multi-enzyme complexes localized at the cytoplasmic surface of the endoplasmic reticulum (synthesis site), and transported to the destination site, the vacuole. Three mechanisms for the vacuolar accumulation of anthocyanin in plant species have been proposed. Previous studies have indicated that glutathione S-transferase (GST) genes from model and ornamental plants are involved in anthocyanin transportation. In the present study, an anthocyanin-related GST, IbGSTF4, was identified and characterized based on transcriptome results. Phylogenetic analysis revealed that IbGSTF4 was most closely correlated to PhAN9 and CkmGST3, the anthocyanin-related GST of Petunia hybrida and Cyclamen. Furthermore, the expression analysis revealed that IbGSTF4 is strongly expressed in pigmented tissues, when compared to green organs, which is in agreement to the ability to correlate with anthocyanin accumulation. A GST activity assay uncovered that the IbGST4 protein owned similar activities with the GST family. Furthermore, the molecular functional complementation of Arabidopsis thaliana mutant tt19 demonstrated that IbGSTF4 might play a vital role in the vacuole sequestration of anthocyanin in sweetpotato. Moreover, the dual luciferase assay revealed that the LUC driven by the promoter of IbGSTF4 could not be directly activated by IbMYB1, suggesting that the regulatory mechanism of anthocyanin accumulation and sequestration in sweetpotato was intricate.
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Affiliation(s)
- Meng Kou
- School of Life Science, Jiangsu Normal University, Xuzhou 221116, PR China; Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District/Sweetpotato Research Institute, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Breeding of Sweetpotato, Ministry of Agriculture, Xuzhou 221131, PR China
| | - Ya-Ju Liu
- School of Life Science, Jiangsu Normal University, Xuzhou 221116, PR China; Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District/Sweetpotato Research Institute, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Breeding of Sweetpotato, Ministry of Agriculture, Xuzhou 221131, PR China
| | - Zong-Yun Li
- School of Life Science, Jiangsu Normal University, Xuzhou 221116, PR China
| | - Yun-Gang Zhang
- Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District/Sweetpotato Research Institute, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Breeding of Sweetpotato, Ministry of Agriculture, Xuzhou 221131, PR China
| | - Wei Tang
- Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District/Sweetpotato Research Institute, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Breeding of Sweetpotato, Ministry of Agriculture, Xuzhou 221131, PR China
| | - Hui Yan
- Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District/Sweetpotato Research Institute, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Breeding of Sweetpotato, Ministry of Agriculture, Xuzhou 221131, PR China
| | - Xin Wang
- Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District/Sweetpotato Research Institute, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Breeding of Sweetpotato, Ministry of Agriculture, Xuzhou 221131, PR China
| | - Xiao-Guang Chen
- Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District/Sweetpotato Research Institute, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Breeding of Sweetpotato, Ministry of Agriculture, Xuzhou 221131, PR China
| | - Zai-Xing Su
- Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District/Sweetpotato Research Institute, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Breeding of Sweetpotato, Ministry of Agriculture, Xuzhou 221131, PR China
| | | | - Qiang Li
- School of Life Science, Jiangsu Normal University, Xuzhou 221116, PR China; Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District/Sweetpotato Research Institute, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Breeding of Sweetpotato, Ministry of Agriculture, Xuzhou 221131, PR China.
| | - Dai-Fu Ma
- School of Life Science, Jiangsu Normal University, Xuzhou 221116, PR China; Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District/Sweetpotato Research Institute, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Breeding of Sweetpotato, Ministry of Agriculture, Xuzhou 221131, PR China.
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10
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Kim HS, Yoon UH, Lee CJ, Kim SE, Ji CY, Kwak SS. Status of research on the sweetpotato biotechnology and prospects of the molecular breeding on marginal lands. ACTA ACUST UNITED AC 2018. [DOI: 10.5010/jpb.2018.45.3.196] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Ho Soo Kim
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea
| | - Ung-Han Yoon
- Genomics Division, National Academy of Agricultural Science, Jeonju 54875, Korea
| | - Chan-Ju Lee
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea
| | - So-Eun Kim
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea
| | - Chang Yoon Ji
- Research & Development Center, Korea Scientific Technique Industry Co., Ltd., 67, Saneop-ro 92, Gwonseon-gu, Suwon-si 16643, Korea
| | - Sang-Soo Kwak
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea
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Yang Y, Wang Y, Jia L, Yang G, Xu X, Zhai H, He S, Li J, Dai X, Qin N, Zhu C, Liu Q. Involvement of an ABI-like protein and a Ca2+-ATPase in drought tolerance as revealed by transcript profiling of a sweetpotato somatic hybrid and its parents Ipomoea batatas (L.) Lam. and I. triloba L. PLoS One 2018; 13:e0193193. [PMID: 29466419 PMCID: PMC5821372 DOI: 10.1371/journal.pone.0193193] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 02/06/2018] [Indexed: 12/14/2022] Open
Abstract
Previously, we obtained the sweetpotato somatic hybrid KT1 from a cross between sweetpotato (Ipomoea batatas (L.) Lam.) cv. Kokei No. 14 and its drought-tolerant wild relative I. triloba L. KT1 not only inherited the thick storage root characteristic of Kokei No. 14 but also the drought-tolerance trait of I. triloba L. The aim of this study was to explore the molecular mechanism of the drought tolerance of KT1. Four-week-old in vitro-grown plants of KT1, Kokei No. 14, and I. triloba L. were subjected to a simulated drought stress treatment (30% PEG6000) for 0, 6, 12 and 24 h. Total RNA was extracted from samples at each time point, and then used for transcriptome sequencing. The gene transcript profiles of KT1 and its parents were compared to identify differentially expressed genes, and drought-related modules were screened by a weighted gene co-expression network analysis. The functions of ABI-like protein and Ca2+-ATPase, two proteins screened from the cyan and light yellow modules, were analyzed in terms of their potential roles in drought tolerance in KT1 and its parents. These analyses of the drought responses of KT1 and its somatic donors at the transcriptional level provide new annotations for the molecular mechanism of drought tolerance in the somatic hybrid KT1 and its parents.
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Affiliation(s)
- Yufeng Yang
- Food Crop Institute, Henan Academy of Agricultural Sciences, Zhengzhou, China
- Key Laboratory of Sweetpotato Biology and Biotechnology, Ministry of Agriculture, China Agricultural University, Beijing, China
| | - Yannan Wang
- Food Crop Institute, Henan Academy of Agricultural Sciences, Zhengzhou, China
- Key Laboratory of Sweetpotato Biology and Biotechnology, Ministry of Agriculture, China Agricultural University, Beijing, China
| | - Licong Jia
- Key Laboratory of Sweetpotato Biology and Biotechnology, Ministry of Agriculture, China Agricultural University, Beijing, China
| | - Guohong Yang
- Food Crop Institute, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Xinzhi Xu
- Food Crop Institute, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Hong Zhai
- Key Laboratory of Sweetpotato Biology and Biotechnology, Ministry of Agriculture, China Agricultural University, Beijing, China
| | - Shaozhen He
- Key Laboratory of Sweetpotato Biology and Biotechnology, Ministry of Agriculture, China Agricultural University, Beijing, China
| | - Junxia Li
- Food Crop Institute, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Xiaodong Dai
- Food Crop Institute, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Na Qin
- Food Crop Institute, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Cancan Zhu
- Food Crop Institute, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Qingchang Liu
- Key Laboratory of Sweetpotato Biology and Biotechnology, Ministry of Agriculture, China Agricultural University, Beijing, China
- * E-mail:
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Li J, Wang C, Han X, Qi W, Chen Y, Wang T, Zheng Y, Zhao X. Transcriptome Analysis to Identify the Putative Biosynthesis and Transport Genes Associated with the Medicinal Components of Achyranthes bidentata Bl. FRONTIERS IN PLANT SCIENCE 2016; 7:1860. [PMID: 28018396 PMCID: PMC5149546 DOI: 10.3389/fpls.2016.01860] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Accepted: 11/25/2016] [Indexed: 05/27/2023]
Abstract
Achyranthes bidentata is a popular perennial medicine herb used for 1000s of years in China to treat various diseases. Although this herb has multiple pharmaceutical purposes in China, no transcriptomic information has been reported for this species. In addition, the understanding of several key pathways and enzymes involved in the biosynthesis of oleanolic acid and ecdysterone, two pharmacologically active classes of metabolites and major chemical constituents of A. bidentata root extracts, is limited. The aim of the present study was to characterize the transcriptome profile of the roots and leaves of A. bidentata to uncover the biosynthetic and transport mechanisms of the active components. In this study, we identified 100,987 transcripts, with an average length of 1146.8 base pairs. A total of 31,634 (31.33%) unigenes were annotated, and 12,762 unigenes were mapped to 303 pathways according to the Kyoto Encyclopedia of Genes and Genomes pathway database. Moreover, we identified a total of 260 oleanolic acid and ecdysterone genes encoding biosynthetic enzymes. Furthermore, the key enzymes involved in the oleanolic acid and ecdysterone synthesis pathways were analyzed using quantitative real-time polymerase chain reaction, revealing that the roots expressed these enzymes to a greater extent than the leaves. In addition, we identified 85 ATP-binding cassette transporters, some of which might be involved in the translocation of secondary metabolites.
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Affiliation(s)
- Jinting Li
- College of Life Sciences, Henan Normal UniversityXinxiang, China
- Engineering Laboratory of Biotechnology for Green Medicinal Plant of Henan ProvinceXinxiang, China
| | - Can Wang
- College of Life Sciences, Henan Normal UniversityXinxiang, China
| | - Xueping Han
- College of Life Sciences, Henan Normal UniversityXinxiang, China
| | - Wanzhen Qi
- College of Life Sciences, Henan Normal UniversityXinxiang, China
| | - Yanqiong Chen
- College of Life Sciences, Henan Normal UniversityXinxiang, China
| | - Taixia Wang
- College of Life Sciences, Henan Normal UniversityXinxiang, China
| | - Yi Zheng
- Boyce Thompson Institute, IthacaNY, USA
| | - Xiting Zhao
- College of Life Sciences, Henan Normal UniversityXinxiang, China
- Engineering Laboratory of Biotechnology for Green Medicinal Plant of Henan ProvinceXinxiang, China
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Si Z, Du B, Huo J, He S, Liu Q, Zhai H. A genome-wide BAC-end sequence survey provides first insights into sweetpotato (Ipomoea batatas (L.) Lam.) genome composition. BMC Genomics 2016; 17:945. [PMID: 27871234 PMCID: PMC5117676 DOI: 10.1186/s12864-016-3302-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2016] [Accepted: 11/15/2016] [Indexed: 11/14/2022] Open
Abstract
Background Sweetpotato, Ipomoea batatas (L.) Lam., is an important food crop widely grown in the world. However, little is known about the genome of this species because it is a highly heterozygous hexaploid. Gaining a more in-depth knowledge of sweetpotato genome is therefore necessary and imperative. In this study, the first bacterial artificial chromosome (BAC) library of sweetpotato was constructed. Clones from the BAC library were end-sequenced and analyzed to provide genome-wide information about this species. Results The BAC library contained 240,384 clones with an average insert size of 101 kb and had a 7.93–10.82 × coverage of the genome, and the probability of isolating any single-copy DNA sequence from the library was more than 99%. Both ends of 8310 BAC clones randomly selected from the library were sequenced to generate 11,542 high-quality BAC-end sequences (BESs), with an accumulative length of 7,595,261 bp and an average length of 658 bp. Analysis of the BESs revealed that 12.17% of the sweetpotato genome were known repetitive DNA, including 7.37% long terminal repeat (LTR) retrotransposons, 1.15% Non-LTR retrotransposons and 1.42% Class II DNA transposons etc., 18.31% of the genome were identified as sweetpotato-unique repetitive DNA and 10.00% of the genome were predicted to be coding regions. In total, 3,846 simple sequences repeats (SSRs) were identified, with a density of one SSR per 1.93 kb, from which 288 SSRs primers were designed and tested for length polymorphism using 20 sweetpotato accessions, 173 (60.07%) of them produced polymorphic bands. Sweetpotato BESs had significant hits to the genome sequences of I. trifida and more matches to the whole-genome sequences of Solanum lycopersicum than those of Vitis vinifera, Theobroma cacao and Arabidopsis thaliana. Conclusions The first BAC library for sweetpotato has been successfully constructed. The high quality BESs provide first insights into sweetpotato genome composition, and have significant hits to the genome sequences of I. trifida and more matches to the whole-genome sequences of Solanum lycopersicum. These resources as a robust platform will be used in high-resolution mapping, gene cloning, assembly of genome sequences, comparative genomics and evolution for sweetpotato. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3302-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zengzhi Si
- Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis and Utilization, Ministry of Education, China Agricultural University, Beijing, 100193, China
| | - Bing Du
- Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis and Utilization, Ministry of Education, China Agricultural University, Beijing, 100193, China
| | - Jinxi Huo
- Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis and Utilization, Ministry of Education, China Agricultural University, Beijing, 100193, China
| | - Shaozhen He
- Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis and Utilization, Ministry of Education, China Agricultural University, Beijing, 100193, China
| | - Qingchang Liu
- Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis and Utilization, Ministry of Education, China Agricultural University, Beijing, 100193, China.
| | - Hong Zhai
- Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis and Utilization, Ministry of Education, China Agricultural University, Beijing, 100193, China.
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