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Wei J, Li H, Huang X, Zhao Y, Ouyang L, Wei M, Wang C, Wang J, Lu G. Elucidating the regulatory role of long non-coding RNAs in drought stress response during seed germination in leaf mustard. PeerJ 2024; 12:e17661. [PMID: 38978758 PMCID: PMC11229683 DOI: 10.7717/peerj.17661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 06/08/2024] [Indexed: 07/10/2024] Open
Abstract
Leaf mustard (Brassica juncea L. Czern & Coss), an important vegetable crop, experiences pronounced adversity due to seasonal drought stress, particularly at the seed germination stage. Although there is partial comprehension of drought-responsive genes, the role of long non-coding RNAs (lncRNAs) in adjusting mustard's drought stress response is largely unexplored. In this study, we showed that the drought-tolerant cultivar 'Weiliang' manifested a markedly lower base water potential (-1.073 MPa vs -0.437 MPa) and higher germination percentage (41.2% vs 0%) than the drought-susceptible cultivar 'Shuidong' under drought conditions. High throughput RNA sequencing techniques revealed a significant repertoire of lncRNAs from both cultivars during germination under drought stress, resulting in the identification of 2,087 differentially expressed lncRNAs (DELs) and their correspondingly linked 12,433 target genes. It was noted that 84 genes targeted by DEL exhibited enrichment in the photosynthesis pathway. Gene network construction showed that MSTRG.150397, a regulatory lncRNA, was inferred to potentially modulate key photosynthetic genes (Psb27, PetC, PetH, and PsbW), whilst MSTRG.107159 was indicated as an inhibitory regulator of six drought-responsive PIP genes. Further, weighted gene co-expression network analysis (WGCNA) corroborated the involvement of light intensity and stress response genes targeted by the identified DELs. The precision and regulatory impact of lncRNA were verified through qPCR. This study extends our knowledge of the regulatory mechanisms governing drought stress responses in mustard, which will help strategies to augment drought tolerance in this crop.
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Affiliation(s)
- Jinxing Wei
- Guangdong University of Petrochemical Technology, Maoming, China
| | - Haibo Li
- Shaoguan University, Shaoguan, China
| | - Xiaoer Huang
- Guangdong University of Petrochemical Technology, Maoming, China
| | - Yongguo Zhao
- Guangdong University of Petrochemical Technology, Maoming, China
| | - Lejun Ouyang
- Guangdong University of Petrochemical Technology, Maoming, China
| | - Mingken Wei
- Guangdong University of Petrochemical Technology, Maoming, China
| | - Chun Wang
- Guangdong University of Petrochemical Technology, Maoming, China
| | - Junxia Wang
- South China Agricultural University, Guangzhou, China
| | - Guangyuan Lu
- Guangdong University of Petrochemical Technology, Maoming, China
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Wei J, Xu L, Shi Y, Cheng T, Tan W, Zhao Y, Li C, Yang X, Ouyang L, Wei M, Wang J, Lu G. Transcriptome profile analysis of Indian mustard (Brassica juncea L.) during seed germination reveals the drought stress-induced genes associated with energy, hormone, and phenylpropanoid pathways. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 200:107750. [PMID: 37210860 DOI: 10.1016/j.plaphy.2023.107750] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 04/14/2023] [Accepted: 05/08/2023] [Indexed: 05/23/2023]
Abstract
Indian mustard (Brassica juncea L. Czern and Coss) is an important oil and vegetable crop frequently affected by seasonal drought stress during seed germination, which retards plant growth and causes yield loss considerably. However, the gene networks regulating responses to drought stress in leafy Indian mustard remain elusive. Here, we elucidated the underlying gene networks and pathways of drought response in leafy Indian mustard using next-generation transcriptomic techniques. Phenotypic analysis showed that the drought-tolerant leafy Indian mustard cv. 'WeiLiang' (WL) had a higher germination rate, antioxidant capacity, and better growth performance than the drought-sensitive cv. 'ShuiDong' (SD). Transcriptome analysis identified differentially expressed genes (DEGs) in both cultivars under drought stress during four germination time points (i.e., 0, 12, 24, and 36 h); most of which were classified as drought-responsive, seed germination, and dormancy-related genes. In the Kyoto Encyclopedia of Genes and Genome (KEGG) analyses, three main pathways (i.e., starch and sucrose metabolism, phenylpropanoid biosynthesis, and plant hormone signal transduction) were unveiled involved in response to drought stress during seed germination. Furthermore, Weighted Gene Co-expression Network Analysis (WGCNA) identified several hub genes (novel.12726, novel.1856, BjuB027900, BjuA003402, BjuA021578, BjuA005565, BjuB006596, novel.12977, and BjuA033308) associated with seed germination and drought stress in leafy Indian mustard. Taken together, these findings deepen our understanding of the gene networks for drought responses during seed germination in leafy Indian mustard and provide potential target genes for the genetic improvement of drought tolerance in this crop.
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Affiliation(s)
- Jinxing Wei
- College of Biology and Food Engineering, Guangdong University of Petrochemical Technology, Maoming, 525000, China; Integrative Microbiology Research Centre, College of Plant Protection, South China Agricultural University, Guangzhou, 510642, China
| | - Linghui Xu
- Integrative Microbiology Research Centre, College of Plant Protection, South China Agricultural University, Guangzhou, 510642, China; Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou, 510642, China
| | - Yu Shi
- Integrative Microbiology Research Centre, College of Plant Protection, South China Agricultural University, Guangzhou, 510642, China
| | - Tianfang Cheng
- Integrative Microbiology Research Centre, College of Plant Protection, South China Agricultural University, Guangzhou, 510642, China
| | - Wenlan Tan
- Integrative Microbiology Research Centre, College of Plant Protection, South China Agricultural University, Guangzhou, 510642, China
| | - Yongguo Zhao
- College of Biology and Food Engineering, Guangdong University of Petrochemical Technology, Maoming, 525000, China
| | - Chunsheng Li
- Hubei Engineering University, Xiaogan, 432000, China
| | - Xinyu Yang
- College of Biology and Food Engineering, Guangdong University of Petrochemical Technology, Maoming, 525000, China
| | - Lejun Ouyang
- College of Biology and Food Engineering, Guangdong University of Petrochemical Technology, Maoming, 525000, China
| | - Mingken Wei
- College of Biology and Food Engineering, Guangdong University of Petrochemical Technology, Maoming, 525000, China
| | - Junxia Wang
- Integrative Microbiology Research Centre, College of Plant Protection, South China Agricultural University, Guangzhou, 510642, China; Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou, 510642, China.
| | - Guangyuan Lu
- College of Biology and Food Engineering, Guangdong University of Petrochemical Technology, Maoming, 525000, China.
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Cao T, Sun J, Shan N, Chen X, Wang P, Zhu Q, Xiao Y, Zhang H, Zhou Q, Huang Y. Uncovering the genetic diversity of yams ( Dioscorea spp.) in China by combining phenotypic trait and molecular marker analyses. Ecol Evol 2021; 11:9970-9986. [PMID: 34367553 PMCID: PMC8328405 DOI: 10.1002/ece3.7727] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 05/12/2021] [Accepted: 05/14/2021] [Indexed: 11/12/2022] Open
Abstract
Yam is an important edible tuber and root plant worldwide; China as one of the native places of yams has many diverse local resources. The goal of this study was to clarify the genetic diversity of the commonly cultivated yam landraces and the genetic relationship between the main yam species in China. In this study, 26 phenotypic traits of 112 yam accessions from 21 provinces in China were evaluated, and 24 simple sequence repeat (SSR) and 29 sequence-related amplified polymorphism (SRAP) markers were used for the genetic diversity analysis. Phenotypic traits revealed that Dioscorea opposita had the highest genetic diversity, followed by D. alata, D. persimilis, D. fordii, and D. esculenta. Among the 26 phenotypic traits, the Shannon diversity indexes of leaf shape, petiole color, and stem color were high, and the range in the variation of tuber-related traits in the underground part was higher than that in the aboveground part. All accessions were divided into six groups by phenotypic trait clustering, which was also supported by principal component analysis (PCA). Molecular marker analysis showed that SSR and SRAP markers had good amplification effects and could effectively and accurately evaluate the genetic variation of yam. The unweighted pair-group method with arithmetic means analysis based on SSR-SRAP marker data showed that the 112 accessions were also divided into six groups, similar to the phenotypic trait results. The results of PCA and population structure analysis based on SSR-SRAP data also produced similar results. In addition, the analysis of the origin and genetic relationship of yam indicated that the species D. opposita may have originated from China. These results demonstrate the genetic diversity and distinctness among the widely cultivated species of Chinese yam and provide a theoretical reference for the classification, breeding, germplasm innovation, utilization, and variety protection of Chinese yam resources.
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Affiliation(s)
- Tianxu Cao
- Agronomy CollegeJiangxi Agricultural UniversityNanchangChina
- School of Advanced Agriculture and BioengineeringYangtze Normal UniversityChongqingChina
- Key Laboratory of Crop Physiology, Ecology and Genetic BreedingJiangxi Agricultural UniversityMinistry of Education of ChinaNanchangChina
| | - Jingyu Sun
- Agronomy CollegeJiangxi Agricultural UniversityNanchangChina
| | - Nan Shan
- Agronomy CollegeJiangxi Agricultural UniversityNanchangChina
| | - Xin Chen
- Agronomy CollegeJiangxi Agricultural UniversityNanchangChina
| | - Putao Wang
- Agronomy CollegeJiangxi Agricultural UniversityNanchangChina
| | - Qianglong Zhu
- Agronomy CollegeJiangxi Agricultural UniversityNanchangChina
| | - Yao Xiao
- Agronomy CollegeJiangxi Agricultural UniversityNanchangChina
| | - Hongyu Zhang
- Agronomy CollegeJiangxi Agricultural UniversityNanchangChina
| | - Qinghong Zhou
- Agronomy CollegeJiangxi Agricultural UniversityNanchangChina
| | - Yingjin Huang
- Agronomy CollegeJiangxi Agricultural UniversityNanchangChina
- Key Laboratory of Crop Physiology, Ecology and Genetic BreedingJiangxi Agricultural UniversityMinistry of Education of ChinaNanchangChina
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Li S, Wang Z, Su Y, Wang T. EST-SSR-based landscape genetics of Pseudotaxus chienii, a tertiary relict conifer endemic to China. Ecol Evol 2021; 11:9498-9515. [PMID: 34306638 PMCID: PMC8293779 DOI: 10.1002/ece3.7769] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 05/04/2021] [Accepted: 05/19/2021] [Indexed: 12/12/2022] Open
Abstract
Pseudotaxus chienii, belonging to the monotypic genus Pseudotaxus (Taxaceae), is a relict conifer endemic to China. Its populations are usually small and patchily distributed, having a low capacity of natural regeneration. To gain a clearer understanding of how landscape variables affect the local adaptation of P. chienii, we applied EST-SSR markers in conjunction with landscape genetics methods: (a) to examine the population genetic pattern and spatial genetic structure; (b) to perform genome scan and selection scan to identify outlier loci and the associated landscape variables; and (c) to model the ecological niche under climate change. As a result, P. chienii was found to have a moderate level of genetic variation and a high level of genetic differentiation. Its populations displayed a significant positive relationship between the genetic and geographical distance (i.e., "isolation by distance" pattern) and a strong fine-scale spatial genetic structure within 2 km. A putatively adaptive locus EMS6 (functionally annotated to cellulose synthase A catalytic subunit 7) was identified, which was found significantly associated with soil Cu, K, and Pb content and the combined effects of temperature and precipitation. Moreover, P. chienii was predicted to experience significant range contractions in future climate change scenarios. Our results highlight the potential of specific soil metal content and climate variables as the driving force of adaptive genetic differentiation in P. chienii. The data would also be useful to develop a conservation action plan for P. chienii.
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Affiliation(s)
- Shufeng Li
- School of Life SciencesSun Yat‐sen UniversityGuangzhouChina
| | - Zhen Wang
- School of Life SciencesSun Yat‐sen UniversityGuangzhouChina
| | - Yingjuan Su
- School of Life SciencesSun Yat‐sen UniversityGuangzhouChina
- Research Institute of Sun Yat‐sen University in ShenzhenShenzhenChina
| | - Ting Wang
- Research Institute of Sun Yat‐sen University in ShenzhenShenzhenChina
- College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
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Raza A, Razzaq A, Mehmood SS, Hussain MA, Wei S, He H, Zaman QU, Xuekun Z, Hasanuzzaman M. Omics: The way forward to enhance abiotic stress tolerance in Brassica napus L. GM CROPS & FOOD 2021; 12:251-281. [PMID: 33464960 PMCID: PMC7833762 DOI: 10.1080/21645698.2020.1859898] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Plant abiotic stresses negative affects growth and development, causing a massive reduction in global agricultural production. Rapeseed (Brassica napus L.) is a major oilseed crop because of its economic value and oilseed production. However, its productivity has been reduced by many environmental adversities. Therefore, it is a prime need to grow rapeseed cultivars, which can withstand numerous abiotic stresses. To understand the various molecular and cellular mechanisms underlying the abiotic stress tolerance and improvement in rapeseed, omics approaches have been extensively employed in recent years. This review summarized the recent advancement in genomics, transcriptomics, proteomics, metabolomics, and their imploration in abiotic stress regulation in rapeseed. Some persisting bottlenecks have been highlighted, demanding proper attention to fully explore the omics tools. Further, the potential prospects of the CRISPR/Cas9 system for genome editing to assist molecular breeding in developing abiotic stress-tolerant rapeseed genotypes have also been explained. In short, the combination of integrated omics, genome editing, and speed breeding can alter rapeseed production worldwide.
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Affiliation(s)
- Ali Raza
- Key Lab of Biology and Genetic Improvement of Oil Crops, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences (CAAS) , Wuhan, China
| | - Ali Razzaq
- Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture , Faisalabad, Pakistan
| | - Sundas Saher Mehmood
- Key Lab of Biology and Genetic Improvement of Oil Crops, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences (CAAS) , Wuhan, China
| | - Muhammad Azhar Hussain
- Key Lab of Biology and Genetic Improvement of Oil Crops, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences (CAAS) , Wuhan, China
| | - Su Wei
- Key Lab of Biology and Genetic Improvement of Oil Crops, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences (CAAS) , Wuhan, China
| | - Huang He
- Key Lab of Biology and Genetic Improvement of Oil Crops, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences (CAAS) , Wuhan, China
| | - Qamar U Zaman
- Key Lab of Biology and Genetic Improvement of Oil Crops, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences (CAAS) , Wuhan, China
| | - Zhang Xuekun
- College of Agriculture, Engineering Research Center of Ecology and Agricultural Use of Wetland of Ministry of Education, Yangtze University Jingzhou , China
| | - Mirza Hasanuzzaman
- Department of Agronomy, Faculty of Agriculture, Sher-e-Bangla Agricultural University , Dhaka, Bangladesh
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Feng T, Jia Q, Meng X, Chen X, Wang F, Chai W, Liang Z. Evaluation of genetic diversity and construction of DNA fingerprinting in Polygonatum Mill. based on EST-SSR and SRAP molecular markers. 3 Biotech 2020; 10:322. [PMID: 32656055 DOI: 10.1007/s13205-020-02316-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Accepted: 06/23/2020] [Indexed: 12/17/2022] Open
Abstract
Polygonatum sibiricum is widely consumed as a traditional Chinese herb and edible plant in China. Despite its nutritional and medical values, research on Polygonatum Mill. has been scarce, particularly as far as its genetic diversity is concerned. In this study, fourteen expressed sequence tag-derived simple sequence repeat (EST-SSR) and seven sequence-related amplified polymorphism (SRAP) markers were used to evaluate the genetic diversity in fifty Polygonatum Mill. accessions. The EST-SSRs and SRAPs produced 173 (90.58%) and 113 (93.39%) polymorphic bands, respectively. Unweighted Pair-Group Method Analysis (UPGMA) based on the combined data matrices of EST-SSRs and SRAPs divided the fifty Polygonatum Mill. accessions into fourteen groups. In addition, accessions of P. cyrtonema Hua obtained from Anhui and Zhejiang provinces were clustered according to their geographic origin. Furthermore, some accessions were gathered together based on species, such as P. kingianum Coll. et Hemsl, P. punctatum Royle ex Kunth, P. odoratum (Mill.) Druce, and P. sibiricum Red., and bootstrap analysis for clustering fully supported the grouping of the accessions. The Analysis of Molecular Variance (AMOVA) results revealed higher variation within populations (95%) rather than among populations (5%), indicating that Polygonatum Mill. has a low genetic differentiation between populations, and Principal Coordinate Analysis (PCoA) greatly supported the results of cluster analysis and AMOVA analysis. Finally, five markers which could produce abundant and stable bands were used to construct DNA fingerprinting database of Polygonatum Mill.. Our results demonstrated the utility of both EST-SSR and SRAP markers to successfully evaluate and identify Polygonatum Mill..
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Affiliation(s)
- Tinghui Feng
- Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018 Zhejiang China
| | - Qiaojun Jia
- Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018 Zhejiang China
| | - Xin Meng
- Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018 Zhejiang China
| | - Xiliang Chen
- Zhejiang WSKOO Biotechnology Co.,Ltd., Wuyi, 321200 Zhejiang China
| | - Feifeng Wang
- Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018 Zhejiang China
| | - Weiguo Chai
- Institute of Biotechnology, Hangzhou Academy of Agricultural Sciences, Hangzhou, 310024 Zhejiang China
| | - Zongsuo Liang
- Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018 Zhejiang China
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