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Goli RC, Mahar K, Manohar PS, Chishi KG, Prabhu IG, Choudhary S, Rathi P, Chinnareddyvari CS, Haritha P, Metta M, Shetkar M, Kumar A, N D CP, Vidyasagar, Sukhija N, Kanaka KK. Insights from homozygous signatures of cervus nippon revealed genetic architecture for components of fitness. Mamm Genome 2024:10.1007/s00335-024-10064-1. [PMID: 39191871 DOI: 10.1007/s00335-024-10064-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Accepted: 08/13/2024] [Indexed: 08/29/2024]
Abstract
This study investigates the genomic landscape of Sika deer populations, emphasizing the detection and characterization of runs of homozygosity (ROH) and their contribution towards components of fitness. Using 85,001 high-confidence SNPs, the investigation into ROH distribution unveiled nuanced patterns of autozygosity across individuals especially in 2 out of the 8 farms, exhibiting elevated ROH levels and mean genome coverage under ROH segments. The prevalence of shorter ROH segments (0.5-4 Mb) suggests historical relatedness and potential selective pressures within these populations. Intriguingly, despite observed variations in ROH profiles, the overall genomic inbreeding coefficient (FROH) remained relatively low across all farms, indicating a discernible degree of genetic exchange and effective mitigation of inbreeding within the studied Sika deer populations. Consensus ROH (cROH) were found to harbor genes for important functions viz., EGFLAM gene which is involved in the vision function of the eye, SKP2 gene which regulates cell cycle, CAPSL involved in adipogenesis, SPEF2 which is essential for sperm flagellar assembly, DCLK3 involved in the heat stress. This first ever study on ROH in Sika deer, to shed light on the adaptive role of genes in these homozygous regions. The insights garnered from this study have broader implications in the management of genetic diversity in this vulnerable species.
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Affiliation(s)
- Rangasai Chandra Goli
- ICAR-National Dairy Research Institute, Karnal, Haryana, India
- ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, India
| | - Karan Mahar
- ICAR-National Dairy Research Institute, Karnal, Haryana, India
| | - Peela Sai Manohar
- ICAR-Indian Veterinary Research Institute, Izatnagar, Uttar Pradesh, India
| | - Kiyevi G Chishi
- ICAR-National Dairy Research Institute, Karnal, Haryana, India
- ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, India
| | | | - Sonu Choudhary
- ICAR-National Dairy Research Institute, Karnal, Haryana, India
- ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, India
| | - Pallavi Rathi
- ICAR-National Dairy Research Institute, Karnal, Haryana, India
- ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, India
| | - Chandana Sree Chinnareddyvari
- ICAR-National Dairy Research Institute, Karnal, Haryana, India
- ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, India
| | - Pala Haritha
- ICAR-National Dairy Research Institute, Karnal, Haryana, India
| | - Muralidhar Metta
- College of Veterinary Science, SVVU, Garividi, Andhra Pradesh, India
| | - Mahantesh Shetkar
- College of Veterinary Sciences and Animal Husbandry, DUVASU, Mathura, Uttar Pradesh, India
| | - Amit Kumar
- ICAR- Indian Institute of Agricultural Biotechnology, Ranchi, Jharkhand, India
| | - Chethan Patil N D
- Department of Agricultural Economics & Extension, Lovely Professional University, Punjab, India
| | - Vidyasagar
- Veterinary College, KVAFSU, Bidar, Karnataka, India
| | - Nidhi Sukhija
- CSB-Central Tasar Research and Training Institute, Ranchi, Jharkhand, India.
| | - K K Kanaka
- ICAR- Indian Institute of Agricultural Biotechnology, Ranchi, Jharkhand, India
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Kumar D, Venkadesan S, Prabha R, Begam S, Dutta B, Mishra DC, Chaturvedi KK, Jha GK, Solanke AU, Sevanthi AM. RiceMetaSys: Drought-miR, a one-stop solution for drought responsive miRNAs-mRNA module in rice. Database (Oxford) 2024; 2024:baae076. [PMID: 39167719 PMCID: PMC11338179 DOI: 10.1093/database/baae076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 05/27/2024] [Accepted: 08/08/2024] [Indexed: 08/23/2024]
Abstract
MicroRNAs are key players involved in stress responses in plants and reports are available on the role of miRNAs in drought stress response in rice. This work reports the development of a database, RiceMetaSys: Drought-miR, based on the meta-analysis of publicly available sRNA datasets. From 28 drought stress-specific sRNA datasets, we identified 216 drought-responsive miRNAs (DRMs). The major features of the database include genotype-, tissue- and miRNA ID-specific search options and comparison of genotypes to identify common miRNAs. Co-localization of the DRMs with the known quantitative trait loci (QTLs), i.e., meta-QTL regions governing drought tolerance in rice pertaining to different drought adaptive traits, narrowed down this to 37 promising DRMs. To identify the high confidence target genes of DRMs under drought stress, degradome datasets and web resource on drought-responsive genes (RiceMetaSys: DRG) were used. Out of the 216 unique DRMs, only 193 had targets with high stringent parameters. Out of the 1081 target genes identified by Degradome datasets, 730 showed differential expression under drought stress in at least one accession. To retrieve complete information on the target genes, the database has been linked with RiceMetaSys: DRG. Further, we updated the RiceMetaSys: DRGv1 developed earlier with the addition of DRGs identified from RNA-seq datasets from five rice genotypes. We also identified 759 putative novel miRNAs and their target genes employing stringent criteria. Novel miRNA search has all the search options of known miRNAs and additionally, it gives information on their in silico validation features. Simple sequence repeat markers for both the miRNAs and their target genes have also been designed and made available in the database. Network analysis of the target genes identified 60 hub genes which primarily act through abscisic acid pathway and jasmonic acid pathway. Co-localization of the hub genes with the meta-QTL regions governing drought tolerance narrowed down this to 16 most promising DRGs. Database URL: http://14.139.229.201/RiceMetaSys_miRNA Updated database of RiceMetaSys URL: http://14.139.229.201/RiceMetaSysA/Drought/.
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Affiliation(s)
- Deepesh Kumar
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi 110012, India
- The Graduate School, ICAR-Indian Agricultural Research Institute, Pusa Campus, New Delhi 110012, India
| | | | - Ratna Prabha
- AKMU, ICAR-Indian Agricultural Research Institute, Pusa Campus, New Delhi 110012, India
| | - Shbana Begam
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi 110012, India
| | - Bipratip Dutta
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi 110012, India
- The Graduate School, ICAR-Indian Agricultural Research Institute, Pusa Campus, New Delhi 110012, India
| | - Dwijesh C Mishra
- ICAR-Indian Agricultural Statistics Research Institute, Pusa Campus, New Delhi 110012, India
| | - K K Chaturvedi
- ICAR-Indian Agricultural Statistics Research Institute, Pusa Campus, New Delhi 110012, India
| | - Girish Kumar Jha
- ICAR-Indian Agricultural Statistics Research Institute, Pusa Campus, New Delhi 110012, India
| | - Amolkumar U Solanke
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi 110012, India
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Dutta G, Alex R, Singh A, Gowane GR, Vohra V, De S, Verma A, Ludri A. Functional transcriptome analysis revealed upregulation of MAPK-SMAD signalling pathways in chronic heat stress in crossbred cattle. INTERNATIONAL JOURNAL OF BIOMETEOROLOGY 2024; 68:1371-1385. [PMID: 38720050 DOI: 10.1007/s00484-024-02672-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 02/14/2024] [Accepted: 03/01/2024] [Indexed: 07/26/2024]
Abstract
Animal geneticists and breeders have the impending challenge of enhancing the resilience of Indian livestock to heat stress through better selection strategies. Climate change's impact on livestock is more intense in tropical countries like India where dairy cattle crossbreeds are more sensitive to heat stress. The main reason for this study was to find the missing relative changes in transcript levels in thermo-neutral and heat stress conditions in crossbred cattle through whole-transcriptome analysis of RNA-Seq data. Differentially expressed genes (DEGs) identified based on the minimum log twofold change value and false discovery rate 0.05 revealed 468 up-regulated genes and 2273 down-regulated significant genes. Functional annotation and pathway analysis of these significant DEGs were compared based on Gene Ontology (Biological process), Kyoto Encyclopedia of Genes and Genome (KEGG), and Reactome pathways using g: Profiler, ShinyGO v0.76, and iDEP.951 web tools. On finding network visualization, the most over-represented and correlated pathways were neuronal and sensory organ development, calcium signalling pathway, Mitogen-activated protein kinase (MAPK) and Smad signalling pathway, Ras-proximate-1, or Ras-related protein 1 (Rap 1) signalling pathway, apoptosis, and oxidative stress. Similarly, down-regulated genes were most expressed in mRNA processing, immune system, B-cell receptor signalling pathway, Nucleotide oligomerization domain (NOD)-like receptors (NLRs) signalling pathway and nonsense-mediated decay (NMD) pathway. The heat stress-responsive genes identified in this study will facilitate our understanding of the molecular basis for climate resilience and heat tolerance in Indian dairy crossbreeds.
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Affiliation(s)
- Gaurav Dutta
- Animal Genetics and Breeding, ICAR-National Dairy Research Institute, Karnal, Haryana, 132001, India
| | - Rani Alex
- Animal Genetics and Breeding, ICAR-National Dairy Research Institute, Karnal, Haryana, 132001, India.
| | - Ayushi Singh
- Animal Genetics and Breeding, ICAR-National Dairy Research Institute, Karnal, Haryana, 132001, India
| | - Gopal R Gowane
- Animal Genetics and Breeding, ICAR-National Dairy Research Institute, Karnal, Haryana, 132001, India
| | - Vikas Vohra
- Animal Genetics and Breeding, ICAR-National Dairy Research Institute, Karnal, Haryana, 132001, India
| | - Sachidanandan De
- Animal Genetics and Breeding, ICAR-National Dairy Research Institute, Karnal, Haryana, 132001, India
| | - Archana Verma
- Animal Genetics and Breeding, ICAR-National Dairy Research Institute, Karnal, Haryana, 132001, India
| | - Ashutosh Ludri
- Animal Genetics and Breeding, ICAR-National Dairy Research Institute, Karnal, Haryana, 132001, India
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Li C, Yan L, Liu Q, Tian R, Wang S, Umer MF, Jalil MJ, Lohani MN, Liu Y, Tang H, Xu Q, Jiang Q, Chen G, Qi P, Jiang Y, Gou L, Yao Q, Zheng Y, Wei Y, Ma J. Integration of transcriptomics, metabolomics, and hormone analysis revealed the formation of lesion spots inhibited by GA and CTK was related to cell death and disease resistance in bread wheat (Triticum aestivum L.). BMC PLANT BIOLOGY 2024; 24:558. [PMID: 38877396 PMCID: PMC11179392 DOI: 10.1186/s12870-024-05212-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Accepted: 05/28/2024] [Indexed: 06/16/2024]
Abstract
BACKGROUND Wheat is one of the important grain crops in the world. The formation of lesion spots related to cell death is involved in disease resistance, whereas the regulatory pathway of lesion spot production and resistance mechanism to pathogens in wheat is largely unknown. RESULTS In this study, a pair of NILs (NIL-Lm5W and NIL-Lm5M) was constructed from the BC1F4 population by the wheat lesion mimic mutant MC21 and its wild genotype Chuannong 16. The formation of lesion spots in NIL-Lm5M significantly increased its resistance to stripe rust, and NIL-Lm5M showed superiour agronomic traits than NIL-Lm5W under stripe rust infection.Whereafter, the NILs were subjected to transcriptomic (stage N: no spots; stage S, only a few spots; and stage M, numerous spots), metabolomic (stage N and S), and hormone analysis (stage S), with samples taken from normal plants in the field. Transcriptomic analysis showed that the differentially expressed genes were enriched in plant-pathogen interaction, and defense-related genes were significantly upregulated following the formation of lesion spots. Metabolomic analysis showed that the differentially accumulated metabolites were enriched in energy metabolism, including amino acid metabolism, carbohydrate metabolism, and lipid metabolism. Correlation network diagrams of transcriptomic and metabolomic showed that they were both enriched in energy metabolism. Additionally, the contents of gibberellin A7, cis-Zeatin, and abscisic acid were decreased in leaves upon lesion spot formation, whereas the lesion spots in NIL-Lm5M leaves were restrained by spaying GA and cytokinin (CTK, trans-zeatin) in the field. CONCLUSION The formation of lesion spots can result in cell death and enhance strip rust resistance by protein degradation pathway and defense-related genes overexpression in wheat. Besides, the formation of lesion spots was significantly affected by GA and CTK. Altogether, these results may contribute to the understanding of lesion spot formation in wheat and laid a foundation for regulating the resistance mechanism to stripe rust.
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Affiliation(s)
- Cong Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Lei Yan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Qian Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Rong Tian
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Surong Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Muhammad Faisal Umer
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Muhammad Junaid Jalil
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Md Nahibuzzaman Lohani
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yanlin Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Huaping Tang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Qiang Xu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Qiantao Jiang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Guoyue Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Pengfei Qi
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yunfeng Jiang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Lulu Gou
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China.
| | - Qifu Yao
- College of Agroforestry Engineering and Planning, Guizhou Key Laboratory of Biodiversity Conservation and Utilization in the Fanjing Mountain Region, Tongren University, Tongren, 554300, China
| | - Youliang Zheng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yuming Wei
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China.
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China.
| | - Jian Ma
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China.
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China.
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Rawat S, Jugran AK, Sharma H. Recent advancements in the physiological, genetic, and genomic research on Rhododendrons for trait improvement. 3 Biotech 2024; 14:164. [PMID: 38808301 PMCID: PMC11128433 DOI: 10.1007/s13205-024-04006-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 05/09/2024] [Indexed: 05/30/2024] Open
Abstract
High species diversity, hybridization potential, broad geographical dispersal range and ornamental characteristics (i.e., attractive size, shape, structure, flowers, and evergreen) have fetched a good international market for Rhododendron. However, most species are restricted to specific geographic areas due to their habitat specificity in acidic soil and cold climates, resulting many species being classified under threat categories of the IUCN. In this review, advances in research on Rhododendron for improvement to floral display quality and stress resistance have been described. The low genetic barrier among species has created opportunities for extensive hybridization and ploidy alteration for introducing quality and adaptive traits during the development of new varieties. Recent technological advances have supported investigations into the mechanism of flower development, as well as cold tolerance and pathogen resistance mechanisms in the Rhododendron. However, most of the species have limited adaptability to drought, line-tolerance, pathogen resistance, and high-temperature conditions and this resistance ability present in few species largely remains unexplored. Additionally, the available genetic diversity and genomic information on species, and possibilities for their application in molecular breeding have been summarized. Overall, genomic resource data are scarce in the majority of the members of this genus. Finally, various research gaps such as genetic mapping of quality traits, understanding the molecular mechanism of quality-related traits and genomic assortment in Rhododendron members have been discussed in the future perspective section. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-024-04006-6.
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Affiliation(s)
- Sandeep Rawat
- Sikkim Regional Centre, G. B. Pant National Institute of Himalayan Environment, Pangthang, Gangtok, Sikkim 737101 India
| | - Arun K. Jugran
- Garhwal Regional Centre, G. B. Pant National Institute of Himalayan Environment, Srinagar, Uttarakhand 246174 India
| | - Himanshu Sharma
- National Agri-Food Biotechnology Institute (NABI), Sector-81, SAS Nagar, Mohali, Punjab 140306 India
- Faculty of Applied Sciences and Biotechnology, Shoolini University, Solan, Himachal Pradesh 173229 India
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Abebe BK, Wang H, Li A, Zan L. A review of the role of transcription factors in regulating adipogenesis and lipogenesis in beef cattle. J Anim Breed Genet 2024; 141:235-256. [PMID: 38146089 DOI: 10.1111/jbg.12841] [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: 09/30/2023] [Revised: 11/25/2023] [Accepted: 11/30/2023] [Indexed: 12/27/2023]
Abstract
In the past few decades, genomic selection and other refined strategies have been used to increase the growth rate and lean meat production of beef cattle. Nevertheless, the fast growth rates of cattle breeds are often accompanied by a reduction in intramuscular fat (IMF) deposition, impairing meat quality. Transcription factors play vital roles in regulating adipogenesis and lipogenesis in beef cattle. Meanwhile, understanding the role of transcription factors in regulating adipogenesis and lipogenesis in beef cattle has gained significant attention to increase IMF deposition and meat quality. Therefore, the aim of this paper was to provide a comprehensive summary and valuable insight into the complex role of transcription factors in adipogenesis and lipogenesis in beef cattle. This review summarizes the contemporary studies in transcription factors in adipogenesis and lipogenesis, genome-wide analysis of transcription factors, epigenetic regulation of transcription factors, nutritional regulation of transcription factors, metabolic signalling pathways, functional genomics methods, transcriptomic profiling of adipose tissues, transcription factors and meat quality and comparative genomics with other livestock species. In conclusion, transcription factors play a crucial role in promoting adipocyte development and fatty acid biosynthesis in beef cattle. They control adipose tissue formation and metabolism, thereby improving meat quality and maintaining metabolic balance. Understanding the processes by which these transcription factors regulate adipose tissue deposition and lipid metabolism will simplify the development of marbling or IMF composition in beef cattle.
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Affiliation(s)
- Belete Kuraz Abebe
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
- Department of Animal Science, Werabe University, Werabe, Ethiopia
| | - Hongbao Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Anning Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Linsen Zan
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
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Hou Q, Yu R, Shang C, Deng H, Wen Z, Qiu Z, Qiao G. Molecular characterization and evolutionary relationships of DOFs in four cherry species and functional analysis in sweet cherry. Int J Biol Macromol 2024; 263:130346. [PMID: 38403208 DOI: 10.1016/j.ijbiomac.2024.130346] [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: 10/16/2023] [Revised: 02/17/2024] [Accepted: 02/19/2024] [Indexed: 02/27/2024]
Abstract
The DOF (DNA binding with one finger) has multiple functions in plants. However, it has received little attention in the research field of cherries. In this study, the evolutionary relationship and molecular characterization of DOF in four cherry species were analyzed, revealing its expression pattern in sweet cherry. There are 23 members in Prunus avium cv. 'Tieton', 88 in Prunus cerasus, 53 in Cerasus × yedoensis, and 27 in Cerasus serrulata. Most of these genes are intron-less or non-intron, with a conserved C2-C2 domain. Due to heterozygosity and chromosomal ploidy, whole-genome duplication (WGD) events occur to varying degrees, and DOF genes are contracted during evolution. Furthermore, these genes are affected by purifying selection pressure. Under low-temperature treatment, the expression of PavDOF2 and PavDOF18 were significantly up-regulated, while that of PavDOF16 is significantly down-regulated. The expression of PavDOF9, PavDOF12, PavDOF14, PavDOF16, PavDOF17, PavDOF18, and PavDOF19 exhibits an increasing trend during flower development and varies during sweet cherry fruit development. PavDOF1, PavDOF8, PavDOF9, and PavDOF15 are localized in the nucleus but is not transcriptionally active. The findings systemically demonstrate the molecular characteristics of DOF in different cherry varieties, providing a basis for further research on the functions of these genes.
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Affiliation(s)
- Qiandong Hou
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang 550025, Guizhou Province, China
| | - Runrun Yu
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang 550025, Guizhou Province, China
| | - Chunqiong Shang
- College of Forestry, Guizhou University/ Institute for Forest Resources & Environment of Guizhou, Guiyang 550025, Guizhou Province, China
| | - Hong Deng
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang 550025, Guizhou Province, China
| | - Zhuang Wen
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang 550025, Guizhou Province, China
| | - Zhilang Qiu
- School of Biology & Engineering, School of Health Medicine Modern Industry, Guizhou Medical University, Guiyang 550025, Guizhou Province, China
| | - Guang Qiao
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang 550025, Guizhou Province, China.
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Hosseinzadeh S, Hasanpur K. Whole genome discovery of regulatory genes responsible for the response of chicken to heat stress. Sci Rep 2024; 14:6544. [PMID: 38503864 PMCID: PMC10951342 DOI: 10.1038/s41598-024-56757-0] [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: 11/11/2023] [Accepted: 03/11/2024] [Indexed: 03/21/2024] Open
Abstract
Long noncoding RNAs (lncRNAs) are functional bridges connecting the genome with phenotypes by interacting with DNA, mRNA, and proteins. Using publically available acute heat stress (AHS)-related RNA-seq data, we discovered novel lncRNAs and tested their association with AHS along with ~ 8800 known lncRNAs and ~ 28,000 mRNA transcripts. Our pipeline discovered a total of 145 potentially novel-lncRNAs. One of them (Fishcomb_p-value = 0.06) along with another novel transcript (annotated as protein-coding; Fishcomb_p-value = 0.03) were identified as significantly associated with AHS. We found five known-lncRNAs and 134 mRNAs transcripts that were significantly associated with AHS. Four novel lncRNAs interact cis-regulated with 12 mRNA transcripts and are targeted by 11 miRNAs. Also six meta-lncRNAs associate with 134 meta-mRNAs through trans-acting co-expression, each targeted by 15 and 216 miRNAs, respectively. Three of the known-lncRNAs significantly co-expressed with almost 97 of the significant mRNAs (Pearson correlation p-value < 0.05). We report the mentioned three known-lncRNAs (ENSGALT00000099876, ENSGALT00000107573, and ENSGALT00000106323) as the most, significantly regulatory elements of AHS in chicken. It can be concluded that in order to alleviate the adverse effects of AHS on chicken, the manipulation of the three regulatory lncRNAs could lead to a more desirable result than the manipulation of the most significant mRNAs.
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Affiliation(s)
- Sevda Hosseinzadeh
- Department of Animal Science, Faculty of Agriculture, University of Tabriz, Tabriz, Iran
| | - Karim Hasanpur
- Department of Animal Science, Faculty of Agriculture, University of Tabriz, Tabriz, Iran.
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Mishra A, Yadav P, Singh K. Host Response of Arabidopsis thaliana Interaction with Fungal Endophytes Involves microRNAs. Mol Biotechnol 2024:10.1007/s12033-024-01051-7. [PMID: 38367181 DOI: 10.1007/s12033-024-01051-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 12/29/2023] [Indexed: 02/19/2024]
Abstract
Plant and fungus interaction is a complex process involving many molecular factors determining the nature of relationship. The enigmatic methodology by which fungal endophytes are able to colonise a plant harmoniously is still inexplicable. Small RNAs have been identified as major regulatory elements under various biotic interactions. However, their role in endophytic plant-fungal interactions remain to be elucidated. Therefore, transcript expression data available on Gene Expression Omnibus for Arabidopsis thaliana was utilised for miRNAs identification under endophytism. The analysis predicted 15 miRNAs with differential expression of which the ath-miRNA398b modulation was significant. Application of psRNAtarget, C-mii, pmiREN, and TarDB provided a pool of 357 target genes for these miRNAs. Protein-protein interaction analysis identified major hub proteins, including BTB/POZ domain-containing protein, beta-Xylosidase-2 (AtBXL2), and Copper/Zinc Superoxide Dismutase-2 (AtSOD2). The quantitative real-time PCR validated the computational prediction and expression for selected target genes AtSOD2, AtBXL2, and AtRCA along with ath-miRNA398b under endophytism. Overall, results indicate that miRNAs have a significant role in regulating Arabidopsis thaliana-endophytic fungal interaction.
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Affiliation(s)
- Anand Mishra
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Post Box No. 06, Palampur, 176061, India
| | - Pooja Yadav
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Post Box No. 06, Palampur, 176061, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Kunal Singh
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Post Box No. 06, Palampur, 176061, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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10
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Ji A, Zheng X, Yang W, Chen M, Ma A, Liu Y, Wei X. Transcriptome analysis reveals the underlying mechanism for over-accumulation of alkaline protease in Bacillus licheniformis. J Appl Microbiol 2024; 135:lxad319. [PMID: 38159929 DOI: 10.1093/jambio/lxad319] [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: 08/31/2023] [Revised: 12/18/2023] [Accepted: 12/29/2023] [Indexed: 01/03/2024]
Abstract
AIMS Bacillus licheniformis AQ is an industrial strain with high production of alkaline protease (AprE), which has great industrial application value. However, how to regulate the production of AprE in the process of industrial fermentation is still not completely clear. Therefore, it is important to understand the metabolic process of AprE production in the industrial fermentation medium. METHODS AND RESULTS In this study, transcriptome sequencing of the whole fermentation course was performed to explore the synthesis and regulation mechanism of AprE in B. licheniformis AQ. During the fermentation process, the AprE got continuously accumulated, reaching a peak of 42 020 U/mL at the fermentation endpoint (48 h). Meanwhile, the highly expressed genes were observed. Compared with the fermentation endpoint, there were 61 genes in the intersection of differentially expressed genes, functioning as catabolic processes, peptidases and inhibitors, chaperones, and folding catalysts. Furthermore, the protein-protein interactions network of AprE was constructed. CONCLUSION This study provides important transcriptome information for B. licheniformis AQ and potential molecular targets for further improving the production of AprE.
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Affiliation(s)
- Anying Ji
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Xianliang Zheng
- AngelYeast Co., Ltd, Yichang 443003, China
- Hubei Provincial Key Laboratory of Yeast Function, Yichang 443003, China
- National Key Laboratory of Agricultural Microbiology, Yichang 443003, China
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Wei Yang
- GeneMind Biosciences Company Limited, Shenzhen 518001, China
| | - Ming Chen
- AngelYeast Co., Ltd, Yichang 443003, China
- Hubei Provincial Key Laboratory of Yeast Function, Yichang 443003, China
- National Key Laboratory of Agricultural Microbiology, Yichang 443003, China
| | - Aimin Ma
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yongfeng Liu
- GeneMind Biosciences Company Limited, Shenzhen 518001, China
| | - Xuetuan Wei
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
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11
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A V, Kumar A, Mahala S, Chandra Janga S, Chauhan A, Mehrotra A, Kumar De A, Ranjan Sahu A, Firdous Ahmad S, Vempadapu V, Dutt T. Revelation of genetic diversity and genomic footprints of adaptation in Indian pig breeds. Gene 2024; 893:147950. [PMID: 37918549 DOI: 10.1016/j.gene.2023.147950] [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: 08/04/2023] [Revised: 10/16/2023] [Accepted: 10/30/2023] [Indexed: 11/04/2023]
Abstract
In the present study, the genetic diversity measures among four Indian domestic breeds of pig namely Agonda Goan, Ghurrah, Ghungroo, and Nicobari, of different agro-climatic regions of country were explored and compared with European commercial breeds, European wild boar and Chinese domestic breeds. The double digest restriction site-associated DNA sequencing (ddRADseq) data of Indian pigs (102) and Landrace (10 animals) were generated and whole genome sequencing data of exotic pigs (60 animals) from public data repository were used in the study. The principal component analysis (PCA), admixture analysis and phylogenetic analysis revealed that Indian breeds were closer in ancestry to Chinese breeds than European breeds. European breeds exhibited highest genetic diversity measures among all the considered breeds. Among Indian breeds, Agonda Goan and Ghurrah were found to be more genetically diverse than Nicobari and Ghungroo. The selection signature regions in Indian pigs were explored using iHS and XP-EHH, and during iHS analysis, it was observed that genes related to growth, reproduction, health, meat quality, sensory perception and behavior were found to be under selection pressure in Indian pig breeds. Strong selection signatures were recorded in 24.25-25.25 Mb region of SSC18, 123.25-124 Mb region of SSC15 and 118.75-119.5 Mb region of SSC2 in most of the Indian breeds upon pairwise comparison with European commercial breeds using XP-EHH. These regions were harboring some important genes such as EPHA4 for thermotolerance, TAS2R16, FEZF1, CADPS2 and PTPRZ1 for adaptability to scavenging system of rearing, TRIM36 and PGGT1B for disease resistance and CCDC112, PIAS1, FEM1B and ITGA11 for reproduction.
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Affiliation(s)
- Vani A
- Division of Animal Genetics, Indian Veterinary Research Institute, Bareilly, UP, India
| | - Amit Kumar
- Division of Animal Genetics, Indian Veterinary Research Institute, Bareilly, UP, India.
| | - Sudarshan Mahala
- Division of Animal Genetics, Indian Veterinary Research Institute, Bareilly, UP, India
| | - Sarath Chandra Janga
- Luddy School of Informatics, Computing, and Engineering, Indiana University, IUPUI, Indianapolis, IN, USA
| | - Anuj Chauhan
- Livestock Production and Management, Indian Veterinary Research Institute, Bareilly, UP, India
| | | | - Arun Kumar De
- Central Island Agricultural Research Institute, Port Blair, Andaman and Nicobar Islands, India
| | - Amiya Ranjan Sahu
- Central Coastal Agricultural Research Institute, Old Goa, Goa, India
| | - Sheikh Firdous Ahmad
- Division of Animal Genetics, Indian Veterinary Research Institute, Bareilly, UP, India
| | - Varshini Vempadapu
- Division of Animal Genetics, Indian Veterinary Research Institute, Bareilly, UP, India
| | - Triveni Dutt
- Livestock Production and Management, Indian Veterinary Research Institute, Bareilly, UP, India
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12
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Sheet S, Jang SS, Kim JH, Park W, Kim D. A transcriptomic analysis of skeletal muscle tissues reveals promising candidate genes and pathways accountable for different daily weight gain in Hanwoo cattle. Sci Rep 2024; 14:315. [PMID: 38172605 PMCID: PMC10764957 DOI: 10.1038/s41598-023-51037-9] [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: 08/08/2023] [Accepted: 12/29/2023] [Indexed: 01/05/2024] Open
Abstract
Cattle traits like average daily weight gain (ADG) greatly impact profitability. Selecting based on ADG considering genetic variability can lead to economic and genetic advancements in cattle breeding. This study aimed to unravel genetic influences on ADG variation in Hanwoo cattle at the skeletal muscle transcriptomic level. RNA sequencing was conducted on longissimus dorsi (LD), semimembranosus (SB), and psoas major (PM) muscles of 14 steers assigned to same feed, grouped by low (≤ 0.71 kg) and high (≥ 0.77 kg) ADG. At P ≤ 0.05 and log2fold > 1.5, the distinct pattern of gene expression was identified with 184, 172, and 210 differentially expressed genes in LD, SB, and PM muscles, respectively. Tissue-specific responses to ADG variation were evident, with myogenesis and differentiation associated JAK-STAT signaling pathway and prolactin signaling pathways enriched in LD and SB muscles, while adipogenesis-related PPAR signaling pathways were enriched in PM muscle. Key hub genes (AXIN2, CDKN1A, MYC, PTGS2, FZD5, SPP1) were upregulated and functionally significant in muscle growth and differentiation. Notably, DPP6, CDKN1A, and FZD5 emerged as possible candidate genes linked to ADG variation. These findings enhance our understanding of genetic factors behind ADG variation in Hanwoo cattle, illuminating skeletal muscle mechanisms influencing ADG.
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Affiliation(s)
- Sunirmal Sheet
- Animal Genomics and Bioinformatics Division, Rural Development Administration, National Institute of Animal Science, Wanju, 55365, Republic of Korea
| | - Sun Sik Jang
- Hanwoo Research Institute, National Institute of Animal Science, RDA, Pyeongchang, 25342, Republic of Korea
| | - Jae Hwan Kim
- Animal Genomics and Bioinformatics Division, Rural Development Administration, National Institute of Animal Science, Wanju, 55365, Republic of Korea
| | - Woncheoul Park
- Animal Genomics and Bioinformatics Division, Rural Development Administration, National Institute of Animal Science, Wanju, 55365, Republic of Korea.
| | - Dahye Kim
- Animal Genomics and Bioinformatics Division, Rural Development Administration, National Institute of Animal Science, Wanju, 55365, Republic of Korea.
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13
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Meng X, Wang M, Luo M, Sun L, Yan Q, Liu Y. Systematic evaluation of multiple NGS platforms for structural variants detection. J Biol Chem 2023; 299:105436. [PMID: 37944616 PMCID: PMC10724692 DOI: 10.1016/j.jbc.2023.105436] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 10/29/2023] [Accepted: 10/31/2023] [Indexed: 11/12/2023] Open
Abstract
Structural variations (SV) are critical genome changes affecting human diseases. Although many hybridization-based methods exist, evaluating SVs through next-generation sequencing (NGS) data is still necessary for broader research exploration. Here, we comprehensively compared the performance of 16 SV callers and multiple NGS platforms using NA12878 whole genome sequencing (WGS) datasets. The results indicated that several SV callers performed well relatively, such as Manta, GRIDSS, LUMPY, TARDIS, FermiKit, and Wham. Meanwhile, all NGS platforms have a similar performance using a single software. Additionally, we found that the source of undetected SVs was mostly from long reads datasets, therefore, the more appropriate strategy for accurate SV detection will be an integration of long and shorter reads in the future. At present, in the period of NGS as a mainstream method in bioinformatics, our study would provide helpful and comprehensive guidelines for specific categories of SV research.
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Affiliation(s)
- Xuan Meng
- School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Miao Wang
- Research Cooperation Department, GeneMind Biosciences Company Limited, Shenzhen, China
| | - Mingjie Luo
- Research Cooperation Department, GeneMind Biosciences Company Limited, Shenzhen, China
| | - Lei Sun
- Research Cooperation Department, GeneMind Biosciences Company Limited, Shenzhen, China
| | - Qin Yan
- Research Cooperation Department, GeneMind Biosciences Company Limited, Shenzhen, China
| | - Yongfeng Liu
- Research Cooperation Department, GeneMind Biosciences Company Limited, Shenzhen, China.
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14
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Jha UC, Nayyar H, Roychowdhury R, Prasad PVV, Parida SK, Siddique KHM. Non-coding RNAs (ncRNAs) in plant: Master regulators for adapting to extreme temperature conditions. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 205:108164. [PMID: 38008006 DOI: 10.1016/j.plaphy.2023.108164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 10/30/2023] [Accepted: 11/02/2023] [Indexed: 11/28/2023]
Abstract
Unusual daily temperature fluctuations caused by climate change and climate variability adversely impact agricultural crop production. Since plants are immobile and constantly receive external environmental signals, such as extreme high (heat) and low (cold) temperatures, they have developed complex molecular regulatory mechanisms to cope with stressful situations to sustain their natural growth and development. Among these mechanisms, non-coding RNAs (ncRNAs), particularly microRNAs (miRNAs), small-interfering RNAs (siRNAs), and long-non-coding RNAs (lncRNAs), play a significant role in enhancing heat and cold stress tolerance. This review explores the pivotal findings related to miRNAs, siRNAs, and lncRNAs, elucidating how they functionally regulate plant adaptation to extreme temperatures. In addition, this review addresses the challenges associated with uncovering these non-coding RNAs and understanding their roles in orchestrating heat and cold tolerance in plants.
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Affiliation(s)
- Uday Chand Jha
- Sustainable Intensification Innovation Lab, Kansas State University, Department of Agronomy, Manhattan, KS 66506, USA; ICAR-Indian Institute of Pulses Research, Kanpur, Uttar Pradesh 208024, India.
| | - Harsh Nayyar
- Department of Botany, Panjab University, Chandigarh, 160014, India.
| | - Rajib Roychowdhury
- Department of Plant Pathology and Weed Research, Institute of Plant Protection, Agricultural Research Organization (ARO) - The Volcani Institute, Rishon Lezion 7505101, Israel
| | - P V Vara Prasad
- Sustainable Intensification Innovation Lab, Kansas State University, Department of Agronomy, Manhattan, KS 66506, USA
| | - Swarup K Parida
- National Institute of Plant Genomic Research, New Delhi, 110067, India
| | - Kadambot H M Siddique
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6001, Australia
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15
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Feng W, Zhang H, Cao Y, Liu Y, Zhao Y, Sun F, Yang Q, Zhang X, Zhang Y, Wang Y, Li W, Lu Y, Fu F, Yu H. Maize ZmBES1/BZR1-1 transcription factor negatively regulates drought tolerance. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 205:108188. [PMID: 37979574 DOI: 10.1016/j.plaphy.2023.108188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 10/28/2023] [Accepted: 11/09/2023] [Indexed: 11/20/2023]
Abstract
Drought stress is a common abiotic factor and restricts plant growth and development. Exploring maize stress-related genes and their regulatory mechanisms is crucial for ensuring agricultural productivity and food security. The BRI1-EMS1 suppressor (BES1)/brassinazole-resistant 1 (BZR1) transcription factors (TFs) play important roles in plant growth, development, and stress response. However, maize ZmBES1/BZR1s are rarely reported. In the present study, the ZmBES1/BZR1-1 gene was cloned from maize B73 and functionally characterized in transgenic Arabidopsis and rice in drought stress response. The ZmBES1/BZR1-1 protein possessed a conserved bHLH domain characterized by BES1/BZR1 TFs, localized in the nucleus, and showed transcription activation activity. The expression of ZmBES1/BZR1-1 exhibited no tissue specificity but drought-inhibitory expression in maize. Under drought stress, overexpression of ZmBES1/BZR1-1 resulted in the enhancement of drought sensitivity of transgenic Arabidopsis and rice with a lower survival rate, reactive oxygen species (ROS) level and relative water content (RWC) and a higher stomatal aperture and relative electrolyte leakage (REL). The RNA-seq results showed that 56 differentially expressed genes (DEGs) were regulated by ZmBES1/BZR1-1 by binding to E-box elements in their promoters. The GO analysis showed that the DEGs were significantly annotated with response to oxidative stress and oxygen level. The study suggests that the ZmBES1/BZR1-1 gene negatively regulates drought stress, which provides insights into further underlying molecular mechanisms in the drought stress response mediated by BZR1/BES1s.
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Affiliation(s)
- Wenqi Feng
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Hongwanjun Zhang
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yang Cao
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yuan Liu
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yiran Zhao
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Fuai Sun
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Qingqing Yang
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xuecai Zhang
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, 56237, Mexico
| | - Yuanyuan Zhang
- College of Life Science & Biotechnology, Mianyang Teachers' College, Mianyang, 621000, China
| | - Yingge Wang
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Wanchen Li
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yanli Lu
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Fengling Fu
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China.
| | - Haoqiang Yu
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China.
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16
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Azad MF, Dawar P, Esim N, Rock CD. Role of miRNAs in sucrose stress response, reactive oxygen species, and anthocyanin biosynthesis in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2023; 14:1278320. [PMID: 38023835 PMCID: PMC10656695 DOI: 10.3389/fpls.2023.1278320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 10/17/2023] [Indexed: 12/01/2023]
Abstract
In plants, sucrose is the main transported disaccharide that is the primary product of photosynthesis and controls a multitude of aspects of the plant life cycle including structure, growth, development, and stress response. Sucrose is a signaling molecule facilitating various stress adaptations by crosstalk with other hormones, but the molecular mechanisms are not well understood. Accumulation of high sucrose concentrations is a hallmark of many abiotic and biotic stresses, resulting in the accumulation of reactive oxygen species and secondary metabolite anthocyanins that have antioxidant properties. Previous studies have shown that several MYeloBlastosis family/MYB transcription factors are positive and negative regulators of sucrose-induced anthocyanin accumulation and subject to microRNA (miRNA)-mediated post-transcriptional silencing, consistent with the notion that miRNAs may be "nodes" in crosstalk signaling by virtue of their sequence-guided targeting of different homologous family members. In this study, we endeavored to uncover by deep sequencing small RNA and mRNA transcriptomes the effects of exogenous high sucrose stress on miRNA abundances and their validated target transcripts in Arabidopsis. We focused on genotype-by-treatment effects of high sucrose stress in Production of Anthocyanin Pigment 1-Dominant/pap1-D, an activation-tagged dominant allele of MYB75 transcription factor, a positive effector of secondary metabolite anthocyanin pathway. In the process, we discovered links to reactive oxygen species signaling through miR158/161/173-targeted Pentatrico Peptide Repeat genes and two novel non-canonical targets of high sucrose-induced miR408 and miR398b*(star), relevant to carbon metabolic fluxes: Flavonoid 3'-Hydroxlase (F3'H), an important enzyme in determining the B-ring hydroxylation pattern of flavonoids, and ORANGE a post-translational regulator of Phytoene Synthase expression, respectively. Taken together, our results contribute to understanding the molecular mechanisms of carbon flux shifts from primary to secondary metabolites in response to high sugar stress.
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Affiliation(s)
- Md. Fakhrul Azad
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, United States
| | - Pranav Dawar
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, United States
| | - Nevzat Esim
- Department of Molecular Biology and Genetics, Bіngöl University, Bingöl, Türkiye
| | - Christopher D. Rock
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, United States
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17
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Ajila V, Colley L, Ste-Croix DT, Nissan N, Cober ER, Mimee B, Samanfar B, Green JR. Species-specific microRNA discovery and target prediction in the soybean cyst nematode. Sci Rep 2023; 13:17657. [PMID: 37848601 PMCID: PMC10582106 DOI: 10.1038/s41598-023-44469-w] [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: 04/27/2023] [Accepted: 10/09/2023] [Indexed: 10/19/2023] Open
Abstract
The soybean cyst nematode (SCN) is a devastating pathogen for economic and food security considerations. Although the SCN genome has recently been sequenced, the presence of any miRNA has not been systematically explored and reported. This paper describes the development of a species-specific SCN miRNA discovery pipeline and its application to the SCN genome. Experiments on well-documented model nematodes (Caenorhabditis elegans and Pristionchus pacificus) are used to tune the pipeline's hyperparameters and confirm its recall and precision. Application to the SCN genome identifies 3342 high-confidence putative SCN miRNA. Prediction specificity within SCN is confirmed by applying the pipeline to RNA hairpins from known exonic regions of the SCN genome (i.e., sequences known to not be miRNA). Prediction recall is confirmed by building a positive control set of SCN miRNA, based on a limited deep sequencing experiment. Interestingly, a number of novel miRNA are predicted to be encoded within the intronic regions of effector genes, known to be involved in SCN parasitism, suggesting that these miRNA may also be involved in the infection process or virulence. Beyond miRNA discovery, gene targets within SCN are predicted for all high-confidence novel miRNA using a miRNA:mRNA target prediction system. Lastly, cross-kingdom miRNA targeting is investigated, where putative soybean mRNA targets are identified for novel SCN miRNA. All predicted miRNA and gene targets are made available in appendix and through a Borealis DataVerse open repository ( https://borealisdata.ca/dataset.xhtml?persistentId=doi:10.5683/SP3/30DEXA ).
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Affiliation(s)
- Victoria Ajila
- Department of Systems and Computer Engineering, Carleton University, Ottawa, K1S 5B6, Canada
| | - Laura Colley
- Department of Systems and Computer Engineering, Carleton University, Ottawa, K1S 5B6, Canada
| | - Dave T Ste-Croix
- Saint-Jean-sur-Richelieu Research and Development Centre, Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu, J3B 7B5, Canada
| | - Nour Nissan
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, K1A 0C6, Canada
- Department of Biology and Ottawa Institute of Systems Biology, Carleton University, Ottawa, K1S 5B6, Canada
| | - Elroy R Cober
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, K1A 0C6, Canada
| | - Benjamin Mimee
- Saint-Jean-sur-Richelieu Research and Development Centre, Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu, J3B 7B5, Canada
| | - Bahram Samanfar
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, K1A 0C6, Canada
- Department of Biology and Ottawa Institute of Systems Biology, Carleton University, Ottawa, K1S 5B6, Canada
| | - James R Green
- Department of Systems and Computer Engineering, Carleton University, Ottawa, K1S 5B6, Canada.
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18
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Hazra A, Ghosh S, Naskar S, Rahaman P, Roy C, Kundu A, Chaudhuri RK, Chakraborti D. Global transcriptome analysis reveals fungal disease responsive core gene regulatory landscape in tea. Sci Rep 2023; 13:17186. [PMID: 37821523 PMCID: PMC10567763 DOI: 10.1038/s41598-023-44163-x] [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: 03/22/2023] [Accepted: 10/04/2023] [Indexed: 10/13/2023] Open
Abstract
Fungal infections are the inevitable limiting factor for productivity of tea. Transcriptome reprogramming recruits multiple regulatory pathways during pathogen infection. A comprehensive meta-analysis was performed utilizing previously reported, well-replicated transcriptomic datasets from seven fungal diseases of tea. The study identified a cumulative set of 18,517 differentially expressed genes (DEGs) in tea, implicated in several functional clusters, including the MAPK signaling pathway, transcriptional regulation, and the biosynthesis of phenylpropanoids. Gene set enrichment analyses under each pathogen stress elucidated that DEGs were involved in ethylene metabolism, secondary metabolism, receptor kinase activity, and various reactive oxygen species detoxification enzyme activities. Expressional fold change of combined datasets highlighting 2258 meta-DEGs shared a common transcriptomic response upon fungal stress in tea. Pervasive duplication events caused biotic stress-responsive core DEGs to appear in multiple copies throughout the tea genome. The co-expression network of meta-DEGs in multiple modules demonstrated the coordination of appropriate pathways, most of which involved cell wall organization. The functional coordination was controlled by a number of hub genes and miRNAs, leading to pathogenic resistance or susceptibility. This first-of-its-kind meta-analysis of host-pathogen interaction generated consensus candidate loci as molecular signatures, which can be associated with future resistance breeding programs in tea.
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Affiliation(s)
- Anjan Hazra
- Department of Genetics, University of Calcutta, 35, Ballygunge Circular Road, Kolkata, 700019, India
| | - Sanatan Ghosh
- Department of Genetics, University of Calcutta, 35, Ballygunge Circular Road, Kolkata, 700019, India
| | - Sudipta Naskar
- Department of Genetics, University of Calcutta, 35, Ballygunge Circular Road, Kolkata, 700019, India
| | - Piya Rahaman
- Department of Genetics, University of Calcutta, 35, Ballygunge Circular Road, Kolkata, 700019, India
| | - Chitralekha Roy
- Department of Genetics, University of Calcutta, 35, Ballygunge Circular Road, Kolkata, 700019, India
| | - Anirban Kundu
- Plant Genomics and Bioinformatics Laboratory, P.G. Department of Botany, Ramakrishna Mission Vivekananda Centenary College (Autonomous), Rahara, Kolkata, 700118, India
| | | | - Dipankar Chakraborti
- Department of Genetics, University of Calcutta, 35, Ballygunge Circular Road, Kolkata, 700019, India.
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19
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Shi H, Xiong Q, Zhao Z, Zhou L, Yin J, Lu X, Chen X, Wang J. Disruption of the Novel Small Protein RBR7 Leads to Enhanced Plant Resistance to Blast Disease. RICE (NEW YORK, N.Y.) 2023; 16:42. [PMID: 37733139 PMCID: PMC10513991 DOI: 10.1186/s12284-023-00660-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 09/14/2023] [Indexed: 09/22/2023]
Abstract
Plant disease is a threat to global food security. Breeding crops carrying broad-spectrum resistance loci is an effective way to control infectious disease. Disease-resistant mutants are valuable resources for deciphering the underlying mechanisms of plant immunity and could provide genetic loci to generate disease-resistant crops. Here, we identified a rice mutant, rbr7 (rice blast resistance 7), that confers resistance against different strains of Magnaporthe oryzae. Disease-mimicking necrotic lesions started to appear on the leaves of rbr7 four weeks after sowing. Histochemical analysis revealed reactive oxygen species accumulation and cell death accompanied by spontaneous lesion formation in rbr7. Map-based cloning and bulk segregation analysis showed a 2855 bp fragment deletion on chromosome 5, leading to the disruption of the LOC_Os05g28480-coding protein. Transgenic rbr7 complementation plants showed compromised resistance to rice blast, indicating that LOC_Os05g28480, or Rbr7, regulates the rice immune response. Rbr7 encodes a small protein of unknown function with 85 amino acids. Transcriptomic analysis revealed that disruption of RBR7 led to the upregulation of genes responding to salicylic acid, systemic acquired resistance and pathogenesis-related genes. Taken together, our findings reveal insights into a novel small protein involved in regulating plant resistance to rice blast and provide a potential target for crop breeding.
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Affiliation(s)
- Hui Shi
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Qing Xiong
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Zhangjie Zhao
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Lian Zhou
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Junjie Yin
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Xiang Lu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Xuewei Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Jing Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.
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20
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Li Y, Wang J, Li L, Song W, Li M, Hua X, Wang Y, Yuan J, Xue Z. Natural products of pentacyclic triterpenoids: from discovery to heterologous biosynthesis. Nat Prod Rep 2023; 40:1303-1353. [PMID: 36454108 DOI: 10.1039/d2np00063f] [Citation(s) in RCA: 31] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/17/2023]
Abstract
Covering: up to 2022Pentacyclic triterpenoids are important natural bioactive substances that are widely present in plants and fungi. They have significant medicinal efficacy, play an important role in reducing blood glucose and protecting the liver, and have anti-inflammatory, anti-oxidation, anti-fatigue, anti-viral, and anti-cancer activities. Pentacyclic triterpenoids are derived from the isoprenoid biosynthetic pathway, which generates common precursors of triterpenes and steroids, followed by cyclization with oxidosqualene cyclases (OSCs) and decoration via cytochrome P450 monooxygenases (CYP450s) and glycosyltransferases (GTs). Many biosynthetic pathways of triterpenoid saponins have been elucidated by studying their metabolic regulation network through the use of multiomics and identifying their functional genes. Unfortunately, natural resources of pentacyclic triterpenoids are limited due to their low content in plant tissues and the long growth cycle of plants. Based on the understanding of their biosynthetic pathway and transcriptional regulation, plant bioreactors and microbial cell factories are emerging as alternative means for the synthesis of desired triterpenoid saponins. The rapid development of synthetic biology, metabolic engineering, and fermentation technology has broadened channels for the accumulation of pentacyclic triterpenoid saponins. In this review, we summarize the classification, distribution, structural characteristics, and bioactivity of pentacyclic triterpenoids. We further discuss the biosynthetic pathways of pentacyclic triterpenoids and involved transcriptional regulation. Moreover, the recent progress and characteristics of heterologous biosynthesis in plants and microbial cell factories are discussed comparatively. Finally, we propose potential strategies to improve the accumulation of triterpenoid saponins, thereby providing a guide for their future biomanufacturing.
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Affiliation(s)
- Yanlin Li
- Ministry of Education, Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Northeast Forestry University, Harbin, PR China.
- Heilongjiang Key Laboratory of Plant Bioactive Substance Biosynthesis and Utilization, Northeast Forestry University, Harbin, PR China
| | - Jing Wang
- Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, PR China
| | - Linyong Li
- Ministry of Education, Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Northeast Forestry University, Harbin, PR China.
- Heilongjiang Key Laboratory of Plant Bioactive Substance Biosynthesis and Utilization, Northeast Forestry University, Harbin, PR China
| | - Wenhui Song
- Ministry of Education, Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Northeast Forestry University, Harbin, PR China.
- Heilongjiang Key Laboratory of Plant Bioactive Substance Biosynthesis and Utilization, Northeast Forestry University, Harbin, PR China
| | - Min Li
- Ministry of Education, Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Northeast Forestry University, Harbin, PR China.
- Heilongjiang Key Laboratory of Plant Bioactive Substance Biosynthesis and Utilization, Northeast Forestry University, Harbin, PR China
| | - Xin Hua
- Ministry of Education, Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Northeast Forestry University, Harbin, PR China.
- Heilongjiang Key Laboratory of Plant Bioactive Substance Biosynthesis and Utilization, Northeast Forestry University, Harbin, PR China
| | - Yu Wang
- Ministry of Education, Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Northeast Forestry University, Harbin, PR China.
| | - Jifeng Yuan
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, 361102, Fujian, PR China.
| | - Zheyong Xue
- Ministry of Education, Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Northeast Forestry University, Harbin, PR China.
- Heilongjiang Key Laboratory of Plant Bioactive Substance Biosynthesis and Utilization, Northeast Forestry University, Harbin, PR China
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21
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Muyyarikkandy MS, Schlesinger M, Ren Y, Gao M, Liefeld A, Reed S, Amalaradjou MA. In ovo probiotic supplementation promotes muscle growth and development in broiler embryos. Poult Sci 2023; 102:102744. [PMID: 37216887 DOI: 10.1016/j.psj.2023.102744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 04/18/2023] [Accepted: 04/19/2023] [Indexed: 05/24/2023] Open
Abstract
In chickens, muscle development during embryonic growth is predominantly by myofiber hyperplasia. Following hatch, muscle growth primarily occurs via hypertrophy of the existing myofibers. Since myofiber number is set at hatch, production of more muscle fibers during embryonic growth would provide a greater myofiber number at hatch and potential for posthatch muscle growth by hypertrophy. Therefore, to improve performance in broilers, this study investigated the effect of in ovo spray application of probiotics on overall morphometry and muscle development in broiler embryos. For the study, fertile Ross 308 eggs were sprayed with different probiotics; Lactobacillus paracasei DUP 13076 (LP) and L. rhamnosus NRRL B 442 (LR) prior to and during incubation. The embryos were sacrificed on d 7, 10, 14, and 18 for embryo morphometry and pectoralis major muscle (PMM) sampling. Muscle sections were stained and imaged to quantify muscle fiber density (MFD), myofiber cross-sectional area (CSA), and nuclei density. Additionally, gene expression assays were performed to elucidate the effect of probiotics on myogenic genes. In ovo probiotic supplementation was found to significantly improve embryo weight, breast weight, and leg weight (P < 0.05). Further, histological analysis of PMM revealed a significant increase in MFD and nuclei number in the probiotic-treated embryos when compared to the control (P < 0.05). In 18-day-old broiler embryos, myofibers in the treatment group had a significantly smaller CSA (LP: 95.27 ± 3.28 μm2, LR: 178.84 ± 15.1 μm2) when compared to the control (211.41 ± 15.67 μm2). This decrease in CSA was found to be associated with a concomitant increase in MFD (fibers/mm2) in the LP (13,647 ± 482.15) and LR (13,957 ± 463.13) group when compared to the control (7,680 ± 406.78). Additionally, this increase in myofibrillar hyperplasia in the treatment groups was associated with upregulation in the expression of key genes regulating muscle growth including MYF5, MYOD, MYOG, and IGF-1. In summary, in ovo spray application of probiotics promoted overall embryo growth and muscle development in broilers.
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Affiliation(s)
| | - Maya Schlesinger
- Department of Animal Science, University of Connecticut, Storrs, CT 06269, USA
| | - Yuying Ren
- Department of Animal Science, University of Connecticut, Storrs, CT 06269, USA
| | - Mairui Gao
- Department of Animal Science, University of Connecticut, Storrs, CT 06269, USA
| | - Amanda Liefeld
- Department of Animal Science, University of Connecticut, Storrs, CT 06269, USA
| | - Sarah Reed
- Department of Animal Science, University of Connecticut, Storrs, CT 06269, USA
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Zhang Y, He XJ, Barron AB, Li Z, Jin MJ, Wang ZL, Huang Q, Zhang LZ, Wu XB, Yan WY, Zeng ZJ. The diverging epigenomic landscapes of honeybee queens and workers revealed by multiomic sequencing. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2023; 155:103929. [PMID: 36906046 DOI: 10.1016/j.ibmb.2023.103929] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 02/27/2023] [Accepted: 03/02/2023] [Indexed: 05/10/2023]
Abstract
The role of the epigenome in phenotypic plasticity is unclear presently. Here we used a multiomics approach to explore the nature of the epigenome in developing honey bee (Apis mellifera) workers and queens. Our data clearly showed distinct queen and worker epigenomic landscapes during the developmental process. Differences in gene expression between workers and queens become more extensive and more layered during the process of development. Genes known to be important for caste differentiation were more likely to be regulated by multiple epigenomic systems than other differentially expressed genes. We confirmed the importance of two candidate genes for caste differentiation by using RNAi to manipulate the expression of two genes that differed in expression between workers and queens were regulated by multiple epigenomic systems. For both genes the RNAi manipulation resulted in a decrease in weight and fewer ovarioles of newly emerged queens compared to controls. Our data show that the distinct epigenomic landscapes of worker and queen bees differentiate during the course of larval development.
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Affiliation(s)
- Yong Zhang
- Honeybee Research Institute, Jiangxi Agricultural University, Nanchang, Jiangxi, 330045, PR China; Jiangxi Province Honeybee Biology and Beekeeping Nanchang, Jiangxi, 330045, PR China
| | - Xu Jiang He
- Honeybee Research Institute, Jiangxi Agricultural University, Nanchang, Jiangxi, 330045, PR China; Jiangxi Province Honeybee Biology and Beekeeping Nanchang, Jiangxi, 330045, PR China
| | - Andrew B Barron
- Department of Biological Sciences, Macquarie University, North Ryde, NSW, 2109, Australia
| | - Zhen Li
- Honeybee Research Institute, Jiangxi Agricultural University, Nanchang, Jiangxi, 330045, PR China; Jiangxi Province Honeybee Biology and Beekeeping Nanchang, Jiangxi, 330045, PR China
| | - Meng Jie Jin
- Honeybee Research Institute, Jiangxi Agricultural University, Nanchang, Jiangxi, 330045, PR China; Jiangxi Province Honeybee Biology and Beekeeping Nanchang, Jiangxi, 330045, PR China
| | - Zi Long Wang
- Honeybee Research Institute, Jiangxi Agricultural University, Nanchang, Jiangxi, 330045, PR China; Jiangxi Province Honeybee Biology and Beekeeping Nanchang, Jiangxi, 330045, PR China
| | - Qiang Huang
- Honeybee Research Institute, Jiangxi Agricultural University, Nanchang, Jiangxi, 330045, PR China; Jiangxi Province Honeybee Biology and Beekeeping Nanchang, Jiangxi, 330045, PR China
| | - Li Zhen Zhang
- Honeybee Research Institute, Jiangxi Agricultural University, Nanchang, Jiangxi, 330045, PR China; Jiangxi Province Honeybee Biology and Beekeeping Nanchang, Jiangxi, 330045, PR China
| | - Xiao Bo Wu
- Honeybee Research Institute, Jiangxi Agricultural University, Nanchang, Jiangxi, 330045, PR China; Jiangxi Province Honeybee Biology and Beekeeping Nanchang, Jiangxi, 330045, PR China
| | - Wei Yu Yan
- Honeybee Research Institute, Jiangxi Agricultural University, Nanchang, Jiangxi, 330045, PR China; Jiangxi Province Honeybee Biology and Beekeeping Nanchang, Jiangxi, 330045, PR China
| | - Zhi Jiang Zeng
- Honeybee Research Institute, Jiangxi Agricultural University, Nanchang, Jiangxi, 330045, PR China; Jiangxi Province Honeybee Biology and Beekeeping Nanchang, Jiangxi, 330045, PR China.
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23
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Peng G, Liu Z, Zhuang C, Zhou H. Environment-sensitive genic male sterility in rice and other plants. PLANT, CELL & ENVIRONMENT 2023; 46:1120-1142. [PMID: 36458343 DOI: 10.1111/pce.14503] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 11/20/2022] [Accepted: 11/27/2022] [Indexed: 06/17/2023]
Abstract
Environment-sensitive genic male sterility is a type of male sterility that is affected by both genetic and environmental factors. Environment-sensitive genic male sterile lines are not only used in two-line hybrid breeding but are also good materials for studying plant-environment interactions. In this study we review the research progress on environment-sensitive genic male sterility in rice from the perspectives of epigenetic, transcriptional, posttranscriptional, posttranslational and metabolic mechanisms as well as signal transduction processes. While significant progress has been made in the genetics, gene cloning and understanding of the molecular mechanisms of environment-sensitive genic male sterility in recent years, the relevant regulatory network is still poorly understood in rice. We therefore also review studies of environment-sensitive genic male sterility in Arabidopsis and other crops, hoping to promote research in this field in rice. Finally, we analyse the challenges posed by environment-sensitive genic male sterility and provide corresponding suggestions. This review will contribute towards an understanding the molecular genetics of environment-sensitive genic male sterility and its application in two-line hybrid breeding in rice and other species.
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Affiliation(s)
- Guoqing Peng
- Guangdong Laboratory for Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Zhenlan Liu
- Guangdong Laboratory for Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Chuxiong Zhuang
- Guangdong Laboratory for Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Hai Zhou
- Guangdong Laboratory for Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, China
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24
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Li X, Wang X, Ma Q, Zhong Y, Zhang Y, Zhang P, Li Y, He R, Zhou Y, Li Y, Cheng M, Yan X, Li Y, He J, Iqbal MZ, Rong T, Tang Q. Integrated single-molecule real-time sequencing and RNA sequencing reveal the molecular mechanisms of salt tolerance in a novel synthesized polyploid genetic bridge between maize and its wild relatives. BMC Genomics 2023; 24:55. [PMID: 36717785 PMCID: PMC9887930 DOI: 10.1186/s12864-023-09148-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Accepted: 01/23/2023] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND Tripsacum dactyloides (2n = 4x = 72) and Zea perennis (2n = 4x = 40) are tertiary gene pools of Zea mays L. and exhibit many abiotic adaptations absent in modern maize, especially salt tolerance. A previously reported allopolyploid (hereafter referred to as MTP, 2n = 74) synthesized using Zea mays, Tripsacum dactyloides, and Zea perennis has even stronger salt tolerance than Z. perennis and T. dactyloides. This allopolyploid will be a powerful genetic bridge for the genetic improvement of maize. However, the molecular mechanisms underlying its salt tolerance, as well as the key genes involved in regulating its salt tolerance, remain unclear. RESULTS Single-molecule real-time sequencing and RNA sequencing were used to identify the genes involved in salt tolerance and reveal the underlying molecular mechanisms. Based on the SMRT-seq results, we obtained 227,375 reference unigenes with an average length of 2300 bp; most of the unigenes were annotated to Z. mays sequences (76.5%) in the NR database. Moreover, a total of 484 and 1053 differentially expressed genes (DEGs) were identified in the leaves and roots, respectively. Functional enrichment analysis of DEGs revealed that multiple pathways responded to salt stress, including "Flavonoid biosynthesis," "Oxidoreductase activity," and "Plant hormone signal transduction" in the leaves and roots, and "Iron ion binding," "Acetyl-CoA carboxylase activity," and "Serine-type carboxypeptidase activity" in the roots. Transcription factors, such as those in the WRKY, B3-ARF, and bHLH families, and cytokinin negatively regulators negatively regulated the salt stress response. According to the results of the short time series-expression miner analysis, proteins involved in "Spliceosome" and "MAPK signal pathway" dynamically responded to salt stress as salinity changed. Protein-protein interaction analysis revealed that heat shock proteins play a role in the large interaction network regulating salt tolerance. CONCLUSIONS Our results reveal the molecular mechanism underlying the regulation of MTP in the response to salt stress and abundant salt-tolerance-related unigenes. These findings will aid the retrieval of lost alleles in modern maize and provide a new approach for using T. dactyloides and Z. perennis to improve maize.
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Affiliation(s)
- Xiaofeng Li
- grid.80510.3c0000 0001 0185 3134Sichuan Agricultural University, Chengdu, 611130 China
| | - Xingyu Wang
- grid.80510.3c0000 0001 0185 3134Sichuan Agricultural University, Chengdu, 611130 China
| | - Qiangqiang Ma
- grid.80510.3c0000 0001 0185 3134Sichuan Agricultural University, Chengdu, 611130 China
| | - Yunfeng Zhong
- grid.80510.3c0000 0001 0185 3134Sichuan Agricultural University, Chengdu, 611130 China
| | - Yibo Zhang
- grid.80510.3c0000 0001 0185 3134Sichuan Agricultural University, Chengdu, 611130 China
| | - Ping Zhang
- grid.452857.9Chengdu Research Base of Giant Panda Breeding, Chengdu, 61130 China
| | - Yingzheng Li
- grid.80510.3c0000 0001 0185 3134Sichuan Agricultural University, Chengdu, 611130 China
| | - Ruyu He
- grid.80510.3c0000 0001 0185 3134Sichuan Agricultural University, Chengdu, 611130 China
| | - Yang Zhou
- grid.80510.3c0000 0001 0185 3134Sichuan Agricultural University, Chengdu, 611130 China
| | - Yang Li
- Mianyang Teachers’ College School of Urban and Rural Construction and Planning, Mianyany, 621000 China
| | - Mingjun Cheng
- grid.412723.10000 0004 0604 889XInstitute of Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu, 610041 China
| | - Xu Yan
- grid.465230.60000 0004 1777 7721Sericulture Research Institute, Sichuan Academy of Agricultural Sciences, Nanchong, 637000 China
| | - Yan Li
- grid.465230.60000 0004 1777 7721Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 611041 China
| | - Jianmei He
- grid.80510.3c0000 0001 0185 3134Sichuan Agricultural University, Chengdu, 611130 China
| | - Muhammad Zafar Iqbal
- grid.80510.3c0000 0001 0185 3134Sichuan Agricultural University, Chengdu, 611130 China
| | - Tingzhao Rong
- grid.80510.3c0000 0001 0185 3134Sichuan Agricultural University, Chengdu, 611130 China
| | - Qilin Tang
- grid.80510.3c0000 0001 0185 3134Sichuan Agricultural University, Chengdu, 611130 China
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Systematic and benchmarking studies of pipelines for mammal WGBS data in the novel NGS platform. BMC Bioinformatics 2023; 24:33. [PMID: 36721080 PMCID: PMC9890740 DOI: 10.1186/s12859-023-05163-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 01/27/2023] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND Whole genome bisulfite sequencing (WGBS), possesses the aptitude to dissect methylation status at the nucleotide-level resolution of 5-methylcytosine (5-mC) on a genome-wide scale. It is a powerful technique for epigenome in various cell types, and tissues. As a recently established next-generation sequencing (NGS) platform, GenoLab M is a promising alternative platform. However, its comprehensive evaluation for WGBS has not been reported. We sequenced two bisulfite-converted mammal DNA in this research using our GenoLab M and NovaSeq 6000, respectively. Then, we systematically compared those data via four widely used WGBS tools (BSMAP, Bismark, BatMeth2, BS-Seeker2) and a new bisulfite-seq tool (BSBolt). We interrogated their computational time, genome depth and coverage, and evaluated their percentage of methylated Cs. RESULT Here, benchmarking a combination of pre- and post-processing methods, we found that trimming improved the performance of mapping efficiency in eight datasets. The data from two platforms uncovered ~ 80% of CpG sites genome-wide in the human cell line. Those data sequenced by GenoLab M achieved a far lower proportion of duplicates (~ 5.5%). Among pipelines, BSMAP provided an intriguing representation of 5-mC distribution at CpG sites with 5-mC levels > ~ 78% in datasets from human cell lines, especially in the GenoLab M. BSMAP performed more advantages in running time, uniquely mapped reads percentages, genomic coverage, and quantitative accuracy. Finally, compared with the previous methylation pattern of human cell line and mouse tissue, we confirmed that the data from GenoLab M performed similar consistency and accuracy in methylation levels of CpG sites with that from NovaSeq 6000. CONCLUSION Together we confirmed that GenoLab M was a qualified NGS platform for WGBS with high performance. Our results showed that BSMAP was the suitable pipeline that allowed for WGBS studies on the GenoLab M platform.
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Global analysis of the association between pig muscle fatty acid composition and gene expression using RNA-Seq. Sci Rep 2023; 13:535. [PMID: 36631502 PMCID: PMC9834388 DOI: 10.1038/s41598-022-27016-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 12/23/2022] [Indexed: 01/13/2023] Open
Abstract
Fatty acids (FAs) play an essential role as mediators of cell signaling and signal transduction, affecting metabolic homeostasis and determining meat quality in pigs. However, FAs are transformed by the action of several genes, such as those encoding desaturases and elongases of FAs in lipogenic tissues. The aim of the current work was to identify candidate genes, biological processes, and pathways involved in the modulation of intramuscular FA profile from longissimus dorsi muscle. FA profile by gas chromatography of methyl esters and gene expression by RNA-Seq were determined in 129 Iberian × Duroc backcrossed pigs. An association analysis between the muscle transcriptome and its FA profile was performed, followed by a concordance and functional analysis. Overall, a list of well-known (e.g., PLIN1, LEP, ELOVL6, SC5D, NCOA2, ACSL1, MDH1, LPL, LGALS12, TFRC, GOT1, and FBP1) and novel (e.g., TRARG1, TANK, ENSSSCG00000011196, and ENSSSCG00000038429) candidate genes was identified, either in association with specific or several FA traits. Likewise, several of these genes belong to biological processes and pathways linked to energy, lipid, and carbohydrate metabolism, which seem determinants in the modulation of FA compositions. This study can contribute to elucidate the complex relationship between gene expression and FA profile in pig muscle.
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Ajila V, Colley L, Ste-Croix DT, Nissan N, Golshani A, Cober ER, Mimee B, Samanfar B, Green JR. P-TarPmiR accurately predicts plant-specific miRNA targets. Sci Rep 2023; 13:332. [PMID: 36609461 PMCID: PMC9822942 DOI: 10.1038/s41598-022-27283-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 12/29/2022] [Indexed: 01/09/2023] Open
Abstract
microRNAs (miRNAs) are small non-coding ribonucleic acids that post-transcriptionally regulate gene expression through the targeting of messenger RNA (mRNAs). Most miRNA target predictors have focused on animal species and prediction performance drops substantially when applied to plant species. Several rule-based miRNA target predictors have been developed in plant species, but they often fail to discover new miRNA targets with non-canonical miRNA-mRNA binding. Here, the recently published TarDB database of plant miRNA-mRNA data is leveraged to retrain the TarPmiR miRNA target predictor for application on plant species. Rigorous experiment design across four plant test species demonstrates that animal-trained predictors fail to sustain performance on plant species, and that the use of plant-specific training data improves accuracy depending on the quantity of plant training data used. Surprisingly, our results indicate that the complete exclusion of animal training data leads to the most accurate plant-specific miRNA target predictor indicating that animal-based data may detract from miRNA target prediction in plants. Our final plant-specific miRNA prediction method, dubbed P-TarPmiR, is freely available for use at http://ptarpmir.cu-bic.ca . The final P-TarPmiR method is used to predict targets for all miRNA within the soybean genome. Those ranked predictions, together with GO term enrichment, are shared with the research community.
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Affiliation(s)
- Victoria Ajila
- grid.34428.390000 0004 1936 893XDepartment of Systems and Computer Engineering, Carleton University, Ottawa, K1S 5B6 Canada
| | - Laura Colley
- grid.34428.390000 0004 1936 893XDepartment of Systems and Computer Engineering, Carleton University, Ottawa, K1S 5B6 Canada
| | - Dave T. Ste-Croix
- grid.55614.330000 0001 1302 4958Saint-Jean-sur-Richelieu Research and Development Center, Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu, J3B 7B5 Canada
| | - Nour Nissan
- grid.55614.330000 0001 1302 4958Ottawa Research and Development Center, Agriculture and Agri-Food Canada, Ottawa, K1A 0C6 Canada ,grid.34428.390000 0004 1936 893XDepartment of Biology, Carleton University, Ottawa, K1S 5B6 Canada
| | - Ashkan Golshani
- grid.34428.390000 0004 1936 893XDepartment of Biology, Carleton University, Ottawa, K1S 5B6 Canada
| | - Elroy R. Cober
- grid.55614.330000 0001 1302 4958Ottawa Research and Development Center, Agriculture and Agri-Food Canada, Ottawa, K1A 0C6 Canada
| | - Benjamin Mimee
- grid.55614.330000 0001 1302 4958Saint-Jean-sur-Richelieu Research and Development Center, Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu, J3B 7B5 Canada
| | - Bahram Samanfar
- grid.55614.330000 0001 1302 4958Ottawa Research and Development Center, Agriculture and Agri-Food Canada, Ottawa, K1A 0C6 Canada ,grid.34428.390000 0004 1936 893XDepartment of Biology, Carleton University, Ottawa, K1S 5B6 Canada
| | - James R. Green
- grid.34428.390000 0004 1936 893XDepartment of Systems and Computer Engineering, Carleton University, Ottawa, K1S 5B6 Canada
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Genome-wide identification, characterization and gene expression of BES1 transcription factor family in grapevine (Vitis vinifera L.). Sci Rep 2023; 13:240. [PMID: 36604456 PMCID: PMC9816167 DOI: 10.1038/s41598-022-24407-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 11/15/2022] [Indexed: 01/07/2023] Open
Abstract
BES1, as the most important transcription factor responsible for brassinolide (BR) signaling, has been confirmed to play a significant role in regulating plant growth and the improvement of stress resistance. The transcriptional regulatory mechanism of BES1 has been well elucidated in several plants, such as Arabidopsis thaliana (A. thaliana), Triticum aestivum L. (T. aestivum), and Oryza sativa L. (O. sativa). Nevertheless, the genome-wide analysis of the BES1 family in Vitis vinifera L. (V. vinifera). has not been comprehensively carried out. Thus, we have conducted a detailed analysis and identification of the BES1 transcription factors family in V. vinifera; a total of eight VvBES1 genes was predicted, and the phylogenetic relationships, gene structures, and Cis-acting element in their promoters were also analyzed. BES1 genes have been divided into three groups (I, II and III) based on phylogenetic relationship analysis, and most of VvBES1 genes were in group III. Also, we found that VvBES1 genes was located at seven of the total nineteen chromosomes, whereas VvBES1-2 (Vitvi04g01234) and VvBES1-5 (Vitvi18g00924) had a collinearity relationship, and their three copies are well preserved. In addition, the intron-exon model of VvBES1 genes were mostly conserved, and there existed several Cis-acting elements related to stress resistance responsive and phytohormones responsive in BES1s genes promoter. Moreover, the BES1 expressions were different in different V. vinifera organs, and BES1 expressions were different in different V. vinifera varieties under saline-alkali stress and heat stress, the expression of VvBES1 also changed with the prolongation of saline-alkali stress treatment time. The above findings could not only lay a primary foundation for the further validation of VvBES1 function, but could also provide a reference for molecular breeding in V. vinifera.
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Li C, Fan X, Guo X, Liu Y, Wang M, Zhao XC, Wu P, Yan Q, Sun L. Accuracy benchmark of the GeneMind GenoLab M sequencing platform for WGS and WES analysis. BMC Genomics 2022; 23:533. [PMID: 35869426 PMCID: PMC9308344 DOI: 10.1186/s12864-022-08775-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 07/18/2022] [Indexed: 11/23/2022] Open
Abstract
Background GenoLab M is a recently developed next-generation sequencing (NGS) platform from GeneMind Biosciences. To establish the performance of GenoLab M, we present the first report to benchmark and compare the WGS and WES sequencing data of the GenoLab M sequencer to NovaSeq 6000 and NextSeq 550 platform in various types of analysis. For WGS, thirty-fold sequencing from Illumina NovaSeq platform and processed by GATK pipeline is currently considered as the golden standard. Thus this dataset is generated as a benchmark reference in this study. Results GenoLab M showed an average of 94.62% of Q20 percentage for base quality, while the NovaSeq was slightly higher at 96.97%. However, GenoLab M outperformed NovaSeq or NextSeq at a duplication rate, suggesting more usable data after deduplication. For WGS short variant calling, GenoLab M showed significant accuracy improvement over the same depth dataset from NovaSeq, and reached similar accuracy to NovaSeq 33X dataset with 22x depth. For 100X WES, the F-score and Precision in GenoLab M were higher than NovaSeq or NextSeq, especially for InDel calling. Conclusions GenoLab M is a promising NGS platform for high-performance WGS and WES applications. For WGS, 22X depth in the GenoLab M sequencing platform offers a cost-effective alternative to the current mainstream 33X depth on Illumina.
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Hamim I, Sekine KT, Komatsu K. How do emerging long-read sequencing technologies function in transforming the plant pathology research landscape? PLANT MOLECULAR BIOLOGY 2022; 110:469-484. [PMID: 35962900 DOI: 10.1007/s11103-022-01305-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 07/26/2022] [Indexed: 06/15/2023]
Abstract
Long-read sequencing technologies are revolutionizing the sequencing and analysis of plant and pathogen genomes and transcriptomes, as well as contributing to emerging areas of interest in plant-pathogen interactions, disease management techniques, and the introduction of new plant varieties or cultivars. Long-read sequencing (LRS) technologies are progressively being implemented to study plants and pathogens of agricultural importance, which have substantial economic effects. The variability and complexity of the genome and transcriptome affect plant growth, development and pathogen responses. Overcoming the limitations of second-generation sequencing, LRS technology has significantly increased the length of a single contiguous read from a few hundred to millions of base pairs. Because of the longer read lengths, new analysis methods and tools have been developed for plant and pathogen genomics and transcriptomics. LRS technologies enable faster, more efficient, and high-throughput ultralong reads, allowing direct sequencing of genomes that would be impossible or difficult to investigate using short-read sequencing approaches. These benefits include genome assembly in repetitive areas, creating more comprehensive and exact genome determinations, assembling full-length transcripts, and detecting DNA and RNA alterations. Furthermore, these technologies allow for the identification of transcriptome diversity, significant structural variation analysis, and direct epigenetic mark detection in plant and pathogen genomic regions. LRS in plant pathology is found efficient for identifying and characterization of effectors in plants as well as known and unknown plant pathogens. In this review, we investigate how these technologies are transforming the landscape of determination and characterization of plant and pathogen genomes and transcriptomes efficiently and accurately. Moreover, we highlight potential areas of interest offered by LRS technologies for future study into plant-pathogen interactions, disease control strategies, and the development of new plant varieties or cultivars.
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Affiliation(s)
- Islam Hamim
- Laboratory of Plant Pathology, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Japan
- International Research Fellow of Japan Society for the Promotion of Science, Tokyo, Japan
- Department of Plant Pathology, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Ken-Taro Sekine
- Faculty of Agriculture, University of the Ryukyus, Okinawa, Japan
| | - Ken Komatsu
- Laboratory of Plant Pathology, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Japan.
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Li F, Fan K, Guo X, Liu J, Zhang K, Lu P. Genome-wide identification, molecular evolution and expression analysis of the non-specific lipid transfer protein (nsLTP) family in Setaria italica. BMC PLANT BIOLOGY 2022; 22:547. [PMID: 36443672 PMCID: PMC9703814 DOI: 10.1186/s12870-022-03921-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Accepted: 11/01/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Foxtail millet (Setaria italica L.) is a millet species with high tolerance to stressful environments. Plant non-specific lipid transfer proteins (nsLTPs) are a kind of small, basic proteins involved in many biological processes. So far, the genome of S. italica has been fully sequenced, and a comprehensive understanding of the evolution and expression of the nsLTP family is still lacking in foxtail millet. RESULTS Forty-five nsLTP genes were identified in S. italica and clustered into 5 subfamilies except three single genes (SinsLTP38, SinsLTP7, and SinsLTP44). The proportion of SinsLTPs was different in each subfamily, and members within the same subgroup shared conserved exon-intron structures. Besides, 5 SinsLTP duplication events were investigated. Both tandem and segmental duplication contributed to nsLTP expansion in S. italica, and the duplicated SinsLTPs had mainly undergone purifying selection pressure, which suggested that the function of the duplicated SinsLTPs might not diverge much. Moreover, we identified the nsLTP members in 5 other monocots, and 41, 13, 10, 4, and 1 orthologous gene pairs were identified between S. italica and S. viridis, S. bicolor, Z. mays, O. sativa, and B. distachyon, respectively. The functional divergence within the nsLTP orthologous genes might be limited. In addition, the tissue-specific expression patterns of the SinsLTPs were investigated, and the expression profiles of the SinsLTPs in response to abiotic stress were analyzed, all the 10 selected SinsLTPs were responsive to drought, salt, and cold stress. Among the selected SinsLTPs, 2 paired duplicated genes shared almost equivalent expression profiles, suggesting that these duplicated genes might retain some essential functions during subsequent evolution. CONCLUSIONS The present study provided the first systematic analysis for the phylogenetic classification, conserved domain and gene structure, expansion pattern, and expression profile of the nsLTP family in S. italica. These findings could pave a way for further comparative genomic and evolution analysis of nsLTP family in foxtail millet and related monocots, and lay the foundation for the functional analysis of the nsLTPs in S. italica.
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Affiliation(s)
- Feng Li
- College of Agronomy and Life Sciences, Shanxi Datong University, Datong, 037009, China.
- Research and Development Center of Agricultural Facility Technology, Shanxi Datong University, Datong, 037009, China.
| | - Kai Fan
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xuhu Guo
- College of Agronomy and Life Sciences, Shanxi Datong University, Datong, 037009, China
- Research and Development Center of Agricultural Facility Technology, Shanxi Datong University, Datong, 037009, China
| | - Jianxia Liu
- College of Agronomy and Life Sciences, Shanxi Datong University, Datong, 037009, China
- Research and Development Center of Agricultural Facility Technology, Shanxi Datong University, Datong, 037009, China
| | - Kun Zhang
- College of Agronomy and Life Sciences, Shanxi Datong University, Datong, 037009, China
- Research and Development Center of Agricultural Facility Technology, Shanxi Datong University, Datong, 037009, China
| | - Ping Lu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
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Hassan MH, Omar AM, Daskalakis E, Mohamed AA, Boyd LA, Blanford C, Grieve B, Bartolo PJDS. Multi-Layer Biosensor for Pre-Symptomatic Detection of Puccinia strifformis, the Causal Agent of Yellow Rust. BIOSENSORS 2022; 12:829. [PMID: 36290966 PMCID: PMC9599175 DOI: 10.3390/bios12100829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 09/27/2022] [Accepted: 10/01/2022] [Indexed: 06/16/2023]
Abstract
The yellow rust of wheat (caused by Puccinia striiformis f. sp. tritici) is a devastating fungal infection that is responsible for significant wheat yield losses. The main challenge with the detection of this disease is that it can only be visually detected on the leaf surface between 7 and 10 days after infection, and by this point, counter measures such as the use of fungicides are generally less effective. The hypothesis of this study is to develop and use a compact electrochemical-based biosensor for the early detection of P. striiformis, thus enabling fast countermeasures to be taken. The biosensor that was developed consists of three layers. The first layer mimics the wheat leaf surface morphology. The second layer consists of a sucrose/agar mixture that acts as a substrate and contains a wheat-derived terpene volatile organic compound that stimulates the germination and growth of the spores of the yellow rust pathogen P. s. f. sp. tritici. The third layer consists of a nonenzymatic glucose sensor that produces a signal once invertase is produced by P. striiformis, which comes into contact with the second layer, thereby converting sucrose to glucose. The results show the proof that this innovative biosensor can enable the detection of yellow rust spores in 72 h.
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Affiliation(s)
- Mohamed H. Hassan
- Department of Mechanical, Aerospace and Civil Engineering, University of Manchester, Manchester M13 9PL, UK
| | - Abdalla M. Omar
- Department of Mechanical, Aerospace and Civil Engineering, University of Manchester, Manchester M13 9PL, UK
| | - Evangelos Daskalakis
- Department of Mechanical, Aerospace and Civil Engineering, University of Manchester, Manchester M13 9PL, UK
| | | | | | | | - Bruce Grieve
- Department of Electrical & Electronic Engineering, University of Manchester, Manchester M13 9PL, UK
| | - Paulo JDS. Bartolo
- Department of Mechanical, Aerospace and Civil Engineering, University of Manchester, Manchester M13 9PL, UK
- Singapore 3D Printing Centre, Nanyang Technological University, Singapore 639798, Singapore
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Li L, Liu J, Gong H, Zhao Y, Luo J, Sun Z, Li T. A dominant gene Ihrl1 is tightly linked to and inhibits the gene Ndhrl1 mediating nitrogen-dependent hypersensitive reaction-like phenotype in wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:3563-3570. [PMID: 36030437 DOI: 10.1007/s00122-022-04200-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 08/17/2022] [Indexed: 06/15/2023]
Abstract
Identification and mapping of an inhibitor of Ndhrl1 mediating nitrogen-dependent hypersensitive reaction-like phenotype in wheat. Hypersensitive reaction-like (HRL) traits are characteristic of spontaneous lesions including yellowish spots, brown spots or white-stripe that appeared randomly and dispersedly on all the leaves in the absence of plant pathogens. Our previous studies have shown that the wheat line P7001 showed an HRL trait at low nitrogen supply, and this trait was controlled by the gene Ndhrl1 (Nitrogen-dependent hypersensitive reaction-like 1). In order to investigate the robustness of the trait expression mediated by Ndhrl1 under different genetic backgrounds, seven genetic populations, with P7001 being the common female parent, were constructed and analyzed. F1 plants from six of the seven combinations showed HRL trait and Ndhrl1 segregated in a dominant way of HRL: non-HRL = 3:1 in the six populations (F2). Exceptionally, the F1 plants of P7001/Fielder combination showed non-HRL trait and HRL trait in the F2 population showed a contrasting recessive segregation ratio of HRL: non-HRL = 1:3, suggesting Fielder may have another HRL-related gene. Using 55 K SNP array and PCR-based markers, the HRL-related gene in Fielder was mapped to an interval of 5.63-12.91 Mb on the short arm of chromosome 2B with the flanking markers Yzu660R075552 and Yzu660F075941. A recombinant with genomic region of Fielder at Ndhrl1 locus showing HRL trait demonstrated that Fielder also harbored Ndhrl1 same as P7001. Thus, Fielder carries a single dominant suppressor of Ndhrl1, designated as Ihrl1 (Inhibitor of hypersensitive reaction-like). Interestingly, Ihrl1 is tightly linked to Ndhrl1 and may be also involved in nitrogen metabolic and (or) signaling pathways.
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Affiliation(s)
- Lei Li
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou, China
| | - Jiaqi Liu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou, China
| | - Hao Gong
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou, China
| | - Yang Zhao
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou, China
| | - Jinbiao Luo
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou, China
| | - Zhengxi Sun
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou, China
| | - Tao Li
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou, China.
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China.
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Liu D, Cui Y, Zhao Z, Zhang J, Li S, Liu Z. Transcriptome analysis and mining of genes related to shade tolerance in foxtail millet ( Setaria italica (L.) P. Beauv.). ROYAL SOCIETY OPEN SCIENCE 2022; 9:220953. [PMID: 36249327 PMCID: PMC9532984 DOI: 10.1098/rsos.220953] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 09/20/2022] [Indexed: 06/16/2023]
Abstract
A stereo interplanting system with foxtail millet beneath chestnut trees is an effective planting method to raise the utilization of land in chestnut orchards, increase yields and improve quality of chestnut nuts. Consequently, exploration of genes involved in shade tolerance response in foxtail millet and breeding shade-tolerant varieties have become urgent issues. In this study, RNA-seq of leaf samples from two shade-tolerant varieties and three shade-intolerant varieties of foxtail millet at the booting stage was performed. Comparisons between the varieties revealed that 70 genes were commonly differentially expressed. Moreover, the ratio of net photosynthetic rate under shaded environment to that under light environment could be used as an indicator of shade tolerance. Subsequently, weighted gene co-expression network analysis was employed to construct a co-expression network and modules were correlated with this ratio. A total of 375 genes were identified as potentially relevant to shade tolerance, among which nine genes were also present in the 70 differentially expressed genes, which implied that they were good candidates for genes involved in shade tolerance. Our results provide valuable resources for elucidation of the molecular mechanisms underlying shade tolerance and will contribute to breeding of shade-tolerant foxtail millet that are adapted to the shaded environment under chestnut trees.
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Affiliation(s)
- Dan Liu
- Tianjin Key Laboratory of Crop Genetics and Breeding, Institute of Crop Sciences, Tianjin Academy of Agricultural Sciences, Tianjin, People's Republic of China
| | - Yanjiao Cui
- Department of Life Sciences, Tangshan Normal University, Tangshan, People's Republic of China
| | - Zilong Zhao
- Department of Life Sciences, Tangshan Normal University, Tangshan, People's Republic of China
| | - Jing Zhang
- Department of Life Sciences, Tangshan Normal University, Tangshan, People's Republic of China
| | - Suying Li
- Department of Life Sciences, Tangshan Normal University, Tangshan, People's Republic of China
| | - Zhengli Liu
- Department of Life Sciences, Tangshan Normal University, Tangshan, People's Republic of China
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Samarfard S, Ghorbani A, Karbanowicz TP, Lim ZX, Saedi M, Fariborzi N, McTaggart AR, Izadpanah K. Regulatory non-coding RNA: The core defense mechanism against plant pathogens. J Biotechnol 2022; 359:82-94. [PMID: 36174794 DOI: 10.1016/j.jbiotec.2022.09.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 09/18/2022] [Accepted: 09/21/2022] [Indexed: 12/13/2022]
Abstract
Plant pathogens damage crops and threaten global food security. Plants have evolved complex defense networks against pathogens, using crosstalk among various signaling pathways. Key regulators conferring plant immunity through signaling pathways include protein-coding genes and non-coding RNAs (ncRNAs). The discovery of ncRNAs in plant transcriptomes was first considered "transcriptional noise". Recent reviews have highlighted the importance of non-coding RNAs. However, understanding interactions among different types of noncoding RNAs requires additional research. This review attempts to consider how long-ncRNAs, small-ncRNAs and circular RNAs interact in response to pathogenic diseases within different plant species. Developments within genomics and bioinformatics could lead to the further discovery of plant ncRNAs, knowledge of their biological roles, as well as an understanding of their importance in exploiting the recent molecular-based technologies for crop protection.
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Affiliation(s)
- Samira Samarfard
- Department of Primary Industries and Regional Development, DPIRD Diagnostic Laboratory Services, South Perth, WA, Australia
| | - Abozar Ghorbani
- Nuclear Agriculture Research School, Nuclear Science and Technology Research Institute (NSTRI), Karaj, the Islamic Republic of Iran.
| | | | - Zhi Xian Lim
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Mahshid Saedi
- Department of Plant Protection, Faculty of Agriculture, University of Kurdistan, Sanandaj, the Islamic Republic of Iran
| | - Niloofar Fariborzi
- Department of Medical Entomology and Vector Control, School of Health, Shiraz University of Medical Sciences, Shiraz, the Islamic Republic of Iran
| | - Alistair R McTaggart
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Ecosciences Precinct, Dutton Park, QLD 4102, Australia
| | - Keramatollah Izadpanah
- Plant Virology Research Center, College of Agriculture, Shiraz University, Shiraz, the Islamic Republic of Iran
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Identification and genetic diversity analysis of hybrid offspring of azalea based on EST-SSR markers. Sci Rep 2022; 12:15239. [PMID: 36076046 PMCID: PMC9458661 DOI: 10.1038/s41598-022-18907-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 08/22/2022] [Indexed: 11/23/2022] Open
Abstract
Azalea is a world famous flower with high economic and ornamental value. The breeding of new azalea varieties is mainly done by cross breeding. However, there is a risk that cross breeding may cause errors in the hybrid offspring due to contamination by exogenous pollen. Therefore, the identification of hybrid offspring is an important part of azalea breeding. In this study, the parents of three hybrid combinations and their 88 F1 hybrid offspring were selected to screen 15 pairs of EST-SSR primers to identify the authenticity of azalea hybrid offspring. The results showed that the authenticity of 88 azalea F1 hybrid progenies could be determined by at least four primer pairs. Genetic diversity analysis of azalea hybrid progeny revealed that the number of alleles and polymorphic information content of the progeny increased to different degrees, and the more distant the genetic distance between parents, the richer the polymorphic information. It is suggested that EST-SSR molecular marker can be applied for the early identification and genetic diversity analysis of the progeny of azalea hybrids. This method is of positive significance for improving the breeding efficiency of new varieties and exploring the genetic background of azalea.
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Ge H, Xu J, Hua M, An W, Wu J, Wang B, Li P, Fang H. Genome-wide identification and analysis of ACP gene family in Sorghum bicolor (L.) Moench. BMC Genomics 2022; 23:538. [PMID: 35879672 PMCID: PMC9310384 DOI: 10.1186/s12864-022-08776-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 07/18/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Acyl carrier proteins (ACP) constitute a very conserved carrier protein family. Previous studies have found that ACP not only takes part in the fatty acid synthesis process of almost all organisms, but also participates in the regulation of plant growth, development, and metabolism, and makes plants adaptable to stresses. However, this gene family has not been systematically studied in sorghum. RESULTS Nine ACP family members were identified in the sorghum genome, which were located on chromosomes 1, 2, 5, 7, 8 and 9, respectively. Evolutionary analysis among different species divided the ACP family into four subfamilies, showing that the SbACPs were more closely related to maize. The prediction results of subcellular localization showed that SbACPs were mainly distributed in chloroplasts and mitochondria, while fluorescence localization showed that SbACPs were mainly localized in chloroplasts in tobacco leaf. The analysis of gene structure revealed a relatively simple genetic structure, that there were 1-3 introns in the sorghum ACP family, and the gene structure within the same subfamily had high similarity. The amplification method of SbACPs was mainly large fragment replication, and SbACPs were more closely related to ACPs in maize and rice. In addition, three-dimensional structure analysis showed that all ACP genes in sorghum contained four α helices, and the second helix structure was more conserved, implying a key role in function. Cis-acting element analysis indicated that the SbACPs might be involved in light response, plant growth and development regulation, biotic and abiotic stress response, plant hormone regulation, and other physiological processes. What's more, qRT-PCR analysis uncovered that some of SbACPs might be involved in the adaptive regulation of drought and salt stresses, indicating the close relationship between fatty acids and the resistance to abiotic stresses in sorghum. CONCLUSIONS In summary, these results showed a comprehensive overview of the SbACPs and provided a theoretical basis for further studies on the biological functions of SbACPs in sorghum growth, development and abiotic stress responses.
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Affiliation(s)
- Hanqiu Ge
- Ministry of Agricultural Scientific Observing and Experimental Station of Maize in Plain Area of Southern Region, School of Life Sciences, Nantong University, Nantong, 226019, Jiangsu, People's Republic of China
| | - Jingjing Xu
- Ministry of Agricultural Scientific Observing and Experimental Station of Maize in Plain Area of Southern Region, School of Life Sciences, Nantong University, Nantong, 226019, Jiangsu, People's Republic of China
| | - Mingzhu Hua
- Ministry of Agricultural Scientific Observing and Experimental Station of Maize in Plain Area of Southern Region, School of Life Sciences, Nantong University, Nantong, 226019, Jiangsu, People's Republic of China
| | - Wenwen An
- Ministry of Agricultural Scientific Observing and Experimental Station of Maize in Plain Area of Southern Region, School of Life Sciences, Nantong University, Nantong, 226019, Jiangsu, People's Republic of China
| | - Junping Wu
- Nantong Changjiang Seed Co., Ltd, Nantong, 226368, Jiangsu, People's Republic of China
| | - Baohua Wang
- Ministry of Agricultural Scientific Observing and Experimental Station of Maize in Plain Area of Southern Region, School of Life Sciences, Nantong University, Nantong, 226019, Jiangsu, People's Republic of China.
| | - Ping Li
- Ministry of Agricultural Scientific Observing and Experimental Station of Maize in Plain Area of Southern Region, School of Life Sciences, Nantong University, Nantong, 226019, Jiangsu, People's Republic of China.
| | - Hui Fang
- Ministry of Agricultural Scientific Observing and Experimental Station of Maize in Plain Area of Southern Region, School of Life Sciences, Nantong University, Nantong, 226019, Jiangsu, People's Republic of China.
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Li S, Cui Y, Liu D, Zhao Z, Zhang J, Liu Z. Transcriptome analysis and characterization of genes associated to leaf tannin content in foxtail millet [Setaria italica (L.) P. Beauv.]. BMC Genomics 2022; 23:512. [PMID: 35836120 PMCID: PMC9284691 DOI: 10.1186/s12864-022-08746-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 07/07/2022] [Indexed: 12/13/2022] Open
Abstract
Background Chinese chestnut is an economically important tree species whose yield and quality are seriously affected by red spider attack. Tannins is one of the most important class secondary metabolites in plants, and is closely associated with plant defense mechanisms against insect and herbivory. In our previous studies, it was revealed that several low-tannin foxtail millet varieties growing under the Chinese chestnut trees could attract red spiders to feed on their leaves and protect the chestnut trees from the infestation of red spiders, meanwhile, the growth and yield of foxtail millet plants themselves were not greatly affected. Results To identify genes related to leaf tannin content and selection of foxtail millet germplasm resources with low tannin content for interplanting with Chinese chestnut and preventing the red spider attack, the leaves of 4 varieties with different levels of tannin content were harvested for comparative transcriptome analysis. In total, 335 differentially expressed genes (DEGs) were identified. For acquisition of gene functions and biological pathways they involved in, gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) enrichment analyses were performed, and several DEGs were found to possibly participate in the tannins biosynthesis pathway and transport processes of precursors. In addition, according to the PlantTFDB database, some transcription factors were predicted among the DEGs, suggesting their role in regulation of tannins biosynthesis pathway. Conclusion Our results provide valuable gene resources for understanding the biosynthesis and regulation mechanisms of tannins in foxtail millet, and pave the way for speeding up the breeding of low-tannin varieties through marker-assisted selection, which could be utilized for interplanting with Chinese chestnut trees to confer protection against red spider attack. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08746-8.
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Affiliation(s)
- Suying Li
- Department of Life Sciences, Tangshan Normal University, Tangshan, China
| | - Yanjiao Cui
- Department of Life Sciences, Tangshan Normal University, Tangshan, China
| | - Dan Liu
- Tianjin Key Laboratory of Crop Genetics and Breeding, Institute of Crop Sciences, Tianjin Academy of Agricultural Sciences, Tianjin, China
| | - Zilong Zhao
- Department of Life Sciences, Tangshan Normal University, Tangshan, China
| | - Jing Zhang
- Department of Life Sciences, Tangshan Normal University, Tangshan, China
| | - Zhengli Liu
- Department of Life Sciences, Tangshan Normal University, Tangshan, China.
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Li J, Chen M, Fan T, Mu X, Gao J, Wang Y, Jing T, Shi C, Niu H, Zhen S, Fu J, Zheng J, Wang G, Tang J, Gou M. Underlying mechanism of accelerated cell death and multiple disease resistance in a maize lethal leaf spot 1 allele. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:3991-4007. [PMID: 35303096 DOI: 10.1093/jxb/erac116] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 03/16/2022] [Indexed: 06/14/2023]
Abstract
Multiple disease resistance (MDR) in maize has attracted increasing attention. However, the interplay between cell death and metabolite changes and their contributions to MDR remains elusive in maize. In this study, we identified a mutant named as lesion mimic 30 (les30) that showed 'suicidal' lesion formation in the absence of disease and had enhanced resistance to the fungal pathogen Curvularia lunata. Using map-based cloning, we identified the causal gene encoding pheophorbide a oxidase (PAO), which is known to be involved in chlorophyll degradation and MDR, and is encoded by LETHAL LEAF SPOT1 (LLS1). LLS1 was found to be induced by both biotic and abiotic stresses. Transcriptomics analysis showed that genes involved in defense responses and secondary metabolite biosynthesis were mildly activated in leaves of the les30 mutant without lesions, whilst they were strongly activated in leaves with lesions. In addition, in les30 leaves with lesions, there was overaccumulation of defense-associated phytohormones including jasmonic acid and salicylic acid, and of phytoalexins including phenylpropanoids, lignin, and flavonoids, suggesting that their biosynthesis was activated in a lesion-dependent manner. Taken together, our study implies the existence of an interactive amplification loop of interrupted chlorophyll degradation, cell death, expression of defense-related genes, and metabolite changes that results in suicidal lesion formation and MDR, and this has the potential to be exploited by genetic manipulation to improve maize disease resistance.
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Affiliation(s)
- Jiankun Li
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, Center for Crop Genome Engineering, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Mengyao Chen
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, Center for Crop Genome Engineering, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Tianyuan Fan
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, Center for Crop Genome Engineering, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Xiaohuan Mu
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, Center for Crop Genome Engineering, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Jie Gao
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, Center for Crop Genome Engineering, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Ying Wang
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, Center for Crop Genome Engineering, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Teng Jing
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, Center for Crop Genome Engineering, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Cuilan Shi
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, Center for Crop Genome Engineering, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Hongbin Niu
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, Center for Crop Genome Engineering, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Sihan Zhen
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Junjie Fu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jun Zheng
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Guoying Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jihua Tang
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, Center for Crop Genome Engineering, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
- The Shennong Laboratory, Zhengzhou, Henan 450002, China
| | - Mingyue Gou
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, Center for Crop Genome Engineering, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
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Tempel S, Bedo J, Talla E. From a large-scale genomic analysis of insertion sequences to insights into their regulatory roles in prokaryotes. BMC Genomics 2022; 23:451. [PMID: 35725380 PMCID: PMC9208149 DOI: 10.1186/s12864-022-08678-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 06/07/2022] [Indexed: 12/03/2022] Open
Abstract
Background Insertion sequences (ISs) are mobile repeat sequences and most of them can copy themselves to new host genome locations, leading to genome plasticity and gene regulation in prokaryotes. In this study, we present functional and evolutionary relationships between IS and neighboring genes in a large-scale comparative genomic analysis. Results IS families were located in all prokaryotic phyla, with preferential occurrence of IS3, IS4, IS481, and IS5 families in Alpha-, Beta-, and Gammaproteobacteria, Actinobacteria and Firmicutes as well as in eukaryote host-associated organisms and autotrophic opportunistic pathogens. We defined the concept of the IS-Gene couple (IG), which allowed to highlight the functional and regulatory impacts of an IS on the closest gene. Genes involved in transcriptional regulation and transport activities were found overrepresented in IG. In particular, major facilitator superfamily (MFS) transporters, ATP-binding proteins and transposases raised as favorite neighboring gene functions of IS hotspots. Then, evolutionary conserved IS-Gene sets across taxonomic lineages enabled the classification of IS-gene couples into phylum, class-to-genus, and species syntenic IS-Gene couples. The IS5, IS21, IS4, IS607, IS91, ISL3 and IS200 families displayed two to four times more ISs in the phylum and/or class-to-genus syntenic IGs compared to other IS families. This indicates that those families were probably inserted earlier than others and then subjected to horizontal transfer, transposition and deletion events over time. In phylum syntenic IG category, Betaproteobacteria, Crenarchaeota, Calditrichae, Planctomycetes, Acidithiobacillia and Cyanobacteria phyla act as IS reservoirs for other phyla, and neighboring gene functions are mostly related to transcriptional regulators. Comparison of IS occurrences with predicted regulatory motifs led to ~ 26.5% of motif-containing ISs with 2 motifs per IS in average. These results, concomitantly with short IS-Gene distances, suggest that those ISs would interfere with the expression of neighboring genes and thus form strong candidates for an adaptive pairing. Conclusions All together, our large-scale study provide new insights into the IS genetic context and strongly suggest their regulatory roles. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08678-3.
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Affiliation(s)
- Sebastien Tempel
- Aix Marseille University, CNRS, LCB, Laboratoire de Chimie Bactérienne, 13009, Marseille, France.
| | - Justin Bedo
- Bioinformatics Division, the Walter and Eliza Hall Institute, 1G Royal Parade, Parkville, VIC, 3052, Australia.,School of Computing and Information Systems, the University of Melbourne, Parkville, VIC, 3010, Australia
| | - Emmanuel Talla
- Aix Marseille University, CNRS, LCB, Laboratoire de Chimie Bactérienne, 13009, Marseille, France.
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Li C, Liu H, Wang J, Pan Q, Wang Y, Wu K, Jia P, Mu Y, Tang H, Xu Q, Jiang Q, Liu Y, Qi P, Zhang X, Huang L, Chen G, Wang J, Wei Y, Zheng Y, Gou L, Yao Q, Lan X, Ma J. Characterization and fine mapping of a lesion mimic mutant (Lm5) with enhanced stripe rust and powdery mildew resistance in bread wheat (Triticum aestivum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:421-438. [PMID: 34661696 DOI: 10.1007/s00122-021-03973-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 10/08/2021] [Indexed: 06/13/2023]
Abstract
A novel light intensity-dependent lesion mimic mutant with enhanced disease resistance was physiologically, biochemically, and genetically characterized, and the causative gene was fine mapped to a 1.28 Mbp interval containing 17 high-confidence genes. Lesion mimic mutants are ideal for studying disease resistance and programmed cell death photosynthesis in plants to improve crop yield. In this study, a novel light intensity-dependent lesion mimic mutant (MC21) was obtained from the wheat variety Chuannong16 (CN16) by ethyl methane sulfonate treatment. The mutant initially developed tiny lesion spots on the basal part of the leaves, which then gradually proceeded down to leaf sheaths, stems, shells, and awns at the flowering stage. The major agronomic traits were significantly altered in the mutant compared to that in the wild-type CN16. Furthermore, the mutant exhibited a lesion phenotype with degenerated chloroplast structure, decreased chlorophyll content, increased level of reactive oxygen species, and increased resistance to stripe rust and powdery mildew. Genetic analysis indicated that the lesion phenotype was controlled by a novel single semi-dominant nuclear gene. The target gene was mapped on chromosome arm 2AL located between Kompetitive Allele Specific PCR (KASP) markers, KASP-4211 and KASP-5353, and tentatively termed as lesion mimic 5 (Lm5). The fine mapping suggested that Lm5 was located in a 1.28 Mbp interval between markers KASP-5825 and KASP-9366; 17 high-confidence candidate genes were included in this genomic region. This study provides an important foundational step for further cloning of Lm5 using a map-based approach.
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Affiliation(s)
- Cong Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Hang Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jian Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Qi Pan
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yue Wang
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China
| | - Kunyan Wu
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China
| | - Peiying Jia
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yang Mu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Huaping Tang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Qiang Xu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Qiantao Jiang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yaxi Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Pengfei Qi
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xiaojun Zhang
- College of Agronomy, Shanxi Agricultural University, Taiyuan, 030031, China
| | - Lin Huang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Guoyue Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jirui Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yuming Wei
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Youliang Zheng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Lulu Gou
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Qifu Yao
- College of Agroforestry Engineering and Planning/Guizhou Key Laboratory of Biodiversity Conservation and Utilization in the Fanjing Mountain Region, Tongren University, Tongren, 554300, China.
| | - Xiujin Lan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China.
| | - Jian Ma
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China.
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Heryanto C, Hanly JJ, Mazo-Vargas A, Tendolkar A, Martin A. Mapping and CRISPR homology-directed repair of a recessive white eye mutation in Plodia moths. iScience 2022; 25:103885. [PMID: 35243245 PMCID: PMC8861637 DOI: 10.1016/j.isci.2022.103885] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 12/23/2021] [Accepted: 01/11/2022] [Indexed: 11/29/2022] Open
Abstract
The pantry moth Plodia interpunctella is a worldwide pest of stored food products and a promising laboratory model system for lepidopteran functional genomics. Here we describe efficient methods for precise genome editing in this insect. A spontaneous recessive white-eyed phenotype maps to a frameshift deletion (c.737delC) in the white gene. CRISPR NHEJ mutagenesis of white replicates this phenotype with high rates of somatic biallelic knockout. G0 individuals with mutant clones on both eyes produced 100% mutant progeny, making white an ideal marker for co-conversion when targeting other genes. CRISPR HDR experiments corrected c.737delC and reverted white eyes to a pigmented state in 37% of G0 mosaic adults. These repaired alleles showed practical rates of germline transmission in backcrosses, demonstrating the potential of the technique for precise genome editing. Plodia offers a promising avenue for research in this taxon because of its lab-ready features, egg injectability, and editability. Plodia pantry moths are an emerging model organism for functional genomics in Lepidoptera Spontaneous and CRISPR-induced white mutations yield recessive-white eye phenotypes CRISPR HDR repair with ssODN donor result in practical rates of base editing We provide optimized protocols for Plodia handling and genome editing
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Das R, Fernandez JG. Biomaterials for Mimicking and Modelling Tumor Microenvironment. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1379:139-170. [DOI: 10.1007/978-3-031-04039-9_6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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Zhang H, Xu X, Wang M, Wang H, Deng P, Zhang Y, Wang Y, Wang C, Wang Y, Ji W. A dominant spotted leaf gene TaSpl1 activates endocytosis and defense-related genes causing cell death in the absence of dominant inhibitors. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 310:110982. [PMID: 34315598 DOI: 10.1016/j.plantsci.2021.110982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Revised: 06/13/2021] [Accepted: 06/16/2021] [Indexed: 06/13/2023]
Abstract
The spotted leaf lesion mimic trait simulates cell death in a plant responding to pathogen infection. Some spotted leaf genes are recessive, while others are dominant. A small number of plants with a lesion mimic phenotype appeared in a segregating population obtained by crossing two normal green wheat strains, XN509 and N07216. Here, we clarified the genetic model and its breeding value. Phenotyping of the consecutive progeny populations over six cropping seasons showed that the spotted leaf lesion mimic phenotype was controlled by a dominant gene designated TaSpl1, which was inhibited by two other dominant genes, designated TaSpl1-I1 and TaSpl1-I2. Using bulked segregant analysis RNA-seq (BSR-Seq) and newly developed KASP-PCR markers, the TaSpl1 and TaSpl1-I1 loci in N07216 were mapped to the end of chromosomes 3DS and 3BS, respectively. Plants with the spotted phenotype showed lower levels of stripe rust and powdery mildew than those with the normal green phenotype. Compared with normal leaves, the differentially expressed genes in spotted leaves were significantly enriched in plant-pathogen interaction and endocytosis pathways. There were no differences in the yield parameters of the F5 and F6 sister lines, N13039S with TaSpl1 and N13039 N without TaSpl1. These results provide a greater understanding of spotted leaf phenotyping and the breeding value of the lesion mimic allele in developing disease-resistance varieties.
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Affiliation(s)
- Hong Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, PR China; China-Australia Joint Research Center for Abiotic and Biotic Stress Management, Northwest A&F University, Yangling, Shaanxi, 712100, PR China.
| | - Xiaomin Xu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, PR China
| | - Mengmeng Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, PR China
| | - Hui Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, PR China
| | - Pingchuan Deng
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, PR China
| | - Yaoyuan Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, PR China
| | - Yanzhen Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, PR China
| | - Changyou Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, PR China
| | - Yajuan Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, PR China; Shaanxi Research Station of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, Yangling, Shaanxi, 712100, PR China
| | - Wanquan Ji
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, PR China; Shaanxi Research Station of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, Yangling, Shaanxi, 712100, PR China.
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