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Jiao L, Han C, Zhu J, Zhang P, Ma Y, Dai X, Zhang Y. Transcriptome analysis and development of EST-SSR markers in the mushroom Auricularia heimuer. Sci Rep 2024; 14:12340. [PMID: 38811679 DOI: 10.1038/s41598-024-63080-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Accepted: 05/24/2024] [Indexed: 05/31/2024] Open
Abstract
Auricularia heimuer, the third most frequently cultivated edible mushroom species worldwide, has high medicinal value. However, a shortage of molecular marker hinders the efficiency and accuracy of genetic breeding efforts for A. heimuer. High-throughput transcriptome sequencing data are essential for gene discovery and molecular markers development. This study aimed to clarify the distribution of SSR loci across the A. heimuer transcriptome and to develop highly informative EST-SSR markers. These tools can be used for phylogenetic analysis, functional gene mining, and molecular marker-assisted breeding of A. heimuer. This study used Illumina high-throughput sequencing technology to obtain A. heimuer transcriptome data. The results revealed 37,538 unigenes in the A. heimuer transcriptome. Of these unigenes, 24,777 (66.01%) were annotated via comparison with the COG, Pfam, and NR databases. Overall, 2510 SSRs were identified from the unigenes, including 6 types of SSRs. The most abundant type of repeats were trinucleotides (1425, 56.77%), followed by mononucleotides (391, 15.58%) and dinucleotides (456, 18.17%). Primer pairs for 102 SSR loci were randomly designed for validity confirmation and polymorphism identification; this process yielded 53 polymorphic EST-SSR markers. Finally, 13 pairs of highly polymorphic EST-SSR primers were used to analyze the genetic diversity and population structure of 52 wild A. heimuer germplasms, revealing that the 52 germplasms could be divided into three categories. These results indicated that SSR loci were abundant in types, numbers, and frequencies, providing a potential basis for germplasm resource identification, genetic diversity analysis, and molecular marker-assisted breeding of A. heimuer.
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Affiliation(s)
- Lihe Jiao
- Institute of Microbiology, Heilongjiang Academy of Sciences, Harbin, 150010, China
| | - Chuang Han
- Institute of Microbiology, Heilongjiang Academy of Sciences, Harbin, 150010, China
| | - Jianan Zhu
- Institute of Microbiology, Heilongjiang Academy of Sciences, Harbin, 150010, China
| | - Piqi Zhang
- Institute of Microbiology, Heilongjiang Academy of Sciences, Harbin, 150010, China
| | - Yinpeng Ma
- Institute of Microbiology, Heilongjiang Academy of Sciences, Harbin, 150010, China
| | - Xiaodong Dai
- Institute of Microbiology, Heilongjiang Academy of Sciences, Harbin, 150010, China.
| | - Yunzhi Zhang
- Institute of Microbiology, Heilongjiang Academy of Sciences, Harbin, 150010, China.
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2
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Chen S, Du Z, Zhao P, Wang X, Wu Y, Li H, Cai W. Phylogeographic Pattern of the Assassin Bug Sycanus bifidus Inferred from Mitochondrial Genomes and Nuclear Genes. BIOLOGY 2024; 13:305. [PMID: 38785787 PMCID: PMC11118239 DOI: 10.3390/biology13050305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Revised: 04/24/2024] [Accepted: 04/25/2024] [Indexed: 05/25/2024]
Abstract
The assassin bug Sycanus bifidus has a wide distribution across southern China. This study explored its distribution and evolution by analyzing mitochondrial and nuclear ribosomal RNA genes, revealing how Pleistocene climate and geological changes shaped its phylogeography. We identified two main clades, A and B, that diverged in the Middle Pleistocene. Hainan Island's populations form a unique group within Clade A, suggesting that the Qiongzhou Strait served as a dispersal corridor during glaciation. Rising sea levels likely separated the Hainan population afterward. Ecological niche modeling showed that both populations have been viable since the last interglacial period, with demographic analyses indicating possible expansions during the Middle and Late Pleistocene, driven by favorable climates. This study highlights the significant effects of Pleistocene sea-level and climatic changes on the distribution and evolution of S. bifidus in China.
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Affiliation(s)
- Suyi Chen
- Department of Entomology, MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China; (S.C.); (Z.D.); (X.W.)
- Sanya Institute of China Agricultural University, Sanya 572025, China
| | - Zhenyong Du
- Department of Entomology, MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China; (S.C.); (Z.D.); (X.W.)
- Sanya Institute of China Agricultural University, Sanya 572025, China
| | - Ping Zhao
- Key Laboratory of Environment Change and Resources Use in Beibu Gulf (Ministry of Education) and Guangxi Key Laboratory of Earth Surface Processes and Intelligent Simulation, Nanning Normal University, Nanning 530001, China;
- Department of Plant Protection, Kaili University, Kaili 556000, China
| | - Xuan Wang
- Department of Entomology, MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China; (S.C.); (Z.D.); (X.W.)
- Sanya Institute of China Agricultural University, Sanya 572025, China
| | - Yunfei Wu
- College of Biology and Food Engineering, Chuzhou University, Chuzhou 239000, China;
| | - Hu Li
- Department of Entomology, MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China; (S.C.); (Z.D.); (X.W.)
- Sanya Institute of China Agricultural University, Sanya 572025, China
| | - Wanzhi Cai
- Department of Entomology, MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China; (S.C.); (Z.D.); (X.W.)
- Sanya Institute of China Agricultural University, Sanya 572025, China
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3
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Zhou Y, Peng S, Wang H, Cai X, Wang Q. Review of Personalized Medicine and Pharmacogenomics of Anti-Cancer Compounds and Natural Products. Genes (Basel) 2024; 15:468. [PMID: 38674402 PMCID: PMC11049652 DOI: 10.3390/genes15040468] [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: 04/19/2023] [Revised: 05/11/2023] [Accepted: 05/13/2023] [Indexed: 04/28/2024] Open
Abstract
In recent years, the FDA has approved numerous anti-cancer drugs that are mutation-based for clinical use. These drugs have improved the precision of treatment and reduced adverse effects and side effects. Personalized therapy is a prominent and hot topic of current medicine and also represents the future direction of development. With the continuous advancements in gene sequencing and high-throughput screening, research and development strategies for personalized clinical drugs have developed rapidly. This review elaborates the recent personalized treatment strategies, which include artificial intelligence, multi-omics analysis, chemical proteomics, and computation-aided drug design. These technologies rely on the molecular classification of diseases, the global signaling network within organisms, and new models for all targets, which significantly support the development of personalized medicine. Meanwhile, we summarize chemical drugs, such as lorlatinib, osimertinib, and other natural products, that deliver personalized therapeutic effects based on genetic mutations. This review also highlights potential challenges in interpreting genetic mutations and combining drugs, while providing new ideas for the development of personalized medicine and pharmacogenomics in cancer study.
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Affiliation(s)
- Yalan Zhou
- Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China; (Y.Z.); (S.P.); (H.W.)
| | - Siqi Peng
- Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China; (Y.Z.); (S.P.); (H.W.)
| | - Huizhen Wang
- Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China; (Y.Z.); (S.P.); (H.W.)
| | - Xinyin Cai
- Shanghai R&D Centre for Standardization of Chinese Medicines, Shanghai 202103, China
| | - Qingzhong Wang
- Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China; (Y.Z.); (S.P.); (H.W.)
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Dang Z, Li J, Liu Y, Song M, Lockhart PJ, Tian Y, Niu M, Wang Q. RADseq-based population genomic analysis and environmental adaptation of rare and endangered recretohalophyte Reaumuria trigyna. THE PLANT GENOME 2024; 17:e20303. [PMID: 36740755 DOI: 10.1002/tpg2.20303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 11/30/2022] [Indexed: 06/18/2023]
Abstract
Genetic diversity reflects the survival potential, history, and population dynamics of an organism. It underlies the adaptive potential of populations and their response to environmental change. Reaumuria trigyna is an endemic species in the Eastern Alxa and West Ordos desert regions in China. The species has been considered a good candidate to explore the unique survival strategies of plants that inhabit this area. In this study, we performed population genomic analyses based on restriction-site associated DNA sequencing to understand the genetic diversity, population genetic structure, and differentiation of the species. Analyses of 92,719 high-quality single-nucleotide polymorphisms (SNPs) indicated that overall genetic diversity of R. trigyna was low (HO = 0.249 and HE = 0.208). No significant genetic differentiation was observed among the investigated populations. However, a subtle population genetic structure was detected. We suggest that this might be explained by adaptive diversification reinforced by the geographical isolation of populations. Overall, 3513 outlier SNPs were located in 243 gene-coding sequences in the R. trigyna transcriptome. Potential sites under diversifying selection occurred in genes (e.g., AP2/EREBP, E3 ubiquitin-protein ligase, FLS, and 4CL) related to phytohormone regulation and synthesis of secondary metabolites which have roles in adaptation of species. Our genetic analyses provide scientific criteria for evaluating the evolutionary capacity of R. trigyna and the discovery of unique adaptions. Our findings extend knowledge of refugia, environmental adaption, and evolution of germplasm resources that survive in the Ordos area.
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Affiliation(s)
- Zhenhua Dang
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Jiabin Li
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Yanan Liu
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Miaomiao Song
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Peter J Lockhart
- School of Natural Sciences, College of Sciences, Massey University, Palmerston North, New Zealand
| | - Yunyun Tian
- Ministry of Education Key Laboratory of Herbage & Endemic Crop Biotechnology, School of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Miaomiao Niu
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Qinglang Wang
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
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5
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Deakin S, Coltman DW. Development of a high-density sub-species-specific targeted SNP assay for Rocky Mountain bighorn sheep ( Ovis canadensis canadensis). PeerJ 2024; 12:e16946. [PMID: 38426129 PMCID: PMC10903336 DOI: 10.7717/peerj.16946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 01/24/2024] [Indexed: 03/02/2024] Open
Abstract
Due to their abundance and relative ease of genotyping, single nucleotide polymorphisms (SNPs) are a commonly used molecular marker for contemporary population genetic and genomic studies. A high-density and cost-effective way to type SNP loci is Allegro targeted genotyping (ATG), which is a form of targeted genotyping by sequencing developed and offered by Tecan genomics. One major drawback of this technology is the need for a reference genome and information on SNP loci when designing a SNP assay. However, for some non-model species genomic information from other closely related species can be used. Here we describe our process of developing an ATG assay to target 50,000 SNPs in Rocky Mountain bighorn sheep, using a reference genome from domestic sheep and SNP resources from prior bighorn sheep studies. We successfully developed a high accuracy, high-density, and relatively low-cost SNP assay for genotyping Rocky Mountain bighorn sheep that genotyped ~45,000 SNP loci. These loci were relatively evenly distributed throughout the genome. Furthermore, the assay produced genotypes at tens of thousands of SNP loci when tested on other mountain sheep species and subspecies.
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Affiliation(s)
- Samuel Deakin
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - David W. Coltman
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
- Department of Biology, University of Western Ontario, London, Ontario, Canada
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Zhu J, Wang Y, Chen C, Ji L, Hong X, Liu X, Chen H, Wei C, Zhu X, Li W. Identification of Sex-Specific Markers and Candidate Genes Using WGS Sequencing Reveals a ZW-Type Sex-Determination System in the Chinese Soft-Shell Turtle ( Pelodiscus sinensis). Int J Mol Sci 2024; 25:819. [PMID: 38255893 PMCID: PMC10815769 DOI: 10.3390/ijms25020819] [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: 11/24/2023] [Revised: 01/02/2024] [Accepted: 01/07/2024] [Indexed: 01/24/2024] Open
Abstract
Male and female Chinese soft-shelled turtles (Pelodiscus sinensis) have sex-dimorphic growth patterns, and males have higher commercial value because of their larger size and thicker calipash. Thus, developing sex-specific markers is beneficial to studies on all-male breeding in P. sinensis. Here, we developed an accurate and efficient workflow for the screening of sex-specific sequences with ZW or XY sex determination systems. Based on this workflow, female and male P. sinensis reference genomes of 2.23 Gb and 2.26 Gb were obtained using de novo assembly. After aligning and filtering, 4.01 Mb female-specific sequences were finally identified. Subsequently, the seven developed sex-specific primer pairs were 100% accurate in preliminary, population, and embryonic validation. The presence and absence of bands for the primers of P44, P45, P66, P67, P68, and P69, as well as two and one bands for the PB1 primer, indicate that the embryos are genetically female and male, respectively. NR and functional annotations identified several sex-determining candidate genes and related pathways, including Ran, Eif4et, and Crkl genes, and the insulin signaling pathway and the cAMP signaling pathway, respectively. Collectively, our results reveal that a ZW-type sex-determination system is present in P. sinensis and provide novel insights for the screening of sex-specific markers, sex-control breeding, and the studies of the sex determination mechanism of P. sinensis.
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Affiliation(s)
- Junxian Zhu
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, China;
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China; (Y.W.); (C.C.); (L.J.); (X.H.); (X.L.); (H.C.); (C.W.)
| | - Yongchang Wang
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China; (Y.W.); (C.C.); (L.J.); (X.H.); (X.L.); (H.C.); (C.W.)
| | - Chen Chen
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China; (Y.W.); (C.C.); (L.J.); (X.H.); (X.L.); (H.C.); (C.W.)
| | - Liqin Ji
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China; (Y.W.); (C.C.); (L.J.); (X.H.); (X.L.); (H.C.); (C.W.)
| | - Xiaoyou Hong
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China; (Y.W.); (C.C.); (L.J.); (X.H.); (X.L.); (H.C.); (C.W.)
| | - Xiaoli Liu
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China; (Y.W.); (C.C.); (L.J.); (X.H.); (X.L.); (H.C.); (C.W.)
| | - Haigang Chen
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China; (Y.W.); (C.C.); (L.J.); (X.H.); (X.L.); (H.C.); (C.W.)
| | - Chengqing Wei
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China; (Y.W.); (C.C.); (L.J.); (X.H.); (X.L.); (H.C.); (C.W.)
| | - Xinping Zhu
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, China;
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China; (Y.W.); (C.C.); (L.J.); (X.H.); (X.L.); (H.C.); (C.W.)
| | - Wei Li
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, China;
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China; (Y.W.); (C.C.); (L.J.); (X.H.); (X.L.); (H.C.); (C.W.)
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Yang Z, Luo C, Pei X, Wang S, Huang Y, Li J, Liu B, Kong F, Yang QY, Fang C. SoyMD: a platform combining multi-omics data with various tools for soybean research and breeding. Nucleic Acids Res 2024; 52:D1639-D1650. [PMID: 37811889 PMCID: PMC10767819 DOI: 10.1093/nar/gkad786] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 09/13/2023] [Accepted: 09/15/2023] [Indexed: 10/10/2023] Open
Abstract
Advanced multi-omics technologies offer much information that can uncover the regulatory mechanisms from genotype to phenotype. In soybean, numerous multi-omics databases have been published. Although they cover multiple omics, there are still limitations when it comes to the types and scales of omics datasets and analysis methods utilized. This study aims to address these limitations by collecting and integrating a comprehensive set of multi-omics datasets. This includes 38 genomes, transcriptomes from 435 tissue samples, 125 phenotypes from 6686 accessions, epigenome data involving histone modification, transcription factor binding, chromosomal accessibility and chromosomal interaction, as well as genetic variation data from 24 501 soybean accessions. Then, common analysis pipelines and statistical methods were applied to mine information from these multi-omics datasets, resulting in the successful establishment of a user-friendly multi-omics database called SoyMD (https://yanglab.hzau.edu.cn/SoyMD/#/). SoyMD provides researchers with efficient query options and analysis tools, allowing them to swiftly access relevant omics information and conduct comprehensive multi-omics data analyses. Another notable feature of SoyMD is its capability to facilitate the analysis of candidate genes, as demonstrated in the case study on seed oil content. This highlights the immense potential of SoyMD in soybean genetic breeding and functional genomics research.
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Affiliation(s)
- Zhiquan Yang
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510405, China
| | - Chengfang Luo
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Xinxin Pei
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510405, China
| | - Shengbo Wang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Yiming Huang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Jiawei Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Baohui Liu
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510405, China
| | - Fanjiang Kong
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510405, China
| | - Qing-Yong Yang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural Reclamation Sciences, Shihezi 832000, China
| | - Chao Fang
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510405, China
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Radespiel U, Roos C. Special Issue "Primate Phylogeny and Genetics". Genes (Basel) 2024; 15:68. [PMID: 38254958 PMCID: PMC10815477 DOI: 10.3390/genes15010068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Accepted: 01/02/2024] [Indexed: 01/24/2024] Open
Abstract
New phylogenetic tools and population genetics methods have been developed and vastly advanced over the last decade [...].
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Affiliation(s)
- Ute Radespiel
- Institute of Zoology, University of Veterinary Medicine Hannover, Foundation, Buenteweg 17, 30559 Hannover, Germany
| | - Christian Roos
- Gene Bank of Primates and Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, 37077 Göttingen, Germany
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Dou T, Wang C, Ma Y, Chen Z, Zhang J, Guo G. CoreSNP: an efficient pipeline for core marker profile selection from genome-wide SNP datasets in crops. BMC PLANT BIOLOGY 2023; 23:580. [PMID: 37986037 PMCID: PMC10662547 DOI: 10.1186/s12870-023-04609-w] [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: 09/14/2023] [Accepted: 11/14/2023] [Indexed: 11/22/2023]
Abstract
BACKGROUND DNA marker profiles play a crucial role in the identification and registration of germplasm, as well as in the distinctness, uniformity, and stability (DUS) testing of new plant variety protection. However, selecting minimal marker sets from large-scale SNP dataset can be challenging to distinguish a maximum number of samples. RESULTS Here, we developed the CoreSNP pipeline using a "divide and conquer" strategy and a "greedy" algorithm. The pipeline offers adjustable parameters to guarantee the distinction of each sample pair with at least two markers. Additionally, it allows datasets with missing loci as input. The pipeline was tested in barley, soybean, wheat, rice and maize. A few dozen of core SNPs were efficiently selected in different crops with SNP array, GBS, and WGS dataset, which can differentiate thousands of individual samples. The core SNPs were distributed across all chromosomes, exhibiting lower pairwise linkage disequilibrium (LD) and higher polymorphism information content (PIC) and minor allele frequencies (MAF). It was shown that both the genetic diversity of the population and the characteristics of the original dataset can significantly influence the number of core markers. In addition, the core SNPs capture a certain level of the original population structure. CONCLUSIONS CoreSNP is an efficiency way of core marker sets selection based on Genome-wide SNP datasets of crops. Combined with low-density SNP chip or genotyping technologies, it can be a cost-effective way to simplify and expedite the evaluation of genetic resources and differentiate different crop varieties. This tool is expected to have great application prospects in the rapid comparison of germplasm and intellectual property protection of new varieties.
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Affiliation(s)
- Tingyu Dou
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization (MARA), The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (ICS-CAAS), Beijing, 100081, China
| | - Chunchao Wang
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization (MARA), The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (ICS-CAAS), Beijing, 100081, China
| | - Yanling Ma
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization (MARA), The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (ICS-CAAS), Beijing, 100081, China
| | - Zhaoyan Chen
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization (MARA), The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (ICS-CAAS), Beijing, 100081, China
| | - Jing Zhang
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization (MARA), The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (ICS-CAAS), Beijing, 100081, China
| | - Ganggang Guo
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization (MARA), The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (ICS-CAAS), Beijing, 100081, China.
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10
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González-Gómez JP, Lozano-Aguirre LF, Medrano-Félix JA, Chaidez C, Gerba CP, Betancourt WQ, Castro-Del Campo N. Evaluation of nuclear and mitochondrial phylogenetics for the subtyping of Cyclospora cayetanensis. Parasitol Res 2023; 122:2641-2650. [PMID: 37676306 DOI: 10.1007/s00436-023-07963-8] [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: 07/07/2023] [Accepted: 08/30/2023] [Indexed: 09/08/2023]
Abstract
Cyclospora cayetanensis is an enteric coccidian parasite responsible for gastrointestinal disease transmitted through contaminated food and water. It has been documented in several countries, mostly with low-socioeconomic levels, although major outbreaks have hit developed countries. Detection methods based on oocyst morphology, staining, and molecular testing have been developed. However, the current MLST panel offers an opportunity for enhancement, as amplification of all molecular markers remains unfeasible in the majority of samples. This study aims to address this challenge by evaluating two approaches for analyzing the genetic diversity of C. cayetanensis and identifying reliable markers for subtyping: core homologous genes and mitochondrial genome analysis. A pangenome was constructed using 36 complete genomes of C. cayetanensis, and a haplotype network and phylogenetic analysis were conducted using 33 mitochondrial genomes. Through the analysis of the pangenome, 47 potential markers were identified, emphasizing the need for more sequence data to achieve comprehensive characterization. Additionally, the analysis of mitochondrial genomes revealed 19 single-nucleotide variations that can serve as characteristic markers for subtyping this parasite. These findings not only contribute to the selection of molecular markers for C. cayetanensis subtyping, but they also drive the knowledge toward the potential development of a comprehensive genotyping method for this parasite.
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Affiliation(s)
- Jean P González-Gómez
- Laboratorio Nacional para la Investigación en Inocuidad Alimentaria (LANIIA), Centro de Investigación en Alimentación y Desarrollo, A.C. (CIAD), Carretera a Eldorado km 5.5, Campo El Diez, 80110, Culiacán, Sinaloa, México
| | - Luis F Lozano-Aguirre
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, AP565-A, 62210, Cuernavaca, Morelos, México
| | - José A Medrano-Félix
- Investigadoras e Investigadores por México-Centro de Investigación en Alimentación y Desarrollo, A.C. (CIAD), Laboratorio Nacional Para la Investigación en Inocuidad Alimentaria (LANIIA), Carretera a El dorado km 5.5, Campo El Diez, 80110, Culiacán, Sinaloa, Mexico
| | - Cristobal Chaidez
- Laboratorio Nacional para la Investigación en Inocuidad Alimentaria (LANIIA), Centro de Investigación en Alimentación y Desarrollo, A.C. (CIAD), Carretera a Eldorado km 5.5, Campo El Diez, 80110, Culiacán, Sinaloa, México
| | - Charles P Gerba
- Department of Environmental Science, Water & Energy Sustainable Technology (WEST) Center, University of Arizona, 2959 W, Calle Agua Nueva, Tucson, AZ, 85745, USA
| | - Walter Q Betancourt
- Department of Environmental Science, Water & Energy Sustainable Technology (WEST) Center, University of Arizona, 2959 W, Calle Agua Nueva, Tucson, AZ, 85745, USA
| | - Nohelia Castro-Del Campo
- Laboratorio Nacional para la Investigación en Inocuidad Alimentaria (LANIIA), Centro de Investigación en Alimentación y Desarrollo, A.C. (CIAD), Carretera a Eldorado km 5.5, Campo El Diez, 80110, Culiacán, Sinaloa, México.
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11
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Zhou F, Quan J, Ruan D, Qiu Y, Ding R, Xu C, Ye Y, Cai G, Liu L, Zhang Z, Yang J, Wu Z, Zheng E. Identification of Candidate Genes for Economically Important Carcass Cutting in Commercial Pigs through GWAS. Animals (Basel) 2023; 13:3243. [PMID: 37893967 PMCID: PMC10603759 DOI: 10.3390/ani13203243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 10/08/2023] [Accepted: 10/16/2023] [Indexed: 10/29/2023] Open
Abstract
During the process of pork production, the carcasses of pigs are divided and sold, which provides better economic benefits and market competitiveness for pork production than selling the carcass as a whole. Due to the significant cost of post-slaughter phenotypic measurement, the genetic architecture of tenderloin weight (TLNW) and rib weight (RIBW)-important components of pig carcass economic value-remain unknown. In this study, we conducted genome-wide association studies (GWAS) for TLNW and RIBW traits in a population of 431 Duroc × Landrace × Yorkshire (DLY) pigs. In our study, the most significant single nucleotide polymorphism (SNP) associated with TLNW was identified as ASGA0085853 (3.28 Mb) on Sus scrofa chromosome 12 (SSC12), while for RIBW, it was Affx-1115046258 (172.45 Mb) on SSC13. Through haplotype block analysis, we discovered a novel quantitative trait locus (QTL) associated with TLNW, spanning a 5 kb region on SSC12, and a novel RIBW-associated QTL spanning 1.42 Mb on SSC13. Furthermore, we hypothesized that three candidate genes, TIMP2 and EML1, and SMN1, are associated with TLNW and RIBW, respectively. Our research not only addresses the knowledge gap regarding TLNW, but also serves as a valuable reference for studying RIBW. The identified SNP loci strongly associated with TLNW and RIBW may prove useful for marker-assisted selection in pig breeding programs.
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Affiliation(s)
- Fuchen Zhou
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China; (F.Z.); (J.Q.); (D.R.); (Y.Q.); (R.D.); (C.X.); (Y.Y.); (G.C.); (L.L.); (Z.Z.); (J.Y.)
| | - Jianping Quan
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China; (F.Z.); (J.Q.); (D.R.); (Y.Q.); (R.D.); (C.X.); (Y.Y.); (G.C.); (L.L.); (Z.Z.); (J.Y.)
| | - Donglin Ruan
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China; (F.Z.); (J.Q.); (D.R.); (Y.Q.); (R.D.); (C.X.); (Y.Y.); (G.C.); (L.L.); (Z.Z.); (J.Y.)
| | - Yibin Qiu
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China; (F.Z.); (J.Q.); (D.R.); (Y.Q.); (R.D.); (C.X.); (Y.Y.); (G.C.); (L.L.); (Z.Z.); (J.Y.)
| | - Rongrong Ding
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China; (F.Z.); (J.Q.); (D.R.); (Y.Q.); (R.D.); (C.X.); (Y.Y.); (G.C.); (L.L.); (Z.Z.); (J.Y.)
| | - Cineng Xu
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China; (F.Z.); (J.Q.); (D.R.); (Y.Q.); (R.D.); (C.X.); (Y.Y.); (G.C.); (L.L.); (Z.Z.); (J.Y.)
| | - Yong Ye
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China; (F.Z.); (J.Q.); (D.R.); (Y.Q.); (R.D.); (C.X.); (Y.Y.); (G.C.); (L.L.); (Z.Z.); (J.Y.)
| | - Gengyuan Cai
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China; (F.Z.); (J.Q.); (D.R.); (Y.Q.); (R.D.); (C.X.); (Y.Y.); (G.C.); (L.L.); (Z.Z.); (J.Y.)
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
- Guangdong Zhongxin Breeding Technology Co., Ltd., Guangzhou 510642, China
| | - Langqing Liu
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China; (F.Z.); (J.Q.); (D.R.); (Y.Q.); (R.D.); (C.X.); (Y.Y.); (G.C.); (L.L.); (Z.Z.); (J.Y.)
| | - Zebin Zhang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China; (F.Z.); (J.Q.); (D.R.); (Y.Q.); (R.D.); (C.X.); (Y.Y.); (G.C.); (L.L.); (Z.Z.); (J.Y.)
| | - Jie Yang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China; (F.Z.); (J.Q.); (D.R.); (Y.Q.); (R.D.); (C.X.); (Y.Y.); (G.C.); (L.L.); (Z.Z.); (J.Y.)
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
| | - Zhenfang Wu
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China; (F.Z.); (J.Q.); (D.R.); (Y.Q.); (R.D.); (C.X.); (Y.Y.); (G.C.); (L.L.); (Z.Z.); (J.Y.)
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
- Guangdong Zhongxin Breeding Technology Co., Ltd., Guangzhou 510642, China
- Yunfu Subcenter of Guangdong Laboratory for Lingnan Modern Agriculture, Yunfu 527400, China
| | - Enqin Zheng
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China; (F.Z.); (J.Q.); (D.R.); (Y.Q.); (R.D.); (C.X.); (Y.Y.); (G.C.); (L.L.); (Z.Z.); (J.Y.)
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
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12
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Van Laere AS, Tromme A, Delaval L, Farnir F, Blomet J, Desmecht D. A timely, user-friendly, and flexible marker-assisted speed congenics method. Transgenic Res 2023; 32:451-461. [PMID: 37843753 DOI: 10.1007/s11248-023-00365-7] [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: 06/20/2023] [Accepted: 08/28/2023] [Indexed: 10/17/2023]
Abstract
Mice are the most widely used mammalian animal model worldwide. Their use presents many advantages, including our ability to manipulate their genome. Unfortunately, transgenic mice often need to be introgressed to transfer the transgene of interest in a specific mouse line. This time-consuming process can be shortened using the speed congenics technique. However, the need for a panel of informative markers to evaluate the proportion of donor and receiver genomes in different individuals produced at each generation hinders the utilisation of speed congenics. In this study, we present 255 microsatellites and 10 RFLPs which can be used in 18 marker panels, allowing the easy and fast introgression of genes of interest from three mouse lines commonly used for transgenesis (C57BL/6, 129/Sv and FVB) to six mouse lines relevant for biomedical research (BALB/c, C3H, DBA/1, DBA/2, SJL and SWR/J). In addition, our markers analysis confirmed a recently described lack of isogeny in well-established inbred mouse lines available from commercial breeders.
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Affiliation(s)
- Anne-Sophie Van Laere
- Department of Pathology, FARAH, Faculty of Veterinary Medicine, University of Liege, Liège, Belgium
- Laboratoires Prevor, Moulin de Verville, 95670, Valmondois, France
| | - Audrey Tromme
- Department of Pathology, FARAH, Faculty of Veterinary Medicine, University of Liege, Liège, Belgium
- Laboratoires Prevor, Moulin de Verville, 95670, Valmondois, France
| | - Laetitia Delaval
- Department of Pathology, FARAH, Faculty of Veterinary Medicine, University of Liege, Liège, Belgium
- Laboratoires Prevor, Moulin de Verville, 95670, Valmondois, France
| | - Frédéric Farnir
- Biostatistics and Bioinformatics, FARAH, Faculty of Veterinary Medicine, University of Liege, Liège, Belgium
| | - Joël Blomet
- Laboratoires Prevor, Moulin de Verville, 95670, Valmondois, France
| | - Daniel Desmecht
- Department of Pathology, FARAH, Faculty of Veterinary Medicine, University of Liege, Liège, Belgium.
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13
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Mosa KA, Ahmed AE, Hazem Y, Kanawati IS, Abdullah A, Hernandez-Sori L, Ali MA, Vendrame W. Insights into cryopreservation, recovery and genetic stability of medicinal plant tissues. Fitoterapia 2023; 169:105555. [PMID: 37295757 DOI: 10.1016/j.fitote.2023.105555] [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: 02/18/2023] [Revised: 05/24/2023] [Accepted: 05/28/2023] [Indexed: 06/12/2023]
Abstract
Several plant secondary metabolites are used in the production of different pharmaceuticals based on their biological activities. The conservation and sustainable use of medicinal plants is important for the industrial production of plant-based medicines. Different cryopreservation methods are used for long-term culture preservation, which allows fast regeneration of the preserved plant material with the maintenance of its primary original traits. These methods could ensure the sustainable indefinite supply of plant tissues for theoretically unlimited periods of time, and have gained considerable attention in recent years. It is important to assess the recovery rate and the genetic stability of the recovered plant tissues after cryopreservation because cryopreservation efficiency differs among plant tissues and species. This review lays particular emphasis on the pharmaceutical applications of plant secondary metabolites that are produced through tissue culture approaches, highlighting the methods used for their cryopreservation, as well as their recovery and genetic stability.
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Affiliation(s)
- Kareem A Mosa
- Department of Applied Biology, College of Sciences, University of Sharjah, P.O. Box 27272, Sharjah, United Arab Emirates; Department of Biotechnology, Faculty of Agriculture, Al-Azhar University, Cairo, Egypt.
| | - Amro E Ahmed
- Department of Applied Biology, College of Sciences, University of Sharjah, P.O. Box 27272, Sharjah, United Arab Emirates
| | - Yousef Hazem
- Department of Applied Biology, College of Sciences, University of Sharjah, P.O. Box 27272, Sharjah, United Arab Emirates
| | - Israa S Kanawati
- Department of Applied Biology, College of Sciences, University of Sharjah, P.O. Box 27272, Sharjah, United Arab Emirates
| | - Amenah Abdullah
- Department of Applied Biology, College of Sciences, University of Sharjah, P.O. Box 27272, Sharjah, United Arab Emirates
| | - Lazaro Hernandez-Sori
- Laboratory for Plant Breeding and Conservation of Genetic Resources, Bioplant Center, University of Ciego de Ávila, 69450 Ciego de Ávila, Cuba
| | - Muna A Ali
- Department of Applied Biology, College of Sciences, University of Sharjah, P.O. Box 27272, Sharjah, United Arab Emirates
| | - Wagner Vendrame
- Environmental Horticulture Department, University of Florida, Florida, USA
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14
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Liu H, Cheng H, Xu J, Hu J, Zhao C, Xing L, Wang M, Wu Z, Peng D, Yu N, Liu J. Genetic diversity and population structure of Polygonatum cyrtonema Hua in China using SSR markers. PLoS One 2023; 18:e0290605. [PMID: 37651363 PMCID: PMC10470896 DOI: 10.1371/journal.pone.0290605] [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: 04/05/2023] [Accepted: 08/11/2023] [Indexed: 09/02/2023] Open
Abstract
Polygonatum cyrtonema Hua is a perennial herbaceous plant of the Polygonatum genus, belonging to the Liliaceae family, with significant medicinal and nutritional value. In China, this species is a traditional medicinal and edible herb with a long history of application and is widely appreciated by the people. However, as the demand for medicinal herbs continues to grow, excessive harvesting has led to the depletion of wild resources and the risk of genetic erosion. In addition, the chaotic cultivation of varieties and the lack of high quality germplasm resources have led to inconsistent quality of medical materials. Therefore, it is urgent to conduct genetic diversity evaluation of this species and establish a sound conservation plan. This study assessed the genetic diversity and population structure of 96 samples collected from seven regions in China using the simple sequence repeat (SSR) molecular marker technology. In this study, a total of 60 alleles (Na) were detected across the 10 polymorphic SSR markers used, with an average of 6.0 alleles generated per locus. The values of polymorphic information content (PIC) values ranged from 0.3396 to 0.8794, with an average value of 0.6430. The average value of the effective number of alleles (Ne) was 2.761, and the average value of the Shannon's information index (I) was 1.196. The population structure analysis indicates that the Polygonatum cyrtonema Hua germplasm can be classified into three subpopulations (JZ, QY, JD) at the molecular level, which corresponds to the previous subgroups identified based on individual plant phenotypic traits. Analysis of Molecular Variance (AMOVA) showed that 74% of the genetic variation was between individuals within populations in different regions. The phylogenetic analysis of the 96 germplasm samples divided them into three main populations. The QY and JD subpopulations are largely clustered together, which could be attributed to their mountainous distribution and the local climate environment. The genetic differentiation coefficient (Fst) value was low at 0.065, indicating relatively low population differentiation. The ratio of the genetic differentiation coefficient (Fst) between the JZ population and the other two populations (QY and JD) is much higher than the ratio between the QY and JD populations. Based on the clustering results and the ratio of the genetic differentiation coefficient (Fst), it can be inferred that the genetic relationship between the QY and JD subpopulations is closer, with a certain degree of genetic differentiation from the JZ subpopulation. This study supports the conservation of germplasm resources of Polygonatum cyrtonema Hua in China and provides new parental material for germplasm genetic improvement and breeding programs.
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Affiliation(s)
- Heng Liu
- Department of Biopharmaceuticals, College of Pharmacy, Anhui University of Chinese Medicine, Hefei, Anhui Province, China
| | - He Cheng
- Department of Biopharmaceuticals, College of Pharmacy, Anhui University of Chinese Medicine, Hefei, Anhui Province, China
| | - Jun Xu
- Department of Biopharmaceuticals, College of Pharmacy, Anhui University of Chinese Medicine, Hefei, Anhui Province, China
| | - Jiayi Hu
- Department of Biopharmaceuticals, College of Pharmacy, Anhui University of Chinese Medicine, Hefei, Anhui Province, China
| | - Chenchen Zhao
- Department of Biopharmaceuticals, College of Pharmacy, Anhui University of Chinese Medicine, Hefei, Anhui Province, China
| | - Lihua Xing
- Department of Biopharmaceuticals, College of Pharmacy, Anhui University of Chinese Medicine, Hefei, Anhui Province, China
- MOE-Anhui Joint Collaborative Innovation Center for Quality Improvement of Anhui Genuine Chinese Medicinal Materials, Hefei, Anhui Province, China
| | - Mengjin Wang
- Department of Biopharmaceuticals, College of Pharmacy, Anhui University of Chinese Medicine, Hefei, Anhui Province, China
| | - Zhendong Wu
- Anhui Qingyang County Jiuhua traditional Chinese Medicinal Materials Technology Co., Ltd, Chizhou City, Anhui Province, China
| | - Daiyin Peng
- Department of Biopharmaceuticals, College of Pharmacy, Anhui University of Chinese Medicine, Hefei, Anhui Province, China
- MOE-Anhui Joint Collaborative Innovation Center for Quality Improvement of Anhui Genuine Chinese Medicinal Materials, Hefei, Anhui Province, China
| | - Nianjun Yu
- Department of Biopharmaceuticals, College of Pharmacy, Anhui University of Chinese Medicine, Hefei, Anhui Province, China
- MOE-Anhui Joint Collaborative Innovation Center for Quality Improvement of Anhui Genuine Chinese Medicinal Materials, Hefei, Anhui Province, China
| | - Junling Liu
- Department of Biopharmaceuticals, College of Pharmacy, Anhui University of Chinese Medicine, Hefei, Anhui Province, China
- Anhui Provincial Institutes for Food and Drug Control, Hefei, Anhui Province, China
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15
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Savadi S, Muralidhara BM, Venkataravanappa V, Adiga JD. Genome-wide survey and characterization of microsatellites in cashew and design of a web-based microsatellite database: CMDB. FRONTIERS IN PLANT SCIENCE 2023; 14:1242025. [PMID: 37670858 PMCID: PMC10475544 DOI: 10.3389/fpls.2023.1242025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Accepted: 07/31/2023] [Indexed: 09/07/2023]
Abstract
The cashew is an edible tree nut crop having a wide range of food and industrial applications. Despite great economic importance, the genome-wide characterization of microsatellites [simple sequence repeats (SSRs)] in cashew is lacking. In this study, we carried out the first comprehensive genome-wide microsatellites/SSRs characterization in cashew and developed polymorphic markers and a web-based microsatellite database. A total of 54526 SSRs were discovered in the cashew genome, with a mean frequency of 153 SSRs/Mb. Among the mined genome-wide SSRs (2-6 bp size motifs), the dinucleotide repeat motifs were dominant (68.98%) followed by the trinucleotides (24.56%). The Class I type of SSRs (≥20 bp) were 45.10%, while Class II repeat motifs (≥12-<20 bp) were 54.89% of the total genomic SSRs discovered here. Further, the AT-rich SSRs occurred more frequently in the cashew genome (84%) compared to the GC-rich SSRs. The validation of the in silico-mined genome-wide SSRs by PCR screening in cashew genotypes resulted in the development of 59 polymorphic SSR markers, and the polymorphism information content (PIC) of the polymorphic SSR markers ranged from 0.19 to 0.84. Further, a web-based database, "Cashew Microsatellite Database (CMDB)," was constructed to provide access to the genome-wide SSRs mined in this study as well as transcriptome-based SSRs from our previous study to the research community through a user-friendly searchable interface. Besides, CMDB provides information on experimentally validated SSRs. CMDB permits the retrieval of SSR markers information with the customized search options. Altogether, the genome-wide SSRs characterization, the polymorphic markers and CMDB database developed in this study would serve as valuable marker resources for DNA fingerprinting, germplasm characterization, genetic studies, and molecular breeding in cashew and related Anacardium species.
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Affiliation(s)
- Siddanna Savadi
- ICAR- Directorate of Cashew Research (DCR), Puttur, Karnataka, India
| | - B. M. Muralidhara
- ICAR-Indian Institute of Horticultural Research (IIHR), CHES, Madikeri, Karnataka, India
| | - V. Venkataravanappa
- ICAR-Indian Institute of Horticultural Research (IIHR), CHES, Madikeri, Karnataka, India
| | - J. D. Adiga
- ICAR- Directorate of Cashew Research (DCR), Puttur, Karnataka, India
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16
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Nantongo JS, Odoi JB, Agaba H, Gwali S. Genetic diversity and population structure of Vernonia amygdalina Del. in Uganda based on genome wide markers. PLoS One 2023; 18:e0283563. [PMID: 37494370 PMCID: PMC10370736 DOI: 10.1371/journal.pone.0283563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Accepted: 03/09/2023] [Indexed: 07/28/2023] Open
Abstract
Determining the extent and distribution of genetic diversity is an essential component of plant breeding. In the present study, we explored the genetic diversity and population structure of Vernonia amygdalina, a fodder, vegetable and medicinal species of Africa and some parts of Yemen. Most empirical studies demonstrate that populations that are separated by geographic or ecological factors may experience genetic differentiation resulting from restricted gene flow between populations. A total of 238 individuals were sampled from two populations: i) Lake Victoria crescent (LVC) and ii) Southern and Eastern Lake Kyoga basin (SEK) agroecological zones of Uganda and genotyped using DArT platform. Of the two populations, the overall mean observed heterozygosity (Ho) was low to medium (Ho = 0.07[silicoDArTs] and 0.2[SNPs]). Inbreeding levels were also very low (-0.04 to -0.08) suggesting the presence of random mating. Partitioning of genetic structure in the two populations indicated that SEK exhibited a higher genetic diversity than LVC. The principal coordinates analysis (PCA) showed no geographical structuring, consistent with the low genetic differentiation (Fst = 0.00) and the low Euclidean genetic distance (1.38-1.39) between the LVC and SEK populations. However, STRUCTURE analysis with admixture models revealed weak possible genetic clusters with very small genetic distance among them. Overall, the results suggest low genetic diversity and weak genetic differentiation between the two populations. One possible explanation of the results could be the presence of human assisted gene flow over long distances.
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Affiliation(s)
- Judith S Nantongo
- National Forestry Resources Research Institute, Kifu, Mukono, Uganda
| | - Juventine B Odoi
- National Forestry Resources Research Institute, Kifu, Mukono, Uganda
| | - Hillary Agaba
- National Forestry Resources Research Institute, Kifu, Mukono, Uganda
| | - Samson Gwali
- National Forestry Resources Research Institute, Kifu, Mukono, Uganda
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17
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Li Z, Chen Y, Li Y, Zeng Y, Li W, Ma X, Huang L, Shen Y. Whole-Genome Resequencing Reveals the Diversity of Patchouli Germplasm. Int J Mol Sci 2023; 24:10970. [PMID: 37446145 DOI: 10.3390/ijms241310970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 06/27/2023] [Accepted: 06/27/2023] [Indexed: 07/15/2023] Open
Abstract
As an important medicinal and aromatic plant, patchouli is distributed throughout most of Asia. However, current research on patchouli's genetic diversity is limited and lacks genome-wide studies. Here, we have collected seven representative patchouli accessions from different localities and performed whole-genome resequencing on them. In total, 402,650 single nucleotide polymorphisms (SNPs) and 153,233 insertions/deletions (INDELs) were detected. Based on these abundant genetic variants, patchouli accessions were primarily classified into the Chinese group and the Southeast Asian group. However, the accession SP (Shipai) collected from China formed a distinct subgroup within the Southeast Asian group. As SP has been used as a genuine herb in traditional Chinese medicine, its unique molecular markers have been subsequently screened and verified. For 26,144 specific SNPs and 16,289 specific INDELs in SP, 10 of them were validated using Polymerase Chain Reaction (PCR) following three different approaches. Further, we analyzed the effects of total genetic variants on genes involved in the sesquiterpene synthesis pathway, which produce the primary phytochemical compounds found in patchouli. Eight genes were ultimately investigated and a gene encoding nerolidol synthetase (PatNES) was chosen and confirmed through biochemical assay. In accession YN, genetic variants in PatNES led to a loss of synthetase activity. Our results provide valuable information for understanding the diversity of patchouli germplasm resources.
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Affiliation(s)
- Zhipeng Li
- Institute of Medicinal Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510000, China
| | - Yiqiong Chen
- Institute of Medicinal Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510000, China
| | - Yangyan Li
- Institute of Medicinal Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510000, China
| | - Ying Zeng
- Institute of Medicinal Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510000, China
| | - Wanying Li
- Institute of Medicinal Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510000, China
| | - Xiaona Ma
- Institute of Medicinal Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510000, China
| | - Lili Huang
- Institute of Medicinal Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510000, China
| | - Yanting Shen
- Institute of Medicinal Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510000, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100000, China
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Xu W, Wang J, Tian C, Shi W, Wang L. Genome-Wide Development of Polymorphic Microsatellite Markers and Genetic Diversity Analysis for the Halophyte Suaeda aralocaspica (Amaranthaceae). PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12091865. [PMID: 37176923 PMCID: PMC10181123 DOI: 10.3390/plants12091865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 04/14/2023] [Accepted: 04/28/2023] [Indexed: 05/15/2023]
Abstract
Suaeda aralocaspica, which is an annual halophyte, grows in saline deserts in Central Asia with potential use in saline soil reclamation and salt tolerance breeding. Studying its genetic diversity is critical for effective conservation and breeding programs. In this study, we aimed to develop a set of polymorphic microsatellite markers to analyze the genetic diversity of S. aralocaspica. We identified 177,805 SSRs from the S. aralocaspica genome, with an average length of 19.49 bp, which were present at a density of 393.37 SSR/Mb. Trinucleotide repeats dominated (75.74%) different types of motifs, and the main motif was CAA/TTG (44.25%). We successfully developed 38 SSR markers that exhibited substantial polymorphism, displaying an average of 6.18 alleles with accompanying average polymorphism information content (PIC) value of 0.516. The markers were used to evaluate the genetic diversity of 52 individuals collected from three populations of S. aralocaspica in Xinjiang, China. The results showed that the genetic diversity was moderate to high, with a mean expected heterozygosity (He) of 0.614, a mean Shannon's information index (I) of 1.23, and a mean genetic differentiation index (Fst) of 0.263. The SSR markers developed in this study provide a valuable resource for future genetic studies and breeding programs of S. aralocaspica, and even other species in Suaeda.
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Affiliation(s)
- Wei Xu
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiancheng Wang
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Turpan Eremophytes Botanical Garden, Chinese Academy of Sciences, Turpan 838008, China
| | - Changyan Tian
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wei Shi
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lei Wang
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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Li JW, Li H, Liu ZW, Wang YX, Chen Y, Yang N, Hu ZH, Li T, Zhuang J. Molecular markers in tea plant (Camellia sinensis): Applications to evolution, genetic identification, and molecular breeding. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 198:107704. [PMID: 37086694 DOI: 10.1016/j.plaphy.2023.107704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 04/03/2023] [Accepted: 04/13/2023] [Indexed: 05/03/2023]
Abstract
Tea plants have a long cultivation history in the world, and the beverage (tea) made from its leaves is well known in the world. Due to the characteristics of self-incompatibility, long-term natural and artificial hybridization, tea plants have a very complex genetic background, which make the classification of tea plants unclear. Molecular marker, one type of genetic markers, has the advantages of stable inheritance, large amount of information, and high reliability. The development of molecular marker has facilitated the understanding of complex tea germplasm resources. So far, molecular markers had played important roles in the study of the origin and evolution, the preservation and identification of tea germplasms, and the excellent cultivars breeding of tea plants. However, the information is scattered, making it difficult to understand the advance of molecular markers in tea plants. In this paper, we summarized the development process and types of molecular markers in tea plants. In addition, the application advance of these molecular markers in tea plants was reviewed. Perspectives of molecular markers in tea plants were also systematically provided and discussed. The elaboration of molecular markers in this paper should help us to renew understanding of its application in tea plants.
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Affiliation(s)
- Jing-Wen Li
- Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Hui Li
- Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Zhi-Wei Liu
- Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Yong-Xin Wang
- Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Yi Chen
- Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Ni Yang
- Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Zhi-Hang Hu
- Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Tong Li
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, China
| | - Jing Zhuang
- Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing, China.
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Pei D, Song S, Kang J, Zhang C, Wang J, Dong T, Ge M, Pervaiz T, Zhang P, Fang J. Characterization of Simple Sequence Repeat (SSR) Markers Mined in Whole Grape Genomes. Genes (Basel) 2023; 14:genes14030663. [PMID: 36980935 PMCID: PMC10048371 DOI: 10.3390/genes14030663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 02/25/2023] [Accepted: 03/01/2023] [Indexed: 03/09/2023] Open
Abstract
SSR (simple sequence repeat) DNA markers are widely used for genotype DNA identification, QTL mapping, and analyzing genetic biodiversity. However, SSRs in grapes are still in their early stages, with a few primer pairs accessible. With the whole-genome sequencing (WGS) of several grape varieties, characterization of grape SSR changed to be necessary not only to genomics but to also help SSR development and utility. Based on this, we identified the whole-genome SSR of nine grape cultivars (‘PN40024’, ‘Cabernet Sauvignon’, ‘Carménère’, ‘Chardonnay’, ‘Merlot’, ‘Riesling’, ‘Zinfandel’, ‘Shine Muscat’, and ‘Muscat Hamburg’) with whole-genome sequences released publicly and found that there are great differences in the distribution of SSR loci in different varieties. According to the difference in genome size, the number of SSRs ranged from 267,385 (Cabernet Sauvignon) to 627,429 (Carménère), the density of the SSR locus in the genome of nine cultivars was generally 1 per Kb. SSR motif distribution characteristic analysis of these grape cultivars showed that the distribution patterns among grape cultivars were conservative, mainly enriched in A/T. However, there are some differences in motif types (especially tetranucleotides, pentanucleotides, and hexanucleotides), quantity, total length, and average length in different varieties, which might be related to the size of the assembled genome or the specificity of variety domestication. The distribution characteristics of SSRs were revealed by whole-genome analysis of simple repeats of grape varieties. In this study, 32 pairs of primers with lower polymorphism have been screened, which provided an important research foundation for the development of molecular markers of grape variety identification and the construction of linkage maps of important agronomic traits for crop improvement.
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Affiliation(s)
- Dan Pei
- Fruit Crop Genetic Improvement and Seedling Propagation Engineering Center of Jiangsu Province, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Siyan Song
- Zhenjiang Institute of Agricultural Sciences in Hilly Area of Jiangsu Province, Zhenjiang 212400, China
| | - Jun Kang
- Fruit Crop Genetic Improvement and Seedling Propagation Engineering Center of Jiangsu Province, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Chuan Zhang
- Fruit Crop Genetic Improvement and Seedling Propagation Engineering Center of Jiangsu Province, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Jing Wang
- Fruit Crop Genetic Improvement and Seedling Propagation Engineering Center of Jiangsu Province, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Tianyu Dong
- Fruit Crop Genetic Improvement and Seedling Propagation Engineering Center of Jiangsu Province, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Mengqing Ge
- Fruit Crop Genetic Improvement and Seedling Propagation Engineering Center of Jiangsu Province, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Tariq Pervaiz
- Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA 22963, USA
| | - Peian Zhang
- Fruit Crop Genetic Improvement and Seedling Propagation Engineering Center of Jiangsu Province, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Jinggui Fang
- Fruit Crop Genetic Improvement and Seedling Propagation Engineering Center of Jiangsu Province, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
- Correspondence:
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Vieira JL, de Oliveira LO, Barrigossi JAF, Guedes RNC, Smagghe G, Maebe K. Disentangling a Neotropical pest species complex: genetic diversity and population structure of the native rice stink bug Oebalus poecilus and the invasive O. ypsilongriseus. PEST MANAGEMENT SCIENCE 2023; 79:959-968. [PMID: 36317949 DOI: 10.1002/ps.7267] [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: 08/02/2022] [Accepted: 11/01/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND A first step in any pest management initiative is recognizing the existing problem - identifying the pest species and its abundance and dispersal capacities. This is not simple and even more challenging when insidious (invasive) species are involved constituting a pest complex. Understanding a species' population diversity and structure can provide a better understanding of its adaptation and relative pest potential. Such is the need for the native rice stink bug Oebalus poecilus and the invasive O. ypsilongriseus in low and high flatlands of South America. RESULTS The genetic structure differed between both rice stink bug species (FST = 0.157, P = 0.001), where 84% of the overall genetic variability takes place within species and three genetic groups were recognized through Bayesian approach (K = 3). Oebalus poecilus exhibited slightly higher genetic diversity (HE = 0.253) and structuring (FST = 0.050, P = 0.001) than the invasive O. ypsilongriseus (HE = 0.211; FST = 0.038, P = 0.013). Nonetheless, only the former exhibited significant correlation between genetic and geographic distances (r = 0.48, P = 0.013). CONCLUSION Despite the pointed peculiarities, the obtained results indicate overlap in both species' occurrence and similar genetic structure allowing for a compound problem to be dealt with as the complex requires managing without, as yet, a prevailing species or a niche specialization. © 2022 Society of Chemical Industry.
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Affiliation(s)
- Juliana L Vieira
- Departamento de Entomologia, Universidade Federal de Viçosa, Viçosa, Brazil
- Laboratory Agrozoology, Department Plant and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Luiz O de Oliveira
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Viçosa, Brazil
| | | | | | - Guy Smagghe
- Laboratory Agrozoology, Department Plant and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Kevin Maebe
- Laboratory Agrozoology, Department Plant and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
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Genetic monitoring on the world's first MSC eco-labeled common octopus (O. vulgaris) fishery in western Asturias, Spain. Sci Rep 2023; 13:2730. [PMID: 36792695 PMCID: PMC9932175 DOI: 10.1038/s41598-023-29463-6] [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: 06/05/2022] [Accepted: 02/06/2023] [Indexed: 02/17/2023] Open
Abstract
Octopus vulgaris (Cuvier, 1797) is a cephalopod species with great economic value. In western Asturias (northwest of Spain), O. vulgaris artisanal fisheries are relatively well monitored and conditionally eco-labeled by the Marine Stewardship Council (MSC). Despite this, the Asturian octopus stocks have not been genetically assessed so far. In order to improve the current fishery plan and contrast the octopus eco-label validity in Asturias, 539 individuals from five regions of the O. vulgaris geographic distribution, including temporal samplings in Asturias, were collected and genotyped at thirteen microsatellite loci. All the samples under analysis were in agreement with Hardy-Weinberg expectations. Spatial levels of genetic differentiation were estimated using F-statistics, multidimensional scaling, and Bayesian analyses. Results suggested that the O. vulgaris consists of at least four genetically different stocks coming from two ancestral lineages. In addition, temporal analyses showed stability in terms of genetic variation and high NE (> 50) for several generations in different localities within Asturias, pointing out to indeed sustainable fishery exploitation levels. Even though, the current Asturias fishery plan shows no significant genetic damages to the stocks, the regional-specific management plans need systematic genetic monitoring schemes as part of an efficient and preventive regional fishery regulation strategy.
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23
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Li H, Tahir ul Qamar M, Yang L, Liang J, You J, Wang L. Current Progress, Applications and Challenges of Multi-Omics Approaches in Sesame Genetic Improvement. Int J Mol Sci 2023; 24:3105. [PMID: 36834516 PMCID: PMC9965044 DOI: 10.3390/ijms24043105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/16/2023] [Accepted: 01/20/2023] [Indexed: 02/09/2023] Open
Abstract
Sesame is one of the important traditional oil crops in the world, and has high economic and nutritional value. Recently, due to the novel high throughput sequencing techniques and bioinformatical methods, the study of the genomics, methylomics, transcriptomics, proteomics and metabonomics of sesame has developed rapidly. Thus far, the genomes of five sesame accessions have been released, including white and black seed sesame. The genome studies reveal the function and structure of the sesame genome, and facilitate the exploitation of molecular markers, the construction of genetic maps and the study of pan-genomes. Methylomics focus on the study of the molecular level changes under different environmental conditions. Transcriptomics provide a powerful tool to study abiotic/biotic stress, organ development, and noncoding RNAs, and proteomics and metabonomics also provide some support in studying abiotic stress and important traits. In addition, the opportunities and challenges of multi-omics in sesame genetics breeding were also described. This review summarizes the current research status of sesame from the perspectives of multi-omics and hopes to provide help for further in-depth research on sesame.
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Affiliation(s)
- Huan Li
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Muhammad Tahir ul Qamar
- Integrative Omics and Molecular Modeling Laboratory, Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), Faisalabad 38000, Pakistan
| | - Li Yang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Junchao Liang
- Jiangxi Province Key Laboratory of Oil Crops Biology, Crop Research Institute, Nanchang Branch of National Center of Oil Crops Improvement, Jiangxi Academy of Agricultural Sciences, Nanchang 330000, China
| | - Jun You
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Linhai Wang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
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24
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Evaluating genetic diversity of geographically diverse populations of Embelia ribes Burm f., a highly medicinal woody liana from the Western Ghats of India, using random amplified polymorphic DNA (RAPD) and intersimple sequence repeats (ISSR) markers. Mol Biol Rep 2023; 50:1603-1615. [PMID: 36528661 DOI: 10.1007/s11033-022-08099-1] [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: 02/21/2022] [Accepted: 11/08/2022] [Indexed: 12/23/2022]
Abstract
BACKGROUND Embelia ribes Burm f. (Primulaceae) is a medicinal and vulnerable woody liana distributed throughout India. Embelin, a well-recognized active phytoconstituents in berries, is commonly used in ayurvedic formulations. Due to over-exploitation, the status of the plant is vulnerable. Previous studies on this species mainly focused on its phytochemical analysis, which led to overexploitation and loss of the germplasm. METHODS AND RESULTS In the present study, 20 RAPD and 18 ISSR markers were employed to assess genetic divergence in 40 genotypes of E. ribes collected from different parts of the Western Ghats of India. In RAPD analysis, all 40 accessions with 20 RAPD primers amplified 282 fragments, with 83.91% average polymorphism and with an average of 14.10 bands per primer. The size of amplicons varied from 200 to 2500 bp. While, ISSR primers produced 203 fragments of which 161 were polymorphic with an average of 11.28 bands per primer with 73.25% average polymorphism. The size of amplicons ranges from 200 to 2500 bp. RAPD and ISSR markers were also assessed by calculating polymorphic information content (PIC) to discriminate the genotypes; the average PIC value for RAPD, ISSR, and combined RAPD + ISSR markers obtained was more than 0.50 suggesting the informativeness of markers. UPGMA analysis based on Jaccard's similarity coefficient for RAPD, ISSR, and RAPD + ISSR data reveals that 40 accessions of E. ribes were depicted in four clusters. The clustering pattern of all individuals in PCoA analysis agreed with the UPGMA dendrograms, which further confirms the genetic relationships explained by cluster analysis. AMOVA analysis of RAPD, ISSR, and combined marker system revealed variation within the population, ranging from 41 to 44%, and among the population, it ranged from 56 to 59%. CONCLUSION The present study provides an optimized method for evaluating the genetic diversity of Embelia ribes using RAPD and ISSR markers which are useful for further sustainable utilization and conservation of natural populations in the Western Ghats of India.
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Huang P, Hameed R, Abbas M, Balooch S, Alharthi B, Du Y, Abbas A, Younas A, Du D. Integrated omic techniques and their genomic features for invasive weeds. Funct Integr Genomics 2023; 23:44. [PMID: 36680630 DOI: 10.1007/s10142-023-00971-y] [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: 12/08/2022] [Revised: 01/01/2023] [Accepted: 01/11/2023] [Indexed: 01/22/2023]
Abstract
Many emerging invasive weeds display rapid adaptation against different stressful environments compared to their natives. Rapid adaptation and dispersal habits helped invasive populations have strong diversity within the population compared to their natives. Advances in molecular marker techniques may lead to an in-depth understanding of the genetic diversity of invasive weeds. The use of molecular techniques is rapidly growing, and their implications in invasive weed studies are considered powerful tools for genome purposes. Here, we review different approach used multi-omics by invasive weed studies to understand the functional structural and genomic changes in these species under different environmental fluctuations, particularly, to check the accessibility of advance-sequencing techniques used by researchers in genome sequence projects. In this review-based study, we also examine the importance and efficiency of different molecular techniques in identifying and characterizing different genes, associated markers, proteins, metabolites, and key metabolic pathways in invasive and native weeds. Use of these techniques could help weed scientists to further reduce the knowledge gaps in understanding invasive weeds traits. Although these techniques can provide robust insights about the molecular functioning, employing a single omics platform can rarely elucidate the gene-level regulation and the associated real-time expression of weedy traits due to the complex and overlapping nature of biological interactions. We conclude that different multi-omic techniques will provide long-term benefits in launching new genome projects to enhance the understanding of invasive weeds' invasion process.
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Affiliation(s)
- Ping Huang
- Institute of Environment and Ecology, School of Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, People's Republic of China
| | - Rashida Hameed
- Institute of Environment and Ecology, School of Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, People's Republic of China
| | - Manzer Abbas
- School of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, 644000, Sichuan Province, People's Republic of China
| | - Sidra Balooch
- Institute of Botany, Bahauddin Zakariya University, Multan, Punjab, Pakistan
| | - Badr Alharthi
- Department of Biology, University College of Al Khurmah, Taif University, PO. Box 11099, Taif, 21944, Saudi Arabia
| | - Yizhou Du
- Faculty of Engineering, School of Computer Science, University of Sydney, Sydney, New South Wales, Australia
| | - Adeel Abbas
- Institute of Environment and Ecology, School of Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, People's Republic of China.
| | - Afifa Younas
- Department of Botany, Lahore College for Women University, Lahore, Pakistan
| | - Daolin Du
- Institute of Environment and Ecology, School of Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, People's Republic of China.
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Xiang N, Lu B, Yuan T, Yang T, Guo J, Wu Z, Liu H, Liu X, Qin R. De Novo Transcriptome Assembly and EST-SSR Marker Development and Application in Chrysosplenium macrophyllum. Genes (Basel) 2023; 14:genes14020279. [PMID: 36833206 PMCID: PMC9956384 DOI: 10.3390/genes14020279] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 01/16/2023] [Accepted: 01/17/2023] [Indexed: 01/26/2023] Open
Abstract
Chrysosplenium macrophyllum Oliv., belonging to the family Saxifragaceae, is a traditional and unique Chinese herbal medicine. However, the lack of adequate molecular markers has hampered the progress regarding population genetics and evolution within this species. In this research, we used the DNBSEQ-T7 Sequencer (MGI) sequencing assay to analyze the transcriptome profiles of C. macrophyllum. SSR markers were developed on the basis of transcriptomic sequences and further validated on C. macrophyllum and other Chrysosplenium species. The genetic diversity and structure of the 12 populations were analyzed by using polymorphic expressed sequence tag simple sequence repeat (EST-SSR) markers. A potential pool of 3127 non-redundant EST-SSR markers were identified for C. macrophyllum in this study. The developed EST-SSR markers had high amplification rates and cross-species transferability in Chrysosplenium. Our results also showed that the natural populations of C. macrophyllum had a high level of genetic diversity. Genetic distance, principal component analysis, and popular structure analysis revealed that all 60 samples clustered into two major groups that were consistent with their geographical origins. This study provided a batch of highly polymorphic EST-SSR molecular markers that were developed via transcriptome sequencing. These markers will be of great significance for the study of the genetic diversity and evolutionary history of C. macrophyllum and other Chrysosplenium species.
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Affiliation(s)
- Niyan Xiang
- Laboratory of Extreme Environmental Biological Resources and Adaptive Evolution, Research Center for Ecology, School of Sciences, Tibet University, Lhasa 850000, China
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central Minzu University, Wuhan 430074, China
| | - Bojie Lu
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central Minzu University, Wuhan 430074, China
| | - Tao Yuan
- Laboratory of Extreme Environmental Biological Resources and Adaptive Evolution, Research Center for Ecology, School of Sciences, Tibet University, Lhasa 850000, China
| | - Tiange Yang
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central Minzu University, Wuhan 430074, China
| | - Jiani Guo
- Laboratory of Extreme Environmental Biological Resources and Adaptive Evolution, Research Center for Ecology, School of Sciences, Tibet University, Lhasa 850000, China
| | - Zhihua Wu
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Hong Liu
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central Minzu University, Wuhan 430074, China
| | - Xing Liu
- Laboratory of Extreme Environmental Biological Resources and Adaptive Evolution, Research Center for Ecology, School of Sciences, Tibet University, Lhasa 850000, China
- State Key Laboratory of Hybrid Rice, Laboratory of Plant Systematics and Evolutionary Biology, College of Life Sciences, Wuhan University, Wuhan 430072, China
- Correspondence: (X.L.); (R.Q.)
| | - Rui Qin
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central Minzu University, Wuhan 430074, China
- Correspondence: (X.L.); (R.Q.)
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Rai MK. Start codon targeted (SCoT) polymorphism marker in plant genome analysis: current status and prospects. PLANTA 2023; 257:34. [PMID: 36622439 DOI: 10.1007/s00425-023-04067-6] [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: 07/05/2022] [Accepted: 01/04/2023] [Indexed: 06/17/2023]
Abstract
The present review illustrates a comprehensive overview of the start codon targeted (SCoT) polymorphism marker and their utilization in various applications related to genetic and genomic studies. Start codon targeted (SCoT) polymorphism marker, a targeted fingerprinting marker technique, has gained considerable importance in plant genetics, genomics, and molecular breeding due to its many desirable features. SCoT marker targets the region flanking the start codon, a highly conserved region in plant genes. Therefore, it can distinguish genetic variations in a specific gene that link to a specific trait. It is a simple, novel, cost-effective, highly polymorphic, and reproducible molecular marker for which there is no need for prior sequence information. In the recent past, SCoT markers have been employed in many commercially important and underutilized plant species for a variety of applications, including genetic diversity analysis, interspecific/generic genetic relationships, cultivar/hybrid/species identification, sex determination, construction of linkage map, association mapping/analysis, differential gene expression, and genetic fidelity analysis of tissue culture-raised plants. The main aim of this review is to provide up-to-date information on SCoT markers and their application in many commercially important and underutilized plant species, mainly progress made in the last 8-10 years.
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Affiliation(s)
- Manoj K Rai
- Department of Environmental Science, Indira Gandhi National Tribal University, Amarkantak, MP, 484887, India.
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28
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Chen L, Duan L, Sun M, Yang Z, Li H, Hu K, Yang H, Liu L. Current trends and insights on EMS mutagenesis application to studies on plant abiotic stress tolerance and development. FRONTIERS IN PLANT SCIENCE 2023; 13:1052569. [PMID: 36684716 PMCID: PMC9846265 DOI: 10.3389/fpls.2022.1052569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Accepted: 12/01/2022] [Indexed: 06/17/2023]
Abstract
Ethyl methanesulfonate (EMS)-induced mutagenesis is a powerful tool to generate genetic resource for identifying untapped genes and characterizing the function of genes to understand the molecular basis of important agronomic traits. This review focuses on application of contemporary EMS mutagenesis in the field of plant development and abiotic stress tolerance research, with particular focuses on reviewing the mutation types, mutagenesis site, mutagen concentration, mutagenesis duration, the identification and characterization of mutations responsible for altered stress tolerance responses. The application of EMS mutation breeding combined with genetic engineering in the future plant breeding and fundamental research was also discussed. The collective information in this review will provide good insight on how EMS mutagenesis is efficiently applied to improve abiotic stress tolerance of crops with the utilization of Next-generation sequencing (NGS) for mutation identification.
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Affiliation(s)
- Liuzhu Chen
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, China
| | - Liu Duan
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, China
| | - Minghui Sun
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, China
| | - Zhuo Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, China
| | - Hongyu Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, China
| | - Keming Hu
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, China
- Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province/Key Laboratory of Crop Genetics and Physiology of Jiangsu Province, Yangzhou University, Yangzhou, China
| | - Hong Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, China
| | - Li Liu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, China
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Cao X, Zhang Q, He Y, Che H, Lin Y, Luo D, West JS, Xu X. Genetic Analysis of Colletotrichum siamense Populations from Different Hosts and Counties in Hainan, China, Using Microsatellite Markers. PLANT DISEASE 2023; 107:60-66. [PMID: 35666218 DOI: 10.1094/pdis-03-22-0576-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Colletotrichum siamense was demonstrated as the dominant species among Colletotrichum spp. that infected rubber tree, areca palm, and coffee in Hainan, China. However, the extent of genetic differentiation within the species C. siamense in relation to geographical regions and host species is not known. In this study, 112 C. siamense isolates were genotyped with 12 microsatellite markers. In total, there were 99 multilocus genotypes. Results from permutational multivariate analysis of variance and analysis of molecular variance indicated that there was no significant genetic differentiation between fungal populations with respect to host, location (county), and year. Discriminant analysis of principal components and STRUCTURE analysis showed that C. siamense isolates grouped into three clusters; further analysis confirmed that there were significant (P < 0.001) genetic differences among the three clusters. However, each cluster had isolates from different hosts, counties, or years, supporting the lack of genetic differentiation with respect to host, county, and year. Statistical analyses of allelic associations indicated some evidence for recombination within the populations defined on the basis of host or county. The present findings provide insights into the genetic structure of C. siamense on the three perennial host species in Hainan and suggest that the disease on these three crops can be effectively considered as one disease and, hence, needs to be controlled simultaneously in mixed plantations.
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Affiliation(s)
- Xueren Cao
- Key Laboratory of Integrated Pest Management on Tropical Crops, Ministry of Agriculture, Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Qun Zhang
- Analysis and Test Center, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Yongxiang He
- College of Plant Protection, Hainan University, Haikou 570228 China
| | - Haiyan Che
- Key Laboratory of Integrated Pest Management on Tropical Crops, Ministry of Agriculture, Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Yating Lin
- Key Laboratory of Integrated Pest Management on Tropical Crops, Ministry of Agriculture, Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Daquan Luo
- Key Laboratory of Integrated Pest Management on Tropical Crops, Ministry of Agriculture, Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | | | - Xiangming Xu
- NIAB EMR, New Road, East Malling, Kent ME19 6BJ, U.K
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El-Esawi MA, Elashtokhy MMA, Shamseldin SAM, El-Ballat EM, Zayed EM, Heikal YM. Analysis of Genetic Diversity and Phylogenetic Relationships of Wheat ( Triticum aestivum L.) Genotypes Using Phenological, Molecular and DNA Barcoding Markers. Genes (Basel) 2022; 14:34. [PMID: 36672774 PMCID: PMC9858705 DOI: 10.3390/genes14010034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 12/13/2022] [Accepted: 12/16/2022] [Indexed: 12/25/2022] Open
Abstract
Wheat (Triticum aestivum L.) is a key food crop, accounting for approximately 765 million tons produced worldwide. The present study evaluated 16 wheat genotypes using 19 morphological and phenological traits, 16 molecular markers (Inter Simple Sequence Repeats and Start Codon Targeted; ISSR and SCoT) and rbcL and matK plastid gene barcoding. The 16 wheat genotypes showed significant genetic variation using the markers assayed. Cell plot of phenological parameters revealed significant differences among the 16-day-old seedlings of wheat genotypes at Z1.1 growth stage. Collectively, W2 genotype had the lowest shoot length (SL), length of first internodes (LFI) and leaf area (LA) values, while W8 genotype had the highest diameter of first internode (DFI) and LA values. Furthermore, W7 genotype had the maximum plant biomass (PB) and leaf width (LW) values. Geometric models grouped wheat kernels into "rounded" and "nearly elongated". Estimates of heritability (H2) for these morphological characters ranged from 4.93 to 100%. The highest H2 values were recorded for root number (RN) (100%) followed by SL (88.72%), LFI (88.30%), LA (87.76%) and Feret diameter (86.68%), while the lowest H2 value was recorded for DFI (4.93%). Furthermore, highly significant genotypic and phenotypic correlations were also observed among those traits. Reproducible fingerprinting profiles and high levels of polymorphism (PPB%) of SCoT (95.46%) and ISSR (82.41%) were recorded, indicating that they are effective tools for detecting genetic variation levels among wheat genotypes. The informativeness of markers were measured through estimation of polymorphic information content (PIC), resolving power (RP) and marker index (MI). The RP and PPB% of SCoT were significantly higher compared to those of ISSR. Comparatively, the two molecular markers were effective for studying genetic diversity among wheat genotypes, but SCoT markers were more informative. Moreover, based on the two chloroplast DNA regions (rbcL and matK), MatK was found to be more reliable for differentiating among T. aestivum genotypes. Taken together, using all the studied attributes, a clear taxonomic relationship can be used to identify T. aestivum species and improve their pragmatic production and development.
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Affiliation(s)
| | | | - Sahar A. M. Shamseldin
- Botany Department, Women ’s College for Arts, Science and Education, Ain Shams University, Cairo 11566, Egypt
| | - Enas M. El-Ballat
- Botany Department, Faculty of Science, Tanta University, Tanta 31527, Egypt
| | - Ehab M. Zayed
- Cell Study Research Department, Field Crops Research Institute Agricultural Research Center, Giza 12619, Egypt
| | - Yasmin M. Heikal
- Botany Department, Faculty of Science, Mansoura University, Mansoura 35516, Egypt
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Genetic diversity of the Chinese medicinal plant Astragali Radix based on transcriptome-derived SSR markers. ELECTRON J BIOTECHN 2022. [DOI: 10.1016/j.ejbt.2022.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
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Haryani Y, Halid NA, Guat GS, Nor-Khaizura MAR, Hatta MAM, Sabri S, Radu S, Hasan H. High prevalence of multiple antibiotic resistance in fermented food-associated lactic acid bacteria in Malaysia. Food Control 2022. [DOI: 10.1016/j.foodcont.2022.109558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Qiao Y, Zhang X, Li Z, Song Y, Sun Z. Assembly and comparative analysis of the complete mitochondrial genome of Bupleurum chinense DC. BMC Genomics 2022; 23:664. [PMID: 36131243 PMCID: PMC9490909 DOI: 10.1186/s12864-022-08892-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 09/15/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Bupleurum chinense(B. chinense) is a plant that is widely distributed globally and has strong pharmacological effects. Though the chloroplast(cp) genome of B. chinense has been studied, no reports regarding the mitochondrial(mt) genome of B. chinense have been published yet. RESULTS The mt genome of B.chinense was assembled and functionally annotated. The circular mt genome of B. chinense was 435,023 bp in length, and 78 genes, including 39 protein-coding genes, 35 tRNA genes, and 4 rRNA genes, were annotated. Repeat sequences were analyzed and sites at which RNA editing would occur were predicted. Gene migration was observed to occur between the mt and cp genomes of B. chinense via the detection of homologous gene fragments. In addition, the sizes of plant mt genomes and their GC content were analyzed and compared. The sizes of mt genomes of plants varied greatly, but their GC content was conserved to a greater extent during evolution. Ka/Ks analysis was based on code substitutions, and the results showed that most of the coding genes were negatively selected. This indicates that mt genes were conserved during evolution. CONCLUSION In this study, we assembled and annotated the mt genome of the medicinal plant B. chinense. Our findings provide extensive information regarding the mt genome of B. chinense, and help lay the foundation for future studies on the genetic variations, phylogeny, and breeding of B. chinense via an analysis of the mt genome.
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Affiliation(s)
- Yonggang Qiao
- College of Life Sciences, Shanxi Agricultural University, Taigu, 030801, Shanxi, China.
| | - Xinrui Zhang
- College of Life Sciences, Shanxi Agricultural University, Taigu, 030801, Shanxi, China
| | - Zheng Li
- College of Life Sciences, Shanxi Agricultural University, Taigu, 030801, Shanxi, China
| | - Yun Song
- College of Life Sciences, Shanxi Agricultural University, Taigu, 030801, Shanxi, China
| | - Zhe Sun
- College of Life Sciences, Shanxi Agricultural University, Taigu, 030801, Shanxi, China
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Soares IMN, Polonio JC, Zequi JAC, Golias HC. Molecular techniques for the taxonomy of Aedes Meigen, 1818 (Culicidae: Aedini): A review of studies from 2010 to 2021. Acta Trop 2022; 236:106694. [PMID: 36122762 DOI: 10.1016/j.actatropica.2022.106694] [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: 07/18/2022] [Revised: 08/23/2022] [Accepted: 09/15/2022] [Indexed: 11/19/2022]
Abstract
The original description of Aedes Meigen in 1818, written in Latin, was very brief and included a single species, Aedes cinereus. In the last two decades the genus Aedes (Meigen, 1818) has undergone several revisions and reclassifications, with the current proposal being described by Wilkerson in 2015. However, the available keys for morphological identification are still not sufficient to differentiate cryptic species, damaged species, or those with confusing taxonomy. The current study aims to identify and describe the main taxonomic proposals and molecular methodologies available for the identification of the genus Aedes published between the years 2010 and 2021. The main molecular techniques used to identify the genus in the last 10 years, are: Multiplex PCR, DNA barcoding, nuclear and mitochondrial markers, environmental DNA, and bacterial microbiome analysis. This review highlights that there are catalogued data for only a few species of the genus Aedes, being restricted to medically important taxa such as Aedes albopictus and Aedes aegypti. The integrative taxonomy approach is a possibility to reconcile morphological and molecular data to improve species delimitation, contributing to future revisions of the genus.
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Affiliation(s)
| | - Julio Cesar Polonio
- Department of Cell Biology, Genetics and Biotechnology, State University of Maringá (UEM), Brazil
| | | | - Halison Correia Golias
- Department of Cell Biology, Genetics and Biotechnology, State University of Maringá (UEM), Brazil; Department of Humanities, Microbiology Laboratory, Federal Technological University of Paraná (UTFPR), Marcilio Dias Street, 635, Apucarana, Paraná, Brazil.
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Multiomics Molecular Research into the Recalcitrant and Orphan Quercus ilex Tree Species: Why, What for, and How. Int J Mol Sci 2022; 23:ijms23179980. [PMID: 36077370 PMCID: PMC9456323 DOI: 10.3390/ijms23179980] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/29/2022] [Accepted: 08/30/2022] [Indexed: 11/17/2022] Open
Abstract
The holm oak (Quercus ilex L.) is the dominant tree species of the Mediterranean forest and the Spanish agrosilvopastoral ecosystem, “dehesa.” It has been, since the prehistoric period, an important part of the Iberian population from a social, cultural, and religious point of view, providing an ample variety of goods and services, and forming the basis of the economy in rural areas. Currently, there is renewed interest in its use for dietary diversification and sustainable food production. It is part of cultural richness, both economically (tangible) and environmentally (intangible), and must be preserved for future generations. However, a worrisome degradation of the species and associated ecosystems is occurring, observed in an increase in tree decline and mortality, which requires urgent action. Breeding programs based on the selection of elite genotypes by molecular markers is the only plausible biotechnological approach. To this end, the authors’ group started, in 2004, a research line aimed at characterizing the molecular biology of Q. ilex. It has been a challenging task due to its biological characteristics (long life cycle, allogamous, high phenotypic variability) and recalcitrant nature. The biology of this species has been characterized following the central dogma of molecular biology using the omics cascade. Molecular responses to biotic and abiotic stresses, as well as seed maturation and germination, are the two main objectives of our research. The contributions of the group to the knowledge of the species at the level of DNA-based markers, genomics, epigenomics, transcriptomics, proteomics, and metabolomics are discussed here. Moreover, data are compared with those reported for Quercus spp. All omics data generated, and the genome of Q. ilex available, will be integrated with morphological and physiological data in the systems biology direction. Thus, we will propose possible molecular markers related to resilient and productive genotypes to be used in reforestation programs. In addition, possible markers related to the nutritional value of acorn and derivate products, as well as bioactive compounds (peptides and phenolics) and allergens, will be suggested. Subsequently, the selected molecular markers will be validated by both genome-wide association and functional genomic analyses.
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Xu J, Yang B, Li M, Li Z, Tu Y, Tang L, He G. Research on germplasm diversity of Amomum villosum. Lour in genuine producing area. PLoS One 2022; 17:e0268246. [PMID: 36044470 PMCID: PMC9432772 DOI: 10.1371/journal.pone.0268246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 04/25/2022] [Indexed: 12/02/2022] Open
Abstract
Background Genuine Chinese medicine is produced from medicinal plant cultivated in a specific region and is of better quality and efficacy, more consistently qualified and famous than that from the same medicinal plant cultivated in other regions. The cultivating region of genuine medicinal plant is known as the genuine producing area. Yangchun City, which is in Guangdong Province of China, is a genuine producing area for the famous Chinese medicine Amomi Fructus (also called Sharen). Amomi Fructus is the ripe and dry fruit of the Zingiberaceae plant A. villosum Lour.. A. villosum was introduced from the Persian Gulf region and has been cultivated in China for over 1000 years. Until now there are no reports on screening for good germplasm of A. villosum. Methods The contents of volatile oil and bornyl acetate of Amomi Fructus from 14 populations were determined with GC method, and the relative contents of the main chemical components in the volatile oils were determined with GC-MS method. Evaluation and variance analysis of the comprehensive quality of the 14 samples were conducted by means of a multi-indicator entropy-weight TOPSIS model (Technique for Order Preference by Similarity to an Ideal Solution) combined with OPLS-DA (Orthogonal Partial Least Squares Discrimination Analysis) and HCA (Hierarchical Clustering Analysis). The ISSR (Inter-Simple Sequence Repeat) molecular marker technique and the UPGMA (unweighted pair-group method with arithmetic means) were employed to analyze the genetic relationship among A. villosum populations. Results The contents of volatile oil and bornyl acetate differed significantly among the different populations, but the main chemical component in the volatile oil was the same in all the samples, which was bornyl acetate. OPLS-DA results showed that 9 indicators were the main factors influencing the quality differences among the 14 populations. The entropy-weight TOPSIS results showed that there were significant differences in the comprehensive qualities of the 12 populations from the genuine producing area. The best quality of fruit was found in the genuine producing area of Chunwan Town; the qualities of 33% of genuine fruits were lower than that of non-genuine fruits. Twenty-three DNA fragments were obtained by ISSR-PCR amplification using four ISSR primers, eleven of which were polymorphic loci, which accounted for 47.8%. The similarity coefficients (GS) of different populations of A. villosum ranged from 0.6087 to 0.9565. Conclusion There are significant differences among different populations of A. villosum in terms of the kinds of major chemical components and their contents, comprehensive quality and genetic diversity. The germplasm resources of A. villosum are rich in the genuine producing area. It means superior germplasm could be selected in the area. The comprehensive quality of the fruit of A. villosum from the non-genuine producing area is better than some of that from genuine producing area, proving that the non-genuine producing area can also produce Amomi Fructus with excellent quality.
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Affiliation(s)
- Jie Xu
- School of Traditional Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
- Guangdong Yifang Pharmaceutical Co., Ltd., Guangdong Provincial Key Laboratory of Traditional Chinese Medicine Formula Granule, Foshan, Guangdong, China
| | - Bohan Yang
- School of Traditional Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
| | - Mingxiao Li
- School of Traditional Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
- Zhuhai Hospital of Integrated Traditional Chinese and Western Medicine, Zhuhai, Guangdong, China
| | - Zixiang Li
- School of Traditional Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
| | - Yuting Tu
- School of Traditional Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
| | - Liyun Tang
- School of Traditional Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
- School of Life Science, South China Agricultural University, Guangzhou, Guangdong, China
| | - Guozhen He
- School of Traditional Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
- * E-mail:
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NAS Y, İLBİ H. Determination of Genetic Diversity in Banana and Bell Pepper Lines Using Molecular Markers. ULUSLARARASI TARIM VE YABAN HAYATI BILIMLERI DERGISI 2022. [DOI: 10.24180/ijaws.1098482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Successful hybrid cultivar breeding is depend on the high genetic diversity of the plant sources, as well as the homozygous and genetically distant lines requiring hybridization. The aim of this study is to determine the genetic distance between the inbred lines of pepper (Capsicum annuum L.) in order to increase efficacy of the breeding program. In this study, the genetic distances between the inbred lines of 44 bell peppers and 35 banana peppers were investigated using the SRAP (Sequence Related Amplified Polymorphism) markers. Based on pattern scores, dendrograms were produced by the UPGMA (unweighted pair-group method of mathematical averages method). Out of the 71 primer combinations tested, 50 combinations revealed polymorphisms among the banana pepper lines, and a total of 123 polymorphic bands were obtained. In the bell pepper lines, 24 SRAP primer combinations were tested and 15 combinations had 25 polymorphic bands. Based on the UPGMA cluster analysis, the pepper lines divided into groups as bell peppers and banana peppers. While the genetic similarity among the banana pepper lines varied between 0.62 and 0.98, the genetic similarity among the bell pepper lines varied between 0.54 and 1.00. As a result, it can be stated that the SRAP markers can be used successfully for determining the genetic distances of the pepper inbred lines thus will help the breeding programme.
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Affiliation(s)
- Yahya NAS
- ŞIRNAK ÜNİVERSİTESİ, ZİRAAT FAKÜLTESİ
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Kaur B, Garcha KS, Bhatia D, Khosa JS, Sharma M, Mittal A, Verma N, Dhatt AS. Identification of single major QTL and candidate gene(s) governing hull-less seed trait in pumpkin. FRONTIERS IN PLANT SCIENCE 2022; 13:948106. [PMID: 36035714 PMCID: PMC9406289 DOI: 10.3389/fpls.2022.948106] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 07/12/2022] [Indexed: 06/01/2023]
Abstract
The hull-less pumpkin (Cucurbita pepo) seed does not require de-hulling before use for human consumption, as a result highly preferred by the oil, nut, and baking industries. In hull-less seeds, a single recessive gene is responsible for the absence of outer thick seed coat layers; however, the genomic region and gene(s) controlling the trait are unclear to date. In this study, four crosses attempted to derive F2 and backcross populations confirmed the single recessive gene inheritance of hull-less seed trait in populations adapted to the sub-tropical climate. The candidate genomic region for hull-less seed trait was identified through the BSA-QTLseq approach using bulks of F2:3 progenies from a cross of HP111 (hulled) and HLP36 (hull-less). A novel genomic region on chromosome 12 ranging from 1.80 to 3.86 Mb was associated with the hull-less seed trait. The re-sequencing data identified a total of 396 SNPs within this region and eight were successfully converted into polymorphic KASP assays. The genotyping of segregating F2 (n = 160) with polymorphic KASP assays resulted in a 40.3 cM partial linkage map and identified Cp_3430407 (10 cM) and Cp_3498687 (16.1 cM) as flanking markers for hull-less locus (Cphl-1). These flanking markers correspond to the 68.28 kb region in the reference genome, and the marker, Cp_3430407 successfully predicted the genotype in 93.33% of the C. pepo hull-less germplasm lines, thus can be used for marker-assisted selection in parents polymorphic for the hull-less seed trait. The Cphl-1-linked genomic region (2.06 Mb) encompasses a total of 182 genes, including secondary cell wall and lignin biosynthesis-related transcriptional factors viz., "NAC" (Cp4.1LG12g04350) and "MYB" (Cp4.1LG12g03120). These genes were differentially expressed in the seeds of hulled and hull-less genotypes, and therefore could be the potential candidate genes governing the hull-less seed trait in pumpkin.
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Affiliation(s)
- Barinder Kaur
- Department of Vegetable Science, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Karmvir Singh Garcha
- Department of Vegetable Science, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Dharminder Bhatia
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Jiffinvir Singh Khosa
- Department of Vegetable Science, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Madhu Sharma
- Department of Vegetable Science, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Amandeep Mittal
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Neha Verma
- Department of Vegetable Science, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Ajmer Singh Dhatt
- Directorate of Research, Punjab Agricultural University, Ludhiana, Punjab, India
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Prasad P, Khatoon U, Verma RK, Sawant SV, Bag SK. Data mining of transcriptional biomarkers at different cotton fiber developmental stages. Funct Integr Genomics 2022; 22:989-1002. [PMID: 35788822 DOI: 10.1007/s10142-022-00878-0] [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: 03/22/2022] [Revised: 06/13/2022] [Accepted: 06/21/2022] [Indexed: 11/04/2022]
Abstract
Advancement of the gene expression study provides comprehensive information on pivotal genes at different cotton fiber development stages. For the betterment of cotton fiber yield and their quality, genetic improvement is a major target point for the cotton community. Therefore, various studies were carried out to understand the transcriptional machinery of fiber leading to the detailed integrative as well as innovative study. Through data mining and statistical approaches, we identified and validated the transcriptional biomarkers for staged specific differentiation of fiber. With the unique mapping read matrix of ~ 200 cotton transcriptome data and sequential statistical analysis, we identified several important genes that have a deciding and specific role in fiber cell commitment, initiation and elongation, or secondary cell wall synthesis stage. Based on the importance score and validation analysis, IQ domain 26, Aquaporin, Gibberellin regulated protein, methionine gamma lyase, alpha/beta hydrolases, and HAD-like superfamily have shown the specific and determining role for fiber developmental stages. These genes are represented as transcriptional biomarkers that provide a base for molecular characterization for cotton fiber development which will ultimately determine the high yield.
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Affiliation(s)
- Priti Prasad
- Molecular Biology and Biotechnology Division, CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226001, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Uzma Khatoon
- Molecular Biology and Biotechnology Division, CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226001, India.,Department of Botany, University of Lucknow, Lucknow, 226001, India
| | - Rishi Kumar Verma
- Molecular Biology and Biotechnology Division, CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226001, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Samir V Sawant
- Molecular Biology and Biotechnology Division, CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226001, India. .,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
| | - Sumit K Bag
- Molecular Biology and Biotechnology Division, CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226001, India. .,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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Yoshiki A, Ballard G, Perez AV. Genetic quality: a complex issue for experimental study reproducibility. Transgenic Res 2022; 31:413-430. [PMID: 35751794 PMCID: PMC9489590 DOI: 10.1007/s11248-022-00314-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 05/30/2022] [Indexed: 11/29/2022]
Abstract
Laboratory animal research involving mice, requires consideration of many factors to be controlled. Genetic quality is one factor that is often overlooked but is essential for the generation of reproducible experimental results. Whether experimental research involves inbred mice, spontaneous mutant, or genetically modified strains, exercising genetic quality through careful breeding, good recordkeeping, and prudent quality control steps such as validation of the presence of mutations and verification of the genetic background, will help ensure that experimental results are accurate and that reference controls are representative for the particular experiment. In this review paper, we will discuss various techniques used for the generation of genetically altered mice, and the different aspects to be considered regarding genetic quality, including inbred strains and substrains used, quality check controls during and after genetic manipulation and breeding. We also provide examples for when to use the different techniques and considerations on genetic quality checks. Further, we emphasize on the importance of establishing an in-house genetic quality program.
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Affiliation(s)
- Atsushi Yoshiki
- Experimental Animal Division, RIKEN BioResource Research Center, Tsukuba, 3050074, Japan.
| | - Gregory Ballard
- Comparative Medicine and Quality, The Jackson Laboratory, Bar Harbor, ME 04609, USA
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Zhang C, Jia C, Liu X, Zhao H, Hou L, Li M, Cui B, Li Y. Genetic Diversity Study on Geographical Populations of the Multipurpose Species Elsholtzia stauntonii Using Transferable Microsatellite Markers. FRONTIERS IN PLANT SCIENCE 2022; 13:903674. [PMID: 35646027 PMCID: PMC9134938 DOI: 10.3389/fpls.2022.903674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 04/21/2022] [Indexed: 06/15/2023]
Abstract
Elsholtzia stauntonii Benth. (Lamiaceae) is an economically important ornamental, medicinal and aromatic plant species. To meet the increasing market demand for E. stauntonii, it is necessary to assess genetic diversity within the species to accelerate the process of genetic improvement. Analysis of the transferability of simple sequence repeat (SSR) markers from related species or genera is a fast and economical method to evaluate diversity, and can ensure the availability of molecular markers in crops with limited genomic resources. In this study, the cross-genera transferability of 497 SSR markers selected from other members of the Lamiaceae (Salvia L., Perilla L., Mentha L., Hyptis Jacq., Leonurus L., Pogostemon Desf., Rosmarinus L., and Scutella L.) to E. stauntonii was 9.05% (45 primers). Among the 45 transferable markers, 10 markers revealed relatively high polymorphism in E. stauntonii. The genetic variation among 825 individuals from 18 natural populations of E. stauntonii in Hebei Province of China was analyzed using the 10 polymorphic SSR markers. On the basis of the SSR data, the average number of alleles (N A), expected heterozygosity (H E), and Shannon's information index (I) of the 10 primers pairs were 7.000, 0.478, and 0.688, respectively. Lower gene flow (N m = 1.252) and high genetic differentiation (F st = 0.181) were detected in the populations. Analysis of molecular variance (AMOVA) revealed that most of the variation (81.47%) was within the populations. Integrating the results of STRUCTURE, UPGMA (Unweighted Pair Group Method with Arithmetic Mean) clustering, and principal coordinate analysis, the 825 samples were grouped into two clusters associated with geographical provenance (southwestern and northeastern regions), which was consistent with the results of a Mantel test (r = 0.56, p < 0.001). Overall, SSR markers developed in related genera were effective to study the genetic structure and genetic diversity in geographical populations of E. stauntonii. The results provide a theoretical basis for conservation of genetic resources, genetic improvement, and construction of a core collection for E. stauntonii.
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Affiliation(s)
- Chenxing Zhang
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, Beijing, China
| | - Chunfeng Jia
- College of Biochemistry and Environmental Engineering, Baoding University, Baoding, China
| | - Xinru Liu
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, Beijing, China
| | - Hanqing Zhao
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, Beijing, China
| | - Lu Hou
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, Beijing, China
| | - Meng Li
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, Beijing, China
| | - Binbin Cui
- College of Biochemistry and Environmental Engineering, Baoding University, Baoding, China
| | - Yingyue Li
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, Beijing, China
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Krokaitė E, Janulionienė R, Jocienė L, Rekašius T, Rajackaitė G, Paulauskas A, Marozas V, Kupčinskienė E. Relating Invasibility and Invasiveness: Case Study of Impatiens parviflora. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.845947] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Data on alien species show that plant invasions are caused by a complex combination of characteristics of invasive species (invasiveness) and characteristics of invaded environment (invasibility). Impatiens parviflora is one of Europe’s top invasive species. The present study aimed to evaluate molecular diversity of populations of highly invasive in Lithuania I. parviflora by applying several DNA markers and relating genetic parameters to abiotic and biotic environment. For sampling, urban forests, riparian forests, and agrarian shrublands were selected. Three different DNA-based techniques, Simple Sequence Repeats (SSR), Inter Simple Sequence Repeat (ISSR) markers, and Random Amplified Polymorphic DNA (RAPD), were used for detecting genetic variation between 21 populations. All population individuals were monomorphic and homozygotic for four loci and heterozygotic for one locus by SSR analysis. Hierarchical analyses of molecular variance at ISSR and RAPD loci revealed significant differentiation of populations depending on geographic zones of the country. Bayesian Structure analyses of molecular data demonstrated existence of many genetic clusters and this finding is in support to multiple introduction of the species. The polymorphism extent at ISSR loci was positively correlated with the total coverage of herbaceous plant species. The coverage by I. parviflora was negatively correlated with the total number of herbaceous species and light in the sites. Our results indicate that Lithuanian sites with I. parviflora might be distinguished by high soil nutrient levels. According to the principal component analysis, the coverage by I. parviflora was a more important variable of populations compared to molecular data or parameters of abiotic environment. In conclusion, complexity of invasibility and invasiveness factors determine the variability of I. parviflora sites, including genetic traits, coverage of invasive species and conditions of environment that were significant and interrelated.
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Bokore FE, Cuthbert RD, Knox RE, Campbell HL, Meyer B, N'Diaye A, Pozniak CJ, DePauw R. Main effect and epistatic QTL affecting spike shattering and association with plant height revealed in two spring wheat (Triticum aestivum L.) populations. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:1143-1162. [PMID: 35306567 PMCID: PMC9033718 DOI: 10.1007/s00122-021-03980-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 10/18/2021] [Indexed: 05/26/2023]
Abstract
A major QTL on chromosome arm 4BS was associated with reduced spike shattering and reduced plant height in coupling phase, and a second major QTL associated with reduced spike shattering was detected on chromosome arm 5AL in the same wheat variety Carberry. Spike shattering can cause severe grain yield loss in wheat. Development of cultivars with reduced shattering but having easy mechanical threshability is the target of wheat breeding programs. This study was conducted to determine quantitative trait loci (QTL) associated with shattering resistance, and epistasis among QTL in the populations Carberry/AC Cadillac and Carberry/Thatcher. Response of the populations to spike shattering was evaluated near Swift Current, SK, in four to five environments. Plant height data recorded in different locations and years were used to determine the relationship of the trait with spike shattering. Each population was genotyped and mapped with the wheat 90 K Illumina iSelect SNP array. Main effect QTL were analyzed by MapQTL 6, and epistatic interactions between main effect QTL were determined by QTLNetwork 2.0. Correlations between height and shattering ranged from 0.15 to 0.49. Carberry contributed two major QTL associated with spike shattering on chromosome arms 4BS and 5AL, detected in both populations. Carberry also contributed two minor QTL on 7AS and 7AL. AC Cadillac contributed five minor QTL on 1AL, 2DL, 3AL, 3DL and 7DS. Nine epistatic QTL interactions were identified, out of which the most consistent and synergistic interaction, that reduced the expression of shattering, occurred between 4BS and 5AL QTL. The 4BS QTL was consistently associated with reduced shattering and reduced plant height in the coupling phase. The present findings shed light on the inheritance of shattering resistance and provide genetic markers for manipulating the trait to develop wheat cultivars.
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Affiliation(s)
- Firdissa E Bokore
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, 1 Airport Road, P.O. Box 1030, Swift Current, SK, S9H 3X2, Canada.
| | - Richard D Cuthbert
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, 1 Airport Road, P.O. Box 1030, Swift Current, SK, S9H 3X2, Canada.
| | - Ron E Knox
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, 1 Airport Road, P.O. Box 1030, Swift Current, SK, S9H 3X2, Canada
| | - Heather L Campbell
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, 1 Airport Road, P.O. Box 1030, Swift Current, SK, S9H 3X2, Canada
| | - Brad Meyer
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, 1 Airport Road, P.O. Box 1030, Swift Current, SK, S9H 3X2, Canada
| | - Amidou N'Diaye
- Department of Plant Sciences and Crop Development Centre, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK, S7N 5A8, Canada
| | - Curtis J Pozniak
- Department of Plant Sciences and Crop Development Centre, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK, S7N 5A8, Canada
| | - Ron DePauw
- Advancing Wheat Technologies, 118 Strathcona Rd SW, Calgary, AB, T3H 1P3, Canada
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Development and Cross-Species Transferability of Novel Genomic-SSR Markers and Their Utility in Hybrid Identification and Trait Association Analysis in Chinese Cherry. HORTICULTURAE 2022. [DOI: 10.3390/horticulturae8030222] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Chinese cherry (Cerasus pseudocerasus (Lindl.) G.Don) is an economically important tetraploid fruiting cherry species native to China. Simple sequence repeats (SSRs)—due to their codominance, polymorphism, and stability—have been widely applied in genetic identification and trait-association analysis. In this study, using comparative genomics strategy and the data of one high-quality whole genome and seven preliminarily assembled genome sequences, we constructed a database containing 25,779 polymorphic SSR loci to efficiently develop novel markers. Sixty-four SSR loci covering eight linkage groups were selected to design primer pairs. Sixty (93.75%) primer pairs yielded specific bands and 32 (50.00%) exhibited moderate-to-high levels of informativeness (PIC ranging from 0.264 to 0.728) in 94 Chinese cherry accessions. A total of 38 primer pairs exhibited high transferability across 13 Cerasus taxa. The marker SAUCps203 was species-specific in C. pseudocerasus by checking with 114 accessions from Cerasus and 16 relatives, suggesting its potential application in accurate identification of Chinese cherry or its interspecific hybrid. Moreover, 1081 out of 1122 individuals from three cross F1 populations of Chinese cherry were identified as true hybrid offspring by using only five SSR markers. Trait association analysis suggested that 20 SSR loci were significantly associated with soluble solids and fruit size, with explained phenotypic variance ranging from 9.02% to 26.35%. This study will provide a basis for SSR-based germplasm identification and further marker-assisted selection (MAS) of Chinese cherry.
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Chan AHE, Saralamba N, Saralamba S, Ruangsittichai J, Thaenkham U. The potential use of mitochondrial ribosomal genes (12S and 16S) in DNA barcoding and phylogenetic analysis of trematodes. BMC Genomics 2022; 23:104. [PMID: 35130837 PMCID: PMC8822746 DOI: 10.1186/s12864-022-08302-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 01/11/2022] [Indexed: 11/10/2022] Open
Abstract
Background Genetic markers like the nuclear ribosomal RNA (rRNA) genes, internal transcribed spacer regions, mitochondrial protein-coding genes, and genomes have been utilized for molecular identification of parasitic trematodes. However, challenges such as the design of broadly applicable primers for the vast number of species within Digenea and the genetic markers’ ability to provide sufficient species-level resolution limited their utility. This study presented novel and broadly applicable primers using the mitochondrial 12S and 16S rRNA genes for Digenea and aimed to show their suitability as alternative genetic markers for molecular identification of orders Plagiorchiida, Echinostomida, and Strigeida. Results Our results revealed that the mitochondrial 12S and 16S rRNA genes are suitable for trematode molecular identification, with sufficient resolution to discriminate closely related species and achieve accurate species identification through phylogenetic placements. Moreover, the robustness of our newly designed primers to amplify medically important parasitic trematodes encompassing three orders was demonstrated through successful amplification. The convenience and applicability of the newly designed primers and adequate genetic variation of the mitochondrial rRNA genes can be useful as complementary markers for trematode molecular-based studies. Conclusions We demonstrated that the mitochondrial rRNA genes could be alternative genetic markers robust for trematode molecular identification and potentially helpful for DNA barcoding where our primers can be widely applied across the major Digenea orders. Furthermore, the potential of the mitochondrial rRNA genes for molecular systematics can be explored, enhancing their appeal for trematode molecular-based studies. The novelty of utilizing the mitochondrial rRNA genes and the designed primers in this study can potentially open avenues for species identification, discovery, and systematics in the future. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08302-4.
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Affiliation(s)
- Abigail Hui En Chan
- Department of Helminthology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Naowarat Saralamba
- Department of Molecular Tropical Medicine and Genetics, Mahidol University, Bangkok, Thailand
| | - Sompob Saralamba
- Mathematical and Economic Modelling (MAEMOD), Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Jiraporn Ruangsittichai
- Department of Medical Entomology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Urusa Thaenkham
- Department of Helminthology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.
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Chaudhary P, Sharma PC. Distribution of simple sequence repeats, transcription factors, and differentially expressed genes in the NGS-based transcriptome of male and female seabuckthorn ( Hippophae salicifolia). J Biomol Struct Dyn 2022; 41:2504-2517. [PMID: 35120412 DOI: 10.1080/07391102.2022.2034669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Seabuckthorn (Hippophae salicifolia) is a perennial, multipurpose wonder plant, popular for its immense medicinal, nutritional, and therapeutic properties. However, due to the lack of whole-genome-based studies, the molecular mechanism governing distinct sexual phenotypes is still not clear. We employed the high-throughput NGS Illumina NovaSeq paired-end technology to generate whole transcriptome profiles of male and female plants of H. salicifolia. In total, 3.2 million raw short reads were generated with an average length of 150 bp, including 50911358 reads from the male leaf tissue samples and 45850364 reads from the female leaf tissue samples. Clustering of the high-quality reads yielded de novo short read assembly of 50259 transcripts of >100 bp length. The final transcripts were assigned Gene Ontology (GO) terms. The digital expression of genes was studied using the DESeq2 of R package that identified 7180 differentially expressed genes (DEGs) between the male and female plant samples. Further, 10,850 simple sequence repeats, and 8,351 transcription factors, distributed in more than 85 transcription families, were also mined from the final assembled transcriptome. Next, COG and KEGG pathway analyses were performed to assign biological functional terms to the DEGs. The findings of the present study will provide a valuable resource for gene expression discovery and other functional genomics studies aiming towards the selection of candidate genes for the development of sex-specific markers in seabuckthorn and other closely related species.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Parneeta Chaudhary
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, New Delhi, India
| | - Prakash Chand Sharma
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, New Delhi, India
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Jain A, Kumar A, Sharma PC. Morphometric and Microsatellite Diversity in Seabuckthorn ( Hippophae rhamnoides L.) Natural Populations Originating from the Different Geographical Regions of the Indian Himalayas. PLANT MOLECULAR BIOLOGY REPORTER 2022; 40:566-578. [PMID: 35261434 PMCID: PMC8891741 DOI: 10.1007/s11105-022-01338-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 02/16/2022] [Indexed: 05/12/2023]
Abstract
UNLABELLED Seabuckthorn (Hippophae rhamnoides L.), an upcoming superfood plant, has attracted researchers' attention worldwide for its medicinal, nutritional, and socio-economic value, along with its characteristic features to sustain extreme climatic conditions. We have studied microsatellite marker-based genetic and morphometric diversity in 93 collections of H. rhamnoides from different geographic sites representing two regions, namely Leh and Lahaul of the Indian Himalayas. Microsatellite markers were isolated using two different approaches, including screening of microsatellite-enriched genomic library, and in silico screening of in-house developed seabuckthorn EST database and whole transcriptome assembly. In Leh and Lahaul collections, 32 and 30 microsatellite markers were found polymorphic, respectively. All the markers developed for H. rhamnoides showed cross-species transferability to H. salicifolia and H. tibetana. Two to six alleles were recorded in the two sets of collections with an average of 3.71 and 3.53 alleles per locus in Leh and Lahaul collections, respectively. Mean polymorphic information content (PIC) values for microsatellite markers were 0.39 and 0.41 for Leh and Lahaul collections, respectively. The average expected heterozygosity was less than the observed heterozygosity. Wright's fixation index (F IS) varied from (-)0.2045 to 1.0 and (-)0.1688 to 1.0 for Leh and Lahaul collections, respectively. Shannon's informative index (I) remained in the range of 0.6745 to 1.8621, and 0.6824 to 1.6308 for Leh and Lahaul collections, respectively. The UPGMA-based combined dendrogram showed clear demarcation between Leh and Lahaul collections, although a few ecotypes were regrouped with collections from the other region. No significant relationship was observed between the morphological distance matrix and molecular marker distance matrix. The findings of the present study may prove helpful in future breeding and conservation strategies aiming for seabuckthorn improvement. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s11105-022-01338-6.
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Affiliation(s)
- Ankit Jain
- Merck Life Science Pvt. Ltd, 8th Floor, Godrej One, Vikhroli (E), Mumbai, India
| | - Ashish Kumar
- Kusuma School of Biological Sciences, Indian Institute of Technology, New Delhi, India
| | - Prakash Chand Sharma
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, New Delhi, India
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Tiwari M, Singh B, Min D, Jagadish SVK. Omics Path to Increasing Productivity in Less-Studied Crops Under Changing Climate-Lentil a Case Study. FRONTIERS IN PLANT SCIENCE 2022; 13:813985. [PMID: 35615121 PMCID: PMC9125188 DOI: 10.3389/fpls.2022.813985] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 04/04/2022] [Indexed: 05/08/2023]
Abstract
Conventional breeding techniques for crop improvement have reached their full potential, and hence, alternative routes are required to ensure a sustained genetic gain in lentils. Although high-throughput omics technologies have been effectively employed in major crops, less-studied crops such as lentils have primarily relied on conventional breeding. Application of genomics and transcriptomics in lentils has resulted in linkage maps and identification of QTLs and candidate genes related to agronomically relevant traits and biotic and abiotic stress tolerance. Next-generation sequencing (NGS) complemented with high-throughput phenotyping (HTP) technologies is shown to provide new opportunities to identify genomic regions and marker-trait associations to increase lentil breeding efficiency. Recent introduction of image-based phenotyping has facilitated to discern lentil responses undergoing biotic and abiotic stresses. In lentil, proteomics has been performed using conventional methods such as 2-D gel electrophoresis, leading to the identification of seed-specific proteome. Metabolomic studies have led to identifying key metabolites that help differentiate genotypic responses to drought and salinity stresses. Independent analysis of differentially expressed genes from publicly available transcriptomic studies in lentils identified 329 common transcripts between heat and biotic stresses. Similarly, 19 metabolites were common across legumes, while 31 were common in genotypes exposed to drought and salinity stress. These common but differentially expressed genes/proteins/metabolites provide the starting point for developing high-yielding multi-stress-tolerant lentils. Finally, the review summarizes the current findings from omic studies in lentils and provides directions for integrating these findings into a systems approach to increase lentil productivity and enhance resilience to biotic and abiotic stresses under changing climate.
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Affiliation(s)
- Manish Tiwari
- Department of Agronomy, Kansas State University, Manhattan, KS, United States
- *Correspondence: Manish Tiwari,
| | - Baljinder Singh
- National Institute of Plant Genome Research, New Delhi, India
| | - Doohong Min
- Department of Agronomy, Kansas State University, Manhattan, KS, United States
| | - S. V. Krishna Jagadish
- Department of Agronomy, Kansas State University, Manhattan, KS, United States
- S. V. Krishna Jagadish,
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Chechetkin VR, Lobzin VV. Ribonucleocapsid assembly/packaging signals in the genomes of the coronaviruses SARS-CoV and SARS-CoV-2: detection, comparison and implications for therapeutic targeting. J Biomol Struct Dyn 2022; 40:508-522. [PMID: 32901577 PMCID: PMC7544952 DOI: 10.1080/07391102.2020.1815581] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Accepted: 08/21/2020] [Indexed: 12/24/2022]
Abstract
The genomic ssRNA of coronaviruses is packaged within a helical nucleocapsid. Due to transitional symmetry of a helix, weakly specific cooperative interaction between ssRNA and nucleocapsid proteins leads to the natural selection of specific quasi-periodic assembly/packaging signals in the related genomic sequence. Such signals coordinated with the nucleocapsid helical structure were detected and reconstructed in the genomes of the coronaviruses SARS-CoV and SARS-CoV-2. The main period of the signals for both viruses was about 54 nt, that implies 6.75 nt per N protein. The complete coverage of the ssRNA genome of length about 30,000 nt by the nucleocapsid would need 4.4 × 103 N proteins, that makes them the most abundant among the structural proteins. The repertoires of motifs for SARS-CoV and SARS-CoV-2 were divergent but nearly coincided for different isolates of SARS-CoV-2. We obtained the distributions of assembly/packaging signals over the genomes with nonoverlapping windows of width 432 nt. Finally, using the spectral entropy, we compared the load from point mutations and indels during virus age for SARS-CoV and SARS-CoV-2. We found the higher mutational load on SARS-CoV. In this sense, SARS-CoV-2 can be treated as a 'newborn' virus. These observations may be helpful in practical medical applications and are of basic interest. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Vladimir R. Chechetkin
- Engelhardt Institute of Molecular Biology of
Russian Academy of Sciences, Moscow,
Russia
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50
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Cheng Z, Ling J, Zhang W, Ding Y. Rapid detection of 17β-estradiol based on shaddock peel derived fluorescent aptasensor for forensic examination. Forensic Sci Int 2021; 331:111153. [PMID: 34952290 DOI: 10.1016/j.forsciint.2021.111153] [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: 05/06/2021] [Revised: 10/24/2021] [Accepted: 12/17/2021] [Indexed: 11/04/2022]
Abstract
17β-estradiol (E2) detection technique had been shown to a potent method for identification of female blood in forensic practice since it was abundant in the healthy female body. Herein, we developed a fluorescent aptasensor based on carbon quatum dots (CQDs) derived from shaddock peel green synthesis for rapid detection of E2 as a useful auxiliary tool of forensic examination. The CQDs conjugated to the aptamer achieved fluorometric detection of E2 in blood and the blood of healthy female from 12 to 60 years old could be sensitive detected with the limit of detection of 0.025 ng/ml, and the analytical process could be completed within 10 min. The aptasensor was also used to assay E2 in forensic samples including blood and blood stain. In all instances, the results were positive when mixed samples involving female sample. This fluorescent aptasensor was proved to be a green, rapid and sensitive detection method of E2, and it exhibited great potential in discrimination of female samples in forensic practice.
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Affiliation(s)
- Zijia Cheng
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha, Hunan, China
| | - Jiang Ling
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha, Hunan, China
| | - Wenqi Zhang
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha, Hunan, China
| | - Yanjun Ding
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha, Hunan, China.
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