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Liu P, Wilson P, Redquest B, Keobouasone S, Manseau M. Seq2Sat and SatAnalyzer toolkit: Towards comprehensive microsatellite genotyping from sequencing data. Mol Ecol Resour 2024; 24:e13929. [PMID: 38289068 DOI: 10.1111/1755-0998.13929] [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: 09/11/2023] [Revised: 12/22/2023] [Accepted: 01/09/2024] [Indexed: 03/06/2024]
Abstract
Accurate and efficient microsatellite loci genotyping is an essential process in population genetics that is also used in various demographic analyses. Protocols for next-generation sequencing of microsatellite loci enable high-throughput and cross-compatible allele scoring, common issues that are not addressed by conventional capillary-based approaches. To improve this process, we have developed an all-in-one software, called Seq2Sat (sequence to microsatellite), in C++ to support automated microsatellite genotyping. It directly takes raw reads of microsatellite amplicons and conducts read quality control before inferring genotypes based on depth-of-read, read ratio, sequence composition and length. We have also developed a module for sex identification based on sex chromosome-specific locus amplicons. To allow for greater user access and complement autoscoring, we developed SatAnalyzer (microsatellite analyzer), a user-friendly web-based platform that conducts reads-to-report analyses by calling Seq2Sat for genotype autoscoring and produces interactive genotype graphs for manual editing. SatAnalyzer also allows users to troubleshoot multiplex optimization by analysing read quality and distribution across loci and samples in support of high-quality library preparation. To evaluate its performance, we benchmarked our toolkit Seq2Sat/SatAnalyzer against a conventional capillary gel method and existing microsatellite genotyping software, MEGASAT, using two datasets. Results showed that SatAnalyzer can achieve >99.70% genotyping accuracy and Seq2Sat is ~5 times faster than MEGASAT despite many more informative tables and figures being generated. Seq2Sat and SatAnalyzer are freely available on github (https://github.com/ecogenomicscanada/Seq2Sat) and dockerhub (https://hub.docker.com/r/rocpengliu/satanalyzer).
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Affiliation(s)
- Peng Liu
- Science and Technology, Environment and Climate Change Canada, Ottawa, Ontario, Canada
| | - Paul Wilson
- Biology Department, Trent University, Peterborough, Ontario, Canada
| | | | - Sonesinh Keobouasone
- Science and Technology, Environment and Climate Change Canada, Ottawa, Ontario, Canada
| | - Micheline Manseau
- Science and Technology, Environment and Climate Change Canada, Ottawa, Ontario, Canada
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Deng P, Du X, Wang Y, Yang X, Cheng X, Huang C, Li T, Li T, Chen C, Zhao J, Wang C, Liu X, Tian Z, Ji W. GenoBaits®WheatplusEE: a targeted capture sequencing panel for quick and accurate identification of wheat-Thinopyrum derivatives. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:36. [PMID: 38291310 DOI: 10.1007/s00122-023-04538-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 12/27/2023] [Indexed: 02/01/2024]
Abstract
KEY MESSAGE A total of 90,000 capture probes derived from wheat and Thinopyrum elongatum were integrated into one chip, which served as an economical genotype for explorating Thinopyrumspecies and their derivatives. Thinopyrum species play a crucial role as a source of new genetic variations for enhancing wheat traits, including resistance to both abiotic and biotic factors. Accurate identification of exogenous chromosome(s) or chromosome segments or genes is essential following the introduction of alien genetic material into wheat, but this task remains challenging. This study aimed to develop a high-resolution wheat-Thinopyrum elongatum array, named GenoBaits®WheatplusEE, to trace alien genetic information by genotyping using a target sequencing system. This GenoBaits®WheatplusEE array included 90,000 capture probes derived from two species and integrated into one chip, with 10,000 and 80,000 originating from wheat and Th. elongatum, respectively. The capture probes were strategically positioned in genes and evenly distributed across the genome, facilitating the development of a roadmap for identifying each alien gene. The array was applied to the high-throughput identification of the alien chromosomes or segments in Thinopyrum and distantly related species and their derivatives. Our results demonstrated that the GenoBaits®WheatplusEE array could be used for direct identification of the breakpoint of alien segments, determine copy number of alien chromosomes, and reveal variations in wheat chromosomes by a single round of target sequencing of the sample. Additionally, we could efficiently and cost-effectively genotype, supporting the exploration of subgenome composition, phylogenetic relationships, and polymorphisms in essential genes (e.g., Fhb7 gene) among Thinopyrum species and their derivatives. We hope that GenoBaits®WheatplusEE will become a widely adopted tool for exporting wild germplasm for wheat improvement in the future.
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Affiliation(s)
- Pingchuan Deng
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Xin Du
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Yanzhen Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
- Center for Agricultural Genetic Resources Research, Shanxi Agricultural University, Taiyuan, 030031, Shanxi, China
| | - Xiaoying Yang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Xiaofang Cheng
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Chenxi Huang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Tingting Li
- College of Bioengineering, Yangling Vocational Technical College, Yangling, 712100, Shaanxi, China
| | - Tingdong Li
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Chunhuan Chen
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Jixin Zhao
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Changyou Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Xinlun Liu
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Zengrong Tian
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Wanquan Ji
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China.
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Li B, Muhammad N, Zhang S, Lan Y, Yang Y, Han S, Liu M, Yang M. Multiple-Genome-Based Simple Sequence Repeat Is an Efficient and Successful Method in Genotyping and Classifying Different Jujube Germplasm Resources. PLANTS (BASEL, SWITZERLAND) 2023; 12:2885. [PMID: 37571038 PMCID: PMC10421302 DOI: 10.3390/plants12152885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 07/23/2023] [Accepted: 08/03/2023] [Indexed: 08/13/2023]
Abstract
Jujube (Ziziphus jujuba Mill.) is a commercially important tree native to China, known for its high nutritional value and widespread distribution, as well as its diverse germplasm resources. Being resilient to harsh climatic conditions, the cultivation of jujube could provide a solution to food insecurity and income for people of arid and semi-arid regions in and outside of China. The evaluation of germplasm resources and genetic diversity in jujube necessitates the use of Simple Sequence Repeat (SSR) markers. SSR markers are highly polymorphic and can be used to evaluate the genetic diversity within and between cultivars of Chinese jujube, and are important for conservation biology, breeding programs, and the discovery of important traits for Chinese jujube improvement in China and abroad. However, traditional methods of SSR development are time-consuming and inadequate to meet the growing research demands. To address this issue, we developed a novel approach called Multiple-Genome-Based SSR identification (MGB-SSR), which utilizes the genomes of three jujube cultivars to rapidly screen for polymorphic SSRs in the jujube genome. Through the screening process, we identified 12 pairs of SSR primers, which were then used to successfully classify 249 jujube genotypes. Based on the genotyping results, a digital ID card was established, enabling the complete identification of all 249 jujube plants. The MGB-SSR approach proved efficient in rapidly detecting polymorphic SSRs within the jujube genome. Notably, this study represents the first successful differentiation of jujube germplasm resources using 12 SSR markers, with 4 markers successfully identifying triploid jujube genotypes. These findings offer valuable information for the classification of Chinese jujube germplasm, thereby providing significant assistance to jujube researchers and breeders in identifying unknown jujube germplasm.
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Affiliation(s)
- Bin Li
- College of Horticulture, Hebei Agricultural University, Baoding 071000, China; (B.L.)
| | - Noor Muhammad
- College of Horticulture, Hebei Agricultural University, Baoding 071000, China; (B.L.)
| | - Shufeng Zhang
- College of Horticulture, Hebei Agricultural University, Baoding 071000, China; (B.L.)
| | - Yunxin Lan
- College of Horticulture, Hebei Agricultural University, Baoding 071000, China; (B.L.)
| | - Yihan Yang
- College of Horticulture, Hebei Agricultural University, Baoding 071000, China; (B.L.)
| | - Shoukun Han
- College of Horticulture, Hebei Agricultural University, Baoding 071000, China; (B.L.)
| | - Mengjun Liu
- College of Horticulture, Hebei Agricultural University, Baoding 071000, China; (B.L.)
- Research Center of Chinese Jujube, Hebei Agricultural University, Baoding 071000, China
| | - Meng Yang
- College of Horticulture, Hebei Agricultural University, Baoding 071000, China; (B.L.)
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Gao L, Li L, Fang B, Fang Z, Xiang Y, Zhang M, Zhou J, Song H, Chen L, Li T, Xiao H, Wan R, Jiang Y, Peng H. Carryover Contamination-Controlled Amplicon Sequencing Workflow for Accurate Qualitative and Quantitative Detection of Pathogens: a Case Study on SARS-CoV-2. Microbiol Spectr 2023; 11:e0020623. [PMID: 37098913 PMCID: PMC10269707 DOI: 10.1128/spectrum.00206-23] [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: 01/13/2023] [Accepted: 04/02/2023] [Indexed: 04/27/2023] Open
Abstract
Carryover contamination during amplicon sequencing workflow (AMP-Seq) put the accuracy of the high-throughput detection for pathogens at risk. The purpose of this study is to develop a carryover contaminations-controlled AMP-Seq (ccAMP-Seq) workflow to enable accurate qualitative and quantitative detection for pathogens. By using the AMP-Seq workflow to detect SARS-CoV-2, Aerosols, reagents and pipettes were identified as potential sources of contaminations and ccAMP-Seq was then developed. ccAMP-Seq used filter tips and physically isolation of experimental steps to avoid cross contamination, synthetic DNA spike-ins to compete with contaminations and quantify SARS-CoV-2, dUTP/uracil DNA glycosylase system to digest the carryover contaminations, and a new data analysis procedure to remove the sequencing reads from contaminations. Compared to AMP-Seq, the contamination level of ccAMP-Seq was at least 22-folds lower and the detection limit was also about an order of magnitude lower-as low as one copy/reaction. By testing the dilution series of SARS-CoV-2 nucleic acid standard, ccAMP-Seq showed 100% sensitivity and specificity. The high sensitivity of ccAMP-Seq was further confirmed by the detection of SARS-CoV-2 from 62 clinical samples. The consistency between qPCR and ccAMP-Seq was 100% for all the 53 qPCR-positive clinical samples. Seven qPCR-negative clinical samples were found to be positive by ccAMP-Seq, which was confirmed by extra qPCR tests on subsequent samples from the same patients. This study presents a carryover contamination-controlled, accurate qualitative and quantitative amplicon sequencing workflow that addresses the critical problem of pathogen detection for infectious diseases. IMPORTANCE Accuracy, a key indicator of pathogen detection technology, is compromised by carryover contamination in the amplicon sequencing workflow. Taking the detection of SARS-CoV-2 as case, this study presents a new carryover contamination-controlled amplicon sequencing workflow. The new workflow significantly reduces the degree of contamination in the workflow, thereby significantly improving the accuracy and sensitivity of the SARS-CoV-2 detection and empowering the ability of quantitative detection. More importantly, the use of the new workflow is simple and economical. Therefore, the results of this study can be easily applied to other microorganism, which has great significance for improving the detection level of microorganism.
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Affiliation(s)
- Lifen Gao
- Institute for Systems Biology, Jianghan University, Wuhan, Hubei, People’s Republic of China
| | - Lun Li
- Institute for Systems Biology, Jianghan University, Wuhan, Hubei, People’s Republic of China
| | - Bin Fang
- Hubei Provincial Centers for Disease Control and Prevention, Wuhan, Hubei, People’s Republic of China
| | - Zhiwei Fang
- Institute for Systems Biology, Jianghan University, Wuhan, Hubei, People’s Republic of China
| | - Yanghai Xiang
- Yueyang Central Hospital, Yueyang, Hunan, People’s Republic of China
| | - Min Zhang
- Yueyang Central Hospital, Yueyang, Hunan, People’s Republic of China
| | - Junfei Zhou
- Institute for Systems Biology, Jianghan University, Wuhan, Hubei, People’s Republic of China
| | - Huiyin Song
- Institute for Systems Biology, Jianghan University, Wuhan, Hubei, People’s Republic of China
| | - Lihong Chen
- Institute for Systems Biology, Jianghan University, Wuhan, Hubei, People’s Republic of China
| | - Tiantian Li
- Institute for Systems Biology, Jianghan University, Wuhan, Hubei, People’s Republic of China
| | - Huafeng Xiao
- Institute for Systems Biology, Jianghan University, Wuhan, Hubei, People’s Republic of China
| | - Renjing Wan
- Institute for Systems Biology, Jianghan University, Wuhan, Hubei, People’s Republic of China
| | - Yongzhong Jiang
- Hubei Provincial Centers for Disease Control and Prevention, Wuhan, Hubei, People’s Republic of China
| | - Hai Peng
- Institute for Systems Biology, Jianghan University, Wuhan, Hubei, People’s Republic of China
- Mingliao Biotechnology Co., Ltd., Wuhan, Hubei, People’s Republic of China
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Tympakianakis S, Trantas E, Avramidou EV, Ververidis F. Vitis vinifera genotyping toolbox to highlight diversity and germplasm identification. FRONTIERS IN PLANT SCIENCE 2023; 14:1139647. [PMID: 37180393 PMCID: PMC10169827 DOI: 10.3389/fpls.2023.1139647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Accepted: 03/27/2023] [Indexed: 05/16/2023]
Abstract
The contribution of vine cultivation to human welfare as well as the stimulation of basic social and cultural features of civilization has been great. The wide temporal and regional distribution created a wide array of genetic variants that have been used as propagating material to promote cultivation. Information on the origin and relationships among cultivars is of great interest from a phylogenetics and biotechnology perspective. Fingerprinting and exploration of the complicated genetic background of varieties may contribute to future breeding programs. In this review, we present the most frequently used molecular markers, which have been used on Vitis germplasm. We discuss the scientific progress that led to the new strategies being implemented utilizing state-of-the-art next generation sequencing technologies. Additionally, we attempted to delimit the discussion on the algorithms used in phylogenetic analyses and differentiation of grape varieties. Lastly, the contribution of epigenetics is highlighted to tackle future roadmaps for breeding and exploitation of Vitis germplasm. The latter will remain in the top of the edge for future breeding and cultivation and the molecular tools presented herein, will serve as a reference point in the challenging years to come.
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Affiliation(s)
- Stylianos Tympakianakis
- Laboratory of Biological and Biotechnological Applications, Department of Agriculture, School of Agricultural Sciences, Hellenic Mediterranean University, Heraklion, Greece
| | - Emmanouil Trantas
- Laboratory of Biological and Biotechnological Applications, Department of Agriculture, School of Agricultural Sciences, Hellenic Mediterranean University, Heraklion, Greece
- Institute of Agri-Food and Life Sciences, Research Center of the Hellenic Mediterranean University, Heraklion, Greece
| | - Evangelia V. Avramidou
- Institute of Mediterranean Forest Ecosystems, Hellenic Agricultural Organisation “DIMITRA“, Athens, Greece
| | - Filippos Ververidis
- Laboratory of Biological and Biotechnological Applications, Department of Agriculture, School of Agricultural Sciences, Hellenic Mediterranean University, Heraklion, Greece
- Institute of Agri-Food and Life Sciences, Research Center of the Hellenic Mediterranean University, Heraklion, Greece
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Liu F, Wang SH, Jia DH, Tan H, Wang B, Zhao RL. Development of Multiple Nucleotide Polymorphism Molecular Markers for Enoki Mushroom ( Flammulina filiformis) Cultivars Identification. J Fungi (Basel) 2023; 9:jof9030330. [PMID: 36983498 PMCID: PMC10056640 DOI: 10.3390/jof9030330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 02/17/2023] [Accepted: 03/06/2023] [Indexed: 03/30/2023] Open
Abstract
The enoki mushroom (Flammulina filiformis) is one of the most important and popular edible mushrooms commercially in China. However, traditional mushroom cultivar identification is challenging due to poor accuracy, heavy workloads, and low reproducibility. To overcome this challenge, we developed a method for identifying F. filiformis strains using multiple nucleotide polymorphism sequencing (MNP-seq). This involved screening 179 universal MNP markers based on whole-genome sequencing data, constructing an MNP sequence library, and performing multiplex PCR amplification and high-sequencing. We further screened 69 core MNP markers and used them to build a neighbor-joining (NJ) phylogenetic tree of 232 cultivated and wild strains. Our analysis showed that all cultivars could be accurately separated by computing genetic similarity values and that the cultivars could be separated into 22 distinct evolutionary pedigrees. The specific value of genetic similarity can be used as the standard to distinguish F. filiformis cultivars, however, it needs to be comprehensively defined by the additional phenotype and biological characteristics of those strains in the future work.
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Affiliation(s)
- Fei Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Shi-Hui Wang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- School of Plant Protection, Jilin Agricultural University, Changchun 130118, China
| | - Ding-Hong Jia
- National-Local Joint Engineering Laboratory of Breeding and Cultivation of Edible and Medicinal Fungi, Sichuan Institute of Edible Fungi, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China
| | - Hao Tan
- National-Local Joint Engineering Laboratory of Breeding and Cultivation of Edible and Medicinal Fungi, Sichuan Institute of Edible Fungi, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China
| | - Bo Wang
- National-Local Joint Engineering Laboratory of Breeding and Cultivation of Edible and Medicinal Fungi, Sichuan Institute of Edible Fungi, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China
| | - Rui-Lin Zhao
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China
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Zhao S, Zhang C, Wang L, Luo M, Zhang P, Wang Y, Malik WA, Wang Y, Chen P, Qiu X, Wang C, Lu H, Xiang Y, Liu Y, Ruan J, Qian Q, Zhi H, Chang Y. A prolific and robust whole-genome genotyping method using PCR amplification via primer-template mismatched annealing. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:633-645. [PMID: 36269601 DOI: 10.1111/jipb.13395] [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: 10/21/2022] [Indexed: 06/16/2023]
Abstract
Whole-genome genotyping methods are important for breeding. However, it has been challenging to develop a robust method for simultaneous foreground and background genotyping that can easily be adapted to different genes and species. In our study, we accidently discovered that in adapter ligation-mediated PCR, the amplification by primer-template mismatched annealing (PTMA) along the genome could generate thousands of stable PCR products. Based on this observation, we consequently developed a novel method for simultaneous foreground and background integrated genotyping by sequencing (FBI-seq) using one specific primer, in which foreground genotyping is performed by primer-template perfect annealing (PTPA), while background genotyping employs PTMA. Unlike DNA arrays, multiple PCR, or genome target enrichments, FBI-seq requires little preliminary work for primer design and synthesis, and it is easily adaptable to different foreground genes and species. FBI-seq therefore provides a prolific, robust, and accurate method for simultaneous foreground and background genotyping to facilitate breeding in the post-genomics era.
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Affiliation(s)
- Sheng Zhao
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing, 210095, China
- Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Cuicui Zhang
- Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Liqun Wang
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Minxuan Luo
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing, 210095, China
- Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Peng Zhang
- Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Yue Wang
- Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Waqar Afzal Malik
- Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Yue Wang
- Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Peng Chen
- Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Xianjin Qiu
- College of Agriculture, Yangtze University, Jingzhou, 434023, China
| | - Chongrong Wang
- Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Hong Lu
- Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Yong Xiang
- Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Yuwen Liu
- Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Jue Ruan
- Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Qian Qian
- Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Haijian Zhi
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yuxiao Chang
- Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
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Zhang J, Yang J, Lv Y, Zhang X, Xia C, Zhao H, Wen C. Genetic diversity analysis and variety identification using SSR and SNP markers in melon. BMC PLANT BIOLOGY 2023; 23:39. [PMID: 36650465 PMCID: PMC9847184 DOI: 10.1186/s12870-023-04056-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 01/10/2023] [Indexed: 06/17/2023]
Abstract
Melon is an important horticultural crop with a pleasant aromatic flavor and abundance of health-promoting substances. Numerous melon varieties have been cultivated worldwide in recent years, but the high number of varieties and the high similarity between them poses a major challenge for variety evaluation, discrimination, as well as innovation in breeding. Recently, simple sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs), two robust molecular markers, have been utilized as a rapid and reliable method for variety identification. To elucidate the genetic structure and diversity of melon varieties, we screened out 136 perfect SSRs and 164 perfect SNPs from the resequencing data of 149 accessions, including the most representative lines worldwide. This study established the DNA fingerprint of 259 widely-cultivated melon varieties in China using Target-seq technology. All melon varieties were classified into five subgruops, including ssp. agrestis, ssp. melo, muskmelon and two subgroups of foreign individuals. Compared with ssp. melo, the ssp. agrestis varieties might be exposed to a high risk of genetic erosion due to their extremely narrow genetic background. Increasing the gene exchange between ssp. melo and ssp. agrestis is therefore necessary in the breeding procedure. In addition, analysis of the DNA fingerprints of the 259 melon varieties showed a good linear correlation (R2 = 0.9722) between the SSR genotyping and SNP genotyping methods in variety identification. The pedigree analysis based on the DNA fingerprint of 'Jingyu' and 'Jingmi' series melon varieties was consistent with their breeding history. Based on the SNP index analysis, ssp. agrestis had low gene exchange with ssp. melo in chromosome 4, 7, 10, 11and 12, two specific SNP loci were verified to distinguish ssp. agrestis and ssp. melon varieties. Finally, 23 SSRs and 40 SNPs were selected as the core sets of markers for application in variety identification, which could be efficiently applied to variety authentication, variety monitoring, as well as the protection of intellectual property rights in melon.
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Affiliation(s)
- Jian Zhang
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agricultural and Forestry Sciences, National Engineering Research Center for Vegetables, Beijing, 100097, China
- Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing, 100097, China
| | - Jingjing Yang
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agricultural and Forestry Sciences, National Engineering Research Center for Vegetables, Beijing, 100097, China
- Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing, 100097, China
| | - Yanling Lv
- Institute of Vegetable, Liaoning Academy of Agricultural Sciences, Shenyang, 110161, China
| | - Xiaofei Zhang
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agricultural and Forestry Sciences, National Engineering Research Center for Vegetables, Beijing, 100097, China
- Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing, 100097, China
| | - Changxuan Xia
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agricultural and Forestry Sciences, National Engineering Research Center for Vegetables, Beijing, 100097, China
- Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing, 100097, China
| | - Hong Zhao
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agricultural and Forestry Sciences, National Engineering Research Center for Vegetables, Beijing, 100097, China
- Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing, 100097, China
| | - Changlong Wen
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agricultural and Forestry Sciences, National Engineering Research Center for Vegetables, Beijing, 100097, China.
- Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing, 100097, China.
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Xu FF, Chen WQ, Liu W, Liu SS, Wang YX, Chen J, Cui J, Zhang X. Genetic structure of Spirometra mansoni (Cestoda: Diphyllobothriidae) populations in China revealed by a Target SSR-seq method. Parasit Vectors 2022; 15:485. [PMID: 36564786 PMCID: PMC9789593 DOI: 10.1186/s13071-022-05568-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 11/02/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND In China, the plerocercoid of the cestode Spirometra mansoni is the main causative agent of human and animal sparganosis. However, the population genetic structure of this parasite remains unclear. In this study, we genotyped S. mansoni isolates with the aim to improve current knowledge on the evolution and population diversity of this cestode. METHODS We first screened 34 perfect simple sequence repeats (SSRs) using all available omic data and then constructed target sequencing technology (Target SSR-seq) based on the Illumina NovaSeq platform. Next, a series of STRUCTURE. clustering, principal component, analysis of molecular variance and TreeMix analyses were performed on 362 worm samples isolated from 12 different hosts in 16 geographical populations of China to identify the genetic structure. RESULTS A total of 170 alleles were detected. The whole population could be organized and was found to be derived from the admixture of two ancestral clusters. TreeMix analysis hinted that possible gene flow occurred from Guizhou (GZ) to Sichuan (SC), SC to Jaingxi (JX), SC to Hubei (HB), GZ to Yunnan (YN) and GZ to Jiangsu (JS). Both neighbor-joining clustering and principal coordinate analysis showed that isolates from intermediate hosts tend to cluster together, while parasites from definitive hosts revealed greater genetic differences. Generally, a S. mansoni population was observed to harbor high genetic diversity, moderate genetic differentiation and a little genetic exchange among geographical populations. CONCLUSIONS A Target SSR-seq genotyping method was successfully developed, and an in-depth view of genetic diversity and genetic relationship will have important implications for the prevention and control of sparganosis.
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Affiliation(s)
- Fang Fang Xu
- grid.207374.50000 0001 2189 3846Department of Parasitology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450001 Henan China
| | - Wen Qing Chen
- grid.207374.50000 0001 2189 3846Department of Parasitology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450001 Henan China
| | - Wei Liu
- grid.257160.70000 0004 1761 0331Research Center for Parasites and Vectors, College of Veterinary Medicine, Hunan Agricultural University, Changsha, 410128 Hunan China
| | - Sha Sha Liu
- grid.207374.50000 0001 2189 3846Department of Parasitology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450001 Henan China
| | - Yi Xing Wang
- grid.207374.50000 0001 2189 3846Department of Parasitology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450001 Henan China
| | - Jing Chen
- grid.207374.50000 0001 2189 3846Department of Parasitology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450001 Henan China
| | - Jing Cui
- grid.207374.50000 0001 2189 3846Department of Parasitology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450001 Henan China
| | - Xi Zhang
- grid.207374.50000 0001 2189 3846Department of Parasitology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450001 Henan China
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10
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Zou M, Jiang S, Wang F, Zhao L, Zhang C, Bao Y, Chen Y, Xia Z. Feature Compression Applications of Genetic Algorithm. Front Genet 2022; 13:757524. [PMID: 35350241 PMCID: PMC8957834 DOI: 10.3389/fgene.2022.757524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 02/21/2022] [Indexed: 11/13/2022] Open
Abstract
With the rapid development of molecular breeding technology and many new varieties breeding, a method is urgently needed to identify different varieties accurately and quickly. Using this method can not only help farmers feel convenient and efficient in the normal cultivation and breeding process but also protect the interests of breeders, producers and users. In this study, single nucleotide polymorphism (SNP) data of 533 Oryza sativa, 284 Solanum tuberosum and 247 Sus scrofa and 544 Manihot esculenta Crantz were used. The original SNPs were filtered and screened to remove the SNPs with deletion number more than 1% or the homozygous genotype 0/0 and 1/1 number less than 2. The correlation between SNPs were calculated, and the two adjacent SNPs with correlation R2 > 0.95 were retained. The genetic algorithm program was developed to convert the genotype format and randomly combine SNPs to calculate a set of a small number of SNPs which could distinguish all varieties in different species as fingerprint data, using Matlab platform. The successful construction of three sets of fingerprints showed that the method developed in this study was effective in animals and plants. The population structure analysis showed that the genetic algorithm could effectively obtain the core SNPs for constructing fingerprints, and the fingerprint was practical and effective. At present, the two-dimensional code of Manihot esculenta Crantz fingerprint obtained by this method has been applied to field planting. This study provides a novel idea for the Oryza sativa, Solanum tuberosum, Sus scrofa and Manihot esculenta Crantz identification of various species, lays foundation for the cultivation and identification of new varieties, and provides theoretical significance for many other species fingerprints construction.
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Affiliation(s)
- Meiling Zou
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agriculture Sciences, Haikou, China.,Hainan University, Haikou, China
| | | | - Fang Wang
- Academy of Agriculture and Forestry Sciences, Qinghai University, Xining, China
| | - Long Zhao
- Hainan University, Haikou, China.,Academy of Agriculture and Forestry Sciences, Qinghai University, Xining, China
| | | | | | | | - Zhiqiang Xia
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agriculture Sciences, Haikou, China.,Hainan University, Haikou, China
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11
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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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12
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Azizi MMF, Lau HY, Abu-Bakar N. Integration of advanced technologies for plant variety and cultivar identification. J Biosci 2021. [DOI: 10.1007/s12038-021-00214-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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13
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Huo Y, Zhao Y, Xu L, Yi H, Zhang Y, Jia X, Zhao H, Zhao J, Wang F. An integrated strategy for target SSR genotyping with toleration of nucleotide variations in the SSRs and flanking regions. BMC Bioinformatics 2021; 22:429. [PMID: 34496768 PMCID: PMC8424866 DOI: 10.1186/s12859-021-04351-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 08/31/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND With the broad application of high-throughput sequencing and its reduced cost, simple sequence repeat (SSR) genotyping by sequencing (SSR-GBS) has been widely used for interpreting genetic data across different fields, including population genetic diversity and structure analysis, the construction of genetic maps, and the investigation of intraspecies relationships. The development of accurate and efficient typing strategies for SSR-GBS is urgently needed and several tools have been published. However, to date, no suitable accurate genotyping method can tolerate single nucleotide variations (SNVs) in SSRs and flanking regions. These SNVs may be caused by PCR and sequencing errors or SNPs among varieties, and they directly affect sequence alignment and genotyping accuracy. RESULTS Here, we report a new integrated strategy named the accurate microsatellite genotyping tool based on targeted sequencing (AMGT-TS) and provide a user-friendly web-based platform and command-line version of AMGT-TS. To handle SNVs in the SSRs or flanking regions, we developed a broad matching algorithm (BMA) that can quickly and accurately achieve SSR typing for ultradeep coverage and high-throughput analysis of loci with SNVs compatibility and grouping of typed reads for further in-depth information mining. To evaluate this tool, we tested 21 randomly sampled loci in eight maize varieties, accompanied by experimental validation on actual and simulated sequencing data. Our evaluation showed that, compared to other tools, AMGT-TS presented extremely accurate typing results with single base resolution for both homozygous and heterozygous samples. CONCLUSION This integrated strategy can achieve accurate SSR genotyping based on targeted sequencing, and it can tolerate single nucleotide variations in the SSRs and flanking regions. This method can be readily applied to divergent sequencing platforms and species and has excellent application prospects in genetic and population biology research. The web-based platform and command-line version of AMGT-TS are available at https://amgt-ts.plantdna.site:8445 and https://github.com/plantdna/amgt-ts , respectively.
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Affiliation(s)
- Yongxue Huo
- Maize Research Center, Beijing Academy of Agricultural and Forest Sciences (BAAFS)/Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing, 100097, China
| | - Yikun Zhao
- Maize Research Center, Beijing Academy of Agricultural and Forest Sciences (BAAFS)/Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing, 100097, China
| | - Liwen Xu
- Maize Research Center, Beijing Academy of Agricultural and Forest Sciences (BAAFS)/Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing, 100097, China
| | - Hongmei Yi
- Maize Research Center, Beijing Academy of Agricultural and Forest Sciences (BAAFS)/Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing, 100097, China
| | - Yunlong Zhang
- Maize Research Center, Beijing Academy of Agricultural and Forest Sciences (BAAFS)/Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing, 100097, China
| | - Xianqing Jia
- Maize Research Center, Beijing Academy of Agricultural and Forest Sciences (BAAFS)/Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing, 100097, China
| | - Han Zhao
- Provincial Key Laboratory of Agrobiology, Institute of Crop Germplasm and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, Jiangsu, China
| | - Jiuran Zhao
- Maize Research Center, Beijing Academy of Agricultural and Forest Sciences (BAAFS)/Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing, 100097, China.
| | - Fengge Wang
- Maize Research Center, Beijing Academy of Agricultural and Forest Sciences (BAAFS)/Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing, 100097, China.
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14
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Shen Y, Wang J, Shaw RK, Yu H, Sheng X, Zhao Z, Li S, Gu H. Development of GBTS and KASP Panels for Genetic Diversity, Population Structure, and Fingerprinting of a Large Collection of Broccoli ( Brassica oleracea L. var. italica) in China. FRONTIERS IN PLANT SCIENCE 2021; 12:655254. [PMID: 34149754 PMCID: PMC8213352 DOI: 10.3389/fpls.2021.655254] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 04/21/2021] [Indexed: 06/12/2023]
Abstract
Broccoli (Brassica oleracea var. italica) is one of the most important and nutritious vegetables widely cultivated in China. In the recent four decades, several improved varieties were bred and developed by Chinese breeders. However, the efforts for improvement of broccoli are hindered by limited information of genetic diversity and genetic relatedness contained within the available germplasms. This study evaluated the genetic diversity, genetic relationship, population structure, and fingerprinting of 372 accessions of broccoli representing most of the variability of broccoli in China. Millions of SNPs were identified by whole-genome sequencing of 23 representative broccoli genotypes. Through several stringent selection criteria, a total of 1,167 SNPs were selected to characterize genetic diversity and population structure. Of these markers, 1,067 SNPs were genotyped by target sequencing (GBTS), and 100 SNPs were genotyped by kompetitive allele specific PCR (KASP) assay. The average polymorphism information content (PIC) and expected heterozygosity (gene diversity) values were 0.33 and 0.42, respectively. Diversity analysis revealed the prevalence of low to moderate genetic diversity in the broccoli accessions indicating a narrow genetic base. Phylogenetic and principal component analyses revealed that the 372 accessions could be clustered into two main groups but with weak groupings. STRUCTURE analysis also suggested the presence of two subpopulations with weak genetic structure. Analysis of molecular variance (AMOVA) identified 13% variance among populations and 87% within populations revealing very low population differentiation, which could be attributed to massive gene flow and the reproductive biology of the crop. Based on high resolving power, a set of 28 KASP markers was chosen for DNA fingerprinting of the broccoli accessions for seed authentication and varietal identification. To the best of our knowledge, this is the first comprehensive study to measure diversity and population structure of a large collection of broccoli in China and also the first application of GBTS and KASP techniques in genetic characterization of broccoli. This work broadens the understanding of diversity, phylogeny, and population structure of a large collection of broccoli, which may enhance future breeding efforts to achieve higher productivity.
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Affiliation(s)
- Yusen Shen
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Jiansheng Wang
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Ranjan K. Shaw
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Huifang Yu
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Xiaoguang Sheng
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Zhenqing Zhao
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Sujuan Li
- Central Laboratory of Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Honghui Gu
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
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15
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Baggett JP, Tillett RL, Cooper EA, Yerka MK. De novo identification and targeted sequencing of SSRs efficiently fingerprints Sorghum bicolor sub-population identity. PLoS One 2021; 16:e0248213. [PMID: 33684158 PMCID: PMC7939377 DOI: 10.1371/journal.pone.0248213] [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: 05/12/2020] [Accepted: 02/22/2021] [Indexed: 11/21/2022] Open
Abstract
Recent plant breeding studies of several species have demonstrated the utility of combining molecular assessments of genetic distance into trait-linked SNP genotyping during the development of parent lines to maximize yield gains due to heterosis. SSRs (Short Sequence Repeats) are the molecular marker of choice to determine genetic diversity, but the methods historically used to sequence them have been burdensome. The ability to analyze SSRs in a higher-throughput manner independent of laboratory conditions would increase their utility in molecular ecology, germplasm curation, and plant breeding programs worldwide. This project reports simple bioinformatics methods that can be used to generate genome-wide de novo SSRs in silico followed by targeted Next Generation Sequencing (NGS) validation of those that provide the most information about sub-population identity of a breeding line, which influences heterotic group selection. While these methods were optimized in sorghum [Sorghum bicolor (L.) Moench], they were developed to be applied to any species with a reference genome and high-coverage whole-genome sequencing data of individuals from the sub-populations to be characterized. An analysis of published sorghum genomes selected to represent its five main races (bicolor, caudatum, durra, kafir, and guinea; 75 accessions total) identified 130,120 SSR motifs. Average lengths were 23.8 bp and 95% were between 10 and 92 bp, making them suitable for NGS. Validation through targeted sequencing amplified 188 of 192 assayed SSR loci. Results highlighted the distinctness of accessions from the guinea sub-group margaritiferum from all other sorghum accessions, consistent with previous studies of nuclear and mitochondrial DNA. SSRs that efficiently fingerprinted margaritiferum individuals (Xgma1 -Xgma6) are presented. Developing similar fingerprints of other sub-populations (Xunr1 -Xunr182) was not possible due to the extensive admixture between them in the data set analyzed. In summary, these methods were able to fingerprint specific sub-populations when rates of admixture between them are low.
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Affiliation(s)
- John P. Baggett
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV, United States of America
| | - Richard L. Tillett
- Nevada Center for Bioinformatics, University of Nevada, Reno, NV, United States of America
| | - Elizabeth A. Cooper
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, United States of America
| | - Melinda K. Yerka
- Department of Agriculture, Veterinary, and Rangeland Sciences, University of Nevada, Reno, NV, United States of America
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16
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Tong J, Sun M, Wang Y, Zhang Y, Rasheed A, Li M, Xia X, He Z, Hao Y. Dissection of Molecular Processes and Genetic Architecture Underlying Iron and Zinc Homeostasis for Biofortification: From Model Plants to Common Wheat. Int J Mol Sci 2020; 21:E9280. [PMID: 33291360 PMCID: PMC7730113 DOI: 10.3390/ijms21239280] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Revised: 11/28/2020] [Accepted: 12/01/2020] [Indexed: 02/07/2023] Open
Abstract
The micronutrients iron (Fe) and zinc (Zn) are not only essential for plant survival and proliferation but are crucial for human health. Increasing Fe and Zn levels in edible parts of plants, known as biofortification, is seen a sustainable approach to alleviate micronutrient deficiency in humans. Wheat, as one of the leading staple foods worldwide, is recognized as a prioritized choice for Fe and Zn biofortification. However, to date, limited molecular and physiological mechanisms have been elucidated for Fe and Zn homeostasis in wheat. The expanding molecular understanding of Fe and Zn homeostasis in model plants is providing invaluable resources to biofortify wheat. Recent advancements in NGS (next generation sequencing) technologies coupled with improved wheat genome assembly and high-throughput genotyping platforms have initiated a revolution in resources and approaches for wheat genetic investigations and breeding. Here, we summarize molecular processes and genes involved in Fe and Zn homeostasis in the model plants Arabidopsis and rice, identify their orthologs in the wheat genome, and relate them to known wheat Fe/Zn QTL (quantitative trait locus/loci) based on physical positions. The current study provides the first inventory of the genes regulating grain Fe and Zn homeostasis in wheat, which will benefit gene discovery and breeding, and thereby accelerate the release of Fe- and Zn-enriched wheats.
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Affiliation(s)
- Jingyang Tong
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing 100081, China; (J.T.); (M.S.); (Y.W.); (Y.Z.); (M.L.); (X.X.)
| | - Mengjing Sun
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing 100081, China; (J.T.); (M.S.); (Y.W.); (Y.Z.); (M.L.); (X.X.)
| | - Yue Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing 100081, China; (J.T.); (M.S.); (Y.W.); (Y.Z.); (M.L.); (X.X.)
| | - Yong Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing 100081, China; (J.T.); (M.S.); (Y.W.); (Y.Z.); (M.L.); (X.X.)
| | - Awais Rasheed
- International Maize and Wheat Improvement Center (CIMMYT) China Office, c/o CAAS, 12 Zhongguancun South Street, Beijing 100081, China;
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Ming Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing 100081, China; (J.T.); (M.S.); (Y.W.); (Y.Z.); (M.L.); (X.X.)
| | - Xianchun Xia
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing 100081, China; (J.T.); (M.S.); (Y.W.); (Y.Z.); (M.L.); (X.X.)
| | - Zhonghu He
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing 100081, China; (J.T.); (M.S.); (Y.W.); (Y.Z.); (M.L.); (X.X.)
- International Maize and Wheat Improvement Center (CIMMYT) China Office, c/o CAAS, 12 Zhongguancun South Street, Beijing 100081, China;
| | - Yuanfeng Hao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing 100081, China; (J.T.); (M.S.); (Y.W.); (Y.Z.); (M.L.); (X.X.)
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17
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Lepais O, Chancerel E, Boury C, Salin F, Manicki A, Taillebois L, Dutech C, Aissi A, Bacles CF, Daverat F, Launey S, Guichoux E. Fast sequence-based microsatellite genotyping development workflow. PeerJ 2020; 8:e9085. [PMID: 32411534 PMCID: PMC7204839 DOI: 10.7717/peerj.9085] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 04/08/2020] [Indexed: 12/21/2022] Open
Abstract
Application of high-throughput sequencing technologies to microsatellite genotyping (SSRseq) has been shown to remove many of the limitations of electrophoresis-based methods and to refine inference of population genetic diversity and structure. We present here a streamlined SSRseq development workflow that includes microsatellite development, multiplexed marker amplification and sequencing, and automated bioinformatics data analysis. We illustrate its application to five groups of species across phyla (fungi, plant, insect and fish) with different levels of genomic resource availability. We found that relying on previously developed microsatellite assay is not optimal and leads to a resulting low number of reliable locus being genotyped. In contrast, de novo ad hoc primer designs gives highly multiplexed microsatellite assays that can be sequenced to produce high quality genotypes for 20-40 loci. We highlight critical upfront development factors to consider for effective SSRseq setup in a wide range of situations. Sequence analysis accounting for all linked polymorphisms along the sequence quickly generates a powerful multi-allelic haplotype-based genotypic dataset, calling to new theoretical and analytical frameworks to extract more information from multi-nucleotide polymorphism marker systems.
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Affiliation(s)
- Olivier Lepais
- INRAE, Univ. Bordeaux, BIOGECO, Cestas, France
- INRAE, Université de Pau et Pays de l’Adour, ECOBIOP, Saint-Peé-sur-Nivelle, France
| | | | | | | | - Aurélie Manicki
- INRAE, Université de Pau et Pays de l’Adour, ECOBIOP, Saint-Peé-sur-Nivelle, France
| | - Laura Taillebois
- INRAE, Université de Pau et Pays de l’Adour, ECOBIOP, Saint-Peé-sur-Nivelle, France
| | | | | | - Cecile F.E. Bacles
- INRAE, Université de Pau et Pays de l’Adour, ECOBIOP, Saint-Peé-sur-Nivelle, France
| | | | - Sophie Launey
- INRAE, Agrocampus Ouest, ESE, Ecology and Ecosystem Health, Rennes, France
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PIDS: A User-Friendly Plant DNA Fingerprint Database Management System. Genes (Basel) 2020; 11:genes11040373. [PMID: 32235513 PMCID: PMC7230844 DOI: 10.3390/genes11040373] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 03/27/2020] [Accepted: 03/29/2020] [Indexed: 11/23/2022] Open
Abstract
The high variability and somatic stability of DNA fingerprints can be used to identify individuals, which is of great value in plant breeding. DNA fingerprint databases are essential and important tools for plant molecular research because they provide powerful technical and information support for crop breeding, variety quality control, variety right protection, and molecular marker-assisted breeding. Building a DNA fingerprint database involves the production of large amounts of heterogeneous data for which storage, analysis, and retrieval are time and resource consuming. To process the large amounts of data generated by laboratories and conduct quality control, a database management system is urgently needed to track samples and analyze data. We developed the plant international DNA-fingerprinting system (PIDS) using an open source web server and free software that has automatic collection, storage, and efficient management functions based on merging and comparison algorithms to handle massive microsatellite DNA fingerprint data. PIDS also can perform genetic analyses. This system can match a corresponding capillary electrophoresis image on each primer locus as fingerprint data to upload to the server. PIDS provides free customization and extension of back-end functions to meet the requirements of different laboratories. This system can be a significant tool for plant breeders and can be applied in forensic science for human fingerprint identification, as well as in virus and microorganism research.
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19
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Guo L, Yang Q, Yang JW, Zhang N, Liu BS, Zhu KC, Guo HY, Jiang SG, Zhang DC. MultiplexSSR: A pipeline for developing multiplex SSR-PCR assays from resequencing data. Ecol Evol 2020; 10:3055-3067. [PMID: 32211176 PMCID: PMC7083706 DOI: 10.1002/ece3.6121] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 02/02/2020] [Accepted: 02/05/2020] [Indexed: 12/15/2022] Open
Abstract
Next-generation sequencing has greatly promoted the investigation of single nucleotide polymorphisms, while studies of simple sequence repeats are sharply decreasing. However, simple sequence repeats still present some advantages in conservation genetics. In this study, an end-to-end pipeline referred to as MultiplexSSR was established to develop multiplex PCR assays in batches with highly polymorphic simple sequence repeats for capillary platforms from resequencing data. The distribution of single sequence repeats in the genome, the error profiles of genotypes and allelotypes, and the increase in the allele length range depending on the number of individuals were investigated. A total of 98% of single sequence repeats presented lengths of less than 100 bp. The error rate of the genotyping and allelotyping of dimeric patterns was ten times higher than those for other patterns. The error rate of allelotyping was less than that of genotyping. The allele length range reached approximate saturation with 10 individuals. This pipeline uses allele numbers to select highly polymorphic loci, masks loci with variation, and applies in silico PCR to improve primer specificity. The application of the developed multiplex SSR-PCR assays validated the pipeline's robustness, showing higher polymorphism and stability for the developed simple sequence repeats and a lower cost for genotyping and providing low-depth resequencing data from less than a dozen individuals for the development of markers. This pipeline fills the gap between next-generation sequencing and multiplex SSR-PCR.
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Affiliation(s)
- Liang Guo
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization Ministry of Agriculture and Rural Affairs South China Sea Fisheries Research Institute Chinese Academy of Fishery Sciences Guangzhou China
- Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry Guangzhou China
| | - Quan Yang
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization Ministry of Agriculture and Rural Affairs South China Sea Fisheries Research Institute Chinese Academy of Fishery Sciences Guangzhou China
- Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry Guangzhou China
- National Demonstration Center for Experimental Fisheries Science Education Shanghai Ocean University Shanghai China
| | - Jing-Wen Yang
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization Ministry of Agriculture and Rural Affairs South China Sea Fisheries Research Institute Chinese Academy of Fishery Sciences Guangzhou China
- Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry Guangzhou China
| | - Nan Zhang
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization Ministry of Agriculture and Rural Affairs South China Sea Fisheries Research Institute Chinese Academy of Fishery Sciences Guangzhou China
- Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry Guangzhou China
| | - Bao-Suo Liu
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization Ministry of Agriculture and Rural Affairs South China Sea Fisheries Research Institute Chinese Academy of Fishery Sciences Guangzhou China
- Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry Guangzhou China
| | - Ke-Cheng Zhu
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization Ministry of Agriculture and Rural Affairs South China Sea Fisheries Research Institute Chinese Academy of Fishery Sciences Guangzhou China
- Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry Guangzhou China
| | - Hua-Yang Guo
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization Ministry of Agriculture and Rural Affairs South China Sea Fisheries Research Institute Chinese Academy of Fishery Sciences Guangzhou China
- Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry Guangzhou China
| | - Shi-Gui Jiang
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization Ministry of Agriculture and Rural Affairs South China Sea Fisheries Research Institute Chinese Academy of Fishery Sciences Guangzhou China
- Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry Guangzhou China
| | - Dian-Chang Zhang
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization Ministry of Agriculture and Rural Affairs South China Sea Fisheries Research Institute Chinese Academy of Fishery Sciences Guangzhou China
- Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry Guangzhou China
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Du H, Yang J, Chen B, Zhang X, Zhang J, Yang K, Geng S, Wen C. Target sequencing reveals genetic diversity, population structure, core-SNP markers, and fruit shape-associated loci in pepper varieties. BMC PLANT BIOLOGY 2019; 19:578. [PMID: 31870303 PMCID: PMC6929450 DOI: 10.1186/s12870-019-2122-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 11/07/2019] [Indexed: 05/24/2023]
Abstract
BACKGROUND The widely cultivated pepper (Capsicum spp.) is one of the most diverse vegetables; however, little research has focused on characterizing the genetic diversity and relatedness of commercial varieties grown in China. In this study, a panel of 92 perfect single-nucleotide polymorphisms (SNPs) was identified using re-sequencing data from 35 different C. annuum lines. Based on this panel, a Target SNP-seq genotyping method was designed, which combined multiplex amplification of perfect SNPs with Illumina sequencing, to detect polymorphisms across 271 commercial pepper varieties. RESULTS The perfect SNPs panel had a high discriminating capacity due to the average value of polymorphism information content, observed heterozygosity, expected heterozygosity, and minor allele frequency, which were 0.31, 0.28, 0.4, and 0.31, respectively. Notably, the studied pepper varieties were morphologically categorized based on fruit shape as blocky-, long horn-, short horn-, and linear-fruited. The long horn-fruited population exhibited the most genetic diversity followed by the short horn-, linear-, and blocky-fruited populations. A set of 35 core SNPs were then used as kompetitive allele-specific PCR (KASPar) markers, another robust genotyping technique for variety identification. Analysis of genetic relatedness using principal component analysis and phylogenetic tree construction indicated that the four fruit shape populations clustered separately with limited overlaps. Based on STRUCTURE clustering, it was possible to divide the varieties into five subpopulations, which correlated with fruit shape. Further, the subpopulations were statistically different according to a randomization test and Fst statistics. Nine loci, located on chromosomes 1, 2, 3, 4, 6, and 12, were identified to be significantly associated with the fruit shape index (p < 0.0001). CONCLUSIONS Target SNP-seq developed in this study appears as an efficient power tool to detect the genetic diversity, population relatedness and molecular breeding in pepper. Moreover, this study demonstrates that the genetic structure of Chinese pepper varieties is significantly influenced by breeding programs focused on fruit shape.
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Affiliation(s)
- Heshan Du
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agricultural and Forestry Sciences, Beijing, 100097, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, National Engineering Research Center for Vegetables, Beijing, 100097, China
| | - Jingjing Yang
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agricultural and Forestry Sciences, Beijing, 100097, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, National Engineering Research Center for Vegetables, Beijing, 100097, China
| | - Bin Chen
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agricultural and Forestry Sciences, Beijing, 100097, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, National Engineering Research Center for Vegetables, Beijing, 100097, China
| | - Xiaofen Zhang
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agricultural and Forestry Sciences, Beijing, 100097, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, National Engineering Research Center for Vegetables, Beijing, 100097, China
| | - Jian Zhang
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agricultural and Forestry Sciences, Beijing, 100097, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, National Engineering Research Center for Vegetables, Beijing, 100097, China
| | - Kun Yang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Sansheng Geng
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agricultural and Forestry Sciences, Beijing, 100097, China.
- Beijing Key Laboratory of Vegetable Germplasm Improvement, National Engineering Research Center for Vegetables, Beijing, 100097, China.
| | - Changlong Wen
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agricultural and Forestry Sciences, Beijing, 100097, China.
- Beijing Key Laboratory of Vegetable Germplasm Improvement, National Engineering Research Center for Vegetables, Beijing, 100097, China.
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Application of high-throughput amplicon sequencing-based SSR genotyping in genetic background screening. BMC Genomics 2019; 20:444. [PMID: 31159719 PMCID: PMC6547574 DOI: 10.1186/s12864-019-5800-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 05/14/2019] [Indexed: 12/05/2022] Open
Abstract
Background Host genetic backgrounds affect gene functions. The genetic backgrounds of genetically engineered organisms must be identified to confirm their genetic backgrounds identity with those of recipients. Marker-assisted backcrossing (MAB), transgenesis and clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (CRISPR/Cas9) editing are three commonly used genetic engineering techniques. However, methods for genetic background screening between genetically engineered organisms and corresponding recipients suffer from low efficiency, low accuracy or high cost. Results Here, we improved our previously reported AmpSeq-SSR method, an amplicon sequencing-based simple sequence repeat (SSR) genotyping method, by selecting SSR loci with high polymorphism among varieties. Ultimately, a set of 396 SSRs was generated and applied to evaluate the genetic backgrounds identity between rice lines developed through MAB, transgenesis, and CRISPR/Cas9 editing and the respective recipient rice. We discovered that the percentage of different SSRs between the MAB-developed rice line and its recipient was as high as 23.5%. In contrast, only 0.8% of SSRs were different between the CRISPR/Cas9-system-mediated rice line and its recipient, while no SSRs showed different genotypes between the transgenic rice line and its recipient. Furthermore, most differential SSRs induced by MAB technology were located in non-coding regions (62.9%), followed by untranslated regions (21.0%) and coding regions (16.1%). Trinucleotide repeats were the most prevalent type of altered SSR. Most importantly, all altered SSRs located in coding regions were trinucleotide repeats. Conclusions This method is not only useful for the background evaluation of genetic resources but also expands our understanding of the unintended effects of different genetic engineering techniques. While the work we present focused on rice, this method can be readily extended to other organisms. Electronic supplementary material The online version of this article (10.1186/s12864-019-5800-4) contains supplementary material, which is available to authorized users.
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Yang J, Zhang J, Han R, Zhang F, Mao A, Luo J, Dong B, Liu H, Tang H, Zhang J, Wen C. Target SSR-Seq: A Novel SSR Genotyping Technology Associate With Perfect SSRs in Genetic Analysis of Cucumber Varieties. FRONTIERS IN PLANT SCIENCE 2019; 10:531. [PMID: 31105728 PMCID: PMC6492046 DOI: 10.3389/fpls.2019.00531] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2019] [Accepted: 04/05/2019] [Indexed: 05/03/2023]
Abstract
Simple sequence repeats (SSR) - also known as microsatellites - have been used extensively in genetic analysis, fine mapping, quantitative trait locus (QTL) mapping, as well as marker-assisted selection (MAS) breeding and other techniques. Despite a plethora of studies reporting that perfect SSRs with stable motifs and flanking sequences are more efficient for genetic research, the lack of a high throughput technology for SSR genotyping has limited their use as genetic targets in many crops. In this study, we developed a technology called Target SSR-seq that combined the multiplexed amplification of perfect SSRs with high throughput sequencing. This method can genotype plenty of SSR loci in hundreds of samples with highly accurate results, due to the substantial coverage afforded by high throughput sequencing. We also detected 844 perfect SSRs based on 182 resequencing datasets in cucumber, of which 91 SSRs were selected for Target SSR-seq. Finally, 122 SSRs, including 31 SSRs for varieties identification, were used to genotype 382 key cucumber varieties readily available in Chinese markets using our Target SSR-seq method. Libraries of PCR products were constructed and then sequenced on the Illumina HiSeq X Ten platform. Bioinformatics analysis revealed that 111 filtered SSRs were accurately genotyped with an average coverage of 1289× at an extremely low cost; furthermore, 398 alleles were observed in 382 cucumber cultivars. Genetic analysis identified four populations: northern China type, southern China type, European type, and Xishuangbanna type. Moreover, we acquired a set of 16 core SSRs for the identification of 382 cucumber varieties, of which 42 were isolated as backbone cucumber varieties. This study demonstrated that Target SSR-seq is a novel and efficient method for genetic research.
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Affiliation(s)
- Jingjing Yang
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agricultural and Forestry Sciences, National Engineering Research Center for Vegetables, Beijing, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, China
| | - Jian Zhang
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agricultural and Forestry Sciences, National Engineering Research Center for Vegetables, Beijing, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, China
| | - Ruixi Han
- Development Center of Science and Technology, Ministry of Agriculture and Rural Affairs of the People’s Republic of China, Beijing, China
| | - Feng Zhang
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agricultural and Forestry Sciences, National Engineering Research Center for Vegetables, Beijing, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, China
| | - Aijun Mao
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agricultural and Forestry Sciences, National Engineering Research Center for Vegetables, Beijing, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, China
| | - Jiang Luo
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agricultural and Forestry Sciences, National Engineering Research Center for Vegetables, Beijing, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, China
| | - Bobo Dong
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agricultural and Forestry Sciences, National Engineering Research Center for Vegetables, Beijing, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, China
| | - Hui Liu
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agricultural and Forestry Sciences, National Engineering Research Center for Vegetables, Beijing, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, China
| | - Hao Tang
- Development Center of Science and Technology, Ministry of Agriculture and Rural Affairs of the People’s Republic of China, Beijing, China
| | - Jianan Zhang
- Molbreeding Biotechnology Company, Shijiazhuang, China
| | - Changlong Wen
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agricultural and Forestry Sciences, National Engineering Research Center for Vegetables, Beijing, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, China
- *Correspondence: Changlong Wen,
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Gao L, Fang Z, Zhou J, Li L, Lu L, Li L, Li T, Chen L, Zhang W, Zhai W, Peng H. Transcriptional insights into the pyramided resistance to rice bacterial blight. Sci Rep 2018; 8:12358. [PMID: 30120263 PMCID: PMC6098014 DOI: 10.1038/s41598-018-29899-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 07/16/2018] [Indexed: 11/30/2022] Open
Abstract
The pyramiding of resistance (R) genes provides broad-spectrum and durable resistance to plant diseases. However, the genetic basis for bacterial blight (BB) resistance remains unclear. The BB R gene pyramided line IRBB54, which expresses xa5 and Xa21, possessed a higher level of resistance than both single R gene lines. Large-scale genotyping of genetic markers in this study revealed similar genetic backgrounds among the near-isogenic lines (NILs), suggesting that resistance in the resistant NILs was mainly conferred by the individual R genes or the interaction between them. Transcriptome analysis demonstrated that more than 50% of the differentially expressed genes (DEGs), and more than 70% of the differentially expressed functions, were shared between IRBB54 and IRBB5 or IRBB21. Most of the DEGs in the resistant NILs were downregulated and are predicted to function in cellular and biological process. The DEGs common among the resistant NILs mainly showed non-additive expression patterns and enrichment in stress-related pathways. The differential expression of agronomic trait-controlled genes in the resistant NILs, especially in IRBB54, indicated the existence of potential side-effects resulting from gene pyramiding. Our findings contribute to the understanding of R gene pyramiding, as well as its effects on targeted and non-targeted trait(s).
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Affiliation(s)
- Lifen Gao
- Institute for Systems Biology, Jianghan University, Wuhan, Hubei, 430056, China
| | - Zhiwei Fang
- Institute for Systems Biology, Jianghan University, Wuhan, Hubei, 430056, China
| | - Junfei Zhou
- Institute for Systems Biology, Jianghan University, Wuhan, Hubei, 430056, China
| | - Lun Li
- Institute for Systems Biology, Jianghan University, Wuhan, Hubei, 430056, China
| | - Long Lu
- Institute for Systems Biology, Jianghan University, Wuhan, Hubei, 430056, China
| | - Lili Li
- Institute for Systems Biology, Jianghan University, Wuhan, Hubei, 430056, China
| | - Tiantian Li
- Institute for Systems Biology, Jianghan University, Wuhan, Hubei, 430056, China
| | - Lihong Chen
- Institute for Systems Biology, Jianghan University, Wuhan, Hubei, 430056, China
| | - Weixiong Zhang
- Institute for Systems Biology, Jianghan University, Wuhan, Hubei, 430056, China
| | - Wenxue Zhai
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Hai Peng
- Institute for Systems Biology, Jianghan University, Wuhan, Hubei, 430056, China.
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24
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Bagshaw AT. Functional Mechanisms of Microsatellite DNA in Eukaryotic Genomes. Genome Biol Evol 2017; 9:2428-2443. [PMID: 28957459 PMCID: PMC5622345 DOI: 10.1093/gbe/evx164] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/23/2017] [Indexed: 02/06/2023] Open
Abstract
Microsatellite repeat DNA is best known for its length mutability, which is implicated in several neurological diseases and cancers, and often exploited as a genetic marker. Less well-known is the body of work exploring the widespread and surprisingly diverse functional roles of microsatellites. Recently, emerging evidence includes the finding that normal microsatellite polymorphism contributes substantially to the heritability of human gene expression on a genome-wide scale, calling attention to the task of elucidating the mechanisms involved. At present, these are underexplored, but several themes have emerged. I review evidence demonstrating roles for microsatellites in modulation of transcription factor binding, spacing between promoter elements, enhancers, cytosine methylation, alternative splicing, mRNA stability, selection of transcription start and termination sites, unusual structural conformations, nucleosome positioning and modification, higher order chromatin structure, noncoding RNA, and meiotic recombination hot spots.
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