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Martínez-Guardiola C, Parreño R, Candela H. MAPtools: command-line tools for mapping-by-sequencing and QTL-Seq analysis and visualization. PLANT METHODS 2024; 20:107. [PMID: 39014443 PMCID: PMC11253474 DOI: 10.1186/s13007-024-01222-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Accepted: 06/10/2024] [Indexed: 07/18/2024]
Abstract
BACKGROUND Classical mutagenesis is a powerful tool that has allowed researchers to elucidate the molecular and genetic basis of a plethora of processes in many model species. The integration of these methods with modern massively parallel sequencing techniques, initially in model species but currently also in many crop species, is accelerating the identification of genes underlying a wide range of traits of agronomic interest. RESULTS We have developed MAPtools, an open-source Python3 application designed specifically for the analysis of genomic data from bulked segregant analysis experiments, including mapping-by-sequencing (MBS) and quantitative trait locus sequencing (QTL-seq) experiments. We have extensively tested MAPtools using datasets published in recent literature. CONCLUSIONS MAPtools gives users the flexibility to customize their bioinformatics pipeline with various commands for calculating allele count-based statistics, generating plots to pinpoint candidate regions, and annotating the effects of SNP and indel mutations. While extensively tested with plants, the program is versatile and applicable to any species for which a mapping population can be generated and a sequenced genome is available. AVAILABILITY AND IMPLEMENTATION MAPtools is available under GPL v3.0 license and documented as a Python3 package at https://github.com/hcandela/MAPtools .
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Affiliation(s)
- César Martínez-Guardiola
- Instituto de Bioingeniería, Universidad Miguel Hernández de Elche, Campus de Elche, Elche, 03202, Spain
| | - Ricardo Parreño
- Instituto de Bioingeniería, Universidad Miguel Hernández de Elche, Campus de Elche, Elche, 03202, Spain
| | - Héctor Candela
- Instituto de Bioingeniería, Universidad Miguel Hernández de Elche, Campus de Elche, Elche, 03202, Spain.
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Li X, Kumar S, Brenneman KV, Anderson TJC. Bulk segregant linkage mapping for rodent and human malaria parasites. Parasitol Int 2022; 91:102653. [PMID: 36007706 DOI: 10.1016/j.parint.2022.102653] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 08/18/2022] [Accepted: 08/19/2022] [Indexed: 11/25/2022]
Abstract
In 2005 Richard Carter's group surprised the malaria genetics community with an elegant approach to rapidly mapping the genetic basis of phenotypic traits in rodent malaria parasites. This approach, which he termed "linkage group selection", utilized bulk pools of progeny, rather than individual clones, and exploited simple selection schemes to identify genome regions underlying resistance to drug treatment (or other phenotypes). This work was the first application of "bulk segregant" methodologies for genetic mapping in microbes: this approach is now widely used in yeast, and across multiple recombining pathogens ranging from Aspergillus fungi to Schistosome parasites. Genetic crosses of human malaria parasites (for which Richard Carter was also a pioneer) can now be conducted in humanized mice, providing new opportunities for exploiting bulk segregant approaches for a wide variety of malaria parasite traits. We review the application of bulk segregant approaches to mapping malaria parasite traits and suggest additional developments that may further expand the utility of this powerful approach.
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Affiliation(s)
- Xue Li
- Program in Disease Intervention and Prevention, Texas Biomedical Research Institute, San Antonio, TX, USA.
| | - Sudhir Kumar
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Katelyn Vendrely Brenneman
- Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Tim J C Anderson
- Program in Disease Intervention and Prevention, Texas Biomedical Research Institute, San Antonio, TX, USA.
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Li Z, Xu Y. Bulk segregation analysis in the NGS era: a review of its teenage years. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 109:1355-1374. [PMID: 34931728 DOI: 10.1111/tpj.15646] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 11/27/2021] [Accepted: 12/14/2021] [Indexed: 06/14/2023]
Abstract
Bulk segregation analysis (BSA) utilizes a strategy of pooling individuals with extreme phenotypes to conduct economical and rapidly linked marker screening or quantitative trait locus (QTL) mapping. With the development of next-generation sequencing (NGS) technology in the past 10 years, BSA methods and technical systems have been gradually developed and improved. At the same time, the ever-decreasing costs of sequencing accelerate NGS-based BSA application in different species, including eukaryotic yeast, grain crops, economic crops, horticultural crops, trees, aquatic animals, and insects. This paper provides a landscape of BSA methods and reviews the BSA development process in the past decade, including the sequencing method for BSA, different populations, different mapping algorithms, associated region threshold determination, and factors affecting BSA mapping. Finally, we summarize related strategies in QTL fine mapping combining BSA.
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Affiliation(s)
- Zhiqiang Li
- Adsen Biotechnology Co., Ltd., Urumchi, 830022, China
| | - Yuhui Xu
- Adsen Biotechnology Co., Ltd., Urumchi, 830022, China
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Lup SD, Wilson-Sánchez D, Andreu-Sánchez S, Micol JL. Easymap: A User-Friendly Software Package for Rapid Mapping-by-Sequencing of Point Mutations and Large Insertions. FRONTIERS IN PLANT SCIENCE 2021; 12:655286. [PMID: 34040621 PMCID: PMC8143052 DOI: 10.3389/fpls.2021.655286] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 03/18/2021] [Indexed: 05/15/2023]
Abstract
Mapping-by-sequencing strategies combine next-generation sequencing (NGS) with classical linkage analysis, allowing rapid identification of the causal mutations of the phenotypes exhibited by mutants isolated in a genetic screen. Computer programs that analyze NGS data obtained from a mapping population of individuals derived from a mutant of interest to identify a causal mutation are available; however, the installation and usage of such programs requires bioinformatic skills, modifying or combining pieces of existing software, or purchasing licenses. To ease this process, we developed Easymap, an open-source program that simplifies the data analysis workflows from raw NGS reads to candidate mutations. Easymap can perform bulked segregant mapping of point mutations induced by ethyl methanesulfonate (EMS) with DNA-seq or RNA-seq datasets, as well as tagged-sequence mapping for large insertions, such as transposons or T-DNAs. The mapping analyses implemented in Easymap have been validated with experimental and simulated datasets from different plant and animal model species. Easymap was designed to be accessible to all users regardless of their bioinformatics skills by implementing a user-friendly graphical interface, a simple universal installation script, and detailed mapping reports, including informative images and complementary data for assessment of the mapping results. Easymap is available at http://genetics.edu.umh.es/resources/easymap; its Quickstart Installation Guide details the recommended procedure for installation.
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Zhang Z, Jung PP, Grouès V, May P, Linster C, Glaab E. BSA4Yeast: Web-based quantitative trait locus linkage analysis and bulk segregant analysis of yeast sequencing data. Gigascience 2019; 8:5505542. [PMID: 31141611 PMCID: PMC6571488 DOI: 10.1093/gigascience/giz060] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Revised: 02/15/2019] [Accepted: 04/30/2019] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Quantitative trait locus (QTL) mapping using bulk segregants is an effective approach for identifying genetic variants associated with phenotypes of interest in model organisms. By exploiting next-generation sequencing technology, the QTL mapping accuracy can be improved significantly, providing a valuable means to annotate new genetic variants. However, setting up a comprehensive analysis framework for this purpose is a time-consuming and error-prone task, posing many challenges for scientists with limited experience in this domain. RESULTS Here, we present BSA4Yeast, a comprehensive web application for QTL mapping via bulk segregant analysis of yeast sequencing data. The software provides an automated and efficiency-optimized data processing, up-to-date functional annotations, and an interactive web interface to explore identified QTLs. CONCLUSIONS BSA4Yeast enables researchers to identify plausible candidate genes in QTL regions efficiently in order to validate their genetic variations experimentally as causative for a phenotype of interest. BSA4Yeast is freely available at https://bsa4yeast.lcsb.uni.lu.
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Affiliation(s)
- Zhi Zhang
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 7 avenue des Hauts Fourneaux, L-4362 Esch-sur-Alzette, Luxembourg
| | - Paul P Jung
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 7 avenue des Hauts Fourneaux, L-4362 Esch-sur-Alzette, Luxembourg
| | - Valentin Grouès
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 7 avenue des Hauts Fourneaux, L-4362 Esch-sur-Alzette, Luxembourg
| | - Patrick May
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 7 avenue des Hauts Fourneaux, L-4362 Esch-sur-Alzette, Luxembourg
| | - Carole Linster
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 7 avenue des Hauts Fourneaux, L-4362 Esch-sur-Alzette, Luxembourg
| | - Enrico Glaab
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 7 avenue des Hauts Fourneaux, L-4362 Esch-sur-Alzette, Luxembourg
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Dougherty L, Singh R, Brown S, Dardick C, Xu K. Exploring DNA variant segregation types in pooled genome sequencing enables effective mapping of weeping trait in Malus. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:1499-1516. [PMID: 29361034 PMCID: PMC5888915 DOI: 10.1093/jxb/erx490] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Accepted: 12/19/2017] [Indexed: 05/19/2023]
Abstract
To unlock the power of next generation sequencing-based bulked segregant analysis in allele discovery in out-crossing woody species, and to understand the genetic control of the weeping trait, an F1 population from the cross 'Cheal's Weeping' × 'Evereste' was used to create two genomic DNA pools 'weeping' (17 progeny) and 'standard' (16 progeny). Illumina pair-end (2 × 151 bp) sequencing of the pools to a 27.1× (weeping) and a 30.4× (standard) genome (742.3 Mb) coverage allowed detection of 84562 DNA variants specific to 'weeping', 92148 specific to 'standard', and 173169 common to both pools. A detailed analysis of the DNA variant genotypes in the pools predicted three informative segregation types of variants: (type I) in weeping pool-specific variants, and (type II) and (type III) in variants common to both pools, where the first allele is assumed to be weeping linked and the allele shown in bold is a variant in relation to the reference genome. Conducting variant allele frequency and density-based mappings revealed four genomic regions with a significant association with weeping: a major locus, Weeping (W), on chromosome 13 and others on chromosomes 10 (W2), 16 (W3), and 5 (W4). The results from type I variants were noisier and less certain than those from type II and type III variants, demonstrating that although type I variants are often the first choice, type II and type III variants represent an important source of DNA variants that can be exploited for genetic mapping in out-crossing woody species. Confirmation of the mapping of W and W2, investigation into their genetic interactions, and identification of expressed genes in the W and W2 regions provided insight into the genetic control of weeping and its expressivity in Malus.
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Affiliation(s)
- Laura Dougherty
- Horticulture Section, School of Integrative Plant Science, Cornell University, USA
| | - Raksha Singh
- Horticulture Section, School of Integrative Plant Science, Cornell University, USA
| | - Susan Brown
- Horticulture Section, School of Integrative Plant Science, Cornell University, USA
| | | | - Kenong Xu
- Horticulture Section, School of Integrative Plant Science, Cornell University, USA
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Singh VK, Khan AW, Saxena RK, Sinha P, Kale SM, Parupalli S, Kumar V, Chitikineni A, Vechalapu S, Sameer Kumar CV, Sharma M, Ghanta A, Yamini KN, Muniswamy S, Varshney RK. Indel-seq: a fast-forward genetics approach for identification of trait-associated putative candidate genomic regions and its application in pigeonpea (Cajanus cajan). PLANT BIOTECHNOLOGY JOURNAL 2017; 15:906-914. [PMID: 28027425 PMCID: PMC5466435 DOI: 10.1111/pbi.12685] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Revised: 12/19/2016] [Accepted: 12/20/2016] [Indexed: 05/05/2023]
Abstract
Identification of candidate genomic regions associated with target traits using conventional mapping methods is challenging and time-consuming. In recent years, a number of single nucleotide polymorphism (SNP)-based mapping approaches have been developed and used for identification of candidate/putative genomic regions. However, in the majority of these studies, insertion-deletion (Indel) were largely ignored. For efficient use of Indels in mapping target traits, we propose Indel-seq approach, which is a combination of whole-genome resequencing (WGRS) and bulked segregant analysis (BSA) and relies on the Indel frequencies in extreme bulks. Deployment of Indel-seq approach for identification of candidate genomic regions associated with fusarium wilt (FW) and sterility mosaic disease (SMD) resistance in pigeonpea has identified 16 Indels affecting 26 putative candidate genes. Of these 26 affected putative candidate genes, 24 genes showed effect in the upstream/downstream of the genic region and two genes showed effect in the genes. Validation of these 16 candidate Indels in other FW- and SMD-resistant and FW- and SMD-susceptible genotypes revealed a significant association of five Indels (three for FW and two for SMD resistance). Comparative analysis of Indel-seq with other genetic mapping approaches highlighted the importance of the approach in identification of significant genomic regions associated with target traits. Therefore, the Indel-seq approach can be used for quick and precise identification of candidate genomic regions for any target traits in any crop species.
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Affiliation(s)
- Vikas K. Singh
- International Crops Research Institute for the Semi‐Arid TropicsPatancheruTelangana StateIndia
| | - Aamir W. Khan
- International Crops Research Institute for the Semi‐Arid TropicsPatancheruTelangana StateIndia
| | - Rachit K. Saxena
- International Crops Research Institute for the Semi‐Arid TropicsPatancheruTelangana StateIndia
| | - Pallavi Sinha
- International Crops Research Institute for the Semi‐Arid TropicsPatancheruTelangana StateIndia
| | - Sandip M. Kale
- International Crops Research Institute for the Semi‐Arid TropicsPatancheruTelangana StateIndia
| | - Swathi Parupalli
- International Crops Research Institute for the Semi‐Arid TropicsPatancheruTelangana StateIndia
| | - Vinay Kumar
- International Crops Research Institute for the Semi‐Arid TropicsPatancheruTelangana StateIndia
| | - Annapurna Chitikineni
- International Crops Research Institute for the Semi‐Arid TropicsPatancheruTelangana StateIndia
| | - Suryanarayana Vechalapu
- International Crops Research Institute for the Semi‐Arid TropicsPatancheruTelangana StateIndia
| | | | - Mamta Sharma
- International Crops Research Institute for the Semi‐Arid TropicsPatancheruTelangana StateIndia
| | - Anuradha Ghanta
- Agricultural Research Station (ARS)‐TandurProfessor Jayashankar Telangana State Agricultural University (PJTSAU)HyderabadTelangana StateIndia
| | - Kalinati Narasimhan Yamini
- Agricultural Research Station (ARS)‐TandurProfessor Jayashankar Telangana State Agricultural University (PJTSAU)HyderabadTelangana StateIndia
| | - Sonnappa Muniswamy
- Agricultural Research Station (ARS)‐GulbargaUniversity of Agricultural Sciences (UAS)RaichurKarnatakaIndia
| | - Rajeev K. Varshney
- International Crops Research Institute for the Semi‐Arid TropicsPatancheruTelangana StateIndia
- School of Plant Biology and Institute of AgricultureThe University of Western AustraliaCrawleyWAAustralia
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