دورية أكاديمية
haploMAGIC: accurate phasing and detection of recombination in multiparental populations despite genotyping errors.
| العنوان: | haploMAGIC: accurate phasing and detection of recombination in multiparental populations despite genotyping errors. |
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| المؤلفون: | Montero-Tena JA; Department of Agrobioinformatics, IFZ Research Center for Biosystems, Land Use and Nutrition, Justus Liebig University, Heinrich Buff Ring 26, 35392 Giessen, Germany., Abdollahi Sisi N; Department of Plant Breeding, IFZ Research Center for Biosystems, Land Use and Nutrition, Justus Liebig University, Heinrich Buff Ring 26, 35392 Giessen, Germany., Kox T; NPZ Innovation GmbH, Hohenlieth-Hof, 24363 Holtsee, Germany., Abbadi A; NPZ Innovation GmbH, Hohenlieth-Hof, 24363 Holtsee, Germany., Snowdon RJ; Department of Plant Breeding, IFZ Research Center for Biosystems, Land Use and Nutrition, Justus Liebig University, Heinrich Buff Ring 26, 35392 Giessen, Germany., Golicz AA; Department of Agrobioinformatics, IFZ Research Center for Biosystems, Land Use and Nutrition, Justus Liebig University, Heinrich Buff Ring 26, 35392 Giessen, Germany. |
| المصدر: | G3 (Bethesda, Md.) [G3 (Bethesda)] 2024 Aug 07; Vol. 14 (8). |
| نوع المنشور: | Journal Article |
| اللغة: | English |
| بيانات الدورية: | Publisher: Oxford University Press Country of Publication: England NLM ID: 101566598 Publication Model: Print Cited Medium: Internet ISSN: 2160-1836 (Electronic) Linking ISSN: 21601836 NLM ISO Abbreviation: G3 (Bethesda) Subsets: MEDLINE |
| أسماء مطبوعة: | Publication: 2021- : [Oxford] : Oxford University Press Original Publication: Bethesda, MD : Genetics Society of America, 2011- |
| مواضيع طبية MeSH: | Recombination, Genetic* , Polymorphism, Single Nucleotide* , Genotyping Techniques*/methods , Haplotypes*, Brassica napus/genetics ; Software ; Genotype ; Genome, Plant ; Crossing Over, Genetic |
| مستخلص: | Recombination is a key mechanism in breeding for promoting genetic variability. Multiparental populations (MPPs) constitute an excellent platform for precise genotype phasing, identification of genome-wide crossovers (COs), estimation of recombination frequencies, and construction of recombination maps. Here, we introduce haploMAGIC, a pipeline to detect COs in MPPs with single-nucleotide polymorphism (SNP) data by exploiting the pedigree relationships for accurate genotype phasing and inference of grandparental haplotypes. haploMAGIC applies filtering to prevent false-positive COs due to genotyping errors (GEs), a common problem in high-throughput SNP analysis of complex plant genomes. Hence, it discards haploblocks not reaching a specified minimum number of informative alleles. A performance analysis using populations simulated with AlphaSimR revealed that haploMAGIC improves upon existing methods of CO detection in terms of recall and precision, most notably when GE rates are high. Furthermore, we constructed recombination maps using haploMAGIC with high-resolution genotype data from 2 large multiparental populations of winter rapeseed (Brassica napus). The results demonstrate the applicability of the pipeline in real-world scenarios and showed good correlations in recombination frequency compared with alternative software. Therefore, we propose haploMAGIC as an accurate tool at CO detection with MPPs that shows robustness against GEs. Competing Interests: Conflicts of interest The author(s) declare no conflict of interest. (© The Author(s) 2024. Published by Oxford University Press on behalf of The Genetics Society of America.) |
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| معلومات مُعتمدة: | German Research Foundation |
| فهرسة مساهمة: | Keywords: MPP; Multiparent Advanced Generation Inter-Cross (MAGIC); Multiparental Populations; genotyping; oilseed rape; recombination |
| تواريخ الأحداث: | Date Created: 20240529 Date Completed: 20240807 Latest Revision: 20240809 |
| رمز التحديث: | 20240809 |
| مُعرف محوري في PubMed: | PMC11304941 |
| DOI: | 10.1093/g3journal/jkae109 |
| PMID: | 38808682 |
| قاعدة البيانات: | MEDLINE |
Full Text Finder | تدمد: | 2160-1836 |
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| DOI: | 10.1093/g3journal/jkae109 |