Genomic Rearrangements Considered as Quantitative Traits
Genomic Rearrangements Considered as Quantitative Traits
Abstract To understand the population genetics of structural variants (SVs), and their effects on phenotypes, we developed an approach to mapping SVs, particularly transpositions, segregating in a sequenced population, and which avoids calling SVs directly. The evidence for a potential SV at a locus is indicated by variation in the counts of short-reads that map anomalously to the locus. These SV traits are treated as quantitative traits and mapped genetically, analogously to a gene expression study. Association between an SV trait at one locus and genotypes at a distant locus indicate the origin and target of a transposition. Using ultra-low-coverage (0.3x) population sequence data from 488 recombinant inbred Arabidopsis genomes, we identified 6,502 segregating SVs. Remarkably, 25% of these were transpositions. Whilst many SVs cannot be delineated precisely, PCR validated 83% of 44 predicted transposition breakpoints. We show that specific SVs may be causative for quantitative trait loci for germination, fungal disease resistance and other phenotypes. Further we show that the phenotypic heritability attributable to sequence anomalies differs from, and in the case of time to germination and bolting, exceeds that due to standard genetic variation. Gene expression within SVs is also more likely to be silenced or dysregulated. This approach is generally applicable to large populations sequenced at low-coverage, and complements the prevalent strategy of SV discovery in fewer individuals sequenced at high coverage.
Osborne Edward J.、Gan Xiangchao、Bhomra Amarjit、Belfield Eric、Jones Jonathan、Kover Paula、Mott Richard、Nordborg Magnus、Kahles Andr¨|、Harberd Nicholas P、Imprialou Martha、Goram Richard、R?tsch Gunnar、Stegle Oliver、Greenhalgh Robert、Lempe Janne、Tsiantis Miltos、Robert-Seilaniantz Alexandre、Visscher Anne、Hein Jotun、Steffen Joshua G.、Clark Richard M.
Department of Biology, University of Utah, Salt Lake CityMax Planck Institute for Plant Breeding ResearchWellcome Trust Centre for Human Genetics, University of OxfordDepartment of Plant Sciences, University of OxfordThe Sainsbury Laboratory, Norwich Research ParkDept of Biology and Biochemistry, University of BathWellcome Trust Centre for Human Genetics, University of Oxford||UCL Genetics Institute, University College LondonGregor Mendel Institute of Molecular Plant BiologyMemorial Sloan-Kettering Cancer CenterDepartment of Plant Sciences, University of OxfordWellcome Trust Centre for Human Genetics, University of OxfordJohn Innes CentreMemorial Sloan-Kettering Cancer CenterEuropean Bioinformatics InstituteDepartment of Biology, University of Utah, Salt Lake CityMax Planck Institute for Plant Breeding ResearchMax Planck Institute for Plant Breeding ResearchUMR INRA-Agrocampus Ouest-Universit¨| de Rennes 1Department of Plant Sciences, University of Oxford||Department of Comparative Plant and Fungal Biology, Royal Botanic Gardens KewDepartment of Statistics, University of OxfordDepartment of Biology, University of Utah, Salt Lake CityDepartment of Biology, University of Utah, Salt Lake City||Center for Cell and Genome Science, University of Utah
遗传学植物学生物科学研究方法、生物科学研究技术
Osborne Edward J.,Gan Xiangchao,Bhomra Amarjit,Belfield Eric,Jones Jonathan,Kover Paula,Mott Richard,Nordborg Magnus,Kahles Andr¨|,Harberd Nicholas P,Imprialou Martha,Goram Richard,R?tsch Gunnar,Stegle Oliver,Greenhalgh Robert,Lempe Janne,Tsiantis Miltos,Robert-Seilaniantz Alexandre,Visscher Anne,Hein Jotun,Steffen Joshua G.,Clark Richard M..Genomic Rearrangements Considered as Quantitative Traits[EB/OL].(2025-03-28)[2025-07-22].https://www.biorxiv.org/content/10.1101/087387.点此复制
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