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Inferring the Genomic Landscape of Recombination Rate Variation in European Aspen (Populus tremula)
Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC). Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap.
Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC). Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik.ORCID-id: 0000-0002-9771-467x
Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysiologisk botanik. Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Umeå Plant Science Centre (UPSC).ORCID-id: 0000-0002-5249-604X
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2020 (engelsk)Inngår i: G3: Genes, Genomes, Genetics, ISSN 2160-1836, E-ISSN 2160-1836, Vol. 10, nr 1, s. 299-309Artikkel i tidsskrift (Fagfellevurdert) Published
Abstract [en]

The rate of meiotic recombination is one of the central factors determining genome-wide levels of linkage disequilibrium which has important consequences for the efficiency of natural selection and for the dissection of quantitative traits. Here we present a new, high-resolution linkage map for Populus tremula that we use to anchor approximately two thirds of the P. tremula draft genome assembly on to the expected 19 chromosomes, providing us with the first chromosome-scale assembly for P. tremula (Table 2). We then use this resource to estimate variation in recombination rates across the P. tremula genome and compare these results to recombination rates based on linkage disequilibrium in a large number of unrelated individuals. We also assess how variation in recombination rates is associated with a number of genomic features, such as gene density, repeat density and methylation levels. We find that recombination rates obtained from the two methods largely agree, although the LD-based method identifies a number of genomic regions with very high recombination rates that the map-based method fails to detect. Linkage map and LD-based estimates of recombination rates are positively correlated and show similar correlations with other genomic features, showing that both methods can accurately infer recombination rate variation across the genome. Recombination rates are positively correlated with gene density and negatively correlated with repeat density and methylation levels, suggesting that recombination is largely directed toward gene regions in P. tremula.

sted, utgiver, år, opplag, sider
GENETICS SOCIETY AMERICA , 2020. Vol. 10, nr 1, s. 299-309
Emneord [en]
linkage disequilibrium, linkage map, linked selection, methylation, nucleotide diversity, recombination
HSV kategori
Identifikatorer
URN: urn:nbn:se:umu:diva-167954DOI: 10.1534/g3.119.400504ISI: 000506031000027PubMedID: 31744900OAI: oai:DiVA.org:umu-167954DiVA, id: diva2:1396266
Tilgjengelig fra: 2020-02-25 Laget: 2020-02-25 Sist oppdatert: 2020-02-25bibliografisk kontrollert

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Bernhardsson, CarolinaSchiffthaler, BastianRobinson, Kathryn MJansson, StefanStreet, NathanielIngvarsson, Pär K.
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