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Linkage‐linkage disequilibrium dissection of the epigenetic quantitative trait loci (epiQTLs) underlying growth and wood properties in Populus
Author(s) -
Lu Wenjie,
Xiao Liang,
Quan Mingyang,
Wang Qingshi,
ElKassaby Yousry A.,
Du Qingzhang,
Zhang Deqiang
Publication year - 2020
Publication title -
new phytologist
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.742
H-Index - 244
eISSN - 1469-8137
pISSN - 0028-646X
DOI - 10.1111/nph.16220
Subject(s) - epigenetics , biology , genetics , quantitative trait locus , linkage disequilibrium , dna methylation , population , genetic architecture , phenotype , gene , genetic linkage , association mapping , methylation , single nucleotide polymorphism , evolutionary biology , gene expression , genotype , demography , sociology
Increasing evidence indicates that DNA methylation is heritable and serves as an essential marker contributing to phenotypic variation. Linkage‐linkage disequilibrium mapping was used to decipher the epigenetic architecture underlying nine growth and wood property traits in a linkage population (550 F 1 progeny) and a natural population (435 unrelated individuals) of Populus using methylation‐sensitive amplification polymorphism (MSAP)‐based analysis. The interactions between genetic and epigenetic variants in the causative genes was further unveiled using expression quantitative trait methylation (eQTM) and nucleotide (eQTN) mapping strategies. A total of 163 epigenetic quantitative trait loci (epiQTLs; LOD ≥ 3.0), explaining 1.7–44.5% of phenotypic variations, were mapped to a high‐resolution epigenetic map with 19 linkage groups, which was supported by the significant MSAP associations ( P < 0.001) in the two populations. There were 23 causal genes involved in growth regulation and wood formation, whose markers were located in epiQTLs and associated with the same traits in both populations. Further eQTN and eQTM mapping showed that causal genetic and epigenetic variants within the 23 candidate genes may interact more in trans in gene expression and phenotype. The present study provides strategies for investigating epigenetic architecture and the interaction between genetic and epigenetic variants modulating complex traits in forest trees.