Linkage‐linkage disequilibrium dissection of the epigenetic quantitative trait loci (epiQTLs) underlying growth and wood properties in Populus

Abstract

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 F1 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.

Climate sensitivity of Cryptomeria japonica in two contrasting environments: Perspectives from QTL mapping

“…This includes research on life history stages, climate (i.e., experiments covering wider geographical locations), and other environmental conditions (e.g., soil conditions; [67]). The epigenetic effects on genotypes might also be important for the growth response observed in the present study [68,69]. Additionally, because our study was conducted using local varieties from the Kyushu region, additional studies capturing wider genetic variation (e.g., populations from natural forests) with different approaches-such as genome-wide association study (GWAS)-are necessary to generalize the findings of this study.…”

Genome-Wide Association Study of Wood Anatomical and Morphological Traits in Populus trichocarpa

“…We compared our GWAS results with previous GWAS studies for similar traits in P. trichocarpa (Wegrzyn et al, 2010;Porth et al, 2013a;Porth et al, 2013b;Evans et al, 2014;McKown et al, 2014b;Chhetri et al, 2019) and other Populus species including P. deltoides (Fahrenkrog et al, 2017), P. euphratica (Ma et al, 2013;Jia et al, 2020) and P. tomentosa (Quan et al, 2016;Chen B. et al, 2018;Quan et al, 2019;Lu et al, 2020). We found very minimal overlap in the genes and/or gene families detected.…”

“…Jia et al (2020) identified 82 genes related to seed salinity tolerance in P. euphratica, including a zinc finger protein similar to one that we detected for leaf abaxial density that regulates gas exchange in plants. Lu et al (2020) identified 23 genes involved in three growth and six wood property traits and Quan et al (2019) identified 203 lignin biosynthetic genes, 81 TF genes, 36 microRNAs and 71 long non-coding RNA genes for 10 growth and wood property traits in the same P. tomentosa population. However, these studies have no apparent overlap in gene functions for similar morphology or wood property traits in our study.…”

Quantitative Epigenetics: A New Avenue for Crop Improvement

“…To overcome limitations, integrated genetic mapping by combining linkage and linkage-disequilibrium is recommended. Recently, an integrated linkage and linkage-disequilibrium mapping was conducted for the identification of epiQTLs in plants [89]. Using 550 F1s and 435 natural germplasm accessions a huge number of epiQTLs (163 epiQTLs) were found to be associated with growth and wood properties in Populus.…”

“…Using 550 F1s and 435 natural germplasm accessions a huge number of epiQTLs (163 epiQTLs) were found to be associated with growth and wood properties in Populus. Further, 23 causal genes present within epiQTL regions showed cause and effect relationship as revealed by the coregulation of eQTN (expression quantitative trait nucleotide) and eQTM (expression quantitative trait methylation) [89].…”