Identification of additive, dominant, and epistatic variation conferred by key genes in cellulose biosynthesis pathway in Populus tomentosa

Abstract

Economically important traits in many species generally show polygenic, quantitative inheritance. The components of genetic variation (additive, dominant and epistatic effects) of these traits conferred by multiple genes in shared biological pathways remain to be defined. Here, we investigated 11 full-length genes in cellulose biosynthesis, on 10 growth and wood-property traits, within a population of 460 unrelated Populus tomentosa individuals, via multi-gene association. To validate positive associations, we conducted single-marker analysis in a linkage population of 1,200 individuals. We identified 118, 121, and 43 associations (P< 0.01) corresponding to additive, dominant, and epistatic effects, respectively, with low to moderate proportions of phenotypic variance (R2). Epistatic interaction models uncovered a combination of three non-synonymous sites from three unique genes, representing a significant epistasis for diameter at breast height and stem volume. Single-marker analysis validated 61 associations (false discovery rate, Q ≤ 0.10), representing 38 SNPs from nine genes, and its average effect (R2 = 3.8%) nearly 2-fold higher than that identified with multi-gene association, suggesting that multi-gene association can capture smaller individual variants. Moreover, a structural gene–gene network based on tissue-specific transcript abundances provides a better understanding of the multi-gene pathway affecting tree growth and lignocellulose biosynthesis. Our study highlights the importance of pathway-based multiple gene associations to uncover the nature of genetic variance for quantitative traits and may drive novel progress in molecular breeding.

Genetic architecture underlying the lignin biosynthesis pathway involves noncoding RNAs and transcription factors for growth and wood properties in Populus

“…Previously, substantial regulatory networks have been reported for wood formation in trees (Du et al ., ; Zhou et al ., ), and they dissected a well‐characterized pathway involves in a fraction of major genes, such as miR397a (Lu et al ., ) and the MYB gene family (Patzlaff et al ., ). Here, we dissected the multigene genetic network underlying lignin biosynthesis pathway includes lncRNAs, miRNAs and TFs, which provides a more comprehensive genetic networks for wood formation and captures the major loci in noncoding transcripts.…”

Genetic architecture of growth traits in Populus revealed by integrated quantitative trait locus (QTL) analysis and association studies

“…() and Du et al . (). Positive dominance is defined as occurring when the mean phenotypic value of the heterozygous class is higher than the value across both homozygous classes, based on least square means, whereas negative dominance is defined as occurring when the average value of the heterozygous class is lower (not a recessive lethal).…”

Estimation of number and size of QTL effects in forest tree traits

“…1a). An interesting and comparable real data example of these phenomena is the study of Du et al (2015) where significant markers from an association study on a population of Populus tomentosa with 460 individuals were validated in 1200 F1 individuals from a hybrid cross. Those markers that could be validated for the same trait in the F1 population showed on average 58% larger PVE in the F1 cross in comparison to the association mapping population.…”

“…Finally, it should be emphasized that a few studies included in this paper did try to reduce or correct for the issues originating from single locus analysis, such as the Beavis effect (Ma et al 2010) or bias due to LD (McKown et al 2014;Porth et al 2013) between significant markers (Peres-Neto et al 2006). Others used the recommended approach to validate and reestimate the effects in an independent population (Dillon et al 2012;Dillon et al 2010;Du et al 2015;Tian et al 2014) which also is a considerable improvement in this respect.…”