Time‐specific and pleiotropic quantitative trait loci coordinately modulate stem growth in Populus

Abstract

In perennial woody plants, the coordinated increase of stem height and diameter during juvenile growth improves competitiveness (i.e. access to light); however, the factors underlying variation in stem growth remain unknown in trees. Here, we used linkage-linkage disequilibrium (linkage-LD) mapping to decipher the genetic architecture underlying three growth traits during juvenile stem growth. We used two Populus populations: a linkage mapping population comprising a full-sib family of 1,200 progeny and an association mapping panel comprising 435 unrelated individuals from nearly the entire natural range of Populus tomentosa. We mapped 311 quantitative trait loci (QTL) for three growth traits at 12 timepoints to 42 regions in 17 linkage groups. Of these, 28 regions encompassing 233 QTL were annotated as 27 segmental homology regions (SHRs). Using SNPs identified by whole-genome re-sequencing of the 435-member association mapping panel, we identified significant SNPs (P ≤ 9.4 × 10 ) within 27 SHRs that affect stem growth at nine timepoints with diverse additive and dominance patterns, and these SNPs exhibited complex allelic epistasis over the juvenile growth period. Nineteen genes linked to potential causative alleles that have time-specific or pleiotropic effects, and mostly overlapped with significant signatures of selection within SHRs between climatic regions represented by the association mapping panel. Five genes with potential time-specific effects showed species-specific temporal expression profiles during the juvenile stages of stem growth in five representative Populus species. Our observations revealed the importance of considering temporal genetic basis of complex traits, which will facilitate the molecular design of tree ideotypes.

Construction of a high-density genetic map and QTL mapping of leaf traits and plant growth in an interspecific F1 population of Catalpa bungei × Catalpa duclouxii Dode

“…In recent years, examination of the dynamic QTLs for plant growth characteristics in a continuous set of time points has been performed; for example, Du et al mapped the growth traits of poplar at 12 successive time points and found that some QTLs were specific to one time point, while some QTLs were found at several continuous or discontinuous time points, which may be due to their specific functions in plant growth at different growth stages [63]. In the present study, QTLs for plant height at five time points were mapped, and 8 QTLs were detected at more than one time point for a cumulative PVE of 61.4%.…”

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

“…Several large-scale genome-wide association studies have identified the underlying genetic architecture related to morphological, physiological, wood property and chemistry, salinity tolerance, and disease resistance traits ( Ma et al, 2013 ; McKown et al, 2014b ; Muchero et al, 2015 ; Zhang et al, 2018 ; Bdeir et al, 2019 ; Quan et al, 2019 ; Jia et al, 2020 ; Lu et al, 2020 ). Furthermore, the biology of wood formation, cell wall ultrastructure and composition, and cell wall recalcitrance are fairly well studied ( Groover et al, 2010 ; Wegrzyn et al, 2010 ; Studer et al, 2011 ; Du et al, 2013 ; Porth et al, 2013a ; Porth et al, 2013b ; Muchero et al, 2015 ; Porth et al, 2015 ; Allwright et al, 2016 ; Du et al, 2016 ; Escamez et al, 2017 ; Fahrenkrog et al, 2017 ; Johnson et al, 2017 ; Xi et al, 2017 ; Du et al, 2018 ; Gandla et al, 2018 ; Du et al, 2019 ) and a few studies have also recognized the role of microRNA in controlling tree growth and wood property traits in Populus ( Quan et al, 2016 ; Chen B. et al, 2018 ). However, the genetic architecture underlying wood anatomical traits such as vessel size and density are relatively uncharacterized, despite the importance of these traits for cell wall composition and the overall performance of the tree.…”

Genetic dissection of the gene coexpression network underlying photosynthesis in Populus

“…The MLM considers the effects of population structure ( Q ) and kinship coefficients ( K ). The Q and K matrix were obtained as described by Du et al (). QVALUE software in R was used to correct for multiple testing with the positive false discovery rate (FDR) method (Storey, ).…”

“…Association mapping is a genetic approach that has been used to dissect the natural allelic variation responsible for complex quantitative traits in perennial trees (Du et al , ). The genetic variation of quantitative traits is classified into additive, dominance and epistatic effects, which are conferred by numerous genes/alleles in multiple biological networks (Du et al , ).…”