A comprehensive genomic scan reveals gene dosage balance impacts on quantitative traits in Populus trees

Abstract

Gene dosage variation and the associated changes in gene expression influence a wide variety of traits, ranging from cancer in humans to yield in plants. It is also expected to affect important traits of ecological and agronomic importance in forest trees, but this variation has not been systematically characterized or exploited. Here we performed a comprehensive scan of the Populus genome for dosage-sensitive loci affecting quantitative trait variation for spring and fall phenology and biomass production. The study population was a large collection of clonally propagated F1 hybrid lines of Populus that saturate the genome 10-fold with deletions and insertions (indels) of known sizes and positions. As a group, the phenotypic means of the indel lines consistently differed from control nonindel lines, with an overall negative effect of both insertions and deletions on all biomass-related traits but more diverse effects and an overall wider phenotypic distribution of the indel lines for the phenology-related traits. We also investigated the correlation between gene dosage at specific chromosomal locations and phenotype, to identify dosage quantitative trait loci (dQTL). Such dQTL were detected for most phenotypes examined, but stronger effect dQTL were identified for the phenology-related traits than for the biomass traits. Our genome-wide screen for dosage sensitivity in a higher eukaryote demonstrates the importance of global genomic balance and the impact of dosage on life history traits.

Genetic Regulation of Vessel Morphology in Populus

“…Thus, indels generated phenotypic variation beyond the variation caused by allelic segregation. Consistent with previous findings ( Bastiaanse et al, 2019 ), as a group lines with lesions had an overall negative effect on growth, as illustrated here by significantly lower tree heights for the lesion group ( Table 2 ). Additional traits with significantly smaller means in the lesion line group included MVD and BT, while lesion lines had a larger mean for VF ( Table 2 ).…”

Chromoanagenesis from radiation-induced genome damage in Populus

“…In this population, ~58% of the lines carried large-scale genomic insertions and deletions (indels) [ 20 ], induced by gamma-irradiation of pollen grains before fertilization. Each F1 line was characterized by a unique set of indels randomly distributed along the 19 chromosomes of the poplar genome [ 19 , 20 ]. Interestingly, two of these lines exhibited dosage variation consistent with chromoanagenesis.…”

“…The two poplar lines carrying the shattered chromosomes did not exhibit significant phenotypic differences compared to their siblings. One of the two was sufficiently robust to be selected amongst the F1 individuals that were clonally propagated and transferred to a field for a population-wide phenotyping experiment [ 20 , 21 ], and did not exhibit extreme phenotypic behaviors in the traits analyzed.…”

Transcriptome Profiling Provides Insight into the Genes in Carotenoid Biosynthesis during the Mesocarp and Seed Developmental Stages of Avocado (Persea americana)

“…Besides, gene dosage (isoform number) increase of most carotenoid biosynthetic-related genes could also accelerate the carotenoid accumulation. Previous studies revealed gene dosage balance impacts on agronomic traits in plants, and defined the linkage between quantitative trait and gene dosage variation [44,45,46]. Consequently, we might imply that the gene dosage variation and the associated changes in gene expression of these unigenes might be important for controlling the carotenoid contents in avocado during the mesocarp and seed developmental stage.…”