Genome Anchored QTLs for Biomass Production in Hybrid Populus Grown Under Contrasting Environments
Wellington Muchero, Mitchell M Sewell, Priya Ranjan, Lee E Gunter, Timothy J Tschaplinski, Tongming Yin, and Gerald A Tuskan
2013 January 29, PLoS ONE 8(1): e54468; doi:10.1371/journal.pone.0054468 —
Traits related to biomass production were analyzed for the presence of quantitative trait loci (QTLs) in a Populus trichocarpa Ã P. deltoides F2 population. A genetic linkage map composed of 841 SSR, AFLP, and RAPD markers and phenotypic data from 310 progeny were used to identify genomic regions harboring biomass QTLs. Twelve intervals were identified, of which BM-1, BM-2, and BM-7 were identified in all three years for both height and diameter. One putative QTL, BM-7, and one suggestive QTL exhibited significant evidence of over-dominance in all three years for both traits. Conversely, QTLs BM-4 and BM-6 exhibited evidence of under-dominance in both environments for height and diameter. Seven of the nine QTLs were successfully anchored, and QTL peak positions were estimated for each one on the P. trichocarpa genome assembly using flanking SSR markers with known physical positions. Of the 3,031 genes located in genome-anchored QTL intervals, 1,892 had PFAM annotations. Of these, 1,313, representing 255 unique annotations, had at least one duplicate copy in a QTL interval identified on a separate scaffold. This observation suggests that some QTLs identified in this study may have shared the same ancestral sequence prior to the salicoid genome duplication in Populus.
Table 1. QTLs associated with height and diameter identified in Populus family 331 F2 pedigree based on linkage-group- (LG) and genome-wise LOD significance thresholds (GW).
Table 2. Suggestive QTLs associated with height and diameter identified in Populus family 331 F2 pedigree.
Figure 1. LOD traces for QTL BM-2 on LG II based on 4-year height (red) and 4-year diameter (green) measured in Clatskanie and 4-year height measured in Boardman (purple). Broken horizontal line represents linkage groupwise LOD significance threshold calculated based on 1,000 permutations at the 0.05 significance level.
Table 3. AMMI analysis results for location specificity in QTL detection between the Clatskanie and Boardman sites.
Muchero W, Sewell MM, Ranjan P, Gunter LE, Tschaplinski TJ, et al. (2013) Genome Anchored QTLs for Biomass Productivity in Hybrid Populus Grown under Contrasting Environments. PLoS ONE 8(1): e54468. doi:10.1371/journal.pone.0054468