Consecutive distant-QTL hotspots in adjacent genomic regions could explain the expression variations of a large number of s-traits, sc-traits, or e-traits (Supplementary file 8 in Dryad [ Wang et al., 2015]).
This new coarse categorization presented from two to four categories for each trait (Supplementary Table 4 for the decreased number of categories).
See Supplementary Information for trait definitions.
We noted SNPs from a range of genes influencing the same lipid trait (Supplementary Material, Table S2).
To test this, we ran the association analysis for rs11855415 using the absolute value of the standardized PegQ score as a quantitative trait (Supplementary Material, Fig. S6).
On the basis of the significant blocks we identified within several genes for each trait (Supplementary Table S11), we identified four exclusive multi-haplotype combinations with numerous genetic variants for three traits—holocellulose, lignin, and tree height (Supplementary Fig. S3).
For each individual, genetic predisposition scores (GPS) were calculated for each of the traits separately (HDL-C, LDL-C, TC, TG) by adding all of the scores for each risk-allele associated with that trait (Supplementary Table 1).
On the basis of these additive SNPs simultaneously associated to each trait (Supplementary Table S6), we identified phenotypic variation among possible genotype combinations for the same trait and some genotype combinations that may be useful for selection breeding.
The mutations detected showed a largely uniform distribution and did not preferentially accumulate near the T-DNA insertion site or near loci involved in the glutelin-reduced trait (Supplementary Fig. S2).
A significant difference of three yield-contributing SW (14 32 g with 87% H), NP (48 142 g with 78% H) and NB (15 31 with 72% H) quantitative traits (Supplementary Table S6) and one abiotic and biotic stress tolerant PH trait in 229 RIL mapping individuals and two parental accessions across 2 yrs based on ANOVA was observed.
The GREB1 region harbours many other SNPs reported to be genome-wide significantly associated with other traits and conditions, with GREB1 in particular associated with obesity-related traits (Supplementary data, Table SI).
