SSRs involved in important MTAs identified through different approaches or their combinations.

<p>SSRs involved in important MTAs identified through different approaches or their combinations.</p

Significant marker-trait associations identified through multi-trait mixed model (MTMM) and qualified FDR criteria.

<p>MTMM was performed for pair of correlated traits (for significant and high correlation; p value ≤0.05, r² value ≥ 2.5).</p

SSR genetic linkage maps of homoeologous group 3 chromosomes showing markers-trait associations (markers associated with different traits are shown by solid circles with different colours), black bar given below the solid circle represents that MTA qualified FDR criterion; markers are indicated to the right and map distances (cM) are indicated to the left of the vertical bar (based on the consensus linkage map of Somers et al. [76].

<p>MTAs identified through all three approaches (SLST, MLMM and MTMM) are highlighted with pink.</p

SSR genetic linkage maps of homoeologous group 4 chromosomes showing markers-trait associations (markers associated with different traits are shown by solid circles with different colours); markers are indicated to the right and map distances (cM) are indicated to the left of the vertical bar (based on the consensus linkage map of Somers et al. [76].

<p>SSR genetic linkage maps of homoeologous group 4 chromosomes showing markers-trait associations (markers associated with different traits are shown by solid circles with different colours); markers are indicated to the right and map distances (cM) are indicated to the left of the vertical bar (based on the consensus linkage map of Somers et al. [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0159343#pone.0159343.ref076" target="_blank">76</a>].</p

Plots of observed p-values (on y-axis) vs. expected p-values (on x-axis) for the 14 different traits using different association mapping models.

<p>Plots of observed p-values (on y-axis) vs. expected p-values (on x-axis) for the 14 different traits using different association mapping models.</p

Frequency distribution of morphological, yield related and quality traits used for association mapping.

<p>Frequency distribution of morphological, yield related and quality traits used for association mapping.</p

List of significant MTAs involving nine SSR markers which did not qualify FDR criteria but reported in earlier studies.

<p>List of significant MTAs involving nine SSR markers which did not qualify FDR criteria but reported in earlier studies.</p

SSR genetic linkage maps of homoeologous group 6 chromsomes showing markers-trait associations (markers associated with different traits are shown by solid circles with different colours), black bar given below the solid circle represents that MTA qualified FDR criterion; markers are indicated to the right and map distances (cM) are indicated to the left of the vertical bar (based on the consensus linkage map of Somers et al. [76]).

<p>SSR genetic linkage maps of homoeologous group 6 chromsomes showing markers-trait associations (markers associated with different traits are shown by solid circles with different colours), black bar given below the solid circle represents that MTA qualified FDR criterion; markers are indicated to the right and map distances (cM) are indicated to the left of the vertical bar (based on the consensus linkage map of Somers et al. [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0159343#pone.0159343.ref076" target="_blank">76</a>]).</p

Relationships between the phenotypic traits and population structure computed using the mean values across environments.

<p>Probability (p-value) and r² values (%) for phenotype–population structure relationship are based on the multiple regression analysis.</p

Epistatic interactions using main effect markers (identified by SLST, MLMM and MTMM) for 13 traits along with their p-value.

<p>Epistatic interactions using main effect markers (identified by SLST, MLMM and MTMM) for 13 traits along with their p-value.</p