Association Mapping of Seed Oil and Protein Content in <i>Sesamum indicum</i> L. Using SSR Markers

<div><p>Sesame is an important oil crop for the high oil content and quality. The seed oil and protein contents are two important traits in sesame. To identify the molecular markers associated with the seed oil and protein contents in sesame, we systematically performed the association mapping among 369 worldwide germplasm accessions under 5 environments using 112 polymorphic SSR markers. The general linear model (GLM) was applied with the criteria of log<i>P</i>≥3.0 and high stability under all 5 environments. Among the 369 sesame accessions, the oil content ranged from 27.89%–58.73% and the protein content ranged from 16.72%–27.79%. A significant negative correlation of the oil content with the protein content was found in the population. A total of 19 markers for oil content were detected with a R² value range from 4% to 29%; 24 markers for protein content were detected with a R² value range from 3% to 29%, of which 19 markers were associated with both traits. Moreover, partial markers were confirmed using mixed linear model (MLM) method, which suggested that the oil and protein contents are controlled mostly by major genes. Allele effect analysis showed that the allele associated with high oil content was always associated with low protein content, and vice versa. Of the 19 markers associated with oil content, 17 presented near the locations of the plant lipid pathway genes and 2 were located just next to a fatty acid elongation gene and a gene encoding Stearoyl-ACP Desaturase, respectively. The findings provided a valuable foundation for oil synthesis gene identification and molecular marker assistant selection (MAS) breeding in sesame.</p></div

Information of candidate genes related to the markers associated with OC traits.

<p>Note: ^aRelated genes are the genes containing or close to the screened markers.</p>b<p>Nearby lipid genes refer to the genes located in the upstream and downstream of 500 Kb far from the marker.</p>c<p>Only one of the homologous genes is listed in the table.</p><p>— refers to no known lipid genes in the location.</p

AIC and maximum log likelihood values of 24 genetic models estimated using an iterated ECM (IECM) algorithm.

*<p>These models were selected as candidate models with smaller AIC values.</p

Association mapping of PC trait using GLM method under the 5 environments.

<p>The markers associated with the PC trait under 5 environments are listed in the table.</p

QTL analysis of seed color trait in F₂ and F₃ families using winQTLCart program.

<p>QTL analysis of seed color trait in F₂ and F₃ families using winQTLCart program.</p

Disequilibrium matrix of 112 SSR polymorphic sites with both the X-axis and Y-axis.

<p>The matrix is divided into two regions by the diagonal line. The upper right region indicates the D′ value of each SSR couples, and the corresponding blocks in the lower left region indicates the significance of D′. Various value intervals of the D′ or P values are shown in different colors according to the right color columns.</p

Phenotypic variation of the seed oil and protein contents in the 369 accessions under 5 environments.

<p>Phenotypic variation of the seed oil and protein contents in the 369 accessions under 5 environments.</p

Genetic composition of individuals based on Bayesian posterior probability.

<p>According to the Bayesian posterior probability, the natural population of 369 worldwide sesame lines is divided into two groups in green and red colors, respectively.</p

Estimation of 2^nd order genetic parameters for seed color trait.

<p>σ²_p: Phenotypic variance.</p><p>σ²_mg: Major gene variance.</p><p>σ²_pg: Polygene variance.</p><p>σ²: Environmental variance.</p><p>h²_mg (%): Heritability of major gene(s).</p><p>h²_pg (%): Heritability of polygenes.</p

Estimation of 1^st order genetic parameters for seed color trait.

<p>Estimation of 1^st order genetic parameters for seed color trait.</p