Identification of QTLs and allelic effect controlling lignan content in sesame (Sesamum indicum L.) using QTL-seq approach

Abstract

Sesame (Sesamum indicum L.), an oilseed crop, is gaining worldwide recognition for its healthy functional ingredients as consumption increases. The content of lignans, known for their antioxidant and anti-inflammatory effects, is a key agronomic trait that determines the industrialization of sesame. However, the study of the genetics and physiology of lignans in sesame is challenging, as they are influenced by multiple genes and environmental factors, therefore, the understanding of gene function and synthetic pathways related to lignan in sesame is still limited. To address these knowledge gaps, we conducted genetic analyses using F7 recombinant inbred line (RIL) populations derived from Goenbaek and Gomazou as low and high lignin content variants, respectively. Using the QTL-seq approach, we identified three loci, qLignan1-1, qLignan6-1, and qLignan11-1, that control lignan content, specifically sesamin and sesamolin. The allelic effect between loci was evaluated using the RIL population. qLignan6-1 had an additive effect that increased lignan content when combined with the other two loci, suggesting that it could be an important factor in gene pyramiding for the development of high-lignan varieties. This study not only highlights the value of sesame lignan, but also provides valuable insights for the development of high-lignan varieties through the use of DNA markers in breeding strategies. Overall, this research contributes to our understanding of the importance of sesame oil and facilitates progress in sesame breeding for improved lignan content.

Keywords: DNA marker; QTL-seq; lignan; oilseed; sesame.

FIGURE 1

Frequency distribution of lignan content in the population of Goenbaek × Gomazou Recombinant Inbred Lines (RILs). Arrows indicate the mean lignin content of the parental variants. The average lignan content is represented in low and high bulk, respectively.

FIGURE 2

QTL-seq analysis for the identification of major effect QTLs controlling lignan content in sesame. (A) SNP/Indel-index plot for high- (green) and low-lignan (yellow) bulks, and △SNP/InDel-index (blue) based on ‘Goenbaek’ as a reference. (B) SNP/Indel-index plots for high- (green) and low-lignan (yellow) bulks, and △SNP/InDel-index (blue) based on ‘Gomazou’ as a reference. The average index value was plotted using red lines using a sliding window approach of 1 Mb intervals with 50 kb increments. The △SNP/InDel-index obtained by subtracting the SNP/InDel-index of low-lignan bulk from the SNP/InDel-index of high-lignan bulk was calculated with the statistical confidence interval under the null hypothesis of no QTL (orange, p < 0.01; and light green, p < 0.05). The three major effect QTLs with the |△SNP/InDel-index|≥ 0.7 were shadowed in red on chromosome 1, 6, and 11, and designated as qLignan1-1, qLignan6-1, and qLignan11-1, respectively.

FIGURE 3

qRT-PCR analysis of selected genes mapped in the KEGG pathway for the discovery of candidate genes. Relative expression of five genes in seeds at 15 and 30 days after flowering (FT) between Goenbaek (GB, orange) and Gomazou (GM, green). Error bars represent standard errors of three biological replicates. Statistically significant differences are indicated as a p-value <0.05, *, <0.01, **, and <0.001, ***.

FIGURE 4

Comparison of lignan content effects across alleles between three QTLs. (A) Results of the effect of the lignan content of individual alleles. Genotype ‘A’ refers to alleles derived from the parent, Goenbaek, and ‘B’ refers to alleles derived from Gomazou. Statistically significant differences are indicated as a p-value <0.01, **, and <0.001, ***. (B) Results of the effect of the lignan content by combinations of alleles. Each QTL designation denotes alleles in the group with higher lignan content as large. Post hoc tests were used to indicate statistical significance.