Identification of Candidate Genes Regulating the Seed Coat Color Trait in Sesame (Sesamum indicum L.) Using an Integrated Approach of QTL Mapping and Transcriptome Analysis.

Chun Li,Haiyang Zhang,Yinghui Duan,Hongmei Miao,Libin Wei,Ming Ju

doi:10.3389/fgene.2021.700469

Abstract

Seed coat color is an important seed quality trait in sesame. However, the genetic mechanism of seed coat color variation remains elusive in sesame. We conducted a QTL mapping of the seed coat color trait in sesame using an F2 mapping population. With the aid of the newly constructed superdense genetic linkage map comprised of 22,375 bins distributed in 13 linkage groups (LGs), 17 QTLs of the three indices (i.e., L, a, and b values) of seed coat color were detected in seven intervals on four LGs, with a phenotype variance explanation rate of 4.46–41.53%. A new QTL qSCa6.1 on LG 6 and a QTL hotspot containing at least four QTLs on LG 9 were further identified. Variants screening of the target intervals showed that there were 84 genes which possessed the variants that were high-impact and co-segregating with the seed coat color trait. Meanwhile, we performed the transcriptome comparison of the developing seeds of a white- and a black-seeded variety, and found that the differentially expressed genes were significantly enriched in 37 pathways, including three pigment biosynthesis related pathways. Integration of variants screening and transcriptome comparison results suggested that 28 candidate genes probably participated in the regulation of the seed coat color in sesame; of which, 10 genes had been proved or suggested to be involved in pigments biosynthesis or accumulation during seed formation. The findings gave the basis for the mechanism of seed coat color regulation in sesame, and exhibited the effects of the integrated approach of genome resequencing and transcriptome analysis on the genetics analysis of the complex traits.

Highlights

Sesame (Sesamum indicum L.) is a specific and important oilseed crop with a long cultivation history (Bedigian, 2003)
In order to clarify the genetic background of the seed coat color in sesame, we firstly investigated the phenotypic variation of the seed coat color trait of the F2 population in 2016 (Supplementary Table 1 and Supplementary Figure 1)
A superdense genetic linkage map was constructed for sesame by genome resequencing and an updated map construction pipeline

Summary

Introduction

Sesame (Sesamum indicum L.) is a specific and important oilseed crop with a long cultivation history (Bedigian, 2003). For sesame seeds, seed coat color varies from white, shallow yellow, yellow, golden, brown, gray, reddish brown, and other medium colors, to black. Black sesame seeds are shown to possess abundant nutritional facts (Ganesan and Xu, 2017; Khoo et al, 2017). Some studies showed that the contents of some substances, such as phenolics, vitamins, and phloretin, in black sesame seeds are high (Ha et al, 2017; Wang et al, 2018). In China, black sesame seeds have been used as a traditional Chinese medicine in the last 3,000 years (Wang et al, 2018; Zhang H. et al, 2019)

Methods

Results

Conclusion