Updated sesame genome assembly and fine mapping of plant height and seed coat color QTLs using a new high-density genetic map

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1 Wang et al. BMC Genomics (26) 7:3 DOI.86/s RESEARCH ARTICLE Open Access Updated sesame genome assembly and fine mapping of plant height and seed coat color QTLs using a new high-density genetic map Linhai Wang, Qiuju Xia 2, Yanxin Zhang, Xiaodong Zhu, Xiaofeng Zhu, Donghua Li, Xuemei Ni 2, Yuan Gao, Haitao Xiang 2, Xin Wei, Jingyin Yu, Zhiwu Quan 2* and Xiurong Zhang * Abstract Background: Sesame is an important high-quality oil seed crop. The sesame genome was de novo sequenced and assembled in 24 (version.); however, the number of anchored pseudomolecules was higher than the chromosome number (2n = 2x = 26) due to the lack of a high-density genetic map with 3 linkage groups. Results: We resequenced a permanent population consisting of 43 recombinant inbred lines and constructed a genetic map to improve the sesame genome assembly. We successfully anchored 327 scaffolds onto 3 pseudomolecules. The new genome assembly (version 2.) included 97.5 % of the scaffolds greater than 5 kb in size present in assembly version. and increased the total pseudomolecule length from to Mb with 94.3 % of the genome assembled and 97.2 % of the predicted gene models anchored. Based on the new genome assembly, a bin map including,522 bins spanning 9.99 cm was generated and used to identified 4 quantitative trait loci (QTLs) for sesame plant height and 9 for seed coat color. The plant height-related QTLs explained 3 24 % the phenotypic variation (mean value, 8 %), and 29 of them were detected in at least two field trials. Two major loci (qph-8.2 and qph-3.3) that contributed 23 and 8 % of the plant height were located in 35 and 928-kb spaces on Chr8 and Chr3, respectively. qph-3.3, is predicted to be responsible for the semi-dwarf sesame plant phenotype and contains 2 candidate genes. This is the first report of a sesame semi-dwarf locus and provides an interesting opportunity for a plant architecture study of the sesame. For the sesame seed coat color, the QTLs of the color spaces L*, a*, and b* were detected with contribution rates of 3 46 %. qscb-4. contributed approximately 39 % of the b* value and was located on Chr4 in a 99.9-kb space. A list of 32 candidate genes for the locus, including a predicted black seed coat-related gene, was determined by screening the newly anchored genome. Conclusions: This study offers a high-density genetic map and an improved assembly of the sesame genome. The number of linkage groups and pseudomolecules in this assembly equals the number of sesame chromosomes for the first time. The map and updated genome assembly are expected to serve as a platform for future comparative genomics and genetic studies. * Correspondence: Quanzhiwu@genomics.org.cn; zhangxr@oilcrops.cn Equal contributors 2 Shenzhen Engineering Laboratory of Crop Molecular Design Breeding, BGI-agro, 5883 Shenzhen, China Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops of the Ministry of Agriculture, Wuhan 4362, China 26 Wang et al. Open Access This article is distributed under the terms of the Creative Commons Attribution 4. International License ( which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver ( applies to the data made available in this article, unless otherwise stated.

2 Wang et al. BMC Genomics (26) 7:3 Page 2 of 3 Background The sesame (Sesamum indicum) is a member of the family Pedaliaceae and order Lamiales [] and is a diploid species with 3 pairs of chromosomes (2n = 2x = 26). In our previous study, the sesame genome was estimated to be approximately 357 Mb in size based on de novo sequencing of Zhongzhi No. 3. The assembled genome (version.) was predicted to contain 27,48 protein-coding genes. The version. assembly anchored 5 scaffolds into 6 pseudomolecules that harbored 85.3 % of the assembled genome and 9.7 % of the predicted genes [2, 3]. We attempted to anchor additional scaffolds and contigs to improve the sesame genome assembly and equalize the number of sesame chromosomes. To achieve this goal, a high-quality and dense genetic map is essential. Although two sesame genetic maps have been published [4, 5], they contain more than 3 linkage groups. The numbers of breeding lines and temporary populations usually contribute to the construction of genetic maps [6]. Genetic maps are useful for discovering, dissecting, and manipulating the genes responsible for simple and complex traits in crop plants [7]. A high-quality genetic map not only improves genome assembly but also provides a foundation for mapping the genes or quantitative trait loci (QTLs) that underlie agronomic traits of important oil crops such as the sesame. The sesame seed is useful because of its high oil content and quality. The sesame antioxidative furofuran lignans such as sesamin, are the focus of research in medicine and pharmacology due to their potent pharmacological properties including the ability to decrease blood lipid [8] and cholesterol [9] levels. Moreover, the diploid characteristic, high oil content, small genome size, and smaller number of lipid-related genes distinguish sesame from other polyploid oil crops such as soybean, peanut, and rapeseed and make it a valuable plant model to study oil biosynthesis and various traits [2]. Despite the importance and long history of cultivation of the sesame, few gene loci have been fine-mapped due to a lack of genetic and genomic studies and gene cloning and functional analyses. Plant architecture is crucial for the grain yield and is determined by the plant height (PH) and other traits []. The green revolution was characterized by breeding semi-dwarf or dwarf wheat and rice cultivars to achieve an increased harvest index and improved adaption to the irrigated and fertile environments usually inhabited by taller plants [ 3]. Sesame has a low yield capacity compared to other crop plants due to its high PH, low harvest index, and susceptibility to biotic and abiotic stressors [4]. Mutant sesame lines with a determinate growth habit have been generated to reduce the sesame PH. Unfortunately, this characteristic was linked to short fruiting zone length and low yield [4, 5] phenotypes; thus, new dwarf or semi-dwarf sesame genetic resources must be explored. Another important sesame trait is the seed coat color which varies widely from white to black. Black sesame seeds are favored as food and medication in Asia, whereas white sesame seeds are primarily used to produce oil. Some studies have shown that white sesame seeds typically have higher sesamin or sesamolin content [6], whereas black sesame seeds usually have higher ash and carbohydrate content and lower protein, oil, and moisture ratios [7]. Single nucleotide polymorphisms (SNPs) are the most abundant small-scale form of genetic variation in humans and plants and SNP markers have become increasingly important tools for molecular genetic analyses [8, 9]. Restriction-site associated DNA sequencing (RAD-seq) using next generation sequencing platforms reduces the representation of the genome and allows oversequencing of the nucleotides adjacent to restriction sites; thus, it is a relatively cost-effective and precise method for the detection of SNPs [2]. In this study, we constructed a recombinant inbred line (RIL) population consisting of 43 lines using a newly discovered semidwarf sesame strain. A new high-density sesame genetic map with 3 linkage groups was prepared using RADseq which enabled us to update the sesame genome assembly to a new level and to finely map important agronomic traits such as the PH and seed coat color. Results and discussion Construction of a new sesame genetic map We RAD sequenced the 43 RILs and the two parental lines and generated more than.7 8 paired-end reads. Each line produced a mean of 76.5 Mb of highquality sequence data. All reads were aligned with the Zhongzi No. 3 scaffold sequence which has a total effective genome length of 274 Mb based on analysis using BWA software [2], and 9.97 % of the reads were mapped onto reference sequences across the various lines. Approximately 5.4 % of the reference genome was tagged by RAD-Seq, with a mean value of 4.53-fold coverage. The tags from the two parents Zhongzhi No. 3 and ZZM2748 were subjected to comparative analysis to detect SNPs. After filtering out poor SNPs and those with a significantly distorted segregation ratio (P <.),,924 SNPs were retained for genotyping of the RIL population. Due to the limitation of markernumbers that can be analyzed in JoinMap software, a portion of the SNPs was selected to construct the primary genetic map. Based on the primary genetic map, we rearranged the scaffolds from the previous genome assembly and generated a new sesame genome sequence. Then, a bin map was constructed by joining the consecutive intervals on

3 Wang et al. BMC Genomics (26) 7:3 Page 3 of 3 the genome that lacked a recombination event within the population [22, 23]. The genetic map included,522 bins that could be grouped into 3 sesame linkage groups (SLGs) with a total length of 9.99 cm (Fig., Additional file : Table S). This is the first sesame genetic map in which the number of linkage groups equals the number of chromosome pairs in a sesame cultivar. The lengths of the 3 linkage groups ranged from to cm (mean value, cm). Each linkage group had 84 (SLG2) to 68 (SLG3) bins resulting in a mean interval distance of.72 cm between adjacent bins (Additional file : Table S2). The bin distance was similar to that generated by RAD-Seq (.69 cm) [5], but was shorter than that maps constructed using randomly selective amplification markers mainly (.86 cm) [24] or the specific length amplified fragment sequencing (SLAF-seq) technology (.2 cm) [4]. Furthermore, more than 99 % of the interval distances between adjacent bins were shorter than 6 cm (Additional file 2: Figure S), indicating the high density of the new sesame genetic map. Update of sesame genome assembly The previous de novo sesame assembly provided a total genome assembly of 274 Mb with a scaffold N5 of 2. Mb and 2 scaffolds greater than 5 kb in size. The assembly anchored 5 larger scaffolds into 6 pseudomolecules based on a genetic map that included 46 markers, which harbored 85.3 % of the total genome assembly and 9.7 % of the predicted genes (version.) [2, 3]. Using the genetic map constructed in this study, we anchored another 72 scaffolds or contigs in a new sesame genome assembly (version 2.) and linked together six smaller linkage groups in version. (LG2 and LG6, LG3 and LG4, and LG9 and LG5). Despite the addition of 72 new scaffolds to the new version of the genome assembly, their orders were relatively consistent with the orders of the 5 scaffolds of version.. In total, 2 changes occurred during the reanchoring, including scaffolds that were adjusted in the same pseudomolecules, 4 scaffolds that were relocated to other pseudomolecules, and 6 scaffolds that were split into two parts and relocated separately (Fig. 2; Additional file : Table S3 and S4). The inconsistency might be due to a single misassembly in which contig sequences were erroneously joined into these scaffolds through paired-end links during the initial assembly as reported for Cucumis melo [25, 26]. As a result, 327 scaffolds,(ncluding the split parts) were anchored to 3 pseudomolecules (Table ), which were defined as pseudochromosomes and designated as Chr to Chr3 (Figs. 2 and 3). The lengths of the 327 anchored scaffolds ranged from 325 bp to 7. Mb (mean value, kb; Additional file 2: Figure S2), 97.5 % of the scaffolds with lengths greater than 5 kb in version. were included in the new assembly version. The total length of the assembled pseudomolecules in the new version increased the assembly from Mb to Mb, representing 94.3 % of the genome assembly, and 97.2 % of the predicted gene models were anchored successfully (Fig. 3). There were 5 scaffolds (GenBank accession nos. KI , KI , KI , KI86666., and KI8666.) with lengths greater than 5 kb that were still missing in the 3 newly assembled pseudomolecules. These sequences may represent conserved regions with few mutation sites or lower frequencies of exchange during chromosome recombination. Other high-density genetic maps based on new mapping populations or fluorescence in situ hybridization (FISH) may be required to anchor the remaining scaffold and to make the map more perfect. The mean sesame whole-genome recombination rate (cm/mb) was 4.25; the rate ranged from 3.45 for Chr to 5.38 for Chr. Comparison of the physical and genetic distances between markers revealed that most of the SLGs contained a low recombination region located approximately 5 Mb from the proximal end or center (Additional file 2: Figure S3). QTLs for traits related to sesame PH The sesame plant height is generally determined by the height of the first capsule-bearing node (HFC), capsule zone length (CZL), and tip length without the capsule (TL) traits. The CZL is also related to the node number (NN) and internode length (IL) traits. The mature Zhongzhi No. 3 plants are normally greater than.8 m in height, whereas ZZM2748 is a semi-dwarf cultivar which grows to less than.9 m. Additionally, the two parents exhibited obvious differences in other traits related to PH (Additional file 2: Figure S4). Among the 43 progeny lines, the values for PH, HFC, CZL, TL, IL and NN were (m),.5.6 (m), (m), 5.8 (cm), (cm) and , respectively (Additional file 2: Figures S5 and S6). PH, HFC, and IL fluctuated less than the other traits based on the coefficient of variation (CV) across the three field trials, and higher broad-sense heritabilities were also observed (Additional file : Table S5). Positive and negative transgressive segregation was observed in the RIL population suggesting that a germplasm could be created with the expected PH, CZL, TL, NN, and IL traits independent of environmental effects; however, the negative heterobeltiosis of HFC appeared to depend largely on the environment. PH was correlated with HFC, CZL, TL, NN, and IL (P <.), and strong correlations were observed between PH and HFC and between CZL and NN (Fig. 4a). Interestingly, the correlation between NN and IL was negative across the three trial sites. This result supported the hypothesis that dwarf sesame cultivars could be bred

4 Wang et al. BMC Genomics (26) 7:3 Page 4 of 3 without the loss of yield because reducing the internode length did not appear to affect the capsule node number. Using the bin map, we identified QTLs underlying the sesame PH and the related traits HFC, CZL, TL, NN, and IL. Phenotypic datasets from the three experimental cm SLG SLG_bin. SLG_bin2.2 SLG_bin3.25 SLG_bin4.38 SLG_bin5.58 SLG_bin6.7 SLG_bin7.83 SLG_bin8.96 SLG_bin SLG_bin 2.49 SLG_bin 2.6 SLG_bin SLG_bin SLG_bin4 7.4 SLG_bin SLG_bin SLG_bin SLG_bin8.2 SLG_bin9.25 SLG_bin2.64 SLG_bin2.77 SLG_bin22.43 SLG_bin SLG_bin SLG_bin SLG_bin26 2. SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin68 5. 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SLG7_bin2.3 SLG7_bin3.26 SLG7_bin4.38 SLG7_bin5.5 SLG7_bin6.6 SLG7_bin7.98 SLG7_bin8. SLG7_bin9.23 SLG7_bin.39 SLG7_bin.52 SLG7_bin2.65 SLG7_bin3.76 SLG7_bin4.9 SLG7_bin5 2.3 SLG7_bin6 2.4 SLG7_bin SLG7_bin8 2.9 SLG7_bin9 4. SLG7_bin SLG7_bin SLG7_bin22.23 SLG7_bin SLG7_bin SLG7_bin SLG7_bin SLG7_bin27 8. SLG7_bin SLG7_bin SLG7_bin3 8.7 SLG7_bin SLG7_bin SLG7_bin SLG7_bin SLG7_bin SLG7_bin SLG7_bin SLG7_bin SLG7_bin SLG7_bin SLG7_bin4 3.2 SLG7_bin SLG7_bin SLG7_bin SLG7_bin SLG7_bin SLG7_bin SLG7_bin SLG7_bin SLG7_bin SLG7_bin SLG7_bin SLG7_bin SLG7_bin SLG7_bin SLG7_bin SLG7_bin SLG7_bin SLG7_bin SLG7_bin SLG7_bin SLG7_bin SLG7_bin SLG7_bin SLG7_bin SLG7_bin66 5. SLG7_bin SLG7_bin SLG7_bin SLG7_bin SLG7_bin SLG7_bin SLG7_bin SLG7_bin SLG7_bin SLG7_bin SLG7_bin SLG7_bin SLG7_bin SLG7_bin SLG7_bin8 6.5 SLG7_bin SLG7_bin SLG7_bin SLG7_bin SLG7_bin SLG7_bin SLG7_bin SLG7_bin SLG7_bin SLG7_bin SLG7_bin SLG7_bin SLG8 SLG8_bin. SLG8_bin2.5 SLG8_bin3.6 SLG8_bin4.57 SLG8_bin5.82 SLG8_bin6.94 SLG8_bin7 2.6 SLG8_bin8 2.3 SLG8_bin SLG8_bin 2.59 SLG8_bin 2.7 SLG8_bin SLG8_bin SLG8_bin SLG8_bin5 4.5 SLG8_bin SLG8_bin SLG8_bin SLG8_bin9 5. SLG8_bin2 5.5 SLG8_bin SLG8_bin SLG8_bin23 6. SLG8_bin SLG8_bin SLG8_bin SLG8_bin SLG8_bin SLG8_bin SLG8_bin3.9 SLG8_bin3.7 SLG8_bin32.48 SLG8_bin33.99 SLG8_bin SLG8_bin SLG8_bin SLG8_bin SLG8_bin SLG8_bin SLG8_bin4 5.7 SLG8_bin4 7. SLG8_bin SLG8_bin SLG8_bin SLG8_bin SLG8_bin SLG8_bin SLG8_bin SLG8_bin SLG8_bin SLG8_bin SLG8_bin SLG8_bin SLG8_bin SLG8_bin SLG8_bin56 3. 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SLG9_bin2.3 SLG9_bin3.29 SLG9_bin4.59 SLG9_bin SLG9_bin SLG9_bin7 9.8 SLG9_bin8.34 SLG9_bin9.47 SLG9_bin.4 SLG9_bin 2.5 SLG9_bin SLG9_bin SLG9_bin4 4.8 SLG9_bin SLG9_bin6 5.6 SLG9_bin SLG9_bin SLG9_bin SLG9_bin2 8.9 SLG9_bin SLG9_bin SLG9_bin SLG9_bin SLG9_bin SLG9_bin SLG9_bin SLG9_bin SLG9_bin SLG9_bin SLG9_bin SLG9_bin SLG9_bin SLG9_bin SLG9_bin SLG9_bin SLG9_bin SLG9_bin SLG9_bin SLG9_bin SLG9_bin SLG9_bin SLG9_bin SLG9_bin SLG9_bin SLG9_bin SLG9_bin SLG9_bin SLG9_bin SLG9_bin5 4.9 SLG9_bin5 4.3 SLG9_bin SLG9_bin SLG9_bin SLG9_bin SLG9_bin SLG9_bin SLG9_bin SLG9_bin SLG9_bin SLG9_bin SLG9_bin SLG9_bin SLG9_bin SLG9_bin SLG9_bin SLG9_bin SLG9_bin SLG9_bin SLG9_bin SLG9_bin SLG9_bin SLG9_bin SLG9_bin SLG9_bin SLG9_bin SLG9_bin SLG9_bin SLG9_bin SLG9_bin SLG9_bin SLG9_bin SLG9_bin SLG9_bin SLG9_bin SLG9_bin SLG9_bin SLG9_bin SLG9_bin SLG9_bin SLG9_bin SLG9_bin SLG9_bin SLG9_bin SLG9_bin SLG9_bin SLG9_bin SLG9_bin SLG9_bin SLG9_bin 76. SLG9_bin 78.7 SLG9_bin SLG9_bin SLG9_bin4 8.9 SLG9_bin SLG9_bin SLG9_bin SLG9_bin SLG9_bin SLG9_bin SLG9_bin SLG9_bin SLG9_bin3 9.4 SLG9_bin4 9.3 SLG9_bin PH: plant height HFC: height of the first capsule bearing node CZL: the capsule zone length SLG SLG_bin. SLG_bin2.56 SLG_bin3.22 SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin8 6.7 SLG_bin SLG_bin 9.8 SLG_bin 2.99 SLG_bin2 3. SLG_bin3 3.5 SLG_bin4 4.2 SLG_bin SLG_bin SLG_bin SLG_bin8 7. SLG_bin SLG_bin SLG_bin2 8.2 SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin9 6.5 SLG_bin 6.3 SLG_bin SLG_bin SLG_bin SLG_bin SLG SLG_bin. SLG_bin2.5 SLG_bin3.27 SLG_bin4.39 SLG_bin SLG_bin SLG_bin SLG_bin8 2.8 SLG_bin SLG_bin 3.6 SLG_bin 3.2 SLG_bin SLG_bin3 4.6 SLG_bin SLG_bin SLG_bin SLG_bin7 8.8 SLG_bin SLG_bin9.58 SLG_bin2.73 SLG_bin2.66 SLG_bin22.79 SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin27 3. SLG_bin SLG_bin SLG_bin3 4.6 SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin5 27. SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin82 5. SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin 67.7 SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin SLG_bin IL: the internode length NN: the node number TL: the tip length without capsule SLG2 SLG2_bin. SLG2_bin2.78 SLG2_bin3 2. SLG2_bin SLG2_bin SLG2_bin SLG2_bin SLG2_bin SLG2_bin SLG2_bin 7.75 SLG2_bin 7.88 SLG2_bin2 8. SLG2_bin SLG2_bin4 8.5 SLG2_bin SLG2_bin SLG2_bin7 8.9 SLG2_bin8 9.4 SLG2_bin9 9.7 SLG2_bin2 9.3 SLG2_bin SLG2_bin SLG2_bin SLG2_bin24.6 SLG2_bin25.33 SLG2_bin SLG2_bin SLG2_bin SLG2_bin SLG2_bin3 5.9 SLG2_bin3 6.3 SLG2_bin SLG2_bin SLG2_bin SLG2_bin SLG2_bin SLG2_bin SLG2_bin SLG2_bin SLG2_bin4 9.7 SLG2_bin4 9.9 SLG2_bin SLG2_bin SLG2_bin SLG2_bin SLG2_bin SLG2_bin SLG2_bin SLG2_bin SLG2_bin SLG2_bin SLG2_bin SLG2_bin SLG2_bin SLG2_bin SLG2_bin SLG2_bin SLG2_bin SLG2_bin SLG2_bin SLG2_bin SLG2_bin SLG2_bin SLG2_bin SLG2_bin SLG2_bin SLG2_bin SLG2_bin SLG2_bin SLG2_bin SLG2_bin SLG2_bin SLG2_bin SLG2_bin SLG2_bin SLG2_bin SLG2_bin SLG2_bin SLG2_bin SLG2_bin SLG2_bin SLG2_bin SLG2_bin SLG2_bin SLG3 SLG3_bin. SLG3_bin2.26 SLG3_bin3.39 SLG3_bin4.52 SLG3_bin5.4 SLG3_bin6.43 SLG3_bin7 2.9 SLG3_bin SLG3_bin SLG3_bin 4.86 SLG3_bin 4.99 SLG3_bin2 5. SLG3_bin SLG3_bin SLG3_bin SLG3_bin SLG3_bin7 6. SLG3_bin8 6.3 SLG3_bin SLG3_bin SLG3_bin SLG3_bin SLG3_bin SLG3_bin SLG3_bin SLG3_bin SLG3_bin SLG3_bin SLG3_bin SLG3_bin3 2.4 SLG3_bin SLG3_bin SLG3_bin SLG3_bin SLG3_bin SLG3_bin SLG3_bin SLG3_bin SLG3_bin SLG3_bin SLG3_bin SLG3_bin SLG3_bin SLG3_bin SLG3_bin SLG3_bin SLG3_bin SLG3_bin SLG3_bin SLG3_bin SLG3_bin SLG3_bin SLG3_bin SLG3_bin SLG3_bin SLG3_bin SLG3_bin SLG3_bin SLG3_bin SLG3_bin SLG3_bin SLG3_bin SLG3_bin SLG3_bin SLG3_bin SLG3_bin SLG3_bin SLG3_bin SLG3_bin SLG3_bin SLG3_bin SLG3_bin SLG3_bin SLG3_bin SLG3_bin SLG3_bin SLG3_bin SLG3_bin SLG3_bin SLG3_bin SLG3_bin SLG3_bin SLG3_bin SLG3_bin SLG3_bin SLG3_bin SLG3_bin SLG3_bin SLG3_bin SLG3_bin SLG3_bin SLG3_bin SLG3_bin SLG3_bin SLG3_bin SCa: seed color space a* SCb: seed color space b* SCl: seed color space l* Fig. High density genetic map of the sesame genome and the mapped QTLs. Positions of the mapped QTLs for plant height (PH), capsule zone length (CZL), height of the first capsule-bearing node (HFC), internode length (IL), node number (NN), and tip length without the capsule (TL). The seed coat color space L*, a*, and b* values are indicated with colored rectangles centered at the peak of each QTL

5 Wang et al. BMC Genomics (26) 7:3 Page 5 of 3 environments were coupled with the genotypic data using Windows QTL Cartographer 2.5 software [27]. The threshold used for the LOD scores to evaluate the statistical significance of the QTL effects was determined using, permutations. In total, 4 QTLs in nine SLGs were detected for the traits with contribution rates of 3 24 % (mean value, 8 %; Table 2, Fig. ). Among them, 4, 5, and 2 QTLs were detected in three, two, and one environment(s), respectively. These loci were not distributed randomly because SLG3, SLG4, SLG8, and SLG9 together contained more than 78 % of the QTLs (Fig. ). Ten QTLs accounting for % of the PH variation were detected. Four of these QTLs (qph-3.2, a scaffold scaffold2_2 scaffold8 scaffold22 scaffold37 scaffold56 scaffold5 scaffold6 scaffold65 scaffold36 LG Chr LG2 Chr2 LG3 Chr3 LG4 Chr4 LG5 Chr5 LG6 Chr6 LG7 scaffold scaffold2_2 scaffold232 scaffold24 scaffold72 scaffold539 scaffold8 scaffold8 scaffold22 scaffold37 scaffold56 scaffold5 scaffold6 scaffold7_2_ scaffold65 scaffold233 scaffold36 scaffold25 scaffold69 scaffold39 scaffold34 scaffold88_ scaffold88_2 scaffold6 scaffold2 scaffold2 scaffold25 scaffold69 scaffold39 scaffold499 scaffold47 scaffold55 scaffold747 scaffold639 scaffold295 scaffold45 scaffold286 scaffold27 scaffold64 scaffold64 scaffold93 scaffold34 scaffold767 scaffold4 scaffold355 scaffold474 scaffold88_2 C726 scaffold6 scaffold2 scaffold2 scaffold28 scaffold7 scaffold37 scaffold4 scaffold92 scaffold343 scaffold52 scaffold24 scaffold scaffold32_2 scaffold32_ scaffold3 scaffold48 scaffold3 scaffold59 scaffold28 C249 C6 scaffold7 scaffold37 scaffold4 scaffold scaffold25 scaffold22 scaffold247 scaffold95 scaffold68 scaffold95 scaffold92 scaffold343 scaffold52 scaffold24 scaffold scaffold32_2 scaffold3 scaffold48 scaffold79 scaffold62 scaffold9 scaffold3 scaffold6 scaffold87 scaffold4 scaffold2 scaffold86 scaffold82 scaffold27 scaffold44 scaffold3 scaffold4 scaffold72 scaffold5 scaffold58 scaffold33 scaffold79 scaffold9 scaffold225 C964 scaffold28 scaffold3 scaffold6 scaffold24 scaffold27 scaffold29 scaffold62 scaffold4 scaffold87 scaffold23 scaffold293 scaffold2 scaffold86 scaffold82 scaffold27 scaffold44 scaffold58 scaffold88 scaffold3 scaffold4 scaffold4 scaffold33 scaffold72 scaffold5 scaffold46 scaffold5_2 scaffold5_ scaffold7_2_ scaffold7_2_2 scaffold69 scaffold22 scaffold9 scaffold29 scaffold78 scaffold38 scaffold68 scaffold67 scaffold5 scaffold87 scaffold5 scaffold46 scaffold5_2 scaffold7_2_2 scaffold466 scaffold59 scaffold26 scaffold92 scaffold973 scaffold69 scaffold9 scaffold2 scaffold74 scaffold226 scaffold22 scaffold383 scaffold29 scaffold38 scaffold29 scaffold68 scaffold67 scaffold65 scaffold87 scaffold9_ scaffold9_2 scaffold4 scaffold78 scaffold3 scaffold63 scaffold54 scaffold85 scaffold2 scaffold3 scaffold7_ scaffold5 scaffold55 scaffold42 scaffold9_2 scaffold4 scaffold24 scaffold78 scaffold3 scaffold8_ scaffold63 scaffold54 scaffold79 scaffold99 scaffold96 scaffold98 scaffold265 scaffold292 scaffold39 scaffold85 scaffold88_ scaffold2 scaffold3 scaffold7_ scaffold5 scaffold55 scaffold8 scaffold62_ scaffold62_2 scaffold52 scaffold scaffold83 scaffold35 scaffold47 scaffold8 scaffold7 scaffold82 scaffold33 scaffold96 scaffold58 scaffold6 Chr7 scaffold256 scaffold8 scaffold62_2 scaffold scaffold238 scaffold52 scaffold2 scaffold353 scaffold3 scaffold26 scaffold368 scaffold249 scaffold73 scaffold2 scaffold78 scaffold83 scaffold35 scaffold47 scaffold275 scaffold8 scaffold7 scaffold86 scaffold82 scaffold324 scaffold75 scaffold77 scaffold33 scaffold379 scaffold9 scaffold96 scaffold44 scaffold58 scaffold28 scaffold6 b scaffold6 LG8 Chr8 scaffold6 scaffold5 Chr9 scaffold5 scaffold59 LG scaffold36 scaffold98 Chr scaffold98 LG scaffold84 scaffold54 Chr scaffold84 scaffold54 scaffold26 Chr2 scaffold26 scaffold42 scaffold36 LG4 scaffold7 scaffold76 scaffold93 Chr3 scaffold243 scaffold5_ scaffold75 scaffold45 scaffold49 scaffold46 scaffold scaffold8_2 scaffold8_ scaffold8 scaffold75 scaffold45 scaffold266 scaffold43 scaffold46 scaffold297 scaffold56 scaffold333 scaffold223 scaffold234 scaffold24 scaffold27 scaffold67 scaffold83 scaffold94 scaffold365 scaffold49 scaffold46 scaffold2272 scaffold235 scaffold347 scaffold254 scaffold2765 scaffold373 C456 C444 C47 C39 C339 C77 C45 C492 C63 C92 C25 C293 C277 C2323 C235 C2385 C2589 C26 C2946 C2977 C2985 C334 scaffold245 C3753 C6 scaffold9 scaffold267 scaffold63 scaffold224 scaffold227 scaffold253 scaffold289 scaffold255 scaffold345 LG9 LG5 scaffold5 scaffold33 scaffold9 scaffold76 scaffold64 scaffold3 scaffold5 scaffold33 scaffold9 scaffold332 scaffold76 scaffold89 scaffold222 scaffold64 scaffold3 scaffold2_ scaffold43 scaffold23 scaffold8 scaffold23 scaffold6 scaffold29 scaffold53 scaffold2_ scaffold43 scaffold376 scaffold37 scaffold363 scaffold84 scaffold9 scaffold2 scaffold25 scaffold242 scaffold22 scaffold23 scaffold8 scaffold23 C548 scaffold6 scaffold285 scaffold29 C46 scaffold6 scaffold47 scaffold4 scaffold scaffold4 scaffold99 scaffold49 scaffold6 scaffold758 scaffold34 scaffold42 scaffold85 scaffold47 scaffold4 C836 scaffold scaffold99 scaffold49 scaffold273 LG6 LG2 scaffold7 scaffold7 scaffold5 scaffold35 scaffold73 scaffold7 scaffold89 scaffold53 scaffold74 scaffold7 scaffold57 scaffold62_ scaffold48 scaffold5 scaffold23 scaffold599 scaffold7 scaffold9_ scaffold35 scaffold73 scaffold7 scaffold89 scaffold64 scaffold252 scaffold53 scaffold74 LG3 scaffold7 scaffold77 scaffold38 scaffold44 scaffold97 scaffold4 scaffold3 scaffold scaffold45 scaffold25 scaffold32 scaffold6 scaffold76 scaffold75 scaffold22 scaffold7 scaffold93 scaffold7 scaffold77 scaffold38 scaffold44 scaffold97 scaffold32_ scaffold4 scaffold3 scaffold C675 scaffold2 scaffold34 scaffold scaffold395 scaffold55 scaffold8 scaffold94 scaffold2 scaffold66 scaffold8 scaffold94 scaffold2 scaffold66 scaffold53 scaffold9 scaffold8_2 scaffold8 scaffold34 Fig. 2 Anchored scaffolds in the current and previously assembled sesame genomes. Green scaffolds indicate anchored scaffolds that are consistent in the current (version 2.) and previously (version.) assembled genomes. Their relative positions are marked with lines. The newly anchored scaffolds in assembly version 2. are highlighted in red. The split scaffolds and relocated scaffolds are indicated in blue. The positions of the six smaller linkage groups in version. (LG9, LG2, LG3, LG4, LG5 and LG6) were indicated with pink lines

6 Wang et al. BMC Genomics (26) 7:3 Page 6 of 3 Table Comparison of the anchored sesame genome versions. and 2. Version 2. V2._scaff_ number V2._size (Mb) Version. V._scaff_ number V._size (Mb) Chr LG 8.58 Chr LG Chr LG Chr LG Chr LG Chr LG Chr LG Chr LG Chr LG9 & LG Chr LG 7.25 Chr LG Chr LG2 & LG6.34 Chr LG3 & LG Total qph-3.3, qph-8.2, and qph-9.2) individually explained more than % of the phenotypic variation (Table 2). We also detected eight HFC, eight CZL, and six TL QTLs. Of them, three of the HFC QTLs (qhfc-3.2, qhfc-9., and qhfc-9.3) and one CZL QTL (qczl-8.) were found to contribute more than % of the phenotype variation at a minimum of two sites. TL might be easily affected by the environment because all of the TL QTLs were detected in only one or two of the three trial sites. Although five QTLs were detected for NN, none of them had a phenotype explanation rate of more than %. Nevertheless, the qnn-3. locus accounted for approximately 9 % of NN and had a pleiotropic effect on CZL (qczl-3.) with a contribution rate of 6.89 %. We also identified loci with pleiotropic effects in other QTLs based on their close or identical locations, particularly in QTLs with higher contribution rates. The qph-8.2 and qph-3.3 QTLs were the two major loci that accounted for 23.3 and 8.7 % of the sesame PH variation, respectively. The qph-8.2 locus was derived from the tall parent with a positive effect of.8 % and was located between bin markers SLG8_bin and SLG8_bin2 in a 35-kb region. This region also contained three other QTLs (qhfc-8.2, qczl-8., and qil- 8.) that accounted for 8.9, 23.84, and 9.45 % of the phenotypic variation in HFC, CZL, and IL, respectively. The qph-3.3 locus was located in a 928-kb region between bin26 and bin27 on SLG3. This region also contained three other QTLs (qhfc-3.2, qczl-3., and qnn-3.2) that accounted for 22., 9.33, and.26 % of the phenotypic variation in HFC, CZL, and NN, respectively. The negative additive effects of these QTLs indicated that the ZZM2748 semi-dwarf parent contributes to a strong decrease in the sesame PH and related traits including HFC, CZL, and NN. Plant height usually decides the plant architecture and contributes to the crop yield. Studies based on mutants with dwarf phenotypes had showed that plant hormones such as gibberellin (GA), auxin, cytokinin (CK), and brassinosteroid (BR) played important roles in determining stem elongation [28, 29]. In sesame, few studies have reported the locus or gene that encodes plant height; the exception is Wu et al.[5], who he detected two QTL with contribution rate no more than 6. However, the relationships of these QTLs were not clear for the inconsistent genetic maps and no sesame reference genomes available for the previous study. We predicted 53 and 2 candidate genes for the flanking bin-marker regions of qph-8.2 and qph-3.3, respectively, on the new assembled pseudomolecule chromosome according to the true confidence intervals (Additional file : Table S6). Annotation of these genes showed some of them may function in regulating of plant height. For example, SIN_593 in the site of qph-3.3 site was predicted to encode an auxin-induced protein and SIN_59 encoded a brassinosteroidinsensitive protein. Further study in the future may be expected to verify their functions. QTL for sesame seed coat color The two parents Zhongzhi No. 3 and ZZM2748 were also distinguishable by seed coat color; the seeds of the former were white and the seeds of the latter were black (Fig. 4b). Genetic analysis showed that black was dominant to white in sesame seed coat color. The black seed coat color was characterized by delayed inheritance or predetermination because the F seeds (F2 organs in theory) produced from a cross between white and black seed sesame plants were always black. The RILs exhibited wide variations in seed coat color. The L*, a*, and b* values for the Zhongzhi No. 3 seed coat color were 64.35, 3.84, and 2.2, respectively, whereas those for ZZM2748 were 25.34,.73, and 2.87, respectively. The L* values for the 43 RILs ranged from 8.6 to and the a* and b* values ranged from.2 to 2.62 and from.74 to 55.77, respectively (Additional file 2: Figure S7). Because L* represents brightness ranging from black to white, a* represents red and b* represents yellow for positive values [3], the measured values and distributions suggest that black, white, and yellow are predominant in the sesame seed coat color space, which is consistent with the observation that the seed coat color segregates in the RILs. Across the Pingyu (PY) and Yangluo (YL) field trial locations, three QTLs (qscl-8., qscl-4., and qscl-.) were detected repeatedly for the L* color space and

7 Chr5 Wang et al. BMC Genomics (26) 7:3 Page 7 of 3 Chr3 Chr Chr Chr2 A B C D E F Chr2 Chr Chr3 Chr9 Chr4 Chr8 Chr6 Chr7 Fig. 3 Distributions of basic elements of the sesame genome in the current assembly. a Pseudomolecules. b Gene density (mrna); the frequency of sites within gene regions per 5 kb ranged from.4 to.6. c DNA transposon element (TE) density; the frequency of sites within the DNA TE regions per 5 kb ranged from to.22. d Retrotransposon element density; the frequency of sites per 5 kb within the retrotransposon element regions ranged from to.7. e GC content; the ratio of GC sites per kb ranged from.32 to.4. f SNP density; the frequency of sites within SNP regions per kb ranged from 5 to 3. Circos software ( was used to construct the diagram made a cumulative contribution of 8 % to the phenotype. Among them, qscl-8. explained approximately 46. % of the L* variation and was located at 73.4 cm on the SLG8 linkage group. This locus was flanked by the adjacent SLG8_bin4 (72.4 cm) and SLG8_bin5 (8.4 cm) bin markers that covered a 2.5-Mb region on pseudochromosome Chr8. The qscl-4. locus was located in a 99.9-kb region on pseudochromosome Chr4 between the bin markers SLG4_bin63 (5.4 cm) and SLG4_bin64 (5.9 cm) and contributed 2.6 % of the L* variation. The qscl-. locus was located at the top of pseudochromosome Chr in a kb region between bin markers SLG_bin ( cm) and SLG_bin2 (.5 cm) and explained 3.7 % of the L* variation. There two QTLs (qsca-8. and qsca-4.) contributed 25.3 and 3.2 % of the color space a* value detected across the PY and YL field trial locations, respectively. Locus qsca-8.2 was detected only at PY with a phenotype explanation rate of 9.2 %. Three QTLs (qscb-4., qscb-8., and qscb-.) were detected for the color

8 Wang et al. BMC Genomics (26) 7:3 a Page 8 of 3 PY WC PH PH HFC HFC CZL TL CZL TL NN NN NL NL - - PH ICH CZL TL NN NL Average YL PH PH ICH HFC CZL CZL TL NN NN NL NL b Fig. 4 (See legend on next page.) TL