Identification of sesame (Sesamum indicum L.) chromosomes using the BAC‐FISH system

Abstract

Sesame (Sesamum indicum L.; Pedaliaceae) is a commercially valuable oilseed crop with high oil content. Its small genome size favours the genomic analysis of key biological processes, such as oil synthesis and metabolism. However, the 13 chromosome pairs of sesame have not been characterised because of technological limitations and their small size. We constructed a BAC library comprising 57,600 BAC clones for sesame. The estimated genome coverage of the sesame BAC library was 13.8×. The successive double colour fluorescence in situ hybridisation (FISH) with bacterial artificial chromosomes (BACs) for sesame was established in this study. Subsequently, the 13 sesame chromosome pairs were individually differentiated using 17 specific BACs for the first time. The schematic of the sesame chromosome set was drawn according to the chromosome relative length and relative position of the BAC signal. The cytogenetic characteristics of sesame chromosomes were also explored. The results provide the technical background required for further cytogenetic map construction, genome assembly and localisation of the DNA sequence in sesame.

Identification of a SiCL1 gene controlling leaf curling and capsule indehiscence in sesame via cross-population association mapping and genomic variants screening

“…The interval C29 between C29_6522236 and C29_6918901 markers contained 90 variants with the P value variation of 3.97 × E − 19 to 3.00 × E − 94 (Additional file 1 : Table S1). According to the interval site of Scaffold C29 and the chromosome nomination described by Zhao et al [ 25 , 26 ], the LG 8 of the cross population corresponded to the Si Chr. 1 of S. indicum .…”

“…In addition, candidate-gene analyses within linked regions have been greatly accelerated by the availability of the complete sequence of the genome [ 32 ]. To accurately carry out the association mapping, we used the fine sesame genome (Yuzhi 11, GCA_001692995.1), SNP genetic map [ 5 ], and the chromosome set annotation system described by Zhao et al [ 25 ] in this study. The high-quality genome supplied the reliable genomic information.…”

“…Raw reads obtained from the Illumina HiSeq 2500 platform were filtered using Trimmomatic 0.33 [ 37 ]. Based on the ultra-dense SNP genetic map [ 5 ] and chromosome annotation results [ 25 ], the genome data of Yuzhi 11 (PRJNA315784) (version 2.0) was re-assembled and applied as the reference genome in this study [ 38 ]. Alignment of re-sequencing data to the reference genome was performed using BWA 0.7.15 with the default settings described by Li and Durbin [ 39 ].…”

“…The target interval was defined as the two-side flanking regions (400 Kb distance) of the SNP/InDel variant with the lowest association P value. Distribution of the genome scaffolds in 13 chromosomes was numbered according to the chromosome annotation described by Zhao et al [ 25 ]. Home-made scripts were used to screen the specific SNPs and InDels of the target interval.…”

A SNP Mutation of SiCRC Regulates Seed Number Per Capsule and Capsule Length of cs1 Mutant in Sesame

“…After filtering, 496,486 SNP/InDel variants were detected for Joint calling. According to the reference sesame genome (Yuzhi 11) and the nomination of the sesame chromosome set [23,26], a total of 423,138 SNP/InDel variants were plotted in 13 chromosomes (Figure 4). Association mapping results showed that the variant site (C11_4680332) with the lowest p -value (5.43E −51 ) was located on the contig 11 of Si Chr.6.…”