title: Updated sesame genome assembly and fine mapping of plant height and seed coat color QTLs using a new high-density genetic map.
abstract: BACKGROUND
  Sesame is an important high-quality oil seed crop. The sesame genome was de novo sequenced and assembled in 2014 (version 1.0); 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 13 linkage groups.
  
  
  RESULTS
  We resequenced a permanent population consisting of 430 recombinant inbred lines and constructed a genetic map to improve the sesame genome assembly. We successfully anchored 327 scaffolds onto 13 pseudomolecules. The new genome assembly (version 2.0) included 97.5 % of the scaffolds greater than 150 kb in size present in assembly version 1.0 and increased the total pseudomolecule length from 233.7 to 258.4 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 1,522 bins spanning 1090.99 cM was generated and used to identified 41 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 18 % of the plant height were located in 350 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 102 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-4.1 contributed approximately 39 % of the b* value and was located on Chr4 in a 199.9-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.
authors.affiliation: 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, 430062, China. linhai827@163.com.
authors.forename: Linhai
authors.initials: L
authors.lastname: Wang
authors.affiliation: Shenzhen Engineering Laboratory of Crop Molecular Design Breeding, BGI-agro, 518083, Shenzhen, China. xiaqiuju@genomics.org.cn.
authors.forename: Qiuju
authors.initials: Q
authors.lastname: Xia
authors.affiliation: 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, 430062, China. 13277065857@163.com.
authors.forename: Yanxin
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: 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, 430062, China. 554656956@qq.com.
authors.forename: Xiaodong
authors.initials: X
authors.lastname: Zhu
authors.affiliation: 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, 430062, China. xfsunny90@163.com.
authors.forename: Xiaofeng
authors.initials: X
authors.lastname: Zhu
authors.affiliation: 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, 430062, China. ldh360681@163.com.
authors.forename: Donghua
authors.initials: D
authors.lastname: Li
authors.affiliation: Shenzhen Engineering Laboratory of Crop Molecular Design Breeding, BGI-agro, 518083, Shenzhen, China. nixuemei@genomics.cn.
authors.forename: Xuemei
authors.initials: X
authors.lastname: Ni
authors.affiliation: 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, 430062, China. gaoyuan0612@163.com.
authors.forename: Yuan
authors.initials: Y
authors.lastname: Gao
authors.affiliation: Shenzhen Engineering Laboratory of Crop Molecular Design Breeding, BGI-agro, 518083, Shenzhen, China. xianghaitao@genomics.cn.
authors.forename: Haitao
authors.initials: H
authors.lastname: Xiang
authors.affiliation: 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, 430062, China. weixin8002@gmail.com.
authors.forename: Xin
authors.initials: X
authors.lastname: Wei
authors.affiliation: 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, 430062, China. yujyinfor@gmail.com.
authors.forename: Jingyin
authors.initials: J
authors.lastname: Yu
authors.affiliation: Shenzhen Engineering Laboratory of Crop Molecular Design Breeding, BGI-agro, 518083, Shenzhen, China. Quanzhiwu@genomics.org.cn.
authors.forename: Zhiwu
authors.initials: Z
authors.lastname: Quan
authors.affiliation: 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, 430062, China. zhangxr@oilcrops.cn.
authors.forename: Xiurong
authors.initials: X
authors.lastname: Zhang
mesh_terms: D002874:Chromosome Mapping; D008040:Genetic Linkage; D018745:Genome, Plant / Q000235:genetics*; D005838:Genotype; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D040641:Quantitative Trait Loci / Q000235:genetics*; D012639:Seeds / Q000235:genetics / Q000254:growth & development; D031685:Sesamum / Q000235:genetics*