title: Deep resequencing reveals allelic variation in Sesamum indicum.
abstract: BACKGROUND
  Characterization of genome-wide patterns of allelic variation and linkage disequilibrium can be used to detect reliable phenotype-genotype associations and signatures of molecular selection. However, the use of Sesamum indicum germplasm for breeding is limited by the lack of polymorphism data.
  
  
  RESULTS
  Here we describe the massively parallel resequencing of 29 sesame strains from 12 countries at a depth of ≥ 13-fold coverage for each of the samples tested. We detected an average of 127,347 SNPs, 17,961 small InDels, and 9,266 structural variants per sample. The population SNP rate, population diversity (π) and Watterson's estimator of segregating sites (θw) were estimated at 8.6 × 10⁻³, 2.5 × 10⁻³ and 3.0 × 10⁻³ bp⁻¹, respectively. Of these SNPs, 23.2% were located within coding regions. Polymorphism patterns were nonrandom among gene families, with genes mediating interactions with the biotic or abiotic environment exhibiting high levels of polymorphism. The linkage disequilibrium (LD) decay distance was estimated at 150 kb, with no distinct structure observed in the population. Phylogenetic relationships between each of the 29 sesame strains were consistent with the hypothesis of sesame originating on the Indian subcontinent. In addition, we proposed novel roles for adenylate isopentenyltransferase (ITP) genes in determining the number of flowers per leaf axil of sesame by mediating zeatin biosynthesis.
  
  
  CONCLUSIONS
  This study represents the first report of genome-wide patterns of genetic variation in sesame. The high LD distance and abundant polymorphisms described here increase our understanding of the forces shaping population-wide sequence variation in sesame and will be a valuable resource for future gene-phenotype and genome-wide association studies (GWAS).
authors.forename: Linhai
authors.initials: L
authors.lastname: Wang
authors.forename: Xuelian
authors.initials: X
authors.lastname: Han
authors.forename: Yanxin
authors.initials: Y
authors.lastname: Zhang
authors.forename: Donghua
authors.initials: D
authors.lastname: Li
authors.forename: Xin
authors.initials: X
authors.lastname: Wei
authors.forename: Xia
authors.initials: X
authors.lastname: Ding
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: D000483:Alleles; D014644:Genetic Variation; D018745:Genome, Plant; D006239:Haplotypes; D059014:High-Throughput Nucleotide Sequencing; D015810:Linkage Disequilibrium; D010641:Phenotype; D017422:Sequence Analysis, DNA; D031685:Sesamum / Q000235:genetics*