Deep resequencing reveals allelic variation in Sesamum indicum

Abstract

BackgroundCharacterization 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.ResultsHere 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.ConclusionsThis 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).Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-014-0225-3) contains supplementary material, which is available to authorized users.

Insight into the evolution and functional characteristics of the pan‐genome assembly from sesame landraces and modern cultivars

“…Wang et al . (,b) pioneered sesame genomic research with the sequencing and assembly of the modern Chinese cultivar Zhongzhi13. Sesame has a small diploid genome (∼357 Mb) and the draft assembly consisted of 274 Mb in 16 linkage groups and contained 27 148 predicted protein‐coding genes (Wang et al ., ).…”

“…Sesame has a wide geographic distribution, but mainly grown in both Asia and Africa (Kobayashi, 1981;Pham et al, 2011). In contrast to many other crop species, cultivated sesame varieties display a high degree of genetic diversity which can be utilized for crop improvement (Dossa et al, 2016;Uncu et al, 2015;Wang et al, 2014a;Wei et al, 2014;Zhang et al, 2012). The genetic and associated phenotypic variation of sesame may be a result of adaptation to diverse growth habitats (Bedigian and Harlan, 1986), as well as the artificial selection pressures resulting in its partially domesticated status (Wei et al, 2015).…”

Assessment of genetic variability in sesame accessions using SSR markers and morpho-agronomic traits

“…The seeds have high nutritional value, due to protein quality and oil, and are also an important source of anti-oxidants compounds, like sesamol and sesamolina, both with anti-hypertensive and anti-cancerous properties (Dar et al, 2015). The sesame plant is easy to handle and has wide environmental adaptation; however, biotic and abiotic stresses may affect the crop yield, depending on the intensity and duration (Gepstein and Glik, 2013;Cooper et al, 2014;Wang et al, 2014). Nowadays, the main challenge of agriculture is to develop technologies to increase food production and allow sustainability, especially under limited resources of the environment.…”

Analysis of genetic variation and potential applications in genome-scale metabolic modeling

“…NGS has allowed de novo assembly of the genomes of thousands of organisms for which no genome sequences were previously available, ranging from complex multicellular organisms (Li et al, 2010 ; Nakamura et al, 2013 ; Pegadaraju et al, 2013 ; Kelley et al, 2014 ) to microorganisms (Soares-Castro and Santos, 2013 ; Yamamoto et al, 2014 ). NGS technologies also provide us with the means to re-sequence organisms (Atsumi et al, 2010 ; Wang et al, 2014 ), i.e., the sequencing of genetically distinct strains that are close enough to a reference strain with a sequenced genome. Re-sequencing is used to determine genetic variants ranging from single nucleotide variants (SNV) to more complex structural variants such as large deletions, inversions, and translocations.…”