Genetic diversity and population structure of the Mediterranean sesame core collection with use of genome-wide SNPs developed by double digest RAD-Seq

Autoři: Merve Basak aff001;  Bulent Uzun aff001;  Engin Yol aff001
Působiště autorů: Department of Field Crops, Faculty of Agriculture, Akdeniz University, Antalya, Turkey aff001
Vyšlo v časopise: PLoS ONE 14(10)
Kategorie: Research Article


The Mediterranean sesame core collection contains agro-morphologically superior sesame accessions from geographically diverse regions in four continents. In the present investigation, the genetic diversity and population structure of this collection was analyzed with 5292 high-quality SNPs discovered by double-digest restriction site associated DNA (ddRAD) sequencing, a cost-effective and flexible next-generation sequencing method. The genetic distance between pairs of accessions varied from 0.023 to 0.524. The gene diversity was higher in accessions from Asia than from America, Africa, and Europe. The highest genetic differentiation was observed between accessions collected from America and Europe. Structure analysis showed the presence of three subpopulations among the sesame accessions, and only six accessions were placed in an admixture group. Phylogenetic tree and principal coordinate analysis clustered the accessions based on their countries of origin. However, no clear division was evident among the sesame accessions with regard to their continental locations. This result was supported by an AMOVA analysis, which revealed a genetic variation among continental groups of 5.53% of the total variation. The large number of SNPs clearly indicated that the Mediterranean sesame core collection is a highly diverse genetic resource. The collection can be exploited by breeders to select appropriate accessions that will provide high genetic gain in sesame improvement programs. The high-quality SNP data generated here should also be used in genome-wide association studies to explore qualitative trait loci and SNPs related to economically and agronomically important traits in sesame.

Klíčová slova:

Asia – Crop genetics – Genetic polymorphism – Molecular genetics – Phylogeography – Plant breeding – Population genetics – Species diversity


1. Weiss EA. Castor, sesame and safflower. Aberdeen: Barnes and Noble Inc.; 1971.

2. Bedigian D, Harlan JR. Evidence for cultivation of sesame in the ancient world. Econ Bot. 1986; 40:137–154.

3. FAO. Faostat. FAO, Rome, Italy. 16 June 2019.

4. Uzun B, Arslan C, Furat S. Variation in fatty acid compositions, oil content and oil yield in a germplasm collection of sesame (Sesamum indicum L.). J Am Oil Chem Soc. 2008; 85:1135–1142.

5. Moazzami AA, Kamal-Eldin A. Sesame seed is a rich source of dietary lignans. J Am Oil Chem Soc. 2006; 83:719–723.

6. Erbas M, Sekerci H, Gul S, Furat S, Yol E, Uzun B. Changes in total antioxidant capacity of sesame (Sesamum sp.)by variety. Asian J Chem. 2009; 21:5549–5555.

7. Ashri A. Sesame. In: Singh RJ, editor. Genetics Resources, Chromosome Engineering and Crop Improvement, Vol. 4, Oilseed Crops. CRC Press; 2007. pp. 231–289.

8. Uzun B, Lee D, Donini P, Cagirgan MI. Identification of a molecular marker linked to the closed capsule mutant trait in sesame using AFLP. Plant Breed. 2003; 122:95–97.

9. Uzun B, Cagirgan MI. Comparison of determinate and indeterminate lines of sesame for agronomic traits. Field Crops Res. 2006; 96:13–18.

10. Ram SG, Sundaravelpandian K, Kumar M, Vinod KK, Bapu JRK, Raveendran TS. Pollen–pistil interaction in the inter-specific crosses of Sesamum sp. Euphytica. 2006; 152:379–385.

11. Ikten C, Catal M, Yol E, Ustun R, Uzun B. Molecular identification, characterization and transmission of phytoplasmas associated with sesame phyllody in Turkey. Eur J Plant Pathol. 2014; 139:217–229.

12. Bisht IS, Mahajan RK, Loknothan TR, Agrawal RC. Diversity in Indian sesame collection and stratification of germplasm accessions in different diversity groups. Genet Resour Crop Evol. 1998; 45:325–335.

13. Arriel NHC, Di Mauro AO, Arriel EF, Trevisoli SHU, et al. Genetic divergence in sesame based on morphological and agronomic traits. Crop Breed Appl. Biotechnol. 2007; 7;253–261.

14. Morris JB. Characterization of sesame (Sesamum indicumL.) germplasm regenerated in Georgia, USA. Genet Resour Crop Evol. 2009; 56:925–936.

15. Yol E, Uzun B. Geographical patterns of sesame (Sesamum indicum L.) accessions grown under Mediterranean environmental conditions, and establishment of a core collection. Crop Sci. 2012; 52:2206–2214.

16. Nimmakayala P, Levi A, Abburi L, Abburi VL, et al. Single nucleotide polymorphisms generated by genotyping by sequencing to characterize genome-wide diversity, linkage disequilibrium, and selective sweeps in cultivated watermelon. BMC Genomics. 2014; 15:767. 25196513

17. Pham TD, Tri MB, Gun W, Tuyen CB, Arnulf MA, Carlsson S. A study of genetic diversity of sesame (Sesamum indicum L.) in Vietnam and Cambodia estimated by RAPD markers. Genet Resour Crop Evol. 2009; 56:679–690.

18. Dar AA, Mudigunda S, Mittal PK, Arumugam N. Comparative assessment of genetic diversity in Sesamum indicum L. using RAPD and SSR markers. 3 Biotech. 2017; 7: 10. 28391476

19. Laurentin HE, Karlovsky P. Genetic relationship and diversity in a sesame (Sesamum indicum L.) germplasm collection using amplified fragment length polymorphism (AFLP). BMC Genet. 2006; 7:10. 16483380

20. Woldesenbet DT, Tesfaye K, Bekele E. Genetic diversity of sesame germplasm collection (Sesamum indicum L.): implication for conservation, improvement and use. Int J Biotechnol Mol Biol Res. 2015; 6:7–18.

21. Wei X, Wang L, Zhang Y, Qi X, et al. Development of simple sequence repeat (SSR) markers of sesame (Sesamum indicum) from a genome survey. Molecules. 2014; 19: 5150–5162. doi: 10.3390/molecules19045150 24759074

22. Wu K, Yang M, Liu H, Tao Y, Mei J, Zhao Y. Genetic analysis and molecular characterization of Chinese sesame (Sesamum indicum L.) cultivars using Insertion-Deletion (InDel) and Simple Sequence Repeat (SSR) markers. BMC Genet. 2014; 15:35. 24641723

23. Wei X, Liu K, Zhang Y, Feng Q, Wang L, Zhao Y, et al. Genetic discovery for oil production and quality in sesame. Nat Commun. 2015; 6:8609. 26477832

24. Cui C, Mei H, Liu Y, Zhang H, Zheng Y. Genetic diversity, population structure, and linkage disequilibrium of an association-mapping panel revealed by genome-wide SNP markers in sesame. Front Plant Sci. 2017; 8:1189.

25. Gupta PK, Roy JK, Prasad M. Single nucleotide polymorphisms: a new paradigm for molecular marker technology and DNA polymorphism detection with emphasis on their use in plants. Curr Sci. 2001; 80:524–535.

26. Ray S, Satya P. Next generation sequencing technologies for next generation plant breeding. Front Plant Sci. 2014; 5;367. 25126091

27. Peterson BK, Weber JN, Kay EH, Fisher HS, Hoekstra HE. Double digest RADseq: an inexpensive method for de novo SNP discovery and genotyping in model and non-model species. PLoS ONE. 2012; 7(5):e37135. 22675423

28. Scheben A, Batley J, Edwards D. Genotyping-by-sequencing approaches to characterize crop genomes: choosing the right tool for the right application. Plant Biotechnol J. 2017; 15:149–161. doi: 10.1111/pbi.12645 27696619

29. Baird NA, Etter PD, Atwood TS, Currey MC, Shiver AL, Lewis ZA, Johnson EA. Rapid SNP discovery and genetic mapping using sequenced RAD markers. PLoS ONE. 2008; 3;e3376. 18852878

30. Da Costa JM, Sorenson MD. Amplification biases and consistent recovery of loci in a double-digest RAD-seq protocol. PLoS ONE. 2014; 9:e106713. 25188270

31. Elshire RJ, Glaubitz JC, Sun Q, Poland JA, Kawamoto K, Buckler ES, Mitchell SE. A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS ONE. 2011; 6:e19379. 21573248

32. Davik J, Sargent DJ, Brurberg MB, Lien S, Kent M, Alsheikh M. A ddRAD based linkage map of the cultivated strawberry, Fragaria xananassa. PLoS ONE. 2015; 10: e0137746. 26398886

33. Chen J, Wang B, Zhang Y, Yue X, Li Z, Liu K. High-density ddRAD linkage and yield-related QTL mapping delimits a chromosomal region responsible for oil content in rapeseed (Brassica napus L.). Breed Sci. 2017; 67:296–306 doi: 10.1270/jsbbs.16116 28744183

34. Jaiswal V, Gupta S, Gahlaut V, Muthamilarasan M, Bandyopadhyay T, Ramchiary N., Prasad M. Genome-wide association study of major agronomic traits in foxtail millet (Setariaitalica L.) using ddRAD sequencing. PloS ONE. 2019; 9:5020.

35. Ma B, Liao L, Peng Q, Fang T, Zhou H, Korban SS, Han Y. Reduced representation genome sequencing reveals patterns of genetic diversity and selection in apple. J Integr Plant Biol. 2017; 59:190–204. doi: 10.1111/jipb.12522 28093854

36. Roy SC, Moitra K, De Sarker D. Assessment of genetic diversity among four orchids based on ddRAD sequencing data for conservation purposes. Physiol Mol Biol Plants. 2017; 23:169–183. doi: 10.1007/s12298-016-0401-z 28250593

37. Lee J-H, Natarajan S, Biswas MK, Shirasawa K, Isobe S, Kim H-T, et al. SNP discovery of Korean short day onion inbred lines using double digest restriction site-associated DNA sequencing. PLoS ONE. 2018; 13:e0201229. 30086138

38. Frankel OH. Genetic perspective of germplasm conservation. In: Arber W, Llimensee K, Peacock WJ, Starlinger P, editors. Genetic Manipulations: Impact on Man and Society. Cambridge: Cambridge University Press; 1984. pp. 161–170.

39. Yol E, Toker R, Golukcu M, Uzun B. Oil content and fatty acid characteristics in Mediterranean sesame core collection. Crop Sci. 2015; 55:2177–2185.

40. Ustun R., Yol E, Ikten C, Catal M, Uzun B. Screening, selection and real-time qPCR validation for phytoplasma resistance in sesame (Sesamum indicum L.). Euphytica. 2017; 213:159.

41. Doyle JJ, Doyle JL. A rapid total DNA preparation procedurefor fresh plant tissue. Focus.1990; 12; 13–15.

42. Girardot C, Scholtalbers J, Sauer S, Su S, Furlong EEM. Je, a versatile suite to handle multiplexed NGS libraries with unique molecular identifiers. BMC Bioinformatics. 2016; 17:419. 27717304

43. Chen S, Zhou Y, Chen Y, Gu J. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics. 2018; 34:884–890.

44. Wang L, Xia Q, Zhang Y, Zhu X, Zhu X, et al. Updated sesame genome assembly and fine mapping of plant height and seed coat color QTLs using a new high-density genetic map. BMC Genomics. 2016; 17:31. 26732604

45. Langmead B, Salzberg SL. Fast gapped-read alignment with bowtie 2. Nature Methods. 2012; 9:357–359. doi: 10.1038/nmeth.1923 22388286

46. Garrison E, Marth G. Haplotype-based variant detection from short-read sequencing. arXiv. 2012; 1207.3907

47. Glaubitz JC, Casstevens TM, Lu F, Harriman J, Elshire RJ, et al. TASSEL-GBS: A high capacity genotyping by sequencing analysis pipeline. PLoS ONE. 2014; 9: e90346. 24587335

48. Lischer HEL, Excoffier L. PGDSpider: An automated data conversion tool for connecting population genetics and genomics programs. Bioinformatics. 2012; 28:298–299. doi: 10.1093/bioinformatics/btr642 22110245

49. Pritchard JK, Stephens M, Donnelly P. Inference ofpopulation genetic structure using multi locus genotype data. Genetics. 2000; 155:945–959. 10835412

50. Evanno G, Regnaut S, Goudet J. Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol. 2005; 14:2611–2620. doi: 10.1111/j.1365-294X.2005.02553.x 15969739

51. Earl DA, vonHoldt BM. STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conserv Genet Resour. 2012; 4:359–361.

52. Ramasamy RK, Ramasamy S, Bindroo BB, Naik VG. STRUCTURE PLOT: a program for drawing elegant STRUCTURE bar plots in user friendly interface. Springerplus. 2014; 13:431.

53. Hammer Ø, Harper DAT, Ryan PD. PAST: Paleontological statistics software package for education and data analysis. Palaeontol Electron. 2001; 4:9.

54. Sokal RR, Michener CD. A statistical method for evaluating systematic relationships. Univ. Kans. Sci. Bull. 1958; 28:1409–1438.

55. Excoffier L, Lischer H. Arlequin suite ver 3.5: A new series of programs to perform population genetics analyses under Linux and Windows. Mol Ecol Resour. 2010; 10: 564–567. doi: 10.1111/j.1755-0998.2010.02847.x 21565059

56. Mohammadi SA, Prasanna BM. Analysis of genetic diversity in crop plants—salient statistical tools and considerations. Crop Sci. 2003; 43:1235–1248.

57. Peakall R, Smouse PE. GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research-an update. Bioinformatics. 2012; 28:2537–2539. doi: 10.1093/bioinformatics/bts460 22820204

58. Bailey T, Krajewski P, Ladunga I, Lefebvre C, Li Q, et al. Practical guidelines for the comprehensive analysis of ChIP-seq data. PLoS Comput Biol. 2013; 9:e1003326. 24244136

59. Bhat KV, Babrekar PP, Lakhanpaul S. Study of genetic diversity in Indian and exotic sesame(Sesamum indicum L.) germplasm using random amplified polymorphic DNA (RAPD) markers. Euphytica.1999; 110:21–33.

60. Ali GM, Yasumoto S, Seki-Katsuta M. Assessment of genetic diversity in sesame (Sesamum indicum L.) detected by amplified fragment length polymorphism markers. Electron J Biotechnol. 2007; 10:12–23.

61. Zhang YX, Zhang XR, Hua W, Wang LH, Che Z. Analysis of genetic diversity among indigenous landraces from sesame (Sesamum indicum L.) core collection in China as revealed by SRAP and SSR markers. Genes Genom. 2010; 32:207–215.

62. Dossa K, Wei X, Zhang Y, Fonceka D, Yang W, et al. Analysis of genetic diversity and population structure of sesame accessions from Africa and Asia as Major centers of its cultivation. Genes. 2016; 7:14.

63. Nachman MW. Single nucleotide polymorphisms and recombination rate in humans. Trends Genet. 2001; 17:481–485. doi: 10.1016/s0168-9525(01)02409-x 11525814

64. Rogozin IB, Pavlov YI. Theoretical analysis of mutation hot spots and their DNA sequence context specificity. Mutat Res. 2003; 544:65–85. doi: 10.1016/s1383-5742(03)00032-2 12888108

65. Liu H, Bayer M, Druka A, Russell JR, Hackett CA, Poland J, et al. An evaluation of genotyping by sequencing (GBS) to map the Breviaristatum-e (ari-e) locus in cultivated barley. BMC Genomics. 2014; 15:104. 24498911

66. Cho YI, Park JH, Lee CW, Ra WH, et al. Evaluation of the genetic diversity and population structure of sesame (Sesamum indicum L.) using microsatellite markers. Genes Genom. 2011; 33:187–195.

67. Van Inghelandt D, Melchinger AE, Lebreton C, Stich B. Population structure and genetic diversity in a commercial maize breeding program assessed with SSR and SNP markers. Theor Appl Genet. 2010; 120:1289–1299. 20063144

68. Paterson A. Genetics and genomics of cotton. In: Paterson A, editor. Plant Genetics and Genomics: Crops and Models. New York: Springer-Verlag; 2009. pp. 493–509.

69. Wei X, Qiao WH, Chen YT, Wang RS. Domestication and geographic origin of Oryza sativa in China: Insights from multilocus analysisof nucleotide variation of O. sativa and O. rufipogon. Mol Ecol. 2012; 21:5073–5087. doi: 10.1111/j.1365-294X.2012.05748.x 22989375

70. Ercan AG, Taskin M, Turgut K. Analysis of genetic diversity in Turkish sesame (Sesamum indicum L.) populations using RAPD markers. Genet. Resour. Crop Evol. 2004; 51:599–607.

71. Gupta PK, Rustgi S, Sharma S, Singh R, Kumar N, Balyan HS. Transferable EST-SSR markers for the study of polymorphismand genetic diversity in bread wheat. Mol Genet Genomic. 2003; 270:315–323.

72. Kumar A, Sharma D, Tiwari A, Jaiswal JP, Singh NK, Sood S. Genotyping-by-sequencing analysis for determining population structure of finger millet germplasm of diverse origins. Plant Genome. 2016; 9:2.

73. Agrama HA, Tuinstra MR. Phylogenetic diversity and relationships among sorghum accessions using SSRs and RAPDs. Afr J Biotechnol. 2003; 2:334–340.

74. Bedigian D. Evolution of sesame revisited: domestication, diversity and prospects. Genet Resour Crop Evol. 2003; 50:779–787.

75. Wang Y, Rashid MAR, Li X, Yao C, et al. Collection and evaluation of genetic diversity and population structure of potato landraces and varieties in china. Front Plant Sci. 2019; 10:139. 30846993

Článek vyšel v časopise


2019 Číslo 10
Nejčtenější tento týden