Skip to main content
SpringerLink
Log in

Genetic diversity of Sesame (Sesamum indicum L) using high throughput diversity array technology

  • Original Research
  • Published:
Journal of Crop Science and Biotechnology Aims and scope Submit manuscript

Abstract

Sesame is an important oil crop widely cultivated in Africa and Asia. Characterization of genetic diversity and population structure of sesame genotypes in these continents can be used to designing breeding methods. In the present study, 300 genotypes comprising 209 Ethiopian landraces, and 75 exotic collections from different African and Asia countries, and 16 varieties were used. The panel was genotyped using two high-throughput diversity array technology markers. A total of 6115 silicoDArT and 6474 SNP markers were reported, of which 5065 silicoDArT and 5821 SNP markers were aligned with the reference sesame genome. For further analysis, it was filtered with an allele frequency for each SNP site and left 2997 high-quality SNPs. All genotypes used in this study were descended from eight geographical origins. The average diversity of the panel was 0.14. Considering the genotypes based on their geographical origin, Africa collections (0.21) without Ethiopian collection was more diverse, when further portioned Africa, North Africa (0.23) collection was more diverse than others, but at the continent level, Asia (0.17) was more diverse than Africa (0.14). The genetic distance among the populations was ranged from 0.015 to 0.394. The populations were clustered into four groups. The structure analysis was divided into four hypothetical ancestral populations and 21 genotypes were an admixture. This indicate genotypes from the same origin didn’t classify on the country of origin. The genetic diversity and population structure guide future research work to design association studies and the systematic utilization of genetic resource.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4

Similar content being viewed by others

References

  • Abate M, Mekbib F (2015) Assessment of genetic diversity in Ethiopian sesame (Sesamum indicum L.) germplasm using random amplified polymorphic DNA (RAPD) markers council for innovative research. J Adv Agric 5:639–649

    Google Scholar 

  • Abate M, Mekbib F, Ayana A, Nigussie M (2015) Genetic variability and association of traits in mid-altitude sesame (Sesamum indicum L.) Germplasm of Ethiopia. Am J Exp Agric 9:1–14

    Google Scholar 

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

    Article  Google Scholar 

  • Basak M, Uzun B, Id EY (2019) Genetic diversity and population structure of the Mediterranean sesame core collection with the use of genome-wide SNPs developed by double digest RAD-Seq, pp 1–15

  • Bastien M, Sonah H, Belzile F (2014) Genome wide association mapping of Sclerotinia sclerotiorum resistance in soybean with a genotyping-by-sequencing approach. The Plant Genome 7:1–13

    Article  Google Scholar 

  • Bedigian D, Harlan JR (1986) Evidence for cultivation of sesame in the ancient world. The New York Botanical Garden 40:137–154

    Google Scholar 

  • Bolibok-Bragoszewska H, Heller-Uszyńska K, Wenzl P, Uszyński G, Kilian A, Rakoczy-Trojanowska M (2009) DArT markers for the rye genome - genetic diversity and mapping. BMC Genomics 10:1–11

    Article  CAS  Google Scholar 

  • Cho YI, Park JH, Lee CW, Ra WH, Chung JW, Lee JR, Ma KH, Lee SY, Lee KS, Lee MCPY (2011) Evaluation of the genetic diversity and population structure of sesame (Sesamum indicum L.) using microsatellite markers. Genes Genomics 33:187–195

    Article  Google Scholar 

  • Courtois B, Audebert A, Dardou A, Roques S, Ghneim-Herrera T, Droc G, Frouin J, Rouan L, Gozé E, Kilian AAN (2013) Genome-wide association mapping of root traits in a japonica rice panel. PLoS ONE 8(11):e78037

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Cruz VMV, Kilian A, Dierig DA (2013) Development of DArT marker platforms and genetic diversity assessment of the US collection of the new oilseed crop lesquerella and related species. PLoS ONE 8:e64062

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • CSA (Central Statistical Agency) (2018) Agricultural sample survey report on area and production of major crops (Private Peasant Holdings, Meher Season)

  • CSA (Central Statistical Agency) (2019) Agricultural sample survey 2019/2020 (2012 E.C.) (September–January 2019/2020) Volume VII report on crop and livestock product utilization (Private Peasant Holdings, Meher Season)

  • Cui C, Mei H, Liu Y, Zhang H, Zheng Y (2017) Genetic diversity, population structure, and linkage disequilibrium of an association-mapping panel revealed by genome-wide SNP markers in sesame. Front Plant Sci 8:1–10

    Google Scholar 

  • Dierig D, Ray DT (2009) New crops breeding: Lesquerella. In: Vollmann J, Rajcan I (eds) Oil crops. Springer, New York, pp 507–516

    Chapter  Google Scholar 

  • Dossa K, Wei X, Zhang Y, Fonceka D, Yang W, Diouf D (2016) Analysis of genetic diversity and population structure of sesame accessions from Africa and Asia as major centers of its cultivation. Genes 7:1–13

    Article  CAS  Google Scholar 

  • Earl DA, VonHoldt BM (2012) STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conserv Genet Resour 4:359–361

    Article  Google Scholar 

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

    Article  CAS  Google Scholar 

  • Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol 14:2611–2620

    Article  CAS  PubMed  Google Scholar 

  • Excoffier L, Lischer HEL (2010) A new series of programs to perform population genetics analyses under Linux and Windows. Mol Ecol Resour 10:564–567

    Article  PubMed  Google Scholar 

  • FAOSTAT. 2019. Food and agriculture organization statistical databases. Accessed from http://www.fao.org/faostat/en/#home

  • Farshadfar M, Farshadfar E (2008) Genetic variability and path analysis of chickpea (Cicer arientinum L.) landraces and lines. J Appl Sci 8:3951–3956

    Article  Google Scholar 

  • Flint-Garcia SA, Thuillet AC, Yu J, Pressoir G, Romero SM, Mitchell SE, Doebley J, Kresovich S, Goodman MM, Buckler ES (2005) Maize association population: a high-resolution platform for quantitative trait locus dissection. Plant J 44:1054–1064

    Article  CAS  PubMed  Google Scholar 

  • Gebremichael DE (2017) Sesame (Sesamum indicum L.) breeding in Ethiopia. Int J Novel Res Life Sci 4:1–11

    Google Scholar 

  • Gebremichael DE, Heiko KP (2011) Genetic variability among landraces of sesame in Ethiopia. Afr Crop Sci J 19:1–13

    Article  Google Scholar 

  • Gidey YT, Kebede SAGG (2012) Extent and pattern of genetic diversity for morpho-agronomic traits in Ethiopian sesame landraces (Sesamum indicum L.). Asian J Agric Res 6:118–128

    Google Scholar 

  • Gupta PK, Rustgi S, Mir RR (2008) Array-based high-throughput DNA markers for crop improvement. Heredity 101:5–18

    Article  CAS  PubMed  Google Scholar 

  • Huang YF, Poland JA, Wight CP, Jackson EW, Tinker NA (2014) Using genotyping-by-sequencing (GBS) for genomic discovery in cultivated oat. PLoS ONE 9:1–16

    Google Scholar 

  • Institute of Biodiversity Conservation (IBC) (2012) Ethiopia: third country report on the state of plant genetic resources for food and agriculture. Addis Ababa, Ethiopia

  • Jarvis DI, Hodgkin T (1998) Wild relatives and crop cultivars: conserving the connection. In The Proceedings of an International Symposium on in situ conservation of plant genetic diversity. George Allen & Unwin, London, UK. pp 163–179

  • Jarvis DI, Hodgkin T (1999) Wild relatives and crop cultivars: detecting natural introgression and farmer selection of new genetic combinations in agroecosystems. Mol Ecol 8:S159–S173

    Article  Google Scholar 

  • Kilian A, Sanewski G, Ko L (2016) The application of DArTseq technology to pineapple. In: XXIX international horticultural congress on horticulture: sustaining lives, livelihoods and landscapes (IHC2014) IV, vol 1111. Humana Press, Totowa, pp 181–188

  • Kilian A, Huttner E, Wenzl P, Jaccoud D, Carling J, Caig V, Evers M, Heller-Uszynska K, Cayla C, Patarapuwadol S, Xia L (2003) The fast and the cheap: SNP and DArT-based whole genome profiling for crop improvement. In Proceedings of the international congress in the wake of the double helix: from the green revolution to the gene revolution. pp 443–461

  • Kilian A, Wenzl P, Huttner E, Carling J, Xia L, Blois H, Caig V, Heller-Uszynska K, Jaccoud D, Hopper C A-KM (2012) Diversity arrays technology: a generic genome profiling technology on open platforms. In: Data production and analysis in population genomics, pp 67–89. Humana Press, Totowa, NJ.

  • Kim DH, Zur G, Danin-Poleg Y, Lee SW, Shim KB, Kang CWKY (2002) Genetic relationships of sesame germplasm collection as revealed by inter-simple sequence repeats. Plant Breeding 121:259–262

    Article  CAS  Google Scholar 

  • Kumar H, Kaur G, Banga S (2012) Molecular characterization and assessment of genetic diversity in sesame (Sesamum indicum L.) germplasm collection using ISSR markers. J Crop Improv 26:540–557

    Article  CAS  Google Scholar 

  • Laidò G, Mangini G, Taranto F, Gadaleta A, Blanco A, Cattivelli L, Marone D, Mastrangelo AM, Papa RDVP (2013) Genetic diversity and population structure of tetraploid wheats ( Triticum turgidum L.) estimated by SSR, DArT and PEdigree data. PLoS ONE 8:1–17

    Article  CAS  Google Scholar 

  • Laurentin HE, Karlovsky P (2006) Genetic relationship and diversity in a sesame (Sesamum indicum L.) germplasm collection using amplified fragment length polymorphism (AFLP). BMC Genet 7:1–10

    Article  CAS  Google Scholar 

  • Lui K (2005) PowerMarker: integrated analysis environment for genetic marker data. Bioinformatics 21:2128–2129

    Article  Google Scholar 

  • Matthies IE, van Hintum T, Weise S, Röder MS (2012) Population structure revealed by different marker types (SSR or DArT) has an impact on the results of genome-wide association mapping in European barley cultivars. Mol Breeding 30:951–966

    Article  Google Scholar 

  • Merve B, Uzun Bulent YE (2019) Genetic diversity and population structure of the Mediterranean sesame core collection with use of genome-wide SNPs developed by double digest RAD-Seq. PLoS ONE 14:1–15

    Google Scholar 

  • Mkamilo GS, Bedigian D (2007) In PROTA (Plant Resources of Tropical Africa/Ressources végétales de l’Afrique tropicale). Wageningen, Netherlands

    Google Scholar 

  • Nei M (1972) Genetic distance between populations. Am Nat 106:283–292

    Article  Google Scholar 

  • Park YCJ, Ra CLW, Lee JCJ (2011) Evaluation of the genetic diversity and population structure of sesame (Sesamum indicum L. ) using microsatellite markers. Genes & Genomics 33:187–195

    Article  Google Scholar 

  • Pritchard JK, Stephens M, Donnelly P (2000) Structure software for population genetics inference (V.2.3.4)

  • Raman H, Raman R, Kilian A, Detering F, Carling J, Coombes N, Diffey S, Kadkol G, Edwards D, McCully MRP (2014) Genome-wide delineation of natural variation for pod shatter resistance in Brassica napus. PLoS ONE. https://doi.org/10.1371/journal.pone.0101673

    Article  PubMed  PubMed Central  Google Scholar 

  • Sánchez-Sevilla JF, Horvath A, Botella MA, Gaston A, Folta K, Kilian A, Denoyes B, Amaya I (2015) Diversity arrays technology (DArT) marker platforms for diversity analysis and linkage mapping in a complex crop, the octoploid cultivated strawberry (Fragaria × ananassa). PLoS ONE 10:1–22

    Article  CAS  Google Scholar 

  • Schaal BA, Hayworth DA, Olsen KM, Rauscher JT, Smith WA (1998) Phylogeographic studies in plants: problems and prospects. Mol Ecol 7:465–474

    Article  Google Scholar 

  • Sharaby N, Butovchenko A (2019) Cultivation technology of sesame seeds and its production in the world and in Egypt. IOP Conf Series: Earth Environ Sci 403:1–8

    Google Scholar 

  • Slatkin M (1987) Gene flow and the geographic structure of natural populations. Science 236:787–792

    Article  CAS  PubMed  Google Scholar 

  • Sonah H, Bastien M, Iquira E, Tardivel A, Légaré G, Boyle B, Normandeau É, Laroche J, Larose S, Jean MBF (2013) An improved genotyping by sequencing (GBS) approach offering increased versatility and efficiency of SNP discovery and genotyping. PLoS ONE 8:1–9

    Article  CAS  Google Scholar 

  • Song XJ, Kuroha T, Ayano M, Furuta T, Nagai K, Komeda N, Segami S, Miura K, Ogawa D, Kamura TST (2015) Rare allele of a previously unidentified histone H4 acetyltransferase enhances grain weight, yield, and plant biomass in rice. Proc Natl Acad Sci USA 112:76–81

    Article  CAS  PubMed  Google Scholar 

  • Tang J, Daroch M, Kilian A, Jeżowski S, Pogrzeba M, Mos M (2015) DArT-based characterisation of genetic diversity in a Miscanthus collection from Poland. Planta 242:985–996

    Article  CAS  PubMed  Google Scholar 

  • Teklu DH, DE Kebede SAG (2014) Assessment of genetic variability, genetic advance, correlation and path analysis for morphological traits in sesame genotypes. Asian J Agric Res 8:181–194

    Google Scholar 

  • Teshome D, Kassahun T, Bekele E (2015) Genetic diversity of sesame germplasm collection (SESAMUM INDICUM L.): implication for conservation, improvement and use. Int J Biotechnol Mol Biol Res 6:7–18

    Article  CAS  Google Scholar 

  • Tewodros T, Kassahun T, Gemechu K, Alemu T (2021) Morphological characteristics and genetic diversity of Ethiopian sesame genotypes. Afr Crop Sci J 29:59–77

    Google Scholar 

  • Vavilov NI (1951) The origin, variation, immunity and breeding of cultivated plants, vol 72. LWW, p 482

  • Wang L, Xia Q, Zhang Y, Zhu X, Zhu X, Li D, Ni X, Gao Y, Xiang H, Wei XYJ (2016) Updated sesame genome assembly and fine mapping of plant height and seed coat color QTLs using a new high-density genetic map. BMC Genomics 17:1–13

    CAS  Google Scholar 

  • Wang Y, Rashid MA, Li X, Yao C, Lu L, Bai J, Li Y, Xu N, Yang Q, Zhang LBG (2019) Collection and evaluation of genetic diversity and population structure of potato landraces and varieties in China. Front Plant Sci 10:1–11

    Google Scholar 

  • Ward JH (1963) Hierarchical grouping to optimize an objective function. J Am Stat Assoc 58:236–244

    Article  Google Scholar 

  • Wei X, Liu K, Zhang Y, Feng Q, Wang L, Zhao Y, Li D, Zhao Q, Zhu X, Zhu XLW (2015) Genetic discovery for oil production and quality in sesame. Nat Commun 6:1–10

    Article  Google Scholar 

  • Wei X, Qiao WH, Chen YT, Wang RS, Cao LR, Zhang WX, Yuan NN, Li ZC, Zeng HLYQ (2012) Domestication and geographic origin of Oryza sativa in China: insights from multilocus analysis of nucleotide variation of O. sativa and O. rufipogon. Mol Ecol 21:5073–5087

    Article  CAS  PubMed  Google Scholar 

  • Wei X, Wang L, Zhang Y, Qi X, Wang X, Ding X, Zhang JZX (2014) Development of simple sequence repeat (SSR) markers of sesame (Sesamum indicum) from a genome survey. Molecules 19:5150–5162

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Wenzl P, Carling J, Kudrna D, Jaccoud D, Huttner E, Kleinhofs A, Kilian A (2004) Diversity Arrays Technology (DArT) for whole-genome profiling of barley. Proc Natl Acad Sci USA 101:9915–9920

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wijnands JHM, Biersteker J, Hiel R (2007) Oilseeds business opportunities in Ethiopia. Ministry of Agriculture, Nature and Food Quality

  • Wu K, Liu H, Yang M, Tao Y, Ma H, Wu W, Zuo YZY (2014) High-density genetic map construction and QTLs analysis of grain yield-related traits in Sesame ( Sesamum indicum L.) based on RAD-Seq technology. BMC Plant Biol 14:1–14

    Article  CAS  Google Scholar 

  • Yang S, Pang W, Ash G, Harper J, Carling J, Wenzl P, Huttner E, Zong XKA (2006) Low level of genetic diversity in cultivated Pigeonpea compared to its wild relatives is revealed by diversity arrays technology. Theor Appl Genet 113:585–595

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  Google Scholar 

  • Zhang Y, Zhang X, Che Z, Wang L, Wei W, Li D (2012) Genetic diversity assessment of sesame core collection in China by phenotype and molecular markers and extraction of a mini-core collection. BMC Genet 13:1

    Article  Google Scholar 

  • Zohary D, Hopf M, Weiss E (2012) Domestication of Plants in the Old World: The origin and spread of domesticated plants in Southwest Asia, Europe, and the Mediterranean Basin. Oxford University Press

    Book  Google Scholar 

Download references

Acknowledgements

The authors are grateful to Ethiopian Biodiversity Institute (EBI) and Assosa, Bako, Gondar, Humera, and, Werer Agricultural Research Centers for their generous provision of collection and improved varieties used in this study. The financial support of Amhara Agricultural Research Institute of (ARARI) and Gondar Agricultural Research Center through BENEFIT-SBN project, is appreciated. The first author further obliged to Addis Ababa University and IGSS program in BecA-ILRI Hub, Nairobi-Kenya for the training provided.

Author information

Authors and Affiliations

  1. College of Natural Sciences, Department of Microbial, Cellular and Molecular Biology, Addis Ababa University, P. O. Box 1176, Addis Ababa, Ethiopia

    Tewodros Tesfaye & Kassahun Tesfaye

  2. Amhara Agricultural Research Institute, Gondar Research Center, P. O. Box 1337, Gondar, Ethiopia

    Tewodros Tesfaye

  3. Ethiopian Institute of Agricultural Research, Holeta Research Center, P. O. Box 2003, Holeta, Ethiopia

    Gemechu Keneni & Tesfahun Alemu

  4. International Livestock Research Institute, Box 30709, Nairobi, 00100, Kenya

    Cathrine Ziyomo

Authors
  1. Tewodros Tesfaye
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Kassahun Tesfaye
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Gemechu Keneni
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Cathrine Ziyomo
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Tesfahun Alemu
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Tewodros Tesfaye.

Ethics declarations

Conflict of interest

The authors declare that they have no competing interests.

Additional information

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary Information

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Tesfaye, T., Tesfaye, K., Keneni, G. et al. Genetic diversity of Sesame (Sesamum indicum L) using high throughput diversity array technology. J. Crop Sci. Biotechnol. 25, 359–371 (2022). https://doi.org/10.1007/s12892-021-00137-x

Download citation

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s12892-021-00137-x

Keywords

Search

Navigation