Hostname: page-component-8448b6f56d-t5pn6 Total loading time: 0 Render date: 2024-04-19T07:24:06.007Z Has data issue: false hasContentIssue false
  • English
  • Français

Effects of domestication bottleneck and selection on fatty acid desaturases in Indian sesame germplasm

Published online by Cambridge University Press:  18 March 2015

Nupur Mondal ,
K. V. Bhat ,
P. S. Srivastava  and
S. K. Sen
Nupur Mondal
Affiliation:
Division of Genomic Research, National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi110 012, India Department of Biotechnology, Jamia Hamdard University, New Delhi110 062, India
K. V. Bhat*
Affiliation:
Division of Genomic Research, National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi110 012, India
P. S. Srivastava
Affiliation:
Department of Biotechnology, Jamia Hamdard University, New Delhi110 062, India
S. K. Sen
Affiliation:
Indian Institute of Technology, Kharagpur, West Bengal, India
*
*Corresponding author. E-mail: kvbhat2014@gmail.com
Get access Rights & Permissions [Opens in a new window]

Abstract

Sesame (Sesamum indicum L.) is one of the oldest and most nutritional oilseed crops, of which domestication history has been poorly understood. This study suggested that sesame has undergone domestication bottleneck during its use for a long time. In this investigation, the molecular analysis included 4.4 Mbp of the genomic DNA of sesame comprising stearoyl acyl desaturase (sad), fatty acid desaturase 2 (fad2) and omega 3 fatty acid desaturase (o3fad) genes in 99 accessions of four populations of sesame germplasm namely: wild species, landraces, improved cultivars and introgressed lines. Results indicated that the improved cultivars and landraces lost 46.6 and 36.7% of nucleotide diversity, respectively, which indicate that the genetic diversity of the crop had been eroded due to selection after domestication. However, there was no significant reduction in genetic diversity of improved cultivars compared with landraces, indicating that unique improved cultivars generated through crosses were of less frequency in this population. Moreover, introgressed lines retained only 17.77% (π) and 4.57% (θ) of landrace diversity. To evaluate the impact of selection across fatty acid biosynthetic pathway, individual nucleotide diversity at three major genes involved in the pathway was surveyed. The analysis between wild and improved cultivars supported positive selection in fad2 and o3fad loci. Though locus-to-locus sequence variation was observed, positive results with two most important loci supported selection after domestication. Reduced diversity in these critical quality governing genes in improved cultivars suggested that future sesame cultivation would benefit from the incorporation of alleles from sesame's wild relatives.

Keywords

crop domesticationfatty acid desaturasegenetic diversitysesameSNP
Type
Research Article
Information
Plant Genetic Resources , Volume 14 , Issue 2 , June 2016 , pp. 81 - 90
Copyright
Copyright © NIAB 2015 

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

Bedigian, D (2003) Evolution of sesame revisited: domestication, diversity and prospects. Genetic Resources and Crop Evolution 50: 779–787.Google Scholar
Bhat, KV, Babrekar, PP and Lakhanpaul, S (1999) Study of genetic diversity in Indian and exotic sesame (Sesamum indicum L.) germplasm using random amplified polymorphic DNA (RAPD) markers. Euphytica 110: 21–33.CrossRefGoogle Scholar
Bittner-Eddy, PD, Crute, IR, Holub, EB and Beynon, JL (2000) RPP13 is a simple locus in Arabidopsis thaliana for alleles that specify downy mildew resistance to different avirulence determinants in Peronospora parasitica . Plant Journal 21: 177–188.Google Scholar
Botella, MA, Parker, JE, Frost, LN, Bittner-Eddy, PD, Beynon, JL, Daniels, MJ, Holub, EB and Jones, JDG (1998) Three genes of the Arabidopsis RPP1 complex resistance locus recognize distinct Peronospora parasitica avirulence determinants. Plant Cell 10: 1847–1860.CrossRefGoogle ScholarPubMed
Brown, GR, Gill, GP, Kuntz, RJ, Langley, CH and Neale, DB (2004) Nucleotide diversity and linkage disequilibrium in loblolly pine. Proceedings of the National Academy of Sciences 101: 15255–15260.Google Scholar
Clark, AG and Kao, TH (1991) Excess nonsynonymous substitution at shared polymorphic sites among self-incompatibility alleles of Solanaceae. Proceedings of the National Academy of Sciences 88: 9823–9827.CrossRefGoogle ScholarPubMed
Duhoon, SS, Sharma, SM, Lakhanpaul, S and Bhat, KV (2004) Sesame. In: Dhillon, BS, Tyagi, RK, Saxena, S and Agrawal, A (eds) Plant Genetic Resources: Oilseed and Cash Crops. Indian Society of Plant Genetic Resources, New Delhi, India: Narosa Publishing House, pp. 136–145.Google Scholar
Excoffier, L and Lischer, HEL (2010) Arlequin suite ver. 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Molecular Ecology Resources 10: 564–567.Google Scholar
Fu, YX and Li, WH (1993) Statistical tests of neutrality of mutations. Genetics 133: 693–709.CrossRefGoogle ScholarPubMed
Fu, Y-B (2011) Genetic evidence for early flax domestication with capsular dehiscence. Genetic Resources and Crop Evolution 58: 1119–1128.Google Scholar
Halliburton, R (2004) Introduction to Population Genetics. Upper Saddle River, NJ: Pearson/Prentice Hall.Google Scholar
Hill, WG and Robertson, A (1968) Linkage disequilibrium in finite populations. Theoretical and Applied Genetics 38: 226–231.CrossRefGoogle ScholarPubMed
Hudson, RR and Kaplan, NL (1985) Statistical properties of the number of recombination events in the history of a sample of DNA sequences. Genetics 111: 147–164.Google Scholar
Hyten, D, Song, Q, Zhu, U, Choi, IY, Nelson, RL, Costa, JM and Specht, JE (2006) Impacts of genetic bottlenecks on soybean genome diversity. Proceedings of the National Academy of Sciences USA 103: 16666–16671.Google Scholar
Ingvarson, PK (2005) Nucleotide polymorphism and linkage disequilbrium within and among natural populations of European Aspen (Populus tremula L., Salicaceae). Genetics 169: 945–953.CrossRefGoogle Scholar
Kawabe, A, Yamane, K and Miyashita, NT (2000) DNA polymorphism at the cytosolic phosphoglucose isomerase (PgiC) locus of the wild plant Arabidopsis thaliana. Genetics 156: 1339–1347.Google Scholar
Kelly, JK (1997) A test of neutrality based on interlocus associations. Genetics 146: 1197–1206.Google Scholar
Librado, P and Rozas, J (2009) DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25: 1451–1452.Google Scholar
Maynard, SJ and Haigh, J (1974) The hitch-hiking effect of a favourable gene. Genetics Research 23: 23–35.Google Scholar
McDowell, JM, Dhandaydham, M, Long, TA, Aarts, MG, Goff, S, Holub, EB and Dangl, JL (1998) Intragenic recombination and diversifying selection contribute to the evolution of downy mildew resistance at the RPP8 locus of Arabidopsis. Plant Cell 10: 1861–1874.CrossRefGoogle Scholar
Mondal, N, Bhat, KV and Srivastava, PS (2010) Variation in fatty acid composition in Indian germplasm of sesame. Journal of the American Oil Chemists' Society 87: 1263–1269.CrossRefGoogle Scholar
Nei, M (1987) Molecular Evolutionary Genetics. New York: Columbia University Press.Google Scholar
Nzikou, JM, Matos, L, Bouanga-Kalou, G, Ndangui, CB, Pambou-Tobi, NPG, Kimbonguila, A and Desobry, S (2009) Chemical composition on the seeds and oil of sesame (Sesamum indicum L.) grown in Congo-Brazzaville. Advance Journal of Food Science and Technology 1: 6–11.Google Scholar
Rozas, J, Gullaud, M, Blandin, G and Aguadé, M (2001) DNA variation at the rp49 gene region of Drosophila simulans: evolutionary inferences from an unusual haplotype structure. Genetics 158: 1147–1155.CrossRefGoogle ScholarPubMed
Saghai-Maroof, MA, Soliman, KM, Jorgensen, RA and Allard, RW (1984) Ribosomal DNA spacer-length polymorphisms in barley: mendelian inheritance, chromosomal location, and population dynamics. Proceedings of the National Academy of Sciences 81: 8014–8018.Google Scholar
Swanson, WJ, Clark, AG, Waldrip-Dail, HM, Wolfner, MF and Aquadro, CF (2001) Evolutionary EST analysis identifies rapidly evolving male reproductive proteins in Drosophila . Proceedings of the National Academy of Sciences 98: 7375–7379.Google Scholar
Tajima, F (1983) Evolutionary relationship of DNA sequences in finite populations. Genetics 105: 437–460.CrossRefGoogle ScholarPubMed
Tajima, F (1989) Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123: 585–595.Google Scholar
Tanksley, SD and McCouch, SR (1997) Seed banks and molecular maps: unlocking genetic potential from the wild. Science 277: 1063–1066.CrossRefGoogle ScholarPubMed
Thompson, JD, Higgins, DG and Gibson, TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic acids research 22: 4673–4680.CrossRefGoogle ScholarPubMed
Ting, CT, Tsaur, SC, Wu, ML and Wu, CI (1998) A rapidly evolving homeobox at the site of a hybrid sterility gene. Science 282: 1501–1504.Google Scholar
Wall, JD (1999) Recombination and the power of statistical tests of neutrality. Genetics Research 74: 65–69.Google Scholar
Watterson, G (1975) On the number of segregating sites in genetical models without recombination. Theoretical population biology 7: 256–276.CrossRefGoogle ScholarPubMed
Wu, J, Saupe, SJ and Glass, NL (1998) Evidence for balancing selection operating at the het-c heterokaryon incompatibility locus in a group of filamentous fungi. Proceedings of the National Academy of Sciences 95: 12398–12403.Google Scholar
Supplementary material: File

Mondal supplementary material

Tables S1-S4

Download Mondal supplementary material(File)
File 143.9 KB