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Analysis of genetic diversity, population structure and linkage disequilibrium in Iranian wheat landraces using SSR markers

Published online by Cambridge University Press:  07 March 2016

Elham Zarei Abbasabad ,
Seyed Abolghasem Mohammadi ,
Mohammad Moghaddam  and
Mohammad Reza Jalal Kamali
Elham Zarei Abbasabad
Affiliation:
Department of Plant Breeding and Biotechnology, Faculty of Agriculture, University of Tabriz, Tabriz, Iran
Seyed Abolghasem Mohammadi*
Affiliation:
Department of Plant Breeding and Biotechnology, Faculty of Agriculture, University of Tabriz, Tabriz, Iran Center of Excellence in Cereal Molecular Breeding, University of Tabriz, Tabriz, Iran
Mohammad Moghaddam
Affiliation:
Department of Plant Breeding and Biotechnology, Faculty of Agriculture, University of Tabriz, Tabriz, Iran Center of Excellence in Cereal Molecular Breeding, University of Tabriz, Tabriz, Iran
Mohammad Reza Jalal Kamali
Affiliation:
CIMMYT (International Maize and Wheat Improvement Center), Karaj, Iran
*
*Corresponding author. E-mail: [email protected]
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Abstract

Population structure and linkage disequilibrium (LD) were investigated in a set of 395 bread wheat landraces including 154 spring, 193 winter, two facultative wheat and 46 unknown growth type collected from different geographical regions of Iran. A total of 53 microsatellite markers distributed in three genomes of wheat were assayed for polymorphism. The 312 polymorphic alleles were served to estimate population structure and analyse the genome-wide LD. The number of alleles ranged from 2 to 18 with an average of 5.89 alleles/locus. Mean of polymorphic information content was 0.6 with a range of 0.15–0.86 and gene diversity varied from 0.16 to 0.88 with an average of 0.64. The population of landraces was highly structured and based on distance-and model-based cluster analyses the 395 landraces were assigned into eight subpopulations: SG1–SG8. Population structure estimates based on simple sequence repeat (SSR) marker data were quantified in a Q matrix and used in calculation of LD between pair of markers. A low overall LD level found in 12–13% (166) of the SSR marker pairs showed significant pairwise LD in r2 ≥ 0.01 and P ≤ 0.001 and six pair showed r2 ≥ 0.05 with P ≤ 0.001. LD clearly decays within the genetic distance of 40–60 cM with r2 ~ 0.05. The results of this study should provide valuable information for future association mapping using this wheat collection.

Keywords

gene diversitylinkage disequilibriummicrosatellite markerspopulation structure
Type
Research Article
Information
Plant Genetic Resources , Volume 15 , Issue 4 , August 2017 , pp. 327 - 334
Copyright
Copyright © NIAB 2016 

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References

Bradbury, PJ, Zhang, Z, Kroon, DE, Casstevens, TM, Ramdoss, Y and Buckler, ES (2007) TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics 23: 2633–2635.CrossRefGoogle ScholarPubMed
Belo, A, Zheng, P, Luck, S, Shen, B, Meyer, DJ, Li, B, Tingey, S and Rafalski, A (2008) Whole genome scan detects an allelic variant of fad2 associated with increased oleic acid levels in maize. Mol Genet Genomics 279: 1–10.CrossRefGoogle ScholarPubMed
Breseghello, F and Sorrells, ME (2006) Association mapping of kernel size and milling quality in wheat (Triticum aestivum L.) cultivars. Genetics 172: 1165–1177.CrossRefGoogle ScholarPubMed
Chao, S, Zhang, WJ, Dubcovsky, J and Sorrells, M (2007) Evaluation of genetic diversity and genome-wide linkage disequilibrium among U.S. wheat (Triticum aestivum L.) germplasm representing different market classes. Crop Science 47: 1018–1030.CrossRefGoogle Scholar
Chen, X, Min, D, Yasir, TA and Hu, YG (2012) Genetic diversity, population structure and linkage disequilibrium in elite Chinese winter wheat investigated with SSR markers. PLos ONE 7: e44510. doi: 10.1371/journal.pone.0044510.Google ScholarPubMed
Excoffier, L (2001) Analysis of population subdivision. In: Balding, D, Bishop, M and Cannings, C (eds) Handbook of Statistical Genetics. New York: John Wiley & Sons, pp. 271–307.Google Scholar
Flint-Garcia, SA, Thornsberry, JM and Buckler, ES (2003) Structure of linkage disequilibrium in plants. Annual Review of Plant Biology 54: 357–374.CrossRefGoogle ScholarPubMed
Garris, AJ, McCouch, SR and Kresovich, S (2003) Population structure and its effects on haplotype diversity and linkage disequilibrium surrounding the xa5 locus of rice Oryza sativa L. Genetics 165: 759–769.CrossRefGoogle ScholarPubMed
Gupta, PK, Rustgi, S and Kulwal, PL (2005) Linkage disequilibrium and association studies in higher plants: present status and future prospects. Plant Molecular Biology 57: 461–485.CrossRefGoogle ScholarPubMed
Hai, L, Wagner, C and Friedt, W (2007) Quantitative structure analysis of genetic diversity among spring bread wheats (Triticum aestivum L.) from different geographical regions. Genetica 130: 213–225.CrossRefGoogle ScholarPubMed
Hamblin, MT, Mitchell, SE, White, GM, Gallego, J, Kukatla, R, Wing, RA, Paterson, AH and Kresovich, S (2004) Comparative population genetics of the panicoid grasses: sequence polymorphism linkage disequilibrium and selection in a diverse sample of Sorghum bicolor . Genetics 167: 471–483.CrossRefGoogle Scholar
Hao, CY, Wang, LF, Ge, HM, Dong, YC and Zhang, XY (2011) Genetic diversity and linkage disequilibrium in Chinese bread wheat (Triticum aestivum L.) revealed by SSR markers. PLoS ONE 6: e17279. doi: 10.1371/journal.pone.0017279.CrossRefGoogle ScholarPubMed
Huang, XQ, Borner, A, Roder, MS and Ganal, MW (2002) Assessing genetic diversity of wheat (Triticum aestivum L.) germplasm using microsatellite markers. Theoretical and Applied Genetics 105: 699–707.CrossRefGoogle ScholarPubMed
Hyten, DL, Choi, IY, Song, Q, Shoemaker, RC, Nelson, RL, Costa, JM, Specht, JE and Cregan, PB (2007) Highly variable patterns of linkage disequilibrium in multiple Soybean populations. Genetics 175: 1937–1944.CrossRefGoogle ScholarPubMed
Jaradat, AA (1991) Levels of phenotypic variation for developmental traits in landrace genotypes of durum wheat (Triticum turgidum ssp. Turgidum L. conv. durum (Desf) MK) from Jordan. Euphytica 51: 265–271.CrossRefGoogle Scholar
Kraakman, ATW, Martinez, F, Mussiraliev, B, Van Eeuwijk, FA and Niks, RE (2006) Linkage disequilibrium mapping of morphological, resistance, and other agronomically relevant traits in modern spring barley cultivars. Molecular Breeding 17: 41–58.CrossRefGoogle Scholar
Kraakman, ATW, Niks, RE, Van der Berg, PMMM, Stam, P and Van Eeuwijk, FA (2004) Linkage disequilibrium mapping of yield and yield stability in modern spring barley cultivars. Genetics 168: 435–446.CrossRefGoogle ScholarPubMed
Kruger, SA, Able, JA, Chalmers, KJ and Langridge, P (2004) Linkage disequilibrium analysis of hexaploid wheat. In: Plant & Animal Genomes XII Conference, 10–14 January, Town & Country Convention Center, Sandiego, CA, p. 321.Google Scholar
Liu, K and Muse, SV (2005) PowerMarker: an integrated analysis environment for genetic marker analysis. Bioinformatics 21: 2128–2129.CrossRefGoogle ScholarPubMed
Maccaferri, M, Sanguineti, MC, Donini, P and Tuberosa, R (2003) Microsatellite analysis reveals a progressive widening of the genetic basis in the elite durum wheat germplasm. Theoretical and Applied Genetics 107: 783–797.CrossRefGoogle ScholarPubMed
Nielsen, NH, Backes, G, Stougaard, J, Andersen, SU and Jahoor, A (2014) Genetic diversity and population structure analysis of European hexaploid bread wheat (Triticum aestivum L.) Varieties. PLoS ONE 9: e94000. doi: 10.1371/journal.pone.0094000.CrossRefGoogle ScholarPubMed
Pritchard, JK, Stephens, M and Donnelly, P (2000) Inference of population structure using multilocus genotype data. Genetics 155: 945–959.CrossRefGoogle ScholarPubMed
Ravel, C, Praud, S, Murigneux, A, Linossier, L, Dardevet, M, Balfourier, F, Dufour, PH, Brunel, D and Charmet, G (2006) Identification of Glu-B1-1as a candidate gene for the quantity of high-molecular-weight glutenin in bread wheat (Triticum aestivum L.) by means of an association study. Theoretical and Applied Genetics 112: 738–743.CrossRefGoogle ScholarPubMed
Rhone, B, Raquin, AL and Goldringer, I (2007) Strong linkage disequilibrium near the selected Yr17 resistance gene in a wheat experimental population. Theoretical and Applied Genetics 114: 787–802.CrossRefGoogle Scholar
Rostoks, N, Ramsay, L, MacKenzie, K, Cardle, L, Bhat, PR, Roose, ML, Svensson, JT, Stein, N, Varshney, RK, Marshall, DF, Graner, A, Close, TJ and Waugh, R (2006) Recent history of artificial outcrossing facilitates whole-genome association mapping in elite inbred crop varieties. Proceedings of the National Academy of Sciences of the United States of America 103: 18656–18661.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 of the United States of America 81: 8014–8018.CrossRefGoogle ScholarPubMed
Skot, L, Humphreys, MO, Armstead, I, Heywood, S, Skot, KP, Sanderson, R, Thomas, ID, Sanderson, R, Chorlton, KH and Hamilton, NRS (2005) An association mapping approach to identify lowering time genes in natural populations of Lolium perenne (L.). Molecular Breeding 15: 233–245.CrossRefGoogle Scholar
Somers, DJ, Banks, T, Depauw, R, Fox, S, Clarke, J, Pozniak, C and McCartney, C (2007) Genome-wide linkage disequilibrium analysis in bread wheat and durum wheat. Genome 50: 557–567.CrossRefGoogle ScholarPubMed
Somers, DJ, Isaac, P and Edwards, K (2004) A high-density microsatellite consensus map for bread wheat (Triticuma estivum L.). Theoretical and Applied Genetics 109: 1105–1114.CrossRefGoogle Scholar
Song, QJ, Shi, JR, Singh, S, Fickus, EW, Cosra, JM, Lewis, J, Gill, BS, Ward, R and Cregan, PB (2005) Development and mapping of microsatellite (SSR) markers in wheat. Theoretical and Applied Genetics 110: 550–560.CrossRefGoogle ScholarPubMed
Stachel, M, Lelley, T, Grausgruber, H and Vollmann, J (2000) Application of microsatellites in wheat (Triticum aestivum L.) for studying genetic differentiation caused by selection for adaptation and use. Theoretical and Applied Genetics 100: 242–248.CrossRefGoogle Scholar
Strelchenko, P, Street, K, Mitrofanova, O, Hill, H, Henry, R and Mackay, M (2008) Comparative assessment of wheat landraces from AWCC, ICARDA and VIR germplasm collections based on the analysis of SSR markers. In: 11th International Wheat Genetics Symposium, 24–29 August 2008, Brisbane, Australia, pp. 309–311.Google Scholar
Thornsberry, JM, Goodman, MM, Doebley, J, Kresovich, S, Nielsen, D and Buckler, ES (2001) Dwarf8 polymorphisms associate with variation in flowering time. Nature Genetics 28: 286–289.CrossRefGoogle ScholarPubMed
Tommasini, L, Schnurbusch, T, Fossati, D, Mascher, F and Keller, B (2007) Association mapping of Stagonospora nodorum blotch resistance in modern European winter wheat varieties. Theoretical and Applied Genetics 115: 697–708.CrossRefGoogle ScholarPubMed
Wang, ML, Barkley, NA and Jenkins, TM (2009) Microsatellite markers in plants and insects. Part I: applications of biotechnology. Genes, Genomes and Genomics 3: 54–67.Google Scholar
Wright, S (1951) The genetical structure of populations. Annals of Eugenics 15: 323–354.CrossRefGoogle ScholarPubMed
Xing, Y, Frei, U, Schejbel, B, Asp, T and Lubberstedt, T (2007) Nucleotide diversity and linkage disequilibrium in 11 expressed resistance candidate genes in Lolium perenne . BMC Plant Biology 7: 43.CrossRefGoogle ScholarPubMed
Yu, JM and Buckler, ES (2006) Genetic association mapping and genome organization of maize. Current Opinion in Biotechnology 17: 1–6.CrossRefGoogle ScholarPubMed
Zhang, DD, Bai, GH, Zhu, CS, Yu, JM and Carver, BF (2010) Genetic diversity, population structure and linkage disequilibrium in U.S. and Elite Winter Wheat. Plant Genome 3: 117–127.CrossRefGoogle Scholar
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