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Genome diversity and population structure analysis of Iranian landrace and improved barley (Hordeum vulgare L.) genotypes using arbitrary functional gene-based molecular markers

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Abstract

Barley (Hordeum vulgare L. subsp. vulgare) is one of the earliest domesticated crop plants, which originated in Fertile Crescent. Genetic diversity analysis in primary gene pool and landraces is an effective strategy for germplasm conservation and utilization in breeding programs. In this study, Eighty-two barley genotypes comprised 22 Iranian improved cultivars and 60 landrace accessions collected from different zones of Iran were assumed for genetic diversity analysis using three gene targeted markers, start codon targeted (SCoT) polymorphism, conserved DNA-derived polymorphism (CDDP) and CAAT box-derived polymorphism (CBDP) in comparison with sequence-related amplified polymorphism (SRAP) markers. A total of 40 primers (10 primers from each marker) detected genetic polymorphism among barley genotypes. Four different marker types showed high level of polymorphism and SRAP markers produced higher number of polymorphic bands (67) in comparisons with SCoT, CDDP and CBDP. Average PIC values for SCoT, CDDP, CBDP and SRAP were 0.33, 0.37, 0.37 and 0.31, respectively. Marker index (MI) in SRAP and CBDP markers was higher than SCoT and CDDP markers. Cluster analysis using CDDP, CBDP and SRAP markers grouped barley genotypes in three distinct groups, while SCoT markers divided genotypes in four clusters. There were positive correlations between similarity matrixes obtained by each marker types. The results from cluster analysis and STRUCTURE analysis using combined data grouped barley genotypes in three clusters and the grouping of genotypes was strongly in agreement with their origins. Results showed that genotypes from west and north-west of Iran grouped in distinct clusters from those originated from north-east and center of Iran. To our knowledge, this is the first detailed report of using gene targeted molecular marker for genetic diversity analysis in barley. Our results showed the efficiency of these markers for genetic diversity analysis in barley and their potential for genome diversity and germplasm conservation.

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References

  • Albayrak G, Gozukirmizi N (1999) RAPD analysis of genetic variation in barley. Turk J Agric For 23:627–630

    Google Scholar 

  • Alipour H, Bihamta MR, Mohammadi V, Peyghambari SA, Bai G, Zhang G (2016) Genotyping-by-Sequencing (GBS) revealed molecular genetic diversity of Iranian wheat landraces and cultivars. Front Plant Sci 8:1293

    Article  Google Scholar 

  • Amirmoradi B, Talebi R, Karami E (2012) Comparison of genetic variationand differentiation among annual Cicer species using start codon targeted (SCoT) polymorphism, DAMD-PCR, and ISSR markers. Plant Syst Evol 298:1679–1688

    Article  CAS  Google Scholar 

  • Assefa A, Labuschagne MT, Viljoen CD (2007) AFLP analysis of genetic relationships between barley (Hordeum vulgare L.) landraces from north Shewa in Ethiopia. Conserv Genet 8:273–280

    Article  Google Scholar 

  • Barati M, Majidi MM, Mirlohi A, Pirnajmodini F, Sharif-Moghaddam N (2015) Response of cultivated and wild barley germplasm to drought stress at different developmental stages. Crop Sci 55:2668–2681

    Article  CAS  Google Scholar 

  • Barati M, Majidi MM, Mirlohi A, Safari M, MoStafavi F, KaraMi Z (2018) Potential of Iranian wild barley (Hordeum vulgare ssp. spontaneum) in breeding for drought tolerance. Cereal Res Commun 46(4):707–716

    Article  CAS  Google Scholar 

  • Bedada G, Westerbergh A, Nevo E, Korol A, Schmid KJ (2014) DNA sequence variation of wild barley Hordeum spontaneum (L.) across environmental gradients in Israel. Heredity 112:646–655

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Carvalho MA (2004) Germplasm characterization of Arachis pintoi Krap. and Greg. (Leguminosae). PhD Thesis, University of Florida, USA

  • Collard BCY, Mackill DJ (2009a) Conserved DNA-derived polymorphism (CDDP): a simple and novel method for generating DNA markers in plants. Plant Mol Bio Rep 27:558–562

    Article  CAS  Google Scholar 

  • Collard BCY, Mackill DJ (2009b) Start codon targeted (SCoT) polymorphism: a simple, novel DNA marker technique for generating gene targeted markers in plants. Plant Mol Bio Rep 27:86–93

    Article  CAS  Google Scholar 

  • Dadbeh H, Alavi Kia SS, Dezhsetan S, Moghaddam Vahed M, Sadeghzadeh B (2015) Genetic variation of Iranian barley landraces, commercial varieties and improved breeding linesusing SSR markers. J Bio & Env Sci 7(2):198–206

    Google Scholar 

  • Elakhdar A, Kumamaru T, Qualset CO, Brueggeman RS, Amer K, Capo-chichi L (2018) Assessment of genetic diversity in Egyptian barley (Hordeum vulgar L.) genotypes using SSR and SNP markers. Genet Resour Crop Evol 65(7):1937–1951

    Article  Google Scholar 

  • El-Esawi MA, Alaraidh IA, Alsahli AA, Ali HM, Alayafi AA, Witczak J, Ahmad A (2018) Genetic variation and alleviation of salinity stress in barley (Hordeum vulgare L.). Molecules 23:2488

    Article  PubMed Central  CAS  Google Scholar 

  • Farahani S, Maleki M, Mehrabi R, Kanouni H, Scheben A, Batley J, Talebi R (2019) Whole genome diversity, population structure and linkage disequilibrium analysis of chickpea (Cicer arietinum L.) advanced breeding lines using genome-wide DArTseq-based SNP markers. Genes 10:676

    Article  CAS  PubMed Central  Google Scholar 

  • Ghaffari P, Talebi R, Keshavarz F (2014) Genetic diversity and geographical differentiation of Iranian landrace, cultivars and exotic chickpea lines as revealed by morphological and microsatellite markers. Physiol Mol Biol Plant 20(2):225–233

    Article  CAS  Google Scholar 

  • Gorji AM, Poczai P, Polgar Z, Taller J (2011) Efficiency of arbitrarily amplified dominant markers (SCOT, ISSR and RAPD) for diagnostic fingerprinting in tetraploid potato. Am J Potato Res 88:226–237

    Article  Google Scholar 

  • Hajibarat Z, Saidi A, Hajibarat Z, Talebi R (2015) Characterization of geneticdiversity in chickpea using SSR markers, Start Codon Targeted Polymorphism(SCoT) and Conserved DNA-Derived Polymorphism (CDDP). Physiol Mol Biol Plant 21(3):365–373

    Article  CAS  Google Scholar 

  • Hamidi H, Talebi R, Keshavarz F (2014) Comparative efficiency of functional gene-based markers, start codon targeted polymorphism (SCoT) and conserved DNA-derived Polymorphism (CDDP) with ISSR markers for diagnostic fingerprinting in wheat (Triticum aestivum L.). Cereal Res Commun 44(4):558–567

    Article  CAS  Google Scholar 

  • Heikrujam M, Kumar J, Agrawal V (2015) Genetic diversity analysis among male and female Jojoba genotypes employing gene targeted molecular markers, start codon targeted (SCoT) polymorphism and CAAT box-derived polymorphism (CBDP) markers. Meta Genes 5:90–97

    Article  Google Scholar 

  • Igwe DO, Afiukwa CA, Ubi BE, Ogbu KI, Ojuederie OB, Ude GN (2017) Assessment of genetic diversity in Vigna unguiculata L. (Walp) accessions using inter-simple sequence repeat (ISSR) and start codon targeted (SCoT) polymorphic markers. BMC Genetic 18(1):98

    Article  CAS  Google Scholar 

  • Ivandic V, Hackett CA, Nevo E, Keith R, Thomas TB (2002) Analysis of sequence repeats (SSRs) in wild barley from the Fertile Crescent: associations with ecology, geography and flowering time. Plant Mole Biol Evol 48:511–527

    Article  CAS  Google Scholar 

  • Jannatabadi AA, Talebi R, Armin M, Jamalabadi J, Baghebani N (2014) Genetic diversity of Iranian landrace chickpea (Cicer arietinum L.) accessions from different geographical origins as revealed by morphological and sequence tagged microsatellite markers. J Plant Biochem Biotech 23(2):225–229

    Article  CAS  Google Scholar 

  • Jones H, Leigh FJ, Mackay I, Bower MA, Smith LMJ, Charles MP, Jones G, Jones MK, Brown TA, Powell W (2008) Population-based resequencing reveals that the flowering time adaptation of cultivated barley originated east of the Fertile Crescent. Mol Biol Evol 25(10):2211–2219

    Article  CAS  PubMed  Google Scholar 

  • Khodayari H, Saeidi H, Akhavan Roofigar A, Rahiminejad MR, Pourkheirandish M, Komatsuda T (2012) Genetic diversity of cultivated barley landraces in Iran measured using microsatellites. Int J Biosci Biochem Bioinfo 2(4):287–290

    Google Scholar 

  • Mariey SA, El-Mansoury MAM, El-Bialy MA (2018) Genetic diversity study of egyptian barley cultivars using sequence-related amplified polymorphism (SRAP) analysis for water stress tolerance. J Sustain Agric Sci 44:21–37

    Google Scholar 

  • Molina-Cano J, Russell J, Moralejo M, Escacena J, Arias G, Powell W (2005) Chloroplast DNA microsatellite analysis supports a polyphyletic origin for barley. Theor Appl Genet 110(4):613–619

    Article  CAS  PubMed  Google Scholar 

  • Nadeem MA, Nawaz MA, Shahid MQ, Doğan Y, Comertpay G, Yıldız M, Hatipoğlu R, Ahmad F, Alsaleh A, Labhane N, Özkan H, Chung G, Baloch FS (2018) DNA molecular markers in plant breeding: current status and recent advancements in genomic selection and genome editing. Biotechnol Biotechnol Equip 32:261–285

    Article  CAS  Google Scholar 

  • Nandha PS, Singh S (2014) Comparative assessment of genetic diversity between wild and cultivated barley using gSSR and EST-SSR markers. Plant Breed 133:28–35

    Article  CAS  Google Scholar 

  • Pakseresht F, Talebi R, Karami E (2013) Comparative assessment of ISSR, DAMD and SCoT markers for evaluation of genetic diversity and conservation of chickpea (Cicer arietinum L.) landraces genotypes collected from north-west of Iran. Physiol Mol Biol Plant 19(4):563–574

    Article  CAS  Google Scholar 

  • Paliwal R, Singh R, Singh AK, Kumar S, Kumar A, Majumdar RS (2013) Molecular characterization of Giloe (Tinospora cordifolia Willd. Miers ex Hook. F. and Thoms.) accessions using Start Codon Targeted (SCoT) markers. Int J Med Aromat Plants 3:413–422

    Google Scholar 

  • Park SK, Lee DJ, Baek HJ, Lee J, Farooq M (2011) Study of the genetic diversity of Korean, Chinese and Japanese landraces of barley (Hordeum vulgare L.) using microsatellites. Biodiv Res Conserv 23:3–13

    Google Scholar 

  • Peakall R, Smouse PE (2006) GenAlEx 6: genetic analysis in Excel. Population genetic software for teaching and research. Mol Ecol Notes 6:288–295

    Article  Google Scholar 

  • Perrier X, Jacquemoud-Collet JP (2006) DARwin software, http://darwin.cirad.fr/darwin

  • Perrier X, Flori A, Bonnot F (2003) Data analysis methods. In: Hamon P, Seguin M, Perrier X, Glaszmann JC (eds) Genetic diversity of cultivated tropical plants. Science Publishers, Enfield, pp 43–76

    Google Scholar 

  • Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Rahimi M, Majidi Hervan I, Valizadeh M, Darvish Kajori F, Ebrahimpour F (2014) Genetic diversity among wild and cultivated barley by ISSR marker. Bull Env Pharmacol Life Sci 3(10):57–62

    Google Scholar 

  • Rubenstein DK, Heisey P, Shoemaker R, Sullivan J, Frisvold G (2005) Crop genetic resources: an economic appraisal. United States Department of Agriculture (USDA). Econ Info Bull; No:2. (www.ers.usda.gov)

  • Saghai-Maroof MA, Soliman KM, Jorgensen RA, Allard RW (1984) Ribosomal DNA sepacer-length polymorphism in barley: mendelian inheritance, chromosomal location, and population dynamics. Proc Natl Acad Sci USA 81:8014–8019

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Saidi A, Daneshvar Z, Hajibarat Z (2018) Comparison of genetic variation of Anthurium (Anthurium andraeanum) cultivars using SCoT, CDDP and RAPD markers. Plant Tissue Cult Biotechnol 28(2):171–182

    Article  Google Scholar 

  • Saroei E, Cheghamirza K, Zarei L (2017) Genetic diversity of characteristics in barley cultivars. Genetika 49(2):495–510

    Article  Google Scholar 

  • Seyedimoradi H, Talebi R, Fayaz F (2016) Geographical diversity pattern in Iranian landrace durum wheat (Triticum turgidum) accessions using start codon targeted polymorphism and conserved DNA-derived polymorphism markers. Environ Experimen Biol 14:63–68

    Article  Google Scholar 

  • Shahlaei A, Torabi S, Khosroshahli M (2014) Efficacy of SCoT and ISSR markers in assessment of tomato (Lycopersicum esculentum Mill.) genetic diversity. Int J Biol Sci 5:14–22

    CAS  Google Scholar 

  • Shakhatreh Y, Baum M, Haddad N, Alrababah M, Ceccarelli S (2016) Assessment of genetic diversity among Jordanian wild barley (Hordeum spontaneum) genotypes revealed by SSR markers. Genets Resour Crop Evol 63(5):813–822

    Article  CAS  Google Scholar 

  • Shekhawat JK, Rai MK, Shekhawat NS, Kataria V (2018) Exploring genetic variability in Prosopis cineraria using two gene targeted CAAT box-derived polymorphism (CBDP) and start codon targeted (SCoT) polymorphism markers. Mol Biol Rep 45:2359–2367

    Article  CAS  PubMed  Google Scholar 

  • Singh AK, Rana MK, Singh S, Kumar S, Kumar R, Singh R (2014) CAAT box-derived polymorphism (CBDP): a novel promoter-targeted molecular marker for plants. J Plant Biochem Biotech 23:175–183

    Article  CAS  Google Scholar 

  • Stein N, Prasad M, Scholz U, Thiel T, Zhang H, Wolf M, Kota R, Varshney RK, Perovic D, Grosse I, Graner A (2007) A 1,000-loci transcript map of the barley genome: new anchoring points for integrative grass genomics. Theor Appl Genet 114(5):823–839

    Article  CAS  PubMed  Google Scholar 

  • Talebi R, Nosrati S, Etminan A, Naji AM (2018) Genetic diversity and population structure analysis of landrace and improved safflower (Cartamus tinctorious L.) germplasm using arbitrary functional gene-based molecular markers. Biotechnol Biotechnol Equip 32(5):1183–1194

    Article  CAS  Google Scholar 

  • Tanno K, Taketa K, Komatsuda T (2002) A DNA marker closely linked to the vrs1 locus (row-typed gene) indicates multiple origins of six-rowed cultivated barley (Hordeum vulgare L.). Theor Appl Genet 104:54–60

    Article  CAS  PubMed  Google Scholar 

  • Tanyolac B (2003) Inter-simple sequence repeat (ISSR) and RAPD variation among wild barley (Hordeum. vulgare subsp. spontaneum) populations from west Turkey. Genet Resour Crop Evol 50(6):611–614

    Article  CAS  Google Scholar 

  • Tomar P, Malik CP (2016) Genetic diversity assessment in Trachyspermum ammi L. Sprague using CDDP and CBDP markers. J Plant Sci Res 32:27–36

    Google Scholar 

  • Turuspekov Y, Abugalieva S, Ermekbayev K, Sato K (2014) Genetic characterization of wild barley populations (Hordeum vulgare ssp. spontaneum) from Kazakhstan based on genome wide SNP analysis. Breed Sci 64(4):399–403

    Article  PubMed  PubMed Central  Google Scholar 

  • Varshney RV, Grosse I, Hahnel U, Siefken R, Prasad M, Stein N, Langridge P, Altschmied L, Graner A (2006) Genetic mapping and BAC assignment of EST-derived SSR markers shows non-uniform distribution of genes in the barley genome. Theor Appl Genet 113:239–250

    Article  CAS  PubMed  Google Scholar 

  • Wang Y, Ren X, Sun D, Sun G (2015) Origin of worldwide cultivated barley revealed by NAM-1 gene and grain protein content. Front Plant Sci 6:803

    PubMed  PubMed Central  Google Scholar 

  • Xiong F, Zhong R, Han Z, Jiang J, He L, Zhuang W, Tang R (2011) Start codon targeted polymorphism for evaluation of functional genetic variation and relationships in cultivated peanut (Arachis hypogaea L.) genotypes. Mol Biol Rep 38(5):3487–3494

    Article  CAS  PubMed  Google Scholar 

  • Yang S, Wei Y, Qi P, Zheng Y (2008) Sequence polymorphisms and phylogenetic relationships of hina gene in wild barley from Tibet, China. Agric Sci China 7(7):796–803

    Article  CAS  Google Scholar 

  • Zohary D, Hopf M (1993) Domestication of plants in the old world: the origin and spread of cultivated plants in West Asia, Europe and the Nile Valley, 2nd edn. Clarendon Press, Oxford

    Google Scholar 

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Acknowledgements

The study was conducted as a part of Msc thesis of first author and supported by Islamic Azad University, Sanandaj Branch, Iran. We are grateful to Iranian Cereal Research Institute for providing barley genotypes used in this study.

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Authors and Affiliations

  1. Department of Agronomy & Plant Breeding, Sanandaj Branch, Islamic Azad University, Sanandaj, Iran

    Diyar Abubakr Ahmed & Reza Talebi

  2. Horticulture Department, College of Agricultural Engineering Sciences, University of Sulaimani, Sulaimani, Iraq

    Nawroz Abdul-razzak Tahir

  3. College of Biology, University of Garmian, Kefri, Iraq

    Sirwan Hassan Salih

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  1. Diyar Abubakr Ahmed
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  2. Nawroz Abdul-razzak Tahir
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  3. Sirwan Hassan Salih
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  4. Reza Talebi
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Correspondence to Reza Talebi.

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Ahmed, D.A., Tahir, N.Ar., Salih, S.H. et al. Genome diversity and population structure analysis of Iranian landrace and improved barley (Hordeum vulgare L.) genotypes using arbitrary functional gene-based molecular markers. Genet Resour Crop Evol 68, 1045–1060 (2021). https://doi.org/10.1007/s10722-020-01047-7

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