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Genetic variability and population structure of Agropyron desertorum accessions from Iran based on inter simple sequence repeat (ISSR) assay

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Abstract

The genetic diversity of 34 A. desertorum accessions was studied using 28 ISSR primers. A total of 448 loci were amplified in the A. desertorum genome, and 402 (90%) of them were polymorphic. The primer (AG)8YC produced the greatest number of polymorphic fragments, while the primer (AC)8YA produced the lowest number. The number of effective alleles ranged between 1.26 and 1.57. The highest value of Shanon index belonged to primer (GA)8T, while the highest value of Nei index (0.33) was detected for primers (GA)8T, (TC)8C, and (GACA)4. Primer (GA)8GCC with PIC = 0.40 was the best informative marker in the evaluation of A. desertorum genetic diversity. Genetic similarity among studied accessions was between 0.45 (G03 and G17) and 0.80 (G01 and G11). Using Bayesian and WPGMA classification algorithms, the A. desertorum germplasm was divided into two major subgroups (Red and Green), which consisted of 13 and 17 accessions, respectively, and also admixture accessions. Late-maturing accessions were distinguished from early-maturing accessions and mostly localized in the Green subgroup. The Red subgroup had more private alleles as well as heterozygosity compared with the Green subgroup and therefore also had promising selection potential. Totally, ISSR markers could distinguish early mature genotypes, and this is significant for increased forage yield. Likewise, the recognized heterotic groups could help breeders select highly polymorphic genotypes in polycross breeding.

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Data availability

The datasets generated during and/or analysed during the current study are available from the corresponding author on reasonable request.

References

  • Absattar T, Absattarova A, Fillipova N, Otemissova A, Shavrukov Y (2018) Diversity array technology (DArT) 56K analysis, confirmed by SNP markers, distinguishes one crested wheatgrass Agropyron species from two others found in Kazakhstan. Mol Breeding 38:37

    Article  Google Scholar 

  • Alam MA, Juraimi AS, Rafii MY, Hamid AA, Arolu IW, Abdul Latif M (2015) Genetic diversity analysis among collected purslane (Portulaca oleracea L.) accessions using ISSR markers. CR Biol 338:1–11

    Article  Google Scholar 

  • Arghavani A, Asghari A, Shokrpour M, Mohammaddost C (2010) Genetic diversity in ecotypes of two Agropyron species using RAPD markers. Res J Environ Sci 4:50–56

    Article  CAS  Google Scholar 

  • Ayaz A, Zaman W, Saqib S, Ullah F, Mahmood T (2020) Phylogeny and diversity of lamiaceae based on rps14 gene in Pakistan. Genetika 52:435–452

    Article  Google Scholar 

  • Bor NL (1970) Gramineae. In: Iranica Flora, Rechinger KH (eds) Akademische Druk-u. Verlagsanstalt, Graz, pp 571–573

    Google Scholar 

  • Che Y, Yang Y, Yang X, Li X, Li L (2015) Phylogenetic relationship and diversity among Agropyron Gaertn. germplasm using SSRs markers. Plant Syst Evol 301:163–170

    Article  Google Scholar 

  • Copete A, Moreno R, Cabrera A (2018) Characterization of a world collection of Agropyron cristatum accessions. Genet Resour Crop Evol 65:1455–1469

    Article  Google Scholar 

  • Doyle J, Doyle J (1987) A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull 19:11–15

    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 

  • Farshadfar M, Nowrozi R, Safari H, Shirvani H, Amjadian M (2018) Assessment of genetic diversity in Agropyron desertorum accessions using ISSR molecular marker. Futur of Food J Food Agric Soc 6:20–29

    Google Scholar 

  • Frankham R, Briscoe DA, Ballou JD (2002) Introduction to conservation genetics. Cambridge University Press, Cambridge

    Book  Google Scholar 

  • Godwin ID, Aitken EA, Smith LW (1997) Application of inter simple sequence repeat (ISSR) markers to plant genetics. Electrophoresis 18:1524–8

    Article  CAS  PubMed  Google Scholar 

  • Govindaraj M, Vetriventhan M, Srinivasan M (2015) Importance of genetic diversity assessment in crop plants and its recent advances: an overview of its analytical perspectives. Genet Res Int 2015:431487

    CAS  PubMed  PubMed Central  Google Scholar 

  • Han H, Qiu R, Liu Y, Zhou X, Gao C, Pang Y, Zhao Y (2022) Analysis of chloroplast genomes provides insights into the evolution of Agropyron. Front Genet 13:832809

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hayward AC, Tollenaere R, Dalton-Morgan J, Batley J (2015) Molecular marker applications in plants. Methods Mol Biol 1245:13–27

    Article  CAS  PubMed  Google Scholar 

  • Jafari AA, Seydemohammadi AR, Abdi N, Madah AH (2008) Seed and hay production in 31 genotypes of desert wheatgrass (Agropyron desertorum) using drought tolerance indices. Iran J Range Desert Res 15:114–128

    Google Scholar 

  • Jombart T, Devillard S, Balloux F (2010) Discriminant analysis of principal components: a new method for the analysis of genetically structured populations. BMC Genet 11:94

    Article  PubMed  PubMed Central  Google Scholar 

  • Li H, Jiang B, Wang J, Lu Y, Zhang J, Pan C, Yang X, Li X, Liu W, Li L (2017) Appling of novel powdery mildew resistance genes from Agropyron cristatum chromosome 2P’. Theor Appl Genet 130:109–121

    Article  CAS  PubMed  Google Scholar 

  • Mohammadi R, Panahi B, Amiri S (2020) ISSR Based study of fine fescue (Festuca ovina L.) highlighted the genetic diversity of Iranian accessions. Cytol Genet 54:257–263

    Article  Google Scholar 

  • Mohammadi R, Amiri S, Montakhabi Kalajahi V (2022) ISSR markers efficiency to assess cool-season grass species genetic diversity and phylogenetic relationships. Proc Natl Acad Sci India Sect B Biol Sci 92:691–699

    Article  CAS  Google Scholar 

  • Nei M (1973) Analysis of gene diversity in subdivided populations. Proc Natl Acad Sci USA 70:3321–3323

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Novembre J (2016) Pritchard, Stephens, and Donnelly on population structure. Genetics 204:391–393

    Article  PubMed  PubMed Central  Google Scholar 

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

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

  • Rahnemoun B, Hatami Maleki H, Mohammadi R (2018) Genetic variability in different accessions of Agropyron based on morphological traits. Modares J Biotechnol 9:517–523

    Google Scholar 

  • Razi M, Amiri ME, Darvishzadeh R, Doulati Baneh H, Alipour H, Martínez-Gómez P (2020) Assessment of genetic diversity of cultivated and wild Iranian grape germplasm using retrotransposon-microsatellite amplified polymorphism (REMAP) markers and pomological traits. Mol Biol Rep 47:7593–7606

    Article  CAS  PubMed  Google Scholar 

  • Reddy MP, Sarla N, Siddiq EA (2002) Inter simple sequence repeat (ISSR) polymorphism and its application in plant breeding. Euphytica 128:9–17

    Article  Google Scholar 

  • Sakamoto S (1964) Cytogenetical problems in Agropyron hybrids. Seiken Jiho 16:38–47

    Google Scholar 

  • Salgotra RK, Stewart CN (2020) Functional markers for precision plant breeding. Int J Mol Sci 21:4792

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Serrote CML, Reiniger LRS, Silva KB, Rabaiolli SMDS, Stefanel CM (2019) Determining the polymorphism information content of a molecular marker. Gene 5:144175

    Google Scholar 

  • Spataro G, Tiranti B, Arcaleni P, Bellucci E, Attene G, Papa R, Zeuli PS, Negri V (2011) Genetic diversity and structure of a worldwide collection of Phaseolus coccineus L. Theor Appl Genet 122:1281–1291

    Article  CAS  PubMed  Google Scholar 

  • Wu Q, Zang F, Ma Y, Zheng Y, Zang D (2020) Analysis of genetic diversity and population structure in endangered Populus wulianensis based on 18 newly developed EST-SSR markers. Glob Ecol Conserv 24:e01329

    Article  Google Scholar 

  • Yeh FC, Yang RC, Boyle T (1999) POPGENE version 1.31, Microsoft Window-based freeware for population genetic analysis. University of Alberta and Centre for International Forestry Research

Download references

Acknowledgment

The authors thank the University of Maragheh and the Agricultural Biotechnology Research Institute of Iran for lab facilities.

Funding

This work was supported by university of Maragheh and Author Hamid Hatami Maleki has received research support from University of Maragheh.

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Authors and Affiliations

  1. Department of Plant Production and Genetics, Faculty of Agriculture, University of Maragheh, Maragheh, Iran

    Hamid Hatami Maleki & Mina Hasanzadeh

  2. Department of Genomics, Branch for Northwest & West Region, Agricultural Biotechnology Research, Institute of Iran, Agricultural Research, Education and Extension Organization (AREEO), Tabriz, Iran

    Reza Mohammadi

  3. Department of Horticultural Sciences, Mahabad Branch, Islamic Azad University, Mahabad, Iran

    Mousa Arshad

  4. Department of Horticultural Science, Faculty of Agriculture, University of Urmia, Urmia, Iran

    Maryam Rafiee

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  1. Hamid Hatami Maleki
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  2. Reza Mohammadi
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  4. Mina Hasanzadeh
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Contributions

All authors contributed to the study conception and design. Material preparation, data collection and analysis were performed by RM and HHM, MH, MA, MR and HHM. The first draft of the manuscript was written by HHM and all authors commented on previous versions of the manuscript. All authors read and approved the final manuscript.

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Correspondence to Hamid Hatami Maleki.

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Maleki, H.H., Mohammadi, R., Arshad, M. et al. Genetic variability and population structure of Agropyron desertorum accessions from Iran based on inter simple sequence repeat (ISSR) assay. Genet Resour Crop Evol 70, 2511–2520 (2023). https://doi.org/10.1007/s10722-023-01579-8

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