Analysis of genetic relationships between broomrape populations from different countries using ISSR markers

Authors

DOI:

https://doi.org/10.15835/nbha52113590

Keywords:

diversity, gene flow, genetic differentiation, genetic structure, ISSR markers, O. cumana, phylogenetic relationship

Abstract

Orobanche cumana, commonly known as sunflower broomrape, poses a significant risk to sunflower cultivation in areas located along the Black Sea and across Europe. A study was conducted to analyze the genetic diversity and differentiation among populations of this parasitic plant originating from Bulgaria, Turkey, Republic of Moldova, and Romania. A total of 269 individuals from 23 populations were genotyped using 13 ISSR markers. The frequency distribution of alleles in the broomrape populations from Romania, Turkey and Bulgaria is more homogeneous than that from Moldavian populations. However, according to genetic diversity parameters O. cumana populations from Moldova and Turkey were more variable (total gene diversity Ht=0.188; 0.214), than those from Bulgaria and Romania (Ht=0.112; 0.067). The highest values of gene diversity within populations (Hs = 0.138) were found in Turkish broomrape. The value of Gst ranged between 0.359-0.516, indicating a very high level of genetic differentiation among populations. These results are consistent with low Nm values (0.468-0.895). Pairwise differentiation index (PhiPT) and Nei’s unbiased measures of genetic distance (GD) showed similar patterns, indicating a maximum (PhiPT=0.500; GD=0.261) and, respectively, minimum (PhiPT=0.238; GD=0.079) values between broomrape from Turkey and Romania, respectively, Romania and Moldova. Dendrogram constructed using the UPMGA method based on Nei's genetic distances and Pearson's dissimilarity clustered together Moldavian and Romanian broomrape and grouped in two separate clusters populations belonging to Bulgaria and Turkey. The PCA analysis confirmed the results of UPGMA clusterization. Overall, both methods suggest that the groupings of broomrape are partly determined by its geographical origin, as well as by the genetic differences and similarities accumulated over time, and are not related to virulence.

References

Abdalla MMF, Shafik MM, Attia SM, Ghannam HA (2016). Molecular characterization of Orobanche crenata in Egypt using ISSR markers and its relation to faba bean breeding. Biotechnology Journal International 16(3):1-11. https://doi.org/10.9734/BJI/2016/27216

Ali A, Wang J-D, Pan Y-B, Deng Z-H, Chen Z-W, Chen R-K, Gao S-J (2017). Molecular identification and genetic diversity analysis of Chinese sugarcane (Saccharum spp. hybrids) varieties using SSR markers. Tropical Plant Biology 10(4):194-203. https://doi.org/10.1007/s12042-017-9195-6

Amiteye S (2021). Basic concepts and methodologies of DNA marker systems in plant molecular breeding. Heliyon 7(10):e08093. https://doi.org/10.1016/j.heliyon.2021.e08093

Bendaoud F, Kim G, Larose H, Westwood JH, Zermane N, Haak DC (2022). Genotyping-by-sequencing analysis of reveals genetic differentiation. Ecology and Evolution 12(3):e8750. https://doi.org/10.1002/ece3.8750

Benharrat H, Veronesi C, Theodet C, Thalouarn P (2002). Orobanche species and population discrimination using intersimple sequence repeat (ISSR). Weed Research 42(6):470-475. https://doi.org/10.1046/j.1365-3180.2002.00305.x

Bivol I, Barbacar N (2013). RAPD and SCAR markers to study of the nature of inheritance and genetic polymorphism of hybrid collection of the cowpea (Vigna unguiculata (L.) Walp.). Romanian Biotechnological Letters Journal 18(5):8634-8644.

Buso GSC, Rangel PH, Ferreira ME (1998). Analysis of genetic variability of South American wild rice populations (Oryza glumaepatula) with isozymes and RAPD markers. Molecular Ecology 7(1):107- https://doi.org/117. 10.1046/j.1365-294x.1998.00321.x

Chen H, Yang H, Qiang W-Y (2016). Genetic diversity of ten Vicia unijuga populations by ISSR markers. Acta Prataculturae Sinica 25(9):96-103. https://doi.org/10.11686/cyxb2015547

Chen L, Pan T, Qian H, Zhang M, Yang G, Wang X (2021). Genetic diversity and population structure revealed by SSR markers on endemic species Osmanthus serrulatus Rehder from Southwestern Sichuan Basin, China. Forests 12(10):1365. https://doi.org/10.3390/f12101365

Clapco S, Martea R, Duca M (2020). Relaţia dintre distanţa genetică şi distanţa geografică la unele populaţii de Orobanche cumana Wallr. din Republica Moldova. Relationship between genetic distance and geographical distance in some populations of Orobanche cumana Wallr. from Republic of Moldova. Ştiinţa Agricolă 1:73-80. https://doi.org/10.5281/zenodo.3893057

Cvijović I, Good BH, Desai MM (2018). The effect of strong purifying selection on genetic diversity. Genetics 209(4):1235-1278. https://doi.org/10.1534/genetics.118.301058

Duca M, Bivol I (2022). The study of ISSR-markers polymorphism in broomrape populations from Bulgaria. In: VIth International Symposium Advanced Biotechnologies – Achievements and Prospects, October 3-4, 2022, Chisinau, Republic of Moldova, pp 26-28.

Duca M, Bivol I (2023). Genetic diversity of broomrape populations from different geographical origins assessed by ISSR markers. Helia 46(79). https://doi.org/10.1515/helia-2023-0014

Duca M, Joiţa-Păcureanu M, Port A, Martea R, Boicu A, Rîşnoveanu L, Clapco S (2020). Genetic diversity analysis of sunflower broomrape populations from Republic of Moldova using ISSR markers. Romanian Agricultural Research 37:89-97. https://doi.org/10.59665/rar3712

Dwivedi S, Singh S, Chauhan UK, Tiwari MK (2018). Inter and intraspecific genetic diversity (RAPD) among three most frequent species of macrofungi (Ganoderma lucidum, Leucoagricus sp. and Lentinus sp.) of Tropical Forest of Central India. Journal of Genetic Engineering and Biotechnology 16(1):133-141. https://doi.org/10.1016/j.jgeb.2017.11.008

Franks SJ, Hamann E, Weis AE (2018). Using the resurrection approach to understand contemporary evolution in changing environments. Evolutionary Applications 11:17-28. https://doi.org/10.1111/eva.12528

Gagne G, Roeckel-Drevet P, Grezes-Besset B, Shindrova P, Ivanov P, Grand-Ravel C, ... Nicolas P (1998). Study of the variability and evolution of Orobanche cumana populations infesting sunflower in different European countries. Theoretical and Applied Genetics 96:1216-22. https://doi.org/10.1007/s001220050859

Gheţea LG, Motoc RM, Popescu CF, Barbacar N, Bărbării LE, Constantinescu CM, … Savin G (2012). Assessment of Diversity in Grapevine Gene Pools from Romania and Republic of Moldova, Based on SSR Markers Analysis. In: Maldonado AIL (Eds). Horticulture. IntechOpen, pp 43-60.

Gompert Z, Lucas L, Buerkle CA, Forister ML, Fordyce JA, Nice CC (2014). Admixture and the organization of genetic diversity in a butterfly species complex revealed through common and rare genetic variants. Molecular Ecology 23:4555-4573. https://doi.org/10.1111/mec.12811

Harris EE, Meyer D (2006). The molecular signature of selection underlying human adaptations. American Journal of Physical Anthropology 43:89-130. https://doi.org/10.1002/ajpa.20518

Ivanović Ž, Marisavljević D, Marinković R, Mitrović P, Blagojević J, Nikolić I, Pavlović D (2021). Genetic diversity of Orobanche cumana populations in Serbia. The Plant Pathology Journal 37(6):512-520. https://doi.org/10.5423/PPJ.OA.04.2021.0066

Joshi SP, Ranjekar PK, Gupta VS (1999). Molecular markers in plant genome analysis. Current Science 77(2):230-240. https://www.jstor.org/stable/24102526

Khamassi K, Abbes Z, Tani E, Katsileros A, Guenni K, Rouissi M, … Kharrat M (2023). Genetic structure and diversity analysis of Tunisian Orobanche spp. and Phelipanche spp. using molecular markers. Applied Sciences 13:11622. https://doi.org/10.3390/app132111622

Kim H, Lei P, Wang A, Liu S, Zhao Y, Huang F, … Meng F (2021). Genetic diversity of castor bean (Ricinus communis L.) revealed by ISSR and RAPD markers. Agronomy 11(3):457. https://doi.org/10.3390/agronomy11030457

Linck E, Battey CJ (2019). Minor allele frequency thresholds strongly affect population structure inference with genomic datasets. Molecular Ecology Resources 19(3):639-647. https://doi.org/10.1111/1755-0998.12995

Luz GC, Strioto DK, Mangolin CA, Machado MFPS (2020). ISSR markers to assess genetic diversity of cultivated populations from artificial selection of Stevia rebaudiana (Bert.) Bertoni. Breeding Science 70(4):508-514. https://doi.org/10.1270/jsbbs.20014

Moghadam FAM, Qaderi A, Sharifi-Sirchi G (2021). Evaluation of genetic diversity of 17 populations (Lepidium sativum L.) plant collected from different regions of Iran by RAPD Marker. ACS Agricultural Science & Technology 1(6):684-690. https://doi.org/10.1021/acsagscitech.1c00182

National Research Council (2013). Genetic diversity in free-ranging horse and Burro populations. In: Using Science to Improve the BLM Wild Horse and Burro Program: A Way Forward. Washington, DC: The National Academies Press. pp 167-194. https://doi.org/10.17226/13511

Reddy MP, Sarla N, Siddiq EA (2002). Inter simple sequence repeat (ISSR) polymorphism and its application in plant breeding. Euphytica 128(1):9-17. https://doi.org/10.1023/A:1020691618797

Román B, Satovic Z, Rubiales D, Torres AM, Cubero JI, Katzir N, Joel DM (2002). Variation among and within populations of the parasitic weed Orobanche crenata from Spain and Israel revealed by inter simple sequence repeat markers. Phytopathology 92(12):1262-1266. https://doi.org/10.1094/PHYTO.2002.92.12.1262

Sambrook J, Russell D (2001). Molecular cloning. A laboratory manual. Cold Spring Harbor Laboratory Press, New York.

Sarwat M (2012). ISSR: a reliable and cost-effective technique for detection of DNA polymorphism. Methods in Molecular Biology 862:103-121. https://doi.org/10.1007/978-1-61779-609-8_9

Sharawy S, Karakish E (2015). Taxonomic relationships of some species of Orobanche L. evidence from RAPD-PCR and ISSR markers. Pakistan Journal of Botany 47(2):437-452. https://www.pakbs.org/pjbot/PDFs/47(2)/08.pdf

Shi BX, Zhang J, Gu YG, Lai CX, Lei ZH, Sha H, ... Zhao J (2019). Application of ISSR markers to reveal the genetic diversity of sunflower broomrape in China. Chinese Journal of Oil Crop Sciences 41(4):629-637. https://doi.org/10.7505/j.issn.1007-9084.2019.04.018

Slatkin M (1987). Gene flow and the geographic structure of natural populations. Science 236(4803):787-792. https://doi.org/10.1126/science.3576198

Stoyanov K, Gevezova M, Denev I (2012). Identification of ISSR markers for studying the biodiversity of Bulgarian representatives of genus Orobanche subsection Minores. Biotechnology & Biotechnological Equipment 26(1):2743-2749. https://doi.org/10.5504/BBEQ.2011.0139

Wright S (1951). The genetical structure of populations. Annals of Eugenics 15(1):323-354. https://doi.org/10.1111/j.1469-1809.1949.tb02451.x

Wright S (1978). Evolution and the Genetics of Populations. Vol. 4. Variability within and among Natural Populations. University of Chicago Press, Chicago.

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Published

2024-02-22

How to Cite

DUCA, M., BIVOL, I., MUTU, A., PORT, A., & CLAPCO, S. (2024). Analysis of genetic relationships between broomrape populations from different countries using ISSR markers. Notulae Botanicae Horti Agrobotanici Cluj-Napoca, 52(1), 13590. https://doi.org/10.15835/nbha52113590

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Research Articles
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DOI: 10.15835/nbha52113590