Evaluation of genetic variation in einkorn wheat originated from west Iran using microsatellite markers

Document Type : Research Paper

Authors

1 Department of Agronomy and Plant Breeding, Faculty of Agricultural Science and Engineering, Razi University, Kermanshah, Iran

2 Associate Professor, Department of Agronomy and Plant Breeding, College of Agriculture, Ilam University, Ilam, Iran

Abstract

Objective
Genetic diversity in field crops and their wild ancestors plays important role in breeding programs. The aim of this study was to investigate the genetic diversity of einkorn (Triticum monococcum L. ssp. boeoticum) wheat genotypes collected from western parts of Iran using SSR markers.
 
Material and methods
In this study, genetic variation of 163 genotypes from 34 populations of einkorn wheat collected from western parts of Iran was investigated using 19 SSR loci developed in the A genome of hexaploid wheat.
 
Results
In the investigation of 163 einkorn genotypes using 19 microsatellite loci were generated 151 polymorphic alleles with an average of 7.94 per locus. The content of polymorphic information content (PIC) in the studied einkorn genotypes ranged from 0.64 for Xgwm480-3A locus to 0.89 for Xgwm4-4A locus. The mean content of polymorphic information in the studied genotypes was 0.77. According to the results, Xgwm4-4A, Xgwm610-4A and Xgwm282-7A loci were identified as the most suitable primers for studying genetic diversity and differentiation of einkorn wheat genotypes. The mean of Shannon coefficient of 0.16 indicated moderate variation in genotypes under study. The average percentage of polymorphic gene loci in the 34 studied populations was 36.74 and the average heterozygosity was 0.114. Based on analysis of molecular variance for 34 populations, the variations between and within populations were calculated as 7% and 93%, respectively. Cluster analysis based on Jaccard coefficients and UPGMA algorithm classified the einkorn genotypes into 10 distinct groups. The results of the principal coordinate analysis revealed that the two primary vectors explained 29.33% and 24.01% of the total molecular genetic variance, respectively.
 
Conclusion
The results indicated the usefulness of microsatellite markers in identifying and grouping einkorn wheat genotypes, so that the obtained information could be used in breeding projects, germplasm conservation planning and collection of einkorn wheat populations.

Keywords


پهلوانی سمیه، ایزانلو علی، پارسا سهیل، قادری محمدقادر (1395) ارتباط بین صفات کیفی دانه و نشانگرهای مولکولی SSR در برخی از ژنوتیپ‌های گندم نان. پژوهشنامه اصلاح گیاهان زراعی 8 (19)، 36-25.
خارستانی هادی، نصراله نژادقمی علی‌اصغر، مهرابی علی‌اشرف (1292) بررسی تنوع ژنتیکی گندم‌های اینکورن با استفاده از نشانگرهای ریزماهواره. مجله الکترونیک تولید گیاهان زراعی 6 (2)، 16-1.
زرگانی مهدی؛ رنجبر غلامعلی؛ ابراهیم‌نژاد شاهپور (1394) بررسی مولکولی تنوع ژنتیکی درلاین‌های دابل هاپلوئید گندم نان با استفاده از نشانگرهای SSR. پژوهشنامه اصلاح گیاهان زراعی 7 (15)، 95-88 .
عبدالهی سیسی نیر؛ محمدی سیدابوالقاسم؛ علوی‌کیا سید سیامک؛ صادق‌زاده بهزاد (1391) کاربرد نشانگرهای EST-SSR در تعیین ساختار ژنتیکی توده‌های بومی و ارقام اصلاح شده جو و تمایز آنها. سومین همایش ملی بیوتکنولوژی کشاورزی ، مشهد، ایران.
قاسمی نسرین؛ میرفخرایی رضاقلی؛ و عباسی علیرضا (1398) بررسی تنوع ژنتیکی ارقام گندم نان (Triticum aestivum L.) با استفاده از نشانگرهای ریزماهواره. پژوهشنامه اصلاح گیاهان زراعی، 11 (29)،  9-16.
کافی هانیه، نوابپور سعید، زینلی­نژاد خلیل، پهلوانی محمدهادی (1397) ارزیابی تنوع ژنتیکی ژنوتیپ‌های گندم نان ایرانی و خارجی با استفاده از نشانگرهای  SSR. ژنتیک نوین 13 (2)، 311-307.
کوهستانی محمد؛ صادق‌زاده بهزاد؛ ابراهیمی محمدعلی؛ یوسفی ولی‌اله (1395) شناسایی نشانگرهای SSR پیوسته با صفات زراعی در گندم دوروم. دومین کنگره بین المللی و چهاردهمین کنگره ملی ژنتیک ایران 3-1 خرداد، تهران؛ ایران.
محمدی مجید؛ میرفخرایی رضاقلی؛ عباسی علیرضا (1392) مطالعه تنوع ژنتیکی گندم نان (.Triticum aestivum L) به کمک نشانگرهای ریزماهواره و تجزیه ارتباطی برای صفات فیزیولوژیک تحت تنش سرمای بهاره .ژنتیک نوین 3، 279-288.
نظری مریم؛ و عبدالشاهی روح‌اله (1393) بررسی تنوع ژنتیکی ارقام گندم نان (Triticum aestivum L.) از طریق صفات مورفوفیزیولوژیک و نشانگرهای مولکولی SSR. مجله بیوتکنولوژی کشاورزی،  6 (3): 231-215.
واجد ابراهیمی محمدتقی؛ محمدآبادی محمدرضا؛ اسماعیلی‌زاده علی (1396) بررسی تنوع ژنتیکی چهار نژاد از گوسفندان موجود در ایران با استفاده از  نشانگرهای ریزماهواره‌ای. فنآوری زیستی در کشاورزی 16، 59-67.
واجدابراهیمی محمدتقی، محمدآبادی محمدرضا، اسمعیلی زاده کشکوئیه علی (1394) بررسی تنوع ژنتیکی پنج جمعیت گوسفند ایرانی با استفاده از نشانگرهای ریزماهواره‌ای. مجله بیوتکنولوژی کشاورزی 7(4)، 158-143.
References
Abdollahi-Sisi N, Mohammadi SA, Alavikia S, Sadeghzadeh B (2012) Analysis of genetic diversity in barley improved and landraces using SSR. Proceeding of 3rd Iranian Agricultural Biotechnology Congress. 3-5 September, Ferdowsi University of Mashhad, Iran (In Persian).
Anderson JA, Churchill GA, Autrique JE et al. (1993) Optimizing parental selection for genetic linkage maps. Genome 36, 181-186.
Arzani A, Ashraf M (2017) Cultivated ancient wheats (Triticum spp.): A potential source of health-beneficial food products. Compr Rev Food Sci Food Saf 16, 477-488.
Chambers GK, Macavoy ES (2000) Microsatellites: consensus and controversy. Comp Biochem Physiol B Biochem Mol Biol 126, 455-476.
Doyle JJ, Doyle, JL (1990) Isolation of plant DNA from fresh tissue. Focus 12, 13-15.
FAO. 2017. FAOSTAT Database. Available online at: http://www.fao.org/faostat/en/#data/QC
Gupta PK, Varshney RK (2005) Cereal genomics: an overview. Springer 1-18.
Ghasemi N, Mirfarkhai RH, Abbasi AS (2019) Genetic diversity of bread wheat (Triticum aestivum L.) cultivars using microsatellite markers. J Crop Breed Res 29, 9-16 (In Persian).
Hammer K, Filatenko AA, Korzun V (2000) Microsatellite markers - a new tool for distinguishing diploid wheat species. Genet Resour Crop Evol 47, 497-505.
Harlan JR, Zohary D (1996) Cultivated einkorn=Triticum monococcum L.subsp. monococcum (Triticum mono monococcum); wild einkorn=T. m. boeoticum; and Triticum monococcum L. subsp. aegiliopoides (Triticum mono aegilopoides). Sci 153, 1074-1080.
Ismaili A, Nazarian Firoozabadi F, Samiey K. and Drikvand R (2017) Assessment of genetic diversity among rain-fed wheat genotypes,using intron-exon semi random primers. J Cell Mol Res (Iranian Journal of Biology) 30, 121-129.
Jannik JL, Bink MC, Jansen RC (2001) Using complex plant pedigrees to map valuable genes. Trends Plant Sci 6, 337–42.
Kafi H, Navabpour S, Zaynali Nezhad KH, Pahlavani MH (2018) Evaluation of genetic diversity in Iranian and exotic wheat genotypes using SSR markers. Mod Genet 13, 307-311 (In Persian).
Kalivas A, Xanthopoulos F, Kehagia O, Tsaftaris AS (2011) Agronomic characterization genetic diversity and association analysis of cotton cultivars using simple sequence repeat molecular markers. Genet Mol Res 10, 208-217.
Kharestani H, Nasrolah Nejad Qomi AA, Mehrabi AA (2013) Genetic diversity assessment of Einkorn wheat by using microsatellite markers. EJCP 6, 1-16 (In Persian).
Kouhestani M, Sadeghzadeh S, Ebrahimi MA, Yousefi A (2016) Identification of SSR markers associated with agronomic traits in durum wheat. International & National Genetics Congress. Venue: Shahid Beheshti University, International Congress Center, Tehran, I. R of Iran.
Kumar R, Kumar A, Kumar SA, Radha J (2012) Evaluation of genetic diversity in rice sing simple sequence repeats (SSR) markers. Afr J Biotechnol 84, 14956-14995.
Liu J, Liu L, Hou N, Zhang A (2007) Genetic diversity of wheat gene pool of recurrent selection assessed by microsatellite markers and morphological traits. Euphytica 155, 249-258.
Mardia KV, Kent JT and Bibby JM (1979) Multivariate analysis. Academic press.
Maxted NBV, Ford-Lloyd SL, Jury SP, Kell MA Scholten. (2006) Towards a definition of a crop wild relative. Biodivers Conserv 15, 2673-2685.
Mir Drikvand R, Khyrolahi A, Ebrahimi A, Rezvani M (2015) Study of Genetic Diversity among Some Rainfed Bread and Durum Wheat Genotypes, Using SSR Markers. Plant Genet Res 1, 35-44 (In Persian).
Mizumoto K, Hirosawa S,Nakamura C, Takumi S (2002) Nuclear and chloroplast genome genetic diversity in the wild einkorn wheat (Triticum urartu), revealed by AFLP and SSLP analyses. Hered 137, 208-214.
Mohammadi SA, Prasanna BM (2003) Analysis of genetic diversity in crop plants-Salient statistical tools and considerations. Crop Sci 43, 1235-1248
Mohammadi M, Mirfakhraii RG, Abbasi A (2013) Genetic diversity in bread wheat (Triticum aestivumL.) as revealed by microsatellite markers and association analysis of physiological traits related to spring cold stress. Mod Genet 3, 279-288 (In Persian).
Naghavi MR, Malaki M, Alizadeh H et al. (2009) An assessment of genetic diversity in wild diploid wheat Triticum boeoticum from west of Iran using RAPD, AFLP and SSR markers. J Agron Sci Technol 11, 585-598.
Nazari M, Abdolshahi R (2014) Evaluation of genetic diversity in bread wheat cultivars (Triticum aestivum L.) using morpho-physiological traits and SSR markers. J Agric Biotechnol 6, 215-231 (In Persian).
Nei, M, Li WH (1979) Mathematical model for studying genetic variation in terms of restriction endonucleases. Proceedings of the National Academy of Science 76, 5269-5273.
Pahlavani S, Izanloo A, Parsa S, Ghaderi MG (2016) Association between Grain Quality Traits and SSR Molecular Markers in Some Bread Wheat Genotypes. J Crop Breed 19, 25-36 (In Persian).
Pirseyedi SM, Mardi M, Naghavi MR et al. (2006) Evaluation of genetic diversity and identification of informative markers for morphological characters in Sardari derivative wheat lines. Pak J Agric Biotechnol Sci 9, 2411-2418.
Rafalski JA, Vogel JM, Morgante M et al. (1996) Generating and using DNA markers in plants. Nonmammalian Genomic Analysis. A Practical Guide 75-134.
Roussel V, Leisova L, Exbrayat F et al. (2005) SSR allelic diversity changes in 480 European bread wheat varieties released from 1840 to 2000. Theor Appl Genet 111, 162-170.
Salehi M, Arzani A, Talebi M, Rokhzadi A (2018) Genetic diversity of wheat wild relatives using SSR markers. Genet 50, 131-141.
Salvi S, Tuberosa R (2005) To clone or not to clone plant QTLs: present and future challenges. Trends Plant Sci 10, 297-304.
Vajed Ebrahimi MT, Mohammad Abadi MR, Esmailizadeh AK (2016) Analysis of genetic diversity in five Iranian sheep population using microsatellites markers. Agric Biotechnol J 7, 143-158 (In Persian).
Vajed Ebrahimi MT, Mohammadabadi MR, Esmailizadeh AK (2017) Genetic Diversity Analysis of Four Sheep Breeds Existing in Iran Using Microsatellite Markers. Agric Biotechnol 8, 59-66 (In Persian).
Wang H, Wang X, Chen P, Liu D (2007) Assessment of genetic diversity of Yunnan, Tibetan and Xinjiang wheat using SSR markers. J Genet Genom 34, 623-633.
Warschefsky E, Penmetsa RV, Cook DR, von Wettberg EJB (2014) Back to the wilds: tapping evolutionary adaptations for resilient crops through systematic hybridization with crop wild relatives. Am J Bot 101, 1791-1800.
Williams JGK, Kubelik AR, Livak KJ et al. (1990) DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Res 18, 6531-6535.
Zargani M, Ranjbar GA, Ebrahim Nejad Sh (2015) Molecular assessment of genetic diversity among bread wheat (Triticum aestivum L.) doubled haploid lines using SSR markers. J Crop Breed 7, 88-95 (In Persian).
Zhang HY, Liu XZ, Li TS, Yang YM­ (2006) ­ Genetic diversity among Flue-cured tobacco (Nicotiana tabacum L.) revealed by amplified fragment length polymorphism. ­ Bot­ Stud 47, 223-229.