Molecular variation and genetic relationships among Aegilops tauschii accessions based on CAAT-box derived polymorphism

Document Type : Research Paper

Authors

1 Islamic Azad university of Isfahan

2 Department of Plant breeding and Biotechnology, Kermanshah Branch, Islamic Azad University, Kermanshah, Iran

3 Associate Professor, Department of Agronomy and plant breeding, Isfahan (Khorasgan) Branch, Islamic Azad University, Isfahan, Iran

4 ilam university

5 Professor, Department of Agronomy and plant breeding, Isfahan (Khorasgan) Branch, Islamic Azad University, Isfahan, Iran

Abstract

Objective
The importance of wild relatives in wheat breeding has caused a lot of investigations to study the genetic diversity and population structures in different species of wild wheat, using various molecular markers. The purpose of this study was to investigate the molecular diversity of 90 different accessions of Aegilops tauschiiand analyzing the genetic structure for clustering the populations using CAAT box-derived polymorphism (CBDP) markers.
 
 
 
Materials and methods
In the present study, the genetic diversity and population structure of 90 different accessions of Ae. tauschii collected from different geographical areas of Iran, was evaluated using 12 CBDP primers.
Results
Based on the results, the 12 primers amplified 141 bands in which 91 were polymorphic with an average of 7.58 bands pre primer. The polymorphism information content (PIC) and marker index (MI) for the CBDP primers ranged from 0.40 to 0.49 and 1.49 to 4.99, respectively. Primers CB9, CB12 and CB1 showed a high efficiency in genetic discrimination of evaluated accessions. Population structure analysis classified evaluated accessions into three main groups with 10, 18 and 30 accessions respectively and other accessions recognized as a mixture accessions. In this study, subpopulation NO.1 had the highest values of genetic diversity indices such as number of effective alleles (Ne), Shannon index (I) and heterozygosity (He). Among Ae. tauschii populations a very low genetic differentiation (Gst: 0.03) and high gene flow (Nm: 18.58) were observed. The dendrogram resulted from cluster analysis categorized the assessed accessions into three clusters which accordance with genetic structural analysis results.
Conclusions
Overall, the results of different parameters showed that the CBDP, is an appropriate marker system for assessing the genetic diversity of Aegilops tauschii accessions. Regarding to the results of genetic structural analysis and diversity parameters, a conservation program is recommended for management of Aegilops germplasm as a valuable genetic resource in the wheat breeding programs.

Keywords

References

بهادر یاسر؛محمدآبادی محمدرضا؛خضریامین؛اسدی مهدیه؛مدحتی لیلا (1395) مطالعهتنوعژنتیکیجمعیتهایزنبورعسلاستانکرمانبااستفادهازنشانگرهای  ISSR. پژوهش‌هایتولیداتدامی13(1)، 192-186.
پورابوقداره علیرضا؛ اطمینان علیرضا؛ شوشتری لیا؛ ملکی تبریزی ندا (1398) ارزیابی مقایسه‌ای نشانگرهای CBDP و SCoT در بررسی تنوع ژنتیکی موجود در توده‌های مختلف Aegilops. مجله بیوتکنولوژی کشاورزی 11 (4)، 174-153.‎
واجدابراهیمی محمدتقی؛ محمدآبادی محمدرضا؛ اسماعیلی زاده علی (1394) ‎بررسی تنوع ژنتیکی پنج جمعیت گوسفند ایرانی با استفاده از نشانگرهای ریزماهواره ای‎. مجله بیوتکنولوژی کشاورزی 7 (4)، 143-158.‎
Reference
Ahmadi J, Pour-Aboughadareh A, Fabriki-Ourang S et al. (2018a) Screening wild progenitors of wheat for salinity stress at early stages of plant growth: insight into potential sources of variability for salinity adaptation in wheat. Crop Pasture Sci 69, 649–58.
Ahmadi J, Pour-Aboughadareh A, Fabriki-Ourang S, Mehrabi A-A, Siddique KHM (2018b) Screening wheat germplasm for seedling root architectural traits under contrasting water regimes: potential sources of variability for drought adaptation. Arch Agron Soil Sci 64, 1351–1365.
Ahmadi J, Pour-Aboughadareh A, Ourang SF, Mehrabi AA, Siddique KHM (2018c) Wild relatives of wheat: Aegilops–Triticum accessions disclose differential antioxidative and physiological responses to water stress. Acta Physiol Plant 40, 90.
Anderson JA, Churchill GA, Autrique JE, et al. (1993) Optimizing parental selection for genetic linkage maps. Genome 36, 181–186
Baghizadeh A, Bahaaddini M, Mohamadabadi MR, Askari N (2009) Allelic Variations in Exon 2 of Caprine MHC Class II DRB3 Gene in Raeini Cashmere Goat. Am-Eurasian J Agric Environment Sci 6, 454-459.
Bahador Y, Mohammadabadi MR, Khezri A, Asadi M, Medhati L (2016) Study of Genetic Diversity in Honey Bee Populations in Kerman Province using ISSR Markers. Res Anim Prod 7 (13), 186-192 (In Persian).
Bansal M, Kaur S, Dhaliwal HS, Bains NS, Bariana H S, Chhuneja P, et al (2017) Mapping of Aegilops umbellulata-derived leaf rust and stripe rust resistance loci in wheat. Plant Pathol 66, 38–44.
Benoist C, O'hare K, Breathnach R, Chambon P (1980) The ovalbumin gene-sequence of putative control regions. Nucleic Acid Res 8, 127–142.
Cheniany M, Ebrahimzadeh H, Salimi A, Niknam V (2007) Isozyme variation in some populations of wild diploid wheats in Iran. Biochem Syst Ecol 35, 363–371.
Colmer TD, Flowers TJ, Munns R (2006) Use of wild relatives to improve salt tolerance in wheat. J Exp Bot 57, 1059–1078. 
Ditta A, Zhou Z, Cai X et al (2018) Assessment of genetic diversity, population structure, and evolutionary relationship of uncharacterized genes in a novel germplasm collection of diploid and allotetraploid Gossypium accessions using EST and mgenomic SSR markers. Int J of Mol Sci 19, 2401.    
Doyle JJ, Doyle JL (1987) A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochemical Bulletin 19, 11-15.
Dubcovsky J, Dvorak J (2007) Genome plasticity a key factor in the success of polyploid wheat under domestication. Science 316, 1862–6.
Dulai S, Molnár I, Szopkó D et al. (2014) Wheat- Aegilops biuncialis amphiploids have efficient photosynthesis and biomass production during osmotic stress. J Plant Physiol 171, 509–517.
Dumolin-Lapegue S, Demesure B, Fineschi S, Le Corre V, Petit RJ (1997) Phylogeographic structure of white oaks throughout the European continent. Genetics 146, 1475–1487.
Ebrahimi Z, Mohammadabadi MR, Esmailizadeh A, Khezri A (2015) Association of PIT1 gene and milk protein percentage in Holstein cattle J Livest Sci Technol 3 (1), 41-49.
Eltaher S, Sallam A, Belamkar V, Emara HA, Nower AA, Salem KFM (2018) Genetic Diversity and Population Structure of F3:6 Nebraska Winter Wheat Genotypes Using Genotyping-By-Sequencing. Front Genet9, 76. 
Etminan A, Pour-Aboughadareh A, Mehrabi AA, Shooshtari L, Ahmadi-Rad A, Moradkhani H (2019) Molecular characterization of the wild relatives of wheat using CAAT-box derived polymorphism. Plant Biosyst 153, 398-405.
Etminan A, Pour-Aboughadareh A, Mohammadi R et al. (2018a) Applicability of CAAT box- derived polymorphism (CBDP) markers for analysis of genetic diversity in durum wheat. Cereal Res Commun 46, 1–9.
 Etminan A, Pour-Aboughadareh A, Noori A et al. (2018b) Genetic relationships and diversity among wild Salvia accessions revealed by ISSR and SCoT markers. Biotechnol & Biotechnol Equi 32, 610–617. 
Falahati-Anbaran M, Habashi AA, Esfahany M, Mohammadi SA & Ghareyazie B (2006) Study of genetic diversity and relationships of diploid and tetraploid annual medics using Microsatellite markers. Journal of Science and Technology of Agricultural and Natural Resources 10(3), 349-358 (In Persian).
Giraldo OP (2019) Political ecology and agriculture. 1st Edition, Springer, Cham.
Hamidi H, Talebi R, Keshavarzi, 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 42, 558-567.
Kahiluoto H, Kaseva J, Balek J, et al. (2019) Decline in climate resilience of European wheat. Proceedings of the National Academy of Sciences of the United States of America 116, 123–128.
Khodabakhshzadeh R, Mohammadabadi MR, Moradi H et al. (2015) Identify of G―›A point mutation at positions 477 and 721 in exon 2 of GDF9 gene in Kermani sheep. Modern Genet J 10, 261-268 (In Persian)
Kihara H (1944) Discovery of the DD-analyser, one of the ancestors of vulgare wheat.  Biol Agric Hortic 19:889–90.
Liu B, Martre P, Ewert F, et al. (2018) Global wheat production with 1.5 and 2.0 ◦C above pre-industrial warming. Global Change Biol 25, 1428–1444.
Liu W, Rouse M, Friebe B, et al. (2011) Discovery and molecular mapping of a new gene conferring resistance to stem rust, Sr53, derived from Aegilops geniculata and characterization of spontaneous translocation stocks with reduced alien chromatin. Chromosome Res 19, 669–682.
Lopes M, El-Basyoni I, Baenziger P, Singh S, Royo C, Ozbek K, Aktas H, Ozer E, Ozdemir F, Manickavelu A, Ban T, Vikram P (2015) Exploiting genetic diversity from landraces in wheat breeding for adaptation to climate change. J. Exp. Bot 66, 3477-3486.
Mahjoob BH, Najafi-Zarini and Hashemi SHR (2014) Assessment of genetic relationships among 36 Brassica genotypes using ISSR molecular markers. J Crop Breed 6, 96-106.
Mayer KFX, Rogers J, Dole el J, et al (2014) A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome. Science, 345. 
McFadden ES, Sears ER (1946) The origin of Triticum spelta and its free-threshing hexaploid relatives. J Hered 37, 107–16.
Moazeni SM, Mohammadabadi MR, Sadeghi M et al. (2016) Association of the melanocortin-3(MC3R) receptor gene with growth and reproductive traits in Mazandaran indigenous chicken. J. Livest. Sci. Technol 4, 51-56.
Moghadaszadeh M, Mohammadabadi MR, Esmailizadeh Koshkoieh A (2015) Association of Exon 2 of BMP15 Gene with the Litter Size in the Raini Cashmere Goat. Genet the 3rd Millennium 13, 4062-4067.
Moghaddam M, Ehdaie B, Waines G. 2000. Genetic diversity of wild diploid wheat Triticum urartu Tum. ex. Gandil. revealed by isozyme markers. Genet Res Crop Evol 47, 323–334.
Moradkhani H, Mehrabi A, Etminan A, Pour-Aboughadareh A (2015) Molecular diversity and phylogeny of Triticum-Aegilops species possessing D genome revealed by SSR and ISSR markers. Plant Breed Seed Sci 81, 71-95.
Moradkhani H, Pour-Aboughadareh AR, Mehrabi AA, Etminan A (2012) Evaluation of genetic relationships of Triticum-Aegilops species possessing D genome in different ploidy levels using microsatellites. Int J Agri Crop Sci 23, 1746–1751.
Mousavifard SS, Saeidi H, Rahiminejad MR, Shamsadini M (2015) Molecular analysis of diversity of diploid Triticum species in Iran using ISSR markers. Genet Resour Crop Evol 62, 387–394.
Naghavi M, Maleki M, Tabatabaei S (2009) Efficiency of floristic and molecular markers to determine diversity in Iranian populations of T. boeoticum. World Acad Sci Eng Technol 3, 42–44.
Naghavi MR, Hajikaram M, Taleei AR, Jafar Aghaee M (2010) Microsatellite analysis of genetic diversity and population genetic structure of Aegilops tauschii Coss. in Northern Iran. Genet Res Crop Evol 57, 423-430.
Nei M (1978) Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics 89, 583-590.
Olivera PD, Rouse MN, Jin Y (2018) Identification of new sources of resistance to wheat stem rust in Aegilops spp. in the tertiary gene pool of wheat. Front Plant Sci 9, 1719–1726.
Olson EL, Rouse MN, Pumphrey MO, et al. (2013) Introgression of stem rust resistance genes SrTA10187 and SrTA10171 from Aegilops tauschii to wheat. Theor Appl Genet 126, 2477–2484.
Petersen G, Seberg O, Yde M, Berthelsen K (2006) Phylogenetic relationships of Triticum and Aegilops and evidence for the origin of the a, B, and D genomes of common wheat (Triticum aestivum). Mol Phylogenet Evol 39, 70.
Pont C, Salse J (2017) Wheat paleohistory created asymmetrical genomic evolution. Curr Opin Plant Biol 36, 29–37.
Pour-Aboughadareh A, Ahmadi J, Mehrabi AA, et al. (2017a) Assessment of genetic diversity among Iranian Triticum germplasm using agro-morphological traits and start codon targeted (SCoT) markers. Cereal Res Commun 45, 574–586.
Pour-Aboughadareh A, Ahmadi J, Mehrabi AA, Moghaddam M, Etminan A (2017b) Evaluation of agro-morphological diversity in wild relatives of wheat collected in Iran. J Agr Sci Tech 19, 943–956.
Pour-Aboughadareh A, Etminan A, Shooshtari L, Maleki-Tabrizi N (2019) Comparative assessment of SCoT and CBDP markers for investigation of genetic diversity existing in different Aegilops species. Agric Biotechnol J 11 (4), 153-174. (In Persian)
Pour-Aboughadareh A, Mohmoudi M, Ahmadi J, Moghaddam M, Mehrabi AA, Alavikia SS. 2017c. Agro-morphological and molecular variability in Triticum boeoticum accessions from Zagros Mountains, Iran. Genet Res Crop Evol 64, 545–556.
Prevost A, Wilkinson MJ (1999) A new system of comparing PCR primers applied to ISSR fingerprinting of potato cultivars. Theor Appl Genet 98, 107–112.
Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multi locus genotype data. Genetics 155, 945–959.
Putman AI, Carbone I (2014) Challenges in analysis and interpretation of microsatellite data for population genetic studies. Ecol Evol 4, 4399–4428.
Saeidi H, Rahiminejad MR, Vallian S, Heslop-Harrison JS (2006) Biodiversity of diploid D-genome Aegilops tauschii Coss. in Iran measured using microsatellites. Genet Resour Crop Evol 53, 1477–1484.
Salse J, Chagué V, Bolot S, et al. (2008) New insights into the origin of the B genome of hexaploid wheat: evolutionary relationships at the SPA genomic region with the S genome of the diploid relative Aegilops speltoides. BMC Genomics 9, 555.
Singh AK, Rana MK, Singh S, et al. (2014) CAAT box-derived polymorphism (CBDP): a novel promoter-targeted molecular marker for plants. Journal of Plant Biochemistry and Biotechnology 23,175–183.
Sohail Q, Shehzad T, Kilian A, et al. (2012) Development of diversity array technology (DArT) markers for assessment of population structure and diversity in Aegilops tauschii. Breed Sci 62, 38–45.
Tahernezhad Z, Zamani MJ, Solouki M, Zahravi M, Imamjomeh AA, Jafaraghaei M, Bihamta MR (2010) ‘Genetic diversity of Iranian Aegilops tauschii Coss. using microsatellite molecular markers and morphological traits. Mol Bio Rep 37, 3413–3420.
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(4), 143-158 (In Persian).
Varshney RK, Chabane K, Hendre PS, et al. (2007) Comparative assessment of EST-SSR, EST-SNP and AFLP markers for evaluation of genetic diversity and conservation of genetic resources using wild, cultivated and elite barleys. Plant Sci 173, 638–649.
Wang IJ (2013) Examining the full effects of landscape hetero-geneity on spatial genetic variation: a multiple matrix regression approach for quantifying geographic and ecological isolation. Evol 16, 175–182.
Yan W, Li J, Zheng D, Friedman C, Wang H, et al. (2019) Analysis of genetic population structure and diversity in Mallotus oblongifolius using ISSR and SRAP markers. PeerJ 7, e7173. 
Zamanianfard Z, Etminan A, Mohammadi R, Shooshtari L (2015) Evaluation of Molecular Diversity of durum wheat genotypes using ISSR markers, Biol Forum7(1), 214-218.
Zhuravlev YN, Reunova GD, Kats IL, Muzarok TI, Bondar AA (2010) Genetic variability and population structure of endangered Panax ginseng in the Russian Primorye. Chine
Agricultural Biotechnology Journal
Volume 13, Issue 1
April 2021
Pages 57-74

Files

Share

How to cite

Statistics