Screening of some Iranian Commercial Apricot Cultivars by SSR Markers for Identification of Synonyms

Document Type : Research Article

Authors

• Mehdi Rezaei
• Mitra Rahmati
• Abdolreza Kavand
• Morteza Hemati
• Seyyed Reza Kazemi

Seed and Plant Certification and Registration Institite, Agricultural Research Education and Extention Organization (AREEO), Karaj, Iran

https://doi.org/10.22067/jhs.2021.61722.0

Abstract

Introduction: Apricot (Prunus armeniaca L.) as an important fruit crop belongs to the Amygdaloideae in the Rosacea family and is grown in regions with Mediterranean climates in the world. Apricot species were classified into six eco-geographical groups including: Central Asian, East Chinese, North Chinese, Dzhungar-Zailij, Irano-Caucasian and European. Iranian genotypes which belong to the Irano-Caucasian group are mostly self-incompatible with low chill requirement. The high level of genetic diversity in Iranian apricots is due to sexual reproduction by seeds during the years. In Iran, many of apricot local varieties have been relocated between provinces and subsequently, in some cases their names, have been changed over the years. Hence, to determine the genetically different cultivars and detection of synonyms, screening of apricot germplasm seems necessary in Iran.
Materials and Methods: Thirty eight commercial genotypes of apricot with five biological replications were collected from 14 nurseries in West Azarbaijan, East Azarbaijan, Esfahan, Semnan, Alborz, and Tehran Provinces in Iran. Additionally Orang Red apricot (Porteghali) included in the study as an outgroup sample. Also DNA sample of previously registered apricots in national list were used in this study. Young and healthy leaves of each cultivar were sampled and stored at -70 °C. Samples were powdered using mortar and pestle in presence of liquid nitrogen. CTAB extraction buffer was used for nucleic acid extraction. Quantity and quality of extracted DNA were measured by spectrophotometry and agarose gel electrophoresis.
Thermal cycles were done in Eppendorf thermocycler and the cycling program were set on one cycle of 94°C for 4 minute, 30 cycles of  94°C for 30 seconds, annealing temperature of each primer for 30 seconds and 72°C for 30 seconds followed by one cycle of 72°C for 5 minutes. PCR products were resolved on 10% polyacrylamide gels in 1x TBE buffer. GelRed (Biotium) was applied for gel staining and amplified bands were revealed by UV (300 nm). Eight SSR markers which showed more diversity were selected and scored. Polymorphic alleles were scored as one for presence and zero for absence. For detection of off types, samples were classified by Paired Group method and Euclidean algorithm in PAST software. Then the data of off-types were removed from the dataset and samples were reclassified by the method. Principal Coordinate Analysis (PCoA) was carried out using PAST software. Genetic diversity indices were evaluated in Popgene 32 software.   
Results and Discussion: Eight SSR loci produced 124 alleles with the average 15.5 allele per locus. Nei’s gene diversity and Shannon’s information index were 0.32 and 0.48, respectively which showed high level of diversity in this collection. Distance matrix based on Nei’s gene diversity showed that the most genetic distance (0.74) was between Askar Abadi and Zodras, Mahali Goushti Zodras and Nasiri cultivars. Clustering of samples indicated that some samples including 19 (Shahroudi), 59 (Nakhjavan), 107 (Shahroudi), 127 (Soltani), 137 (Ghavami), 144 (Tabraze) and 156 (Daneshkade) were off-types.
For identification of synonyms the off-type samples were disregarded. Cluster analysis illustrated that some local cultivars with different names had same genetic backgrounds. Thus, the names of these samples should be unified in the germplasm. Depicted graph based on first and second coordinates in PCoA demonstrated that the 38 collected groups of apricots are genetically 26 distinct cultivars and there are some duplicates in the germplasm. Results showed that three loci including UDP98-021, UDP98-409 and UDP98-411 were able to distinguish all 26 genotypes. To check the genetic identity of saplings with the same name, some cultivars including Jahangiri, Askar Abadi, Shamlou, Saltanati, Shahroudi, Shams, Tabarze and Rajab Ali were collected from two different nurseries. Surprisingly, the results showed that Nasiri, Tabraze and Shahroudi which were sampled twice from distinct nurseries and provinces, despite of identical names, had different genetic backgrounds.
Conclusion: Detected off-types among five biological replications of local varieties propagated asexually by nurseries showed that there was not sufficient attention in the selection of propagating material in the nurseries. In this context, establishment of foundation blocks by public sector and mother orchards by private sector of economy from Iranian apricot local varieties can be an effective solution so that nursery operators can provide certified propagating material for production of certified nursery stocks. Moreover, seed and plant certification and registration institute should made inspection and testing procedures in mother orchards and nurseries to ensure that propagated trees are healthy, genetically uniform and original.

Keywords

• Cluster analysis
• Germplasm management
• Molecular marker
• Synonym

20.1001.1.20084730.1400.35.4.4.0

Main Subjects

• Breeding and Biotechnology of Plant and Flower

References

1. Albuquerque H.Y.G., Oliveira E.J. Brito A.C., Andrade L.R.B., Carmo C.D., Morgante C.V., Vieira E.A., Moura E.F., and Faleiro F.G. 2019. Identification of duplicates in cassava germplasm banks based on single-nucleotide polymorphisms (SNPs). Scientia Agrocola 76(4): 328-336.
2. Food and Agriculture Organization of the United Nations. 2018. FAOSTAT statistical database. Rome, FAO.
3. Gross B.L., Volk G.M., Richards M.Ch. Forsline P.L., Fazi, G., and Chao T. 2012. Identification of ‘‘Duplicate’’ Accessions within the USDA-ARS National Plant Germplasm System Malus Collection. Journal of American Society for Horticultural Science 137(5): 333-342.
4. Gürcan K., Öcal N., Yılmaz K.U., Ullah S., Erdoğan A., and Zengin Y. 2015. Evaluation of Turkish apricot germplasm using SSR markers: Genetic diversity assessment and search for Plum pox virus resistance alleles. Scientia Horticultura 193: 155–164.
5. Hormaza J.I. 2002. Molecular characterization and similarity relationships among apricot (Prunus armeniaca) genotypes using simple sequence repeats. Theoretical and Applied Genetics 104(3): 321–328.
6. Janatizadeh A., Fatahimoghadam M.R., Zamani Z., and Zeraatgar H. 2011. Study of genetic diversity in some apricot cultivars and genotypes using morphological and RAPD Markers. Journal of Iranian Horticultural Science 42(3): 255-265.
7. Khadari B., Breton C., Moutier N., Roger J.P., Besnard G., Berville A., and Dosba F. 2003. The use of molecular markers for germplasm management in a French olive collection. Theoretical and Applied Genetics 106: 521-529.
8. Khadivi-Khub A., Yarahmadi M., Jannatizadeh A., and Ebrahimi A. 2015. Genetic relationships and diversity of common apricot (Prunus armeniaca) based on simple sequence repeat (SSR) markers. Biochemical and Systematic Ecology 61: 366–371.
9. Layne R.E.C., Bailey C.H., and Hough L.F. 1996. Apricots. P. 79-111 In: Janick, J., Moore, J.N. (Eds.), Fruit Breeding: Tree and Tropical Fruits, vol. II. John Wiley and Sons, New York.
10. Maghuly F., Fernandez E.B., Ruthner S., Pedryc A., and Laimer M. 2005. Microsatellite variability in apricots (Prunus armeniaca) reflects their geographic origin and breeding history. Tree Genetics and Genomes 1(4): 151–165.
11. Mohamadzadeh S., Bouzari N., and Abdosi V. 2013. Evaluation of pomological, morphological and genetic characteristics in some Iranian apricot cultivars and genotypes. Journal of Iranian Horticultural Science 44(2): 179-191.
12. Naghavi M.R., Ghareyazi B., Hosseini Salekdeh Gh. 2013. Molecular Markers. University of Tehran Press. Tehran. (In Persian)
13. Pedryc A., Ruthner S., Hermán R., Krska B., Hegedűs A., and Halász J. 2009. Genetic diversity of apricot revealed by a set of SSR markers from linkage group G1. Scientia Horticultura 121(1): 19–26.
14. Raji R., Jannatizadeh A., Fattahi R., and Esfahlani M.A. 2014. Investigation of variability of apricot (Prunus armeniaca) using morphological traits and microsatellite markers. Scientia Horticultura 176: 225–231.
15. Rehder A. 1967. Manual of Cultivated Trees and Shrubs Hardy in North America: Exclusive of the Subtropical and Warmer Temperate Regions, 2^nd Eds Macmillan, NewYork.
16. Saghai-Maroof M.A., Soliman K.M., Jorgensen R.A., and Allard R.W. 1984. Ribosomal DNA spacer-length polymorphism in barley: Mendelian inheritance, chromosomal location, and population dynamics. Proceedings of the National Academy of Sciences of the United States of America 81: 8014–8019.
17. Sánchez-Pérez R., Ruiz D., Dicenta F., Egea J., and Martínez-Gómez P. 2005. Application of simple sequence repeat (SSR) markers in apricot breeding: molecular characterization, protection, and genetic relationships. Scientia Horticultura 103(3): 305–315.
18. Tautz D. 1989. Hyper-variability of simple sequences as a general source for polymorphic DNA markers. Nucleic Acids Research 17(16): 6463–6471.
19. Tian-Ming H., Xue-Sen C., Zheng X., Jiang-Sheng G., Pei-Jun L., Wen L., Qing L., and Yan W. 2006. Using SSR markers to determine the population genetic structure of wild apricot (Prunus armeniaca) in the Ily Valley of West China. Genetic Resources and Crop Evolution 543: 563–572.
20. Trujillo I., Ojeda M.A. Urdiroz N.M., Potter D., Barranco D., Rallo L., and Diez C.M. 2013. Identification of the worldwide olive germplasm bank of Córdoba (Spain) using SSR and morphological markers. Tree Genetics and Genomes 10: 141-155.