Evaluating and Identification of Genetic Variation of some of Pomegranate (Punica granatum) Genotypes using DNA barcoding (ITS)

Document Type : Research Paper

Authors

1 Assistant Professor, Horticulture Crops Research Department, Agricultural Research, Education and Extension Organization (AREEO), Hamedan, Iran

2 Department of Plant Breeding and Biotechnology, Faculty of Agriculture, Shahrekord University

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

Abstract

Objective
Iran is one of the few countries where the origin of pomegranate (Punica granatum L.) in the world. About half of the pomegranate genotypes are endangered. Despite the similarity between some genotypes in terms of appearance, there are differences between anthocyanins, phytochemicals, antioxidants, etc., of them that are very much affected by the environment (especially stress) and require DNA barcoding. For this reason, more accurate molecular studies, especially DNA identification, are necessary to aid in classification, identification of the required genotype, non-incorrect naming of genotypes, and identification of cultivars. By performing this research, it is possible to reduce the volume of genotypes and eliminate duplicate and similar genotypes in Saveh pomegranate collection to reduce their maintenance and management costs. Also used to select the best plant barcode to identify, differentiate and determine the diversity of genotypes for use in breeding programs.
Materials and methods
In this study, 58 genotypes in Saveh pomegranate collection were examined by ITS barcode region. After receiving the sequences, first all the sequences blast in the NCBI site for the accuracy of the desired area and after sure of the desired plant area (pomegranate), the quality of the sequences was measured with Chromas software and in addition to deleting the M13 sequence, the beginning and end sequences and poor-quality sequences were deleted. Then, for multiple alignments by clustalW method, bioinformatics analysis was performed using MEGA software.
Results
The results showed that the success rate of propagation in this area by PCR was 79%. Also, the success rate of sequencing in this area was 74.68%. The GC content of this area was 64.23%. The lowest genetic distance for this region (0.005) was between the genotypes of Malls Tabas with Chatroud Shirin and the Torsh Dorag Rafsanjan with Globland Bafgh and the highest genetic distance (5.314) was between the genotypes of Gol Magasi Taft with Dane Siyah Ardestan, Poost Ghermez Zanjan, Malas Paveh, Peyvndi Ashkzar and Dane Ghermez Zavareh genotypes. The results of phylogenetic tree also showed that wild genotypes of Tamin Khash, Domezeh Bagh Malek Izeh and Dorag Malas Bajestan and Gol Magasi Taft were each in separate groups and other genotypes were in other groups.
Conclusions
In general, Ardestan, Khash, Gol Magasi Taft, Malas Peyvandi Ashkzar, Zanjan, Paveh, Zavareh and Ravar genotypes had the highest genetic diversity and distance with other genotypes that according to other characteristics of genotypes, they can be used as parents for breeding programs. Also, considering that this region, unlike other regions, carries both paternal and maternal genes and due to the facilitation of reproduction and the success of their sequences, was identified as a suitable region to show genetic diversity between genotypes which can be used in future research.

Keywords

References

احمدی کریم، عبادزاه حمیدرضا، حاتمی فرشاد و همکاران (1400). آمارنامه کشاورزی (جلد سوم). وزارت جهاد کشاورزی.
اسدی فاطمه، دژستان سارا، قهرمانزاده رباب و همکاران (1394). بارکد گذاری DNA برخی از گیاهان دارویی.  فصلنامه علمی زیست فناوری گیاهان زراعی 5، 40-31.
References
Ahmadi K, Ebadzadeh HR, Hatami F, et al. (2021) Agricultural statistics (3rd Vol.). Ministry of Agriculture-Jahad, Iran (In Persian).
Asadi F, Dezhestan S, Ghahremanzadeh R, et al. (2016) DNA barcoding of some local medicinal plants of Ardabil province. Crop Biotech 10, 31-40 (In Persian).
Basaki T, Khayam Nekouei M, Choukan R, Mardi M (2016) Evaluation of Iranian pomegranate collection using simple sequence repeat and morphological traits. Crop Breed J 6, 67-78.
Brown AHD (1995) The core collection at the crossroads. In: Hodkin T, Brown AHD. Van Hintum TJL et al. (Eds.), Core collections of plant genetic resources. International Plant Genetic Resources Institute (IPGRI). John Wiley and Sons, Chichester, pp. 3-19.
Castro C (2015) DNA barcodes in Fig cultivars (Ficus carica L.) using ITS regions of ribosomal DNA, the psbA-trnH spacer and the matK coding sequence. Am J Plant Sci 6, 95-102.
Chase MW. Cowan RS. Hollingsworth PM, et al. (2007) A proposal for a standardized protocol to barcode all land plants. Taxon 56, 295-299.
Hajibabaei M, Singer GAC, Hebert PDN, Hickey DA (2007) DNA barcoding: how it complements taxonomy, molecular phylogenetics and population genetics. Trends Genet 23, 167-172.
Hajiahmadi Z, Talebi M, Sayed-Tabatabaei BE (2013) Studying genetic variability of pomegranate (Punica granatum L.) based on chloroplast DNA and barcode genes. Mol Biotechnol 55, 249-259.
Jalikop SH, Sampath Kumar P (1990) Use of a gene marker to study the mode of pollination in pomegranate (Punica granatum L.). J Hortic Sci 65, 221-223.
Kress WJ, Wurdack KJ, Zimmer EA, et al. (2005) Use of DNA barcodes to identify flowering plants. Proc Natl Acad Sci USA 102, 8369-8374.
Kress WJ (2017) Plant DNA barcodes: applications today and in the future. J Syst Evol 55, 291-307.
Liu J, Yan HF, Ge XJ (2016) The use of DNA barcoding on recently diverged species in the genus Gentiana (Gentianaceae) in China. Plos One 11(4): 1-14.
Pirseyedi SM, Valizadehgan S, Mardi M, et al. (2010) Isolation and characterization of novel microsatellite markers in pomegranate (Punica geranatum L.). Int J Mol Sci 11, 2010-2016.
Teixeira da Silva JA, Rana TS, Narzary D, et al. (2013) Pomegranate biology and biotechnology: A review. Sci Hortic-Amsterdam160, 85-107.
Tamura K, Peterson D, Peterson N, et al. (2011) MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28, 2731-2739.
De Vere N, Rich TCG, Ford CR, et al. (2012) DNA barcoding the native flowering plants and conifers of wales. Plos One 7(6), e37945.
Yao PC, Gao HY, Wei YN, et al. (2017) Evaluating sampling strategy for DNA barcoding study of coastal and inland halo tolerant Poaceae and Chenopodiaceae: A case study for increased sample size.  Plos One 12(9), e0185311.
Agricultural Biotechnology Journal
Volume 15, Issue 1
April 2023
Pages 107-124

Files

Share

How to cite

Statistics