Volume 18, Issue 2 (4-2026)
J Crop Breed 2026, 18(2): 173-184 |
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Raeisi F, Fahmideh L, Fakheri B A, Keykhasaber M. (2026). Phylogenetic Classification of Some Date Palm Cultivars in Sistan and Baluchestan Province Based on the matK Chloroplasty Gene. J Crop Breed. 18(2), 173-184. doi:10.61882/jcb.2026.1588
URL: http://jcb.sanru.ac.ir/article-1-1588-en.html
URL: http://jcb.sanru.ac.ir/article-1-1588-en.html
1- Department of Plant Breeding and Biotechnology, Faculty of Agriculture, University of Zabol, Zabol, Iran
2- Department of Plant Breeding and Biotechnology, Plant Production Faculty, Gorgan University of Agricultural Sciences and Natural Resources, Gorgan, Iran
3- Department of Plant Pathology, Faculty of Agriculture, University of Zabol, Zabol, Iran
2- Department of Plant Breeding and Biotechnology, Plant Production Faculty, Gorgan University of Agricultural Sciences and Natural Resources, Gorgan, Iran
3- Department of Plant Pathology, Faculty of Agriculture, University of Zabol, Zabol, Iran
Abstract: (253 Views)
Extended Abstract
Background: The date palm (Phoenix dactylifera L.) is a monocotyledonous plant from the Palmaceae, which is cultivated in many countries from tropical and subtropical regions, including Iran. Today, owing to the progress of technology, molecular identification methods have special importance in systematic studies. One of these methods is DNA barcoding, which is species identification based on the sequences of conserved DNA regions that provide a valuable tool for assessing phylogenetic relationships. In this method, the comparison of the sequences of special conserved DNA fragments is used to study the diversity of populations and determine the relationships between different species. Accordingly, different regions of nuclear DNA (ITS, ITS2) and chloroplast (rbcL, matK, trnH-psbA, atpF-atpH, nhdJ, and psbK-psbI) have been suggested as important barcodes in plants. The matK chloroplast gene, which has a high evolutionary speed at the nucleotide and amino acid levels, is one of the most suitable chloroplast genes for the analysis of phylogeny and evolutionary relationships in a range of taxonomic levels from species to genus, phylum and even super phylum, in Angiosperms in particular. This gene can be used individually or together with other genes to identify and introduce unknown species. Examining the genetic diversity of the available germplasm reserves is essential for the improvement and propagation of cultivars with desirable traits, and the first step in this process is to identify the existing cultivars and classify them. Due to the importance of producing dates in Iran, browsing for new cultivars, breeding existing cultivars, and studying the existing diversity between different cultivars are among important strategies to improve the quantity and quality of date palm production. However, there are not enough studies on the investigation of the relationship or genetic distance of different date palm cultivars using suitable genetic markers. Therefore, the main objective of this research was to determine the capability of the matK marker for the analysis of genetic diversity and phylogenetic relationships of the studied date palm cultivars.
Methods: In this research, the chloroplast gene matK was used to investigate the genetic diversity among 15 local date varieties from Saravan and Jalgh, Nahok, and Sinokan regions of Sistan and Baluchistan Province. DNA was extracted from young leaves of different cultivars using the Dellaporta (1993) method, and then the quality and quantity of DNA was determined using 1.5% agarose gel electrophoresis and a spectrophotometer. PCR was performed using specific primers of the matk gene, and a fragment of about 900 bp was amplified and sent for sequencing. The quality of the sequencing results was examined and then aligned using BioEdit software, and the regions with low sequencing quality were removed from the 3' and 5' ends. Next, the sequences were blasted for alignment with other sequences in the NCBI database to examine the degree of similarity with other registered sequences. After sequence alignment, key genetic parameters, including the total number of mutations, nucleotide diversity, the number of mutation sites, and the extent of their variation, were comprehensively analyzed. Then, MEGA7 software was used to determine the relationships and genetic distance between the studied cultivars, and the UPGMA method was also used to draw a phylogeny tree.
Results: The comparison of the sequences showed a high homology between these sequences and the sequences of P. dactylifera species available in the gene bank. Sequencing results of the investigated cultivars were registered in the NCBI database. The results of the current research showed that a total of 1019 positions were identified for the matk marker used in this study, 672 positions of which included deletions and additions, and 347 positions were without deletions or additions. Fifteen haplotypes and four conserved DNA regions were identified in this population. The numerical value dN/dS was 0.169, and the genetic distance ranged from 0.019 to 1.238. The highest genetic distance (1.238) was observed between the samples of Halile20 from Saravan and Pimazo16 from Jalgh. After drawing the phylogeny tree, the studied cultivars were divided into three branches, in which Halileh 20 from Saravan was located in the first branch. The Pimazo 16 variety from Jalgh was placed in the second branch. The third branch was divided into two sub-branches, in which there were a total of six numbers in the first sub-branch and a total of seven numbers in the second sub-branch. According to this classification, Halileh 20 of Saravan is the most distant from the other varieties.
Conclusion: Based on the obtained results, it can be concluded that the use of the matk marker has been useful and suitable for studying and understanding the diversity and intraspecies relationships of date palms. Therefore, it is possible to suggest the use of this barcode in addition to other suitable molecular in future date palm studies to investigate genetic diversity.
Background: The date palm (Phoenix dactylifera L.) is a monocotyledonous plant from the Palmaceae, which is cultivated in many countries from tropical and subtropical regions, including Iran. Today, owing to the progress of technology, molecular identification methods have special importance in systematic studies. One of these methods is DNA barcoding, which is species identification based on the sequences of conserved DNA regions that provide a valuable tool for assessing phylogenetic relationships. In this method, the comparison of the sequences of special conserved DNA fragments is used to study the diversity of populations and determine the relationships between different species. Accordingly, different regions of nuclear DNA (ITS, ITS2) and chloroplast (rbcL, matK, trnH-psbA, atpF-atpH, nhdJ, and psbK-psbI) have been suggested as important barcodes in plants. The matK chloroplast gene, which has a high evolutionary speed at the nucleotide and amino acid levels, is one of the most suitable chloroplast genes for the analysis of phylogeny and evolutionary relationships in a range of taxonomic levels from species to genus, phylum and even super phylum, in Angiosperms in particular. This gene can be used individually or together with other genes to identify and introduce unknown species. Examining the genetic diversity of the available germplasm reserves is essential for the improvement and propagation of cultivars with desirable traits, and the first step in this process is to identify the existing cultivars and classify them. Due to the importance of producing dates in Iran, browsing for new cultivars, breeding existing cultivars, and studying the existing diversity between different cultivars are among important strategies to improve the quantity and quality of date palm production. However, there are not enough studies on the investigation of the relationship or genetic distance of different date palm cultivars using suitable genetic markers. Therefore, the main objective of this research was to determine the capability of the matK marker for the analysis of genetic diversity and phylogenetic relationships of the studied date palm cultivars.
Methods: In this research, the chloroplast gene matK was used to investigate the genetic diversity among 15 local date varieties from Saravan and Jalgh, Nahok, and Sinokan regions of Sistan and Baluchistan Province. DNA was extracted from young leaves of different cultivars using the Dellaporta (1993) method, and then the quality and quantity of DNA was determined using 1.5% agarose gel electrophoresis and a spectrophotometer. PCR was performed using specific primers of the matk gene, and a fragment of about 900 bp was amplified and sent for sequencing. The quality of the sequencing results was examined and then aligned using BioEdit software, and the regions with low sequencing quality were removed from the 3' and 5' ends. Next, the sequences were blasted for alignment with other sequences in the NCBI database to examine the degree of similarity with other registered sequences. After sequence alignment, key genetic parameters, including the total number of mutations, nucleotide diversity, the number of mutation sites, and the extent of their variation, were comprehensively analyzed. Then, MEGA7 software was used to determine the relationships and genetic distance between the studied cultivars, and the UPGMA method was also used to draw a phylogeny tree.
Results: The comparison of the sequences showed a high homology between these sequences and the sequences of P. dactylifera species available in the gene bank. Sequencing results of the investigated cultivars were registered in the NCBI database. The results of the current research showed that a total of 1019 positions were identified for the matk marker used in this study, 672 positions of which included deletions and additions, and 347 positions were without deletions or additions. Fifteen haplotypes and four conserved DNA regions were identified in this population. The numerical value dN/dS was 0.169, and the genetic distance ranged from 0.019 to 1.238. The highest genetic distance (1.238) was observed between the samples of Halile20 from Saravan and Pimazo16 from Jalgh. After drawing the phylogeny tree, the studied cultivars were divided into three branches, in which Halileh 20 from Saravan was located in the first branch. The Pimazo 16 variety from Jalgh was placed in the second branch. The third branch was divided into two sub-branches, in which there were a total of six numbers in the first sub-branch and a total of seven numbers in the second sub-branch. According to this classification, Halileh 20 of Saravan is the most distant from the other varieties.
Conclusion: Based on the obtained results, it can be concluded that the use of the matk marker has been useful and suitable for studying and understanding the diversity and intraspecies relationships of date palms. Therefore, it is possible to suggest the use of this barcode in addition to other suitable molecular in future date palm studies to investigate genetic diversity.
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