Volume 15, Issue 46 (7-2023)
J Crop Breed 2023, 15(46): 156-165 |
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Shahbaz B, Soltani Howyzeh M, Shariati V. (2023). Large Scale Identification of SSR Molecular Markers Using RNA Sequencing in Yarrow (Acillea millefolium L.). J Crop Breed. 15(46), 156-165. doi:10.61186/jcb.15.46.156
URL: http://jcb.sanru.ac.ir/article-1-1235-en.html
URL: http://jcb.sanru.ac.ir/article-1-1235-en.html
1- Department of Genetics and Plant Breeding, Ahvaz Branch, Islamic Azad University, Ahvaz, Iran
2- Department of Genetics and Plant Breeding, Ahvaz Branch, Islamic Azad University, Ahvaz, Iran,
3- Molecular Biotechnology Department, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran
2- Department of Genetics and Plant Breeding, Ahvaz Branch, Islamic Azad University, Ahvaz, Iran,
3- Molecular Biotechnology Department, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran
Abstract: (1899 Views)
Extended Abstract
Introduction: The medicinal plant Yarrow (Achillea millefolium L.) due to its medicinal and industrial functions is one of valuable pastureland plant in Iran and the world.
Materials and methods: In this study the Illumina Hiseq 2500 platform used to identify the microsatellites markers by transcriptome sequencing of the leaf and inflorescence of Yarrow.
Results: According to the de novo sequencing results of the medicinal plant Yarrow cultivated in the Research Institute of Forests and Rangelands, 9450 single transcript sequences (6920 single gene sequences) containing 10,570 potential microsatellites were identified. The most common types of microsatellites were dinucleotides (62%), followed by trinucleotides (2748, 26%), and mononucleotides (7%), respectively. In total, 69% of the microsatellites were classified as second class (10 to 20 nucleotides), and 31% were first class (more than 20 nucleotides). The frequency of microsatellites in the transcriptome of inflorescence was one per10 kb assembled sequences. According to unigenes annotation results, totally 1,762 (22.3%), 4723 (53.3%), 3714 (47.5%), 4517 (51.3%) and 5189 (60.7%) unigenes annotated from all databases of KAAS, Arabidopsis, UniProt, NCBI database Non-redundant proteins and sunflower respectively. Among 8542 clustered unigenes containing microsatellite, 38440 unigene sequences (45%) were classified as functional and categorized as 52 clusters.
Conclusion: Among all the categorized monomers, 3220 (65%) belonged to the "metabolic process" category, of which 90 (3%) belonged to the "secondary metabolic process" category. The introduction of these markers can be used for future studies of selection using markers, genetic diversity, and genetic maps in this medicinal plant breeding programs.
Introduction: The medicinal plant Yarrow (Achillea millefolium L.) due to its medicinal and industrial functions is one of valuable pastureland plant in Iran and the world.
Materials and methods: In this study the Illumina Hiseq 2500 platform used to identify the microsatellites markers by transcriptome sequencing of the leaf and inflorescence of Yarrow.
Results: According to the de novo sequencing results of the medicinal plant Yarrow cultivated in the Research Institute of Forests and Rangelands, 9450 single transcript sequences (6920 single gene sequences) containing 10,570 potential microsatellites were identified. The most common types of microsatellites were dinucleotides (62%), followed by trinucleotides (2748, 26%), and mononucleotides (7%), respectively. In total, 69% of the microsatellites were classified as second class (10 to 20 nucleotides), and 31% were first class (more than 20 nucleotides). The frequency of microsatellites in the transcriptome of inflorescence was one per10 kb assembled sequences. According to unigenes annotation results, totally 1,762 (22.3%), 4723 (53.3%), 3714 (47.5%), 4517 (51.3%) and 5189 (60.7%) unigenes annotated from all databases of KAAS, Arabidopsis, UniProt, NCBI database Non-redundant proteins and sunflower respectively. Among 8542 clustered unigenes containing microsatellite, 38440 unigene sequences (45%) were classified as functional and categorized as 52 clusters.
Conclusion: Among all the categorized monomers, 3220 (65%) belonged to the "metabolic process" category, of which 90 (3%) belonged to the "secondary metabolic process" category. The introduction of these markers can be used for future studies of selection using markers, genetic diversity, and genetic maps in this medicinal plant breeding programs.
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