De Novo SNP Discovery and Genotyping of Iranian <i>Pimpinella</i> Species Using ddRAD Sequencing
The species of <i>Pimpinella</i>, one of the largest genera of the family Apiaceae, are traditionally cultivated for medicinal purposes. In this study, high-throughput double digest restriction-site associated DNA sequencing technology (ddRAD-seq) was used to identify single nucleotide p...
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MDPI AG
2021-06-01
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| Series: | Agronomy |
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| Online Access: | https://www.mdpi.com/2073-4395/11/7/1342 |
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| author | Shaghayegh Mehravi Gholam Ali Ranjbar Ghader Mirzaghaderi Anita Alice Severn-Ellis Armin Scheben David Edwards Jacqueline Batley |
| author_facet | Shaghayegh Mehravi Gholam Ali Ranjbar Ghader Mirzaghaderi Anita Alice Severn-Ellis Armin Scheben David Edwards Jacqueline Batley |
| author_sort | Shaghayegh Mehravi |
| collection | DOAJ |
| description | The species of <i>Pimpinella</i>, one of the largest genera of the family Apiaceae, are traditionally cultivated for medicinal purposes. In this study, high-throughput double digest restriction-site associated DNA sequencing technology (ddRAD-seq) was used to identify single nucleotide polymorphisms (SNPs) in eight <i>Pimpinella</i> species from Iran. After double-digestion with the enzymes HpyCH4IV and HinfI, a total of 334,702,966 paired-end reads were de novo assembled into 1,270,791 loci with an average of 28.8 reads per locus. After stringent filtering, 2440 high-quality SNPs were identified for downstream analysis. Analysis of genetic relationships and population structure, based on these retained SNPs, indicated the presence of three major groups. Gene ontology and pathway analysis were determined by using comparison SNP-associated flanking sequences with a public non-redundant database. Due to the lack of genomic resources in this genus, our present study is the first report to provide high-quality SNPs in <i>Pimpinella</i> based on a de novo analysis pipeline using ddRAD-seq. This data will enhance the molecular knowledge of the genus <i>Pimpinella</i> and will provide an important source of information for breeders and the research community to enhance breeding programs and support the management of <i>Pimpinella</i> genomic resources. |
| first_indexed | 2024-03-10T09:54:48Z |
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| institution | Directory Open Access Journal |
| issn | 2073-4395 |
| language | English |
| last_indexed | 2024-03-10T09:54:48Z |
| publishDate | 2021-06-01 |
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| record_format | Article |
| series | Agronomy |
| spelling | doaj.art-74d54138f5ac4f8a9291bf97bc5c093b2023-11-22T02:27:59ZengMDPI AGAgronomy2073-43952021-06-01117134210.3390/agronomy11071342De Novo SNP Discovery and Genotyping of Iranian <i>Pimpinella</i> Species Using ddRAD SequencingShaghayegh Mehravi0Gholam Ali Ranjbar1Ghader Mirzaghaderi2Anita Alice Severn-Ellis3Armin Scheben4David Edwards5Jacqueline Batley6School of Biological Sciences, University of Western Australia, Perth, WA 6009, AustraliaDepartment of Plant Breeding and Biotechnology, Faculty of Crop Sciences, Sari Agricultural Sciences and Natural Resources University, Sari 4818168984, IranDepartment of Agronomy and Plant Breeding, College of Agriculture, University of Kurdistan, Kurdistan, Sari 4818168984, IranSchool of Biological Sciences, University of Western Australia, Perth, WA 6009, AustraliaSimons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USASchool of Biological Sciences, University of Western Australia, Perth, WA 6009, AustraliaSchool of Biological Sciences, University of Western Australia, Perth, WA 6009, AustraliaThe species of <i>Pimpinella</i>, one of the largest genera of the family Apiaceae, are traditionally cultivated for medicinal purposes. In this study, high-throughput double digest restriction-site associated DNA sequencing technology (ddRAD-seq) was used to identify single nucleotide polymorphisms (SNPs) in eight <i>Pimpinella</i> species from Iran. After double-digestion with the enzymes HpyCH4IV and HinfI, a total of 334,702,966 paired-end reads were de novo assembled into 1,270,791 loci with an average of 28.8 reads per locus. After stringent filtering, 2440 high-quality SNPs were identified for downstream analysis. Analysis of genetic relationships and population structure, based on these retained SNPs, indicated the presence of three major groups. Gene ontology and pathway analysis were determined by using comparison SNP-associated flanking sequences with a public non-redundant database. Due to the lack of genomic resources in this genus, our present study is the first report to provide high-quality SNPs in <i>Pimpinella</i> based on a de novo analysis pipeline using ddRAD-seq. This data will enhance the molecular knowledge of the genus <i>Pimpinella</i> and will provide an important source of information for breeders and the research community to enhance breeding programs and support the management of <i>Pimpinella</i> genomic resources.https://www.mdpi.com/2073-4395/11/7/1342<i>Pimpinella</i>ddRAD SequencingSNP markerspopulation structurede novo analysisgene ontology |
| spellingShingle | Shaghayegh Mehravi Gholam Ali Ranjbar Ghader Mirzaghaderi Anita Alice Severn-Ellis Armin Scheben David Edwards Jacqueline Batley De Novo SNP Discovery and Genotyping of Iranian <i>Pimpinella</i> Species Using ddRAD Sequencing Agronomy <i>Pimpinella</i> ddRAD Sequencing SNP markers population structure de novo analysis gene ontology |
| title | De Novo SNP Discovery and Genotyping of Iranian <i>Pimpinella</i> Species Using ddRAD Sequencing |
| title_full | De Novo SNP Discovery and Genotyping of Iranian <i>Pimpinella</i> Species Using ddRAD Sequencing |
| title_fullStr | De Novo SNP Discovery and Genotyping of Iranian <i>Pimpinella</i> Species Using ddRAD Sequencing |
| title_full_unstemmed | De Novo SNP Discovery and Genotyping of Iranian <i>Pimpinella</i> Species Using ddRAD Sequencing |
| title_short | De Novo SNP Discovery and Genotyping of Iranian <i>Pimpinella</i> Species Using ddRAD Sequencing |
| title_sort | de novo snp discovery and genotyping of iranian i pimpinella i species using ddrad sequencing |
| topic | <i>Pimpinella</i> ddRAD Sequencing SNP markers population structure de novo analysis gene ontology |
| url | https://www.mdpi.com/2073-4395/11/7/1342 |
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