Analysis on single nucleotide polymorphisms of the PeTPS-(-)Apin gene in Pinus elliottii
Resin-tapping forests of slash pine (Pinus elliottii) have been set up across Southern China owing to their high production and good resin quality, which has led to the rapid growth of the resin industry. In this study, we aimed to identify molecular markers associated with resin traits in pine tree...
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| Veröffentlicht in: | PloS one 2022-05, Vol.17 (5), p.e0266503-e0266503 |
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| creator | Lei, Lei Zhang, Lu Cai, Junhuo Yi, Min Zhao, Heng Ma, Jikai Lai, Meng Jin, Cangfu |
| description | Resin-tapping forests of slash pine (Pinus elliottii) have been set up across Southern China owing to their high production and good resin quality, which has led to the rapid growth of the resin industry. In this study, we aimed to identify molecular markers associated with resin traits in pine trees, which may help develop marker-assisted selection (MAS).
PeTPS-(-)Apin gene was cloned by double primers (external and internal). DnaSP V4.0 software was used to evaluate genetic diversity and linkage disequilibrium. SHEsis was used for haplotype analysis. SPSS was used for ANOVA and χ2 test. DnaSP v4.0 software was used to evaluate genetic diversity.
The full length PeTPS-(-)Apin gene was characterized and shown to have 4638 bp, coding for a 629-amino acid protein. A total of 72 single nucleotide polymorphism (SNP) loci were found. Three SNPs (CG615, AT641 and AG3859) were significantly correlated with α -pinene content, with a contribution rate > 10%. These SNPs were used to select P. elliottii with high α-pinene content, and a 118.0% realistic gain was obtained.
The PeTPS-(-)Apin gene is not uniquely decisive for selection of plus slash pines with stable production, high yield, and good quality, but it can be used as a reference for selection of other resin-producing pines and other resin components. |
| doi_str_mv | 10.1371/journal.pone.0266503 |
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PeTPS-(-)Apin gene was cloned by double primers (external and internal). DnaSP V4.0 software was used to evaluate genetic diversity and linkage disequilibrium. SHEsis was used for haplotype analysis. SPSS was used for ANOVA and χ2 test. DnaSP v4.0 software was used to evaluate genetic diversity.
The full length PeTPS-(-)Apin gene was characterized and shown to have 4638 bp, coding for a 629-amino acid protein. A total of 72 single nucleotide polymorphism (SNP) loci were found. Three SNPs (CG615, AT641 and AG3859) were significantly correlated with α -pinene content, with a contribution rate > 10%. These SNPs were used to select P. elliottii with high α-pinene content, and a 118.0% realistic gain was obtained.
The PeTPS-(-)Apin gene is not uniquely decisive for selection of plus slash pines with stable production, high yield, and good quality, but it can be used as a reference for selection of other resin-producing pines and other resin components.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0266503</identifier><identifier>PMID: 35622849</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Amino acids ; Analysis ; Biology and Life Sciences ; Chi-square test ; Cloning ; Computer and Information Sciences ; Gene expression ; Gene polymorphism ; Genetic aspects ; Genetic diversity ; Genomes ; Gums and resins ; Haplotypes ; Industrial production ; Linkage disequilibrium ; Marker-assisted selection ; Markers ; Mutation ; Nucleotides ; Pine ; Pine trees ; Pinus elliottii ; Polymorphism ; Properties ; Raw materials ; Research and Analysis Methods ; Resins ; Single nucleotide polymorphisms ; Single-nucleotide polymorphism ; Software ; Trees ; Turpentine ; Variance analysis ; α-Pinene</subject><ispartof>PloS one, 2022-05, Vol.17 (5), p.e0266503-e0266503</ispartof><rights>COPYRIGHT 2022 Public Library of Science</rights><rights>2022 Lei et al. This is an open access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>2022 Lei et al 2022 Lei et al</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><cites>FETCH-LOGICAL-c542t-618219d00207eabe8ba73c2fd2efa8c11f93b8ed1ef2937360d946e3d937a3cd3</cites><orcidid>0000-0002-0059-2128 ; 0000-0003-2168-0546</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC9140247/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC9140247/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,864,885,2101,2927,23865,27923,27924,53790,53792,79471,79472</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/35622849$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><contributor>Sharma, Himanshu</contributor><creatorcontrib>Lei, Lei</creatorcontrib><creatorcontrib>Zhang, Lu</creatorcontrib><creatorcontrib>Cai, Junhuo</creatorcontrib><creatorcontrib>Yi, Min</creatorcontrib><creatorcontrib>Zhao, Heng</creatorcontrib><creatorcontrib>Ma, Jikai</creatorcontrib><creatorcontrib>Lai, Meng</creatorcontrib><creatorcontrib>Jin, Cangfu</creatorcontrib><title>Analysis on single nucleotide polymorphisms of the PeTPS-(-)Apin gene in Pinus elliottii</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>Resin-tapping forests of slash pine (Pinus elliottii) have been set up across Southern China owing to their high production and good resin quality, which has led to the rapid growth of the resin industry. In this study, we aimed to identify molecular markers associated with resin traits in pine trees, which may help develop marker-assisted selection (MAS).
PeTPS-(-)Apin gene was cloned by double primers (external and internal). DnaSP V4.0 software was used to evaluate genetic diversity and linkage disequilibrium. SHEsis was used for haplotype analysis. SPSS was used for ANOVA and χ2 test. DnaSP v4.0 software was used to evaluate genetic diversity.
The full length PeTPS-(-)Apin gene was characterized and shown to have 4638 bp, coding for a 629-amino acid protein. A total of 72 single nucleotide polymorphism (SNP) loci were found. Three SNPs (CG615, AT641 and AG3859) were significantly correlated with α -pinene content, with a contribution rate > 10%. These SNPs were used to select P. elliottii with high α-pinene content, and a 118.0% realistic gain was obtained.
The PeTPS-(-)Apin gene is not uniquely decisive for selection of plus slash pines with stable production, high yield, and good quality, but it can be used as a reference for selection of other resin-producing pines and other resin components.</description><subject>Amino acids</subject><subject>Analysis</subject><subject>Biology and Life Sciences</subject><subject>Chi-square test</subject><subject>Cloning</subject><subject>Computer and Information Sciences</subject><subject>Gene expression</subject><subject>Gene polymorphism</subject><subject>Genetic aspects</subject><subject>Genetic diversity</subject><subject>Genomes</subject><subject>Gums and resins</subject><subject>Haplotypes</subject><subject>Industrial production</subject><subject>Linkage disequilibrium</subject><subject>Marker-assisted selection</subject><subject>Markers</subject><subject>Mutation</subject><subject>Nucleotides</subject><subject>Pine</subject><subject>Pine trees</subject><subject>Pinus elliottii</subject><subject>Polymorphism</subject><subject>Properties</subject><subject>Raw materials</subject><subject>Research and Analysis Methods</subject><subject>Resins</subject><subject>Single nucleotide polymorphisms</subject><subject>Single-nucleotide polymorphism</subject><subject>Software</subject><subject>Trees</subject><subject>Turpentine</subject><subject>Variance 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on single nucleotide polymorphisms of the PeTPS-(-)Apin gene in Pinus elliottii</title><author>Lei, Lei ; Zhang, Lu ; Cai, Junhuo ; Yi, Min ; Zhao, Heng ; Ma, Jikai ; Lai, Meng ; Jin, Cangfu</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c542t-618219d00207eabe8ba73c2fd2efa8c11f93b8ed1ef2937360d946e3d937a3cd3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2022</creationdate><topic>Amino acids</topic><topic>Analysis</topic><topic>Biology and Life Sciences</topic><topic>Chi-square test</topic><topic>Cloning</topic><topic>Computer and Information Sciences</topic><topic>Gene expression</topic><topic>Gene polymorphism</topic><topic>Genetic aspects</topic><topic>Genetic diversity</topic><topic>Genomes</topic><topic>Gums and resins</topic><topic>Haplotypes</topic><topic>Industrial production</topic><topic>Linkage disequilibrium</topic><topic>Marker-assisted selection</topic><topic>Markers</topic><topic>Mutation</topic><topic>Nucleotides</topic><topic>Pine</topic><topic>Pine trees</topic><topic>Pinus elliottii</topic><topic>Polymorphism</topic><topic>Properties</topic><topic>Raw materials</topic><topic>Research and Analysis Methods</topic><topic>Resins</topic><topic>Single nucleotide polymorphisms</topic><topic>Single-nucleotide polymorphism</topic><topic>Software</topic><topic>Trees</topic><topic>Turpentine</topic><topic>Variance analysis</topic><topic>α-Pinene</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Lei, Lei</creatorcontrib><creatorcontrib>Zhang, Lu</creatorcontrib><creatorcontrib>Cai, Junhuo</creatorcontrib><creatorcontrib>Yi, Min</creatorcontrib><creatorcontrib>Zhao, Heng</creatorcontrib><creatorcontrib>Ma, Jikai</creatorcontrib><creatorcontrib>Lai, Meng</creatorcontrib><creatorcontrib>Jin, 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One</addtitle><date>2022-05-27</date><risdate>2022</risdate><volume>17</volume><issue>5</issue><spage>e0266503</spage><epage>e0266503</epage><pages>e0266503-e0266503</pages><issn>1932-6203</issn><eissn>1932-6203</eissn><abstract>Resin-tapping forests of slash pine (Pinus elliottii) have been set up across Southern China owing to their high production and good resin quality, which has led to the rapid growth of the resin industry. In this study, we aimed to identify molecular markers associated with resin traits in pine trees, which may help develop marker-assisted selection (MAS).
PeTPS-(-)Apin gene was cloned by double primers (external and internal). DnaSP V4.0 software was used to evaluate genetic diversity and linkage disequilibrium. SHEsis was used for haplotype analysis. SPSS was used for ANOVA and χ2 test. DnaSP v4.0 software was used to evaluate genetic diversity.
The full length PeTPS-(-)Apin gene was characterized and shown to have 4638 bp, coding for a 629-amino acid protein. A total of 72 single nucleotide polymorphism (SNP) loci were found. Three SNPs (CG615, AT641 and AG3859) were significantly correlated with α -pinene content, with a contribution rate > 10%. These SNPs were used to select P. elliottii with high α-pinene content, and a 118.0% realistic gain was obtained.
The PeTPS-(-)Apin gene is not uniquely decisive for selection of plus slash pines with stable production, high yield, and good quality, but it can be used as a reference for selection of other resin-producing pines and other resin components.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>35622849</pmid><doi>10.1371/journal.pone.0266503</doi><orcidid>https://orcid.org/0000-0002-0059-2128</orcidid><orcidid>https://orcid.org/0000-0003-2168-0546</orcidid><oa>free_for_read</oa></addata></record> |
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| source | DOAJ Directory of Open Access Journals; Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals; Public Library of Science (PLoS); PubMed Central; Free Full-Text Journals in Chemistry |
| subjects | Amino acids Analysis Biology and Life Sciences Chi-square test Cloning Computer and Information Sciences Gene expression Gene polymorphism Genetic aspects Genetic diversity Genomes Gums and resins Haplotypes Industrial production Linkage disequilibrium Marker-assisted selection Markers Mutation Nucleotides Pine Pine trees Pinus elliottii Polymorphism Properties Raw materials Research and Analysis Methods Resins Single nucleotide polymorphisms Single-nucleotide polymorphism Software Trees Turpentine Variance analysis α-Pinene |
| title | Analysis on single nucleotide polymorphisms of the PeTPS-(-)Apin gene in Pinus elliottii |
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