Exploring the genetic basis of gene transcript abundance and metabolite levels in loblolly pine (Pinus taeda L.) using association mapping and network construction
Abstract Background Identifying genetic variations that shape important complex traits is fundamental to the genetic improvement of important forest tree species, such as loblolly pine (Pinus taeda L.), which is one of the most commonly planted forest tree species in the southern U.S. Gene transcrip...
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| Format: | Article |
| Language: | English |
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BMC
2018-11-01
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| Series: | BMC Genetics |
| Subjects: | |
| Online Access: | http://link.springer.com/article/10.1186/s12863-018-0687-7 |
| _version_ | 1811292184046993408 |
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| author | Mengmeng Lu Candace M. Seeve Carol A. Loopstra Konstantin V. Krutovsky |
| author_facet | Mengmeng Lu Candace M. Seeve Carol A. Loopstra Konstantin V. Krutovsky |
| author_sort | Mengmeng Lu |
| collection | DOAJ |
| description | Abstract Background Identifying genetic variations that shape important complex traits is fundamental to the genetic improvement of important forest tree species, such as loblolly pine (Pinus taeda L.), which is one of the most commonly planted forest tree species in the southern U.S. Gene transcripts and metabolites are important regulatory intermediates that link genetic variations to higher-order complex traits such as wood development and drought response. A few prior studies have associated intermediate phenotypes including mRNA expression and metabolite levels with a limited number of molecular markers, but the identification of genetic variations that regulate intermediate phenotypes needs further investigation. Results We identified 1841 single nucleotide polymorphisms (SNPs) associated with 191 gene expression mRNA phenotypes and 524 SNPs associated with 53 metabolite level phenotypes using 2.8 million exome-derived SNPs. The identified SNPs reside in genes with a wide variety of functions. We further integrated the identified SNPs and the associated expressed genes and metabolites into networks. We described the SNP-SNP interactions that significantly impacted the gene transcript abundance and metabolite level in the networks. Key loci and genes in the wood development and drought response networks were identified and analyzed. Conclusions This work provides new candidate genes for research on the genetic basis of gene expression and metabolism linked to wood development and drought response in loblolly pine and highlights the efficiency of using association-mapping-based networks to discover candidate genes with important roles in complex biological processes. |
| first_indexed | 2024-04-13T04:41:40Z |
| format | Article |
| id | doaj.art-901c52f10e8b465c8da671d85389798c |
| institution | Directory Open Access Journal |
| issn | 1471-2156 |
| language | English |
| last_indexed | 2024-04-13T04:41:40Z |
| publishDate | 2018-11-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genetics |
| spelling | doaj.art-901c52f10e8b465c8da671d85389798c2022-12-22T03:01:59ZengBMCBMC Genetics1471-21562018-11-0119111310.1186/s12863-018-0687-7Exploring the genetic basis of gene transcript abundance and metabolite levels in loblolly pine (Pinus taeda L.) using association mapping and network constructionMengmeng Lu0Candace M. Seeve1Carol A. Loopstra2Konstantin V. Krutovsky3Department of Ecosystem Science and Management, Texas A&M UniversityUSDA-ARS Midwest AreaDepartment of Ecosystem Science and Management, Texas A&M UniversityDepartment of Ecosystem Science and Management, Texas A&M UniversityAbstract Background Identifying genetic variations that shape important complex traits is fundamental to the genetic improvement of important forest tree species, such as loblolly pine (Pinus taeda L.), which is one of the most commonly planted forest tree species in the southern U.S. Gene transcripts and metabolites are important regulatory intermediates that link genetic variations to higher-order complex traits such as wood development and drought response. A few prior studies have associated intermediate phenotypes including mRNA expression and metabolite levels with a limited number of molecular markers, but the identification of genetic variations that regulate intermediate phenotypes needs further investigation. Results We identified 1841 single nucleotide polymorphisms (SNPs) associated with 191 gene expression mRNA phenotypes and 524 SNPs associated with 53 metabolite level phenotypes using 2.8 million exome-derived SNPs. The identified SNPs reside in genes with a wide variety of functions. We further integrated the identified SNPs and the associated expressed genes and metabolites into networks. We described the SNP-SNP interactions that significantly impacted the gene transcript abundance and metabolite level in the networks. Key loci and genes in the wood development and drought response networks were identified and analyzed. Conclusions This work provides new candidate genes for research on the genetic basis of gene expression and metabolism linked to wood development and drought response in loblolly pine and highlights the efficiency of using association-mapping-based networks to discover candidate genes with important roles in complex biological processes.http://link.springer.com/article/10.1186/s12863-018-0687-7Gene expressionMetabolismEpistasisStress responseWood developmentSNP |
| spellingShingle | Mengmeng Lu Candace M. Seeve Carol A. Loopstra Konstantin V. Krutovsky Exploring the genetic basis of gene transcript abundance and metabolite levels in loblolly pine (Pinus taeda L.) using association mapping and network construction BMC Genetics Gene expression Metabolism Epistasis Stress response Wood development SNP |
| title | Exploring the genetic basis of gene transcript abundance and metabolite levels in loblolly pine (Pinus taeda L.) using association mapping and network construction |
| title_full | Exploring the genetic basis of gene transcript abundance and metabolite levels in loblolly pine (Pinus taeda L.) using association mapping and network construction |
| title_fullStr | Exploring the genetic basis of gene transcript abundance and metabolite levels in loblolly pine (Pinus taeda L.) using association mapping and network construction |
| title_full_unstemmed | Exploring the genetic basis of gene transcript abundance and metabolite levels in loblolly pine (Pinus taeda L.) using association mapping and network construction |
| title_short | Exploring the genetic basis of gene transcript abundance and metabolite levels in loblolly pine (Pinus taeda L.) using association mapping and network construction |
| title_sort | exploring the genetic basis of gene transcript abundance and metabolite levels in loblolly pine pinus taeda l using association mapping and network construction |
| topic | Gene expression Metabolism Epistasis Stress response Wood development SNP |
| url | http://link.springer.com/article/10.1186/s12863-018-0687-7 |
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