Exploring the genetic basis of gene transcript abundance and metabolite levels in loblolly pine (Pinus taeda L.) using association mapping and network construction

Mengmeng Lu,Candace M Seeve,Carol A Loopstra,Konstantin V Krutovsky

doi:10.1186/s12863-018-0687-7

Abstract

BackgroundIdentifying 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.ResultsWe 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.ConclusionsThis 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.

Highlights

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
Eckert et al [10] detected 28 Single nucleotide polymorphism (SNP)-metabolite associations in loblolly pine. These seminal studies identified candidate genes and alleles associated with gene expression and metabolite phenotypes, but the limited number of molecular markers used in these studies constrain our understanding of the genetic basis underlying these complex intermediate phenotypes
Significant associations between SNPs and phenotypes We identified a total of 2562 associations between 1841 SNPs and 191 gene expression phenotypes and 524 associations between 524 SNPs and 53 metabolite concentration phenotypes (Fig. 1a, Additional file 1: Tables S1 and S2)

Summary

Introduction

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. The majority of previous genetic studies on loblolly pine have focused on the dissection of adaptive or commercially important traits, including growth, wood properties, or drought tolerance [4,5,6,7], while only a few studies have sought to associate intermediate phenotypes, such as levels of transcripts and metabolites with genome-wide genetic variation. Eckert et al [10] detected 28 SNP-metabolite associations in loblolly pine These seminal studies identified candidate genes and alleles associated with gene expression and metabolite phenotypes, but the limited number of molecular markers used in these studies constrain our understanding of the genetic basis underlying these complex intermediate phenotypes

Methods

Results

Conclusion