生物
单核苷酸多态性
遗传学
候选基因
表型
数量性状位点
基因
局部适应
性状
SNP公司
适应(眼睛)
人口
基因型
计算生物学
人口学
社会学
神经科学
作者
Benoit Talbot,Ting‐Wen Chen,Shawna J. Zimmerman,Stéphane Joost,Andrew J. Eckert,Taylor M. Crow,Devrim Semizer-Cuming,Chitra Seshadri,Stéphanie Manel
标识
DOI:10.1093/jhered/esw077
摘要
Population genomic analysis can be an important tool in understanding local adaptation. Identification of potential adaptive loci in such analyses is usually based on the survey of a large genomic dataset in combination with environmental variables. Phenotypic data are less commonly incorporated into such studies, although combining a genome scan analysis with a phenotypic trait analysis can greatly improve the insights obtained from each analysis individually. Here, we aimed to identify loci potentially involved in adaptation to climate in 283 Loblolly pine (Pinus taeda) samples from throughout the species' range in the southeastern United States. We analyzed associations between phenotypic, molecular, and environmental variables from datasets of 3082 single nucleotide polymorphism (SNP) loci and 3 categories of phenotypic traits (gene expression, metabolites, and whole-plant traits). We found only 6 SNP loci that displayed potential signals of local adaptation. Five of the 6 identified SNPs are linked to gene expression traits for lignin development, and 1 is linked with whole-plant traits. We subsequently compared the 6 candidate genes with environmental variables and found a high correlation in only 3 of them (R2 > 0.2). Our study highlights the need for a combination of genotypes, phenotypes, and environmental variables, and for an appropriate sampling scheme and study design, to improve confidence in the identification of potential candidate genes.
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