ORCID Profile
0000-0003-4077-1590
Current Organisation
West Virginia University
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Publisher: Frontiers Media SA
Date: 08-10-2019
Publisher: Springer Science and Business Media LLC
Date: 07-2006
DOI: 10.1038/NRG1877
Abstract: Can heritable traits in a single species affect an entire ecosystem? Recent studies show that such traits in a common tree have predictable effects on community structure and ecosystem processes. Because these 'community and ecosystem phenotypes' have a genetic basis and are heritable, we can begin to apply the principles of population and quantitative genetics to place the study of complex communities and ecosystems within an evolutionary framework. This framework could allow us to understand, for the first time, the genetic basis of ecosystem processes, and the effect of such phenomena as climate change and introduced transgenic organisms on entire communities.
Publisher: Wiley
Date: 08-04-2019
DOI: 10.1111/NPH.15777
Abstract: Genome‐wide association studies (GWAS) have great promise for identifying the loci that contribute to adaptive variation, but the complex genetic architecture of many quantitative traits presents a substantial challenge. We measured 14 morphological and physiological traits and identified single nucleotide polymorphism (SNP)‐phenotype associations in a Populus trichocarpa population distributed from California, USA to British Columbia, Canada. We used whole‐genome resequencing data of 882 trees with more than 6.78 million SNPs, coupled with multitrait association to detect polymorphisms with potentially pleiotropic effects. Candidate genes were validated with functional data. Broad‐sense heritability ( H 2 ) ranged from 0.30 to 0.56 for morphological traits and 0.08 to 0.36 for physiological traits. In total, 4 and 20 gene models were detected using the single‐trait and multitrait association methods, respectively. Several of these associations were corroborated by additional lines of evidence, including co‐expression networks, metabolite analyses, and direct confirmation of gene function through RNAi. Multitrait association identified many more significant associations than single‐trait association, potentially revealing pleiotropic effects of in idual genes. This approach can be particularly useful for challenging physiological traits such as water‐use efficiency or complex traits such as leaf morphology, for which we were able to identify credible candidate genes by combining multitrait association with gene co‐expression and co‐methylation data.
Publisher: Wiley
Date: 26-07-2013
DOI: 10.1111/NPH.12422
Abstract: Establishing links between phenotypes and molecular variants is of central importance to accelerate genetic improvement of economically important plant species. Our work represents the first genome‐wide association study to the inherently complex and currently poorly understood genetic architecture of industrially relevant wood traits. Here, we employed an Illumina Infinium 34 K single nucleotide polymorphism ( SNP ) genotyping array that generated 29 233 high‐quality SNP s in c . 3500 broad‐based candidate genes within a population of 334 unrelated P opulus trichocarpa in iduals to establish genome‐wide associations. The analysis revealed 141 significant SNP s ( α ≤ 0.05) associated with 16 wood chemistry/ultrastructure traits, in idually explaining 3–7% of the phenotypic variance. A large set of associations (41% of all hits) occurred in candidate genes preselected for their suggested a priori involvement with secondary growth. For ex le, an allelic variant in the FRA 8 ortholog explained 21% of the total genetic variance in fiber length, when the trait's heritability estimate was considered. The remaining associations identified SNP s in genes not previously implicated in wood or secondary wall formation. Our findings provide unique insights into wood trait architecture and support efforts for population improvement based on desirable allelic variants.
No related grants have been discovered for Stephen DiFazio.