Joint linkage and association mapping of complex traits in shrub willow (Salix purpurea L.)

Carlson, Craig H.; Gouker, Fred E.; Crowell, Chase R.; Evans, Luke; DiFazio, Stephen P.; Smart, Christine D.; Smart, Lawrence B.

doi:10.1093/aob/mcz047

Title: Joint linkage and association mapping of complex traits in shrub willow (Salix purpurea L.)

Journal Article · Mon Apr 22 00:00:00 EDT 2019 · Annals of Botany

DOI:https://doi.org/10.1093/aob/mcz047· OSTI ID:1611037

Carlson, Craig H. ^[1]; Gouker, Fred E. ^[1]; Crowell, Chase R. ^[2]; Evans, Luke ^[3]; DiFazio, Stephen P. ^[4]; Smart, Christine D. ^[2];

^[1]

Horticulture Section, School of Integrative Plant Science, Cornell University, Cornell AgriTech, Geneva, NY, USA
Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Cornell AgriTech, Geneva, NY, USA
Institute for Behavioral Genetics and Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
Department of Biology, West Virginia University, Morgantown, WV, USA

Abstract Background and AimsIncreasing energy demands and the necessity to reduce greenhouse gas emissions are key motivating factors driving the development of lignocellulosic crops as an alternative to non-renewable energy sources. The effects of global climate change will require a better understanding of the genetic basis of complex adaptive traits to breed more resilient bioenergy feedstocks, like willow (Salix spp.). Shrub willow is a sustainable and dedicated bioenergy crop, bred to be fast-growing and high-yielding on marginal land without competing with food crops. In a rapidly changing climate, genomic advances will be vital for the sustained improvement of willow and other non-model bioenergy crops. Here, joint genetic mapping was used to exploit genetic variation garnered from both recent and historical recombination events in S. purpurea. MethodsA panel of North American naturalized S. purpurea accessions and full-sib F2S. purpurea population were genotyped and phenotyped for a suite of morphological, physiological, pest and disease resistance, and wood chemical composition traits, collected from multi-environment and multi-year replicated field trials. Controlling for population stratification and kinship in the association panel and spatial variation in the F2, a comprehensive mixed model analysis was used to dissect the complex genetic architecture and plasticity of these important traits. Key ResultsIndividually, genome-wide association (GWAS) models differed in terms of power, but the combined approach, which corrects for yearly and environmental co-factors across datasets, improved the overall detection and resolution of associated loci. Although there were few significant GWAS hits located within support intervals of QTL for corresponding traits in the F2, many large-effect QTL were identified, as well as QTL hotspots. ConclusionsThis study provides the first comparison of linkage analysis and linkage disequilibrium mapping approaches in Salix, and highlights the complementarity and limits of these two methods for elucidating the genetic architecture of complex bioenergy-related traits of a woody perennial breeding programme.

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Research Organization:: Cornell Univ., Ithaca, NY (United States)

Sponsoring Organization:: USDOE Office of Science (SC)

DOE Contract Number:: SC0008375

OSTI ID:: 1611037

Journal Information:: Annals of Botany, Vol. 124, Issue 4; ISSN 0305-7364

Publisher:: Oxford University Press

Country of Publication:: United States

Language:: English

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