TY - JOUR
T1 - Large effect quantitative trait loci for salicinoid phenolic glycosides in Populus
T2 - Implications for gene discovery
AU - Woolbright, Scott A.
AU - Rehill, Brian J.
AU - Lindroth, Richard L.
AU - DiFazio, Stephen P.
AU - Martinsen, Gregory D.
AU - Zinkgraf, Matthew S.
AU - Allan, Gerard J.
AU - Keim, Paul
AU - Whitham, Thomas G.
N1 - Funding Information:
The authors gratefully acknowledge the contributions of the following individuals: Phil Service, Tom Sisk, Jen Schweitzer, Joe Bailey, Celine Caseys, Christian Lexer, Justin McGrath, Karl Broman, Danny Arends, Stephanie Woolbright, and Tricia Covington. Special thanks to Brad Blake and Phil Patterson (NAU Greenhouse); the students, faculty, and staff of the NAU Department of Biological Sciences; the NAU Cottonwood and Pinyon Ecology Groups; and the Postdoctoral Fellows Program and the Genomic Ecology of Global Change (GEGC) theme at the University of Illinois Carl R. Woese Institute for Genomic Biology (IGB). Funding and other support were provided by the UA Little Rock Department of Biology and College of Arts, Letters, and Sciences; the Phoenix chapter of the ARCS Foundation; NSF FIBR grant DEB-0425908, NSF MacroSystems grant DEB-1340852, and NSF DBI-1126840 for establishing the Southwest Experimental Garden Array.
Publisher Copyright:
© 2018 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.
PY - 2018/4
Y1 - 2018/4
N2 - Genomic studies have been used to identify genes underlying many important plant secondary metabolic pathways. However, genes for salicinoid phenolic glycosides (SPGs)—ecologically important compounds with significant commercial, cultural, and medicinal applications—remain largely undescribed. We used a linkage map derived from a full-sib population of hybrid cottonwoods (Populus spp.) to search for quantitative trait loci (QTL) for the SPGs salicortin and HCH-salicortin. SSR markers and primer sequences were used to anchor the map to the V3.0 P. trichocarpa genome. We discovered 21 QTL for the two traits, including a major QTL for HCH-salicortin (R2 =.52) that colocated with a QTL for salicortin on chr12. Using the V3.0 Populus genome sequence, we identified 2,983 annotated genes and 1,480 genes of unknown function within our QTL intervals. We note ten candidate genes of interest, including a BAHD-type acyltransferase that has been potentially linked to PopulusSPGs. Our results complement other recent studies in Populus with implications for gene discovery and the evolution of defensive chemistry in a model genus. To our knowledge, this is the first study to use a full-sib mapping population to identify QTL intervals and gene lists associated with SPGs.
AB - Genomic studies have been used to identify genes underlying many important plant secondary metabolic pathways. However, genes for salicinoid phenolic glycosides (SPGs)—ecologically important compounds with significant commercial, cultural, and medicinal applications—remain largely undescribed. We used a linkage map derived from a full-sib population of hybrid cottonwoods (Populus spp.) to search for quantitative trait loci (QTL) for the SPGs salicortin and HCH-salicortin. SSR markers and primer sequences were used to anchor the map to the V3.0 P. trichocarpa genome. We discovered 21 QTL for the two traits, including a major QTL for HCH-salicortin (R2 =.52) that colocated with a QTL for salicortin on chr12. Using the V3.0 Populus genome sequence, we identified 2,983 annotated genes and 1,480 genes of unknown function within our QTL intervals. We note ten candidate genes of interest, including a BAHD-type acyltransferase that has been potentially linked to PopulusSPGs. Our results complement other recent studies in Populus with implications for gene discovery and the evolution of defensive chemistry in a model genus. To our knowledge, this is the first study to use a full-sib mapping population to identify QTL intervals and gene lists associated with SPGs.
KW - Populus
KW - community and ecosystem genetics
KW - defensive chemistry genes
KW - foundation species
KW - quantitative trait loci mapping
KW - salicinoid phenolic glycoside
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U2 - 10.1002/ece3.3932
DO - 10.1002/ece3.3932
M3 - Article
AN - SCOPUS:85043370857
VL - 8
SP - 3726
EP - 3737
JO - Ecology and Evolution
JF - Ecology and Evolution
SN - 2045-7758
IS - 7
ER -