A Genetic Map for the Lobatae

Arpita Konar, Olivia Choudury, Oliver Gailing, Mark V. Coggeshall, Margaret E. Staton, Scott Emrich, John E. Carlson, and Jeanne Romero-Severson

Published May 2016 International Oaks No. 27: 181–188

Abstract

Genetic maps constructed with sequenced markers have enduring value for ordering contigs generated during genome sequencing projects, providing a context with which to interpret population and quantitative genetic patterns of variation, testing hypotheses about the genetic architecture loci contributing to adaptive evolution and molecular breeding to combat biotic and abiotic stress. However, controlled crosses are not feasible in many species of ecologically important and economically valuable hardwood forest trees. Parentage analysis of open pollinated seed from a single tree of Quercus rubra L. (Quercus section Lobatae) revealed that one pollen parent accounted for the plurality of the seed set. A genotyping strategy focused on identifying the progeny of this pollinator in subsequent years revealed that the same pollen parent accounted for a majority or plurality of the seed set across all years. Our framework map, constructed on 399 full sibs includes 33 gSSR and 35 EST-SSR designed from Q. rubra and 39 EST-SSR previously mapped in the pedunculate oak Q. robur L., the latter set enabling us to tag all 12 linkage groups to the linkage groups of Q. robur. We also used a reduced representation sequencing technology to generate 78,725 ddRAD (double digest restriction site associated DNA) tags. Our current consensus map includes the framework markers and 1,277 ddRAD tags. We find the ddRAD tag approach useful, but the technology has the limitation of poor efficiency in useful marker recovery and requires bioinformatic expertise costing many times more than the initial sequencing.

Keywords

comparative mapping, Quercus, Fagaceae, heterologous markers, ddRAD tags

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