Low-temperature soluble carbohydrate accumulations are commonly associated with anthocyanin coloration, attenuated growth, and cold adaptation of cool-season grasses. A total of 647 AFLP markers were tested for associations with anthocyanin coloration, tiller formation, leaf formation, cumulative leaf length, percent soluble carbohydrate, and dry matter regrowth among replicated clones of an admixed Leymus wildrye breeding population evaluated in low-temperature growth chambers. The admixed breeding population was derived from a heterogeneous population of L. cinereus × L. triticoides F₁ hybrids, with two additional generations of open pollination. Two AFLP linkage maps, constructed from two full-sib mapping populations derived from the same F₁ hybrid population, were integrated to produce a framework consensus map used to examine the distribution of marker-trait associations in the admixed F₁OP₂ population. Thirty-seven linkage blocks, spanning 258 cM (13.6%) of the 1895 cM consensus map, contained 119 (50%) of the 237 markers showing at least one possible trait association (P < 0.05).="" moreover,="" 28="" (68%)="" of="" the="" 41="" most="" significant="" marker-trait="" associations="">P < 0.005)="" were="" located="" in="" 15="" qtl="" linkage="" blocks="" spanning="" 112.9="" cm="" (6%)="" of="" the="" linkage="" map.="" the="" coincidence="" of="" these="" 28="" significant="" marker-trait="" associations,="" and="" many="" less="" significant="" associations,="" in="" 15="" relatively="" small="" linkage="" blocks="" (0.6="" cm="" to="" 21.3="" cm)="" provides="" evidence="" of="" admixture="" linkage="" disequilibrium="" qtls="" (ald="" qtls)="" in="" this="" heterogeneous="" breeding="" population.="" at="" least="" four="" of="" the="" remaining="" 13="" putative="" marker-trait="" associations="">P < 0.005)="" were="" located="" in="" genetic="" map="" regions="" lacking="" other="" informative="" markers.="" the="" complexity="" of="" marker-trait="" associations="" results="" from="" heterogeneity="" within="" and="" substantial="" divergence="" among="" the="" parental="">