A major shattering QTL has been located on chromosome 2 of wildrice (Zizania palustris). Using the cMap map comparison tool at www.gramene.org, the wildrice chromosome 2 QTL region was compared to the rice SSR map. Rice SSR markers in the syntenous region were chosen and tested in a wildrice breeding population segregating for shattering. A 250 bp amplicon from the RM106 marker was observed to co-segregate with the shattering trait in the breeding population K2EF-C3. Three hundred fifty eight phenotyped individuals were genotyped at the RM106 locus. The marker correctly predicted 100% (5) shattering phenotypes and revealed that 47% (171) non-shattering phenotypes carried the shattering allele although exhibiting a non-shattering phenotype. One hundred fifty two individuals in the open pollinated K2EF-C3 breeding population were genotyped at the RM106 locus. This population was the result of 3 cycles of recurrent phenotypic selection for non-shattering. All 152 individuals exhibited a non-shattering phenotype. Sixty nine individuals exhibited a shattering genotype and 65 individuals exhibited a non-shattering genotype at the RM106 locus. Eighteen individuals in the population either did not amplify or did not have DNA available. Selfed seeds were collected from the 65 individuals with the non-shattering RM106 genotype. The progeny from each selfed plant were genotyped at the RM106 locus and phenotyped to determine the stability of non-shattering selection at the RM106 locus.