Genotypic data changes family rank for growth and quality traits in a black walnut (Juglans nigra L.) progeny test

We evaluated eight-year-old seedlings in a black walnut (Juglans nigra L.) progeny test for two quantitative and two qualitative traits. We also used 12 microsatellite markers to genotype the 328 progeny and their maternal parents. Seedling family growth and quality was evaluated based on the progeny test map. These values were compared to family growth and quality after seedlings were genotyped and reassigned to families by parentage assignment software. After genotyping and parentage analysis, about 80 % of the offspring were assigned to the same half-sib family indicated on the planting map. Considerable differences were observed between the ranks of half-sib families based on the planting-map versus the ranks of the families based on the exclusion/assignment of progeny to their family based on genotypes. Analysis of the data without genotypic assignment of progeny to their correct family revealed that the family effect for height was significant, as was family effect for diameter. After seedlings were reassigned to half-sib families based on genotypic information, neither the family effect for height nor the family effect for diameter was significant. The efficiency of the mixed model ANOVA, as measured by Akaike Information Criterion improved by about 30 % after genotyping and exclusion/reassignment of progeny. These results show that genotyping progeny can have a significant effect on the rank of families and potential selection of individuals from a progeny trial, the quality of data analysis, and the efficiency and efficacy of breeding operations.