Genetic Evaluation of Cotton Breeding Resources from the Pee Dee Germplasm Enhancement Program

The Pee Dee Germplasm Enhancement Program encompasses seventy years of breeding for the improvement of cotton fiber quality and yield.  The goal of the present study is to understand the relationships between cultivars released from the breeding program and to leverage this information to identify associations between genetic signatures and superior cultivar performance.  95 diverse lines released from the program across 8 breeding cycles between 1979 and 2002 were genotyped using the CottonSNP63k Array.  Multiple filtering parameters were tested in order to identify a core set of SNP markers for use in this study.  The resulting genotyping calls were compared to pedigree records to identify potential discrepancies or outliers, followed by population structure.  Lastly, marker-trait association were explored using field performance and fiber quality data from a collaborative 14 year-location trial conducted during prior investigations. Here, the results of the population structure analysis and our findings from the GWAS are presented.