Development and validation of an optimized marker set for genomic selection in southern US rice breeding programs

The potential of genomic selection (GS) to increase the efficiency of breeding programs has been clearly demonstrated; however, the implementation of GS in rice (Oryza sativa L.) breeding programs has been limited. In recent years, efforts have begun to work toward implementing GS into the Louisiana State University (LSU) Agricultural Center rice breeding program. One of the first steps for successful GS implementation is to establish a suitable marker set for the target germplasm and a reliable, cost-effective genotyping platform capable of providing informative marker data with an adequate turnaround time. The objective of this study was to develop a marker set for routine GS and demonstrate its effectiveness in southern U.S. rice germplasm. The utility of the resulting marker set, the LSU500, for GS applications was demonstrated using four years of breeding data across 7,607 experimental lines and four elite biparental populations. The predictive ability of GS ranged from 0.13 to 0.78 for key traits across different market classes and yield trials. Comparisons between phenotypic selection and GS within biparental populations demonstrates similar performance of GS compared with phenotypic selection in predicting future performance. The prediction accuracies obtained with the LSU500 marker set demonstrates the utility of this marker set for cost-effective GS applications in southern U.S. rice breeding programs. The LSU500 marker set has been established through the genotyping service provider Agriplex Genomics, and in the future, it will undergo improvements to reduce the cost and increase the accuracy of GS.