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

Area of Science:

• Plant breeding
• Genetics
• Agricultural science

Background:

• Genomic selection (GS) offers significant potential to improve crop breeding efficiency.
• Implementation of GS in rice (Oryza sativa L.) breeding programs has faced limitations.
• The Louisiana State University (LSU) Agricultural Center is actively working to integrate GS into its rice breeding program.

Purpose of the Study:

• To develop a cost-effective marker set for routine genomic selection in rice.
• To demonstrate the effectiveness of the developed marker set in southern U.S. rice germplasm.
• To establish a reliable genotyping platform for timely marker data acquisition.

Main Methods:

• Development of the LSU500 marker set for southern U.S. rice germplasm.
• Application of the LSU500 marker set using four years of breeding data.
• Analysis of 7,607 experimental lines and four elite biparental populations.
• Evaluation of predictive ability for key traits across different market classes and yield trials.

Main Results:

• The LSU500 marker set demonstrated utility for genomic selection applications.
• Predictive ability of GS ranged from 0.13 to 0.78 for key rice traits.
• Genomic selection showed comparable performance to phenotypic selection in predicting future performance within biparental populations.

Conclusions:

• The LSU500 marker set is effective for cost-effective genomic selection in southern U.S. rice breeding.
• The established marker set provides informative marker data with adequate turnaround time.
• Future improvements aim to further reduce costs and increase the accuracy of GS in rice.