Molecular plant breeding with the aid of molecular markers has played an important role in modern plant breeding over the last two decades. Many marker-based predictions for quantitative traits have been made to enhance parental selection, but the trait prediction accuracy remains generally low, even with the aid of dense, genome-wide SNP markers. Researchers from Agriculture & Agri-Food Canada and the University of Saskatchewan review the prediction issues in molecular plant breeding and the applicability of an RNA-Seq technique for developing function-associated specific trait (FAST) SNP markers. To understand whether and how FAST SNP markers could enhance trait prediction, they also performed a theoretical reasoning on the effectiveness of these markers in a trait-specific prediction, and verified the reasoning through computer simulation. To the end, the search yielded an alternative to regular genomic selection with FAST SNP markers that could be explored to achieve more accurate trait-specific prediction. Continuous search for better alternatives is encouraged to enhance marker-based predictions for an individual quantitative trait in molecular plant breeding.
Capturing genes of major and minor effects for a quantitative trait of interest through RNA-Seq function-associated specific trait (FAST) SNP markers in molecular plant breeding. Marker-specific selection uses the specific markers developed from the major QTL of the trait to select desirable parents. Genomic selection applies genome-wide random markers to estimate breeding values in various traits for parental selection. The derived alternative named trait-specific marker selection (TSMS) employs FAST SNP markers developed from RNA-Seq to predict individual performances in a trait of interest for parental selection.