Abstract
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. To search for more accurate trait-specific prediction with informative SNP markers, we conducted a literature review on the prediction issues in molecular plant breeding and on 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, we 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.
Highlights
Molecular plant breeding with the aid of molecular markers has played an important role in modern plant breeding over the last two decades (Moose and Mumm, 2008)
To facilitate the development of functionassociated specific trait (FAST) SNP markers through RNA-Seq (Figure 3), we proposed a new procedure, following the principle of BSR-Seq developed by Liu S. et al (2012) and the methods used by Salem et al (2012) and Ramirez-Gonzalez et al (2015)
The good examples are the successful developments of FAST SNP markers through RNA-Seq in fish and 175 putative SNP markers associated with Yr15, a major disease resistance gene for wheat yellow rust (RamirezGonzalez et al, 2015)
Summary
Molecular plant breeding with the aid of molecular markers has played an important role in modern plant breeding over the last two decades (Moose and Mumm, 2008). The good examples are the successful developments of FAST SNP markers through RNA-Seq in fish (e.g., see Salem et al, 2012; Ulloa et al, 2015) and 175 putative SNP markers associated with Yr15, a major disease resistance gene for wheat yellow rust (RamirezGonzalez et al, 2015) Built upon these leading efforts, our derived alternative will provide an option for plant breeders with new procedures to develop and focus on a set of FAST SNP markers for trait prediction to enhance parental selection. Our synthesis is encouraging, as continuous search for better alternatives based on the other genetic characteristics of a quantitative trait is possible and may yield more accurate trait prediction for molecular plant breeding
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