Genetic Gain from Phenotypic and Genomic Selection for Quantitative Resistance to Stem Rust of Wheat

Stem rust of wheat (Triticum aestivum L.), caused by Puccinia graminis f. sp. tritici, is a globally important disease that can cause severe yield loss. Since the emergence of Ug99, a group of races capable of infecting up to 90% of the worlds’ wheat cultivars, breeding for quantitative stem rust resistance (QSRR) has become important for developing varieties with durable resistance. Genomic selection (GS) is a breeding method that could increase rates of genetic gain for quantitative traits because selection can occur earlier in the breeding cycle. Selection experiments comparing GS based on markers only and phenotypic selection (PS) have not been conducted in crop species. Our objectives were to compare realized gain from GS based on markers only with that of PS for QSRR using equal selection intensities; determine if gains realized are consistent with theoretical expectations; and compare the impact of GS and PS on inbreeding, genetic variance, and correlated response for pseudo-black chaff (PBC), a correlated trait. In two years, GS led to a 31±11% increase in QSRR and a 138±22% increase in PBC; PS led to a 42±12% increase in QSRR and a180±70% increase in PBC. Selection responses were significant and agreed with theoretical expectations. Gains per unit time from GS and PS were equal, but GS led to significantly lower genetic variance. These results show that, while GS and PS can lead to equal rates of short-term gains, GS can reduce genetic variance more rapidly.