Evaluation of genomic selection and marker-assisted selection in Miscanthus and energycane

Although energycane (Saccharum spp. hybrids) is widely used as a source of lignocellulosic biomass for bioethanol, breeding this crop for disease resistance is challenging due to its narrow genetic base. Therefore, efforts are underway to introgress novel sources of genetic resistance from Miscanthus into energycane. Given that disease resistance in energycane could be either qualitative or quantitative in nature, careful examination of a wide variety of genomic-enabled breeding approaches will be crucial to the success of such an undertaking. Here we examined the efficiency of both genomic selection (GS) and marker-assisted selection (MAS) for traits simulated under different genetic architectures in F₁ and BC₁ populations of Miscanthus × Miscanthus and sugarcane × sugarcane crosses. We observed that the performance of MAS was comparable and sometimes superior to GS for traits simulated with four quantitative trait nucleotides (QTNs). In contrast, as the number of simulated QTN increased, all four GS models that were evaluated tended to outperform MAS, select more phenotypically optimal F₁ individuals, and accurately predict simulated trait values in subsequent BC₁ generations. We therefore conclude that GS is preferable to MAS for introgressing genetic sources of horizontal disease resistance from Miscanthus to energycane, while MAS remains a suitable option for introgressing vertical disease resistance.