Identifying quantitative trait loci (QTLs) and developing diagnostic markers linked to orange rust resistance in sugarcane (Saccharum spp.)

Authors: YANG, XIPING - University Of Florida; Islam, Md; Sood, Sushma; MAYA, STEPHANIE - University Of Florida; HANSON, ERIK - University Of Florida; Comstock, Jack; WANG, JIANPING - University Of Florida

Submitted to: Frontiers in Plant Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/2/2018
Publication Date: 3/19/2018
Citation: Yang, X., Islam, M.S., Sood, S.G., Maya, S., Hanson, E.A., Comstock, J.C., Wang, J. 2018. Identifying quantitative trait loci (QTLs) and developing diagnostic markers linked to orange rust resistance in sugarcane (Saccharum spp.). Frontiers in Plant Science. 9:350. https://doi.org/10.3389/fpls.2018.00350.
DOI: https://doi.org/10.3389/fpls.2018.00350

Interpretive Summary: As an important economic crop, sugarcane is contributing up to 80% of table sugar used in the world. However, sugarcane production is vulnerable due to several diseases. Orange rust is one of the major diseases impacting sugarcane production worldwide. Identifying quantitative trait loci (QTL) and developing diagnostic markers are valuable for breeding programs to expedite release of superior sugarcane cultivars for disease control. Three QTL controlling orange rust resistance in sugarcane were identified for the first time ever accounting for total of 78% of phenotypic variation. We further developed diagnostic markers for marker assisted selection of orange rust resistance based on sugarcane putative resistance genes and sugarcane simple sequence repeats in the QTL intervals. A PCR-based Resistance gene-derived maker, G1 was developed, which showed significant association with orange rust resistance. The putative QTL and marker developed in this study can be effectively utilized in sugarcane breeding programs to facilitate the selection process, thus contributing to the sustainable agriculture for orange rust disease control.

Technical Abstract: Sugarcane (Saccharum spp.) is an important economic crop, contributing up to 80% of table sugar used in the world and has become a promising feedstock for biofuel production. Sugarcane production has been threatened by many diseases, and fungicide applications for disease control have been opted out for sustainable agriculture. Orange rust is one of the major diseases impacting sugarcane production worldwide. Identifying quantitative trait loci (QTL) and developing diagnostic markers are valuable for breeding programs to expedite release of superior sugarcane cultivars for disease control. In this study, an F1 segregating population derived from a cross between two hybrid sugarcane clones, CP95-1039 and CP88-1762, was evaluated for orange rust resistance in replicated trials. Three QTL controlling orange rust resistance in sugarcane were identified for the first time ever, which can explain 58, 12 and 8% of the phenotypic variation, separately. We further developed diagnostic markers for maker assisted selection of orange rust resistance based on sugarcane putative resistance genes and sugarcane simple sequence repeats in the QTL intervals. A PCR-based Resistance gene-derived marker, G1 was developed, which showed significant association with orange rust resistance. The putative QTL and marker developed in this study can be effectively utilized in sugarcane breeding programs to facilitate the selection process, thus contributing to the sustainable agriculture for orange rust disease control.