Combining genomic selection with genome-wide association analysis identified a large-effect QTL and improved selection for red rot resistance in sugarcane

Anthony O'Connell; Jasmin Deo; Emily Deomano; Xianming Wei; Phillip Jackson; Karen S Aitken; Ramaswamy Manimekalai; Krishnasamy Mohanraj; Govinda Hemaprabha; Bakshi Ram; Rasappa Viswanathan; Prakash Lakshmanan

doi:10.3389/fpls.2022.1021182

Combining genomic selection with genome-wide association analysis identified a large-effect QTL and improved selection for red rot resistance in sugarcane

Front Plant Sci. 2022 Oct 31:13:1021182. doi: 10.3389/fpls.2022.1021182. eCollection 2022.

Authors

Affiliations

¹ Sugar Research Australia Limited, Brisbane, QLD, Australia.
² Commonwealth Scientific and Industrial Research Organisation (CSIRO) Agriculture and Food, Queensland Bioscience Precinct, St Lucia, QLD, Australia.
³ Sugarcane Breeding Institute, Coimbatore, India.
⁴ Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China.
⁵ Interdisciplinary Research Center for Agriculture Green Development in Yangtze River Basin (CAGD), College of Resources and Environment, Southwest University, Chongqing, China.
⁶ Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, QLD, Australia.

Abstract

Red rot caused by the fungus Colletotrichum falcatum is the main disease limiting sugarcane productivity in several countries including the major producer India. The genetic basis for red rot resistance is unclear. We studied a panel of 305 sugarcane clones from the Australian breeding program for disease response phenotype and genotype using an Affymetrix^® Axiom^® array, to better understand the genetic basis of red rot resistance. SNP markers highly significantly associated with red rot response (≤ 10^-8) were identified. Markers with largest effect were located in a single 14.6 Mb genomic region of sorghum (the closest diploid relative of sugarcane with a sequenced genome) suggesting the presence of a major-effect QTL. By genomic selection, the estimated selection accuracy was ~0.42 for red rot resistance. This was increased to ~0.5 with the addition of 29 highly significant SNPs as fixed effects. Analysis of genes nearby the markers linked to the QTL revealed many biotic stress responsive genes within this QTL, with the most significant SNP co-locating with a cluster of four chitinase A genes. The SNP markers identified here could be used to predict red rot resistance with high accuracy at any stage in the sugarcane breeding program.

Keywords: GWAS; genome wide association study; genomic selection; molecular breeding; red rot; sugarcane.