Identification of QTLs for smut resistance in sugarcane using a bi-parental mapping population

Authors: CORTES, JOSE - LSU Agcenter; GUTIERREZ, ANDRES - LSU Agcenter; HOY, JEFFREY - LSU Agcenter; Hale, Anna; BAISAKH, NIRANJAN - LSU Agcenter

Submitted to: Gene
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/14/2023
Publication Date: 12/17/2023
Citation: Cortes, J.D., Gutierrez, A.F., Hoy, J.W., Hale, A.L., Baisakh, N. 2023. Identification of QTLs for smut resistance in sugarcane using a bi-parental mapping population. Gene. 2352-4073. https://doi.org/10.1016/j.plgene.2023.100445.
DOI: https://doi.org/10.1016/j.plgene.2023.100445

Interpretive Summary: Sugarcane smut is a major disease in industries across the world. The main strategy for overcoming the disease is to breed varieties which are resistant. While effective, this approach is slow and cumbersome and requires many years of repeated disease screening to obtain reliable results. Unfavorable and variable environmental conditions, inconsistency between ratings for disease susceptibility, and continued loss of susceptible varieties from the program are some of the challenges encountered. The development and use of Deoxyribonucleic acid(DNA) markers associated with resistance to smut disease may overcome some of these challenges and allow for more accurate and rapid identification of resistant varieties. In this study, a genetic analysis was conducted using a family of sugarcane generated from a cross between susceptible female parent and a resistant male parent to identify DNA regions associated with resistance to the disease. DNA markers which were spread across multiple sugarcane chromosomes were identified that were linked to resistance to the disease. Genes near the DNA markers are known to be involved in disease resistance. If further studies in additional populations validate the results seen in this test, these markers have the potential to hasten breeding for smut resistant sugarcane varieties.

Technical Abstract: Sugarcane smut, caused by Sporisorium scitamineum, is a major disease worldwide. Breeding resistant cultivars is the main management strategy. However, occasional failure to detect susceptible clones due to unfavorable environmental conditions, inconsistency in disease ratings between experiments, and continued clone losses due to susceptibility are some of the challenges for this strategy. The development and use of molecular markers associated with smut resistance may overcome these limitations allowing more accurate identification of resistant parents and progeny. A genetic analysis was conducted using an inoculated population of 162 F1 progeny from a biparental cross between susceptible/female and resistant/male parents to identify quantitative trait loci (QTLs) associated with resistance. A total of 1,574 single dose (SD) single-nucleotide polymorphisms (SNP) markers used to construct a genetic map resulted in 253 linkage groups (LGs) of which 150 LGs were assigned to the female parent and 204 LG to the male parent with a genome coverage of 24,580 cM. (Composite) interval mapping with different sub-populations with selective genotyping identified six consistent QTLs that cumulatively explained 25.74% of the phenotypic variance with LOD scores ranging from 3.17 to 23.7. Four out of 12 SNP markers closest to the QTL peaks explained more than 10% of the variance for resistance in the heterozygous condition. Genes known to be involved in disease resistance, such as cellulose synthase, expansin, protein degradation, and receptor-kinase were linked to the genomic regions associated with smut resistance. The markers upon validation in different populations can be utilized for marker-assisted selection.