Identification and validation of two quantitative trait loci for dwarf bunt in the resistant cultivar 'UI Silver'

Authors: JOSHI, PABITRA - University Of Idaho; DHILLON, GURIQBAL SINGH - University Of Idaho; GAO, YAOTIAN - University Of Idaho; KAUR, AMANDEEP - University Of Idaho; WHEELER, JUSTIN - University Of Idaho; Chen, Xianming; KRAUSE, WILLIAM - Oregon State University; KRAUSE, MARGARET - Oregon State University; CHEN, JIANLI - University Of Idaho

Submitted to: Theoretical and Applied Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/2/2024
Publication Date: 1/7/2025
Citation: Joshi, P., Dhillon, G., Gao, Y., Kaur, A., Wheeler, J., Chen, X., Krause, W., Krause, M.R., Chen, J. 2025. Identification and validation of two quantitative trait loci for dwarf bunt in the resistant cultivar 'UI Silver'. Theoretical and Applied Genetics. 2025(138). Article 18. https://doi.org/10.1007/s00122-024-04795-7.
DOI: https://doi.org/10.1007/s00122-024-04795-7

Interpretive Summary: Dwarf bunt is a devastating fungal disease of wheat that can cause complete loss of grain yield and quality during epidemics. Traditional breeding for dwarf bunt resistance requires multiple years of field screening under stringent conditions, with disease assessment possible only near or after plant maturity. Molecular marker-assisted selection offers a more efficient alternative to traditional selection methods. This study aimed to identify quantitative trait loci (QTL) and associated molecular markers for use in dwarf bunt cultivar improvement through marker-assisted breeding. A doubled haploid (DH) mapping population of 135 lines, derived from the bunt-resistant cultivar 'UI Silver' and the susceptible line 'Shaan89150', was evaluated for dwarf bunt resistance in a field nursery in Logan, Utah, USA over three growing seasons (2017, 2018 and 2023). The population was genotyped using the Illumina 90K SNP iSelect marker platform. Using the inclusive composite interval mapping (ICIM) method, a major QTL was consistently identified on chromosome arm 6DL across all environments, explaining phenotypic variations ranging from 15.29% to 35.50%. Another QTL was detected on chromosome arm 6DS, explaining approximately 11% of the phenotypic variation. These two QTL exhibited additive × additive effects on increasing resistance within the DH population. Kompetitive Allele-Specific PCR (KASP) markers were developed within the QTL intervals and employed in a diverse winter wheat panel, confirming the association of the 6DL QTL with dwarf bunt resistance. This study suggests that UI Silver and additional resistant cultivars containing these two QTL are valuable parental lines for improving dwarf bunt resistance through marker-assisted selection. These germplasms are also essential resources for understanding gene functions via map-based gene cloning.

Technical Abstract: Dwarf bunt, caused by Tilletia controversa, is a devastating fungal disease of wheat that can cause complete loss of grain yield and quality during epidemics. Traditional breeding for dwarf bunt resistance requires multiple years of field screening under stringent conditions, with disease assessment possible only near or after plant maturity. Molecular marker-assisted selection offers a more efficient alternative to traditional selection methods. This study aimed to identify quantitative trait loci (QTL) and associated molecular markers for use in dwarf bunt cultivar improvement through marker-assisted breeding. A doubled haploid (DH) mapping population of 135 lines, derived from the bunt-resistant cultivar 'UI Silver' and the susceptible line 'Shaan89150', was evaluated for dwarf bunt resistance in a field nursery in Logan, Utah, USA over three growing seasons (2017, 2018 and 2023). The population was genotyped using the Illumina 90K SNP iSelect marker platform. Using the inclusive composite interval mapping (ICIM) method, a major QTL, Qdb.ssdhui-6DL, was consistently identified on chromosome arm 6DL across all environments, explaining phenotypic variations ranging from 15.29% to 35.50%. Another QTL, Qdb.ssdhui-6DS, was detected on chromosome arm 6DS, explaining approximately 11% of the phenotypic variation. These two QTL exhibited additive × additive effects on increasing resistance within the DH population. Kompetitive Allele-Specific PCR (KASP) markers were developed within the QTL intervals and employed in a diverse winter wheat panel, confirming the association of the 6DL QTL with dwarf bunt resistance. This study suggests that UI Silver and additional resistant cultivars containing these two QTL are valuable parental lines for improving dwarf bunt resistance through marker-assisted selection. These germplasms are also essential resources for understanding gene functions via map-based gene cloning.