Genome wide association study of common resistance to rust species in tetraploid wheat

Authors: MARONE, DANIELA - Crea-Research Centre For Cereal And Industrial Crops; LAIDO, GIOVANNI - Crea-Research Centre For Cereal And Industrial Crops; SACCOMANNO, ANTONIETTA - Crea-Research Centre For Cereal And Industrial Crops; PETRUZZINO, GIUSEPPE - Crea-Research Centre For Cereal And Industrial Crops; GIARETTA AZEVEDO, CLEBER - Crea-Research Centre For Cereal And Industrial Crops; DE VITA, PASQUALE - Crea-Research Centre For Cereal And Industrial Crops; MASTRANGELO, ANNA MARIA - Crea-Research Centre For Cereal And Industrial Crops; GADALETA, AGATA - University Of Bari; AMMAR, KARIM - International Maize & Wheat Improvement Center (CIMMYT); BASSI, FILIPPO - The International Center For Agricultural Research In The Dry Areas(ICARDA); WANG, MAINAN - Washington State University; Chen, Xianming; RUBIALES, DIEGO - Institute For Sustainable Agriculture; MATNY, OADI - University Of Minnesota; STEFFENSON, BRIAN - University Of Minnesota; PECCHIONI, NICOLA - Crea-Research Centre For Cereal And Industrial Crops

Submitted to: Frontiers in Plant Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/11/2023
Publication Date: 1/2/2024
Citation: Marone, D., Laido, G., Saccomanno, A., Petruzzino, G., Giaretta Azevedo, C.V., De Vita, P., Mastrangelo, A., Gadaleta, A., Ammar, K., Bassi, F.M., Wang, M., Chen, X., Rubiales, D., Matny, O., Steffenson, B.J., Pecchioni, N. 2024. Genome wide association study of common resistance to rust species in tetraploid wheat . Frontiers in Plant Science. 14. Article 1290643. https://doi.org/10.3389/fpls.2023.1290643.
DOI: https://doi.org/10.3389/fpls.2023.1290643

Interpretive Summary: Rusts of genus Puccinia are wheat pathogens. Stem, leaf, and stripe rust can occur singularly or in mixed infections and pose a threat to wheat production globally for the wide dispersal of their spores. The development of durably resistant cultivars is the most sustainable mean for their control. Many resistance genes have been identified, characterized, genetically mapped and cloned; several quantitative trait loci (QTL) for resistance have also been described. However, few studies considered resistance to all three rust pathogens in a given germplasm. A genome-wide association study (GWAS) was carried out to identify loci associated with resistance to the three rusts in a collection of 230 inbred lines of tetraploid wheat including 128 durum wheat accessions, previously genotyped with SNP markers. The wheat panel was phenotyped in field and growth chamber experiments across different countries; then, GWAS was performed. In total 9, 34, and 5 QTL were identified in the A and B genomes for resistance to stem rust, leaf rust, and stripe rust, respectively, at both seedling and adult plant stages. Only one QTL on chromosome 4A was found effective against all the three rusts at the seedling stage. Six QTL conferring resistance to two rust species at the adult plant stage were mapped: three on chromosome 1B, and one each on 5B, 7A and 7B. Fifteen QTL conferring seedling resistance to two rusts were mapped: five on chromosome 2B, three on 7B, two each on 5B and 6A, and one each on 1B, 2A and 7A. Most of the QTL identified were specific for a single rust species or race of a species. Candidate genes were identified within the confidence intervals of QTL conferring resistance against at least two rust species by using the annotations of the durum (cv. 'Svevo') and wild emmer wheat (‘Zavitan’) reference genomes. The 22 identified loci conferring resistance to two or three rust species may be useful for breeding new and potentially durable resistant wheat cultivars.

Technical Abstract: Rusts of genus Puccinia are wheat pathogens. Stem (black; Sr), leaf (brown; Lr), and stripe (yellow; Yr) rust, caused by Puccinia graminis f. sp. tritici (Pgt), Puccinia triticina (Pt), and Puccinia striiformis f. sp. tritici (Pst), can occur singularly or in mixed infections and pose a threat to wheat production globally for the wide dispersal of their urediniospores. The development of durably resistant cultivars is the most sustainable mean for their control. Many resistance genes have been identified, characterized, genetically mapped and cloned; several quantitative trait loci (QTL) for resistance have also been described. However, few studies considered resistance to all three rust pathogens in a given germplasm. A genome-wide association study (GWAS) was carried out to identify loci associated with resistance to the three rusts in a collection of 230 inbred lines of tetraploid wheat (128 being Triticum turgidum ssp. durum), previously genotyped with SNPs. The wheat panel was phenotyped in field and growth chamber experiments across different countries; then, mixed linear model (MLM) GWAS was performed. In total 9, 34, and 5 QTL were identified in the A and B genomes for resistance to Pgt, Pt, and Pst, respectively, at both seedling and adult plant stages. Only one QTL on chromosome 4A was found effective against all the three rusts at the seedling stage. Six QTL conferring resistance to two rust species at the adult plant stage were mapped: three on chromosome 1B, and one each on 5B, 7A and 7B. Fifteen QTL conferring seedling resistance to two rusts were mapped: five on chromosome 2B, three on 7B, two each on 5B and 6A, and one each on 1B, 2A and 7A. Most of the QTL identified were specific for a single rust species or race of a species. Candidate genes were identified within the confidence intervals of QTL conferring resistance against at least two rust species by using the annotations of the durum (cv. 'Svevo') and wild emmer wheat (‘Zavitan’) reference genomes. The 22 identified loci conferring resistance to two or three rust species may be useful for breeding new and potentially durable resistant wheat cultivars.