Haplotype variants of Sr46 in Aegilops tauschii, the diploid D genome progenitor of wheat

Authors: ATHIYANNAN, NAVEENKUMAR - Csiro, Black Mountain Laboratories; LONG, YUNMING - North Dakota State University; KANG, HOUYANG - North Dakota State University; CHANDRAMOHAN, SUTHA - Csiro, Black Mountain Laboratories; BHATT, DHARA - Csiro, Black Mountain Laboratories; ZHANG, QIJUN - North Dakota State University; Klindworth, Daryl; Rouse, Matthew; Friesen, Timothy; MCINTOSH, ROBERT - University Of Sydney; ZHANG, PENG - University Of Sydney; FORREST, KERRIE - Agribio, Centre For Agribioscience; HAYDEN, MATHEW - Agribio, Centre For Agribioscience; PATPOUR, MEHRAN - Aarhus University; HOVMOLLER, MOGENS - Aarhus University; HICKEY, LEE - University Of Queensland; AYLIFFE, MICHAEL - Csiro, Black Mountain Laboratories; Cai, Xiwen; LAGUDAH, EVANS - Csiro, Black Mountain Laboratories; PERIYANNAN, SAMBASIVAM - Csiro, Black Mountain Laboratories; Xu, Steven

Submitted to: Theoretical and Applied Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/17/2022
Publication Date: 6/24/2022
Citation: Athiyannan, N., Long, Y., Kang, H., Chandramohan, S., Bhatt, D., Zhang, Q., Klindworth, D.L., Rouse, M.N., Friesen, T.L., MciIntosh, R., Zhang, P., Forrest, K., Hayden, M., Patpour, M., Hovmoller, M.S., Hickey, L.T., Ayliffe, M., Cai, X., Lagudah, E.S., Periyannan, S., Xu, S.S. 2022. Haplotype variants of Sr46 in Aegilops tauschii, the diploid D genome progenitor of wheat. Theoretical and Applied Genetics. 135: 2627-2639. https://doi.org/10.1007/s00122-022-04132-w.
DOI: https://doi.org/10.1007/s00122-022-04132-w

Interpretive Summary: Bread wheat is a polyploid crop with three genomes A, B, and D. The goatgrass species, Aegilops tauschii, is the D-genome progenitor and it is frequently used as a source of desirable genes for improving modern wheat. Several genes including Sr33, Sr45, and Sr46 for resistance to wheat stem rust were previously identified and cloned from the D-genome progenitor. In this study, we identified two stem rust resistance genes located in the chromosomal region harboring Sr46 in three lines of Aegilops tauschii. Gene cloning and sequence analysis revealed that the two genes differ in their encoded proteins from Sr46 by one and two amino acids, respectively, indicating that they are new forms (haplotypes) of Sr46. Based on the gene nomenclature in wheat, we designated the original Sr46 haplotypes as Sr46_h1 and two new haplotypes as Sr46_h2 and Sr46_h3, respectively. The three Sr46 haplotypes, which are effective against all stem rust races tested yet, represent a new source for improving stem rust resistance in wheat. The molecular markers developed in this study will help wheat breeders to efficiently transfer these genes into adapted wheat germplasm and varieties.

Technical Abstract: The Aegilops tauschii (wheat D-genome progenitor) accessions RL 5271 and CPI110672 were identified as resistant to multiple races (including the Ug99 race group) of the wheat stem rust pathogen Puccinia graminis f. sp. tritici (Pgt). This study was conducted to identify the gene(s) conferring stem rust resistance (Sr) in both Ae. tauschii accessions. Genetic analysis of the resistance in RL 5271 identified a single dominant allele (SrRL5271) controlling resistance, whereas a cross of CPI110672 segregated at two loci (SR672.1 and SR672.2). Bulked segregant analysis placed SRRL5271 and Sr672.1 in the SR46 region on chromosome arm 2DS. Molecular marker screening, mapping and genomic sequence analysis identified SrRL5271 and Sr672.1 as an allele of SR46. SrRL5271 and Sr672.1 are identical but differ in sequence from Sr46 (hereafter referred to as Sr46_h1 by following the gene nomenclature in wheat) by a single amino acid (N763K) and are thus designated Sr46_h2). Screening of a panel of Ae. tauschii accessions identified an additional allelic variant that differed from Sr46_h2 by a different amino acid (A648V) and was designated Sr46_h3. By contrast, the susceptible allele from Ae. tauschii accession AL8/78 differed from the resistance alleles by 54 amino acid substitutions (94% nucleotide sequence identity). Cloning and complementation tests of the three resistance haplotypes confirmed their resistance to Pgt race 98-1,2,3,5,6 and partial resistance to Pgt race TTRTF in bread wheat. The three Sr46 haplotypes, with no virulent races detected yet, represent a new source for improving stem resistance in wheat.