Skip to main content
ARS Home » Pacific West Area » Aberdeen, Idaho » Small Grains and Potato Germplasm Research » Research » Publications at this Location » Publication #379945

Research Project: Management of Genetic Resources and Associated Information in the USDA-ARS National Small Grains Collection

Location: Small Grains and Potato Germplasm Research

Title: Comparative sequencing and SNP marker validation for oat stem rust resistance gene Pg6 in a diverse collection of Avena accessions

item Gordon, Tyler
item Jin, Yue
item TINKER, NICHOLAS - Agriculture And Agri-Food Canada
item BEKELE, WUBISHET - Agriculture And Agri-Food Canada
item Gale, Sam
item Bockelman, Harold
item Bonman, John

Submitted to: Theoretical and Applied Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/4/2022
Publication Date: 2/3/2022
Citation: Gordon, T.C., Jin, Y., Tinker, N.A., Bekele, W.A., Gale, S.W., Bockelman, H.E., Bonman, J.M. 2022. Comparative sequencing and SNP marker validation for oat stem rust resistance gene Pg6 in a diverse collection of Avena accessions. Theoretical and Applied Genetics.

Interpretive Summary: Oat stem rust is a devastating foliar disease of oat. Identification of new sources of oat stem rust resistance is an important oat breeding objective as new races of stem rust overcome known resistance genes. A broadly-effective oat stem rust resistance gene, Pg6, was previously identified from a diploid oat (Avena strigosa) accession, CIav 6956. The Pg6 resistance locus was mapped to a 15 million base pair (Mbp) region on A-genome chromosome AA2 and validated using two bi-parental populations. Comparative sequencing within the 15 Mbp region found over 1000 SNPs associated with the Pg6 phenotype. One of these SNP markers was perfectly associated with the Pg6 phenotype in the two populations and closely linked in a diverse group of Avena spp. accessions. The SNP marker was used to postulate the presence of Pg6 in the diverse panel of accessions and identify 22 accessions that likely carry new sources of resistance.

Technical Abstract: Oat stem rust caused by Puccinia graminis f. sp. avenae (Pga) is a devastating disease of oat, and new races of Pga with unique virulence patterns threaten global oat production. Pg6 is a widely effective oat stem rust resistant gene described in the A-genome diploid, A. strigosa. An accession known to carry Pg6, CIav 6956, was crossed with two susceptible A. strigosa accessions, CIav 2524 and PI 573582, to generate 198 F2:3 families and 190 F2:6 RILs, respectively. The genetic map position of Pg6 was determined to be located between 475 and 490 Mbp on diploid chromosome AA2 of a sequenced A. atlantica accession using 238 Illumina SNPs mapped in the RIL population. This region was further refined using association analysis of SNP polymorphisms from whole genome resequenced A-genome accessions. Twenty-four KASP markers were developed from SNPs that showed perfect association between the Pg6 phenotype and 11 resequenced accessions. These markers were validated in the RILs and F2:3 families and the markers most closely linked with resistance were tested in a diverse panel of 253 accessions consisting of oat stem rust differentials, all available diploid Avena spp. accessions, and 41 A. vaviloviana accessions from the National Small Grains Collection. One SNP marker located at 483439497 bp on AA2 was perfectly associated with the Pg6 phenotype in Avena strigosa diploids and was within several Kb of a resistance gene analog, RPP13. The marker results and seedling testing against Pga races DBD, KBD, TJS, and TQL enabled the postulation of Pg6 and potential new sources of resistance in the Avena panel. These results will be used to infer Pg6 presence in other germplasm collections and breeding programs and to assist with introgression, gene pyramiding, and cloning of Pg6.