Relocation of Sr48 to Chromosome 2D Using an Alternative Mapping Population and Development of a Closely Linked Marker Using Diverse Molecular Technologies

Vallence Nsabiyera; Naeela Qureshi; Jianbo Li; Mandeep Randhawa; Peng Zhang; Kerrie Forrest; Urmil Bansal; Harbans Bariana

doi:10.3390/plants12081601

Relocation of Sr48 to Chromosome 2D Using an Alternative Mapping Population and Development of a Closely Linked Marker Using Diverse Molecular Technologies

Plants (Basel). 2023 Apr 10;12(8):1601. doi: 10.3390/plants12081601.

Authors

Vallence Nsabiyera^{1

2}, Naeela Qureshi^{1

3}, Jianbo Li¹, Mandeep Randhawa^{1

4}, Peng Zhang¹, Kerrie Forrest⁵, Urmil Bansal¹, Harbans Bariana^{1

6}

Affiliations

¹ School of Life and Environmental Sciences, Faculty of Science, The University of Sydney Plant Breeding Institute, 107 Cobbitty Road, Cobbitty, NSW 2570, Australia.
² Nabuin Zonal Agricultural Research and Development Institute, National Agricultural Research Organization, Moroto P.O. Box 132, Uganda.
³ International Maize and Wheat Improvement Center (CIMMYT), Carretera Mexico-Veracruz Km. 45, El Batan, Texcoco C.P. 56237, Mexico.
⁴ International Maize and Wheat Improvement Center (CIMMYT), World Agroforestry Centre (ICRAF Campus), UN Avenue, Gigiri, Nairobi P.O. Box 1041-00621, Kenya.
⁵ Agriculture Victoria, AgriBio, Centre for AgriBioscience, 5 Ring Rd., Bundoora, VIC 3083, Australia.
⁶ School of Science, Faculty of Science, Hawkesbury Campus, Western Sydney University, Richmond, NSW 2753, Australia.

Abstract

The Ug99-effective stem rust resistance gene Sr48 was mapped to chromosome 2A based on its repulsion linkage with Yr1 in an Arina/Forno recombinant inbred line (RIL) population. Attempts to identify markers closely linked to Sr48 using available genomic resources were futile. This study used an Arina/Cezanne F_5:7 RIL population to identify markers closely linked with Sr48. Using the Arina/Cezanne DArTseq map, Sr48 was mapped on the short arm of chromosome 2D and it co-segregated with 12 markers. These DArTseq marker sequences were used for BlastN search to identify corresponding wheat chromosome survey sequence (CSS) contigs, and PCR-based markers were developed. Two simple sequence repeat (SSR) markers, sun590 and sun592, and two Kompetitive Allele-Specific PCR (KASP) markers were derived from the contig 2DS_5324961 that mapped distal to Sr48. Molecular cytogenetic analysis using sequential fluorescent in situ hybridization (FISH) and genomic in situ hybridization (GISH) identified a terminal translocation of chromosome 2A in chromosome 2DL of Forno. This translocation would have led to the formation of a quadrivalent involving chromosomes 2A and 2D in the Arina/Forno population, which would have exhibited pseudo-linkage between Sr48 and Yr1 in chromosome 2AL. Polymorphism of the closet marker sunKASP_239 among a set of 178 wheat genotypes suggested that this marker can be used for marker-assisted selection of Sr48.

Keywords: FISH; GISH; Sr48; Ug99; marker-assisted selection (MAS); stem rust; translocation; wheat.

Grants and funding

The first author thanks the Australian Government and the Ugandan Government for funding to pursue his PhD study at the University of Sydney, Australia. We acknowledge the financial support received from the Grains Research Development Corporation (GRDC) Australia.