Genetics of stem rust resistance in South African winter wheat varieties
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Date
2020-01
Authors
Martin, Chemonges
Journal Title
Journal ISSN
Volume Title
Publisher
University of the Free State
Abstract
Stem rust, caused by the fungus Puccinia graminis Pers. f. sp. tritici Eriks. and E. Henn (Pgt), is an important disease of wheat worldwide. Although resistant varieties have been utilised as an effective and efficient way of managing wheat stem rust, the emergence of new and virulent stem rust races threatens wheat cultivation. There is thus a continuous need to search for new sources of stem rust resistance. This study was conducted to elucidate the genetics of stem rust resistance in South African winter wheat varieties. To understand the origin and inheritance of all stage resistance (ASR) to Pgt race PTKST, four resistant varieties Komati, Koonap, Limpopo and SST 387 were crossed with the stem rust susceptible wheat parent Line 37-07. Seedling phenotyping of the F2 and F3 offspring showed that a single dominant gene conferred stem rust resistance in each of the four populations. Allelism tests indicated that either the same gene or closely linked alleles confer resistance in the four wheat varieties. However, allelism tests with Norin 40 (Sr42) and CnsSrTmp (SrTmp) indicated that it is either a closely linked gene, Sr42 or SrTmp that confers resistance to Pgt race PTKST. Multi-race phenotyping ruled out the involvement of Sr42, but suggested the likely presence of SrTmp among South African winter wheat varieties. Simple sequence repeat (SSR) marker genotyping using bulk segregant analysis (BSA) in four F2 mapping populations identified marker loci on chromosome 6DS linked to stem rust resistance in all four varieties. Linkage mapping identified two flanking SSR markers, and barc183 and wms4862 as closely linked [≤2.0 centiMorgan (cM)] to resistance gene(s) in two mapping populations (SST387/Line37-07 and Line37-07/Koonap). In the Line37-07/Komati mapping population, SSR markers psp3200 and barc183 were closely linked (≤2.9 cM). In the Line37-07/Limpopo mapping population, SSR markers wms4528 and barc183 were closely linked (≤0.9 cM). Two single nucleotide polymorphism (SNP) markers, BS00085929 and BS00085937, detecting different alleles in the resistant parents, mapped distally to stem rust resistance gene(s) at an average of 8.4 and 9.2 cM, respectively. Quantitative trait loci (QTL) analysis indicated that psp3200, wms4528, barc183 and wms4862 flanked the stem rust resistance gene(s). Major QTL detected in Komati, SST 387, Koonap and Limpopo explained 73.0, 96.2, 71.4 and 85.2% of phenotypic variation for stem rust resistance to race PTKST, respectively. Flanking SSR markers, wms4862 and barc183, were predictive of stem rust resistance in advanced winter wheat lines, hence confirming the chromosome location and their usefulness in marker-assisted selection (MAS). This study represents the first report of markers developed for stem rust resistance genes in South African winter wheat varieties. Resistant genotypes tested negative for diagnostic SNP markers linked to Sr42, SrTmp and SrCad on chromosome 6DS. From the marker data it can be concluded that the mapped resistance gene(s) are possibly novel or allele(s) of Sr42, SrTmp and/or SrCad. Identification and mapping of an adult plant resistance (APR) gene in the South African winter wheat variety PAN 3161 were conducted by field screening a F2 population and F3 families against Pgt race PTKST. SSR marker genotyping combined with BSA on 128 F2 plants identified markers on the short arm of chromosome 4D as linked to a stem rust resistance gene. SSR marker wmc720 flanked the APR gene SrPan3161 distally at 1.8 cM. Another set of four co-segregating SSR markers gpw7414, gpw8038, wmc52 and cfd23 flanked the APR gene proximally at 1.8 cM. QTL analysis identified a single major QTL explaining 71.5% of the phenotypic variation for resistance to Pgt race PTKST. The flanking markers wmc52, cfd23 and wmc720 were predictive of SrPan3161 in F3 families thus validating the chromosome location and their effectiveness in MAS.
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Keywords
Thesis (Ph.D. (Plant Sciences))--University of the Free State, 2020, Allelism, Inheritance, Markers, Marker-assisted selection, Simple sequence repeat, Single nucleotide polymorphism, Adult plant resistance gene, Stem rust resistance, Wheat stem rust