Genetic analysis of the Puccinia graminis f. sp. tritici and Puccinia triticina populations in southern Africa

["Stem rust","Leaf rust","Genotypes","Phenotypes","Population genetics","Dissertation (M.Sc. (Plant Sciences))--University of the Free State, 2015"]

Selinga, Tonny Ion ; ["Visser, B.","Pretorius, Z. A."]

University of the Free State

Others  :  http://scholar.ufs.ac.za/xmlui/bitstream/11660/2276/1/SelingaTI.pdf

瑞士|英语

来源: University of Iowa

【 摘 要 】

English: The hypothesis of whether genotyping complements phenotyping of Puccinia graminis f. sp. tritici (Pgt) and P. triticina (Pt) was tested. Phenotyping (infection type analysis) has been the method of choice for the identification of races, determination of single-step mutations which amount to asexual reproduction and evaluation of inoculum exchange. However, phenotyping can be labour intensive while the non-viability of spores makes it impossible to identify isolates. Genotyping has been used to confirm the identity of specific races but it has never been used to identify isolates on a large scale. Movement of inoculum has been shown by phenotyping to occur in southern Africa, but not by genotyping.A two stage protocol was used to identify stem rust Ug99 and non-Ug99 isolates collected during the 2010 - 2012 surveys. Generally there was a large agreement between genotypes and phenotypes. The SNP genotypes had high sensitivity for identification of 2SA88 phenotypes [73.3% (95% CI = 63.8% to 81.5%)]. There was a poor correlation (r=0.14) between the SSR genotypes and 26 Pgt resistance genes of the non-Ug99 races. The SSR genotypes had a high sensitivity for identification of 2SA105 [95.5% (95% CI = 77.2% to 99.9%)].However there was strong correlation (r=0.71) between genotypes and 17 Pt resistance genes for Pt isolates. There was a high sensitivity for genotypes to identify 3SA145 [100% (95% CI = 89.72 to 100%)]. It is still not clear whether genotyping is specific in the identification of Pgt and Pt races. Although there was good sensitivity detected, it was difficult to confidently indicate the proportion of isolates with genotypes that could be exclusively found in a single race.Three highly differentiated (FST=0.75) non-Ug99 Pgt and a single Ug99 population were identified in South Africa. Two highly differentiated (FST=0.543; P<0.0001) Pt populations were identified in South Africa. Both the Pgt and Pt populations in South Africa were asexually reproducing. Three Pt populations were detected in southern Africa The fixation index (FST=0.67; P˂0.0001) for the southern African populations was high which suggests that there was significant differentiation between the three southern African populations. The Bayesian model cluster analysis results suggested that there was inoculum exchange between South Africa, Malawi, Zambia and Zimbabwe.