| Wheat stripe rust, caused by the fungal pathogen Puccinia striiformis f. sp. tritici (Pst), is one of the most devastating diseases to wheat all over the world. Breeding resistant cultivars is the most economical and effective method for controlling the stripe-rust disease. The best hope for future genetic improvement of wheat crops lies in exploiting the gene pools of the wild relatives. Wild emmer wheat (Triticum dicoccoides), the progenitors of cultivated wheat, has adapted to a broad range of environments and is a valuable genetic resources that include biotic tolerances, such as stripe rust resistance. With the development of genomics and biostatistics software, association analysis based on the linkage disequilibrium (LD) offers a new method for identifying loci controlling stripe rust. Combination of quantitative trait loci (QTL) mapping and association analysis facilitate dissection of complex traits, which provides important information and markers for molecular breeding in crops,In the present study, new loci or genome regions conferring stripe rust resistance were identified based on association mapping using a large number of EST-related SNP markers. On the other hand, high-density mapping of the stripe rust resistance gene YrH52was constructed based on traditional QTL mapping, which provided a sound basis for further fine mapping and map-based cloning, hence, can speed up genetic improvement of wheat. The main results are summarized as follows:1.Construction of phenotypic database for stripe rust resistance in wild emmer wheat. Stripe rust challenge tests on350wild emmer wheat accessions, originating in Near East Fertile Crescent, were conducted during2011-2012, and2012-2013at Yanting, China. The results indicated that71accessions were completely immune to prevalent stripe rust race,31high resistant,40moderate resistant,134moderate susceptible,74high susceptible, respectively, during2011-2012; while there were86completely immunity,9high resistant,32moderate resistant,21moderate susceptible,202high susceptible to prevalent stripe rust race, respectively, during2012-2013. Among the350wild emmer wheat accessions,49were completely immune to prevalent stripe rust race in two years; hence, these will be a useful core germplasm for mining resistant gene and further studies on breeding utilization in wheat improvement.2. Genetic diversity in the wild emmer wheat. Genotyping data generated by the1,018polymorphic SNP markers were used for genetic diversity analysis, and the results demonstrated that average Nei’s gene diversity and PIC values were0.1841and0.1530, respectively, suggesting a moderate level of genetic diversity. The greater genetic variation in the B genome than in the A genome was detected in this study, which suggested a larger contribution of the B than A genome to wild emmer wheat genetic variation. Comparative analysis of genetic diversity among the seven ecogeographical populations indicated that the greatest genetic diversity was found in the populations from south-east of Turkey and southern of Lebanon, corresponding to the distribution pattern of genetic diversity.3. Population structure in the wild emmer wheat. SNP genotyping data was used for genetic structure analysis, and the results showed that the analyzed wild emmer wheat populations can be divided into two genetically distinct groups:central populations collected from Israel were always separated from marginal populations in Israel, Lebanon, Turkey, and Syria, when K=2to12. Analysis of spatial genetic structure and multiple stepwise regressions demonstrate that inter-population genetic divergence don’t correspond to an isolation-by-distance model, but have a significant correlation with ecological variables. A total of33outlier loci under positive selection were identified according to the hierarchical structure of the populations, and the markers or genome locations were consistent with known patterns of selection that differentiated central populations from marginal populations.4. Linkage disequilibrium (LD) analysis in the wild emmer wheat. A high level of LD was detected in wild emmer wheat. For the whole analyzed germplasm, the percentage of locus pairs with significant (P<0.001) is43.5%, average r2and LD decay distance is0.134and14.3cM, respectively. Besides, LD level displayed considerable variability across the chromosomes, the higher level of LD was observed on chromosome4B and7A; while the lower level of LD was found on chromosome1A,3A, and5A.5. Association mapping of stripe rust response in the wild emmer wheat. A total of30loci significantly associated with stripe rust resistance were detected based on association mapping. These markers could explain5-15%of the total variation, and some of candidate loci were in the same bins where stripe rust resistances QTLs have been previously reported. Analysis of expression patterns for candidate loci displayed altered expression patterns after inoculation with2up-regulated and4down-regulated. Combination expression patterns with function of homologous ESTs for candidate loci, we determined9loci which may be involved in the defense response against stripe rust.6. Construction of high-density genetic mapping of YrH52. Stripe rust tests on F23mapping populations indicated that the segregation ratio for the stripe-rust reaction fitted the theoretical ratio1:2:1, inferring that the stripe-rust resistance gene YrH52is controlled by a single, dominant gene. In the present study, four new markers were found to be linked to the YrH52gene, and linkage distances ranging from0.8to4.5cM; hence, YrH52was flanked by Xhuw23and Xgwm413with map distances of0.8and1.5cM, respectively. |
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