Browsing by Subject "Populationsstruktur"

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Genetic diversity, population structure, and linkage disequilibrium in the context of genome-wide association mapping of northern corn leaf blight resistance
(2012) van Inghelandt, Delphine; Melchinger, Albrecht E.
Besides linkage mapping, association mapping (AM) has become a powerful complement for understanding the genetic basis of complex traits. AM utilizes the natural genetic diversity and the linkage disequilibrium (LD) present in a diverse germplasm set. Setosphaeria turcica is a fungal pathogen that causes northern corn leaf blight (NCLB) in maize. The objective of this thesis research was to set the stage for and perform AM in elite maize breeding populations for NCLB resistance. Information about the genetic diversity and population structure in elite breeding material is of fundamental importance for the improvement of crops. The objectives of my study were to (i) examine the population structure and the genetic diversity in elite maize germplasm based on simple sequence repeat (SSR) markers, (ii) compare these results with those obtained from single nucleotide polymorphism (SNP) markers, and (iii) compare the coancestry coefficient calculated from pedigree records with genetic distance estimates calculated from SSR and SNP markers. The study was based on 1 537 elite maize inbred lines genotyped with 359 SSR and 8 244 SNP markers. My results indicated that both SSR and SNP markers are suitable for uncovering population structure. The same conclusions regarding the structure and the diversity of heterotic pools can be drawn from both markers types. However, fewer SSRs as SNPs are required for this goal, which facilitates the computations, for instance by the STRUCTURE software. Finally, the findings indicated that under the assumption of a fixed budget, modified Roger?s distances and gene diversity could be more precisely estimated with SNPs than with SSRs, and we proposed that between 7 and 11 times more SNPs than SSRs should be used for analyzing population structure and genetic diversity. Association mapping is based on LD shaped by historical recombinations. Many factors affect LD and, therefore, it must be determined empirically in the germplasm under investigation to examine the prospects of genomewide association mapping studies. The objectives of my study were to (i) examine the extent of LD with SSR and SNP markers in 1 537 commercial maize inbred lines belonging to four heterotic pools, (ii) compare the LD patterns determined by these two marker types, (iii) evaluate the number of SNP markers needed to perform genome-wide association analyses, and (iv) investigate temporal trends of LD. The results suggested that SNP markers of the examined density, unlike SSR markers, can be used effectively for association studies in commercial maize germplasm. Based on the decay of LD in the various heterotic pools, between 4 000 and 65 000 SNP markers would be needed to detect with a reasonable power associations with rather large quantitative trait loci (QTL). The 60 K SNP chip currently available for maize seems appropriate to identify QTLs that explain at least 10% of the phenotypic variance. However, to identify QTLs with smaller effects, which is a realistic situation for most traits of interest to maize breeders, a much higher marker density is required. NCLB is a serious foliar disease in maize. In order to unravel the genetic architecture of the resistance against this disease, a vast association mapping panel comprising 1 487 European maize inbred lines was used to (i) identify chromosomal regions affecting flowering time (FT) and NCLB resistance, (ii) examine the epistatic interactions of the identified chromosomal regions with the genetic background on an individual molecular marker basis, and (iii) dissect the correlation between NCLB resistance and FT. We observed for FT, a trait for which already various genetic analyses have been performed in maize, a very well interpretable pattern of SNP associations, suggesting that data from practical plant breeding programs can be used to dissect polygenic traits. Furthermore, we described SNPs associated with NCLB and NCLB corrected for FT resistance that are located in genes for which a direct link to the trait is discernable or which are located in bins of the maize genome for which previously QTLs have been reported. Some of the SNPs showed significant epistatic interactions with markers from the genetic background. The observation that the listed SNPs and their epistatic interactions explained in the entire germplasm set about 10% and in some individual heterotic pools up to 30% of the genetic variance suggests that significant progress towards improving the resistance of maize against NCLB by marker-assisted selection is possible with these markers, without much compromising on late flowering time. Furthermore, these regions are interesting for further research to understand the mechanisms of resistance against NCLB and diseases in general, because some of the genes identified have not been annotated so far for these functions.
Phenotypic and genotypic assessment of traits with relevance for hybrid breeding in European winter wheat
(2015) Langer, Simon Martin; Würschum, Tobias
Hybrid breeding in wheat has recently received increased interest, especially in Europe, and large public and private projects investigating hybrid wheat breeding have been launched. Hybrid breeding has been a great success story for allogamous crops and is seen as a promising approach to increase the yield potential in wheat. Wheat covers more of the world’s surface than any other food crop and is the second main staple crop for human consumption. It can be produced under widely varying conditions and is grown all around the globe, yet, yield gain has declined and is lagging behind the needs of the constantly growing human population. Future challenges in wheat breeding such as the establishment of hybrid varieties and the adaptation of breeding germplasm to increasing stresses caused by climatic changes also in Europe require knowledge-based improvements of relevant traits and phenotyping approaches suited for applied high-throughput plant breeding. A major limitation for the establishment and the production of hybrid wheat is the lack of a cost-efficient hybrid seed production system. This requires the generation of parental ideotypes which maximize the cross-fertilization capability. Male parents should have an extended time of flowering, extrude anthers and widely shed large amounts of viable pollen. Females need increased receptivity for male pollen by opening the glumes and extruding stigmatic hair. Furthermore, male plants should be taller than females and a synchronized timing of flowering between the two parents is also of utmost importance. Employing a set of European elite winter wheat lines, we developed and evaluated phenotyping methods for important floral and flowering traits with relevance for improved cross-pollination (Publication I). We observed high heritabilities for important traits such as ‘pollen mass’ (h2=0.72) and ‘anther extrusion’ (h2=0.91). In addition, genotypic variances were significant which warrants further breeding success. Positive correlations were found among important flowering and floral characteristics which enables the improvement of outcrossing by indirect selection. ‘Pollen mass’ for example, was associated with ‘anther extrusion’, ‘anther length’ and ‘plant height’. Our findings suggest the utility of the developed phenotyping approaches for applied plant breeding and the potential of the traits to assist in the design of the male ideotype for increased cross-fertilization. We investigated the genetic architecture of flowering time and plant height (Publication II and III). A panel of 410 European winter wheat varieties was genotyped by a genotyping-by-sequencing approach and in addition, analyzed for the effects of specific candidate genes. The major factor affecting flowering time was the photoperiod regulator Ppd-D1 (58.2% of explained genotypic variance) followed by Ppd-B1 copy number variation (3.2%). For plant height, the two candidate loci Rht-D1 (37.0%) and Rht-B1 (14.0%) had the largest effects on the trait but contrary to reports in the literature did not contribute to flowering time control. In addition, we identified several small effect QTL and epistatic QTL responsible for fine-adjustments of these two traits. Population structure and genetic relatedness in European elite wheat lines was assessed using different types of markers (Publication IV). Results for relatedness differed for the marker types but consistently showed the absence of a major population structure. Regarding the large wheat genome our results revealed that a high number of markers is necessary as there are regions with only low coverage. Concordantly, we were not able to identify the major flowering locus Ppd-D1 without targeted candidate gene analysis. Observations on the findings on population structure could be confirmed in Publication II and III and in addition, the geographical distribution of important flowering time and plant height genes displayed the historical development of wheat breeding in Europe. This information on genetic relatedness among lines can also be employed to assist the establishment of hybrid wheat.