Browsing by Subject "Mikrosatelliten"

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Genetic diversity in elite lines and landraces of CIMMYT spring bread wheat and hybrid performance of crosses among elite germplasm
(2005) Dreisigacker, Susanne; Melchinger, Albrecht E.
Wheat (Triticum aestivum) is one of the major cereals in the world. During the past years, the world consumption of wheat increased up to nearly 600 million tones, whereas wheat production continuously decreased. Due to land limitations, new production gains must be achieved from improved plant management systems as well as from the development of high yielding varieties. The International Maize and Wheat Improvement Center (CIMMYT) employs different strategies to enhance yield potential in wheat especially for developing countries. For instance, the wheat breeding program focuses on defined mega-environments (MEs), assuming similar growing conditions in certain countries. In the search for useful alleles, breeders often turn back to wild relatives of wheat stored in the CIMMYT gene bank. With the production of synthetic hexaploid bread wheat (SHWs), characteristics from T. durum and T. tauschii can be combined and via backcrossing incorporated into modern breeding materials. Wheat landraces (LCs) are an additional reservoir of resistances to pests and diseases as well as for environmental adaptation. The production of wheat hybrids is seen as a further option to improve yield potential. A considerable amount of genetic diversity among the materials is a prerequisite for all strategies. Due to the worldwide importance of CIMMYT wheat varieties, they represent a suitable source to examine different breeding strategies in wheat. The main objective of our research was to determine the genetic diversity in modern wheat breeding materials and genetic resources at CIMMYT. Specific research questions were: (i) Is the systematic breeding targeted for different MEs reflected in the genetic diversity among breeding lines (Experiment 1)? (ii) Does the production of SHWs (Experiment 2) and the use of LCs (Experiment 3) enhance the genetic variation in modern breeding materials? (iii) Does the development of hybrids represent an option to improve yield potential in wheat? (iv) Is it possible to predict levels of heterosis with the determination of genetic distance (GD) among hybrid parents? (v) Do genomic and EST- derived SSRs differ in the measurement of genetic diversity (Experiments 1 and 3)? (vi) Are GD values based on SSRs correlated with the coefficient of parentage (COP) (Experiments 1 to 4)? In Experiment 1, a total of 68 CIMMYT advanced breeding lines was analyzed with 99 SSRs, of which 51 were EST- and 46 genomic derived SSRs. A high level of genetic diversity (GD = 0.41) was observed among the breeding lines. The majority of variation (91%) was detected among lines targeted to one specific ME, which indicates a broad genetic base of the current CIMMYT breeding materials. Principal coordinate analysis (PCoA) could clearly separate the lines, but they clustered independently from their target MEs. Main explanations are: (i) alleles were selected that provide fitness to several MEs, (ii) adaptation depends only on a small number of genes that were not detected with the SSRs applied, or (iii) too few cycles of selection were considered to separate the germplasm. In Experiment 2, a total of 11 SHWs, 7 recurrent parent lines, and 13 families of backcross-derived lines (SBLs) were analyzed with 90 SSRs. The SHWs clustered far from the SBLs and the recurrent parents in the cluster analyses and PCoA, and formed a distinct germplasm pool with high allelic variation. Two families of SBLs were tested for a selective advantage of the SHW alleles. Six SSRs revealed non-Mendelian inheritance, indicating that the genomic region of SHWs was actively selected for. Thus, the production of SHWs provides a promising approach for the enhancement of genetic variation in modern breeding materials. In Experiment 3, gene bank accessions of 36 LCs from different countries and a total of 119 accessions from nine LCs populations collected in Turkey and Mexico were analysed with 44 and 76 SSRs, respectively. Both LC materials revealed high allelic variation (GD = 0.69 and 0.54). The 36 LC accessions could not be separated according to their continent of origin. An unexpected relationship was observed between the Chilean LC ?Trigo africano? and the Nigerian LCs ?Dikwa?. All of the nine LC populations could be discriminated except for two Turkish LCs collected from the same location. In accordance with previous studies, considerable genetic variation was observed within the LC populations. Our results contributed a lot to the characterisation of the LCs and generated important knowledge for the management of seed bank accessions. In Experiment 4, a total of 112 wheat hybrids and their 22 parental lines were evaluated at two locations in Mexico for grain yield, plant height, days to flowering and maturity. The level of heterosis varied between -15.3% and 14.1%, but was generally too low to compensate for the high costs of hybrid seed production. The correlations between mid-parent values and hybrid performance, as well as between parental line per se performance and general combining ability were significant (P < 0.01) for all traits, and particularly high for grain yield (r = 0.86 and 0.91). PCoA based on 113 SSR markers revealed three groups of parents. However, the correlations of GDs and COPs with the values of heterosis were negative and not significant. Thus, the prospects of large-scale cultivation of hybrid wheat in developing countries are low. The correlations between GDs and COP in Experiments 1 and 3 were generally significant but low. This can be explained by unrealistic assumptions in the calculation of COPs, which ignore the effects of selection and genetic drift. Similarly to genomic SSRs, EST-SSRs did not reflect functional diversity. The latter revealed lower degrees of polymorphism than genomic SSRs in all experiments, but the allele designation was simpler and more reliable. Across all experiments, our study demonstrates that plant breeding does not inevitably lead to a loss of genetic diversity. We confirmed that CIMMYT?s breeding strategies contributed to a successful increase in genetic variation. These results provide useful information to wheat breeders in CIMMYT and other national programs, regarding the use of wild relatives and landraces for the enhancement of the genetic base of wheat germplasm. In addition, our research provides a base of knowledge for future association studies, identification of useful alleles, and their use in marker-assisted selection.
Molecular genetic analysis of modified recurrent full-sib selection in two European F 2 flint maize populations
(2007) Falke, Karen Christin; Melchinger, Albrecht E.
The continuous improvement of breeding material is a main goal in plant breeding. However, many breeding methods result in a reduction of the genetic variation of the breeding material. The primary objective of recurrent selection (RS) methods is to assure a long-term selection response for the target traits while maintaining the genetic variability of the germplasm for continued selection. The main goal of this thesis research was the molecular evaluation of two European F2 flint maize populations under modified recurrent full-sib selection. In detail, the objectives were to (1) investigate linkage mapping with intermating populations, (2) verify the decay of parental linkage disequilibrium (LD) present in the F2 base population through three generations of intermating, (3) identify quantitative trait loci (QTL) of traits under selection, (4) separate the effects of random genetic drift and selection on allele frequency changes during the selection procedure in QTL regions, (5) determine the extent of LD build-up by selection, and (6) analyze the effects of LD on the selection response. Four homozygous inbred lines (A, B, C, and D) were crossed to developed 380 F2:3 lines of population A × B and 140 F3:4 lines of population C × D. The F2 generations of both populations were intermated for three generations by chain crossing to produce F2Syn3 populations. Starting from the F2Syn3 populations, four (A × B) and seven (C × D) cycles of modified recurrent full-sib selection were conducted using a pseudo-factorial mating design. The selection procedure was based on a selection index. For the marker assays, a total of 104 (A × B) and 101 (C × D) SSRs were employed to genotype random subsets of 146 F2:3 lines in A × B and 110 F3:4 lines C × D, 148 F2Syn3 plants and the parents of the 36 selected full-sib families in each cycle of both RS programs. Genetic linkage maps were constructed for population F2:3 (A × B) and F3:4 (C × D) and of both intermated populations F2Syn3. In contrast to earlier studies, mapping methods developed specifically for intermated populations were applied and, thus, the estimated recombination frequencies referred to a single meiosis. Consequently, the map expansion reported in earlier studies was neither expected nor observed. To verify the expected higher mapping resolution of intermated compared with the respective base population, the precision of estimates of the recombination frequencies r was quantified with the average information per individual ir relative to an F2 individual. For infinite population sizes of intermated populations ir > 1 when r < 0.142, however, with a population size of N = 240, as used in our mapping study, ir >1 only when r < 0.04. Therefore, we conclude that random genetic drift has a sizeable effect on ir and, thus, can overrule the advantages of intermating mapping populations. Three generations of intermating were primarily conducted to reduce the initial parental LD between linked loci in the F2 populations and its negative influence on the selection response. Our results demonstrated that the observed decay of LD agreed well with the theoretical expectations. In our modified recurrent full-sib selection program, a comparatively high selection response was reached. An evaluation at the molecular level revealed that further selection response can be expected, because neither fixation nor extinction of alleles was observed at the investigated marker loci. However, using SSR markers we also detected migration effects since the first selection cycles. Selection and random genetic drift are main forces affecting changes in allele frequencies and, therefore, the selection response of RS programs. In our study, we analyzed changes in allele frequencies employing a test that allows the separation of selection and random genetic drift. Significant allele frequency changes due to selection were observed for 23% (C0 vs. C1) and 20% (C0 vs. C4) of all loci in population A × B and for 6% (C0 vs. C1) and 13% (C0 vs. C7) in population C × D. In the base populations F2:3 (A × B) and F3:4 (C × D), several QTL for selection index and its components were detected. At some of them, loci displayed significant allele frequency changes due to selection. Selection is expected to increase the frequency of favorable alleles and simultaneously build up a negative LD between them, which causes a reduction in and, hence, a decline in the selection response. However, the development of LD in our study displayed an erratic change over the selection cycles with only slight increases in positive and negative LD. The reduction in due to a build-up of negative LD is expected only if negative LD is observed at many marker loci. Therefore, we concluded that LD due to selection did not limit the selection response in our RS programs.
Untersuchung der Informativität neuer Mikrosatellitenloci beim Kamel
(2001) Evdotchenko, Dmitri; Geldermann, Hermann
The goal of the investigations was it to use new primers for the representation of polymorphic microsatellite loci in different camel species and to examine new microsatellite loci for Informativity. Some polymorphic loci should be used for the investigation of the genetic differentiation of different dromedary races from Kenya and a bactrian race from Sibiria. For the investigations samples from two species of the old world camels (Camelus bactrianus and Camelus dromedarius) and two species of the new world camels (Llama pacos and Llama glama) were available. As DNA source full blood or leukocyte was used. The representation of the microsatellite loci was carried out with the help of the PCR and following fragment length analysis by means of an automated DNA-Sequencer (A.L.F.). The number of the alleles, their fragment lengths as well as the frequencies of allels and genotypes were computed per locus and taken as original data for estimation of invormativeness. Primer pairs for 34 sequenced loci were tested. 25 of this loci showed specific PCR amplifications with bactrian and dromedary and were therefore included into the further investigations. For instance one third of the loci were found as monomorph, the remaining loci were polymorph. 9 from 17 polymorphic loci showed more than ten alleles in all examined species. The genetic distances between the examined species, computed by means of new microsatellite loci, refer to clear differences between old and new world camels. With the investigations of some dromedary races from Kenya it was shown that the genetic distances estimated on the basis the new marker loci correlated with geographical distances between the races. The investigations supplied thus new informative markers for different genetic analysis in camel. The markers could be also important for the camel breeding (e.g. parentage testing).