Browsing by Subject "Landrassen"

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Assessing the genetic variation of phosphate efficiency in European maize (Zea mays L.)
(2022) Weiß, Thea Mi; Würschum, Tobias
Why should plant breeders in Central Europe care about phosphate efficiency? Soil phosphorus levels have mostly reached high to very high levels over the last decades in intensively farmed, livestock-rich regions. However, the European Union demands a restructuring of the agricultural production systems through setting ambitious goals envisaged in the Farm to Fork Strategy. By 2030, fertilizer use should be reduced by 20 %, nutrient losses by at least 50 %. As a consequence, farmers have to be even more efficient with crop inputs, among them the globally limited resource of phosphorus fertilizers, while maintaining high yields. Plant breeding means thinking ahead. Therefore, phosphate-efficient varieties should be developed to help farmers meet this challenge and reduce the need for additional fertilizers. One prerequisite to reach this target is that genotypic variation for the relevant traits is available. Moreover, approaches that assist selection by accurate but also time- and resource-efficient prediction of genotypes are highly valuable in breeding. Finally, the choice of the selection environment and suitable trait assessment for the improvement of phosphate efficiency under well-supplied conditions, need to be elaborated. In this dissertation, a diverse set of maize genotypes from ancient landraces to modern hybrids was investigated for phosphate efficiency-related traits under well-supplied P soil conditions. Multi-environmental field trials were conducted in 2019 and 2020. The reaction to different starter fertilizer treatments of the 20 commercially most important maize hybrids grown in Germany was studied. In the hybrid trial, the factor environment had a significant effect on the impact of starter fertilizers. Especially in early developmental stages genotypes showed a different response to the application of starter fertilizers. On the overall very well-supplied soils, we observed no significant genotype-by-starter fertilizer interaction. Nonetheless, we identified hybrids, which maintained high yields also if no starter fertilizer was provided. Thus, it seems that sufficient variation is available to select and breed for phosphate efficiency under reduced fertilizer conditions. Furthermore, the concept of phenomic prediction, based on near-infrared spectra instead of marker data to predict the performance of genotypes, was applied to 400 diverse lines of maize and compared to genomic prediction. For this, we used seed-based near-infrared spectroscopy data to perform phenomic selection in our line material, which comprised doubled haploid lines from landraces and elite lines. We observed that phenomic prediction generally performed comparable to genomic prediction or even better. In particular, the phenomic selection approach holds great potential for predictions among different groups of breeding material as it is less prone to artifacts resulting from population structure. Phenomic selection is therefore deemed a useful and cost-efficient tool to predict complex traits, including phosphorus concentration and grain yield, which together form the basis to determine phosphate efficiency. Lastly, 20 different indicators for phosphate efficiency were calculated, the genetic variation of the different measures present in this unique set of lines was quantified, and recommendations for breeding were derived. Of the different measures for phosphate efficiency reported in literature, Flint landraces demonstrated valuable allelic diversity with regard to phosphate efficiency during the seedling stage. Due to the highly complex genetic architecture of phosphate efficiency-related traits, a combination of genomic and phenotypic selection appears best suited for their improvement in breeding. Taken together, phosphate efficiency, including its definition and meaning, is largely dependent on the available phosphorus in the target environment as well as the farm type, which specifies the harvested produce and thereby the entire phosphorus removal from the field. In conclusion, future maize breeding should work in environments that are similar to the future target environments, meaning reduced fertilizer inputs and eventually lower soil P levels. Our results demonstrate that breeding of varieties, which perform well without starter fertilizers is feasible and meaningful under the well-supplied conditions prevalent in Central Europe. For the improvement of the highly complex trait phosphate efficiency through breeding we recommend to apply genomic and phenomic prediction along with classical phenotypic screening of genotypes and by this making our food systems more resilient towards upcoming challenges in agriculture.
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.
Utilization of landraces of European flint maize for breeding and genetic research
(2023) Renner, Juliane; Melchinger, Albrecht E.
Mais ist eine der wichtigsten Kulturarten für die Landwirtschaft weltweit. Seit seiner Domestikation bildeten Landrassen den traditionellen Sortentyp. Durch Selektion und genetische Faktoren entstand eine breite Diversität an panmiktisch vermehrten Populationen, die gut an lokale Bedingungen angepasst waren. Dies änderte sich mit der Einführung der Hybridzüchtung, als nahezu alle Landrassen in der landwirtschaftlichen Produktion und als Ausgangsmaterial für die Züchtung verschwanden. Molekulare Analysen zeigen eine enge genetische Basis des Flint Pools im Vergleich zum Dent Pool. Genetische Ressourcen im Mais gehören zu den umfangreichsten aller Nutzpflanzen. Die Nutzung dieses bislang ungenutzten Reservoirs an genetischer Diversität in Landrassen bietet eine Möglichkeit, um der fortschreitenden Einengung der genetischen Basis entgegenzuwirken und somit den Aufgaben der Pflanzenzüchtung im Hinblick auf eine wachsende Weltbevölkerung sowie den Herausforderungen des Klimawandels und reduzierten Inputs im Anbau gerecht zu werden. Übergeordnetes Ziel dieser Studie war die Evaluierung europäischer Flint-Mais Landrassen, um deren genetische Vielfalt nutzen zu können. Im Speziellen waren die Ziele (i) die Variation in Testkreuzungen europäischer Mais-Landrassen zu bestimmen; (ii) die phänotypische und genotypische Variation der Linien innerhalb und zwischen Landrassen zu beurteilen; (iii) die Eigenleistung dieser Linien mit Elite-Linien sowie Founder-Linien aus dem europäischen Flint-Pool zu vergleichen; (iv) das Potential von doppelhaploiden (DH) Linien aus Landrassen im Vergleich zum Elitematerial für die Züchtung zu analysieren, um die enge genetische Basis des Flint-Pools zu erweitern; (v) die Verwendung von DH-Bibliotheken aus Landrassen für die Assoziationskartierung bis hin zur Eingrenzung kausaler Gene zu demonstrieren; und (vi) Schlussfolgerungen und Leitlinien für die Züchtung und Forschung zu erörtern , um DH-Linien aus Landrassen nutzbar zu machen. In einem ersten Versuch wurde eine umfangreiche Kollektion von 70 europäischen Flint-Landrassen mehrortig in Kombination mit zwei Elite Dent-Testern auf ihre Testkreuzungsleistung hin untersucht. Verglichen mit dem Ertrag moderner Hybriden war der Kornertrag der Testkreuzungen der Landrassen im Durchschnitt um 26 % geringer, jedoch wurde eine hohe genotypische Varianz zwischen den Landrassen für alle Merkmale beobachtet. Die Korrelationen waren mittel bis hoch für die meisten Merkmalskombinationen und entsprachen denen im Elitezuchtmaterial. Die genetische Korrelation der beiden Testkreuzungsserien überstieg 0,74 für alle Merkmale. Dies zeigt, dass es ausreicht die Leistung von Testkreuzungen in Kombination mit einem oder zwei Testern - bestehend aus Einfachkreuzungen des anderen Gen-Pools – zu bewerten, um das Potenzial von Landrassen für die Züchtung zu beurteilen. In einem zweiten Versuch produzierten wir Bibliotheken von DH-Linien der vielversprechendsten Landrassen des vorigen Versuches. Insgesamt wurden 389 DH-Linien aus sechs europäischer Flint Landrassen zusammen mit vier Flint Founder-Linien und 53 Elite Flintlinien auf 16 agronomische Merkmale an vier Standorten geprüft. Die genotypische Varianz (σ^2G) innerhalb der DH-Bibliotheken war größer als die zwischen den Bibliotheken und übertraf auch σ^2G der Elite Flintlinien. Darüber hinaus variierten die Mittelwerte und σ^2G zwischen den DH-Bibliotheken, was zu großen Unterschieden im Brauchbarkeits-Kriterium („usefulness“) führte. Der mittlere Kornertrag der Elite Flintlinien übertraf den der Flint Founder-Linien um 25 % und der DH-Bibliotheken um 62 %, was auf den beträchtlichen Zuchtfortschritt im Elitematerial hinweist sowie auf die erhebliche genetische Bürde, welche in den DH-Bibliotheken vorliegt. Die Brauchbarkeit der besten DH-Linien war trotzdem für viele Merkmale, einschließlich dem Kornertrag, mit der von Elite Flintlinien vergleichbar. Dies zeigt das enorme Potenzial, Landrassen zur Verbreiterung des genetisch engen Elite Flint-Pools zu verwenden. In einem dritten Versuch wurden das genetische Material des vorherigen Versuches mit dem MaizeSNP50 BeadChip von Illumina® genotypisiert und Samen aller Genotypen zur Extraktion und Analyse von 288 Metaboliten mit GC-MS verwendet. Sowohl die agronomischen Merkmale als auch die Metabolit-Daten wurden für eine Assoziationskartierung verwendet. Der schnelle Abfall des Kopplungsungleichgewichts benachbarter Marker in den DH-Bibliotheken im Vergleich zu den Elite Flintlinien führte zu einer hervorragenden Auflösung in der QTL-Kartierung, was durch die Feinkartierung eines QTL (= quantitative trait locus) für Ölgehalt bis zur Phenylalanin Insertion F469 in DGAT1-2 als kausale Variante demonstriert werden konnte. Darüber hinaus wurden für den Metaboliten Allantoin, der im Zusammenhang mit abiotischem Stress steht, Promotorpolymorphismen sowie die Expression einer Allantoinase als vermutete Ursache der Variation identifiziert. Dies gelang trotz der moderaten Größe der Kartierungspopulation. Diese Ergebnisse sind ermutigend, um DH-Bibliotheken von Landrassen für die Assoziationskartierung zu verwenden und QTL bis auf die kausalen Varianten zu entschlüsseln. Eine Erweiterung der Populationsgrößen der DH-Bibliotheken, ähnlich wie sie in anderen Versuchsdesigns in der Literatur verwendet wurden, ist hierbei zu empfehlen, um mit diesem Ansatz QTL zu detektieren, welche lediglich einen kleinen Teil der genetischen Varianz erklären. Dies eröffnet neue Wege zur Nutzung natürlicher und/oder neu geschaffener Allele in der Züchtung. Zusammenfassend zeigen die Ergebnisse dieser Arbeit, dass die genetische Variation europäischer Landrassen bei Flint-Mais eine einzigartige Quelle darstellt, um die fortschreitende Verengung der genetischen Basis des Elitematerials in diesem Gen-Pool umzukehren. Um vielversprechende Landrassen zu identifizieren, schlagen wir folgenden zweistufigen Ansatz vor: (i) Basierend auf der Bewertung der molekularen Diversität werden etwa hundert Landrassen in Leistungsprüfungen auf ihre Anpassungsfähigkeit für die Zielregionen evaluiert und ihre Kombinationsfähigkeit mit dem entgegengesetzten heterotischen Gen-Pool in Testkreuzungen mit einer Einfachkreuzung als Tester bewertet. (ii) Für eine geringe Zahl (< 6) von Landrassen wird anschließend eine große Anzahl von DH-Linien erstellt, welche für die Nutzung in der Assoziationskartierung und/oder genomischen Selektion phänotypisiert und genotypisiert werden, um diese „Goldreserven“ für die Maiszüchtung mit innovativen Methoden zugänglich zu machen.