Browsing by Subject "Disease resistance"

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Capturing wheat phenotypes at the genome level
(2022) Hussain, Babar; Akpınar, Bala A.; Alaux, Michael; Algharib, Ahmed M.; Sehgal, Deepmala; Ali, Zulfiqar; Aradottir, Gudbjorg I.; Batley, Jacqueline; Bellec, Arnaud; Bentley, Alison R.; Cagirici, Halise B.; Cattivelli, Luigi; Choulet, Fred; Cockram, James; Desiderio, Francesca; Devaux, Pierre; Dogramaci, Munevver; Dorado, Gabriel; Dreisigacker, Susanne; Edwards, David; El-Hassouni, Khaoula; Eversole, Kellye; Fahima, Tzion; Figueroa, Melania; Gálvez, Sergio; Gill, Kulvinder S.; Govta, Liubov; Gul, Alvina; Hensel, Goetz; Hernandez, Pilar; Crespo-Herrera, Leonardo Abdiel; Ibrahim, Amir; Kilian, Benjamin; Korzun, Viktor; Krugman, Tamar; Li, Yinghui; Liu, Shuyu; Mahmoud, Amer F.; Morgounov, Alexey; Muslu, Tugdem; Naseer, Faiza; Ordon, Frank; Paux, Etienne; Perovic, Dragan; Reddy, Gadi V. P.; Reif, Jochen Christoph; Reynolds, Matthew; Roychowdhury, Rajib; Rudd, Jackie; Sen, Taner Z.; Sukumaran, Sivakumar; Ozdemir, Bahar Sogutmaz; Tiwari, Vijay Kumar; Ullah, Naimat; Unver, Turgay; Yazar, Selami; Appels, Rudi; Budak, Hikmet
Recent technological advances in next-generation sequencing (NGS) technologies have dramatically reduced the cost of DNA sequencing, allowing species with large and complex genomes to be sequenced. Although bread wheat (Triticum aestivum L.) is one of the world’s most important food crops, efficient exploitation of molecular marker-assisted breeding approaches has lagged behind that achieved in other crop species, due to its large polyploid genome. However, an international public–private effort spanning 9 years reported over 65% draft genome of bread wheat in 2014, and finally, after more than a decade culminated in the release of a gold-standard, fully annotated reference wheat-genome assembly in 2018. Shortly thereafter, in 2020, the genome of assemblies of additional 15 global wheat accessions was released. As a result, wheat has now entered into the pan-genomic era, where basic resources can be efficiently exploited. Wheat genotyping with a few hundred markers has been replaced by genotyping arrays, capable of characterizing hundreds of wheat lines, using thousands of markers, providing fast, relatively inexpensive, and reliable data for exploitation in wheat breeding. These advances have opened up new opportunities for marker-assisted selection (MAS) and genomic selection (GS) in wheat. Herein, we review the advances and perspectives in wheat genetics and genomics, with a focus on key traits, including grain yield, yield-related traits, end-use quality, and resistance to biotic and abiotic stresses. We also focus on reported candidate genes cloned and linked to traits of interest. Furthermore, we report on the improvement in the aforementioned quantitative traits, through the use of (i) clustered regularly interspaced short-palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9)-mediated gene-editing and (ii) positional cloning methods, and of genomic selection. Finally, we examine the utilization of genomics for the next-generation wheat breeding, providing a practical example of using in silico bioinformatics tools that are based on the wheat reference-genome sequence.
Der Einfluss von Wirtsfaktoren der Honigbiene (Apis mellifera L.) auf den Reproduktionserfolg der parasitischen Milbe Varroa destructor (Anderson & Trueman) auf die Auswirkungen einer horizontalen Verbreitung des Parasiten auf den Befall der Bienenvölker
(2014) Frey, Eva; Bessei, Werner
The honey bee colony is faced with a huge number of pathogens, including bee viruses, bacteria, fungi and mites. Among these pathogens, the ectoparasitic mite Varroa destructor is considered the most important parasite of the honey bee worldwide. This mite was discovered at the beginning of the last century in South East Asia within colonies of the original host, the Eastern honey bee Apis cerana. From the middle of the last century the mite has been spread worldwide by transports of infested A. mellifera colonies with dramatic consequences for both, feral and managed honey bee colonies. In the meantime this parasite has become the most serious economic problem for global beekeeping. In temperate climates nearly all honey bee colonies are infested and without yearly Varroa treatments these colonies would collapse within a few years. This confirms that a stable host parasite relationship has not been established yet. Therefore the control of V. destructor still represents the main challenge for beekeeping. The main reason for host damages is the dramatic increase of the Varroa population during the season. Our honey bee colonies are obviously unable to control this population dynamic of the parasite. The increase of the mite population is influenced by the reproductive rate of Varroa females within individual brood cells, by host-parasite-interactions on the colony level and by interactions among honey bee colonies on the population level. The dissertation at hand presents experimental approaches and results at all three levels. On the individual level we were able to demonstrate that age-dependent signals of the honey bee larvae not only activate the oogenesis of the Varroa females but even trigger the further course of mite reproduction. Our studies on the activation of the Varroa reproduction revealed that exclusively larvae within 18 h (worker) and 36 h (drones), respectively, after cell capping were able to stimulate the mite’s oogenesis. Furthermore, we were able to confirm for the first time the presence of a signal in the host larvae allowing the reproducing mites to adjust their own reproductive cycle to the ontogenetic development of the host. Under certain conditions such host signals can even stop an oogenesis of the female mite that has already been started. From an adaptive point of view that sort of a stop signal enables the female mite to save resources for a next reproductive cycle if the own egg development is not sufficiently synchronized with the development of the host. My results indicate that age specific volatiles of the larval cuticle are involved in the regulation of mite reproduction. According to preliminary quantitative GC–MS analysis we suggest certain fatty acid ethyl esters as candidate compounds. These host signals – either involved in the activation or in the interruption of the Varroa reproduction – offer possibilities to influence the reproductive success of Varroa females and might therefore be used for biological control in the future. Within an EU cooperation project we could additionally demonstrate that the so called temporary infertility of Varroa females is significantly correlated with three QTL of the host larvae. This confirms a genetic basis for host resistance factors that inhibit the mite reproduction. For this study we made use of the fact that we had access to a honey bee population at the island of Gotland, Sweden that has survived mite infestation without any treatment for more than 10 years. We crossed a queen from this tolerant population with drones from susceptible colonies to rear hybrid queens and produced a mapping population of haploid drones from these hybrids. Because honey bees have a haplodiploid sex determination, the haploid drones provide an extremely simple and highly efficient model system for genetic studies. Subsequently, we mapped three candidate target regions on chromosomes 4, 7, and 9. Although the individual effect of these three QTL was found to be relatively small, the set of all three had significant impact on the suppression of V. destructor reproduction by epistasis. The detection of this epistatic interaction was only possible because we used the simple genetic make-up of haploid drones. For studies on Varroa resistance on the colony level and for selection programs the interactions among the colonies of the local honey bee population have to be considered. In two experimental approaches I was able to prove that the invasion of Varroa mites from neighboring colonies – often called “reinvasion” – significantly influences the population dynamic of the parasite within the colony. First, we quantified the number of mites invading individual colonies in relation to the invasion pressure (= number and distance of infested colonies). For this approach we made use of an isolated military training area near Münsingen at the Swabian Alb not accessible to other beekeepers. We established ten “mite receiver colonies” continuously treated against V. destructor and placed them at distances of 1m to 1.5 km from four heavily infested “mite donor colonies”. In the donor colonies, we estimated the population of bees, brood, and V. destructor at three week intervals. The invasion of mites into the receiver colonies was recorded every 7-12 days. During the measurement period of about two months, between 85 and 444 mites per colony were introduced into the receiver colonies. Surprisingly, there were no significant differences in the invasion rates in relation to the distance between donor and receiver colonies. The second approach was performed under more realistic field conditions of two experimental apiaries established in regions with high and low bee densities, respectively. Additionally, in this experiment we analyzed the multiplication of the invaded mites. Thereby we confirmed that horizontal transmission plus the reproduction of the invaded Varroa mites can cause an exponential increase of the mite population that may exceed the damage threshold within three months. We were further able to show that the invasion rates – and therefore the final infestation – differ significantly according to the number of honey bee colonies in the neighborhood of the apiary: At the site with a high bee density, the average invasion rate per colony over the entire three and a half months period was 462 mites per colony compared to only 126 mites per colony at the site with a low bee density. As a consequence, the colonies of the apiary at the high bee density site revealed an average final infestation in November of 2,082 mites per colony compared to 340 mites per colony at the low bee density site. The highly infested colonies lost about three times more bees compared to the lower infested colonies – obviously a result of Virus infections transmitted by Varroa mites. With my different approaches I was able to add further elements of knowledge for a better understanding of how host factors and ambient conditions influence the Varroa reproduction within individual brood cells and the population dynamic within a honey bee colony. A better knowledge of these host parasite interactions is essential for the selection of mite resistant colonies and further more important for the development of concepts for an effective Varroa treatment.
Resistance gene analogues as a tool for basic and applied resistance genetics exemplified by sugarcane mosaic virus resistance in maize (Zea mays L.)
(2003) Quint, Marcel; Melchinger, Albrecht E.
With the recent cloning of a number of plant disease resistance genes (R genes) it became apparent that R genes share certain homologies in conserved amino acid domains. PCR amplification of genomic DNA using degenerate primers on the basis of these conserved amino acid domains identified sequences with homologies to plant disease R genes - resistance gene analogues (RGAs). RGAs exist in large numbers in plant genomes and provide new possibilities for the investigation of resistance genetics in general and also for the analysis of certain plant disease resistances. The overall objective of this thesis was to evaluate the use of RGAs for plant breeding for the example of sugarcane mosaic virus (SCMV) resistance in maize. SCMV is one of the most important virus diseases of maize and causes serious yield losses in susceptible cultivars. Owing to the non-persistent manner of transmission, control of aphid vectors by chemical means is not effective and therefore, cultivation of resistant maize varieties is the most efficient method of virus control. Previous studies on the inheritance of oligogenic SCMV resistance located two major quantitative trait loci (QTLs) - Scmv1 and Scmv2 - on chromosomes 6S and 3L, respectively. The objectives of this study were to (1) give an overview on the current status of breeding for virus resistance in maize, (2) identify and genetically map candidate genes for Scmv1 and Scmv2, (3) use potential sequence homologies of linked RGAs for targeted increase of the number of candidate genes in the target regions, (4) convert closely linked amplified fragment length polymorphism (AFLP) markers into codominant, simple PCR-based markers as a tool for marker-assisted selection (MAS) and map-based cloning, (5) evaluate RGAs for the development of molecular markers, MAS, and map-based cloning, and (6) investigate the consequences of duplicate markers for the construction of linkage maps and their implications for MAS and map-based cloning. Three previously published RGAs, pic13, pic21, and pic19 were cloned from six maize inbred lines, converted to cleaved amplified polymorphic sequence (CAPS) markers, and mapped in relation to SCMV R genes (Scmv1, Scmv2) in maize. Pairwise sequence alignments among the six inbreds revealed a frequency of one single nucleotide polymorphism (SNP) per 33 bp for the three RGAs, indicating a high degree of polymorphism and a high probability of success in converting RGAs into codominant CAPS markers compared to other sequences. Therefore, RGAs meet important requirements for the development of molecular markers, i.e., a high degree of polymorphism and availability in great numbers throughout the genome. In contrast to this, the degree of polymorphism for AFLPs closely linked to Scmv1 an Scmv2 was significantly lower in the same six inbred lines compared to RGAs. Only two of eight AFLP markers could be converted into one CAPS and one indel (insertion/deletion) marker. By genetic mapping, pic21 was shown to be different from Scmv2, whereas pic19 and pic13 could be mapped as single-copy markers to the target regions and are candidates for Scmv1 and Scmv2, respectively, due to genetic mapping and consistent restriction patterns of ancestral lines. Subsequently, pic19 was used as candidate for Scmv1 to screen a maize BAC library to identify homologous sequences in the maize genome and to investigate their genomic organisation. Fifteen positive BAC clones were identified and classified into five physically independent contigs consisting of overlapping clones. Genetic mapping clustered three contigs into the same genomic region as Scmv1 on chromosome 6S. The two remaining contigs mapped to the same region as a QTL for SCMV resistance on chromosome 1. Thus, RGAs mapping to a target region can be successfully used to identify further linked candidate sequences. The pic19 homologous sequences of these clones revealed a sequence similarity of 94-98% at the nucleotide level. The high sequence similarity and the multi-locus character of the previously single-copy mapped RGA pic19 show potential problems for the use of RGAs as molecular markers. The existence of ghost markers analogous to ghost QTL was suggested to be a result of simultaneous mapping of several homologous gene family members which cannot be distinguished at the level of PCR. The idea of ghost loci derived by potentially duplicated sequences such as expressed sequence tags (ESTs), AFLPs, or simple sequence repeats (SSRs) was the subject of a theoretical and computer simulation study. Simultaneous amplification of homologous sequences results in an excess of heterozygotes causing distorted segregation ratios. We were able to theoretically prove the existence of such ghost markers resulting in changes of the correct marker orders. If these fictive ghost markers are part of a genetic map which is the subject of MAS or map-based cloning this may have fatal effects like locating a target gene into an incorrect marker interval. This incorrect locus order caused by duplicate marker loci can negatively affect the assignment of target genes to chromosome regions in a map-based cloning experiment, hinder indirect selection for a favourable allele at a QTL, and decrease the efficiency of reducing the chromosome segment attached to the target gene in marker-assisted backcrossing. In conclusion, this thesis demonstrates the use of RGAs for plant breeding and resistance genetics in general. RGAs provide a good source for the development of simple PCR-based markers. Furthermore, RGAs are an excellent tool for MAS, the identification of candidate genes and effective increase of such candidates in target regions using sequence homologies between RGAs. The duplicate nature of RGAs revealed potential problems for genetic mapping of potentially duplicated sequences which are widespread in eukaryote genomes and existent for several types of molecular markers. For resistance genetics in general, investigation of RGAs is important for the understanding of R gene organisation and evolutionary genetics of plant disease resistance.