Resistance Breeding in Apple at Dresden-Pillnitz

Resistance breeding in apple has a long tradition at the Institute of Fruit Breeding now Julius Kuehn-institute in Dresden-Pillnitz. The breeding was aimed at the production of multiple resistance cultivars to allow a more sustainable and environmentally friendly production of apple. In the last decades a series of resistant cultivars (Re®-cultivars) bred in Dresden-Pillnitz has been released, ‘Recolor’ and ‘Rekarda’ in 2006. The main topic in the resistance breeding programme was scab resistance and the donor of scab resistance in most cultivars was Malus x floribunda 821. Due to the development of strains that are able to overcome resistance genes inherited by M. x floribunda 821 and due to the fact that single resistance genes can be broken easily, pyramiding of resistance genes is necessary. Besides scab, fire blight and powdery mildew are the main disease for which a pyramiding of genes is aspired in Pillnitz. Biotechnical approaches are necessary for the early detection of pyramided resistance genes in breeding clones. This paper will give an overview of the resistance breeding of apple in Pillnitz and the methods used

Strawberry breeding for disease resistance in Dresden

Verticillium resistance is one of the most important breeding goals in strawberry resistance breeding at Dresden-Pillnitz. Resistance evaluation of cultivars, advanced selections and seedlings is realized under natural conditions at a provocation field and by artificial inoculation in the greenhouse. Introgression of Fragaria chiloensis L. (Miller) into Fragaria ×ananassa Duch. resulted in highly tolerant breeding selections. After back-crossing with cultivars of F. ×ananassa first genotypes were selected which can be evaluated in experimental cultivar trials at different locations in Germany

Genomic prediction and quantitative trait locus discovery in a cassava training population constructed from multiple breeding stages

Open Access Article; Published online: 11 Dec 2019Assembly of a training population (TP) is an important component of effective genomic selection‐based breeding programs. In this study, we examined the power of diverse germplasm assembled from two cassava (Manihot esculenta Crantz) breeding programs in Tanzania at different breeding stages to predict traits and discover quantitative trait loci (QTL). This is the first genomic selection and genome‐wide association study (GWAS) on Tanzanian cassava data. We detected QTL associated with cassava mosaic disease (CMD) resistance on chromosomes 12 and 16; QTL conferring resistance to cassava brown streak disease (CBSD) on chromosomes 9 and 11; and QTL on chromosomes 2, 3, 8, and 10 associated with resistance to CBSD for root necrosis. We detected a QTL on chromosome 4 and two QTL on chromosome 12 conferring dual resistance to CMD and CBSD. The use of clones in the same stage to construct TPs provided higher trait prediction accuracy than TPs with a mixture of clones from multiple breeding stages. Moreover, clones in the early breeding stage provided more reliable trait prediction accuracy and are better candidates for constructing a TP. Although larger TP sizes have been associated with improved accuracy, in this study, adding clones from Kibaha to those from Ukiriguru and vice versa did not improve the prediction accuracy of either population. Including the Ugandan TP in either population did not improve trait prediction accuracy. This study applied genomic prediction to understand the implications of constructing TP from clones at different breeding stages pooled from different locations on trait accuracy

Contesting Genetic Knowledge-Practices in Livestock Breeding: Biopower, Biosocial Collectivities, and Heterogeneous Resistances

Cattle and sheep breeders in the UK and elsewhere increasingly draw on genetic techniques in order to make breeding decisions. Many breeders support such techniques, while others argue against them for a variety of reasons, including their preference for the ‘traditions' of visual-based and pedigree-based selections. Meanwhile, even for those institutions and breeders who promote genetic techniques, the outcomes are not always as predicted. We build on our recent use of Foucault's discussions of biopower to examine the effects of the introduction of genetic techniques in UK livestock breeding in order to begin to explore the diffuse and capillary nature of resistance within relations of biopower. We focus specifically on how resistance and contestation can be understood through the joint lenses of biopower and an understanding of livestock breeding as knowledge-practices enacted within heterogeneous biosocial collectivities. In some instances these collectivities coalesce around shared endeavour, such as increasing the valency of genetic evaluation within livestock breeding. Yet such mixed collectivities also open up opportunities for counter-conduct: heterogeneous resistances to and contestations of genetic evaluation as something represented as progressive and inevitable. We focus on exploring such modes of resistance using detailed empirical research with livestock breeders and breeding institutions. We demonstrate how in different and specific ways geneticisation becomes problematised, and is contested and made more complex, through the knowledge-practices of breeders, the bodies of animals, and the complex relationships between different institutions in livestock breeding and rearing

The BIOEXPLOIT Project

The EU Framework 6 Integrated Project BIOEXPLOIT concerns the exploitation of natural plant biodiversity for the pesticide-free production of food. It focuses on the pathogens Phytophthora infestans, Septoria tritici, Blumeria graminis, Puccinia spp. and Fusarium spp. and on the crops wheat, barley, tomato and potato. The project commenced in October 2005, comprises 45 laboratories in 12 countries, and is carried out by partners from research institutes, universities, private companies and small-medium enterprises. The project has four strategic objectives covered in eight sub-projects. These objectives relate to (i) understanding the molecular components involved in durable disease resistance, (ii) exploring and exploiting the natural biodiversity in disease resistance, (iii) accelerating the introduction of marker-assisted breeding and genetic engineering in the EU plant breeding industry, and (iv) coordinating and integrating resistance breeding research, providing training in new technologies, disseminating the results, and transferring knowledge and technologies to the industry

Participatory plant breeding in Denmark

Plant breeding gets more and more concentrated on a couple of multinational companies, and financing plant breeding via the traditional royalty founded certification system exclusive for the specific needs in organic farming is not profitable in most field crops. The seed certification system only allows pure line varieties, and the royalty funded breeding system tend to focus on monogenic resistance with s short durability on the marked. To develop new plant genetic material for organic farmers with durable stability and resistance, the Danish Organic Farmers Association has initiated a participatory plant breeding program with the aim to develop varieties and diverse populations for the organic farmers. The project is based within the advisory service in the organisation in cooperation with plant breeding research projects. In this way, it is the hope to overcome the economic and legal barrier for implementation of crop diversity and targeted selection for the different needs in the diverse organic sector

Cisgenesis, a new tool for traditional plant breeding, should be exempted from the regulation on genetically modified organisms in a step by step approach

Modern potato breeding requires over 100,000 seedlings per new variety. Main reasons are (1) the increasing number of traits that have to be combined in this tetraploid vegetatively propagated crop, and (2) an increasing number of traits (e.g., resistance to biotic stress) originates from wild species. Pre-breeding by introgression or induced translocation is an expensive way of transferring single traits (such as R-genes, coding for resistance to biotic stress) to the cultivated plant. The most important obstacle is simultaneous transfer of undesired neighbouring alien alleles as linkage drag. Stacking several genes from different wild sources is increasing this linkage drag problem tremendously. Biotechnology has enabled transformation of alien genes into the plant. Initially, transgenes were originating mainly from microorganisms, viruses or non-crossable plant species, or they were chimeric. Moreover, selection markers coding for antibiotic resistance or herbicide resistance were needed. Transgenes are a new gene source for plant breeding and, therefore, additional regulations like the EU Directive 2001/18/EC were developed. Because of a strong opposition against genetic modification of plants in Europe, the application of this Directive is strict, very expensive, hampering the introduction of genetically modified (GM) crops and the use of this technology by small and medium-sized enterprises (SMEs). Currently, GM crops are almost the exclusive domain of multinationals. Meanwhile, not only transgenes but also natural genes from the plant species itself or from crossable plant species, called cisgenes, are available and the alien selection genes can be avoided in the end product. This opens the way for cisgenic crops without alien genes. The existing EU directive for GM organisms is not designed for this new development. The cisgenes belong to the existing breeders¿ gene pool. The use of this classical gene pool has been regulated already in agreements regarding breeders¿ rights. We are proposing a step by step approach starting with a crop and gene specific derogation and monitoring towards a general exemption of cisgenic plants from the Directive. Two examples, i.e. development of cisgenic potato for resistance to Phytophthora infestans and cisgenic apple for resistance to Venturia inaequalis are discussed shortly for illustration of the importance of cisgenesis as a new tool for traditional plant breeding. Cisgenesis is simplifying introgression and induced translocation breeding tremendously and is highly recommended for SMEs and developing countrie

A major QTL corresponding to the Rk locus for resistance to root-knot nematodes in cowpea (Vigna unguiculata L. Walp.).

Key messageGenome resolution of a major QTL associated with the Rk locus in cowpea for resistance to root-knot nematodes has significance for plant breeding programs and R gene characterization. Cowpea (Vigna unguiculata L. Walp.) is a susceptible host of root-knot nematodes (Meloidogyne spp.) (RKN), major plant-parasitic pests in global agriculture. To date, breeding for host resistance in cowpea has relied on phenotypic selection which requires time-consuming and expensive controlled infection assays. To facilitate marker-based selection, we aimed to identify and map quantitative trait loci (QTL) conferring the resistance trait. One recombinant inbred line (RIL) and two F2:3 populations, each derived from a cross between a susceptible and a resistant parent, were genotyped with genome-wide single nucleotide polymorphism (SNP) markers. The populations were screened in the field for root-galling symptoms and/or under growth-chamber conditions for nematode reproduction levels using M. incognita and M. javanica biotypes. One major QTL was mapped consistently on linkage group VuLG11 of each population. By genotyping additional cowpea lines and near-isogenic lines derived from conventional backcrossing, we confirmed that the detected QTL co-localized with the genome region associated with the Rk locus for RKN resistance that has been used in conventional breeding for many decades. This chromosomal location defined with flanking markers will be a valuable target in marker-assisted breeding and for positional cloning of genes controlling RKN resistance

Identification and mapping of the novel apple scab resistance gene Vd3

Apple scab, caused by the fungal pathogen Venturia inaequalis, is one of the most devastating diseases for the apple growing in temperate zones with humid springs and summers. Breeding programs around the world have been able to identify several sources of resistance, the Vf from Malus floribunda 821 being the most frequently used. The appearance of two new races of V. inaequalis (races 6 and 7) in several European countries that are able to overcome the resistance of the Vf gene put in evidence the necessity of the combination of different resistance genes in the same genotype (pyramiding). Here, we report the identification and mapping of a new apple scab resistance gene (Vd3) from the resistant selection “1980-015-25” of the apple breeding program at Plant Research International, The Netherlands. This selection contains also the Vf gene and the novel V25 gene for apple scab resistance. We mapped Vd3 on linkage group 1, 1 cM to the south of Vf in repulsion phase to it. Based on pedigree analysis and resistance tests, it could be deduced that 1980-015-25 had inherited Vd3 from the founder “D3.” This gene provides resistance to the highly virulent EU-NL-24 strain of race 7 of V. inaequalis capable of overcoming the resistance from Vf and Vg

Resistant and susceptible pea lines harbour different root-rot pathogens and antagonistic fungi

Disease resistance encompasses the mechanisms that allow a plant to withstand or ward off a pathogen. The molecular responses of plants under pathogen attack and the underlying genetics have been extensively studied. However, resistance is not only a trait defined by the warfare between pathogen and host. In fact, resistance is an emergent phenotype of the interactions between the microbial community and the host. Fungal root diseases threaten pea (Pisum sativum L.) cultivation, and therefore a valuable protein source and important crop in low-input farming systems. Resistance in current pea varieties against multiple root pathogens is lacking. In order to acknowledge the rhizosphere microbiome as an integral part of the environment, 261 pea genotypes were screened for resistance on naturally infested field soil in a pot-based experiment. Thereof, eight lines with contrasting disease levels were selected and tested on four soils with different disease pressure in a follow-up pot experiment. Along root rot assessments, pea pathogens (F. solani, F. oxysporum, F. avenaceum, A. euteiches, P. ultimum and D. pinodella) and arbuscular mycorrhizal fungi were quantified in diseased roots using qPCR assays. The amount of fungal DNA detected in the roots differed among the pea genotypes and the four soils and a significant pea genotype x soil interaction was evidenced for several pathogen species. For example, the quantity of F. avenaceum in the roots mostly depends on the soil (two-way ANOVA, p < 0.01) and differs significantly between pea genotypes (p = 0.013). F. oxysporum and F. solani quantities showed significant pea genotype x soil interactions (p < 0.01 for both species). Significant correlations were found between F. avenaceum and F. solani quantity and root rot index (rs = 0.38, p < 0.01 and rs = 0.56, p < 0.01, respectively ). On the other hand, F. oxysporum quantity shows no relationship with root rot (rs = 0.007, p = 0.95). These results suggest differential roles of the microbes in the pea root rot and highlight the importance of incorporating the complexity of the soil microbiome at early stages of resistance screenings and breeding efforts. Resistance breeding against root rot will be challenged by the fact that soil microbes interact with each other and the plant and that their composition varies between different soils. Further insights into plant-microbe interactions and emerging molecular plant breeding tools will fuel future plant breeding