Institut für Pflanzenzüchtung, Saatgutforschung und Populationsgenetik

Permanent URI for this collectionhttps://hohpublica.uni-hohenheim.de/handle/123456789/13

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Genetic variation for tolerance to the downy mildew pathogen Peronospora variabilis in genetic resources of quinoa (Chenopodium quinoa)
(2021) Colque-Little, Carla; Abondano, Miguel Correa; Lund, Ole Søgaard; Amby, Daniel Buchvaldt; Piepho, Hans-Peter; Andreasen, Christian; Schmöckel, Sandra; Schmid, Karl
Background: Quinoa (Chenopodium quinoa Willd.) is an ancient grain crop that is tolerant to abiotic stress and has favorable nutritional properties. Downy mildew is the main disease of quinoa and is caused by infections of the biotrophic oomycete Peronospora variabilis Gaüm. Since the disease causes major yield losses, identifying sources of downy mildew tolerance in genetic resources and understanding its genetic basis are important goals in quinoa breeding. Results: We infected 132 South American genotypes, three Danish cultivars and the weedy relative C. album with a single isolate of P. variabilis under greenhouse conditions and observed a large variation in disease traits like severity of infection, which ranged from 5 to 83%. Linear mixed models revealed a significant effect of genotypes on disease traits with high heritabilities (0.72 to 0.81). Factors like altitude at site of origin or seed saponin content did not correlate with mildew tolerance, but stomatal width was weakly correlated with severity of infection. Despite the strong genotypic effects on mildew tolerance, genome-wide association mapping with 88 genotypes failed to identify significant marker-trait associations indicating a polygenic architecture of mildew tolerance. Conclusions: The strong genetic effects on mildew tolerance allow to identify genetic resources, which are valuable sources of resistance in future quinoa breeding.
Genome-wide association study for in vitro digestibility and related traits in triticale forage
(2024) De Zutter, Anneleen; Piro, Maria Chiara; Maenhout, Steven; Maurer, Hans Peter; De Boever, Johan; Muylle, Hilde; Roldán-Ruiz, Isabel; Haesaert, Geert
Background: Triticale is making its way on dairy farms as an alternative forage crop. This requires the availability of high-yielding triticale varieties with good digestibility. Triticale forage breeding mainly focussed on biomass yield, but efforts to improve digestibility are increasing. We previously investigated the interrelationships among different quality traits in soft dough triticale: starch, acid detergent fibre and in vitro digestibility of organic matter (IVOMD) and of neutral detergent fibre (IVNDFD) of the total plant, IVNDFD and Klason lignin of the stems, and ear proportion and stem length. Here we determine the genetic control of these traits, using a genome-wide association (GWAS) approach. A total of 33,231 DArTseq SNP markers assessed in a collection of 118 winter triticale genotypes, including 101 varieties and 17 breeding lines, were used. Results: The GWAS identified a total of 53 significant marker-trait associations (MTAs). The highest number of significantly associated SNP markers (n = 10) was identified for total plant IVNDFD. A SNP marker on chromosome 1A (4211801_19_C/T; 474,437,796 bp) was found to be significantly associated with ear proportion, and plant and stem IVNDFD, with the largest phenotypic variation for ear proportion (R²p = 0.23). Based on MTAs, candidate genes were identified which were of particular relevance for variation in in vitro digestibility (IVD) because they are putatively involved in plasma membrane transport, cytoskeleton organisation, carbohydrate metabolic processes, protein phosphorylation, and sterol and cell wall biogenesis. Interestingly, a xyloglucan-related candidate gene on chromosome 2R, SECCE2Rv1G0126340, was located in close proximity of a SNP significantly associated with stem IVNDFD. Furthermore, quantitative trait loci previously reported in wheat co-localized with significantly associated SNP markers in triticale. Conclusions: A collection of 118 winter triticale genotypes combined with DArTseq SNP markers served as a source for identifying 53 MTAs and several candidate genes for forage IVD and related traits through a GWAS approach. Taken together, the results of this study demonstrate that the genetic diversity available in this collection can be further exploited for research and breeding purposes to improve the IVD of triticale forage.
Using landscape genomics to infer genomic regions involved in environmental adaptation of soybean genebank accessions
(2025) Haupt, Max; Schmid, Karl
Background: Understanding how crops adapt to specific environmental conditions is becoming increasingly important in the face of accelerating climate change, but the genetics of local adaptation remains little understood for many crops. Landscape genomics can reveal patterns of genetic variation that indicate adaptive diversification during crop evolution and dispersal. Here, we examine genetic differentiation and association signatures with environmental gradients in soybean ( Glycine max ) germplasm groups from China that were inferred from the USDA Soybean Germplasm Collection ( N = 17, 019 accessions) based on population structure and passport information. Results: We recover genes previously known to be involved in soybean environmental adaptation and report numerous new candidate genes in adaptation signatures implicated by genomic resources such as the genome annotation and gene expression datasets to function in flowering regulation, photoperiodism and stress reaction cascades. Linkage disequilibrium network analysis suggested functional relationships between genomic regions with signatures of genetic differentiation, consistent with a polygenic nature of environmental adaptation. We tested whether haplotypes associated with environmental adaptation in China were present in 843 North American and 160 European soybean cultivars and found that haplotypes in major genes for early maturity have been selected during breeding, but also that a large number of haplotypes exhibiting putative adaptive variation for cold regions at high latitudes are underrepresented in modern cultivars. Conclusions: Our results demonstrate the value of landscape genomics analysis of genebank accessions studying crop environmental adaptation and to inform future research and breeding efforts for improved adaptation of soybean and other crops to future climates.

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