Bejo Zaden (Netherlands)

In recent years, accurate and low-cost variant calling has enabled the genotyping of large diversity panels for genome-wide association studies. As a result, phenotyping rather than genotyping is now the rate-limiting step, especially in field experiments. This has created a strong need for high-throughput, accurate, and low-cost in-field phenotyping. Here, we present a genome-wide association study (GWAS) study on 194 field-grown accessions of lettuce (Lactuca sativa). These accessions were non-destructively phenotyped at two time points 15 days apart using a drone equipped with an RGB and multispectral (MSP) camera. Our high-throughput phenotyping approach integrates an RGB- and MSP camera to measure the color and height of lettuce in this large-scale field experiment. We used the mean and other summary statistics, such as median, quantiles, skewness, kurtosis, minimum, and maximum to quantify different aspects of color and height variation in lettuce from the drone images. Using these summary statistics as traits for GWAS, we confirm several previously described genetic associations, now under field conditions, and identify additional novel associations for color and height traits in lettuce.

Biological control of seedborne pathogens and soilborne seedling pathogens through antagonists applied on seeds is an alternative to chemical seed treatments. The survival of coated microorganisms during the various seed processing, storage and distribution steps is essential for the use of beneficial fungi or bacteria on seeds. A study was done to gain insight into the survival potential and variability in survival of representatives of different microbial groups during storage of coated seeds of different crops. Survival of inocula on seeds of Brassica, onion, spinach and perennial ryegrass was tested by plating and for a subset of coated seeds by viability qPCR. A close correlation was found for CFU counts per seed and the estimated number of viable conidia based on strain-specific or generic fungal viability qPCR for conidia of Cladosporium cladosporioides H39 coated on various seed lots. For Lysobacter enzymogenes 3.1 T8, viability qPCR showed survival of cells on coated seeds. However, only few colonies were produced on Tryptone soy agar. Generic fungal and bacterial qPCR and viability qPCR assays with non-coated seeds indicated that only a proportion of the seed microbiota, frequently less than 10 %, are viable. Survival of inocula coated on seeds and stored for three to six months differed between applied microbial groups, formulation of inocula and between laboratories conducting the experiments. From the obtained results it can be concluded that there is a promising potential to improve the often envisaged low survival of inocula coated on seeds. Improved strains selection, improved and adapted seed processing technologies, and developing expertise in microbial seed processing will allow the use of a broader range of fungal and bacterial groups. The application of viability qPCR will support this development as a fast and reliable tool to monitor the survival of microbial inocula coated on seeds.

High seed quality is a prerequisite for successful crop production, making maintenance of seed viability and vigour during storage important. The effects of temperature and humidity on seed ageing are well known, while the negative effect of oxygen in the seed storage environment has been studied less. Here we report on experiments to study the quantitative effect of oxygen on the ageing of seeds. Primed celery seeds were chosen as a model, because of their relatively short shelf life. After equilibration at four relative humidity levels (16, 33, 43 and 60% RH), the seeds were stored at four temperatures (5, 13, 20 and 30°C) and six oxygen levels (1, 5.2, 10, 21, 50 and 99%) for a period up to seven years. Germination tests after storage confirmed a strong shelf life-extending effect of low oxygen conditions, at all four temperatures and the three lower humidity levels. Modelling the viability data revealed a linear double logarithmic relationship between the oxygen concentration and the storage time till a 50% decline in viability (p50), for seeds pe-equilibrated at 16, 33 or 43% RH. The models also showed that each halving of the oxygen concentration increased seed longevity by around 77%. This means that a reduction of the environmental oxygen concentration to a level below 1% increased the shelf life of the primed celery seeds by a factor of twelve. For seeds pre-equilibrated at 60% RH, the effect of lowering the oxygen concentration below 21% was much less or even absent at 30°C, likely due to a different physical or physiological condition of the seeds at this higher humidity level. The large and logarithmic effect of reducing the oxygen level during the dry storage of seeds provides additional opportunities to prolong the shelf life of seeds either for commercial or genebank storage. To estimate the effect of these factors, a model is provided describing the quantitative effect of all three factors, temperature, equilibrium relative humidity and oxygen concentration. Several options for practical application are discussed.

Abstract The balanced segregation of homologous chromosomes during meiosis is essential for fertility and is mediated by crossovers. A strong reduction of crossovers leads to desynapsis, a process in which pairing of homologous chromosomes is abolished before metaphase I. This results in a random segregation of univalent and the production of unbalanced and sterile gametes. However, if desynapsis is combined with another meiotic alteration that restitutes the first meiotic division, then uniform and balanced unreduced gametes, essentially composed of non-recombinant homologs, are produced. This mitosis-like division is of interest to breeders because it transmits most of the parental heterozygosity to the gametes. In potato, desynapsis is a recessive trait that was tentatively mapped to chromosome8. In this article, we have fine-mapped the position of the desynapsis locus and identifiedStMSH4, an essential component of the class I crossover pathway, as the most likely candidate gene. A seven base-pair insertion in the second exon ofStMSH4was found to be associated with desynapsis in our mapping population. We also identified a second allele with a 3820 base-pair insertion and confirmed that both alleles cannot complement each other. Such non-functional alleles appeared to be common in potato cultivars. More than half of the varieties we tested are carriers of mutational load at theStMSH4locus. With this new information, breeders can choose to remove desynaptic alleles from their germplasm to improve fertility or to use them to produce highly uniform unreduced gametes in alternative breeding schemes.

Abstract Seed health is an indispensable prerequisite of food security. While the toolkit of plant protection products is currently limited, evidence suggests that the seed microbiome could protect seeds from pathogens. Thus, given their possible disease suppressive potential, we tested 11 different pathosystems to achieve the following proof-of-concept: seed microbiomes can be beneficial for seed health through conferring disease suppression. This study focused on beetroot, onion, spinach, pepper, coriander, red fescue and perennial ryegrass seeds, with each crop being challenged with one or two from a total of six pathogens, namely Pythium ultimum (or a Pythium sp.), Setophoma terrestris, Fusarium oxysporum, Phytophthora capsici, Laetisaria fuciformis and a mix of Puccinia sp. isolates. Each seed lot of each crop was tested with and without treatment with a disinfectant as a proxy for comparing intact seed microbiomes with seed microbiomes after partial elimination by disinfection. We found disease suppression in two pathosystems. Beetroot and spinach seed lots were able to suppress disease caused by P. ultimum when their microbiomes were intact but not after seed disinfection. We speculate that this relates to the microorganisms residing on and in the seed. Yet, seed microbiome disease suppression was not found in all pathosystems, highlighting the variation in seed morphology, plant cultivars, pathogens and seed disinfection treatments. A holistic understanding of the characteristics of seeds that harbour suppressive microbiomes as well as the pathogens that are sensitive to suppression could lead to more targeted and informed seed processing and treatment and, consequently, to the sustainable management of seedling diseases.