The greatest threat to potato production world-wide is late blight, caused by the oomycete pathogen Phytophthora infestans. A screen of 126 wild diploid Solanum accessions from the Commonwealth Potato Collection (CPC) with P. infestans isolates belonging to the genotype 13-A2 identified resistances in the species S. bulbocastanum, S. capsicibaccatum, S. microdontum, S. mochiquense, S. okadae, S. pinnatisectum, S. polyadenium, S. tarijense, and S. verrucosum. Effector-omics, allele mining, and diagnostic RenSeq (dRenSeq) were utilized to investigate the nature of resistances in S. okadae accessions. dRenSeq in resistant S. okadae accessions 7129, 7625, 3762, and a bulk of 20 resistant progeny confirmed the presence of full-length Rpi-vnt1.1 under stringent mapping conditions and corroborated allele mining results in the accessions 7129 and 7625 as well as Avr-vnt1 recognition in transient expression assays. In contrast, susceptible S. okadae accession 3761 and a bulk of 20 susceptible progeny lacked sequence homology in the 5′ end compared to the functional Rpi-vnt1.1 gene. Further evaluation of S. okadae accessions with P. infestans isolates that have a broad spectrum of virulence demonstrated that, although S. okadae accessions 7129, 7625, and 7629 contain functional Rpi-vnt1.1, they also carry a novel resistance gene. We provide evidence that existing germplasm collections are important sources of novel resistances and that “omic” technologies such as dRenSeq-based genomics and effector-omics are efficacious tools to rapidly explore the diversity within these collections.

Conservation and exploitation of crop wild relative species is an important component in ensuring food security and improving current agricultural output. By identifying agriculturally important characteristics that express favorable response to both biotic and abiotic stress currently unused by breeders, the incorporation of this new genetic material into genetic background stocks may help mitigate problems imposed by climate change, land degradation, and population pressure. This is particularly important in countries that will be more severely affected by the threat of reduced yields. The ability to effectively manage genetic resources collections and integrate unique and diverse data types is crucial in exploring, understanding, and exploiting the diversity contained within genebanks. Providing a common interface through which experimental and background data can be disseminated to both researchers and breeders will bring focus and facilitate community building into research communities. We have taken wild barley (Hordeum spp.) and potato (Solanum spp.) collections along with wheat (Triticum spp.) and maize (Zea mays subsp. mays) and their wild relatives and incorporated this data into web‐based information resources built using the Germinate platform (https://ics.hutton.ac.uk/get-germinate, accessed 4 Apr. 2017). We have tailored these to better meet the demands of researchers by developing both new data visualization tools and integration with current software such as Helium, Flapjack, and CurlyWhirly (https://ics.hutton.ac.uk/software, accessed 4 Apr. 2017) and presented the data in a common platform. While the underlying species differ, the approach taken ensures that tools are compatible across all database instances. We will describe these database instances and show that Germinate offers a common platform that will aid in the exploration and wider use of these species.

Genome-wide QTL analysis of potato tuber carotenoid content was investigated in populations of Solanum tuberosum Group Phureja that segregate for flesh colour, revealing a novel major QTL on chromosome 9. The carotenoid content of edible plant storage organs is a key nutritional and quality trait. Although the structural genes that encode the biosynthetic enzymes are well characterised, much less is known about the factors that determine overall storage organ content. In this study, genome-wide QTL mapping, in concert with an efficient 'genetical genomics' analysis using bulked samples, has been employed to investigate the genetic architecture of potato tuber carotenoid content. Two diploid populations of Solanum tuberosum Group Phureja were genotyped (AFLP, SSR and DArT markers) and analysed for their tuber carotenoid content over two growing seasons. Common to both populations were QTL that explained relatively small proportions of the variation in constituent carotenoids and a major QTL on chromosome 3 explaining up to 71 % of the variation in carotenoid content. In one of the populations (01H15), a second major carotenoid QTL was identified on chromosome 9, explaining up to 20 % of the phenotypic variation. Whereas the major chromosome 3 QTL was likely to be due to an allele of a gene encoding β-carotene hydroxylase, no known carotenoid biosynthetic genes are located in the vicinity of the chromosome 9 QTL. A unique expression profiling strategy using phenotypically distinct bulks comprised individuals with similar carotenoid content provided further support for the QTL mapping to chromosome 9. This study shows the potential of using the potato genome sequence to link genetic maps to data arising from eQTL approaches to enhance the discovery of candidate genes underlying QTLs.

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Risk-assessment studies of virus-resistant transgenic plants (VRTPs