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Genebanks are important suppliers of genetic resources to the genomics research community, and access to the resulting information will allow traditional genebank users to better select genetic material for their breeding and scientific programmes. We discuss herein a possible solution to interconnect these data automatically based on semantic web technology. [ABSTRACT FROM PUBLISHER]

Plant genetic resources are conserved by genebanks mainly in the form of seeds. In most of the cases, the dried seeds can be stored for a considerable period of time, but eventually seed deterioration results in the inability to generate healthy seedlings. Prolonging seed longevity during storage reduces the frequency of regeneration, which is beneficial from a genetic as well as a management point of view. To reduce the rate of deterioration, cool and dry storage conditions are usually practised for long-term seed storage. In spite of the growing body of evidence that seed deterioration is predominantly caused by oxidative processes, the importance of seed storage under anoxic conditions has received little attention from the genebank community. Herein, we report on the effects of anoxia on seed viability, the oxygen uptake by dry seeds in closed containers and the permeability for oxygen of various seed storage containers. Our results confirm that the ageing of dry seeds is accelerated by the presence of oxygen in the storage environment. Therefore, we recommend that genebanks store dry seeds under anoxic conditions to prolong their longevity during ex situ conservation. To reduce the initial rate of viability loss, we further recommend that the period of temporary storage after seed harvest be minimized and also that the seeds are kept during this period under controlled conditions, including anoxia. [ABSTRACT FROM PUBLISHER]

The loss of variation in crops due to the modernization of agriculture has been described as genetic erosion. The current paper discusses the different views that exist on the concept of genetic erosion in crops. Genetic erosion of cultivated diversity is reflected in a modernization bottleneck in the diversity levels that occurred during the history of the crop. Two stages in this bottleneck are recognized: the initial replacement of landraces by modern cultivars; and further trends in diversity as a consequence of modern breeding practices. Genetic erosion may occur at three levels of integration: crop, variety and allele. The different approaches in the recent literature to measure genetic erosion in crops are reviewed. Genetic erosion as reflected in a reduction of allelic evenness and richness appears to be the most useful definition, but has to be viewed in conjunction with events at variety level. According to the reviewed literature, the most likely scenario of diversity trends during modernization is the following: a reduction in diversity due to the replacement of landraces by modern cultivars, but no further reduction after this replacement has been completed. [ABSTRACT FROM AUTHOR]

We examined microsatellite variation in two diploid, outcrossing relatives of Arubidopsis thulium, Arubis petrueu and Arubis lyrutu. The primer sequences were derived from A. thuliunu. About 50% (14 loci) of the A. thuliunu primers could succesfully amplify microsatellites in the related species. Analysis of microsatellite structure in the related species showed that there had been large changes in the microsatellites: there were large differences in repeat numbers and many of the A. thuliunu simple repeats were shorter in the related species. For the loci we compared, the related species had a much lower level of variability at the microsatellites than Japanese wild populations of A. thuliunu. This is presumably related to the different microsatellite structures, because allozyme data showed that the outcrossing relatives were highly polymorphic compared to other outcrossing herbaceous species. Use of microsatellites in assessing variability or phylogenetic relationships between different species requires caution, because changes in microsatellite structure may alter evolutionary rates. [ABSTRACT FROM AUTHOR]

Lettuce (Lactuca sativa L.) is a leafy vegetable crop with ongoing breeding efforts related to quality, resilience, and innovative production systems. To breed resilient and resistant lettuce in the future, valuable genetic variation found in close relatives could be further exploited. Lactuca virosa (2x = 2n = 18), a wild relative assigned to the tertiary lettuce gene pool, has a much larger genome (3.7 Gbp) than Lactuca sativa (2.5 Gbp). It has been used in interspecific crosses and is a donor to modern crisphead lettuce cultivars. Here, we present a de novo reference assembly of L. virosa with high continuity and complete gene space. This assembly facilitated comparisons to the genome of L. sativa and to that of the wild species L. saligna, a representative of the secondary lettuce gene pool. To assess the diversity in gene content, we classified the genes of the 3 Lactuca species as core, accessory, and unique. In addition, we identified 3 interspecific chromosomal inversions compared to L. sativa, which each may cause recombination suppression and thus hamper future introgression breeding. Using 3-way comparisons in both reference-based and reference-free manners, we show that the proliferation of long-terminal repeat elements has driven the genome expansion of L. virosa. Further, we performed a genome-wide comparison of immune genes, nucleotide-binding leucine-rich repeat, and receptor-like kinases among Lactuca spp. and indicated the evolutionary patterns and mechanisms behind their expansions. These genome analyses greatly facilitate the understanding of genetic variation in L. virosa, which is beneficial for the breeding of improved lettuce varieties., Competing Interests: Conflicts of interest The author(s) declare no conflict of interest., (© The Author(s) 2023. Published by Oxford University Press on behalf of The Genetics Society of America.)

Single primer enrichment technology (SPET) is a novel high-throughput genotyping method based on short-read sequencing of specific genomic regions harboring polymorphisms. SPET provides an efficient and reproducible method for genotyping target loci, overcoming the limits associated with other reduced representation library sequencing methods that are based on a random sampling of genomic loci. The possibility to sequence regions surrounding a target SNP allows the discovery of thousands of closely linked, novel SNPs. In this work, we report the design and application of the first SPET panel in lettuce, consisting of 41,547 probes spanning the whole genome and designed to target both coding (~96%) and intergenic (~4%) regions. A total of 81,531 SNPs were surveyed in 160 lettuce accessions originating from a total of 10 countries in Europe, America, and Asia and representing 10 horticultural types. Model ancestry population structure clearly separated the cultivated accessions ( Lactuca sativa ) from accessions of its presumed wild progenitor ( L. serriola ), revealing a total of six genetic subgroups that reflected a differentiation based on cultivar typology. Phylogenetic relationships and principal component analysis revealed a clustering of butterhead types and a general differentiation between germplasm originating from Western and Eastern Europe. To determine the potentiality of SPET for gene discovery, we performed genome-wide association analysis for main agricultural traits in L. sativa using six models (GLM naive, MLM, MLMM, CMLM, FarmCPU, and BLINK) to compare their strength and power for association detection. Robust associations were detected for seed color on chromosome 7 at 50 Mbp. Colocalization of association signals was found for outer leaf color and leaf anthocyanin content on chromosome 9 at 152 Mbp and on chromosome 5 at 86 Mbp. The association for bolting time was detected with the GLM, BLINK, and FarmCPU models on chromosome 7 at 164 Mbp. Associations were detected in chromosomal regions previously reported to harbor candidate genes for these traits, thus confirming the effectiveness of SPET for GWAS. Our findings illustrated the strength of SPET for discovering thousands of variable sites toward the dissection of the genomic diversity of germplasm collections, thus allowing a better characterization of lettuce collections., Competing Interests: DS was employed by the company IGA Technology Services Srl. MB was employed by the company ISI Sementi SpA. DP was employed by the company Limagrain - Vilmorin-Mikado. AL and GB were employed by the company Gautier Semences. CA was employed by the company Sativa Rheinau AG. TZ was employed by the company Zollinger Conseilles Sarl. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Tripodi, Beretta, Peltier, Kalfas, Vasilikiotis, Laidet, Briand, Aichholz, Zollinger, Treuren, Scaglione and Goritschnig.)

Genebanks aim to optimize their storage conditions in order to postpone seed ageing as long as possible. As most genebanks have a relatively short life history, empirical data about seed longevity during ex situ storage are almost absent. Based on seed characteristics, theoretical predictions indicate that cereal seeds can be stored without substantial loss of viability for time periods exceeding 100 years, even under temperatures of a few degrees above zero. Here we present the results of a germination study in wheat and barley, comparing genebank seed samples maintained at different temperatures for 23-33 years. Wheat and barley seed samples stored at -20°C showed a mean germination of 94% and 90%, respectively, indicating no loss of the initial viability determined for the accessions prior to introduction in the collection. Seed samples maintained at 4°C showed a mean germination of 62% for wheat and 75% for barley. In addition to the observed loss of viability, the 4°C samples also showed a loss in vigour as the time period to reach their final germination was about twice as long compared to the -20°C samples. A subset of the wheat accessions tested in 2011 were retested in 2017, showing further reduction in mean germination to 35% for the 4°C samples, while the -20°C samples remained stable at 95%. Several 4°C samples were even close to a complete loss of viability. Considering that wheat and barley are generally regarded as good maintainers, the rapid loss of seed viability observed in the present study indicates that the ex situ seed storage of genetic resources at 4°C should be treated with caution by genebanks, particularly when used for long-term conservation.

Possibilities for using molecular markers to improve genebank efficiency are increasingly present thanks to developments in genebanks and developments in molecular genetics. These possibilities relate to all aspects of genebank management: acquisition, maintenance, characterisation and utilisation. However, two pitfalls should be avoided. The first lies in the neutrality of the most generally used markers, making them less suitable for optimising genetic diversity. The second is related to the considerable costs involved in using molecular markers. In many cases an economical analysis will have to decide if the markers can routinely be used in genebank operations. Some examples of model studies and applications of molecular markers in genebank operations will be presented, in which both genetic and economic aspects will be illustrated briefly. These examples involved existing genebank collections of wild lettuce, cabbage and wild potato.