Genetic Resources最新文献

{"title":"Combined cytogenetic and molecular methods for taxonomic verification and description of Brassica populations deriving from different origins","authors":"C. Falentin, H. Hadj-Arab, F. Aissiou, Claudia Bartoli, G. Bazan, Matéo Boudet, L. Bousset-Vaslin, Marwa Chwikhi, O. Coriton, G. Deniot, J. Ferreira de Carvalho, Laurène Gay, A. Geraci, Pascal Glory, V. Huteau, R. Ilahy, Vincenzo Ilardi, J. A. Jarillo, V. Meglič, Elisabetta Oddo, Mónica Pernas, M. Piñeiro, B. Pipan, T. Rhim, Vincent Richer, F. Rizza, J. Ronfort, M. Rousseau-Gueutin, R. Schicchi, L. Sinkovič, Maryse Taburel, V. Terzi, Sylvain Théréné, M. Tiret, I. Tlili, Marie-Hélène Wagner, Franz Werner Badeck, A. Chèvre","doi":"10.46265/genresj.ryaj6068","DOIUrl":"https://doi.org/10.46265/genresj.ryaj6068","url":null,"abstract":"Agriculture faces great challenges to overcome global warming and improve system sustainability, requiring access to novel genetic diversity. So far, wild populations and local landraces remain poorly explored. This is notably the case for the two diploid species, Brassica oleracea L. (CC, 2n=2x=18) and B. rapa L. (AA, 2n=2x=20). In order to explore the genetic diversity in both species, we have collected populations in their centre of origin, the Mediterranean basin, on a large contrasting climatic and soil gradient from northern Europe to southern sub-Saharan regions. In these areas, we also collected 14 populations belonging to five B. oleracea closely related species. Our objective was to ensure the absence of species misidentification at the seedling stage among the populations collected and to describe thereafter their origins. We combined flow cytometry, sequencing of a species-specific chloroplast genomic region, as well as cytogenetic analyses in case of unexpected results for taxonomic verification. Out of the 112 B. oleracea and 154 B. rapa populations collected, 103 and 146, respectively, presented a good germination rate and eighteen populations were misidentified. The most frequent mistake was the confusion of these diploid species with B. napus. Additionally for B. rapa, two autotetraploid populations were observed. Habitats of the collected and confirmed wild populations and landraces are described in this study. The unique plant material described here will serve to investigate the genomic regions involved in adaptation to climate and microbiota within the framework of the H2020 Prima project ‘BrasExplor’.","PeriodicalId":514160,"journal":{"name":"Genetic Resources","volume":" 84","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-05-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140992878","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identification of genetically plastic forms among Belarusian ancient flax (Linum usitatissimum convar. elongatum Vav. et Ell.) varieties using the Linum Insertion Sequence LIS-1","authors":"Maria Parfenchyk, Valentina Lemesh, Elena Lagunovskaya, Valentina Sakovich, Andrei Buloichik, Elena Guzenko, Lyubov Khotyleva","doi":"10.46265/genresj.dbno8764","DOIUrl":"https://doi.org/10.46265/genresj.dbno8764","url":null,"abstract":"The Linum Insertion Sequence 1 (LIS-1) occurs in the genetically plastic flax genotypes in response to the lack or excess of mineral and water nutrition, but also naturally, and can be transmitted to the progeny. We have analyzed 21 ancient Belarusian varieties of flax Linum usitatissimum convar. elongatum Vav. et Ell. The LIS-1 presence or absence was checked for individual plants in at minimum two generations with primer-specific polymerase chain reaction (PCR) and agarose gel electrophoresis. The studied flax varieties formed four groups: non-responsive varieties (LIS-1 was not found, group NR); responsive, which formed and completely lost the insertion (group R0); responsive, which formed and retained LIS-1 (group R1); and responsive unstable (group R2). A statistically significant difference was found in ‘plant height’ (p < 0.05), ‘technical length of the stem’ (p < 0.05) between R0 and NR, and R2 and NR LIS-1 groups. The machine learning algorithm random forest classifier was used to predict the presence, absence or heterozygosity of LIS-1 in flax plants based on their growth and reproductive characteristics. As a result, the accuracy of the prediction was 98% on test data. In terms of sources for the selection of fibre flax varieties adaptive to environmental challenges, the most promising group consists of responsive varieties that have formed LIS-1 insertion (R0, R1 and R2 groups).","PeriodicalId":514160,"journal":{"name":"Genetic Resources","volume":"134 S446","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141002810","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A public mid-density genotyping platform for cultivated blueberry (Vaccinium spp.)","authors":"Dongyan Zhao, Manoj Sapkota, Jeff Glaubitz, N. Bassil, Molla F Mengist, Massimo Iorizzo, Katarzyna Heller-Uszynska, Marcelo Mollinari, C. Beil, Moira Sheehan","doi":"10.46265/genresj.wqzs1824","DOIUrl":"https://doi.org/10.46265/genresj.wqzs1824","url":null,"abstract":"Small public breeding programmes have many barriers to adopting technology, particularly creating and using genetic marker panels for genomic-based decisions in selection. Here we report the creation of a DArTag panel of 3,000 loci distributed across the tetraploid genome of blueberry (Vaccinium corymbosum) for use in molecular breeding and genomic prediction. The creation of this marker panel brings cost-effective and rapid genotyping capabilities to public and private breeding programmes. The open access provided by this platform will allow genetic data sets generated on the marker panel to be compared and joined across projects, institutions and countries. This genotyping resource has the power to make routine genotyping a reality for any breeder of blueberry.","PeriodicalId":514160,"journal":{"name":"Genetic Resources","volume":"27 10","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-04-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140715608","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The first draft genome sequence of Russian olive (Elaeagnus angustifolia L.) in Iran","authors":"Leila Zirak, R. Khakvar, Nadia Azizpour","doi":"10.46265/genresj.waot8693","DOIUrl":"https://doi.org/10.46265/genresj.waot8693","url":null,"abstract":"Russian olive (Elaeagnus angustifolia L.) is a native tree species of Iran and the Caucasus region growing in both wild habitats and cultivated settings. The area under cultivation of this tree has been increasing in recent years due to its ability to withstand drought and soil salinity. Revealing the complete genome of this tree holds great importance. To achieve this, a local cultivar of Russian olive was sampled from the northwest region of Iran for whole genome sequencing using the Illumina platform resulting in approximately 6GB of raw data. A quality check of the raw data indicated that approximately 45,011,388 read pairs were obtained from sequences totalling around 6.7×109bp with CG content of 31%. To assemble the genome of the Russian olive tree, the raw data was aligned to a reference sequence of the jujube (Ziziphus jujuba) genome, which is the taxonomically closest plant to the Russian olive. Assembly of alignments yielded a genome size of 553,696,299bp consisting of 339,701 contigs. The N50 value was 5,300 with an L50 value of 24,921 and GC content of the Russian olive genome was 31.5%. This research represents the first report on the genome of the Iranian cultivar of the Russian olive tree.","PeriodicalId":514160,"journal":{"name":"Genetic Resources","volume":"59 4","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140746861","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"European genetic resources conservation in a rapidly changing world: three existential challenges for the crop, forest and animal domains in the 21st century","authors":"F. Lefèvre, Danijela Bojkovski, Magda Bou Dagher Kharrat, M. Bozzano, Eléonore Charvolin-Lemaire, S. Hiemstra, H. Kraigher, Denis Laloë, G. Restoux, Suzanne Sharrock, E. Sturaro, Theo van Hintum, M. Westergren, Nigel Maxted","doi":"10.46265/genresj.rejr6896","DOIUrl":"https://doi.org/10.46265/genresj.rejr6896","url":null,"abstract":"Even though genetic resources represent a fundamental reservoir of options to achieve sustainable development goals in a changing world, they are overlooked in the policy agenda and severely threatened. The conservation of genetic resources relies on complementary in situ and ex situ approaches appropriately designed for each type of organism. Environmental and socioeconomic changes raise new challenges and opportunities for sustainable use and conservation of genetic resources.\u0000Aiming at a more integrated and adaptive approach, European scientists and genetic resources managers with long experience in the agricultural crop, animal and forestry domains joined their expertise to address three critical challenges: (1) how to adapt genetic resources conservation strategies to climate change, (2) how to promote in situ conservation strategies and (3) how can genetic resources conservation contribute to and benefit from agroecological systems. We present here 31 evidence-based statements and 88 key recommendations elaborated around these questions for policymakers, conservation actors and the scientific community.\u0000We anticipate that stakeholders in other genetic resources domains and biodiversity conservation actors across the globe will have interest in these crosscutting and multi-actor recommendations, which support several biodiversity conservation policies and practices.","PeriodicalId":514160,"journal":{"name":"Genetic Resources","volume":"39 4","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140253300","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}