11. Genomic insight into the origin, domestication, dispersal, diversification and human selection of Tartary buckwheatYuqi He, Kaixuan Zhang, Yaliang Shi, Mateja Germ, Zlata Luthar, Ivan Kreft, Dagmar Janovská, Vladimir Meglič, Meiliang Zhou, 2024, original scientific article Abstract: Background: Tartary buckwheat, Fagopyrum tataricum, is a pseudocereal crop with worldwide distribution and high nutritional value. However, the origin and domestication history of this crop remain to be elucidated. Results: Here, by analyzing the population genomics of 567 accessions collected worldwide and reviewing historical documents, we find that Tartary buckwheat originated in the Himalayan region and then spread southwest possibly along with the migration of the Yi people, a minority in Southwestern China that has a long history of planting Tartary buckwheat. Along with the expansion of the Mongol Empire, Tartary buckwheat dispersed to Europe and ultimately to the rest of the world. The different natural growth environments resulted in adaptation, especially significant differences in salt tolerance between northern and southern Chinese Tartary buckwheat populations. By scanning for selective sweeps and using a genome-wide association study, we identify genes responsible for Tartary buckwheat domestication and differentiation, which we then experimentally validate. Comparative genomics and QTL analysis further shed light on the genetic foundation of the easily dehulled trait in a particular variety that was artificially selected by the Wa people, a minority group in Southwestern China known for cultivating Tartary buckwheat specifically for steaming as a staple food to prevent lysine deficiency. Conclusions: This study provides both comprehensive insights into the origin and domestication of, and a foundation for molecular breeding for, Tartary buckwheat.
Keywords: domestication, migration, artificial selection, buckwheat, genomics
Published in DiRROS: 31.12.2024; Views: 60; Downloads: 31
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12. Potential of different common (Fagopyrum esculentum Moench) and Tartary (Fagopyrum tataricum (L.) Gaertn.) buckwheat accessions to sustainably manage surrounding weedsY Vieites-Álvarez, MI Hussain, Manuel J. Reigosa, Aleš Kolmanič, Vladimir Meglič, Petra Hlásná Čepková, Meiliang Zhou, Dagmar Janovská, Adela M. Sánchez-Moreiras, 2024, original scientific article Keywords: agroecology, allelopathy, buckwheat, polyphenols, root exudates, sustainable weed management
Published in DiRROS: 31.12.2024; Views: 60; Downloads: 29
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13. AmiCa : atlas of miRNA-gene correlations in cancerNina Hauptman, Jože Pižem, 2024, original scientific article Abstract: The increasing availability of RNA sequencing data has opened up numerous opportunities to analyze various RNA interactions, including microRNA-target interactions (MTIs). In response to the necessity for a specialized tool to study MTIs in cancer and normal tissues, we developed AmiCa (https://amica.omics.si/), a web server designed for comprehensive analysis of mature microRNA (miRNA) and gene expression in 32 cancer types. Data from 9498 tumor samples and 626 normal samples from The Cancer Genome Atlas were obtained through the Genomic Data Commons and used to calculate differential expression and miRNA-target gene (MTI) correlations. AmiCa provides data on differential expression of miRNAs/genes for cancers for which normal tissue samples were available. In addition, the server calculates and presents correlations separately for tumor and normal samples for cancers for which normal samples are available. Furthermore, it enables the exploration of miRNA/gene expression in all cancer types with different miRNA/gene expression. In addition, AmiCa includes a ranking system for genes and miRNAs that can be used to identify those that are particularly highly expressed in certain cancers compared to other cancers, facilitating targeted and cancer-specific research. Finally, the functionality of AmiCa is illustrated by two case studies.
Keywords: miRNA, gene, expression, cancer, correlation, gene prioritization
Published in DiRROS: 31.12.2024; Views: 64; Downloads: 31
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14. Identification of population-informative markers from high-density genotyping data through combined feature selection and machine learning algorithms : Application to European autochthonous and cosmopolitan pig breedsGiuseppina Schiavo, Francesca Bertolini, Samuele Bovo, Giuliano Galimberti, Maria Muñoz, Riccardo Bozzi, Marjeta Čandek-Potokar, Cristina Ovilo, Luca Fontanesi, 2024, original scientific article Keywords: genome, population genomics, random forest, signatures of selection, SNP
Published in DiRROS: 31.12.2024; Views: 46; Downloads: 13
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15. Composition and quality of honey bee feed: the methodology and monitoring of candy boardsSoraia I. Falcão, Michel Bocquet, Robert Chlebo, João C. Barreira, Alessandra Giacomelli, Maja Ivana Smodiš Škerl, Giancarlo Quaglia, 2024, original scientific article Keywords: honey bee, honey bee nutrition, candy boards, supplements, bee healt
Published in DiRROS: 31.12.2024; Views: 37; Downloads: 11
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16. Persistence of autozygosity in crossbreds between autochthonous and cosmopolitan breeds of swine : a simulation studyMaria Chiara Fabbri, Emmanuel Lozada-Soto, Francesco Tiezzi, Marjeta Čandek-Potokar, Samuele Bovo, Giuseppina Schiavo, Luca Fontanesi, Maria Muñoz, Cristina Ovilo, Riccardo Bozzi, 2024, original scientific article Keywords: autozygosity, crossbreeding, local breeds, pigs, quantitative traits loci
Published in DiRROS: 31.12.2024; Views: 50; Downloads: 10
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17. Ogorčica Xiphinema index Thorne & Allen, 1950, prenašalec virusa pahljačavosti listov vinske trteJulija Polanšek, Stanislav Trdan, Saša Širca, 2024, original scientific article Abstract: Virusi na rastlinah povzročajo veliko gospodarsko škodo, saj je zdravljenje okuženih trt praktično nemogoče v poznejši fazi rasti, ali pa so uveljavljeni postopki precej dolgotrajni, prav tako proti virusom trenutno ni učinkovitega pripravka ali ukrepa. Med očem skrite prenašalce virusov spadajo tudi ogorčice – majhni organizmi , ki lahko skupaj z virusi povzročajo velike izgube pridelka. Med takšne ogorčice spada tudi vrsta Xiphinema index. Je glavni prenašalec virusa pahljačavosti listov vinske trte (Grapevine fanleaf virus, GFLV). Vinska trta je glavni gostitelj te rastlinsko-parazitske ogorčice. S svojim značilnim dolgim cevastim bodalom – stiletom prodre in se prehranjuje na mladih koreninicah. Okužba vinske trte z GFLV iz rodu Nepovirus vodi v postopno izrojevanje vinske trte in pozneje v gospodarsko nekonkurenčnost vinograda. Obvladovanje okužb z GFLV v vinogradih je večinoma omejeno na obvladovanje ogorčice X. index, ki pa je izjemno težavno, predvsem zaradi njihove relativno dolge življenjske dobe in prostorske razporeditve v tleh. Kot najbolj učinkovita ukrepa sta se izkazala kolobarjenje na zemljišču, kjer se pojavlja ta ogorčica in praha, a sta ta pristopa ekonomsko neprivlačna, saj je za ta ukrep potrebno pustiti zemljišče pred ponovno zasaditvijo novega vinograda brez vinske trte za več let. V prihodnosti je potrebno pozornost posvetiti področju razvoja novih, okolju prijaznejših in učinkovitejših pristopov obvladovanja virusonosnih ogorčic X. index in nadomestiti uporabo nematocidov
Keywords: rastlinsko-parazitske ogorčice, Xiphinema indeks, nepovirusi, Vitis spp., GFLV, biotično zatiranje
Published in DiRROS: 31.12.2024; Views: 46; Downloads: 19
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18. Total mutual-visibility in Hamming graphsCsilla Bujtás, Sandi Klavžar, Jing Tian, 2025, original scientific article Abstract: If $G$ is a graph and $X\subseteq V(G)$, then $X$ is a total mutual-visibility set if every pair of vertices $x$ and $y$ of $G$ admits a shortest $x,y$-path $P$ with $V(P) \cap X \subseteq \{x,y\}$. The cardinality of a largest total mutual-visibility set of $G$ is the total mutual-visibility number $\mu_{\rm t}(G)$ of $G$. In this paper the total mutual-visibility number is studied on Hamming graphs, that is, Cartesian products of complete graphs. Different equivalent formulations for the problem are derived. The values $\mu_{\rm t}(K_{n_1}\,\square\, K_{n_2}\,\square\, K_{n_3})$ are determined. It is proved that $\mu_{\rm t}(K_{n_1} \,\square\, \cdots \,\square\, K_{n_r}) = O(N^{r-2})$▫, where $N = n_1+\cdots + n_r$, and that $\mu_{\rm t}(K_s^{\,\square\,, r}) = \Theta(s^{r-2})$ for every $r\ge 3$, where $K_s^{\,\square\,, r}$ denotes the Cartesian product of $r$ copies of $K_s$. The main theorems are also reformulated as Turán-type results on hypergraphs.
Keywords: mutual-visibility set, total mutual-visibility set, Hamming graphs, Turán-type problem
Published in DiRROS: 30.12.2024; Views: 60; Downloads: 24
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19. Analiza mladja na Pahernikovi posestiTomaž Rihter, Jurij Diaci, 2024, original scientific article Abstract: Kakovostno naravno pomlajevanje je ključno za sonaravno gospodarjenje, a ker gozdna inventura ne zagotavlja dovolj informacij, smo v letu 2023 izpeljali dodatno vzorčenje mladovja na mreži stalnih vzorčnih ploskev na Pahernikovi posesti. Ugotovili smo sprejemljive povprečne gostote mladja pod 130 cm višine s 15.924 osebki ha-1, mejno zadovoljive gostote mladovja nad 130 cm višine in s premerom < 5 cm z 994 osebki ha-1 in nizke gostote za mladovja med 5 in 10 cm premera z 276 osebki ha-1. Vse mladovje je v poprečju zastiralo 24 % površine tal, pritalna vegetacija pa 11 %. Razlike v gostotah in zastiranju mladovja med nadmorskimi višinami in prostorsko ločenimi deli posesti niso bile izrazite. V mladovju je prevladovala smreka (38 %), sledili sta jelka (32 %) in bukev (26 %). Visok delež jelke je bil na račun visokih gostot v višinskem razredu do 20 cm. V višjih razredih je bilo jelke vse manj, objedenost po rastlinojedi divjadi je bila intenzivnejša. Povprečno objedanje mladja do 1,3 m je znašalo 33 %, jelke pa 39 %. Izpeljana inventarizacija in analiza mladovja nakazujeta možnosti izboljševanja gozdne inventure.
Keywords: gostota in zmes drevesnih vrst, veliki rastlinojedi parkljarji, poškodbe mladovja, smrekovo-jelovo-bukovi gozdovi, jelovja, gozdna inventura
Published in DiRROS: 30.12.2024; Views: 326; Downloads: 23
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20. The effect of forest gaps on the diversity and composition of bacterial communities in mixed-type forest soils across the Carpathian mountainsNejc Suban, Olivera Maksimović, Nataša Šibanc, Tijana Martinović, Eva Dařenová, Matjaž Čater, Tine Grebenc, 2024, original scientific article Abstract: Mixed forests of European beech (Fagus sylvatica L.) and silver fir (Abies alba Mill.) play a vital ecological role in Central and South-Eastern Europe. This study investigates the diversity and composition of soil bacterial communities in these forests, focusing on rhizosphere and bulk soils under varying canopy structures. Soil samples were collected from eight sites along the Carpathian Mountains, including managed forests and the remnants of old growth. Metabarcoding of bacterial communities revealed that alpha diversity (species richness, Shannon index, and evenness) was significantly affected by sampling location but not by forest canopy structure or soil type (rhizosphere and bulk soil). The lowest bacterial diversity was found in the old-growth forest of the Beskidy region, while the highest was recorded in managed forest in Vrancea. Beta diversity analyses showed minimal variation between rhizosphere and bulk soil bacterial communities, with geographic distance being the strongest predictor of community composition. Actinobacteriota and Proteobacteria were the dominant phyla across all sites, with higher relative abundance of Actinobacteriota in all rhizosphere samples compared to bulk soil. Complex combinations of various environmental conditions at each sampling location, including soil parameters (mainly pH and C:N ratio), the age of forest gaps, the type and intensity of disturbances, and species composition of above-ground vegetation, can strongly affect soil bacterial communities. A closer examination of additional environmental variables would be necessary to better explain the observed differences in the diversity and composition of bacterial communities.
Keywords: forest gaps, forest management, soil microbiome, soil, rhizosphere, Carpathians, temperate forest
Published in DiRROS: 30.12.2024; Views: 137; Downloads: 33
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