Gene Bank Research Articles

Cryopreservation of sessile oak (Quercus petraea (Matt.) Liebl.) plumules using aluminium cryo-plates: influence of cryoprotection and drying

Background Quercusseeds that are recalcitrant to desiccation and freezing temperatures cannot be stored in gene banks under conventional conditions. However, the germplasm of some recalcitrant seeded species can be stored in liquid nitrogen (–196 °C). Unfortunately, for many species, among them for almost the whole genus Quercus, an effective cryostorage method is still unknown. In this study, we propose a successful cryostorage protocol for Quercus petraea (Matt.) Liebl. germplasm using plumules (a shoot apical meristem of an embryo) frozen on aluminium cryo-plates.ResultsThe plumules isolated from the acorns of ten provenances were prestored in 0.5 M sucrose solution (for 18 h). To form alginate beads (one plumule per bead), the plumules were placed in the wells of a cryo-plate and embedded in calcium alginate gel. For cryoprotection, the encapsulated plumules were immersed in cryoprotectant solution containing 2.0 M glycerol and different concentrations of sucrose (0.8–1.2 M) for 40 min at 25 °C and desiccated under a laminar flow cabinet for 1.0–4.0 h. Cryo-plates with plumules were directly immersed in liquid nitrogen and then cryostored for 30 min. For rewarming, cryo-plates with plumules were immersed in 1.0 M sucrose solution and rehydrated for 15 min at 25 °C. Survival rates varied from 25.8 to 83.4 were achieved after cryoprotection in 1.0 M sucrose solution and the drying of plumules for 2 h. The in vitro regrowth rate of cryopreserved plumules varied among provenances and was 26–77%.ConclusionsThis study presents, for the first time, a successful, simple and effective protocol for the cryopreservation of Q. petraea germplasm that could be used in gene banks. The experiment was successfully repeated on seeds from various provenances, each yielding similar, good results. However, seed quality and storage time after harvesting are important factors in plumule regrowth after cryopreservation.

Biofloc biosecurity: A revolutionary paradigm in augmenting aquaculture health and resilience against Aeromonashydrophila

This research embarked upon an in-depth exploration of the pioneering concept of biofloc biosecurity, assessing its instrumental role in amplifying fish growth dynamics, hematological indices, biochemical metrics, chemical body composition, and immunological defenses, both pre- and post-infection by Aeromonas hydrophila. By juxtaposing biofloc-reared Oreochromis niloticus against traditionally reared fish, intricate observations of histopathological changes and clinical symptomatology were undertaken. Employing 16S RNA, the bacterial strain Aeromonas hydrophila (ATCC 7966) was precisely identified and banked It into gene bank and given accession number (OR452335). After a preparatory period of ten weeks in the Biofloc system, O. niloticus faced a challenge with Aeromonas hydrophila. Empirical findings revealed that fish from the Biofloc cohort displayed marked advancements across all investigational parameters, before and after infection, as opposed to the control set. In the aftermath of the Aeromonas hydrophila confrontation, biofloc-acclimatized fish manifested an elevated resilience against the bacterial onslaught, displaying superior metrics in growth, hematology, biochemistry, body constitution, and immunological response. Biofloc group showed a strong immune response, particularly in terms of Lysozyme and Total Antioxidant Capacity. Additionally, there was a significant impact on Immunoglobulin and Complement 3 after infection, highlighting the group's increased immune activity. Furthermore, these fish attenuated the pernicious morphological indicators and histopathological anomalies instigated by septicemic bacteria, which otherwise inflict substantial economic detriments upon the aquaculture industry. This research underscores the immense promise biofloc biosecurity holds in bolstering the overall health and performance metrics of cultured O. niloticus.

Metalloprotease Genes Expression in Trichophyton mentagraphytes and Trichophyton simii Contains Genetic Variations Isolated from Iraqi Patients Resistance to Ketoconazole and Amphotericin B

This study aimed to use Real-Time Polymerase Chain Reaction analysis, to discover the metalloprotease genes (MEP1-5) in Trichophyton menagraphytes and Trichophyton simii contained Genetic variations and determine their expression and association with the antifungal resistance of dermatophytes. Two species of dermatophytes (five isolates) were used in this study (diagnosed morphologically and molecularly by ITS region previously), which included the following types are (Trichophyton mentagrophytes, and Trichophyton simii) of them contained variations of the percentage of conformity with the gene bank 99% and they were registered with the gene bank. The two species were tested for antifungal susceptibility by using the disk method. RNA was isolated from sample according to the protocol of TRIzol™ Reagent The genes used in this study were the metalloprotease gene (MEP1-5). The Livak method was used for determining gene expression. All the genes were amplified and normalized to 18S-Rrna as reference genes. All Trichophyton simii isolates contains the five genes MEP 1 to 5 but Trichophyton mentagrophytes one isolate contains five genes (MEP1-5) and others isolate contains four gene MEP 1 to 4. It has been found that Amphotericin B inhibits the MEP 4 and MEP 5 genes other than the MEP1,2,3 genes. The MEP2 and3 recorded the highest increase in gene expression after treatmentin in Trichophyton simii, while in Trichophyton mentagrophytes the MEP1 recorded the highest increase in gene expression after treatment fllowed by MEP2,3,4 respectively. It has been found that Amphotericin B, had a better effect to inhibit the genes of fungi of Trichophyton mentagrophytes, and Trichophyton simii other than Ketoconazole, especially the MEP 5 followed by MEP 4.

Identification of Orissa frog Fejervarya orissaensis from Bangladesh based on 16s and 12s rRNA genes

In this study, we attempted species-level identification of frog specimen collected from Faridpur district of Bangladesh beyond it’s location outside Orissa, India. Specimen was identified morphologically at genus level as Fejervarya sp. belonging to the family Dicroglossidae using finger formula F3>F4>F1=F1 where F denote as toe finger. From the study two nucleotide sequences of 16S and 12S rRNA genes were obtained which contained 508bp and 408bp respectively. The Sequences were submitted to Gene Bank database with the accession number OQ231604 and OQ240197 for 16S and 12S rRNA gene sequences. Furthermore, the 16S rRNA gene sequence was used as molecular bar-code for the identified Orissa frog F. orissaensis species from Bangladesh. GC content of partial 12S and 16S rRNA genes have been calculated as 44% and 45% respectively. For 16S rRNA gene sequence there was no intra specific divergence. Whereas the inter specific polymorphic divergence were calculated 4.13% and 6.3% when the collected Orissa frog F. orissaensis was compared with that of F. iskandari and F. kupitzi, respectively. In case of 12S rRNA gene intra specific divergence was found 2.45% where the inter specific divergence were 4.41% and 6.86% when the collected Orissa frog F. orissaensis was compared with that of F. iskandari and F. limnocaris, respectively. Maximum likelihood tree also indicates that our sample Orissa frog formed a monophyletic group with F. orissaensis in both the cases of 16S and 12S rRNA genes and thus can be concluded as closely related. Therefore, the collected specimen was identified to be belonging to Fejervarya orissaensis which would be first report from Bangladesh outside Orissa, India. Bangladesh J. Zool. 51(3): 301-313, 2023

Diversity, conservation and utilization of grain legumes: A potential source for food and nutritional security in Nepal

Grain legumes are precious crops of Nepal in terms of the dietary protein supplement ample concentration of micronutrients, and role in crop intensification and ameliorating soil fertility. About 11% of the cultivated area is occupied by grain legumes that include lentil, chickpea, grasspea, fieldpea, fababean, pigeonpea, soybean, blackgram, horsegram, ricebean, cowpea, and mungbean. About 100 genera and 379 species of legumes are distributed in diverse agroecological zones ranging from terai to the alpine region of Nepal, with growth habits ranging from annual to perennial shrubs. Out of the 379 species of legumes which include grain, vegetable, and forage legumes, 262 are native, and 20 species belonging to the sub-group Papilionacae are used as food legumes. Highest food legume species diversity has been recorded in Macrotyloma (34 spp.), followed by Crotalaria (18 spp.), Vigna (15 spp.), Lathyrus (7 spp.), Vicia (6 spp.), Cajanus (5 spp.), Trigonella (5 spp.) and Phaseolus (4 spp.). Other genus having 1-3 species includes Cicer (3 spp.), Mukuna (3 spp.), Glycine (2 spp.), Canavila (2 spp.), Pisum (2 spp.), Lablab (2 spp.), Pachyrrhizus (1 sp.), Psophocarpus (1 sp.), Lens (1 sp.) and Cyamopsis (1 sp.). Research on grain legumes was initiated in 1976 and a systematic collection of grain legume landraces was done in 1987 by the Grain Legumes Research Program (GLRP). Past collection missions organized in collaboration with the International Development Research Centre (IDRC), the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), the International Center for Agricultural Research in the Dry Areas (ICARDA), and other institutes have resulted in the collection of 1107 landraces and provided an opportunity for their inclusion in the variety improvement program. National Agricultural Genetic Resources Center (NAGRC) has conserved 2936 landraces of different legumes, 951 landraces have been kept in gene banks of ICARDA center, while GLRP Khajura has active collections of 218 landraces and 627 exotic germplasm of various legume crops. Varietal improvement programs resulted in the development of 51 varieties, while 6 varietes were registered and two varieties were de-notified in food legumes (lentil, chickpea, soybean, cowpea, black gram, mungbean, pigeon pea, rice bean, faba bean, grass pea, and kidney bean).

Genetic diversity analysis of banana using SSR markers

Banana, a crucial fruit crop thriving in tropical and sub-tropical regions, facing a notable challenge of elevated sterility across various cultivated banana genotypes. This sterility issue hampers the cultivation of diverse banana varieties. Therefore, a focused endeavour is crucial to thoroughly investigate the richness of diversity within both wild and cultivated banana genotypes, aiming to preserve it for future utilization. In the present study, 21 Musa genotypes were collected from different places of North-Eastern Region, and conserved in the field gene bank at Department of Horticulture, College of Agriculture, Lembucherra, Tripura during 2015-2022. Molecular characterization and DNA fingerprinting of these banana accessions were performed by employing 16 banana SSR markers. The number of alleles per locus ranged from 15 to 24 with an average 20.375. The expected heterozygosity (He) ranged from 0.564-0.967 with a mean of 0.852, and the polymorphic information content (PIC) varies from 0.638–0.945 (mean = 0.859). Genetic diversity analysis showed dissimilar groups, indicating possibility of involvement of different accuminata and balbisiana types in evaluation of banana in NE region. The outcome of the current study will be useful for des igning banana crops against different stresses

A diverse panel of 755 bread wheat accessions harbors untapped genetic diversity in landraces and reveals novel genetic regions conferring powdery mildew resistance

Key message A bread wheat panel reveals rich genetic diversity in Turkish, Pakistani and Iranian landraces and novel resistance loci to diverse powdery mildew isolates via subsetting approaches in association studies.Wheat breeding for disease resistance relies on the availability and use of diverse genetic resources. More than 800,000 wheat accessions are globally conserved in gene banks, but they are mostly uncharacterized for the presence of resistance genes and their potential for agriculture. Based on the selective reduction of previously assembled collections for allele mining for disease resistance, we assembled a trait-customized panel of 755 geographically diverse bread wheat accessions with a focus on landraces, called the LandracePLUS panel. Population structure analysis of this panel based on the TaBW35K SNP array revealed an increased genetic diversity compared to 632 landraces genotyped in an earlier study and 17 high-quality sequenced wheat accessions. The additional genetic diversity found here mostly originated from Turkish, Iranian and Pakistani landraces. We characterized the LandracePLUS panel for resistance to ten diverse isolates of the fungal pathogen powdery mildew. Performing genome-wide association studies and dividing the panel further by a targeted subsetting approach for accessions of distinct geographical origin, we detected several known and already cloned genes, including the Pm2a gene. In addition, we identified 22 putatively novel powdery mildew resistance loci that represent useful sources for resistance breeding and for research on the mildew-wheat pathosystem. Our study shows the value of assembling trait-customized collections and utilizing a diverse range of pathogen races to detect novel loci. It further highlights the importance of integrating landraces of different geographical origins into future diversity studies.

Effect of Pre-treatments on Germination of Pterocarpus marsupium Roxb. for Developing Field Gene-Banks in Eastern India

Aims: Pterocarpus marsupium Roxb. is an important timber species with high medicinal properties belonging to the Fabaceae family. The species is severely threatened by anthropogenic and ecological pressures coupled with less natural regeneration. No results in vegetative propagation methods and very less germination is reported for the species under nursery conditions. This study investigates the germination potential of P. marsupium seeds under the prevailing climatic conditions of regions in eastern India. Place and Duration of Study: The study was carried out at the ICFRE - Institute of Forest Productivity (IFP), Lalgutwa, Ranchi, during the 24th to the 32nd Meteorological Standard Week (MSW) of 2022, spanning from June to August. Methodology: Seeds were collected from three CPTs selected from natural forests of Jharkhand, Bihar and West Bengal and the experiment was carried out following split plot design. Observations on several germination parameters and seed vigour indices were recorded until eight weeks after sowing and subjected to factor multivariate analysis of variance (MANOVA) in SPSS 25.0. Results: The experiment revealed that alternate wetting and drying of seeds significantly (P <. 001) outperformed all other treatments with a highest germination percentage of 60±1.196%. Accessions from Jharkhand and West Bengal exhibited significantly (P < .001) better vigour indices (1959.8, 1855.35 for SVI-I and 538.715, 527.742 for SVI-II, respectively) compared to the accession from Bihar (1796.49 and 532.618 for SVI-I and SVI-II). Although the study did not find any significant interaction between the treatments and accession, there was a statistically significant impact on the aggregate dependent variables (F (126,503.279) = 1.579, P <. 001; Wilks' Λ = .077). Conclusion: The results of this study report an economically feasible and rapid seed treatment method for establishing field gene banks of P. marsupium in eastern India to aid its ex-situ conservation practices.

Diversity of actinomycetes on plant rhizosphere of karst ecosystem of Gorontalo, Indonesia

Abstract. Retnowati Y, Kandowangko NY, Katili AS, Pembengo W. 2024. Diversity of actinomycetes on plant rhizosphere of karst ecosystem of Gorontalo, Indonesia. Biodiversitas 25: 907-915. The objective of this study was to isolate and identify the actinomycetes associated with the rhizosphere of plants in the karst ecosystem. This study was descriptive-quantitative. Soil sampling was conducted at three locations of the karst ecosystem of Gorontalo, i.e., Bangga Hills at Bangga Bubaa Coastal area of Gorontalo District, Hills around Lake Limboto of Gorontalo District, and Oluhuta Beach Hills at Bone Bolango District. Rhizosphere-soil sample was collected from 15-30 cm of soil depth. Isolation of actinomycetes was performed using the plate method. The screening of phosphate-solubilizing bacteria was based on the ability to solubilize phosphates indicated by the clear zone on the Pikovskaya medium. Identification of actinomycetes bacteria based on morphology and molecular characters. The morphology character included the color of aerial and substrate mycelium. Molecular characteristics based on the sequence of 16S rRNA gene compared to sequence data on the gene bank of NCBI. The phylogenetic tree reconstruction was based on the Neighbor-joining algorithm. The results successfully found six isolates, including three actinomycetes isolates, two non-actinomycetes bacteria, and one yeast. They were isolated from the rhizosphere of Malastoma malabathrum, Chromolaena odorata, Cycas rumphii, Leucaena leucocephala, and Jatropha curcas. The actinomycetes isolate showed plant-growth-promoting potential indicated by solubilizing phosphate and Indole 3-Acetic Acid production activities. Based on the molecular analysis, actinomycetes were closely related to Streptomyces aegyptia (MT505707.1:42-1426), Streptomyces sp. GGCR-6 (MH718844.1:5-1391), and Streptomyces carpaticus strain PES-A23 (MH712039).

Biological Study with Morphological Characterization of Flower Phenology in Garcinia indica (Choisy)

Characterization flowering patten in Garcinia indica was studied using different age groups planted in a field gene bank. Flowering commenced in five-year-old trees (5YP) in all age groups targeted to study. followed by four-year-old trees. The first flowering was recorded during 3-4th week of November and continued for ten weeks among the plants. G. indica accessions with mixed sexuality were recorded where, the majority of bisexual flowers with female and male flower were there in the same plant. However, flower appearance started in 3rd week of November and extended up to December 3rd week and the maximum number of trees flowered in 1st week of December. Most of the accessions recorded 50 per cent flowering on 2nd and 3rd week of January. The duration of flowering varied from 8 to 10 weeks. Majority of the flowers were observed to be auxiliary and some of them were terminal. Traits such as petal length, sepal length, stamen length and style length did not exhibit significant differences among the accessions studied. However, pollen viability varied among the accessions. Maximum per cent (88.33%) of viable pollen were recorded in 5YP-1 and minimum (82%) in 5YP-3 & 15 with the mean value of 45.68%.

Isolation, molecular characterization and antibiogram of Lactic acid bacteria from dairy cattle sources of Mizoram, India

A total of 250 samples of dairy cattle sources comprised of 100 cattle faeces, 75 raw milk, and 75 fermented milk samples which were randomly collected from different areas of Aizawl district of Mizoram that have been analyzed bacteriologically for enumeration and isolation of Lactic acid bacteria (LAB). The 90 phenotypically positive LAB isolates were further analyzed molecularly by 16S-rRNA gene analysis and 42 isolates were found positive. A total of 20 PCR positive LAB isolates were randomly selected and sequenced, out of which 11 isolates were positive for LAB after sequence analysis, belonging to six species of LAB, namely Lactibantibacillus plantarum (4), Lactobacillus fermentum (2), Lactobacillus brevis (2), Bacillus coagulance (1), Enterococcus faecium (1) and Weissella cibaria (1). The phylogenetic tree was constructed to check the relatedness of the strains with other referral LAB strains from NCBI gene bank. These 11 isolates were further analyzed for antibiogram. All 11 LAB strains tested for antibiotic sensitivity were 100% resistant to kanamycin, whereas intermediate resistance was shown by Lactobacillus brevis FM046 to clindamycin and three strains namely Lactobacillus fermentum FM011, Bacillus coagulans FM033 and Lactobacillus brevis FM046 to penicillin. All the 11 LAB strains were 100% sensitive to most of the tested antibiotics namely amikacin, ampicillin, azithromycin, cefoxitin, cefpodoxime, ceftriaxone, erythromycin, gentamicin and rifampicin. The LAB strains detected from the dairy cattle sources of Mizoram with sensitive antibiogram might be further studied for their probiotic potential.

Mapping the genetic architecture of low-temperature stress tolerance in citron watermelon.

Sweet-fleshed watermelon (Citrullus lanatus) is an important vegetable crop of the tropical origin. It is widely grown and consumed around the world for its hydration and nutritional quality values. Low-temperature stress can affect early planting, seedling establishment, and expansion of crop production to new areas. A collection of 122 citron watermelon (Citrullus amarus) accessions were obtained from the USDA's National Plant Germplasm Repository System gene bank in Griffin, GA. The accessions were genotyped using whole genome resequencing to generate single nucleotide polymorphisms (SNPs) molecular markers and screened under cold-stressed and non-stressed control conditions. Four low-temperature stress tolerance related traits including shoot biomass, vine length, maximum quantum efficiency of photosystem II, and chlorophyll content were measured under cold-stressed and non-stressed control treatment conditions. Correlation analysis revealed the presence of positive relationships among traits. Broad-sense heritability for all traits ranged from 0.35 to 0.73, implying the presence of genetic contributions to the observed phenotypic variation. Genomic regions underlying these traits across several citron watermelon chromosomes were identified. Four low-temperature stress tolerance related putative candidate genes co-located with the peak SNPs from genome-wide association study. These genomic regions and marker information could potentially be used in molecular breeding to accelerate genetic improvements for low-temperature stress tolerance in watermelon.

Molecular Characterization of Vigna unguiculata (L.) Walp Collection based on ISSR Markers

Background: In Azerbaijan, cow pea is one of the fundamental legumes. This study was carried out at the Institute of Genetic Resources, Azerbaijan National Academy of Sciences to evaluate genetic diversity in 28 cowpea accessions from Azerbaijan national gene bank. The aim of this study was to evaluate the genotypic diversity, relatedness and population structure among local cow pea resources available in Azerbaijan and the cultivated VIR accessions based on ISSR markers. Methods: The studies were conducted in 2017-2019 at the Institute of Genetic Resources (IGR) of the National Academy of Sciences (NAS) of Azerbaijan. 28 samples were used as research material: 10 of them were local forms and 18 were samples obtained from VIR. Sowing of collection samples was carried out in duplicate with an area of food of one plant 10 ´ 45 cm at the optimum time, in the at the end of April. Result: In the study, 28 alleles were synthesized for the collection with five ISSR markers, with an average polymorphism index of 75%. The rich genetic diversity (GMO = 0.80; PIC = 0.34) was found in the collection. Statistical analyzes have shown that the efficiency of the UBC 835 and the UBC 818 premieres was high. The average genetic distance index in the cow pea collection was 0.33. 71% of the samples were genetically identifiable and 29% revealed that the genotype was identical across the studied loci. PCoA and cluster analysis identified 3 genetically distinct groups within the collection, with the first two coordinates explaining 57% of this genetic variation.

Novel SNP markers for flowering and seed quality traits in faba bean (Vicia faba L.): characterization and GWAS of a diversity panel.

Faba bean (Vicia faba L.) is a legume crop grown in diverse climates worldwide. It has a high potential for increased cultivation to meet the need for more plant-based proteins in human diets, a prerequisite for a more sustainable food production system. Characterization of diversity panels of crops can identify variation in and genetic markers for target traits of interest for plant breeding. In this work, we collected a diversity panel of 220 accessions of faba bean from around the world consisting of gene bank material and commercially available cultivars. The aims of this study were to quantify the phenotypic diversity in target traits to analyze the impact of breeding on these traits, and to identify genetic markers associated with traits through a genome-wide association study (GWAS). Characterization under field conditions at Nordic latitude across two years revealed a large genotypic variation and high broad-sense heritability for eleven agronomic and seed quality traits. Pairwise correlations showed that seed yield was positively correlated to plant height, number of seeds per plant, and days to maturity. Further, susceptibility to bean weevil damage was significantly higher for early flowering accessions and accessions with larger seeds. In this study, no yield penalty was found for higher seed protein content, but protein content was negatively correlated to starch content. Our results showed that while breeding advances in faba bean germplasm have resulted in increased yields and number of seeds per plant, they have also led to a selection pressure towards delayed onset of flowering and maturity. DArTseq genotyping identified 6,606 single nucleotide polymorphisms (SNPs) by alignment to the faba bean reference genome. These SNPs were used in a GWAS, revealing 51 novel SNP markers significantly associated with ten of the assessed traits. Three markers for days to flowering were found in predicted genes encoding proteins for which homologs in other plant species regulate flowering. Altogether, this work enriches the growing pool of phenotypic and genotypic data on faba bean as a valuable resource for developing efficient breeding strategies to expand crop cultivation.

Using ddRADseq to assess the genetic diversity of in-farm and gene bank cacao resources in the Baracoa region, eastern Cuba, for use and conservation purposes.

The Baracoa region, eastern Cuba, hosts around 80 % of the country cacao (Theobroma cacao L.) plantations. Cacao plants in farms are diverse in origin and propagation, with grafted and hybrid plants being the more common ones. Less frequent are plants from cuttings, TSH progeny, and traditional Cuban cacao. A national cacao gene bank is also present in Baracoa, with 282 accessions either prospected in Cuba or introduced from other countries. A breeding program associated with the gene bank started in the 1990s based on agro-morphological descriptors. The genetic diversity of cacao resources in Baracoa has been poorly described, except for traditional Cuban cacao, affecting the proper development of the breeding program and the cacao planting policies in the region. To assess the population structure and genetic diversity of cacao resources in Baracoa region, we genotyped plants from both cacao gene bank (CG) and cacao farms (CF) applying a new ddRADseq protocol for cacao. After data processing, two SNPs datasets containing 11,425 and 6,481 high-quality SNPs were generated with 238 CG and 135 CF plants, respectively. SNPs were unevenly distributed along the 10 cacao chromosomes and laid mainly in noncoding regions of the genome. Population structure analysis with these SNP datasets identified seven and four genetic groups in CG and CF samples, respectively. Clustering using UPGMA and principal component analysis mostly agree with population structure results. Amelonado was the predominant cacao ancestry, accounting for 49.22 % (CG) and 57.73 % (CF) of the total. Criollo, Contamana, Iquitos, and Nanay ancestries were detected in both CG and CF samples, while Nacional and Marañon backgrounds were only identified in CG. Genetic differentiation among CG (FST ranging from 0.071 to 0.407) was higher than among CF genetic groups (FST: 0.093-0.282). Genetic diversity parameters showed similar values for CG and CF samples. The CG and CF genetic groups with the lowest genetic diversity parameters had the highest proportion of Amelonado ancestry. These results should contribute to reinforcing the ongoing breeding program and updating the planting policies on cacao farms, with an impact on the social and economic life of the region.

Crop-to-wild gene flow in wild coffee species: the case of Coffea canephora in the Democratic Republic of the Congo.

Plant breeders are increasingly turning to crop wild relatives (CWRs) to ensure food security in a rapidly changing environment. However, CWR populations are confronted with various human-induced threats, including hybridization with their nearby cultivated crops. This might be a particular problem for wild coffee species, which often occur near coffee cultivation areas. Here, we briefly review the evidence for wild Coffea arabica (cultivated as Arabica coffee) and Coffea canephora (cultivated as Robusta coffee) and then focused on C. canephora in the Yangambi region in the Democratic Republic of the Congo. There, we examined the geographical distribution of cultivated C. canephora and the incidence of hybridization between cultivated and wild individuals within the rainforest. We collected 71 C. canephora individuals from home gardens and 12 C. canephora individuals from the tropical rainforest in the Yangambi region and genotyped them using genotyping-by-sequencing (GBS). We compared the fingerprints with existing GBS data from 388 C. canephora individuals from natural tropical rainforests and the INERA Coffee Collection, a Robusta coffee field gene bank and the most probable source of cultivated genotypes in the area. We then established robust diagnostic fingerprints that genetically differentiate cultivated from wild coffee, identified cultivated-wild hybrids and mapped their geographical position in the rainforest. We identified cultivated genotypes and cultivated-wild hybrids in zones with clear anthropogenic activity, and where cultivated C. canephora in home gardens may serve as a source for crop-to-wild gene flow. We found relatively few hybrids and backcrosses in the rainforests. The cultivation of C. canephora in close proximity to its wild gene pool has led to cultivated genotypes and cultivated-wild hybrids appearing within the natural habitats of C. canephora. Yet, given the high genetic similarity between the cultivated and wild gene pool, together with the relatively low incidence of hybridization, our results indicate that the overall impact in terms of risk of introgression remains limited so far.

Genomic characterization of dryland adaptation in endangered Anxi cattle in China.

Local species exhibit distinctive indigenous characteristics while showing unique productive and phenotypic traits. However, the advent of commercialization has posed a substantial threat to the survival of indigenous species. Anxi cattle, an endangered native breed in China, have evolved unique growth and reproductive characteristics in extreme desert and semidesert ecosystems. In this study, we conducted a genomic comparison of 10 Anxi cattle genomes with those of five other global populations/breeds to assess genetic diversity and identify candidate genomic regions in Anxi cattle. Population structure and genetic diversity analyses revealed that Anxi cattle are part of the East Asian cattle clade, exhibiting higher genetic diversity than commercial breeds. Through selective sweep analysis, we identified specific genetic variations linked to the environmental adaptability of Anxi cattle. Notably, we identified several candidate genes, including CERS3 involved in regulating skin permeability and antimicrobial functions, RBFOX2 associated with cardiac development, SLC16A7 participated in the regulation of pancreatic endocrine function, and SPATA3 related to reproduction. Our findings revealed the distinctive genomic features of Anxi cattle in dryland environments, provided invaluable insights for further research and breed preservation, and had important significance for enriching the domestic cattle breeding gene bank.

Essential oil variation of Achillea filipendulina populations in farm condition

ABSTRACT Achillea filipendulina is a native aromatic plant with antibacterial and anti-inflammatory properties. This research aimed to determine and compare the essential oil content and composition of different populations of this plant in farm condition. Seeds provided by the Natural Resources Gene Bank of Iran were sown in a field experiment over two years. Essential oils from the aerial parts of all populations, at full flowering stage, were obtained by hydro-distillation and analysed by gas chromatography (GC) and gas chromatography-mass spectrometry (GC/MS). The oil yields ranged from 0.13% to 1.20%. Twenty-six compounds were identified with 1,8-cineole (2.0–73.5%), santolina alcohol (14.2–35%) and borneol (0.6–20.4%) as major components. Cluster analysis divided all accessions into two clusters. The main compounds in cluster 1 (two populations) were santolina alcohol, borneol, cis-chrysanthenyl acetate, bornyl acetate and α-pinene. The oils in Cluster 2 contained borneol, cis-chrysanthenyl acetate and high amount of 1,8-cineole (22.6–73.5%) as main components.

Hilly, Semi-Mountainous and Mountainous Areas Harbor Landraces Diversity: The Case of Messinia (Peloponnese-Greece)

Landraces are identified for their genetic diversity and heritage value. Geographically isolated areas are gradually recognized for their agricultural diversity and importance in conservation. One of the consequences of agricultural intensification is an increase in crop uniformity and hence a reduction in the landraces’ genetic resources. Messinia, located in Southwest Peloponnese, Greece, is characterized by a diverse terrain and smallholdings. The geomorphological character of the area and farmers’ selections have led to new landraces (local varieties) with unique traits and specific adaptations. A total of 110 villages/settlements were visited between 2013–2016, aiming to explore the existing wealth of landraces and the degree of genetic erosion. The genetic material collected and the testimonies extracted from local communities were compared to data from past expeditions, gene banks, and portal databases. Of the 427 collected samples, the majority belonged to annual vegetable or pulse species, indicating the genetic diversity of the groups, which was likely related to their culinary value. Perennial crops are priced both as commercial and staple crops, with olive trees dominating the agricultural landscape. Genetic erosion and production decline were noticed for cereals. It is concluded that socio-cultural and agricultural trends have a strong influence on the survival of landraces. Without exhausting the agricultural wealth of the region, the present study suggests that Messinia is an agrobiodiversity hotspot that includes neglected crops.

Short Communication: Aplocheilus panchax Hamilton, 1822 Found at Acidic Waters of Abandoned Ex-tin Mining Ponds as Insectivorous Fish and Its Role for Water Quality Improvement

Kepala timah fish or blue panchax is one of the species found at acidic waters of abandoned ex-tin mining pond. Kepala timah fish belongs to the extremophile fishes which can survive in extreme aquatic environments caused by pressure from environmental factors. This study aimed to confirm the kepala timah fish as a species of Aplocheilus panchax and to analyze its natural food habits. Molecular analysis through DNA barcoding was carried out by analyzing the COI gene and confirming the sequence of kepala timah fish in the gene bank on the NCBI website and constructing a phylogenetic tree for kepala timah fish to other A. panchax populations. Analysis of food habits was carried out by identifying the contents of the digestive tract of kepala timah fish which were observed microscopically. The results showed that kepala timah fish found at acidic waters of abandoned ex-tin mining pond was confirmed as Aplocheilus panchax Hamilton, 1822. Some morphological characters confirmed the similarity between kepala timah fish and A. panchax such as a silvery white spot on its head, terminal type of the mouth position, body shape was sagittiform, small dorsal fin on posterior body, and the shape of the caudal fin was rounded or rhomboid. Analysis of the contents of digestive tract showed the food habits of A. panchax found at acidic waters of ex-tin mining pond was insects. The food habits explained that A. panchax was classified as larvivorous or insectivorous fishes. The presence of A. panchax and its metabolic activity at abandoned ex-tin mining ponds can contributed to increasing organic matter in the waters so that it can be beneficial for improving water quality.