Conservation Of Genetic Resources Research Articles

Development of a robust SNP marker set for genotyping diverse gene bank collections of polyploid roses

BackgroundDue to genetic depletion in nature, gene banks play a critical role in the long-term conservation of plant genetic resources and the provision of a wide range of plant genetic diversity for research and breeding programs. Genetic information on accessions facilitates gene bank management and can help to conserve limited resources and to identify taxonomic misclassifications or mislabelling. Here, we developed SNP markers for genotyping 4,187 mostly polyploid rose accessions from large rose collections, including the German Genebank for Roses.ResultsWe filtered SNP marker information from the RhWag68k Axiom SNP array using call rates, uniformity of the four allelic dosage groups and chromosomal position to improve genotyping efficiency. After conversion to individual PACE® markers and further filtering, we selected markers with high discriminatory power. These markers were used to analyse 4,187 accessions with a mean call rate of 91.4%. By combining two evaluation methods, the mean call rate was increased to 95.2%. Additionally, the robustness against the genotypic groups used for calling was evaluated, resulting in a final set of 18 markers. Analyses of 94 pairs of assumed duplicate accessions included as controls revealed unexpected differences for eight pairs, which were confirmed using SSR markers. After removing the duplicates and filtering for accessions that were robustly called with all 18 markers, 141 out of the 1,957 accessions showed unexpected identical marker profiles with at least one other accession in our PACE® and SSR analysis. Given the attractiveness of NGS technologies, 13 SNPs from the marker set were also analysed using amplicon sequencing, with 76% agreement observed between PACE® and amplicon markers.ConclusionsAlthough sampling error cannot be completely excluded, this is an indication that mislabelling occurs in rose collections and that molecular markers may be able to detect these cases. In future applications, our marker set could be used to develop a core reference set of representative accessions, and thus optimise the selection of gene bank accessions.

A Comparative Metabolomics Study of the Potential Marker Compounds in Feces from Different Hybrid Offspring of Huainan Pigs.

As a notable native Chinese genetic population, the Huainan pig has an exceptional meat quality but a low percentage of lean meat and subpar genetic performance. To better exploit the superior genetic traits of the Huainan pig and address knowledge gaps regarding the optimization of its hybrid offspring, this study used Huainan pigs as the maternal line and bred them with Yorkshire, Landrace, and Berkshire sires. This approach produced three hybrid combinations: Yorkshire × Huainan (YH), Landrace × Huainan (LH), and Berkshire × Huainan (BH). The body size, fat ratio, and average backfat thickness of these hybrid progeny were evaluated under the same feeding management and nutritional circumstances. The results revealed that the average backfat thickness of YH was significantly lower than that of LH and BH. In order to better understand the causes of these variations, fecal samples were taken from three pigs in each group for metabolomic analysis. A total of 2291 metabolites were identified, including benzene derivatives (16.6%), amino acids and their metabolites (14.5%), and organic acids (13.4%), with pyruvaldehyde and norethindrone acetate elevated in YH compared to LH and BH. In addition, the three hybrid pig groups commonly exhibited differences in the "glycerophospholipid metabolism" pathway. This variation may also contribute to differences in their fat ratio and backfat thickness. Our findings provide a novel perspective on the role of hybrid vigor in advancing the genetic population of Huainan pigs, while also revealing the unique metabolic characteristics of the YH with regard to fat deposition. This study is expected to enhance the conservation and effective utilization of genetic resources within the Huainan pig population.

Comparative ultrastructural and transcriptomic profile analysis of skin tissues from indigenous, improved meat, and dairy goat breeds

BackgroundHigh-quality goatskins are valuable byproducts usually produced by indigenous goat breeds with poorer production performance in Asia and Africa. However, the genetic and molecular mechanisms underpinning goatskin’s biomechanical properties (e.g., tensile strength) remain elusive. Mechanistic exploration of these traits could greatly aid the genetic improvement and genetic resource conservation of native breeds in these regions. To fulfill this purpose, we collected skin tissues from three goat breeds: Huai goat (HG), a Chinese native variety producing high-quality goatskins; Yudong meat goat (YDMG), a crossbreed of HG and Boer goat; Henan dairy goat (HNDG), a dairy goat breed.ResultsScanning electronic microscopy analysis of skin tissues found that the collagen fiber diameters, collagen fibril diameters, and crimps significantly differed among the three goat breeds; however, collagen fibril diameters are similar in HG and HNDG. A sum of 230, 775, and 86 differentially expressed genes (DEGs) were identified from YDMG versus HNDG, HG versus HNDG, and YDMG versus HG, respectively. Functional enrichment analysis suggested that signaling pathways involved in fatty acid, retinol, steroid metabolisms, and GO items related to the physical properties of the skin (e.g., collagen-containing extracellular matrix) are significantly overrepresented in DEGs identified from meat versus dairy goats. Furthermore, 106 DEGs (e.g., COL1A1, COL1A2, and SPARC) showed specific expression patterns in HG and YDMG versus HNDG. Items about biophysical features of skin (e.g., extracellular matrix organization and ECM proteoglycans) are markedly enriched. Protein-protein interaction analysis suggested that two growth factors (IGF1 and PDGFD) are latent collagen and other ECM protein expression modulators.ConclusionUltrastructural analysis of goat skin tissues suggested that collagen fibril diameter is not a major factor affecting goatskin quality. Transcriptomic profiles unveiled core genes and associated biological processes potentially involved in regulating goatskin quality. These discoveries shined new light on deeper understanding the mechanisms of hide-related traits in goat and other livestock.

Genomic signal selection analysis reveals genes related to the lambing trait of Hotan sheep.

Lambing in ewes is a complex and crucial aspect of sheep production that directly influences economic viability and production efficiency. In the present study, we analyzed the genomes of single lamb (SLE) and twin lamb (TLE) Hotan sheep to elucidate the genetic mechanisms underlying lamb production in Hotan sheep. In this study, we used genome-wide resequencing to analyze the genomes of Hotan sheep exhibiting SLE and TLE traits. To identify the population genetic structure and linkage disequilibrium associated with SLE and TLE traits, we employed two complementary genome selection signals: the interpopulation genetic differentiation index (FST) and nucleotide diversity (Pi). Subsequently, we performed gene annotation and enrichment analyses of the selected regions of the obtained genome. Our analysis generated 801 Gb of sequence data, from which 31,864,651 high-quality single nucleotide polymorphic loci were identified. We identified 290 selected regions and 332 genes across the Hotan sheep genome by using two widely adopted selective scanning detection methods (FST statistics and Piratio). Functional annotation and enrichment analysis of these genes identified 13 genes associated with the lambing rate, which were enriched in pathways such as the transforming growth factor-β (TGF-β) signaling pathway (BMPR2, ID2, SMAD7, THBS1, and RBX1), renal cell carcinoma (PAK1, ELOC), inositol phosphate metabolism (PLCZ), non-homologous terminal junction (RAD50), ABC transporters (ABCC4), and the NET pathway (H2B, H4, and H2A). This study employed selective elimination analysis to identify candidate genes involved in the regulation of lambing trait in Hotan sheep. By investigating the molecular mechanisms underlying lambing rate in Hotan sheep, we developed molecular markers for twin lambing to enhance reproductive performance and promote the conservation and development of outstanding genetic resources in local Xinjiang sheep.

LC-MS metabolomics uncovers potential biomarkers of semen cryo-injury in goats.

Semen cryopreservation acts a crucial role in enhancing breed improvement and conserving genetic resources. However, it often leads to decreased sperm activity and reduced pregnancy rates. Despite significant advancements in semen freezing techniques for goats, the precise factors and mechanisms causing cryo-injury remain unclear. In this study, we examined the motility characteristics of fresh semen versus frozen-thawed semen and investigated changes in the metabolite profiles of seminal plasma using liquid chromatograph-mass spectrometry (LC-MS). A total of 364 differentially expressed metabolites (DEMs) were identified between fresh and frozen-thawed semen samples. Among these, 185 metabolites were significantly up-regulated, while 179 were down-regulated (p<0.05). The majority of these DEMs belonged to lipids and lipid-like molecules, as well as organic acids and derivatives. The Kyoto Encyclopedia of Genes and Genomes (KEGG) indicated that these DEMs were primarily involved in pathways related to amino acid synthesis and metabolism. Additionally, metabolite set enrichment analysis (MSEA) underscored the critical role of amino acid synthesis and metabolic pathways in semen cryopreservation. Specific metabolites such as alanine, proline, phenylalanine, tryptophan, tyrosine, adenosine, citric acid, flavin adenine dinucleotide (FAD), and choline emerged as potential biomarkers for sperm cryo-injury in goats. These findings provide valuable insights into enhancing the quality of semen cryopreservation in goats, contributing to improved breeding and genetic resource conservation efforts.

Genetic structure of cattle of the siberian branch by microsatellite loci

Molecular-genetic methods are essential tools for the utilization and conservation of animal genetic resources. These methods facilitate more efficient management and control of breeding programs within livestock production systems. For studying the genetic diversity of a population, the use of STR markers is relevant due to the high variability of repeats. This study presents a genetic characterization of a Holstein and Black Pied cattle population (n = 10233) in Western Siberia using 12 microsatellite loci (BM1818, BM1824, BM2113, ETH10, ETH225, ETH3, INRA023, SPS115, TGLA126, TGLA122, TGLA227, TGLA53). A total of 145 alleles were identified across all loci, with frequencies ranging from 0.00005 to 0.68961. The highest level of genetic diversity was observed at the TGLA122 locus (25 alleles) with an average number of effective alleles (Ne) of 4.5. The least polymorphic locus was BM1824 (7 alleles) with an average Ne of 3.27. The average observed (Ho) and expected (He) heterozygosity across all loci was 0.6. The highest variability was observed at the TGLA53 locus, with a Wright’s fixation index (Fis) of 0.161, indicating a heterozygote deficiency. A similar deficiency was observed at the BM1818 locus. All other loci exhibited a positive Fis, with the highest value observed at the ETH3 locus (-0.074), indicating an excess of heterozygotes. The average Fis across all loci was -0.02, suggesting a sufficient level of heterozygosity within the studied population. These findings provide valuable information for population studies and practical breeding programs aiming to manage genetic diversity and improve selection efficiency in this cattle population.

Effects of Supplementation of Different Antioxidants to Cryopreservation Extender on the Post-Thaw Quality of Rooster Semen-A Meta-Analysis.

The standardization of the semen cryopreservation technique could be an effective tool in poultry for the conservation of genetic resources. During this process, the production of reactive oxygen species increases, leading to oxidative stress that causes damage to the spermatozoa. To reduce this effect, the addition of exogenous antioxidants in the cryopreservation diluent has been reported to be effective. Multiple antioxidants such as catalase, vitamin E, cysteamine, ergothioneine, and serine have been studied in roosters. Therefore, the present investigation aims to perform a meta-analysis to determine if the use of the aforementioned antioxidants added to the cryopreservation extender produces an improvement in semen quality parameters in roosters after thawing. After collecting the data, a discriminant canonical analysis was performed to determine which of the selected semen quality traits provided the most information, with hypo-osmotic swelling test (HOST), viability, and total motility variables showing the highest discriminatory power. However, according to the descriptive statistics, catalase and serine are the antioxidants that improve a greater number of seminal quality parameters, and since catalase gives the most favorable results for most of the discriminating variables, it could be the antioxidant of choice.

Analysis of genetic diversity and environmental associations of wild citron (Citrus medica L.) in northeast India

Citron (Citrus medica L.) is a major citrus fruit crop known for its medicinal, nutritional, and aromatic uses. Native to northeast India, Myanmar, and south China, citron is cultivated mostly in the Mediterranean and South Asian countries. The truly wild populations of citron are found in the hills and valleys of northeast India. The extent of genetic diversity in wild citron in relation to environmental variables has not been documented. In the present study, we analyzed genetic diversity and environmental association of wild populations of C. medica in northeast India using 15 polymorphic nuclear SSR (simple sequence repeat) markers and 21 environmental variables. SSR profiling revealed a moderate genetic diversity (Ho = 0.40; He = 0.41; I = 0.70). Neighbor-joining (NJ) and principal coordinate analysis (PCoA) grouped 16 natural populations into two genetic clusters. Bayesian structure results showed two genetic populations with a high admixture of individuals. Analysis of molecular variance (AMOVA) revealed low genetic differentiation (Fst = 0.14; P < 0.001), indicative of high gene flow (Nm = 1.53) in citron. The isolation by distance (IBD) analysis showed a weak correlation, indicating that geographic distance was not a determining factor for genetic distance in C. medica populations. The higher metrics of outcrossing rate (tm > 0.9) revealed outbreeding nature of the species. The genetic diversity of citron showed a positive correlation with precipitation of driest month and precipitation of coldest quarter, but negative with mean diurnal range and isothermality. Overall, the results of the present study could benefit the conservation and management of citron resources and their natural habitat in northeast India. Genetically highly diverse populations identified in the present study can be used for conservation and utilization of citron genetic resources.

Freezability of Semen Collected from Ganders of 12 Breeds Covered by the Polish Genetic Resources Conservation Program

Abstract A rapid decline in wild animal biodiversity, as well as in the number of local livestock breeds of lower economical values, makes species and breeds protection and creation of genetic reserves a necessity and a challenge of the 21st century. For birds, semen freezing is still the best method of gene preservation ex situ in vitro. The aim of the presented study was to assess the susceptibility to freezing process and to establish the semen gene bank of twelve goose breeds covered by the Polish genetic resources conservation program. Sexually mature ganders were randomly selected from four northern local breeds: Kartuska, Pomorska, Rypinska, Suwalska, four southern local breeds: Garbonosa, Kielecka, Lubelska, Podkarpacka, and four foreign goose breeds: Kuban, Landes, Roman and Slovakian. Each breed was represented by 12 males, twelve repetitions were carried out. Semen samples were frozen in a computer-controlled cryogenic chamber using a method developed for White Koluda goose. The basic evaluation criterion was sperm morphology in fresh and freeze-thawed semen assessed in nigrosine-eosin stained histological smears. The percentage of live in total and live normal sperm in the fresh semen differed significantly (P&lt;0.05) between breeds. Semen of Kartuska and Suwalska ganders (northern breeds), contained the highest percent of live sperm – 94.4 and 94.1 respectively, including 52.5% and 54.2% of live normal sperm, while the lowest number of these forms was observed for Slovakian goose – 86.4% and 29.2%, respectively. The freezing process resulted in a significant (P&lt;0.05) reduction in the total number of live and live normal sperm and an increase in dead sperm in all groups. Cryopreservation process was the most effective in case of Suwalska goose semen (28.4% of live normal cells in thawed semen) and the less profitable for Landes (7.4% of live normal cells). The analyses showed significant differences between breeds in sperm morphology in fresh and thawed semen. Moreover, the high proportion of live spermatozoa in the fresh semen did not guarantee a high proportion of spermatozoa after thawing, indicating the differences in semen susceptibility to cryopreservation process depending on goose breed.

The Elimination of Viroids through In Vitro Thermotherapy and a Meristem Tip Culture from a New Limonime Hybrid (Citrus x limon var. limon (L.) Burm. f. x Citrus latifolia var. latifolia)

Viruses and viroids pose a significant challenge in citriculture, and their control is crucial for plant health. This study evaluated the effectiveness of in vitro thermotherapy combined with a meristem tip culture for eliminating citrus exocortis viroid (CEVd) and hop stunt viroid (HSVd) from a new limonime hybrid (Citrus x limon var. limon x Citrus latifolia var. latifolia). The elimination success was confirmed by RT-PCR assays. The in vitro elimination rate for CEVd during the shoot proliferation stage (43%) was higher than for HSVd (21%). Accordingly, in the subsequent rooting stage, the in vitro elimination rate for CEVd (50%) was higher than for HSVd (33%). Successful CEVd and HSVd eradication at a 100% rate was confirmed in the ex vitro acclimatized plants in the greenhouse. The study also established an efficient micropropagation protocol. The optimal treatment for in vitro shoot induction was 0.5–2 mg L−1 benzyladenine (BA) + 0.5 mg L−1 gibberellic acid (GA3) + 0.25 mg L−1 naphthalene acetic acid (NAA), while for shoot elongation, it was 0.5 mg L−1 BA + 0.5 mg L−1 kinetin (KIN) + 0.5 mg L−1 GA3 + 0.25 mg L−1 NAA. Rooting was best promoted by 1 mg L−1 NAA. This study provides valuable insights for the mass production of viroid-free propagation material in this new lemon x lime hybrid, contributing to the conservation of genetic resources in citrus breeding programs through the combined application of in vitro thermotherapy and an in vitro meristem tip culture, a novel and highlighted achievement reported for the first time in this study.

Genetic analysis of village pear (Pyrus communis L.) cultivar populations in northeastern Türkiye

AbstractPear (Pyrus communis L.) stands out as a prominent fruit species in temperate regions worldwide. The Çoruh River basin, nestled in the lower Caucasus in Türkiye, serves as a valuable repository of pear germplasm. To elucidate the genetic structure of pear populations in this region, 84 village pear cultivar genotypes (land races) from six villages, sample garden collections (SCC), and wild Panta root stock populations were analysed using eleven microsatellite markers. Genetic diversity and structure analyses indicated that village pear cultivar populations exhibit substantial genetic diversity and admixture. This diversity is attributed to local farming practices such as phenotypic selection and widespread dispersal of clonal materials. The genetic structure analysis, combined with the identification of private alleles, indicates that the pear genetic resources in the Çoruh river basin likely has originated from two gene pool sources, specifically the Meydancık and Camili village pear traditional cultivar populations. The Camili village pear cultivar population as a new in situ genetic reserve site has been proposed. Despite the existence an ex situ conservation site, the study suggests inadequateness of SCC as an ex situ site in capturing the full extent of genetic diversity of village pear cultivar genetic resources. Thus, enriching the genetic diversity in the SCC ex situ site is essential for effective pear genetic resource conservation in the Çoruh river basin. These findings contribute valuable insights for the development of targeted conservation strategies, ensuring the preservation of pear genetic resources in this region.

Molecular Mechanisms Underlying Freezing Tolerance in Plants: Implications for Cryopreservation.

Cryopreservation is a crucial technique for the long-term ex situ conservation of plant genetic resources, particularly in the context of global biodiversity decline. This process entails freezing biological material at ultra-low temperatures using liquid nitrogen, which effectively halts metabolic activities and preserves plant tissues over extended periods. Over the past seven decades, a plethora of techniques for cryopreserving plant materials have been developed. These include slow freezing, vitrification, encapsulation dehydration, encapsulation-vitrification, droplet vitrification, cryo-plates, and cryo-mesh techniques. A key challenge in the advancement of cryopreservation lies in our ability to understand the molecular processes underlying plant freezing tolerance. These mechanisms include cold acclimatization, the activation of cold-responsive genes through pathways such as the ICE-CBF-COR cascade, and the protective roles of transcription factors, non-coding RNAs, and epigenetic modifications. Furthermore, specialized proteins, such as antifreeze proteins (AFPs) and late embryogenesis abundant (LEA) proteins, play crucial roles in protecting plant cells during freezing and thawing. Despite its potential, cryopreservation faces significant challenges, particularly in standardizing protocols for a wide range of plant species, especially those from tropical and subtropical regions. This review highlights the importance of ongoing research and the integration of omics technologies to improve cryopreservation techniques, ensuring their effectiveness across diverse plant species and contributing to global efforts regarding biodiversity conservation.

RECORDING, PRESERVATION, IMPROVEMENT AND USE OF AUTOCHTHONOUS GENETIC RESOURCES OF PLANTS IN THE REGION OF KORÇA

Korça, although a small area on the surface, stands out for its climatic, land and orthographic diversity. This has made that the genetic diversity, both in spontaneous and cultivated plants per area unit, to be quite wide. After the industrial revolution, there has been an exploitation on a large scale which has led to the narrowing of this biodiversity and in some cases, to their disappearance Collection is the first step in conservation of genetic resources. This includes a series of activities from germplasm exploration, collection of field materials, processing, documentation, to submission for storage Plant exploration was carried out at the time of flowering. At this stage was also determined, the most suitable deadline for the second visit during which the materials will be collected. Most germplasm collections were based on seed collection. Through the study, we identified resources with important genetic values of cultivars and autochthonous populations of the Korça region, such as corn, beans, tomatoes, peppers, onions, cabbage, leeks, watermelons, melons, fodder peas, apples, pears, walnuts, chestnut etc. The next important step is the introduction into the schemes of genetic improvement of seed production of plant forms, especially those that are of interest to farmers. From an economic point of view, this project made a contribution to the reduction of genetic erosion.

Caracterización morfoagronómica de poblaciones de maíz criollo (Zea mays L.), provincia de Manabí, Ecuador

Ecuador is a country with a wide genetic diversity of maize and there are populations of native maize conserved by farmers that have not yet been characterized. These genetic resources could be conserved and used in plant breeding programs. The objective of this research was to characterize the morpho-agronomic diversity of 38 populations of native maize from the province of Manabí, Ecuador, using 19 quantitative and 11 qualitative morpho-agronomic descriptors. During the dry season of 2022 (July - December) at the Portoviejo Experimental Station of the National Institute of Agricultural Research (INIAP), plots of 8 m2 were established for each population of native maize, with 0.3 m between plants and 0.8 m between furrows and each furrow was 5 m long. Cluster analysis showed the formation of four groups, where the populations of hard kernels with large ears and soft kernels with short ears were separated into different groups. The quantitative variables ear height, panicle length, percentage of lodging, number of kernels per row and biomass of the inflorescence rachis recorded "D" indices of 0.75, showing themselves as discriminant variables in the formation of the groups, while the most discriminating qualitative variables were kernel type (χ2 = 49.09***, P= 0.742, V= 0.64), kernel color (χ2= 51.955***, P= 0.75, V=0.64), row arrangement (χ2= 18.11*, P=0.56, V=0.39), and kernel surface shape (χ2 = 20.52*, P=0.58, V=0.41). The native maize races identified were Candela, Cubano, Tuxpeño, Tusilla, and Uchima, observing significant genetic diversity in the populations studied. It was concluded that the characterized native maize populations were a valuable genetic resource for the conservation and use of this cereal. Keywords: genotypes, landraces, genetic variability, conservation of genetic resources.

Understanding the Significance of Raffinose Family Oligosaccharides in Seed Physiology

Seed vigour and longevity are pivotal agronomic traits with profound implications for crop yield, food security, and the global economy. Seed longevity, often defined by the duration of seed viability, is crucial for effective gene bank management, influencing seed regeneration cycles and ensuring the long-term conservation of plant genetic resources. The inevitable process of seed deterioration, driven by a complex network of biochemical reactions, leads to altered metabolism and damage to critical cellular components such as membranes, DNA, mitochondria, proteins, and the antioxidative defence system. In recent research, Raffinose family oligosaccharides (RFOs) have emerged as key contributors to enhancing seed vigour and longevity. These sugars perform multiple functions in plants, including tolerance to abiotic and biotic stresses, regulation of seed germination, and maintenance of desiccation tolerance, all of which are essential for overall seed health. Studies suggest that RFOs significantly bolster seed vigour and longevity through mechanisms such as cytoplasmic vitrification, water replacement, and osmoprotection in dried seeds. These oligosaccharides are particularly abundant in the seeds of leguminous crops and are also found in roots and specialized storage organs. The glassy state formed by RFOs is vital for protecting cells from oxidative damage caused by reactive oxygen species (ROS), enhancing the stability of enzymes, and preventing deleterious conformational changes in proteins. Furthermore, delaying the degradation of RFOs has been shown to inhibit premature germination, underscoring their critical role in early seedling development and successful crop establishment.

Economic Evaluation of Conservation through Use of an Araucaria angustifolia Provenance and Progeny Test.

Araucaria angustifolia is a species known for its valuable wood and nuts, but it is threatened with extinction. The plantation of forests for genetic resource conservation is a complementary strategy designed to reduce the species' genetic variability loss. This study aimed to evaluate the technical and economic viability of A. angustifolia for genetic conservation through use. The analyzed provenance and progeny trial was established in 1982 in Itapeva, Brazil. It was structured using a compact family blocks design with 110 open-pollinated progenies from five natural populations, three replicates, ten plants per subplot, and 3.0 m × 2.0 m spacing. After 33 years, the trial was evaluated for total height, diameter at breast height, wood volume, and survival. The variance components and genetic parameter estimates were performed using Restricted Maximum Likelihood/Best Linear Unbiased Prediction methods (REML/BLUP) methods with the Selegen software (version 2014). The production and management scenarios were obtained using the SisAraucaria software (version 2003). Sensitivity analysis and economic parameter estimates were obtained through various economic evaluation methods using the Planin software (version 1995). In general, the genetic parameters indicated that the population has enough variability for both conservation and breeding purposes, suggesting technical viability for the establishment of a seed orchard. The economic parameters indicated that the commercialization of wood and araucaria nuts proved to be more profitable than wood production by itself. In conclusion, araucaria genetic conservation through use is a technically and economically viable ex situ conservation strategy.

Chromosome-level genome assembly of the medicinal insect Blaps rhynchopetera using Nanopore and Hi-C technologies.

Blaps rhynchopetera Fairmaire is a significant medicinal resource in southwestern China. We utilized Nanopore and Hi-C technologies in combination to generate a high-quality, chromosome-level assembly of the B. rhynchopetera genome and described its genetic features. Genome surveys revealed that B. rhynchopetera is a highly heterozygous species. The assembled genome was 379.24Mb in size, of which 96.03% was assigned to 20 pseudochromosomes. A total of 212.93Mb of repeat sequences were annotated, and 26,824 protein-coding genes and 837 noncoding RNAs were identified. Phylogenetic analysis indicated the divergence of the ancestors of B. rhynchopetera and its closely related species Tenebrio molitor at about 85.6 million years ago. The colinearity analysis showed that some chromosomes of B. rhynchopetera may have had fission events, and it has a good synteny relationship with Tribolium castaneum. Furthermore, in the enrichment analyses, the gene families related to detoxification and immunity of B. rhynchopetera facilitated the understanding of its environmental adaptations, which will serve as a valuable research resource for pest control strategies and conservation efforts of beneficial insects. This high-quality reference genome will also contribute to the conservation of insect species diversity and genetic resources.

Population structure and breed identification of Chinese indigenous sheep breeds using whole genome SNPs and InDels

BackgroundAccurate breed identification is essential for the conservation and sustainable use of indigenous farm animal genetic resources. In this study, we evaluated the phylogenetic relationships and genomic breed compositions of 13 sheep breeds using SNP and InDel data from whole genome sequencing. The breeds included 11 Chinese indigenous and 2 foreign commercial breeds. We compared different strategies for breed identification with respect to different marker types, i.e. SNPs, InDels, and a combination of SNPs and InDels (named SIs), different breed-informative marker detection methods, and different machine learning classification methods.ResultsUsing WGS-based SNPs and InDels, we revealed the phylogenetic relationships between 11 Chinese indigenous and two foreign sheep breeds and quantified their purities through estimated genomic breed compositions. We found that the optimal strategy for identifying these breeds was the combination of DFI_union for breed-informative marker detection, which integrated the methods of Delta, Pairwise Wright's FST, and Informativeness for Assignment (namely DFI) by merging the breed-informative markers derived from the three methods, and KSR for breed assignment, which integrated the methods of K-Nearest Neighbor, Support Vector Machine, and Random Forest (namely KSR) by intersecting their results. Using SI markers improved the identification accuracy compared to using SNPs or InDels alone. We achieved accuracies over 97.5% when using at least the 1000 most breed-informative (MBI) SI markers and even 100% when using 5000 SI markers.ConclusionsOur results provide not only an important foundation for conservation of these Chinese local sheep breeds, but also general approaches for breed identification of indigenous farm animal breeds.

Effect of Supplementation of a Cryopreservation Extender with Pectoliv30 on Post-Thawing Semen Quality Parameters in Rooster Species.

Sperm cryopreservation is a fundamental tool for the conservation of avian genetic resources; however, avian spermatozoa are susceptible to this process. To cope with the high production of reactive oxygen species (ROS), the addition of exogenous antioxidants is beneficial. Pectoliv30 is a substance derived from alperujo, and in this study, its effect was analyzed on seminal quality after its addition to the cryopreservation extender of roosters at different concentrations. For this purpose, 16 Utrerana breed roosters were used, and seminal collection was performed in six replicates, creating a pool for each working day with ejaculates of quality. After cryopreservation, one sample per treatment and replicate was thawed, and several seminal quality parameters were evaluated. Statistical analysis revealed numerous correlations between these variables, both positive and negative according to the correlation matrix obtained. Furthermore, the chi-squared automatic interaction detection (CHAID) decision tree (DT) reported significant differences in the hypo-osmotic swelling test (HOST) variable between groups. Moreover, results for this parameter were more desirable at high concentrations of Pectoliv30. The application of this substance extracted from the by-product alperujo as an antioxidant allows the improvement of the post-thawing seminal quality in roosters and facilitates optimization of the cryopreservation process as a way to improve the conservation programs of different endangered poultry breeds.

Review on Morphological and Molecular Characterization for Tea (&lt;em&gt;Camellia sinensis&lt;/em&gt; [L.] O. Kuntze var. &lt;em&gt;sinensis&lt;/em&gt;) Breeding

Tea (Camellia sinensis) is the world’s second most consuming beverage and one of the major exporting plantation crops in Sri Lanka. Tea yield is highly influenced by weather conditions, shoot density, shoot weight and genetic factors which inherited by tea plants. Development of vegetative propagated cultivars has led to a genetic bottleneck condition in tea plantation. Therefore, it is important to understand the genetic variability through proper characterization for a successful breeding program. Morphological characterization is a cost-effective method and molecular characterization based on molecular markers such as RAPD and ISSR give more reliable data and it is a perfect method for the conservation of genetic resources. The genetic diversity of tea can be conserved ex-situ and in-situ in the fields and gene banks These approaches will reduce the time taken for conventional breeding of tea and aid in development of superior cultivars.