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Abstract Bartonella are vector-borne gram-negative facultative intracellular bacteria that can infect a wide spectrum of mammals, and are recognized as emerging human pathogens. This study aimed to investigate the prevalence and molecular characteristics of Bartonella infections in small mammals within the Qinghai Menyuan section of Qilian Mountain National Park, China. Small mammals were captured, and the liver, spleen and kidney were collected for Bartonella detection and identification using a combination of real-time PCR targeting the transfer-mRNA (ssrA) gene and followed by sequencing of the citrate synthase (gltA) gene. A total of 52 rodents were captured, and 36 rodents were positive for Bartonella, with a positivity rate of 69.23% (36/52). Bartonella was detected in Cricetulus longicaudatus, Microtus oeconomus, Mus musculus, and Ochotona cansus. The positivity rate was significantly different in the different habitats. Two Bartonella species were observed, including Bartonella grahamii and Bartonella heixiaziensis, and B. grahamii was the dominant epidemic strain in this area. Phylogenetic analysis showed that B. grahamii mainly clustered into two clusters, which were closely related to the Apodemus isolates from China and Japan and the local plateau pika isolates, respectively. In addition, genetic polymorphism analysis showed that B. grahamii had high genetic diversity, and its haplotype had certain regional differences and host specificity. Overall, high prevalence of Bartonella in small mammals in the Qinghai Menyuan section of Qilian Mountain National Park. B. grahamii is the dominant strain with high genetic diversity and potential pathogenicity to humans, and corresponding control measures should be considered.

Abstract Numerous plant taxa are threatened by habitat destruction or overexploitation. To overcome these threats, new methods are urgently needed for rescuing threatened and endangered plant species. Here, we review the genetic consequences of threats to species populations. We highlight potential advantages of genome editing for mitigating negative effects caused by new pathogens and pests or climate change where other approaches have failed. We propose solutions to protect threatened plants using genome editing technology unless absolutely necessary. We further discuss the challenges associated with genome editing in plant conservation to mitigate the decline of plant diversity.

Abstract Sea cucumbers are deposit feeding members of marine benthic communities. The over-exploitation of sea cucumber natural stocks, especially in the Mediterranean basin, is having negative impacts on the marine ecosystem. This concerns had led the Italian government to take legal actions to preserve these important marine resources. The aim of this study was to evaluate the level of genetic diversity and population structures within two sympatric Holothuria sea cucumber species, H. polii and H. tubulosa, across ten Mediterranean areas along Italy. A 323 bp portion of the COI mitochondrial gene was sequenced in a total of 441 holothurians (251 H. polii, 177 H. tubulosa and 13 from other species). Genetic diversity analyses and analysis of molecular variance (AMOVA) suggest that H. polii and H. tubulosa species are distinct, but within and among populations are homogeneous, indicating active gene flows across the Mediterranean areas investigated. H. polii showed a lower genetic diversity than H. tubulosa, probably related to differences in life history traits. Phylogenetic analyses showed a clear differentiation between the two species, even if six specimens morphologically assigned to a species clustered within the other species, indicating a possible occurrence of hybridization events. These data will be useful in implementing conservation actions for these holothurian genetic resources.

Abstract Background Multidrug- or rifampicin-resistant tuberculosis (TB; MDR/RR-TB) is a significant public health threat. However, the mechanisms involved in its transmission in Sichuan, China are unclear. To provide a scientific basis for MDR/RR-TB control and prevention, we investigated the drug-resistance characteristics, genetic diversity, and transmission dynamics and analyzed the demographic and clinical characteristics of patients to identify risk factors for the acquisition of MDR/RR-TB in Sichuan, Western China. Methods Whole-genome sequencing was performed using a sample comprised of all MDR/RR-TB strains isolated from patients with pulmonary TB (≥ 15 years) at the 22 surveillance sites in Sichuan province between January 2019 and December 2021, to analyze genotypic drug resistance and genetic diversity. Moreover, we performed statistical analyses of the epidemiological characteristics and risk factors associated with the transmission dynamics of MDR/RR-TB. Results The final analysis included 278 MDR/RR TB strains. Lineage 2.2, the major sub-lineage, accounted for 82.01% (228/278) of isolates, followed by lineage 4.5 (9.72%, 27/278), lineage 4.4 (6.83%, 19/278), and lineage 4.2 (1.44%, 4/278). The drug resistance rates, ranging from high to low, were as follows: isoniazid (229 [82.37%]), streptomycin (177 [63.67%]), ethambutol (144 [51.80%]), pyrazinamide (PZA, 119 [42.81%]), fluoroquinolones (FQs, 93 [33.45%]). Further, the clofazimine, bedaquiline, and delamanid resistance rates were 2.88, 2.88, and 1.04%, respectively. The gene composition cluster rate was 32.37% (90/278). In addition, 83.81% (233/278) of MDR/RR-TB cases were determined to be likely caused by transmission. Finally, patients infected with lineage two strains and strains with the KatG S315T amino acid substitution presented a higher risk of MDR/RR-TB transmission. Conclusion Transmission plays a significant role in the MDR/RR-TB burden in Sichuan province, and lineage 2 strains and strains harboring KatG S315T have a high probability of transmission. Further, high levels of FQ and PZA drug resistance suggest an urgent need for drug susceptibility testing prior to designing therapeutic regimens. New anti-TB drugs need to be used standardly and TB strains should be regularly monitored for resistance to these drugs.

Papaya leaf curl China virus (PaLCuCNV) is a damaging plant pathogen causing substantial losses to crop. The complete genomes of three PaLCuCNV isolates from Ageratum conyzoides were obtained and combined with the 68 reference isolates in GenBank for comprehensive genetic diversity analyses using specialized computational tools. Sequence alignment revealed nucleotide sequence similarity ranging from 85.3% to 99.9% among 71 PaLCuCNV isolates. Employing phylogenetic analysis, 71 PaLCuCNV sequences were clustered into five groups, with no significant correlation observed between genetic differentiation and either host species or geographical origin. Additionally, 13 recombination events across all PaLCuCNV isolates were identified. Genetic diversity analysis indicated the ongoing expansion and evolution of PaLCuCNV populations, supported by a neutral model. Moreover, significant genetic differentiation was observed among distinct viral populations, primarily attributed to genetic drift. Overall, our findings provide valuable insights into the detection, genetic variation, and evolutionary dynamics of PaLCuCNV.

The Nivkhs are a small ethnic group indigenous of the Russian Far East, living in the Khabarovsk Territory and on Sakhalin Island, descending from the ancient inhabitants of these territories. In the Nivkhs, a specific Sakhalin-Amur anthropological type is prevalent. They are quite isolated, due to long isolation from contacts with other peoples. The gene pool of the Nivkhs and other Far Eastern and Siberian populations was characterized using a genome-wide panel of autosomal single-nucleotide polymorphic markers and Y chromosome haplogroups. Bioinformatic processing of frequencies of autosomal SNPs, Y chromosome haplogroups and YSTR haplotypes showed that the Nivkh gene pool is very different from the other populations’. Analysis of the SNP frequencies using the PCA method divided the Far Eastern populations in full accordance with the territories of their residence into the northern group of the Chukchi and Koryaks and the southern group, including the Nivkhs and Udege. The remoteness of the Nivkhs coincides with their geographic localization, with the Nivkhs and Udege demonstrating the greatest kinship. The Nivkhs have a specific component of their gene pool, which is present with much less frequency in the Udege and Transbaikal Evenks. According to the IBD blocks, the genotypes of the Nivkhs show a very small percentage of coincidence with the Udege, Koryaks, Evenks and Chukchi, the value of which is the lowest compared to the IBD blocks among all other Siberian populations. The Nivkh-specific composition of haplogroups and YSTR haplotypes was shown. In the Nivkhs, the C2a1 haplogroup is divided into three sublines, which have a fairly ancient origin and are associated with the ancestors of modern northern Mongoloids. The Nivkh haplogroup O2a1b1a2a-F238 is found among residents of China and Myanmar. The Q1a1a1-M120 line is represented among the Nivkhs, Koryaks, Evenks and Yukaghirs. Phylogenetic analysis of individual Y chromosomal haplogroups demonstrated the closeness of the Nivkh gene pool with the ancient population of the Amur and Okhotsk regions, the Koryaks, the Tungus peoples and the population of Southeast Asia. The Nivkh gene pool confirms the relative smallness of their ancestral groups without mixing with other populations.

Abstract Background Plant mutagenesis creates novel alleles, thereby increasing genetic and phenotypic diversity. The availability of the faba bean (Vicia faba L.) reference genome and a growing set of additional genomic resources has increased the scientific and practical value of mutant collections. We aimed to genotype and morphologically phenotype a historical faba bean mutant collection developed and characterized by Jan Sjödin (1934–2023) over half a century ago in order to increase its value to researchers. The collection was genotyped using high-throughput single-primer enrichment technology (SPET) assays. Results We used 11,073 informative single nucleotide polymorphism (SNP) markers spanning the faba bean genome to genotype 52 mutant lines along with the background line, cv. Primus. A range of flower, seed, leaf, and stipule mutations were observed. The analysis of population structure revealed a shallow structure with no major subpopulations. Principal component and cluster analyses revealed, to a minor extent, that the mutants clustered by their phenotype. Conclusions The mutants’ phenotypic variation and shallow structure indicate that the Sjödin faba bean collection has the potential to play a significant role in faba bean breeding and in genetic and functional studies.

Abstract [Objective] Through identification and analysis of disease resistance of the field- and indoorgrowing seedlings, the distribution of disease resistance of Gossypium barbadense germplasm resources was mastered, providing a basis for screening high resistant resources to Verticillium wilt. [Methods] 238 G. barbadense germplasm resources of our research group were used as objects. In 2023, the field plot test for the natural disease was carried out in KEL and AWT, and the resistance of G. barbadense resources to V. wilt was identified and evaluated by indoor inoculation. [Results] The genetic diversity of 15 indexes of 238 G. barbadense germplasm resources was analyzed. The coefficient of variation was ranged from 2.00% to 36.97%, with an average of 16.05%. Resistance identification in different environments showed that the coefficient of variation was ranged from 8.40% to 71.06%. Based on the analysis of four different environments, no germplasm resources with complete immunity and high resistance to V. wilt were identified, and 30 resistant materials, 194 resistant materials, and 14 susceptible materials were identified. [Conclusion] Most of the planting resources of G. barbadense have resistance to V. wilt. Therefore, it is necessary to identify and select germplasm resources with strong resistance to V. wilt from G. barbadense germplasm resources.

Abstract Background The shea tree is a well-known carbon sink in Africa that requires a sustainable conservation of its gene pool. However, the genetic structure of its population is not well studied, especially in Côte d’Ivoire. In this study, 333 superior shea tree genotypes conserved in situ in Côte d’Ivoire were collected and genotyped with the aim of investigating its genetic diversity and population structure to facilitate suitable conservation and support future breeding efforts to adapt to climate change effects. Results A total of 7,559 filtered high-quality single nucleotide polymorphisms (SNPs) were identified using the genotyping by sequencing technology. The gene diversity (HE) ranged between 0.1 to 0.5 with an average of 0.26, while the polymorphism information content (PIC) value ranged between 0.1 to 0.5 with an average of 0.24, indicating a moderate genetic diversity among the studied genotypes. The population structure model classified the 333 genotypes into three genetic groups (GP1, GP2, and GP3). GP1 contained shea trees that mainly originated from the Poro, Tchologo, and Hambol districts, while GP2 and GP3 contained shea trees collected from the Bagoué district. Analysis of molecular variance (AMOVA) identified 55% variance within populations and 45% variance within individuals, indicating a very low genetic differentiation (or very high gene exchange) between these three groups (F ST = 0.004, gene flow Nm = 59.02). Morphologically, GP1 displayed spreading tree growth habit, oval nut shape, higher mean nut weight (10.62 g), wide leaf (limb width = 4.63 cm), and small trunk size (trunk circumference = 133.4 cm). Meanwhile, GP2 and GP3 showed similar morphological characteristics: erect and spreading tree growth habit, ovoid nut shape, lower mean nut weight (GP2: 8.89 g; GP3: 8.36 g), thin leaf (limb width = 4.45 cm), and large trunk size ( GP2: 160.5 cm, GP3: 149.1 cm). A core set of 100 superior shea trees, representing 30% of the original population size and including individuals from all four study districts, was proposed using the “maximum length sub-tree function” in DARwin v. 6.0.21. Conclusion These findings provide new knowledge of the genetic diversity and population structure of Ivorian shea tree genetic resources for the design of effective collection and conservation strategies for the efficient use of inbreeding.

Abstract Whole genome sequences (WGS) of 185 North American Thoroughbred horses were compared to quantify the number and frequency of variants, diversity of mitotypes, and autosomal runs of homozygosity (ROH). Of the samples, 82 horses were born between 1965 and 1986 (Group 1); the remaining 103, selected to maximize pedigree diversity, were born between 2000 and 2020 (Group 2). Over 14.3 million autosomal variants were identified with 4.5–5.0 million found per horse. Mitochondrial sequences associated the North American Thoroughbreds with 9 of 17 clades previously identified among diverse breeds. Individual coefficients of inbreeding, estimated from ROH, averaged 0.266 (Group 1) and 0.283 (Group 2). When SNP arrays were simulated using subsets of WGS markers, the arrays over-estimated lengths of ROH. WGS-based estimates of inbreeding were highly correlated (r > 0.98) with SNP array-based estimates, but only moderately correlated (r = 0.40) with inbreeding based on 5-generation pedigrees. On average, Group 1 horses had more heterozygous variants (P

UNLABELLED: Botrytis cinerea Pers. Fr. (teleomorph: Botryotinia fuckeliana) is a necrotrophic fungal pathogen that attacks a wide range of plants. This updated pathogen profile explores the extensive genetic diversity of B. cinerea, highlights the progress in genome sequencing, and provides current knowledge of genetic and molecular mechanisms employed by the fungus to attack its hosts. In addition, we also discuss recent innovative strategies to combat B. cinerea. TAXONOMY: Kingdom: Fungi, phylum: Ascomycota, subphylum: Pezizomycotina, class: Leotiomycetes, order: Helotiales, family: Sclerotiniaceae, genus: Botrytis, species: cinerea. HOST RANGE: B. cinerea infects almost all of the plant groups (angiosperms, gymnosperms, pteridophytes, and bryophytes). To date, 1606 plant species have been identified as hosts of B. cinerea. GENETIC DIVERSITY: This polyphagous necrotroph has extensive genetic diversity at all population levels shaped by climate, geography, and plant host variation. PATHOGENICITY: Genetic architecture of virulence and host specificity is polygenic using multiple weapons to target hosts, including secretory proteins, complex signal transduction pathways, metabolites, and mobile small RNA. DISEASE CONTROL STRATEGIES: Efforts to control B. cinerea, being a high-diversity generalist pathogen, are complicated. However, integrated disease management strategies that combine cultural practices, chemical and biological controls, and the use of appropriate crop varieties will lessen yield losses. Recently, studies conducted worldwide have explored the potential of small RNA as an efficient and environmentally friendly approach for combating grey mould. However, additional research is necessary, especially on risk assessment and regulatory frameworks, to fully harness the potential of this technology.

Cytogenetic and molecular studies hold significant importance in plant breeding programs. In the case of moringa, such studies are scarce. Therefore, the objective of this research was to determine the chromosomal number and genetic diversity parameters in two phenotypes of Moringa oleifera Lam. (short and long capsule) using chromosomal analysis and ISSR markers, respectively. Cytogenetic analyses were conducted using the “Somatic chromosomes in root apices” technique, with acetocarmine and papain for staining. It was possible to identify 2N = 28 chromosomes in a single cell of the long capsule phenotype, ranging in size from 0.05 to 0.10 μm. Cells in both moringa phenotypes were observed in prophase, metaphase, anaphase, and telophase. High genetic variability was found in both phenotypes of moringa, as indicated by a Shannon index of 0.81. Additionally, the principal component analysis and UPGMA (Unweighted Pair-Group Method with Arithmetic) groups revealed genetic isolation between the studied moringa phenotypes. The significant polymorphism obtained with most primers suggests that the tested ISSR markers are highly useful for studying genetic diversity in moringa. These findings provide a robust foundation for future research in genetic improvement and conservation of moringa, highlighting the relevance of cytogenetic and molecular studies in this species.

Zoysiagrass is warm-season turfgrass thriving in tropical regions. Despite the adaptive nature, the existence of Indonesian zoysiagrass as well as morphological and genetic characteristics are not available. Therefore, this study aimed to explore Indonesian zoysiagrass from western and eastern parts of the country, as well as its morphological and molecular characteristics. Morphological characteristics was conducted to measure vegetative and reproductive characters while genotyping was performed using 15 simple sequence repeat markers. Morphological characteristics cluster three major groups, namely Group 1 corresponded to short, shorter, and fine leaves. Group 2 corresponded to tall, longer, and fine leaves, fewer seeds, and short spikelet, while Group 3 corresponded to tall, long, and wider leaves, more seeds, and longer spikelet. The results showed that the expected heterozygosity (He = 0.256) was lower than homozygosity (Ho = 0.341). The high level of discriminating capacity, polymorphism, and informativeness of SSR marker was observed (Effective Multiplex Ratio = 4.20, Marker Index = 2.394, and Resolving Power = 1.574). Additionally, population structure generated two subpopulations. Group 1 corresponded to Z. japonica from Sumatera Island and mixed province while Group 2 corresponded to Z. japonica from Central Java and Bali with Z. japonica and Z. matrella from mixed province. In conclusion, the exploration of morphological and genetic diversity from Indonesian zoysiagrass provided useful insight for conservation and future breeding improvement. [ABSTRACT FROM AUTHOR]

Wax moths, Galleria mellonella Linnaeus, 1758 and Achroia grisella Fabricius, 1794 are the key pests of honeybee colonies worldwide. They cause wax comb damages which lead to colony perishing and absconding. To control these pests, their genetic background and evolution should be considered. In this study, genetic diversity and demographic history of 2 species of wax moth were explored based on mitochondrial genes (COI). Wax moths were collected from northeatern part of Thailand for morphological and DNA analyses. G. mellonella and A. grisella sequences from GenBank were included for genetic diversity and demographic history analyses (total of 80 and 26 sequences, respectively). Overall genetic diversity for A. grisella samples from Northeastern Thailand was relatively low (h = 0.467 ± 0.132 and π = 0.00150 ± 0.00042). Likewise, low genetic diversity was also observed in G. mellonella samples (h = 0.280 ± 0.101 and π = 0.00046 ± 0.00017). Among samples from different global regions, the haplotype and nucleotide diversity of A. grisella were 0.834 ± 0.050 and 0.00996 ± 0.00124, respectively. The haplotype and nucleotide diversity of G. mellonella were 0.709 ± 0.034 and 0.01084 ± 0.00279, respectively. The ML tree revealed that these 2 species were separated into 2 major clades (G. mellonella clade and A. grisella clade). All sequences corresponding to G. mellonella formed to a single monophyletic clade, while all the sequences corresponding to A. grisella formed another single monophyletic clade. Clade G. mellonella was divided into 4 subclades designated as Clade Gm1, Gm2, Gm3 and Gm4, whereas A. grisella clade was divided into 3 subclades designated as Clade Ag1, Ag2 and Ag3. The sum of squares deviation (SSD) and Harpending's raggedness index (rg) and the results of Tajima's D and Fu's Fs tests indicated population expansion was not found in either species. [ABSTRACT FROM AUTHOR]

Extended Abstract Background: Chickpea (Cicer arietinum L.) is a legume grown in cool season areas. It is one of the main sources of protein and energy and plays a major role in improving soil fertility. Peas are divided into two classes, Desi and Kabali. The Desi seed is smaller, wrinkled, and darker while Kabli has a lighter, whiter seed color, larger seed size, and smooth surface. The chickpea yield is 1199 kg per hectare in America, 1261 kg per hectare in India, and 409 kg per hectare in Iran. Until 2005, this plant was called an orphan plant due to the insufficient genetic resources in chickpeas, but the plant was known as a plant with a rich genomic resource after many efforts at national and international levels. Further studies on chickpea genetic diversity are important to improve the yield. Chickpeas have plenty of diversity in different geographical regions, and the genetic pattern and the amount of variation within and between these populations should be known to progress breeding programs and effectively use these germplasm collections. The evaluation of genotypes faces two key challenges. The first is the genotype-environment interaction, and the second is the interaction between the studied traits. This study aimed to investigate the genetic diversity in the Desi chickpea germplasm under autumn cultivation conditions, analyze the relationships of morphological-agronomical traits, and select superior genotypes in terms of all morphological-agronomical traits. Methods: This study was conducted on 416 genotypes, including 335 landrace of Iran, 1 ICARDA genotype, and 78 ICRISAT genotypes, along with two checks named Kaka and Pirouz cultivars in the experimental farm of the Dryland Agricultural Research Institute (Kermanshah). The cultivars were evaluated in terms of morphological-agronomic traits, including the number of days to flowering, the number of main branches, the number of secondary branches, the number of pods per plant, plant height, the end number of days to maturity, seed yield, and 100-seed weight (HSW). The experiment was conducted during 2020-2021 under autumn sowing conditions and as an augmentation based on a randomized complete block design with nine blocks. The variance, heritability, and genetic advance were analyzed with the R software packages (augmentedRCBD). The R software package (metan) and (GGEBiplotGUI) were used for the biplot analysis of the genotype by trait. Data were grouped using the K-mean algorithm, single method, and Euclidean distance with R software. The R software package (NbClust) was used to calculate the number of appropriate groups resulting from the cluster analysis. Using the R software package (metan) with the selection index (MGIDI), the top genotypes were ranked based on several traits. Results: The results of the analysis of variance were significant for the number of days to maturity, HSW, and plant height. The highest and the lowest coefficients of variation belonged to the number of secondary branches and days to maturity, respectively. The plant height and HSW traits had high values of heritability and genetic advancement. According to the results of the genotype by trait biplot, genotypes 148, 327, 391, and 277 were in the best conditions in terms of HSW, days to maturity, plant height, and days to flowering. Genotypes 6, 400, 18, 42, 26, 168, 15, and 2 were in the best conditions for the number of pods per plant, seed yield, the number of main branches, and the number of secondary branches per plant. According to the findings of the genotype by trait biplot, most of the selected genotypes were from the landrace of the Iranian chickpea. Clustering was performed using the K-means method, which divided the genotypes into two groups. In the second group, genotypes 6, 18, 148, 327, and 91 had more distances (according to the center of the group) than the other genotypes. Then, 62 genotypes were ranked as the best genotypes in terms of all traits using the MGIDI index. Conclusion: The high genetic diversity of the traits studied in this research indicates the possibility of selection among the genotypes. Plant height and HSW traits have high heritability and genetic advance values, indicating the additive effects of the gene. In studies of the Desi chickpea populations, the breeding method of selection can be used to improve these traits. According to the biplot results, the number of pods per plant had important effects on seed yield in autumn sowing conditions, and it is important in terms of selecting genotypes related to the desired traits. On the other hand, the weight of HSW had a high correlation with the plant height in the Desi chickpea, which is very important in the mechanical harvesting of chickpeas. The superior genotypes selected in this research can be used as parents in future breeding programs of the Desi chickpea under autumn cultivation conditions.

【Objective】The study was conducted to clarify the genetic structure characteristics, genetic diversity level and molecular variation of different geographical populations of Conopomorpha sinensis Bradely, with an aim to provide scientific evidence for the study of its origin and evolution and provide reference information for the control of this pest in different regions.【Method】Using the C. sinensis from5production areas in southern China as materials, using GBS (Genotyping-by-sequencing) technology was used for samples genotyping, then SNP locus was identified with SAMTOOLS software, and phylogenetic tree was constructed according to SNP genotyping results. Finally, principal component analysis was performed.【Result】Sequencing of C. sinensis from5regions was conducted by GBS technology. A total of 27.39 Gb of high-quality effective data were obtained, with an average of 5.48 Gb per sample. A total of 11 767 high-quality single nucleotide polymorphism (SNPs) loci were obtained. Phylogenetic tree analysis showed that the genetic relationship of Luzhou population was far from that of other populations. The results of principal component analysis showed that C. sinensis was divided into2groups in5regions, and the Luzhou population was significantly different from the other4populations. Both principal component analysis and phylogenetic tree analysis revealed that there were obvious differences in genetic level among C. sinensis from different geographical origins. The results of genetic diversity analysis showed that the observed heterozygosity was 0.2099-0.2531, the expected heterozygosity was 0.1937-0.2203, π was 0.2495-0.2748, indicating that the genetic diversity level of C. sinensis population was low. The results of AMOVA analysis showed that the genetic variation between populations (0.87%) was smaller than that within populations (99.13%), indicating that the variation mainly came from within populations rather than between populations.【Conclusion】The genetic diversity level of C. sinensis in different geographical populations was low, while the genetic differentiation degree of Luzhou population in Sichuan was high, and its genetic relationship was distant with other populations.

This study investigated genetic variability, character association, and genetic diversity in ninety-five forage sorghum genotypes, evaluated using a randomized block design for seven fodder quality traits. Analysis of variance revealed significant differences among genotypes for all traits. Genotypes such as G90 (424B), G23 (334B), G87 (CSV21F), G76 (330B), and G45 (373B) exhibit desirable fodder quality traits. Notably, G90 (424B) and G47 (NSS5B) stand out for their superior green forage yield per plant and fodder quality, making them prime candidates for varietal development programs. Crude protein emerged as a crucial selection factor for fodder quality. Green forage yield per plant showed minimal association with the other quality traits. A strong positive correlation was observed among in vitro organic matter digestibility, metabolic energy, crude protein, and ash content. D2 analysis identified five clusters, with genotypes from clusters V and IV recommended for crossing to produce superior transgressive segregants for fodder quality. Acid detergent fibre, crude protein, and ash content significantly contributed to genetic divergence. Considering these selected traits and genotypes, they could be invaluable in future sorghum forage breeding programs aimed at enhancing fodder quality traits.

The present study was carried out to assess the genetic parameters and divergence in 38 rice genotypes for important yield and grain quality traits. Phenotypic coefficient of variation (PCV) exceeded genotypic coefficient of variation (GCV) for all the traits taken for the study, while high heritability was recorded for all the traits, except kernel length to breadth ratio and grain iron content. The trait number of grains per panicle exhibited high heritability (91.00%) and high genetic advance as a percentage of mean suggesting simple selection may be followed to improve the traits. Cluster analysis grouped the genotypes into seven clusters. The highest inter-cluster distance was observed between clusters VII and IV (537.17). Five genotypes excelled in grain yield, ten genotypes for grain zinc content and one genotype for grain iron content over the check variety Rajendra Bhagwati. Despite high variability in grain zinc and iron content, no genotype surpassed the check variety for all three crucial attributes i.e. grain yield, grain zinc and iron content. The experimental material’s variability for grain nutrient status suggests their potential use in biofortification programs.

Diospyros mun A.Chev. ex Lecomte (Ebenaceae), a native evergreen tree in Vietnam, has important economic and ecological values. The absence of effective and reliable molecular markers has hampered the study of D. mun’s genetic diversity and population structure, even though it is an endemic and endangered species. Therefore, significant enrichment of genomic resources is urgently needed to uncover and better understand the genetic architecture of D. mun. This study aims to demonstrate an efficient and reliable tool to explore the polymorphism within D. mun germplasm. It provides a valuable platform for the breeding and conservation of this species and other endangered species worldwide. The Illumina HiSeq™ 4000 sequencing technology was applied for the transcriptomic analysis, genetic differentiation and population structure of D. mun in Vietnam. In this study, the transcriptomes of D. mun were analysed using the Illumina HiSeqTM 4000 sequencing system and a total of 5,588,615,700 base pairs were generated. De novo assembly indicated that 91,134 unigenes were generated (average length = 645.55 bp, N50 = 957 bp, Q20 = 98.08% and Q30 = 94.51%). A total of 92,798 and 21,134 unigenes had significant similarities amongst Nr and Swiss-Prot, respectively. In the GO database, 19,929 unigenes were annotated and these genes were divided into three major categories and 50 subcategories. In the KOG analysis, 18,499 unigenes were annotated and divided into 25 gene function categories. In the KEGG analysis, 12,017 unigenes were annotated. According to the related pathways involved, they could be classified into 56 subclasses. In this study, we have identified a total of 9,391 EST-SSR markers. Ten microsatellite loci were employed to assess the genetic diversity and structure of 82 adult D. mun trees across three populations in Vietnam. The results indicated moderate levels of genetic diversity with PIC = 0.77, NA = 3.9, NE = 2.8, Ho = 0.56 and HE = 0.58 and the fixation index value was recorded as positive for three populations (NS, NH and CP). Genetic differentiation among populations was low (FST = 0.045), suggesting limited gene flow (Nm = 5.34). This result indicates gene exchange between the populations of ancient D. mun from different geographical areas and regions. The analysis of molecular variance (AMOVA) showed that high genetic variation existed within individuals (91%) compared to amongst populations (4%). Genetic structure analysis, DAPC and the NJ tree indicated that the three populations were divided into three main clusters. With this study, we provide a molecular resoureces for the breeding and conservation of D. mun.

Abstract Background Greater yam is a key staple crop grown in tropical and subtropical regions, while its asexual propagation mode had led to non-flowering mutations. How transposable elements contribute to its genetic variations is rarely analyzed. We used transcriptome and whole genome sequencing data to identify active transposable elements (TEs) and genetic variation caused by these active TEs. Our aim was to shed light on which TEs would lead to its intraspecies variation. Results Annotation of de novo assembly transcripts indicated that 0.8 − 0.9% of transcripts were TE related, with LTR retrotransposons (LTR-RTs) accounted for 65% TE transcripts. A large portion of these transcripts were non-autonomous TEs, which had incomplete functional domains. The majority of mapped transcripts were distributed in genic deficient regions, with 9% of TEs overlapping with genic regions. Moreover, over 90% TE transcripts exhibited low expression levels and insufficient reads coverage to support full-length structure assembly. Subfamily analysis of Copia and Gypsy, the two LTR-RTs revealed that a small number of subfamilies contained a significantly larger number of members, which play a key role in generating TE transcript. Based on resequencing data, 15,002 L-RT insertion loci were detected for active LTR-RT members. The insertion loci of LTR-RTs were highly divergent among greater yam accessions. Conclusions This study showed the ongoing transcription and transpositions of TEs in greater yam, despite low transcription levels and incomplete proteins insufficient for autonomous transposition. While our research did not directly link these TEs to specific yam traits such as tuber yield and propagation mode, it lays a crucial foundation for further research on how these TE insertion polymorphisms (TIPs) might be related to variations in greater yam traits and its tuber propagation mode. Future research may explore the potential roles of TEs in trait variations, such as tuber yield and stress resistance, in greater yam.

Abstract Background The salmonid pathogen Flavobacterium psychrophilum poses a significant economic threat to global aquaculture, yet our understanding of its genetic and phenotypic diversity remains incomplete across much of its geographic range. In this study, we characterise the genetic and phenotypic diversity of 70 isolates collected from rainbow trout (Oncorhynchus mykiss) and brown trout (Salmo trutta m. fario) from fish farms in the Czech Republic between 2012 and 2019 to compare their genomic content with all draft or complete genomes present in the NCBI database (n = 187). Results The Czech isolates underwent comprehensive evaluation, including multiplex PCR-based serotyping, genetic analysis, antimicrobial resistance testing, and assessment of selected virulence factors. Multiplex PCR serotyping revealed 43 isolates as Type 1, 23 as Type 2, with sporadic cases of Types 3 and 4. Multi-locus sequence typing unveiled 12 sequence types (ST), including seven newly described ones. Notably, 24 isolates were identified as ST329, a novel sequence type, while 22 were classified as the globally-distributed ST2. Phylogenetic analysis demonstrated clonal distribution of ST329 in the Czech Republic, with these isolates lacking a phage sequence in their genomes. Antimicrobial susceptibility testing revealed a high proportion of isolates classified as non-wild type with reduced susceptibility to oxolinic acid, oxytetracycline, flumequine, and enrofloxacin, while most isolates were classified as wild type for florfenicol, sulfamethoxazole-trimethoprim, and erythromycin. However, 31 isolates classified as wild type for florfenicol exhibited minimum inhibitory concentrations at the susceptibility breakpoint. Conclusion The prevalence of the Czech F. psychrophilum serotypes has evolved over time, likely influenced by the introduction of new isolates through international trade. Thus, it is crucial to monitor F. psychrophilum clones within and across countries using advanced methods such as MLST, serotyping, and genome sequencing. Given the open nature of the pan-genome, further sequencing of strains promises exciting discoveries in F. psychrophilum genomics.

Abstract The current study aimed at population genetic characterization of B. vogeli based on the cytochrome b (cyt b) gene sequences (≥ 685 bp) available in the GenBank. Phylogenetic trees placed all the sequences of B. vogeli in a single large monophyletic clade; however, it was further divided into two subclades (Bv1 and Bv2). Out of seven nucleotide variations observed between Bv1 and Bv2 subclades, four were synonymous (G92A, C170T, T488C and A659G), and three were non-synonymous (G324A, C438A and G465A) resulting in amino acid substitutions at three places (V108I, L146I and V155I). Within different B. vogeli populations, the nucleotide and haplotype diversities were low. The median-joining haplotype network revealed only two haplotypes (Hap_1 and Hap_2). A geographical sub-structuring was noticed in the B. vogeli populations, with moderate genetic differentiation (FST = 0.05000; P

Abstract Background Sheep breeds native to the United Kingdom exhibit a striking diversity of different traits. Some of these traits are highly sustainable, such as seasonal wool shedding in the Wiltshire Horn, and are likely to become more important as pressures on sheep production increase in coming decades. Despite their clear importance to the future of sheep farming, the genetic diversity of native UK sheep breeds is poorly characterised. This increases the risk of losing the ability to select for breed-specific traits from native breeds that might be important to the UK sheep sector in the future. Here, we use 50 K genotyping to perform preliminary analysis of breed relationships and genetic diversity within native UK sheep breeds, as a first step towards a comprehensive characterisation. This study generates novel data for thirteen native UK breeds, including six on the UK Breeds at Risk (BAR) list, and utilises existing data from the publicly available Sheep HapMap dataset to investigate population structure, heterozygosity and admixture. Results In this study the commercial breeds exhibited high levels of admixture, weaker population structure and had higher heterozygosity compared to the other native breeds, which generally tend to be more distinct, less admixed, and have lower genetic diversity and higher kinship coefficients. Some breeds including the Wiltshire Horn, Lincoln Longwool and Ryeland showed very little admixture at all, indicating a high level of breed integrity but potentially low genetic diversity. Population structure and admixture were strongly influenced by sample size and sample provenance – highlighting the need for equal sample sizes, sufficient numbers of individuals per breed, and sampling across multiple flocks. The genetic profiles both within and between breeds were highly complex for UK sheep, reflecting the complexity in the demographic history of these breeds. Conclusion Our results highlight the utility of genotyping data for investigating breed diversity and genetic structure. They also suggest that routine generation of genotyping data would be very useful in informing conservation strategies for rare and declining breeds with small population sizes. We conclude that generating genetic resources for the sheep breeds that are native to the UK will help preserve the considerable genetic diversity represented by these breeds, and safe-guard this diversity as a valuable resource for the UK sheep sector to utilise in the face of future challenges.

Abstract Background The Tibetan sheep is one of the three major primitive sheep breeds in China, representing a unique and high-quality genetic resource in the Qinghai-Tibet Plateau and neighboring high-altitude regions, exhibiting exceptional adaptability to high-altitude climatic environments. However, research on the genetic relationships among different populations of Tibetan sheep at the whole-genome level remains insufficient. This study aims to explore the population structure and historical dynamics among 11 Tibetan sheep populations, accurately assess the genetic diversity within the populations, and providing a theoretical basis for the development of targeted genetic breeding strategies for Tibetan sheep. Results In this study, a total of 10,884,454 high-quality SNPs were obtained. All Tibetan sheep populations exhibited varying degrees of linkage disequilibrium, with similar decay rates; among them, the WT population showed the fastest decay, while the TS population exhibited the slowest decay rate. Analyses using Tajima’s D and π indicated that the genetic diversity levels of the Tibetan sheep populations are generally low. Fst results revealed that most populations exhibited moderate to low levels of genetic differentiation. The effective population size among Tibetan sheep populations showed an increasing trend over time. The evolutionary relationships among Tibetan sheep populations reflect the correlation between their geographical locations and genomic genetic distances, while also indirectly confirming the impact of historical activities such as early human migration, admixture, fusion, and expansion on the population sizes and distributions of Tibetan sheep. Conclusions The results indicate that the genetic diversity levels and genetic differentiation among Tibetan sheep populations are relatively low. In this study, we identified the genetic characteristics of Tibetan sheep populations, which exhibit low levels of diversity, genetic differentiation, and a strong population structure. A deeper genomic exploration of the population structure and diversity status of Tibetan sheep populations will provide theoretical support for subsequent genetic breeding and diversity conservation efforts.

Abstract Key message The strong clonal growth of black locust (Robinia pseudoacacia L.) not only influences the stand structure of natural or artificially established stands, but also the genetic composition of seed harvested from such clonal stands. For the commercial production of genetically diverse seeds, the stand structure should be taken into account or, at best, seeds harvested from seed orchards should be used. Context Black locust is characterised by intensive asexual reproduction through the formation of root suckers. By this means clonal structures can develop within black locust stands, in which ramets of a single clone can dominate extensive areas. Aims We want to analyse to what extent clonal structures within black locust stands negatively influence the genetic composition and diversity in seed harvested in such stands. We discuss how a potential reduction in genetic diversity can be reduced by measures taken during harvesting and whether the harvesting of seed orchards may be a better alternative. Methods We compare the genetic composition and diversity of parent trees and seed harvested from a clonal black locust stand with a seed orchard in which multiple ramets of selected clones were arranged in a randomised design. Results Within the clonal stand, parent contributions to the seed lot analysed proved to be strongly uneven. Selfing rates were high and large full-sib families dominated within the seed lot. Although the relatively strong pollination from unknown pollen donors, probably located outside of the stand, prevented a massive loss of alleles, high selfing rates and the formation of large full-sib families led to an unequal distribution of alleles within the progeny. Within the seed orchard—even though it had a lower number of clones than expected—the randomised design promoted a more diverse pollination pattern. Conclusion We conclude that for black locust, seed orchards have the greater potential to ensure a balanced genetic composition of harvested seed lots. If economic considerations make it necessary to harvest seed stands, this should only be done in a considered manner and, if possible, with knowledge of the clonal structures of the stand.

Introduction. Rotavirus infection is the major cause of severe dehydrating diarrhea requiring hospitalization in young children worldwide. Due to their segmented genome, rotaviruses are capable of gene reassortment, which makes the emergence and spread of genetically novel strains possible. The purpose of this study was to search for unusual rotaviruses circulating in Nizhny Novgorod in 2021‒2023 and their molecular genetic characterization based on all genome segments. Materials and methods. Rotavirus-positive stool samples of children were examined by PCR genotyping and electrophoresis in PAAG. cDNA fragments of each of the 11 genes (VP1‒VP4, VP6, VP7, NSP1‒NSP5), 570 to 850 nucleotide pairs in length were sequenced for the selected strains. The phylogenetic analysis was performed in the MEGA X program. Results. In the study period 2021‒2023, 11 G[P] combinations with a predominance of G3P[8] (59.5%) were identified. Six atypical Rotavirus А (RVA) strains were identified: 2 strains of the G2P[4] genotype (G2-P[4]-I2-R2-C2-M2-A3-N2-T3-E2-H3, G2-P[4]-I2-R2-C2-M2-A3-N2-T3-E3-H2) and 4 G3P[9] strains (all strains had the genotype G3-P[9]-I2-R2-C2-M2-A3-N2-T3-E3-H3). Phylogenetic analysis based on all genes showed an evolutionary relationship between rotaviruses similar to rotaviruses of cats and dogs (BA222-like) and unusual strains of the G2P[4] genotype, for which a mixed combination of genotypes was identified and characterized for the first time. Discussion. The results obtained expand the understanding of the diversity of reassortant RVAs, as well as complement the data on the genotypic structure of the rotavirus population in Nizhny Novgorod. Conclusion. The wide genetic diversity of reassortant RVA can help rotaviruses overcome the immunological pressure provided by natural and vaccine-induced immunity. In this regard, to control the emergence of new variants and assess changes in the virulence of rotaviruses after reassortment processes, continuous molecular monitoring for circulating RVA is necessary.

Spodoptera frugiperda J.E. Smith (Lepidoptera: Noctuidae) is an invasive pest of corn plants spreading throughout the world, including East Nusa Tenggara (NTT), Indonesia. Despite the wide distribution, there is a lack of information on the strain or genetic diversity of the pest in NTT. Therefore, this study aimed to determine the strain of S. frugiperda from several areas in NTT with a molecular method using cytochrome oxidase subunit 1 (COI) and triose phosphate isomerase (Tpi) gene markers. The samples were collected from 3 islands: Timor, Flores, and Sumba. Amplification of the marker genes was carried out using 3 specific primers to identify the strain obtained from samples. Subsequently, polymerase chain reaction (PCR) products were sequenced and the DNA sequences were analyzed using the BioEdit and BLAST programs. Phylogeny analyses were carried out using the MEGA 11 program to verify the strain group of samples with reference isolates from other countries found in GenBank. The PCR results showed product amplicon size 811 bp for the CO1A marker. Based on phylogeny tree analysis using COI marker, S. frugiperda from NTT showed 2 clades, namely corn and rice strains. The characterization results showed that S. frugiperda in NTT comprised 63.6% corn and 36.4% rice strains. COIB classified S. frugiperda from NTT into the h4 haplotype subgroup, while Tpi gene marker was in the corn strain. This study provided valuable information regarding the strain of S. frugiperda in Indonesia to determine the appropriate control strategy.

Abstract African pangolins are hunted for their meat and for use in local traditional medicine, as well as for their scales, which are trafficked internationally, especially to growing Asian markets. Pangolin’s population genetic structure can be used to trace the geographic origins of trafficked scales, but substantial sampling gaps across pangolins’ ranges hinder these efforts. In this study, we documented population structure and dynamics in the two species of African pangolin, the white-bellied pangolin (Phataginus tricuspis) and the giant pangolin (Smutsia gigantea) in the underexplored Republic of Congo. Using the mitochondrial control region and two nuclear markers (beta-fibrinogen and titin), we identified high genetic diversity in both species. We document a distinct mitochondrial lineage of the white-bellied pangolin, which was most likely shaped by river barriers together with dynamics of forest refugia related to the climatic shifts during the Pleistocene. We detected population growth in the white-bellied pangolin coinciding with a dry period during the Pleistocene, suggesting some ability for this typically forest-dwelling species to persist under diverse environmental conditions. Using landscape genetics, we found all but one of the pangolins we sampled at bush meat markets originated locally. A single individual appeared to have been imported to Congo from Cameroon. These findings significantly contribute to our understanding of pangolin population biology and local trade dynamics. In addition, our data from a previously unstudied part of pangolins’ ranges will help us to better understand international wildlife trafficking patterns and to target conservation and protection strategies for these highly vulnerable species.

Abstract Background Melanin in the black-bone chicken’s body is considered the material basis for its medicinal effects and is an economically important trait. Therefore, improving the melanin content is a crucial focus in the breeding process of black-bone chickens. Luning chickens are black-bone chickens, with black beaks, skin, and meat. To investigate the genetic diversity and molecular mechanisms of melanin deposition in Luning chickens, we conducted whole-genome resequencing to analyze their breeding history and identify candidate genes influencing their black phenotype, along with transcriptome sequencing of dorsal skin tissues of male Luning chickens. Results Population structure analysis revealed that Luning chickens tend to cluster independently and are closely related to Tibetan chickens. Runs of homozygosity analysis suggested potential inbreeding in the Luning chicken and Tibetan chicken population. By combining genetic differentiation index (Fst) and nucleotide diversity (θπ) ratios, we pinpointed selected regions associated with melanin deposition. Gene annotation identified 540 genes with the highest Fst value in LOC101750371 and LOC121108313, located on the 68.24–68.58 Mb interval of chromosome Z. Combining genomic and transcriptomic data, we identified ATP5E, EDN3, and LOC101750371 as candidate genes influencing skin color traits in black-bone chickens. Conclusions This study characterized the evolutionary history of Luning chickens and preliminarily excavated candidate genes influencing the genetic mechanism of pigmentation in black-bone chickens, providing valuable insights for the study of animal melanin deposition.

Abstract Background Douglas-fir (Pseudotsuga menziesii [Mirb.] Franco) plays a critical role in the ecology and economy of Western North America. This conifer species comprises two distinct varieties: the coastal variety (var. menziesii) along the Pacific coast, and the interior variety (var. glauca) spanning the Rocky Mountains into Mexico, with instances of inter-varietal hybridization in Washington and British Columbia. Recent investigations have focused on assessing environmental pressures shaping Douglas-fir’s genomic variation for a better understanding of its evolutionary and adaptive responses. Here, we characterize range-wide population structure, estimate inter-varietal hybridization levels, identify candidate loci for climate adaptation, and forecast shifts in species and variety distribution under future climates. Results Using a custom SNP-array, we genotyped 540 trees revealing four distinct clusters with asymmetric admixture patterns in the hybridization zone. Higher genetic diversity observed in coastal and hybrid populations contrasts with lower diversity in inland populations of the southern Rockies and Mexico, exhibiting a significant isolation by distance pattern, with less marked but still significant isolation by environment. For both varieties, we identified candidate loci associated with local adaptation, with hundreds of genes linked to processes such as stimulus response, reactions to chemical compounds, and metabolic functions. Ecological niche modeling revealed contrasting potential distribution shifts among the varieties in the coming decades, with interior populations projected to lose habitat and become more vulnerable, while coastal populations are expected to gain suitable areas. Conclusions Overall, our findings provide crucial insights into the population structure and adaptive potential of Douglas-fir, with the coastal variety being the most likely to preserve its evolutionary path throughout the present century, which carry implications for the conservation and management of this species across their range.

Abstract Zanthoxylum is a versatile economic tree species utilized for its spice, seasoning, oil, medicinal, and industrial raw material applications, and it has a lengthy history of cultivation and domestication in China. This has led to the development of numerous cultivars. However, the phenomenon of mixed cultivars and confusing names has significantly obstructed the effective utilization of Zanthoxylum resources and industrial development. Consequently, conducting genetic diversity studies and cultivar identification on Zanthoxylum are crucial. This research analyzed the genetic traits of 80 Zanthoxylum cultivars using simple sequence repeat (SSR) and inter-Primer Binding Site (iPBS) molecular markers, leading to the creation of a DNA fingerprint. This study identified 206 and 127 alleles with 32 SSR markers and 10 iPBS markers, respectively, yielding an average of 6.4 and 12.7 alleles (Na) per marker. The average polymorphism information content (PIC) for the SSR and iPBS markers was 0.710 and 0.281, respectively. The genetic similarity coefficients for the 80 Zanthoxylum accessions ranged from 0.0947 to 0.9868 and from 0.2206 to 1.0000, with mean values of 0.3864 and 0.5215, respectively, indicating substantial genetic diversity. Cluster analysis, corroborated by principal coordinate analysis (PCoA), categorized these accessions into three primary groups. Analysis of the genetic differentiation among the three Zanthoxylum (Z. bungeanum, Z. armatum, and Z. piperitum) populations using SSR markers revealed a mean genetic differentiation coefficient (Fst) of 0.335 and a gene flow (Nm) of 0.629, suggesting significant genetic divergence among the populations. Molecular variance analysis (AMOVA) indicated that 65% of the genetic variation occurred within individuals, while 35% occurred among populations. Bayesian model-based analysis of population genetic structure divided all materials into two groups. The combined PI and PIsibs value of the 32 SSR markers were 4.265 × 10− 27 and 1.282 × 10− 11, respectively, showing strong fingerprinting power. DNA fingerprints of the 80 cultivars were established using eight pairs of SSR primers, each assigned a unique numerical code. In summary, while both markers were effective at assessing the genetic diversity and relationships of Zanthoxylum species, SSR markers demonstrated superior polymorphism and cultivar discrimination compared to iPBS markers. These findings offer a scientific foundation for the conservation and sustainable use of Zanthoxylum species.

Abstract Background Trueperella pyogenes is an opportunistic pathogen that causes suppurative infections in various animal species, including goats. So far, only limited knowledge of phenotypic and genotypic properties of T. pyogenes isolates from goats has been gathered. In our study, we characterized the phenotypic and genotypic properties of caprine T. pyogenes isolates and established their relationship by Random Amplified Polymorphic DNA-Polymerase Chain Reaction (RAPD-PCR). Results From 2015 to 2023, 104 T. pyogenes isolates were obtained from 1146 clinical materials. In addition, two T. pyogenes isolates were obtained from 306 swabs collected from healthy goats. A total of 51 T. pyogenes isolates were subjected to detailed phenotypic and genotypic characterization. The virulence genotype plo/nanH/nanP/fimA/fimC/luxS was predominant. All of the tested isolates showed the ability to form a biofilm but with different intensities, whereby most of them were classified as strong biofilm formers (72.5%). The high level of genetic diversity among tested caprine T. pyogenes isolates (19 different RAPD profiles) was observed. The same RAPD profiles were found for isolates obtained from one individual, as well as from other animals in the same herd, but also in various herds. Conclusions This study provided important data on the occurrence of T. pyogenes infections in goats. The assessment of virulence properties and genetic relationships of caprine T. pyogenes isolates contributed to the knowledge of the epidemiology of infections caused by this pathogen in small ruminants. Nevertheless, further investigations are warranted to clarify the routes of transmission and dissemination of the pathogen.

Macrophyte habitats exhibit remarkable heterogeneity, encompassing the spatial variation of abiotic and biotic components such as changes in water conditions and weather as well as anthropogenic stressors. Environmental factors are thought to be important drivers shaping the genetic and epigenetic variation of aquatic plants. However, the links among genetic diversity, epigenetic variation, and environmental variables remain largely unclear, especially for clonal aquatic plants. Here, we performed population genetic and epigenetic analyses in conjunction with habitat discrimination to elucidate the environmental factors driving intraspecies genetic and epigenetic variation in hornwort (Ceratophyllum demersum) in a subtropical lake. Environmental factors were highly correlated with the genetic and epigenetic variation of C. demersum, with temperature being a key driver of the genetic variation. Lower temperature was detected to be correlated with greater genetic and epigenetic variation. Genetic and epigenetic variation were positively driven by water temperature, but were negatively affected by ambient air temperature. These findings indicate that the genetic and epigenetic variation of this clonal aquatic herb is not related to the geographic feature but is instead driven by environmental conditions, and demonstrate the effects of temperature on local genetic and epigenetic variation in aquatic systems.

The common walnut (Juglans regia) is one of the most economically important nut trees cultivated worldwide. Despite its importance, no comprehensive evaluation of walnut tree population genetics has been undertaken across the range where it originated, Central Asia. In this study, we investigated the genetic diversity and population structure of 1082 individuals from 46 populations across Central Asia. We found moderate genetic diversity of J. regia across Central Asia, with 46 populations clustered into three groups with a weak relationship between genetic and geographic distance. Our findings reveal that the western Himalaya might be the core region of common walnut genetic diversity in Central Asia and that, except for two populations in Gongliu Wild Walnut Valley, humans might have introduced walnut populations to Xinjiang, China. The observed distribution of the genetic landscape has probably been affected by historical climate fluctuation, breeding system, and prolonged anthropogenic activity. We propose the conservation of the core genetic diversity resources in the western Himalaya and pay special attention to populations from Gongliu in Xinjiang. These findings enhance our understanding of the genetic variation throughout the distribution range of J. regia in Central Asia, which will provide a key prerequisite for evidence-based conservation and management.

The topmouth culter (Culter alburnus) is at the top of the food chain and plays an important role in the maintenance of freshwater ecosystem stability. It is also a commercially important aquaculture fish species in China. To establish conservation strategies and breeding programs, a total of 16 polymorphic microsatellite loci were isolated from transcriptome-derived sequences of C. alburnus. Characterization of these loci was assessed against 1 wild and 3 cultured populations in Huzhou, China. The number of alleles per locus ranged from 3 to 10 with an average of 5.25. A bottleneck effect was observed in all 4 populations; The ChangXing population showed moderate genetic differentiation when compared with other populations (FST values, 0.0695–0.0788). The microsatellite loci would be useful for further studies on population genetic diversity, genetic structure, and assessments of the artificial propagation release effect of C. alburnus.

The objective of the present study was to investigate the morphological variations among collections of okra landraces in order to improve local varieties in Palestine. Eighteen okra accessions from various locations in the West-Bank region were evaluated for morphological variation. Different sixteen morphological traits were used for okra collection evaluation. The results revealed significant differences in seed color, leaf rib color, stem color, branching patterns, and fruit characteristics. Cluster and similarity analysis classified into two main clusters (I and II) with further sub-clusters. Genetic proximity did not strictly align with geographical boundaries, suggesting that factors beyond location influence genetic similarity. Cluster I exhibited greater diversity, with sub-clusters hinting at potential local adaptation. In contrast, Cluster II was smaller and less diverse, implying potentially distinct genetic origins. These findings provide insights for breeding strategies and germplasm conservation.

Water stress is one of the most important limiting abiotic factors for crop plants. The drought resistance was investigated for 35 camelina doubled haploid lines along with a check cultivar (Sohail), under two irrigation conditions (supplementary irrigation and rainfed), during the crop year 2020-2021. The study was conducted in the randomized complete block design by three replications in three regions of Eslamabad-e Gharb, Mahidasht and Mehrgan. The indices of stress sensitivity (SSI), tolerance (Tol), drought resistance (DTI), mean productivity (MP), geometric mean productivity (GMP), harmonic mean (MH), yield stability (YSI) and drought resistance (DI) were calculated using seed yield in two environments of rainfed (Ys) and supplementary irrigation (Yp). There was a significant difference among regions for YS, Yp, MP, GMP, MH, and DTI indices. MP, GMP, MH, DTI and DI indices had significant correlations with two environments. According to MH, MP and GMP, the highest and the lowest drought resistance were observed in the Mehrgan region and Islamabad region, respectively. Mahidasht showed the highest value of drought resistance and Mehrgan showed the lowest value of drought resistance among the lines based on DTI. In addition, the results of the mean comparison, cluster analysis, principal components analysis and the three-dimensional scatter diagram of the lines based on the yield of two environments and the MP index showed that lines 1, 2, 3, 5, 6, 10, 7 and the check cultivar had more drought resistant. These lines had high seed yield in two contrast environments and showed more drought resistance, which is recommendable for breeding programs in the climatic conditions of Kermanshah province.

Understanding patterns of species-genetic diversity correlations (SGDC) is important for conservation purposes because it allows us to infer whether conservation of species diversity (SD) influences conservation of genetic diversity (GD) and the other way around. Here, we studied SGDCs using aquatic macrofauna in a set of 31 urban ponds in the metropolitan area of Stockholm, Sweden. We also estimated how land use and pond environmental factors affect SD and GD. SD was estimated as species richness. GD was estimated in four focal species that differed in their dispersal abilities: Asellus aquaticus (Isopoda), Haliplus ruficollis (Coleoptera), Planorbis planorbis (Gastropoda), Rana temporaria (Amphibia), using double digest restriction associated DNA (ddRAD) sequencing data. There were no significant SGDCs for any of the species. Similarly, GD was not related to land use or pond environment. However, SD had a significant positive correlation with total invertebrate abundance and pond area. Given the absence of significant SGDCs in our study, and the mixed positive and negative patterns found in previous studies reporting SGDCs, we suggest that simultaneously preserving species and genetic diversity in urban areas will prove challenging.

Floodplain forests as one of the most endangered ecosystems in Europe have recently been impacted by fungal pathogens Phytophtora sp. and Hymenoscyphus fraxineus (chalara). Grey poplar (Populus × canescens Aiton Sm.) can be used as one of well adapted tree species for the reforestation of withering stands of ash (Fraxinus sp.). A unique population of grey poplar (Populus × canescens Aiton Sm.) characterized by desirable phenotypic traits was used for this purpose. The gender distribution was asymmetric; out of 155 individuals, 113 were female. Out of 33 different genotypes determined in the population, 15 were used as a source of approved forest reproductive material. Vegetative reproduction methods (ex situ clonal reproduction by micropropagation and cuttings) were developed and used, to rapidly initiate the recovery of forest stands of grey poplar. In total, 940 explants were successfully micropropagated and adapted to natural conditions, to ensure a genetically diverse source of viable plants used for reforestation. Moreover, we used methodological procedures of micropropagation for setting up cryopreservation technique. With respect to long-term storage of valuable grey poplar genotypes, modulation of gene expression by cold hardening during cryopreservation revealed significant changes in a few candidate genes involved in plant cellular processes.

Abstract Background The burden of malaria persists in sub-Saharan Africa and the emergence of artemisinin resistance has introduced complexity to control efforts. Monitoring the efficacy of artemisinin-based treatment for malaria is crucial to address this challenge. This study assessed treatment efficacy of artemether-lumefantrine (AL) and genetic diversity of Plasmodium falciparum isolates in a Nigerian population. Methods Participants presenting with clinical symptoms of uncomplicated malaria at a health centre in Lagos, Nigeria, were screened for P. falciparum. Enrolled participants were treated with AL and monitored through scheduled check-up visits, clinical and laboratory examinations for 28 days. Parasite clearance and genetic diversity were assessed through polymerase chain reaction (PCR) analysis of merozoite surface proteins (msp1 and msp2). The prevalence of drug resistance mutations was assessed by P. falciparum multidrug resistance gene 1 (mdr1) genotyping followed by P. falciparum ubiquitin-specific protease 1 (ubp1) gene sequencing. Results The PCR-uncorrected treatment outcome revealed 94.4% adequate clinical and parasitological response (ACPR) and 5.6% late parasitological failure (LPF) rates. After PCR correction, no suspected LPF case was detected and ACPR 67/67 (100%) was achieved in all the individuals. Moreover, a high prevalence of wild-type alleles for mdr1 N86Y (93.7%), and mdr1 D1246Y (87.5%) was observed. Genetic diversity analysis revealed predominant K1 allelic family for msp1 (90.2%) and FC27 for msp2 (64.4%). Estimated multiplicity of infection (MOI) was 1.7, with the highest MOI observed in the 5–15 years age group. ubp1 sequence analysis identified one nonsynonymous E1528D polymorphism at a low frequency (1.6%). Conclusion The study demonstrated sustained efficacy of AL for treating uncomplicated P. falciparum malaria. Genetic diversity analysis revealed various allelic types, suggesting occurrences of polyclonal infections. Nonetheless, the detection of a significant ubp1 polymorphism could have future implications for the epidemiology of anti-malarial drug resistance in the population.

Abstract Botryosphaeriaceae species are the major causal agents of walnut dieback worldwide, along with Diaporthe species. Botryosphaeria dothidea and Neofusicoccum parvum are the only two Botryosphaeriaceae species associated with this recently emergent disease in France, and little is known about their diversity, structure, origin and dispersion in French walnut orchards. A total of 381 isolates of both species were genetically typed using a sequence-based microsatellite genotyping (SSR-seq) method. This analysis revealed a low genetic diversity and a high clonality of these populations, in agreement with their clonal mode of reproduction. The genetic similarity among populations, regardless of the tissue type and the presence of symptoms, supports the hypothesis that these pathogens can move between fruits and twigs and display latent pathogen lifestyles. Contrasting genetic patterns between N. parvum populations from Californian and Spanish walnut orchards and the French ones suggested no conclusive evidence for pathogen transmission from infected materials. The high genetic similarity with French vineyards populations suggested instead putative transmission between these hosts, which was also observed with B. dothidea populations. Overall, this study provides critical insight into the epidemiology of two important pathogens involved in the emerging dieback of French walnut orchards, including their distribution, potential to mate, putative origin and disease pathways.

Abstract Linseed or flaxseed, native to the Indian subcontinent, had undergone domestication, edaphic selection and evolutionary processes that may have resulted in huge genetic variability in Indian genotypes. To understand the hitherto unexplored genetic diversity for sustainable flaxseed production amid challenges of climate fluctuation and identify trait-specific high-yielding genotypes, 2576 unique linseed accessions were comprehensively evaluated for 36 traits for up to six environments representing two major agroecological zones in India. A wide range of variability was recorded for days to initiation of flowering (42.86–114.99), plant height (43.31–122.88 cm), capsules/plant (64.62–375.87), seed size (6.06–14.44 cm2), thousand seed weight (2.80–11.86 g), seed yield (2.93–17.28 g/plant), oil content (30.14–45.96%) and fatty acid profile especially the key constituent omega-3 fatty acid (25.4–65.88%). Most of the traits such as plant height, flowering time, seed yield, seed and capsule size showed a high or moderately high level of variance coupled with high broad sense heritability indicating precise capturing of less heritable quantitative traits. The infraspecific classification of the tested collection revealed the seed/oil type (2498 accessions) as the dominant morphotype over dual-purpose/fiber flax (78 accessions) in the conserved collection. Correlation analysis indicated a significant positive association between flowering time, plant height, days to maturity and oil content. Trait-specific superior genotypes for earliness (50% flowering in 11 g), capsules/plant (> 350), oil content (> 45%) and fatty acid composition (> 65% alpha-linolenic acid) were identified to aid genetic improvement of linseed and to broaden the narrow genetic base.

Abstract Melioidosis caused by Burkholderia pseudomallei (Bp) is a public health threat. Genomic-epidemiology research on this deadly disease is scarce. We investigated whole-genome sequences of Bp isolates in relation to environmental source and drug susceptibility. In total, 563 Bp isolates were collected from 11 Northeast Thai provinces during the period 2004–2021. Patients (n = 530 isolates), infected animals (n = 8), and environmental sources (n = 25) provided samples. Phylogenetic analysis revealed genetic diversity among the Bp isolates, including numerous well-supported clusters of varying sizes. Through in-depth analysis of 38 monophyletic clades (MCs), we found eleven associated with province of origin (p-value

Abstract Background The tropical legume Mucuna pruriens (L.) DC. can meet three agricultural needs: low-cost protein, high-value medicines, and green manure or cover crops. But like other underutilized crops, it needs more modern breeding resources. Identifying marker-trait associations (MTAs) can facilitate marker-assisted breeding and crop improvement. Recent studies have demonstrated the feasibility of identifying MTAs using a small number of accessions ( 10% from mixed linear model offer a solid resource base for improving this crop. This is the first report on association mapping in M. pruriens and our results are expected to assist with marker-assisted breeding and identifying candidate genes in this promising legume.

Abstract Biogeographic barriers to gene flow are central to studies of plant phylogeography. There are many physical and geographic barriers in China, but few studies have used molecular ecological evidence to investigate the natural geographic isolation barrier of the Qinling Mountains-Huaihe River Line (QHL). Allium macrostemon is a precious Chinese perennial herb belonging to the Amaryllidaceae family. It is used as a food and medicine, with a variety of health and healing properties. Five SSR markers, three chloroplast DNA (cpDNA) markers (psbA-trnH, rps16 and trnL-F), one nuclear ribosomal DNA (nrDNA) marker (ITS), and simplified genome GBS sequencing were used to analyse the genetic diversity and structure of A. macrostemon. Combining SSR, cpDNA, nrDNA ITS data and GBS analysis results, we divided A. macrostemon populations into northern and southern groups, with the southern group further divided into southwestern and central-southeastern groups. Niche simulation results reveal that the distribution area of A. macrostemon will reach its maximum in the future. These data indicate that the regional separation of A. macrostemon has been maintained by the combined influence of a geographical barrier and Quaternary climate, and that the back-and-forth fluctuations of QHL and Quaternary climate have played an important role in this process. QHL acts as a north-south dividing line in phylogeography and population genetic structure, promoting physical geographic isolation. This study provides a theoretical basis for the conservation, development, and utilization of A. macrostemon resources. It further provides a reference for understanding the systematic geographical pattern of the large-scale spatial distribution of plants in China and enriches our understanding of Quaternary plant evolution in areas with complex terrain.