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Introduction: The incidence of nontuberculous mycobacterial (NTM) infections has increased worldwide, attracting attention in routine diagnostic settings, particularly among patients with suspected tuberculosis. This study aimed to acquire knowledge of NTM infections in patients with suspected tuberculosis and to evaluate the genetic diversity of the strains. Methods: In this study, 230 clinical specimens were collected from suspected tuberculosis patients. Following decontamination with N-Acetyl-L-cysteine–sodium hydroxide (NALC-NaOH), the sediments of specimens were inoculated onto Löwenstein–Jensen medium and then incubated at 37°C for 8 weeks. The samples that yielded positive cultures were evaluated through the sequencing of conserved fragments of IS6110 and hsp65. For those samples that were not identified as part of the M. tuberculosis complex (MTC) by IS6110 PCR, further analysis was conducted via PCR to detect fragments of the hsp65 gene. Results: Twenty-one NTM species were isolated from 230 clinical specimens (14 NTM from pulmonary specimens and 7 from extrapulmonary specimens). Among these, 12 (57.14%) were rapid-growing mycobacteria (RGM), and 9 (42.85%) were slow-growing mycobacteria (SGM). No M. avium complex (MAC) was identified in any of the specimens. Notably, the M. kansasii , M. gordonae , and M. abscessus strains presented significant genetic diversity. Conclusions: The prevalence of infections attributed to nontuberculous species surpasses that attributed to tuberculosis. These findings underscore the importance of exploring NTM species in individuals suspected of having TB. [ABSTRACT FROM AUTHOR]

Strict biennials are among the least known lifecycles in plant ecology due to their rarity in nature, and their population genetics still remain unknown. The present study addressed the strict biennial lifecycle and associated population genetics of Pedicularis hallaisanensis , an endangered endemic plant in Korea. All P. hallaisanensis individuals were counted in August from 2021 to 2023 in the wild population of Gayasan National Park, and lifecycle and morphological changes were monitored monthly. A de novo draft genome and single nucleotide polymorphism (SNP) analysis were used to study the population's genetic structure. P. hallaisanensis strictly requires a 2-year lifecycle per generation, including 8 and 10 months of growing periods as a first-year seedling and second-year adult, respectively. Facultative annual and perennial lifecycles were undetected, resulting in odd-year and even-year flowering cohorts. Permutational multivariate analysis of variance on the detected 3,716 SNPs demonstrated that the flowering group (p < 0.005), microhabitat (p < 0.001), and their interaction (p < 0.01) had a significant effect on genetic structure, which was differentiated between odd-year and even-year flowering cohorts. Other cluster analyses also showed that a microhabitat under historical anthropogenic interventions contained lowered genetic diversity due to a decreased genetic distance between odd-year and even-year flowering cohorts (p < 0.05). Overall, the findings suggest that excessive anthropogenic interventions should be avoided to preserve genetic diversity in the wild P. hallaisanensis population. Moreover, conservation programs for similar biennial plants should collect wild breeds from both odd-year and even-year flowering cohorts to improve the genetic diversity of artificially propagated individuals. [ABSTRACT FROM AUTHOR]

Pseudomonas syringae pv. tomato (Pst) is the causal agent of bacterial speck disease in tomatoes. The Pto/Prf gene cluster from Solanum pimpinellifolium was introgressed into several modern tomato cultivars and provided protection against Pst race 0 strains for many decades. However, virulent Pst race 1 strains that evade Pto -mediated immunity now predominate in tomato-growing regions worldwide. Here we report the identification of resistance to a Pst race 1 strain (Pst 19) in the wild tomato accession S. pimpinellifolium LA1589 (hereafter LA1589), using our rapid high-throughput seedling screen. LA1589 supports less bacterial growth than cultivars, and does not exhibit a hypersensitive response to Pst 19. We tested an existing set of 87 Inbred Backcross Lines (IBLs) derived from a cross between susceptible Solanum lycopersicum E-6203 and Solanum pimpinellifolium LA1589 for resistance to Pst 19. Using single-marker analysis, we identified three genomic regions associated with resistance. Bacterial growth assays on IBLs confirmed that these regions contribute to resistance in planta. We also mapped candidate genes associated with resistance in a cross between the Solanum lycopersicum var. lycopersicum cultivar Heinz BG-1706 and S. pimpinellifolium LA1589. By comparing candidates from the two mapping approaches, we were able to identify 3 QTL and 5 candidate genes in LA1589 for a role in resistance to Pst 19. This work will assist in molecular marker-assisted breeding to protect tomato from bacterial speck disease. [ABSTRACT FROM AUTHOR]

Sweet potato (Ipomoea batatas) is a crucial crop for food security and economic stability in many regions, including Costa Rica. This study aimed to assess the prevalence and genetic diversity of two major viruses associated with sweet potato virus disease (SPVD) in Costa Rica: sweet potato feathery mottle virus (SPFMV) and sweet potato chlorotic stunt virus (SPCSV). A total of 50 leaf samples displaying typical viral disease symptoms were collected from major sweet potato‐growing regions. Using multiplex reverse transcription (RT)‐PCR, SPFMV was detected in 82% of the samples and SPCSV in 52%, with a coinfection rate of 48%. Genetic analysis revealed that SPFMV isolates belonged predominantly to phylogenetic group B, while SPCSV isolates clustered with the West African (WA) strain. The low genetic diversity within these viral populations suggests a limited number of initial infection events followed by local spread. Riboprobe technology was evaluated as an alternative to RT‐PCR for virus detection. While the riboprobes for SPFMV demonstrated sensitivity comparable to RT‐PCR, the SPCSV riboprobes showed slightly lower sensitivity, particularly when using crude leaf extracts. Despite this, riboprobes offer significant advantages in terms of cost and ease of use for large‐scale screening. Our findings underscore the need for robust diagnostic and management strategies to control SPVD and highlight the importance of continuous monitoring and research to mitigate the impact of viral diseases on sweet potato production in Costa Rica. These insights contribute to the global understanding of SPVD and support collaborative efforts in plant pathology research. [ABSTRACT FROM AUTHOR]

Bread wheat (Triticum aestivum) became a globally dominant crop after incorporating the D genome from the donor species Aegilops tauschii , but the evolutionary history that shaped the D genome during this process remains to be clarified. Here, we propose a renewed evolutionary model linking Ae. tauschii and the hexaploid wheat D genome by constructing an ancestral haplotype map covering 762 Ae. tauschii and hexaploid wheat accessions. We dissected the evolutionary trajectories of Ae. tauschii lineages and reported a few independent intermediate accessions, demonstrating that low-frequency inter-sublineage gene flow had enriched the diversity of Ae. tauschii. We discovered that the D genome of hexaploid wheat was inherited from a unified ancestral template, but with a mosaic composition that was highly mixed and derived mainly from three Ae. tauschii L2 sublineages located in the Caspian coastal region. This result suggests that early agricultural activities facilitated innovations in D-genome composition and finalized the success of hexaploidization. We found that the majority (51.4%) of genetic diversity was attributed to novel mutations absent in Ae. tauschii , and we identified large Ae. tauschii introgressions from various lineages, which expanded the diversity of the wheat D genome and introduced beneficial alleles. This work sheds light on the process of wheat hexaploidization and highlights the evolutionary significance of the multi-layered genetic diversity of the bread wheat D genome. By constructing a pan-ancestry haploblock map for the Triticum–Aegilops D genome covering 762 Aegilops tauschii and hexaploid wheat accessions, this study discovered that hexaploid wheat inherited a conserved ancestral genomic template across the D genome. Furthermore, the study elucidated its mosaic composition, which was mainly contributed by three Ae. tauschii L2 sublineages located in the Caspian coastal region. [ABSTRACT FROM AUTHOR]

Introduction: With its distinctive evolutionary rate and inheritance patterns separate from the nuclear genome, mitochondrial genome analysis has become a prominent focus of current research. Dendrobium hancockii Rolfe, a species of orchid with both medicinal and horticultural value, will benefit from the application of the fully assembled and annotated mitochondrial genome. This will aid in elucidating its phylogenetic relationships, comparative genomics, and population genetic diversity. Methods: Based on sequencing results from Illumina combined with PacBio and Nanopore, the mitochondrial genome map of D. hancockii was constructed. Comparative analysis was conducted from the perspectives of phylogeny across multiple species, selection pressure on protein-coding genes, and homologous segments. The population diversity of D. hancockii was analyzed using single nucleotide polymorphism (SNP) data from the mitochondrial genome and single-copy nuclear genes. Results and discussion: This research constructed a circular mitochondrial map for D. hancockii , spanning 523,952 bp, containing 40 unique protein-coding genes, 37 transfer RNA genes, and 4 ribosomal RNA genes. Comparative analysis of mitochondrial genes from 26 land plants revealed a conserved gene cluster, " rpl16-ccmFn-rps3-rps19 ," particularly within the Dendrobium genus. The mitochondrial genome of D. hancockii exhibits a lower point mutation rate but significant structural variation. Analysis of 103 resequencing samples identified 19,101 SNP sites, dividing D. hancockii into two major groups with limited gene flow between them, as supported by population diversity, genetic structure analysis, principal component analysis, and phylogenetic trees. The geographical distribution and genetic differentiation of D. hancockii into two major groups suggest a clear phytogeographical division, likely driven by ancient geological or climatic events. The close alignment of mitochondrial data with nuclear gene data highlights the potential of the mitochondrial genome for future studies on genetic evolution in this species. [ABSTRACT FROM AUTHOR]

Chrysanthemums are versatile ornamental plants, and improving leaf and flower traits is an important breeding objective. Distant hybridization is a powerful method for plant breeding and genetic improvement, whereas the genetic basis in interspecific F1 progeny of chrysanthemums needs to be better understood for breeding purposes. In this study, the leaf and floral traits of the 273 reciprocal interspecific F1 hybrids of diploid C. dichrum (YSJ) and C. nankingense (JHN) were analyzed along with their SNP-derived genetic structure to elucidate the influence of differences in genetic background between the parents on the hybrid performance. We then performed a genome-wide association analysis (GWAS) to reveal the investigated traits' genomic loci and candidate genes. Considerable phenotypic variation (8.81% ~ 55.78%) and heterosis with transgressive segregation in both directions were observed in the reciprocal progenies. We observed a higher level of phenotypic variation in JHN × YSJ rather than in YSJ × JHN. Also, a significant reciprocal effect was observed for most examined traits. Based on the SNP data, we separated the hybrid progenies into three groups (I, II, and III), albeit imperfectly dependent on the cross directions, except for some reciprocal hybrids clustering into group II. Group I from YSJ × JHN and Group III from YSJ × JHN differed with contrasting FST and π ratios, indicating the genetic changes in the reciprocal populations. The outcome of GWAS via the IIIVmrMLM method detected 339 significant quantitative trait nucleotides (QTNs) and 40 suggestive QTNs, and the phenotypic variation explained by a single QTN ranged from 0.26% to 7.42%. Within 100 kb upstream and downstream of the important QTNs, we discovered 49 known genes and 39 new candidate genes for the investigated leaf and floral traits. Our study provides profound insights into the genetic architecture of reciprocal hybrid progenies of chrysanthemum species, facilitating future breeding activities. [ABSTRACT FROM AUTHOR]

Background: The present investigation was conducted at Agricultural College and Research Institute, Killikulam, Tamil Nadu during the year 2022-2023 involving 220 groundnut genotypes along with a resistant and susceptible check towards validation of phenotypic extremities on yield and its contributing traits besides screening against late leaf spot resistance. Methods: The data collected from two hundred and twenty germplasm along with check varieties for thirteen quantitative traits. The collected data were subjected to statistical analysis (Mahalanobis, 1936) besides interpreted by various genetic tools such as PCV, GCV, heritability and GAM. Further, ten plants were selected at random from each genotype and observation on late leaf spot disease was recorded based on modified 9 point scale. Result: Molecular analysis for LLS resistance among the groundnut germplasm had shown the concurrent superiority in terms of yield and resistance to late leaf spot disease among the genotypes ICG 15233, ICG 8760, ICG 76, ICG 111, ICG 297, ICG 405, ICG 238, ICG 4598, ICG 5051, ICG 6057, ICG 8253, ICG 8285, ICG 10701 and ICG 15234. Hence, these genotypes can be exploited to develop a disease resistance and high yielding groundnut culture. [ABSTRACT FROM AUTHOR]

Saburai goat (Capra hircus) developed by the farmers at Tanggamus Regency, Indonesia and originated from the crossbreeding between Boer buck and Ettawa grade doe for meat production purpose. This study aimed to evaluate Saburai goat based on two ISSR markers of (AG)9C and (GA)9C. This study uses 28 adult Saburai does. Results showed that a total of 13 DNA fragments were observed according to two ISSR markers with a total of 11 polymorphic loci. However, the PIC value in (AG)9C ISSR marker was higher than (GA)9C ISSR marker. According to both ISSR markers, Saburai goat can be characterized into two clusters. In conclusion, the genetic diversity in Saburai goats is high and potential to improve with molecular selection. [ABSTRACT FROM AUTHOR]

Pinus sylvestris var. mongolica plays a crucial role in the ecological restoration and industrial raw material production of arid and semiarid regions in northern China. The widespread degradation of its near‐mature plantation (over 30 years) is a significant concern, having been a topic of interest in recent decades. In this study, the genetic diversity and population genetic structure were assessed using 12 simple sequence repeat (SSR) markers within 11 native provenance populations and eight plantation populations. Additionally, variations in eight morphological traits of their offspring were evaluated at three sites in northern China. The results revealed high genetic diversity and weak genetic differentiation among the native provenance populations. The mean number of alleles (Na), allelic richness (Ar), expected heterozygosity (He), and Shannon–Wiener diversity index (I) were 5.492, 4.679, 0.550, and 1.120, respectively, and the genetic differentiation coefficient (FST) was 0.022. Significant population effects of tree height and height to live crown base (HCB), as well as interactions of population with site and block within site, were observed in tree height, HCB, stem diameter at breast height (DBH), stem volume (VOL), crown shape (CS), and disease grade (DG). The genetic diversity parameters based on SSR markers and breeding values of tree height, DBH, HCB, VOL, and stem form (SF) of plantation populations were found to be lower than those of native provenance populations. Significant positive correlations were identified between the mean effective number of alleles per locus (Ne) and VOL as well as He and crown width (CW). Furthermore, the maximum temperature of the warmest month (BIO5) and the silt content (T_SILT) were identified as significant factors influencing genetic diversity parameters and morphological variation, respectively. The findings provide scientific support for the reduction of plantation degradation, the effective restoration, and the sustainable management of forests for this species. [ABSTRACT FROM AUTHOR]

Pine stem rust, the most damaging and widespread forest disease occurring in pine trees in the Northern Hemisphere, is primarily caused by Cronartium species (Pucciniales, Melampsorineae). While the phylogenetic relationships of major Cronartium species have been largely elucidated, there is limited understanding of their species diversity and the evolutionary processes shaping their distribution patterns. In this work, we performed broad sampling and sequencing of Cronartium taxa in China together with additional sequence data and other accessions in NCBI to investigate the diversification and to estimate the divergence time of major evolutionary events in this genus. Molecular dating analysis suggested that the divergence of the genus Cronartium probably was around 91.78 Ma during the Upper Cretaceous. It is believed that Cronartium species may have originated in Asia and North America, with intercontinental dispersals occurring primarily during the Middle Eocene, Middle Miocene, and Pliocene. These dispersal events likely took place through the North Atlantic Land Bridge, the De Geer Route, and the Bering Land Bridge, and subsequently diverged through sporadic dispersal and vicariance events. Furthermore, our analysis of host associations revealed that the diversification of Cronartium species was correlated with their telial‐hosts, and some species may have experienced host jump events, indicating a complex interplay between host specificity and pathogen–host interaction during Cronartium evolution. [ABSTRACT FROM AUTHOR]

Assessing patterns of genetic diversity within and among closely related congeners is important for evaluating the conservation status of rare plant taxa. We used nuclear microsatellite genotyping to examine the genetic relatedness among three Physaria taxa on the Kaibab Plateau in northern Arizona. Over 100 species of Physaria are recognized, and are widely distributed in Western North America. On the Kaibab Plateau several taxa occur, including Physaria arizonica and two subspecies of P. kingii, P. kingii subsp. latifolia and P. kingii subsp. kaibabensis. The latter subspecies, the Kaibab bladderpod, is rare and endemic to the Kaibab Plateau and is a potential candidate to be listed under the Endangered Species Act. Morphological characters, primarily flower color, have been used to distinguish P. kingii subsp. kaibabensis from other subspecies. Here we aim to assess its genetic diversity and differentiation as compared to congeners on and around the Kaibab Plateau. We genotyped DNA obtained from leaf samples from 463 individuals collected from 26 sites representing the three putative taxa (12 P. kingii subsp. kaibabensis, 8 P. kingii subsp. latifolia, and 6 P. arizonica). Our results showed that all samples initially identified as P. kingii subsp. latifolia and P. kingii subsp. kaibabensis on the Kaibab Plateau form a single genetic cluster that is well‐differentiated from P. kingii subsp. latifolia sampled from sites off the plateau or P. arizonica on or off the plateau. For P. kingii on the plateau, our findings do not support the previous subspecies designations based on morphological characters. While additional studies of P. kingii will further resolve taxonomic uncertainties within this species, our findings indicate that the Kaibab Plateau population is genetically diverse and genetically distinct, and federal protection is justified in light of the threats faced on the Kaibab Plateau and its limited range. [ABSTRACT FROM AUTHOR]

The Ogasawara Islands, representing an oceanic island ecosystem in Japan, have a notably high rate of endemic species akin to other oceanic islands globally. Pittosporum parvifolium is a critically endangered shrub with only four remaining individuals in its natural habitat on the Ogasawara Islands. Current conservation efforts encompass both in situ and ex situ approaches for P. parvifolium. However, these efforts face challenges stemming from the lack of critical conservation information. Therefore, we explored P. parvifolium's genetic diversity and implications for conservation. We utilized simple sequence repeat markers to scrutinize genetic diversity within both in situ and ex situ populations, revealing notably rich diversity among both. The in situ genetic diversity was significantly high despite the few extant individuals. In addition, many of the ex situ peculiar genotypes were absent in individuals conserved in situ. This investigation also provides insights into the reproductive strategies and combinations of selfing and outcrossing. The results of the present study recommend conservation to maximize genetic diversity in P. parvifolium by promoting cross‐pollination among in situ individuals and by introducing individuals with unique genotypes into ex situ stocks. [ABSTRACT FROM AUTHOR]

Magnaporthe oryzae, a filamentous heterothallic ascomycete fungus that serves as the causative agent of rice blast disease, is globally distributed in rice-growing regions. Populations shaped by environmental factors and human intervention play important roles in the formation of genetic structure. In this study, population structures and spatiotemporal dynamics were investigated based on large-scale whole genomic sequences of rice-infecting M. oryzae around the world. By analyzing these genetic structures, we identified divergent clades that crossed geographic boundaries. While we observed associations between the isolates and their geographic origins, we also found that there were frequent migration events occurring across Asia in main rice cultivation regions. Within Asia, China was the migration origin, facilitating gene flows to Japan and South Korea. Since the 1970s, the genetic diversity of M. oryzae populations in China has also shown a steadily increasing trend, continuing through to the 2020s. Additionally, our analysis of the evolutionary history of Asian M. oryzae populations provided insights into the population expansion that has taken place in recent decades. Overall, our findings indicate that human-mediated gene flows played a pivotal role in shaping the genetic structure of M. oryzae. [ABSTRACT FROM AUTHOR]

Simple Summary: The whitefly pest, Bemisia tabaci, is an economically important pest given its role in the transmission of plant virus diseases such as cassava mosaic disease (CMD), which continues to devastate cassava productivity in Nigeria. Previous studies have shown that the ability of whiteflies to transmit plant viruses is dependent on several factors, chief of which is its biotype. Given that whiteflies are often morphologically indistinguishable, it is therefore important to explore the genetic diversity of whiteflies towards developing adequate management strategies for CMD in Nigeria. This study therefore investigated the genetic diversity and distribution of B. tabaci genotypes present in cassava farms surveyed across South West and North Central, Nigeria, while also assessing the presence of cassava mosaic begomoviruses (CMBs). The obtained whitefly samples were genotyped using the mitochondrial cytochrome oxidase I (mtCOI) marker. This study identified four genetic groups of B. tabaci, with the Sub-Saharan Africa 1 (SSA1) group being the most predominant. This research also detected African cassava mosaic virus (ACMV) and East African cassava mosaic virus (EACMV) in specific subgroups, providing insights for developing improved management strategies to mitigate cassava mosaic disease (CMD) in Nigeria. Whitefly Bemisia tabaci (Gennadium, Hemiptera) causes severe damage to cassava plants through excessive feeding on leaves and transmitting viruses, such as African cassava mosaic virus (ACMV), East African cassava mosaic virus (EACMV), and ipomoviruses that cause cassava brown streak disease. Currently, little is known about the molecular diversity and distribution of whitefly species in the major cassava-growing zones of Nigeria. This study aimed to address the knowledge gap by assessing the genetic diversity, distribution, and associated cassava mosaic begomoviruses (CMBs) in whiteflies across South West and North Central, Nigeria. Whitefly samples were systematically collected from cassava plants during georeferenced epidemiological surveys in 2017, 2020, and 2022. The samples were genotyped using the mitochondrial cytochrome oxidase I (mtCOI) marker, and CMBs were detected by PCR with virus-specific primers. Phylogenetic analyses revealed four distinct genetic groups of B. tabaci: Sub-Saharan Africa 1 (SSA1; 84.8%), SSA2 (1.4%), SSA3 (13.1%), and Mediterranean (MED) (0.7%). The SSA1 group was the predominant and most widely distributed genotype across the surveyed zones, with three subgroups identified: SSA1-SG1, SSA1-SG3, and SSA1-SG5. The second most frequently identified genotype, SSA3, was restricted to the North Central zone, along with the SSA2 group, which was only identified in two North Central states (Niger and Plateau). African cassava mosaic virus (ACMV) was detected in SSA1-SG1, SSA1-SG5, and SSA3, whereas EACMV was found in only the SSA1-SG3. The findings of this study will aid in developing better whitefly management strategies to reduce the impact of CMD on cassava production in Nigeria. [ABSTRACT FROM AUTHOR]

(1) Background: Buffaloes are crucial livestock species for food and service in tropical and subtropical regions. Buffalo genetics, particularly in indigenous Chinese breeds such as the Xiangxi white buffalo (XWB), remains an intriguing area of study due to its unique traits and regional significance. (2) Methods: This investigation utilized the whole-genome sequences of twenty XWBs (newly sequenced), along with eighty published whole-genome sequences of other buffalo breeds (including Guizhou white buffalo, river buffalo, and Chinese buffalo in the Yangtze River). Using whole-genome sequencing analysis technology, the population structure, genomic diversity, and selection signatures of XWB were determined. (3) Results: This study revealed that the XWB, being phylogenetically positioned in the middle and lower reaches of the Yangtze River, exhibited substantial genomic diversity. Employing four selection sweep detection methods (CLR, iHS, π-ratio, and FST), several genes were positively identified for adaptive traits in the XWB, including coat color phenotypes (ASIP, KIT), the nervous system (GRIK2), reproduction (KCNIP4), growth and development (IFNAR1, BMP6, HDAC9, MGAT4C, and SLC30A9), the body (LINGO2, LYN, and FLI1), immunity (IRAK3 and MZB1), and lactation (TP63, LPIN1, SAE1). (4) Conclusions: In conclusion, this study enhances our understanding of the genetic distinctiveness and adaptive traits of XWB, highlighting selection signatures crucial for future breeding and conservation and ensuring sustainable use of this vital livestock resource. [ABSTRACT FROM AUTHOR]

Background/Objectives: Orenburg goats are renowned for their soft down that acts as a substrate for warm clothing, particularly shawls that have an international reputation. As with many local livestock breeds, however, the Orenburg is presently at risk of extinction, an issue that can be addressed by assessing population genetic diversity and, thereafter, encouraging as much outbreeding as possible. Using single-nucleotide polymorphism (SNP)-based data, therefore, we analyzed the genetic diversity and population structure of modern Orenburg goats using samples collected from an expedition to Orenburg Oblast in 2024. Methods: We applied the Goat SNP50 BeadChip (Illumina, San Diego, CA, USA) for the genotyping of Orenburg goats from modern and archived populations. SNP genotypes of three Orenburg populations sampled in 2017 and 2019, Altai Mountain, Altai White, and Soviet Mohair breeds, were added to the dataset. Results: Principal component analysis and network and admixture analyses demonstrated that the genetic background inherent to the archived group of Orenburg goats was maintained in all modern populations. Values of genetic diversity indicators in modern populations were compatible with those obtained in comparison groups. Runs of homozygosity (ROH) were found in all the Orenburg goat populations (with a mean ROH length of 72.6–108.9 Mb and mean ROH number of 28–36). Genomic inbreeding based on ROH was low in all the Orenburg populations (FROH = 0.03–0.045). Conclusions: We showed that the ancestral background is retained in present-day Orenburg goats sampled in 2024. We provide the genetic basis through which certain breeder animals may be selected and bred traditionally or ex situ through a conservation program of gamete preservation. [ABSTRACT FROM AUTHOR]

Background/Objectives: Understanding the genetic diversity of soybean genotypes can provide valuable information that guides parental selection and the design of an effective hybridization strategy in a soybean breeding program. In order to identify genetically diverse, complementary, and prospective parental lines for breeding, this study set out to ascertain the genetic diversity, relationships, and population structure among 35 soybean genotypes based on agro-morphological traits and Single Nucleotide Polymorphic (SNP) marker data. Methods/Results: Cluster analysis, based on agro-morphological traits, grouped the studied genotypes into four clusters. The first two principal components accounted for 62.8% of the total phenotypic variation, where days to 50% flowering, days to 95% maturity, grain yield, shattering score, and lodging score had high and positive contributions to the total variation. Using the SNP marker information, mean values of 0.16, 0.19, 0.067, and 0.227 were obtained for minor allele frequency (MAF), polymorphic information content (PIC), observed heterozygosity (Ho), and expected heterozygosity (He), respectively. Using different clustering approaches (admixture population structure, principal component scatter plot, and hierarchical clustering), the studied genotypes were grouped into four major clusters. Conclusions:The agro-morphological and molecular analysis results indicated the existence of moderate genetic diversity among the studied genotypes. The traits identified to be significantly related to yield provide valuable information for the genetic improvement of soybeans for yield. [ABSTRACT FROM AUTHOR]

Although a lack of diversity in genetic studies is an acknowledged obstacle for personalized medicine and precision public health, Latin American populations remain particularly understudied despite their heterogeneity and mixed ancestry. This gap extends to COVID-19 despite its variability in susceptibility and clinical course, where ethnic background appears to influence disease severity, with non-Europeans facing higher hospitalization rates. In addition, access to high-quality samples and data is a critical issue for personalized and precision medicine, and it has become clear that the solution lies in biobanks. The creation of the Chilean COVID-19 Biorepository reported here addresses these gaps, representing the first nationwide multicentric Chilean initiative. It operates under rigorous biobanking standards and serves as one of South America's largest COVID cohorts. A centralized harmonization strategy was chosen and included unified standard operating procedures, a sampling coding system, and biobanking staff training. Adults with confirmed SARS-CoV-2 infection provided broad informed consent. Samples were collected to preserve blood, plasma, buffy coat, and DNA. Quality controls included adherence to the standard preanalytical code, incident reporting, and DNA concentration and absorbance ratio 260/280 assessments. Detailed sociodemographic, health, medication, and preexisting condition data were gathered. In five months, 2262 participants were enrolled, pseudonymized, and sorted by disease severity. The average Amerindian ancestry considering all participant was 44.0% [SD 15.5%], and this value increased to 61.2% [SD 19.5%] among those who self-identified as Native South Americans. Notably, 279 participants self-identified with one of 12 ethnic groups. High compliance (>90%) in all assessed quality controls was achieved. Looking ahead, our team founded the COVID-19 Genomics Network (C19-GenoNet) focused on identifying genetic factors influencing SARS-CoV-2 outcomes. In conclusion, this bottom-up collaborative effort aims to promote the integration of Latin American populations into global genetic research and welcomes collaborations supporting this endeavor. Interested parties are invited to explore collaboration opportunities through our catalog, accessible online. [ABSTRACT FROM AUTHOR]

Understanding population structure is a priority for evaluating population dynamics of commercially fished cephalopods under fishing pressure and environmental changes. This study employed a multidisciplinary approach to clarify the population structure of Loliolus (Nipponololigo) uyii, a common squid in inshore fisheries. Sampling was conducted multiple times to cover the distribution range across the East China Sea and South China Sea. High haplotype diversity was revealed by three gene markers (COI, 16S and ODH). Two geographical clades with significant genetic differentiation were divided through phylogenetic trees and haplotype networks. The boundary between the two clades is delineated by the Dongshan population in the southern East China Sea. Furthermore, the neutrality tests and mismatch analysis suggested that L. (N.) uyii populations may have undergone population expansion. Correspondingly, statolith differences in lateral dome and posterior indentation, along with high classification success, further supported the genetic division. The overall difference in statolith shape also efficiently identified seasonal groups in the Beibu Gulf lacking genetic differentiation. This result offers new insights into the influence of genetic and environmental factors on statolith shape. The integrated results provide a comprehensive understanding of the population structure of L. (N.) uyii, laying the foundation for resource development and the conservation of the species. [ABSTRACT FROM AUTHOR]

Genetic diversity and ecology are two important aspects of vector species crucial to a full understanding of disease epidemiology. In this study, we examined genetic diversity, genetic structure and the physiochemical parameters of the breeding habitats of the two significant black fly vector species, Simulium chumpornense Takaoka and Kuvangkadilok and S. nodosum Puri, from Laos. Genetic diversity of S. chumpornense in Laos was relatively high with maximum genetic divergence of 3.05% but no significant genetic differentiation between populations. Comparisons with conspecific populations from Thailand also found no genetic differentiation between the two countries. This possibly related to the recent history of this species, as a very recent (31,000 years ago) historical population expansion was detected. Physicochemical parameters of the breeding habitats suggest the ability to utilize diverse stream sizes from small flows (1 m wide) to huge rivers (290 m or more wide). Populations of S. nodosum from Laos had low genetic diversity with maximum genetic divergence of 2.56% and no genetic structuring among populations. Comparisons with those reported from other countries revealed five genetically divergent lineages (I–V) with minimum genetic divergence of 1.36%. The majority (42 of 52) of specimens from Laos belonged to lineage I and the remaining (10) comprised lineage II. Lineage I is the largest and representative of specimens from Thailand, Myanmar, Vietnam, Taiwan and Laos. Population history analysis revealed that lineage I had undergone recent demographic expansion dating back to 7000 years ago. This very recent population expansion resembles others reported from Thailand and possibly indicates a response to increasing human and domestic animals following the agricultural revolution. Breeding sites of S. nodosum are diverse in respect to elevation, velocity, water conductivity and streambed particle size. The ability to utilize a wide variety of breeding sites could promote the production of a large adult population, which can be a pest for humans and other animals. [ABSTRACT FROM AUTHOR]

The fragmented forests of the Kenya highlands, known for their exceptional species richness and endemism, are among the world's most important biodiversity hotspots. However, detailed studies on the fauna of these ecosystems—especially specialist species that depend on moist forests, which are particularly threatened by habitat fragmentation—are still limited. In this study, we used mitochondrial genes (cytochrome b and the displacement loop) and a nuclear marker (retinol-binding protein 3) to investigate genetic and morphological diversity, phylogenetic associations, historical divergence, population dynamics, and phylogeographic patterns in two rodent species—the soft-furred mouse (Praomys jacksoni) and the African wood mouse (Hylomyscus endorobae)—across Kenya's forest landscapes. We found a complex genetic structure, with P. jacksoni exhibiting greater genetic diversity than H. endorobae. The Mt. Kenya P. jacksoni populations are significantly genetically different from those in southwestern forests (Mau Forest, Kakamega Forest, and Loita Hills). In contrast, H. endorobae presented no observable biogeographic structuring across its range. The genetic diversity and geographic structuring patterns highlighted selectively strong effects of forest fragmentation and differing species' ecological and evolutionary responses to these landscape changes. Our findings further underscore the need for expanded sampling across Kenya's highland forests to better understand species' changing diversity and distribution patterns in response to the impacts of human-mediated habitat changes. These insights are critical for informing conservation strategies to preserve biodiversity better in this globally important region. [ABSTRACT FROM AUTHOR]

This study investigates the influence of internal factors on growth dynamics in four Cyprinus carpio varieties, three Romanian strains (Frăsinet, Ineu, and Podu Iloaiei) and the Koi variety. Fish were measured for total length, maximum height, and weight at four ontogenic stages, namely 7 days post-hatch, 3 months (0+), 18 months old (1+), and 36 months (2+). Weight Gain (WG), Specific Growth Rate (SGR), Relative Growth Rate (RGR), Fulton's condition factor, and the profile index were calculated and analyzed. Results revealed significant intervariety differences in growth performance and physiological condition across life stages. At the 2+ stage, Podu Iloaiei exhibited the highest WG (849.73 ± 4.09 g), while Koi showed the lowest (403.99 ± 14.21 g). Koi demonstrated a unique growth pattern, with the highest SGR (0.18 ± 0.00% day−1) and RGR (0.98 ± 0.05 g day−1) at the 2+ stage. Fulton's condition factor varied markedly, with Frăsinet showing the highest value at 7 days post-hatch (149.57 ± 17.485) and Koi the lowest at the 1+ stage (0.63 ± 0.011). The profile index decreased with age in all varieties, with Podu Iloaiei showing the most dramatic change from 4.22 ± 0.149 at 7 days to 2.18 ± 0.004 at 2+. These findings highlight the complex interplay between genetic and developmental factors in carp varieties, offering new insights for tailored breeding programs and aquaculture practices. [ABSTRACT FROM AUTHOR]

This study aimed to compare and assess the genetic diversity and trends among the introduced family provenance, first-cycle superior trees breeding provenance, and improved-generation superior trees breeding provenance of Pinus elliottii using EST-SSR markers. The goal was to provide a foundation for advanced genetic improvement and sustainable utilization of P. elliottii in Jiangxi Province. A total of 417 individuals were analyzed for their genetic diversity and population structure using 19 pairs of SSR markers. The analysis identified 103 alleles across all the samples, with an average of 5.421 alleles per locus. Compared to other coniferous species, P. elliottii exhibited a moderate to high level of genetic diversity (I = 0.862, He = 0.457). Analysis of the molecular variance (AMOVA) revealed that 97.90% of the genetic variation occurred within provenances, consistent with a low genetic differentiation coefficient (Fst = 0.016 < 0.05) and high gene flow (Nm = 15.715) among provenances. In addition, analysis using STRUCTURE v. 2.3.4 software divided the 417 germplasm samples into two distinct groups, corroborating the results of the principal coordinates analysis (PCoA) and the unweighted pair group method with arithmetic (UPGMA) clustering analysis. Overall, the germplasm resources of P. elliottii exhibited rich genetic diversity, with the majority of the genetic variation occurring within provenances. For the genetic improvement of high-resin-yielding slash pines, breeding programs should prioritize populations with high genetic diversity while carefully selecting superior individuals from within those populations. These findings provide a solid foundation for breeding high-resin-yielding varieties and for future research on the sustainable utilization of these valuable resources. [ABSTRACT FROM AUTHOR]

Simple Summary: This study analyzes fecal samples from Siberian roe deer in the Greater Khingan Range of Heilongjiang Province, using mitochondrial DNA and microsatellite markers to explore the population's genetic characteristics. The findings indicate a high level of genetic diversity within the Siberian roe deer population, alongside notable genetic differentiation among groups. Furthermore, this research offers vital insights for the conservation and management of Siberian roe deer and provides valuable data for the protection of local Northeast tigers (Pantheratigris altaica). This study focuses on the Siberian roe deer population in the Greater Khingan Mountains, Northeast China. The cold temperate forest ecosystem in this area is distinctive. The Siberian roe deer is a crucial ecological indicator species, and its living conditions hold significant importance for ecological balance. From the winter of 2019 to 2022, 269 fecal samples of Siberian roe deer were collected from four protected areas in the northern part of the Greater Khingan Mountains, Heilongjiang Province. These samples were comprehensively analyzed using mitochondrial DNA and microsatellite markers, combined with conservation genetics evaluation methods. The results revealed that 244 individuals were identified in the fecal samples. The results of a Cyt b genetic analysis of the samples indicated that the haplotype and nucleotide diversity were 88.1% and 20.3%, respectively. The evaluation of 14 pairs of microsatellite loci showed that the average number of alleles was 11.2, and the average expected and observed heterozygosity were 0.672 and 0.506, respectively. Therefore, the overall genetic diversity level is high, but some populations of Siberian roe deer are at risk. AMOVA analysis and STRUCTURE Bayesian clustering confirmed the existence of obvious genetic differentiation among the populations. Historical studies have shown that the HZ and SH populations underwent the earliest diffusion events, and the BJC and SL populations also exhibited related signs (HZ: Huzhong Nature Reserve in the Greater Khingan Mountains; SH: Shuanghe National Nature Reserve in Heilongjiang Province; BJC: Heilongjiang Beijicun National Nature Reserve; SL: Songling District in Heilongjiang Province). Mismatch distribution and neutral tests indicated no expansion events or bottleneck effects in the population, and the inbreeding coefficient was positive, suggesting the possibility of inbreeding. The development potential of the population in the future varies among the various local populations. This study supports the biodiversity of Siberian roe deer at the genetic level to save the population and provides important scientific basis and reference for the protection and management of Siberian roe deer. [ABSTRACT FROM AUTHOR]

Simple Summary: Pine woods have suffered major damage from the beetle Monochamus alternatus, which spreads the nematode Bursaphelenchus xylophilus and poses a serious threat to conifers like Pinus massoniana. In order to fill the knowledge gap regarding the phylogeography of M. alternatus, specific simple sequence repeat (SSR) primers were designed as part of this work. To find polymorphic SSRs, researchers sequenced M. alternatus specimens from three different locations using the Red-seq approach. After additional analysis, 95,612 SSR loci were found, most of which were repeats of mononucleotide (51.43%), dinucleotide (28.79%), and trinucleotide (16.74%) repeats. Eighteen pairs of SSR primers were selected for their stability and high polymorphism, with genetic typing showing an average allele count of 3–8, heterozygosity (Ho) from 0.13 to 0.73, PIC values ranging from 0.29 to 0.78, and Shannon's index between 0.59 and 1.80. The study resulted in 16 usable SSR primer pairs, enhancing research capabilities in phylogeography, genetic mapping, and functional genomics of M. alternatus. Monochamus alternatus, a pest posing a serious threat to coniferous species, such as Pinus massoniana, has had devastating effects on pine forests due to its association with Bursaphelenchus xylophilus. The creation of unique simple sequence repeat (SSR) primers for M. alternatus is crucial, as there has been little study of the species' phylogeography. The aim of this study was to identify and create polymorphic SSR primers by sequencing samples of M. alternatus obtained from three different sampling points using the restriction site-associated DNA sequencing (Red-seq) approach. Subsequently, supplementary samples were integrated, and genetic typing was performed utilizing the identified polymorphic primers. Through comprehensive analysis, a total of 95,612 SSR loci were identified. Among these, mononucleotide repeats (51.43%), dinucleotide repeats (28.79%), and trinucleotide repeats (16.74%) predominated among the SSR motif types. Ultimately, 18 pairs of SSR primers were screened out, demonstrating stable amplification and high polymorphism. Genetic typing revealed that the mean number of alleles (Na) for these primer pairs ranged from 3 to 8, observed heterozygosity (Ho) ranged from 0.133 to 0.733, polymorphic information content (PIC) ranged from 0.294 and 0.783, and Shannon's index (I) ranged from 0.590 to 1.802. This study effectively produced 16 pairs of SSR primers that can be applied to different populations of M. alternatus. As a result, important tools for furthering studies on the phylogeography of pine wood nematodes, creating genetic maps, gene mapping, and carrying out in-depth investigations into gene function have been made available. [ABSTRACT FROM AUTHOR]

Scots pine is a crucial component of ecosystems in Europe and Asia and a major utility species that comprises more than 60% of total forest production in Poland. Despite its importance, the genetic relationships between key conservation and the commercial value of Scots pine ecotypes in Poland remain unclear. To address this problem, we analyzed 27 populations (841 trees) of the most valuable Polish Scots pine ecotypes, including the oldest natural stands in all 24 regions of provenance established for the species in the country. By examining maternally inherited mitochondrial markers, nuclear microsatellite loci, and thousands of SNP markers from a genotyping array, we evaluated the genetic structure between and within them. These multilevel genomic data revealed high genetic similarity and a homogeneous structure in most populations, suggesting a common historical origin and admixture of populations after the postglacial recolonization of Central Europe. This research presents novel data on existing genomic resources among local ecotypes defined within strictly managed Polish regions of provenance, challenging their validity. Formal tests of the progeny of seed stands are needed to check whether the diversity in adaptation and quantitative traits still supports the delineation of provenance regions. In parallel, the health status of selected populations and the viability of seeds from these regions should be monitored to detect early‐stage symptoms of their environmental stress. It seems reasonable that periodic shortages of forest reproductive material (FRM) in a given region of provenance could be supplemented with the one from other regions that match their climatic envelope. Together, our results have important implications for the management of native Scots pine stands, particularly elite breeding populations, as they contribute to the discussion of the boundaries of provenance regions and the transfers of FRM that face increasing climate change. [ABSTRACT FROM AUTHOR]

Mandarin fruits with good physicochemical quality are desired for the fresh fruit market. The ease of crosses among citrus taxa has been used to expand genetic variability and select new varieties for different fruit markets. With the aim of selecting new commercial varieties, eleven hybrids obtained from the cross between Murcott tangor and Ponkan mandarin were grafted on Rangpur lime rootstock and evaluated for genetic and phenotypical characteristics. It was observed that there are significant differences in the fruit shape, content, and organoleptic characteristics in juice and differential responses to Alternaria alternate, the causal agent of the Alternaria brown spot (ABS) disease. The phenotypic and molecular characterization showed two groups of hybrids, those that resemble Ponkan and others with characteristics closer to the parental Murcott. There are significant differences in the period of fruit maturation among the hybrids and their parents. Considering the parents stand out as the main commercial varieties in the Brazilian mandarin fresh fruit market, these new hybrids have great potential for commercial acceptance and could be an excellent option to extend the period of supply of mandarins. Genetic and phenotypical information will be fundamental for the registration and/or protection of new varieties, which are essential steps that precede the commercial release to the producer. [ABSTRACT FROM AUTHOR]

Cacao (Theobroma cacao L.) is a tropical tree species belonging to the Malvaceae, which originated in the lowland rainforests of the Amazon. It is a major agricultural commodity, which contributes towards the Gross Domestic Product of West African countries, where it accounts for about 70% of the world's production. Understanding the genetic diversity of genetic resources in a country, especially for an introduced crop such as cacao, is crucial to their management and effective utilization. However, very little is known about the genetic structure of the cacao germplasm from Sierra Leone and Togo based on molecular information. We assembled cacao germplasm accessions (235 from Sierra Leone and 141 from Togo) from different seed gardens and farmers' fields across the cacao-producing states/regions of these countries for genetic diversity and population structure studies based on single nucleotide polymorphism (SNP) markers using 20 highly informative and reproducible KASP–SNPs markers. Genetic diversity among these accessions was assessed with three complementary clustering methods, including model-based population structure, discriminant analysis of principal components (DAPC), and phylogenetic trees. STRUCTURE and DAPC exhibited some consistency in the allocation of accessions into subpopulations or groups, although some discrepancies in their groupings were noted. Hierarchical clustering analysis grouped all the individuals into two major groups, as well as several sub-clusters. We also conducted a network analysis to elucidate genetic relationships among cacao accessions from Sierra Leone and Togo. Analysis of molecular variance (AMOVA) revealed high genetic diversity (86%) within accessions. A high rate of mislabeling/duplicate genotype names was revealed in both countries, which may be attributed to errors from the sources of introduction, labeling errors, and lost labels. This preliminary study demonstrates the use of KASP–SNPs for fingerprinting that can help identify duplicate/mislabeled accessions and provide strong evidence for improving accuracy and efficiency in cacao germplasm management as well as the distribution of correct materials to farmers. [ABSTRACT FROM AUTHOR]

Transposable elements (TEs) are found in the genomes of almost all eukaryotes. They have a characteristic structure that ensures their transposition activity, as a result of which TEs can make changes in the structure and functioning of the genome. Through coevolution with the genome, TE sequences can be domesticated. "Molecular domestication" refers to the cooptation of a TE sequence, as a result of which it begins to perform a useful function in the host genome. In bivalves, DNA transposons of the TLEWI subfamily have been identified, which have signs of domestication, as well as spliceosomal introns, which makes them similar to eukaryotic genes. To test the domestication hypothesis, this work carried out an intraspecific analysis of the presence of TLEWI transposons in the Pacific oyster (Crassostrea gigas) and their transcriptional activity in various tissues, during ontogeny and under the influence of internal and external factors. As a result, intraspecific heterogeneity was revealed in the presence of potentially functional copies and expression of transposase genes. For example, for two elements, a dependence of transcriptional activity on the stages of ontogenesis, as well as on temperature, was revealed. This suggests that functional (possibly domesticated) alleles have been conserved in individual populations of the Pacific oyster. The accumulation of additional data will allow us to discover populations that retain active TLEWI transposase genes and to determine whether these genes have been domesticated by the genome. [ABSTRACT FROM AUTHOR]

In Xinjiang, previous reports of cystic echinococcosis (CE) in livestock have focused on West and Middle Tianshan Mountains. In contrast, there is an absence of research on CE in the East Tianshan Mountains. To determine the epidemiology and genetic diversity of Echinococcus granulosus sensu stricto (s.s.) in domestic animals in the East Tianshan Mountains, Xinjiang, China, the livers and lungs of 1773 domestic animals were examined, between January 2023 and March 2023, and 40 cysts were collected. Polymerase chain reaction was used for the molecular diagnosis of the cysts. Statistical results showed that the overall prevalence of echinococcosis in sheep was 6.92% (114/1646), which was significantly higher than that in cattle (1.57%, 2/127). A total of 40 cyst isolates were obtained, including 38 from sheep and 2 from cattle. Genomic DNA was extracted, and the mitochondrial cytochrome c oxidase subunit 1 (cox1) gene was amplified by PCR to obtain the target 850 bp fragment. The results revealed that all the isolates had the G1 genotype, with similarities ranging from 98.88–100%. Haplotype network analysis revealed 32 haplotypes of the cox1 gene, among which Hap_7 was the main haplotype. Furthermore, haplotype diversity (Hd = 0.313 ± 0.093) and nucleotide diversity (π = 0.00173 ± 0.00079) were lower in the East Tianshan Mountains than in other regions, indicating that the populations are genetically less differentiated. Tajima’s D and Fu’s Fs tests were negative (p ≤ 0.01), indicating an expansion of the population in the East Tianshan Mountains of Xinjiang, similar to the results previously reported for Xinjiang. The low fixation index (Fst) ranged from negative values (Gansu Province) to 0.30346 (Mongolia), indicating that the genetic differentiation between the East Tianshan Mountains and Gansu, and Tibet, Xinjiang was relatively low, with frequent gene flow. In this survey, two ‘new’ haplotypes were identified in the East Tianshan livestock. In addition, two different haplotypes of liver and lung infections were found in one cattle. This survey provides information on the epidemiology and genetic diversity of E. granulosus s.s. in the East Tianshan Mountains of Xinjiang, China. [ABSTRACT FROM AUTHOR]

Babesia spp. and Theileria spp. are tick-borne apicomplexan protozoa that can cause disease in animals and humans. Deer are considered reservoirs for a wide variety of Piroplasmida species, including some potentially zoonotic. This study aimed to investigate the occurrence and genetic diversity of piroplasmids in wild deer sampled in four Brazilian states (São Paulo, Mato Grosso do Sul, Paraná and Goiás). For this purpose, extracted DNA samples from 181 deer buffy coat samples (138 Blastocerus dichotomus, 26 Subulo gouazoubira, 4 Mazama jucunda, 3 Mazama rufa and 10 Ozotocerus bezoarticus) were subjected to a nested PCR (nPCR) assay based on the 18S rRNA gene in order to perform a screening for piroplasmids and characterized based on the near-complete 18S rRNA, hsp70 and cox-3 genes. As a result, 75.14% (136/181) samples were positive for piroplasmids. Of these, 108 (79.41%), 101 (74.26%) and 67 (49.26%) were positive to near complete 18S rRNA, hsp70 and cox-3 genes, respectively. Phylogenetic analyses based on three molecular markers showed similar topology to each other. All sequences obtained in the present study were positioned into the Theileria sensu stricto clade, forming a distinct clade, albeit close to T. cervi. Most sequences grouped together into a large clade divided into subclades, which were often related to deer genus/species, showing that Theileria lineages seemed to show specificity according to deer genus/species. Two 18S rRNA sequences (one obtained from S. gouazoubira and another from M. jucunda) were positioned into a different clade, apart from other sequences detected in this study, indicating that different species of Theileria occur in deer from Brazil. Two subclusters were observed in the phylogenetic analysis based on the hsp70 gene: the first containing only sequences detected in marsh deer and the second grouping sequences detected in brocket deer (Mazama spp. and S. gouazoubira). The latter was also divided into smaller clades that grouped Theileria genotypes according to deer species (M. jucunda, M. rufa and S. gouazoubira). This study provides the first molecular evidence of Theileria infection in M. jucunda, as well as co-infection by distinct Theileria (sub)species/genotypes in the same deer was evidenced. Finally, this study expanded the knowledge on the diversity of Theileria spp. infecting deer from South America. [ABSTRACT FROM AUTHOR]

The decline in bee diversity, largely driven by habitat loss, climate change and invasive species, is well‐documented. Within this context, the genus Megachile Latreille, 1802 (Hymenoptera: Megachilidae), a diverse group of solitary leafcutter bees, lacks comprehensive species‐level conservation and taxonomic assessments, potentially concealing population declines and extinctions.Megachile pruina is one of Bermuda's three bee species and possibly the last native bee on the island. Formerly distributed widely across the island, it is now restricted to a small 11.5 ha area within the Castle Harbour Islands Nature Reserve.Classified as 'Vulnerable' under the Bermuda Protected Species Act, its taxonomic and conservation status remains uncertain, particularly its evolutionary relationships with populations in the United States.Here, we analyse nuclear genomes and mitochondrial genomes to reveal that Bermuda's M. pruina population is genetically distinct from mainland US populations and show no close association with any sampled US population, suggesting that Bermuda's represent a unique evolutionary lineage.Our genetic diversity assessment shows lower genetic diversity in Bermuda's population compared with the United States, highlighting a higher level of vulnerability than originally thought.We recommend maintaining its current protection status and advocate for the pressing need of expanding ecological and biological studies to facilitate appropriate conservation and monitoring measures. [ABSTRACT FROM AUTHOR]

A number of consequences of climate change, notably salinity, put global food security at risk by impacting the development and production of lentils. Salinity-induced stress alters lentil genetics, resulting in severe developmental issues and eventual phenotypic damage. Lentils have evolved sophisticated signaling networks to combat salinity stress. Lentil genomics and transcriptomics have discovered key genes and pathways that play an important role in mitigating salinity stress. The development of saline-smart cultivars can be further revolutionized by implementing proteomics, metabolomics, miRNAomics, epigenomics, phenomics, ionomics, machine learning, and speed breeding approaches. All these cutting-edge approaches represent a viable path toward creating saline-tolerant lentil cultivars that can withstand climate change and meet the growing demand for high-quality food worldwide. The review emphasizes the gaps that must be filled for future food security in a changing climate while also highlighting the significant discoveries and insights made possible by omics and other state-of-the-art biotechnological techniques. [ABSTRACT FROM AUTHOR]

Since European settlement of Australia, substantial areas of subtropical rainforest have been cleared. More recently, effort is being made to restore areas of this ecological community. The financial investment and increasing reliance on ecological restoration in biodiversity conservation justifies a need for better understanding of how to improve success at the genetic level. This research measures genetic diversity (allelic richness [Rs], expected heterozygosity [He], and inbreeding using Wright's coefficient [FIS]) for expected neutral DNA markers in three Australian subtropical rainforest trees—White booyong (Argyrodendron trifoliolatum), Watkin's fig (Ficus watkinsiana), and Native tamarind (Diploglottis australis). Wild and restored populations of these species were compared in two neighboring regions in Northeast New South Wales (the Tweed Caldera and the Big Scrub). There were no statistically significant differences in Rs or He between wild and restored populations for any of the target species. Inbreeding was significantly higher in one of the restored versus wild population comparisons: F. watkinsiana in the Tweed (restored F = 0.20; wild F = −0.02; p = 0.01). The comparable levels of genetic diversity observed in restored and wild populations targeted in this study are likely due to informed practitioner perspectives and practices, staged plantings over several years, and high genetic diversity and low genetic differentiation within source populations. [ABSTRACT FROM AUTHOR]

The UN Decade on Ecosystem Restoration will result in an unprecedented need for seeds. Agricultural production, or the growing of plants under controlled conditions to produce desired resources, can be a helpful tool for providing the quantities of seeds needed for large‐scale restoration. In some ecosystems, agricultural production of native plant seeds is part of the restoration process. This is particularly true for native plants that are similar to major food crops, such as native grasses. However, conventional crops have contrasting characteristics (e.g. fast growing, high yield for a focused use) from those desired in restored vegetation (plants capable of surviving and providing ecosystem services in variable environments). This contrast leads to significant, often opposing differences in desirable characteristics in crop versus natural systems. Examples include rapid germination in domesticated crops versus seed dormancy in wild plants, uniform germination, growth and flowering versus bet‐hedging strategies, or high seed retention versus seed dispersal. While it may be useful to maximize productivity of native plants in agricultural environments with similar trait modifications, for restoration, the demands of the natural environment should be primary, and agricultural production should aim to maximize the diversity, function, and evolutionary potential of native species. Any perceived benefits that come from the production of large quantities of inexpensive seeds that cannot meet the needs of wild communities are short‐sighted. We suggest research directions that will be needed to meld agricultural production needs with those of restoration practitioners, as a challenge for those invested in the procurement and use of wild seeds. [ABSTRACT FROM AUTHOR]

The East Asian finless porpoise, Neophocaena asiaeorientalis sunameri, is an endangered species that inhabits the coastal marine environments of East Asia. In the present study, we investigated the overall infection status of anisakid nematodes in East Asian finless porpoises from three sea sectors off the Korean Peninsula. The genetic diversity and population genetic structure of the identified nematode species were evaluated. The prevalence of all stages of anisakid nematodes collected from the stomach was 57.55% (61 among the 106 porpoises examined), and 16 of the hosts were found to have adult worms. The mean number of infected adults was 211 (± 419.54, 5–1455 per host). Only one species of anisakids, Anisakis pegreffii, was identified from randomly selected worms by molecular approaches. Analysis of the mitochondrial (mt) cox2 partial gene in 50 newly generated sequences of A. pegreffii revealed 24 haplotypes, including 14 new haplotypes. We observed below-average levels of nucleotide diversity and haplotype diversity compared to other seas around the world. The mtDNA cox2 haplotypes of the species in the three Korean sea areas showed no genetic structure, suggesting well-connected gene flow within these areas. This study represents the first record of a definitive host of A. pegreffii in Korean waters, providing important information regarding anisakids genetic diversity in the cetacean species inhabiting limited regions. [ABSTRACT FROM AUTHOR]

Societal Impact Statement: Table grape production is a traditional practice in southeastern Spain, where locals have produced fresh grapes and raisins for centuries. Many of these vines are now centenary, and they represent a useful source of diversity for developing future table grape varieties with improved traits. Genetic analysis showed that many of the local varieties identified in this study were traditional varieties from Western Mediterranean countries. Others were not identified, and they might be old grape varieties of previous importance in the region. The conservation and characterization of these varieties could be key to ensuring current and future vineyard sustainability. Summary: Current worldwide table grape production focuses on a reduced number of Vitis vinifera L. varieties. However, traditional farmers have grown many table grape varieties for centuries, as they provided a steady source of fresh fruit and raisins. These ancient living genotypes potentially store a genetic diversity that can be used now to ensure future grape production.Here we focused on the study of grapevines found across Almería, one of the Spanish regions with longer tradition in table grape production. After an exhaustive inspection, we located 220 old (some centenary) vines producing grapes consumed by owners or in abandoned areas no longer devoted to agriculture.Some of these vines were identified by comparing their simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) genetic profiles with available data from international databases. We found that, while grape growers' efforts focused on the cultivation of traditional grape varieties from Western Mediterranean regions, they also cultivated few exogenous varieties if they provided additional fruit features. Other vines were found to have genetic profiles that did not match reference datasets. Interestingly, some of them were found in multiple locations, suggesting they are endangered varieties with some previous relevance in the region. Besides, first‐degree relationships support the autochthonous origin of many of these unidentified genotypes.Locals kept a high number of different grapevine varieties, now considered reservoirs of genetic diversity. Traditional farming practices have been useful to prevent the loss of this diversity, which now needs to be preserved and further studied to contribute to the sustainability of viticultural systems. [ABSTRACT FROM AUTHOR]

Societal Impact Statement: All US commercial maize (Zea mays) is a single race, "Corn Belt Dent," and its genetic base has been in decline for at least 40 years. Independent genotyping can only be conducted after patent and licensing restrictions have expired, a period of 20 years. These restrictions also impede a molecular based assessment of the standing crop by the United States Department of Agriculture (USDA) as recommended by experts. Data blanks about landscape vulnerability put farmers at risk of crop failure and the public at risk of food insecurity. Understanding maize diversity experts' perspectives and analysis helps describe the contours of these data blanks and inform policy recommendations. Summary: Recommendations by the Maize Crop Germplasm Committee to the United States Department of Agriculture (USDA) for a molecular based vulnerability assessment on the US standing maize (Zea mays) crop have not been acted on because of intellectual property and licensing restrictions. This research explores maize diversity experts' access to data and perceptions and analysis of the standing crop.The data come from semi‐structured interviews conducted with 44 maize diversity experts in the public and private sectors.Experts explain that genetic data blanks restrict non‐industry research, describe public sector concerns that standing diversity is narrow(ing), and find historic sources of pedigree data in Plant Variety Protection and patent records are no longer reliable. Some interviewees perceive that industry monitoring of standing diversity is in their best financial interest. Industry participants describe concentration in US maize allows them to control diversity over time, while public researchers discuss efficiency of scale narrowing genetic diversity and global concentration spreading this trend.Knowledge gaps about genetic diversity in US commercial maize are designed through patents, contracts, non‐disclosure agreements, and confidentiality agreements by patent holders who do not want their inbred lines genotyped by competitors. This restricts research and knowledge flow about genetic information into public networks. The Maize Crop Germplasm Committee is a node for knowledge flow; however, the lack of mechanisms for action suggests it is performative. We recommend all protections used on seed include exemptions for research, breeding, and seed saving; an independent assessment of how industry monitors standing diversity; and a molecular analysis of the standing crop conducted by the USDA. All US commercial maize (Zea mays) is a single race, "Corn Belt Dent," and its genetic base has been in decline for at least 40 years. Independent genotyping can only be conducted after patent and licensing restrictions have expired, a period of 20 years. These restrictions also impede a molecular‐based assessment of the standing crop by the United States Department of Agriculture (USDA) as recommended by experts. Data blanks about landscape vulnerability put farmers at risk of crop failure and the public at risk of food insecurity. Understanding maize diversity experts' perspectives and analysis helps describe the contours of these data blanks and inform policy recommendations. [ABSTRACT FROM AUTHOR]

Summary: As a non‐collinear expression form of genetic information, chimeric RNAs increase the complexity of transcriptome in diverse organisms. Although chimeric RNAs have been identified in plants, few common features have been revealed. Here, we systemically explored the landscape of chimeric RNAs across multi‐accession and multi‐tissue using pan‐genome and transcriptome data of four plants: rice, maize, soybean, and Arabidopsis. Among the four species, conserved characteristics of breakpoints and parental genes were discovered. In each species, chimeric RNAs displayed a high level of diversity among accessions, and the clustering of accessions using chimeric events was generally concordant with clustering based on genomic variants, implying a general relationship between genetic variations and chimeric RNAs. Through mass spectrometry, we confirmed a fusion protein OsNDC1‐OsGID1L2 and observed its subcellular localization, which differed from the original proteins. Phenotypic cues in transgenic rice suggest the potential functions of OsNDC1‐OsGID1L2. Moreover, an intriguing chimeric event Os01g0216500–Os01g0216900, generated by a large deletion in basmati rice, also exists in another accession without the deletion, demonstrating its convergence in evolution. Our results illuminate the characteristics and hint at the evolutionary implications of plant chimeric RNAs, which serve as a supplement to genetic variations, thus expanding our understanding of genetic diversity. [ABSTRACT FROM AUTHOR]

The Central African Republic (CAR) is characterized by widespread HIV epidemic with notable prevalence and genetic diversity. We herein analysed the genetic diversity of atypical non‐M HIV‐1 strains. In‐house serotyping assays for variants of HIV‐1 (M, N, O, P) and HIV‐2 were used to test a biological collection of 6092 HIV‐seropositive blood samples collected between 2003 and 2014 at the Institut Pasteur de Bangui. Samples indicative of recombinant M/O groups, HIV‐2, or those that yield doubtful/negative results underwent further PCR tests and sequencing. We found six atypical HIV strains: specifically, three (0.05%) HIV‐1 group O strains (subtype H) detected in samples from 2005, 2008 and 2009, alongside three (0.05%) HIV‐2 strains (two group A and one group B) identified in samples from 2007 and 2009. HIV‐1/O strains showed a genetic link to Cameroon and Gabon strains. This study highlights the dominance of HIV‐1/M in the CAR's HIV epidemic over time and underscores the infrequent occurrence of HIV‐1 group O and HIV‐2 strains. These findings validate the efficacy of WHO‐recommended HIV testing protocols and emphasize the need for adaptive surveillance and management strategies to confront the complexities introduced by the genetic diversity of HIV strains. [ABSTRACT FROM AUTHOR]

Aim: We examined range‐wide genetic variation in a widespread white oak species in western North America to determine phylogeographic patterns (including possible latitudinal gradients) and investigate their underlying causes. Location: Western North America. Taxon: Quercus garryana (Fagaceae). Methods: We sampled Q. garryana at 117 locations throughout its range and related species of white oaks in 8 additional populations. We sequenced DNA from four variable intergenic plastid spacers and the ribosomal nuclear ITS region. We constructed haplotype networks and phylogenetic trees, mapped the geographical distributions of plastid haplotypes, and analysed genetic diversity patterns. Results: We identified 25 plastid haplotypes that clustered in two major groups, each showing pronounced genetic variation with latitude. In contrast, ITS showed little or no geographical or phylogenetic variation. Quercus garryana shared several plastid haplotypes with related white oaks and was not differentiated from these species by ITS. Plastid haplotype diversity in Q. garryana was highest in the central part of its range and sharply reduced to the north. Two haplotypes (one from each haplotype group) occurred in the northern third of the range, with only one at the northern range limit. Populations at the southern range limit were characterised by distinct haplotypes. Main Conclusions: Genetic patterns of Q. garryana have been shaped both by post‐Pleistocene climate change, interacting with features of the landscape, and by hybridisation with other white oaks. The species contains substantial genetic variation with strong spatial structuring of plastid haplotypes, indicating (1) early divergence of southern (Sierra Nevada) and northern populations, and (2) northward dispersal during the Holocene resulting in greatly reduced genetic diversity in its northern range. Species that can adjust their ranges with changing climates may remain susceptible to loss of genetic variation, potentially affecting their ability to persist in novel conditions at northern range margins. [ABSTRACT FROM AUTHOR]

The olive psyllid, Euphyllura olivina Costa (Hemiptera: Psyllidae), causes considerable damage in the olive groves of the Mediterranean area, resulting in significant loss in olive oil production. The present work aims to gain a first overview on the genetic diversity of this species in Tunisia by analyzing patterns of genetic variability in the mitochondrial cytochrome oxidase subunit 1 (COI) and the nuclear Internal Transcribed Spacer marker (ITS). Our analyses revealed low genetic differentiation among the studied populations, with low nucleotide and haplotype diversity. These results are associated with frequent rare variants and high gene flow exchange, suggesting recent colonization followed by population expansion across the invaded range. We cannot exclude the possibility that the low genetic diversity results in part from a reduction in the population size associated with poor performance under the current climatic conditions. Future investigations could benefit from the inclusion of additional genetic markers, including microsatellites, or population genomic approaches, to trace more accurately the demographic history and genetic differentiation of the olive psyllid. [ABSTRACT FROM AUTHOR]

Nepal has 15 distinct agroecosystems spread across three major agroecozones: Tarai, Mid Hill, and High Hill. These regions support a rich variety of agrobiodiversity. This paper examines the significance of native agrobiodiversity within each of these agroecosystems for diversified food, nutrition, health, business and environment. The information presented is derived from various literature sources, discussions with key experts, and the authors' own experiences. Each of these agroecosystems has cultivated and preserved numerous unique species, landraces, and genotypes of agrobiodiversity, including crops, forages, livestock, agro-insects, agro-microorganisms, and aquatic genetic resources. This agrobiodiversity is deeply connected with local cultures, traditional knowledge, and skills. The high diversity of agricultural genetic resources (AGRs) within Nepal's relatively small area is a crucial factor for ensuring food security, nutrition, health, business opportunities, and environmental sustainability. Many niche products, prized for their purity, quality, taste, health benefits, and nutritional value, are sold at premium prices. However, the focus on production-centric agricultural programs over the years has led to the replacement of many niche-specific varieties by more uniform and limited ones. Introducing new genotypes into a particular agroecosystem may undermine the principles of ecological agriculture. Therefore, it is essential to enhance the competitiveness of native AGRs and associated indigenous technologies within each agroecosystem. [ABSTRACT FROM AUTHOR]

Background and Objectives: The deficiency of essential amino acids such as methionine, lysine, and tryptophan in maize protein presents a significant challenge in meeting nutritional demand. Comprehensive evaluation of maize germplasm for variability of essential amino acids, protein content, starch content, and β‐carotene contents in grains, along with their relationships with yield and its associated traits, is a prerequisite for strengthening genetic enhancement for nutritional traits. Thus, the current study presents the profiling of 60 maize inbred lines across 11 nutritional quality and yield, aiming to identify variability in these traits and potential donor candidates for commercial breeding. Findings: The test inbreds exhibited significant variations in the content of grain methionine (0.04%–0.28%), tryptophan (0.019%–0.069%), lysine (0.063%–0.318%), protein (9.31%–11.80%), starch (58.32%–70.88%), and β‐carotene (2.38 ppm–6.79 ppm). Additionally, variations were noted in grain yield (0.87–2.52 t ha−1). Inter‐relationship analyses suggested the feasibility of simultaneous selection of essential amino acids (methionine, tryptophan, lysine) and β‐carotene. The germplasm stock was clustered, and potential diverse donors identified were recommended for utilization in breeding programs. Furthermore, the use of Attenuated Total Reflectance‐Fourier Transform Infrared (ATR‐FTIR) spectroscopy for screening high methionine and high lysine lines in large germplasm based on differences in peak intensity at 2922 cm−1 and 1110 cm−1 was reported, respectively. Conclusions: The multilocation experiment revealed genetic diversity in both nutritional quality and yield across the 60 inbreds. The absence of a negative correlation between the amino acids and β‐carotene indicates the possibility of the development of hybrids with elevated essential amino‐acid levels combined with high β‐carotene content. Significance and Novelty: This is the first holistic report on the variability of nutritional quality traits coupled with yield in maize germplasm. Identified nutrient‐rich inbreds will serve as valuable germplasm in maize biofortification programs. AT‐FTIR is proposed as an easy screening technique and the first report, which can be employed for the initial screening of a large set of germplasm for methionine and lysine content. [ABSTRACT FROM AUTHOR]

Mesona chinensis Benth (MCB), also known as Platostoma palustre, is a highly significant medicinal and edible plant in China and Southeast Asian countries. The cultivated seedlings of MCB are primarily local farm varieties propagated through cuttings, with many being domesticated from wild species. This has led to an unclear and mixed source, as well as uneven quality of MCB. Hence, it is imperative to collect, preserve, evaluate, and identify the germplasm resources of MCB. This study aimed to evaluate the genetic diversity and identify the germplasm of eight core MCB resources using morphology, cytology, and EST-SSR molecular markers. Morphological observations showed significant variation in the inflorescences, leaves, stems, and corolla tissues. Scanning electron microscope (SEM) observations demonstrated significant differences in the number of stomata between the abaxial and adaxial sides of leaves. Furthermore, out of 192 primer pairs of EST-SSR molecular markers, 9 were suitable for constructing fingerprints. A total of 31 alleles were detected, with an average of 3.444 alleles per locus. The number of effective alleles (Ne) of 9 EST-SSR loci ranged from 1.473 (TDF139) to 3.877 (TDF166), while the Shannon Information index (I) per locus ranged from 0.601 (TDF139) to 1.461 (TDF166). The average value of observed heterozygosity (Ho) was 0.681, while the expected heterozygosity (He) was 0.523. The mean value of fixation index (F) was -0.294, while the mean heterozygosity within populations (Hs) was 0.762. The polymorphism information content (PIC) ranged from 0.295 (TDF139) to 0.701 (TDF166) across the 9 loci, with an average PIC value of 0.466. These results indicated that the selected EST-SSR primers exhibited high levels of polymorphism. Notably, TDF166 played a prominent role in exploring the genetic diversity of MCB. Furthermore, the Nei's genetic distance among the eight germplasm resources exhibited significant variation, resulting in the division of all germplasm resources into six subclades. This suggested the presence of abundant genetic diversity within the MCB germplasm resources used in this study. This study provided a foundation for the conservation, management, and future breeding of MCB germplasm resources. [ABSTRACT FROM AUTHOR]

Polyandrous mating, where females mate with multiple males, can be caused by male manipulation, primarily benefiting males. Females, conversely, may suffer costs without direct benefits. According to the good gene hypothesis, females should choose superior males to pass on good genes to their offspring in lek-breeding species. However, when females are compelled to mate against their preference, which leads to polyandrous mating, indirect genetic costs arise, with lower-quality males fathering some offspring. Despite these costs, polyandrous mating may potentially benefit females through fertilization insurance and increased genetic diversity. This study investigated the costs and benefits of polyandrous mating in the lek-chorusing treefrog (Zhangixalus prasinatus) by comparing clutch fertilization success, offspring performance (embryo viability, survival, growth, development) linked to fitness, and allelic diversity between the clutches after monandrous and polyandrous mating. Our results showed that polyandrous mating (1) did not increase fertilization success, (2) did not affect embryo viability, offspring survival, growth, or development, but (3) increased genetic diversity. Additionally, we found that primary males (chosen by females) sired more offspring than peripheral males (not chosen by females). The small proportion of the clutch sired by peripheral males suggests that polyandrous mating in Z. prasinatus may be driven by males to pursue reproductive success, and may, as a by-product, potentially benefit females by increasing their offspring's genetic diversity. Therefore, peripheral males achieve higher reproductive success, while females lack apparent costs, which is suggested to be a likely reason for the moderate frequency of polyandrous mating in this species. Significance statement: Our study investigates the impact of polyandrous mating on female emerald treefrogs (Zhangixalus prasinatus). Our findings reveal that while polyandrous mating neither enhances nor reduces fertilization success, embryo viability, offspring survival, growth, or development, it does increase genetic diversity within clutches. Although this genetic diversity may be a by-product of male reproductive strategies, it potentially offers females indirect genetic benefits, which may help explain the moderate frequency of polyandrous mating in this species. Our research contributes to a deeper understanding of mating systems and reproductive strategies in lek-breeding anurans. [ABSTRACT FROM AUTHOR]

Coccoloba uvifera L. (Polygonacaeae), named also seagrape, is an ectomycorrhizal (ECM) Caribbean beach tree, introduced pantropically for stabilizing coastal soils and producing edible fruits. This review covers the pantropical distribution and micropropagation of seagrape as well as genetic diversity, functional traits and use of ECM symbioses in response to salinity, both in its native regions and areas where it has been introduced. The ECM fungal diversity associated with seagrape was found to be relatively low in its region of origin, with Scleroderma bermudense Coker being the predominant fungal species. In regions of introduction, seagrape predominantly associated with Scleroderma species, whereas S. bermudense was exclusively identified in Réunion and Senegal. The introduction of S. bermudense is likely through spores adhering to the seed coats of seagrape, suggesting a vertical transmission of ECM colonization in seagrape by S. bermudense. This ECM fungus demonstrated its capacity to enhance salt tolerance in seagrape seedlings by reducing Na concentration and increasing K and Ca levels, consequently promoting higher K/Na and Ca/Na ratios in the tissues of ECM seedlings vs. non-ECM plants in nursery conditions. Moreover, the ECM symbiosis positively influenced growth, photosynthetic and transpiration rates, chlorophyll fluorescence and content, stomatal conductance, intercellular CO2, and water status, which improved the performance of ECM seagrape exposed to salt stress in planting conditions. The standardization of seagrape micropropagation emerges as a crucial tool for propagating homogeneous plant material in nursery and planting conditions. This review also explores the use of the ECM symbiosis between seagrape and S. bermudense as a strategy for restoring degraded coastal ecosystems in the Caribbean, Indian Ocean, and West African regions. [ABSTRACT FROM AUTHOR]

Pleurotus pulmonarius is prized by consumers for its distinct flavor, strong aroma, and dense, crispy texture. Although China has extensive germplasm resources for P. pulmonarius, only a limited number of cultivars are commercially available. A comprehensive evaluation and detailed analysis of P. pulmonarius germplasm, alongside the exploration of superior germplasm resources, are essential for developing new varieties. In this study, we resequenced the genomes of 47 P. pulmonarius strains collected nationwide, identifying a total of 4,430,948 single nucleotide polymorphism (SNP) loci. After filtering based on minor allele frequency and data integrity, 181,731 high-quality SNP markers were retained. Phylogenetic analysis grouped the strains into six clusters, with strains from similar geographical regions clustering together. Most CBS strains formed a single cluster; cultivated varieties exhibited higher genetic similarity, whereas wild strains displayed greater diversity. Principal component analysis (PCA) and population structure analyses, using the same SNP markers, corroborated the phylogenetic findings. DNA fingerprinting, derived from 369 core SNPs, further underscored the genetic diversity among strains. Significant morphological variation was observed, with strains in groups ZP, CBS, and WHLJ exhibiting notably higher yields and cap widths compared to other groups. Correlation analysis revealed associations among various phenotypes, while genome-wide association study (GWAS) identified multiple SNP markers within candidate genes linked to agronomic traits, most of which were controlled by multiple genes. This research offers a molecular-level characterization and evaluation of P. pulmonarius germplasm resources, providing a scientific basis for enriching available germplasm and advancing breeding materials. [ABSTRACT FROM AUTHOR]

Background The head louse, Pediculus humanus capitis , is an obligate ectoparasite and its infestation remains a major public health issue worldwide. Determining the genetic characteristics of the existing clades is essential to identify the population structure and to develop head lice-control programs. Hence, we aimed to investigate the genetic diversity of head lice among infested individuals in northern Iran. Methods Adult head lice were collected from 100 infested individuals referring to the health centers throughout five geographical regions in Mazandaran Province, Iran. Partial fragments of the mitochondrial cytb gene were amplified by PCR, then consequently sequenced. Results The results of the phylogenetic tree of collected head lice confirmed the existence of two clades, A and B, in the studied areas. Thirteen haplotypes were detected in the studied populations, of which 11 were novel haplotypes. Clade A was the dominant form and accounted for 75% of samples, while clade B included the rest. Haplotype and nucleotide diversity were 0.999 and 0.0411, respectively. Conclusions Clade A and B of Pediculus humanus capitis exist among the human populations of northern Iran. We observed high genotypic diversity of this head lice. [ABSTRACT FROM AUTHOR]