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Introduction: The Xinjiang Mongolians, located along the Silk Road, migrated westward from Northeast Asia in the 13th and 14th centuries. Despite its significance, genetic studies on Xinjiang Mongolians have been limited compared to other Mongolian populations. Methods: In this study, we analyzed the non-recombining region of the Ychromosome in 165 Xinjiang Mongolian males using 108 biallelic markers and 44 STRs. Results and discussion: Our study identified prevalent haplogroups C2a1a3-F1918 (10%), C2a1a2-M48 (8%), N1a1a-M178 (5%), and R1a1a-M17 (10%) in the Xinjiang Mongolians. Additionally, our study suggested a genetic affinity between Xinjiang Mongolians and Inner Mongolia Mongolian populations, as well as other ethnic groups from northwest China, based on the PCA analysis. The Network analysis revealed distinct branching expansion patterns in haplogroups C2a1a3a-F3796, C2a1a2-M48, and N1a1a-M178, with estimated timeframes aligning with Genghis Khan's invasion of Xinjiang in the Yuan Dynasty. Notably, our analysis of the R1a1aM17 Network highlighted the role of Xinjiang Mongolians in the expansion of Turkicspeaking populations in Xinjiang and surrounding regions. The integration of ancient DNA data suggested that the high frequency haplogroups C2a1a3a-F3796, C2a1a2M48, and N1a1a-M178 could be traced back to their origin in Northeast Asia. Furthermore, the estimated TMRCA of haplogroup R1a1a-M17 implied cultural and genetic influences from Turkic populations during the Qagatay Khanate period. Overall, our study provided a genetic explanation for the ethnic origin of Xinjiang Mongolians, highlighting their migration from Northeast Asia and subsequent assimilation with the local populations in Xinjiang. [ABSTRACT FROM AUTHOR]

The North East Hill Region (NEHR) of India is home to diverse maize landraces including pigmented accessions rich in antioxidants and nutritional properties. The present study attempted to characterize a representative collection of this mostly unexplored diversity. Altogether eighty-three local maize landraces from the seven hill states of the NEHR were studied with special emphasis on pigmentation diversity. For the morphological traits, a significant ANOVA indicated the presence of substantial genetic variability for which selection would be fruitful. A number of these accessions were found to have traits that help cope with moisture stress, improve stalk strength and optimize photosynthesis. Principal component analysis studies for the yield attributing traits indicated that ear weight was most variable. The bleaching/histological studies confirmed that anthocyanin pigment when present was always restricted to the aleurone layer of the kernels, typical of blue maize. Quantitative analysis for kernel anthocyanin/phlobaphene content also revealed genetic differences among the accessions. Genetic analysis using the model-based STRUCTURE indicated significant population structuring among the accessions. Specifically, for the pigmentation diversity studies both principal coordinate analysis and neighbour joining methods revealed near concurrent population structuring due in part to the high differentiation of seven of the twenty-one pigmentation specific loci studied. The results obtained provide comprehensive evidence of a significant amount of genetic differentiation among the landraces under study. Landraces are valuable reservoirs of favourable alleles for which selection can be made and, as in this study, identify accessions for breeding maize with enhanced levels of beneficial secondary metabolites. [ABSTRACT FROM AUTHOR]

【Objective】The genetic diversity and evolutionary characters of Chishui black bone chicken populations were studied, which provided theoretical basis for evaluation of germplasm resource of Chishui black bone chicken, preservation and utilization of genetic resources. 【Method】The full sequence of Cytb gene of 60 Chishui black bone chickens were tested by PCR amplification and sequencing, and then the genetic diversity and evolution were analyzed by bioinformatics. 【Result】The full-length of Cytb gene in Chishui black bone chicken were 1 143 bp, with the proportions of 24. 1% base T, 36. 4% C, 27. 5% A and 12% G respectively. A total of 13 variable sites were found and all were transversions. The haplotype diversity (Hd), nucleotide diversity (Pi) and average nucleotide differences (K) were 0. 796, 0. 001 91 and 2. 180 respectively. The haplotype network showed that Hap3 and Hap2 were the dominant haplotypes in the whole 9 haplotypes of Cytb gene sequence in Chishui black bone chicken. The phylogenetic tree constructed by the 9 haplotypes of Cytb gene sequence in Chishui black bone chicken and Cytb gene sequence in 5 red jungle fowl subspecies suggested that Hap1were clustered with GGS12, and Hap2 were clustered with GGM1. Hap6, Hap7 and Hap3 clustered with GGM3 into one branch; Hap8 and Hap9 were clustered with GGS3;GGS4 was clustered with GGM2; Hap4 and Hap5 clustered into another branch. 【Conclusion】The genetic diversity of Chishui black bone chicken is high, and which probably originates from Gallus gallus spadiceus and Gallus gallus murghi. [ABSTRACT FROM AUTHOR]

The taxonomy of the Heliothinae subfamily is complex, often becoming an obstacle in the identification of these species, especially during the larval stage. An alternative is the use of molecular methods such as the PCR-RFLP technique (or Restriction Fragment Length Polymorphism), which helps to aid and complement the identification of some Heliothine species. The aim of this study was to establish the PCR-RFLP profile using molecular markers for the identification of four Heliothine species. Specific primers were constructed for the amplification of the cytochrome oxidase subunit I (COI) and elongation factor 1 alpha (EF-1α) genes for identifying Helicoverpa armigera, H. zea, H. gelotopoeon, and Chloridea virescens species. In the digestion of the COI gene with the BfaI enzyme, fragments of 294 bp and 321 bp were obtained for H. armigera, while there was no digestion for H. zea, H. gelotopoeon, and C. virescens. The HpaI enzyme produced fragments of 58 bp and 557 bp for H. gelotopoeon, while there was no digestion for H. armigera, H. zea, and C. virescens. The digestion of the EF-1α gene with the EcoRV enzyme produced fragments of 142 bp and 964 bp for C. virescens, while there was no cleavage for the other heliothines. These molecular markers can help the entomologists, aiding in the discrimination between H. zea, H. armigera, H. gelotopoeon, and C. virescens, and can also be used as a tool for monitoring the spread of these pests in agricultural regions. [ABSTRACT FROM AUTHOR]

Cardamom is one of the prominent plants with significant economic value in the Banyumas Regency, Central Java, Indonesia. Although Javanese cardamom is traditionally categorized under Amomum compactum, the morphological variations observed create ambiguity about its exact species status. DNA barcoding using the maturase K (matK) and ribulose-bisphosphate carboxylase (rbcL) genes is proven as a reliable technique to elucidate the taxonomic status of morphological variable plant cultivars. This study aimed to characterize cardamom from Banyumas Regency using morphological and molecular approaches for taxonomic status identification and genetic diversity evaluation. The matK and rbcL genes were selected as genetic markers and sequenced using a bidirectional sequencing technique. Morphological examination showed significant color variations at the cardamom stem base. All samples had high genetic identities to reference species in databases and were supported by high query cover and zero e-values. Therefore, molecular characterization, alongside geographic distribution assessment, established that this plant belongs to a single species, Amomum compactum. Additionally, the analysis conducted showed a low level of genetic diversity, as evidenced by haplotype and nucleotide diversity. Low-level genetic diversity provides additional data to convince that cardamon in Banyumas Regency belongs to a single species. These results are essential data in seed selection for further cultivation. [ABSTRACT FROM AUTHOR]

Background: Lablab purpureus L. is a legume appropriate to grow in tropical environment as it is adaptable to a broad temperature spectrum, rainfall and altitudes. It develops well under humid and warm conditions at temperatures ranging between 18oC and 30oC. It is a drought hardy crop grown in humid and semi-arid regions. The species is propagated by seed and can be sown alone or intercropped; planted near hedges or near other less leafy plants to climb on. Lablab purpureus L. has a flowering response of shortday, with early and late flowering types. Some landraces flower after sowing as early as 55 days. It is predominantly self pollinated although some out crossing is known to occur. Methods: In this study, Lablab purpureus L. genetic diversity were analyzed utilizing AFLP markers on ten Indian Lablab purpureus L. accessions at Department of Botany, Bundelkhand University, Jhansi during 2019-20. Five primers set were used for checking the diversity in Lablab purpureus L. and the marker performance were measured by using 4 parameters i.e. PIC, Mean resolving Power, Resolving Power and MI. Result: A total of 52 bands were generated, of which 45 bands (88.46%) were polymorphic which varies from 6 (M-CAT/E-ACT ) to 13 (M-CAC/E-ACC, M-CAC/E-ACT) with mean of 9.00 bands per primer. The PIC value ranges between 0.55 and 0.76 with a mean value of 0.64. The average value of matrix index is 3.04. Higher the MI, better the marker is. The value of RP ranges between 2.60 and 7.80 with a mean value of 4.68. In the UPGMA dendrogram, the 10 accessions were separated into two main clusters with all the primers used. In this study, we have shown that molecular markers can be used successfully to understand the genetic structure of the accessions of Lablab purpureus L. and identified a series of sequence-specific markers that potentially could be used in Lablab purpureus L. genetic mapping analyses. Since Lablab purpureus L. has been considered as a promising crop because of its wide spectrum of adaptability to different ecological conditions than other legumes, participatory evaluation at an early breeding stage could shape the variety being developed to increase the productivity and other traits as well as for utilization as food. [ABSTRACT FROM AUTHOR]

Background: The present study aims at assessment of genetic diversity in 43 extra early pigeonpea genotypes with 41 simple sequence repeat markers. Methods: In the present investigation, 41 HASSR markers were used to assess the genetic diversity. Similarity matrices were utilized to construct the unweighted pair group method with Arithmetic average dendrogram using NTSYs PC software. Result: Out of 41 HASSR markers, 21 markers were showed distinct banding pattern, while 11 markers were showed monomorphic banding pattern and remaining 9 markers showed no banding pattern or not amplified. Cluster analysis done using HASSR markers revealed that ICPL87119 was found to be the most diverse. This genotype also found to be resistant to wilt. Based on similarity coefficients and cluster analysis genotypes ICPL87119, ICPL84031, ICPL88014, ICPL161, ICPL87091 and CORG9701 were genetically more distant from other genotypes studied and these varieties can be used for their desirable characteristics in breeding programs for pigeonpea improvement. [ABSTRACT FROM AUTHOR]

Bartonella spp. are intracellular bacteria associated with several re-emerging human diseases. Small mammals play a significant role in the maintenance and spread of Bartonella spp. Despite the high small mammal biodiversity in South Africa, there is limited epidemiological information regarding Bartonella spp. in these mammals. The main aim of this study was to determine the prevalence and genetic diversity of Bartonella spp. from wild small mammals from 15 localities in 8 provinces of South Africa. Small mammals (n = 183) were trapped in the Eastern Cape, Free State, Gauteng, Limpopo, Mpumalanga, Northern Cape, North West, and Western Cape provinces of South Africa between 2010 and 2018. Heart, kidney, liver, lung, and spleen were harvested for Bartonella DNA screening, and prevalence was determined based on the PCR amplification of partial fragments of the 16S-23S rRNA intergenic spacer (ITS) region, gltA, and rpoB genes. Bartonella DNA was detected in Aethomys chrysophilus, Aethomys ineptus, Gerbillurus spp., Lemniscomys rosalia, Mastomys coucha, Micaelamys namaquensis, Rhabdomys pumilio, and Thallomys paedulcus. An overall prevalence of 16.9% (31/183, 95% CI: 12.2%-23%) was observed. Bartonella elizabethae, Bartonella grahamii, and Bartonella tribocorum were the zoonotic species identified, while the remaining sequences were aligned to uncultured Bartonella spp. with unknown zoonotic potential. Phylogenetic analyses confirmed five distinct Bartonella lineages (I-V), with lineage IV displaying strong M. coucha host specificity. Our results confirm that South African wild small mammals are natural reservoirs of a diverse assemblage of Bartonella spp., including some zoonotic species with high genetic diversity, although prevalence was relatively low. [ABSTRACT FROM AUTHOR]

Dispersal is an important life history trait that plays a crucial role in avoiding inbreeding. Uncovering the dispersal pattern of a threatened species facilitates conservation efforts. Most species of Galliformes are forest-dwelling terrestrial birds with a weak dispersal ability and high conservation priorities. However, little is known about the dispersal behavior and dispersal pattern of Galliformes species such as Reeves's pheasant Syrmaticus reevesii , a globally vulnerable species endemic to China. Here, we integrated behavioral and genetic analyses to investigate the dispersal pattern of Reeves's pheasant. Our results revealed that both females and males would disperse, although the overall dispersal pattern was more likely to be male-biased. Reeves's pheasant population had a low level of genetic diversity and a mild level of inbreeding. Speculation low genetic diversity was resulted from fragmented habitat, and male-biased dispersal may reduce the opportunity of inbreeding. Our research indicated that sex-biased dispersal patterns may be a behavioral mechanism adopted by wildlife to avoid inbreeding in a fragmented habitat. [ABSTRACT FROM AUTHOR]

The red swamp crayfish (Procambarus clarkii) has become one of China's most important freshwater aquaculture species. As the epicenter of crayfish cultivation, Hubei province provides the majority of germplasm resources for breeding applications. However, the genetic diversity and population structure of P. clarkii in this area remains largely incomplete, hindering the effective utilization of these germplasm resources. In this study, 20 polymorphic microsatellites were developed and used to investigate genetic diversity and differentiation in representative P. clarkii populations from five cultivated and five wild populations in Hubei province. A total of 169 alleles were discovered at these loci, and the average polymorphic information content was calculated as 0.584. Diversity index of expected heterozygosity (He) indicated a relatively medium genetic diversity across all populations (0.431 ~ 0.565), while wild populations exhibited higher genetic diversity (He = 0.542) compared to that in cultured populations (He = 0.478). The average value of pairwise population differentiation index (Fst) was 0.108, manifesting a moderate level of genetic differentiation among populations. Analysis of molecular variance between ten populations revealed that genetic variation mostly resided within individuals (79.4%), with slightly higher variation observed in cultured populations (84.79%) compared to that in wild populations (80.52%). Bayesian assignment, dendrogram, and principal component analysis grouped the genotypes into three clusters with wide variation among the accessions. These results reflected substantial genetic differentiation presented in P. clarkii populations. Our findings shed light on the diversity status of P. clarkii in Hubei province and will be great value for genetic improvement through selective breeding. [ABSTRACT FROM AUTHOR]

Myotis septentrionalis (Northern Long-eared Bat) has recently suffered a >90% decline in population size in North America due to white-nose syndrome (WNS). We assessed genetic diversity, population structure, current effective population size, and demographic history of M. septentrionalis distributed across the United States to determine baseline levels pre-WNS. We analyzed RADseq data from 81 individuals from Kentucky, Louisiana, Michigan, Minnesota, North Carolina, Oklahoma, and Wisconsin. Additionally, we examined population genetic structure using discriminant analysis of principal components, fastStructure, and STRUCTURE. We then estimated effective population size and demographic history using fastsimcoal2. Similar levels of genetic diversity were found across all samples. We found no population genetic structure in the varied analyses from these contemporary samples. The best model for demographic history estimated a rapid population expansion followed by a slower expansion approximately 340,000 years ago. The vagility of M. septentrionalis , along with male dispersal and random mating, may provide a buffer against serious bottleneck effects stemming from rapid population declines due to WNS. This research provides a baseline for tracking and monitoring the influence of WNS on genetic diversity such as potential reduced diversity or increased population structuring in the future. [ABSTRACT FROM AUTHOR]

This study combined population genetics and parentage analysis to obtain foundational data for the conservation of Magnolia kwangsiensis. M. kwangsiensis is a Class I tree species that occurs in two disjunct regions in a biodiversity hotspot in southwest China. We assessed the genetic diversity and structure of this species across its distribution range to support its conservation management. Genetic diversity and population structure of 529 individuals sampled from 14 populations were investigated using seven nuclear simple sequence repeat (nSSR) markers and three chloroplast DNA (cpDNA) fragments. Parentage analysis was used to evaluate the pollen and seed dispersal distances. The nSSR marker analysis revealed a high genetic diversity in M. kwangsiensis, with an average observed (Ho) and expected heterozygosities (He) of 0.726 and 0.687, respectively. The mean and maximum pollen and seed dispersal distances were 66.4 and 95.7 m and 535.4 and 553.8 m, respectively. Our data revealed two distinct genetic groups, consistent with the disjunct geographical distribution of the M. kwangsiensis populations. Both pollen and seed dispersal movements help maintain genetic connectivity among M. kwangsiensis populations, contributing to high levels of genetic diversity. Both genetically differentiated groups corresponding to the two disjunct regions should be recognized as separate conservation units. [ABSTRACT FROM AUTHOR]

Background: Non-pharmaceutical measures and travel restrictions have halted the spread of coronavirus disease 2019 (COVID-19) and influenza. Nonetheless, with COVID-19 restrictions lifted, an unanticipated outbreak of the influenza B/Victoria virus in late 2021 and another influenza H3N2 outbreak in mid-2022 occurred in Guangdong, southern China. The mechanism underlying this phenomenon remains unknown. To better prepare for potential influenza outbreaks during COVID-19 pandemic, we studied the molecular epidemiology and phylogenetics of influenza A(H3N2) and B/Victoria that circulated during the COVID-19 pandemic in this region. Methods: From January 1, 2018 to December 31, 2022, we collected throat swabs from 173,401 patients in Guangdong who had acute respiratory tract infections. Influenza viruses in the samples were tested using reverse transcription-polymerase chain reaction, followed by subtype identification and sequencing of hemagglutinin (HA) and neuraminidase (NA) genes. Phylogenetic and genetic diversity analyses were performed on both genes from 403 samples. A rigorous molecular clock was aligned with the phylogenetic tree to measure the rate of viral evolution and the root-to-tip distance within strains in different years was assessed using regression curve models to determine the correlation. Results: During the early period of COVID-19 control, various influenza viruses were nearly undetectable in respiratory specimens. When control measures were relaxed in January 2020, the influenza infection rate peaked at 4.94% (39/789) in December 2021, with the influenza B/Victoria accounting for 87.18% (34/39) of the total influenza cases. Six months later, the influenza infection rate again increased and peaked at 11.34% (255/2248) in June 2022; influenza A/H3N2 accounted for 94.51% (241/255) of the total influenza cases in autumn 2022. The diverse geographic distribution of HA genes of B/Victoria and A/H3N2 had drastically reduced, and most strains originated from China. The rate of B/Victoria HA evolution (3.11 × 10−3, P < 0.05) was 1.7 times faster than before the COVID-19 outbreak (1.80 × 10−3, P < 0.05). Likewise, the H3N2 HA gene's evolution rate was 7.96 × 10−3 (P < 0.05), which is 2.1 times faster than the strains' pre-COVID-19 evolution rate (3.81 × 10−3, P < 0.05). Conclusions: Despite the extraordinarily low detection rate of influenza infection, concealed influenza transmission may occur between individuals during strict COVID-19 control. This ultimately leads to the accumulation of viral mutations and accelerated evolution of H3N2 and B/Victoria viruses. Monitoring the evolution of influenza may provide insights and alerts regarding potential epidemics in the future. [ABSTRACT FROM AUTHOR]

The conservation biology field underscores the importance of understanding genetic diversity and gene flow within plant populations and the factors that influence them. This study employs Simple Sequence Repeat (SSR) molecular markers to investigate the genetic diversity of the endangered plant species Saussurea involucrata, offering a theoretical foundation for its conservation efforts. Utilizing sequencing results to screen SSR loci, we designed and scrutinized 18 polymorphic microsatellite primers across 112 samples from 11 populations in the Bayinbuluke region. Our findings reveal high genetic diversity (I = 0.837, He = 0.470) and substantial gene flow (Nm = 1.390) among S. involucrata populations (China, Xinjiang), potentially attributed to efficient pollen and seed dispersal mechanisms. Principal Coordinate Analysis (PCoA) indicates a lack of distinct genetic structuring within the Bayinbuluke populations. The cluster analysis using STRUCTURE reflected the genetic structure of S. involucrata to a certain extent compared with PCoA. The results showed that all samples were divided into four groups. To safeguard this species, we advocate for the in situ conservation of all S. involucrata populations in the area. The SSR markers developed in this study provide a valuable resource for future genetic research on S. involucrata. [ABSTRACT FROM AUTHOR]

Background and Objectives: Cherry is one of the most important fruits consumed in the world, which has a good taste, aroma and appearance. Currently, the only important commercial variety of cherry is Takdan-eMashhad cultivar in the country. This cultivar has considerable quantitative and qualitative characteristics, but the self-incompatibility and diversity in the clones in it lead to a decrease in the productivity of the introduced pollinators and the resulting decrease in yield in some years. This study was carried out with the aim of introducing cultivars with high yield and fruit quality and compatible with the climatic conditions of Iran. Materials and Methods: In order to investigate the compatibility of new imported cherry cultivars and to increase the diversity of existing cultivars in the country and to achieve high-yielding cultivars of a number of new cherry cultivars named ‘Lapins’, ‘Sweet Ann’, ‘Sweet heart’, ‘Early Star’, ‘Vera’, ‘Celeste’, ‘Sunburst’ and two control cultivars named ‘Takdan-eMashhad’ and ‘Siyah-e-Mashhad’ grafted on mahaleb rootstock were evaluated in the form of randomized complete block design with three replications for 3 years in Khorasan Razavi province. Results: There was a difference between cultivars in terms of the beginning and end of flowering; thus, ‘Celeste’ cultivar was the earliest flowering (6 April) and ‘Takdan-e-Mashhad’ cultivar was the late flowering (12 April). The fruit harvesting time of the cherry cultivars was also different, so that ‘Early Star’ cultivar was the earliest (27 May) and ‘Takdan-e-Mashhad’ cultivar was the latest (3 July). In the examination of morphological traits, it was found that the height of cultivars varied between 326.66 cm in 'Celeste' cultivar and 497.22 cm in 'Siyah-eMashhad' cultivar. Also, the maximum width of the crown and diameter of the trunk were respectively in the variety "Siyah-e-Mashhad" with the values of 316.66 cm and 49.66 cm. The highest number of spur per 100 cm of branch length (38.06) was related to 'Celeste' cultivar and the lowest number of spur (24.76) was related to 'Lapins' cultivar. In the investigation of the pomological characteristics of studied cherry cultivars, it was found that the shape of the fruit varies from kidney (‘Vera’, ‘Sunburst’, ‘Takdane-Mashhad’ and ‘Siyah-e-Mashhad’) to heart-shaped (‘Sweet heart’, ‘Sweet ann’, ‘Lapins’, ‘Celeste’, ‘Early Star’) among the cultivars. There was also variation in the skin color of the fruits, so that there was four groups: bright red (‘Lapins’), red (‘Sunburst’, ‘Sweet heart’, ‘Sweet ann’), dark red (‘Siyah-e-Mashhad’) and blackish red (‘Takdan-e-Mashhad’, ‘Vera’, ‘Celeste’) were divided. The fruit weight was variable among the cultivars studied; thus, the highest fruit weight (10.03) was observed in ‘Takdan-e-Mashhad’ cultivar and the lowest fruit weight (6.08) was observed in ‘Vera’ cultivar. In terms of yield, a significant difference was observed among the cultivars studied; Thus, the highest yield (31.63 kg per tree) was observed in ‘Sweet heart’ cultivar and the lowest yield (4.99 kg per tree) was observed in ‘Siyah-e-Mashhad’ cultivar. The stone weight also varied from 0.20 in the ‘Vera’ to 0.50 in the ‘Takdan-e-Mashhad’ cultivar. The length of the fruit peduncle was also different among the cultivars; thus, the highest length of fruit peduncle (4.55 cm) was observed in ‘Siyah-e-Mashhad’ cultivar and the lowest length of fruit peduncle (2.90 cm) was observed in ‘Celeste’ cultivar. Soluble solids varied from 23.95% in ‘Sweet heart’ to 18.38% in ‘Lapins’ cultivar. Acidity and pH also showed differences among the cultivars studied; So that the highest acidity and pH respectively (0.186% - 3.74) in ‘Vera’ and ‘Celeste’ cultivars and the lowest acidity and pH (0.142 - 3.42) in ‘Sunburst’ and ‘Siyah-e-Mashhad’ cultivars. Conclusion: 'Celeste' cultivar is considered as the earliest flowering cultivar with the lowest height, the highest number of Spur, and the shortest fruit peduncle length. Also, the 'Takdan-e-Mashhad' cultivar with the highest fruit weight and the 'Sweet Heart' cultivar with the highest amount of soluble solids and yield are important. This research can be used to increase diversity in cherry production, which is highly needed by the consumer market. [ABSTRACT FROM AUTHOR]

Background and Objectives: Tea (Camellia sinensis (L.) O. Kuntze) is the most consumed beverage in the world after water and an important commercial plant with economic value in northern Iran. Over the years, various tea plants have been cultivated in Iran's tea gardens by seed method, which has led to a high diversity in them. Since most gardeners have propagated the plant sexually, tea gardens vary in quality. Therefore, determining the genetic diversity and relatedness of plants has an important role to support breeding and breeding programs. Materials and Methods: In this study, 28 tea plants attributed to Darjeeling region along with eight Iranian samples and eight samples imported from Sri Lanka were investigated for genetic diversity using ISSR markers. After sampling from young and fully developed leaves, their genomic DNA was extracted and 16 ISSR markers were used to investigate the genetic relationships of 44 tea samples. The obtained data were analyzed by the simple similarity coefficient for the ISSR markers and the cluster was designed based on the UPGMA algorithm. Population structure analysis was also done by POPGENE program. Results: The use of 16 ISSR primers produced 158 bands, of which 116 bands showed polymorphism, and based on this, the percentage of polymorphism was calculated as 73.42%. The PIC test showed a range of 0.45 to 0.50 and this indicator was 0.49 for all markers. The results of Cophentic test showed that SM similarity coefficient and UPGMA algorithm are the most suitable for cluster analysis. Based on the obtained data, the range of similarity was found in the range of 0.376 to 0.880 with an average of 0.626. In the cluster analysis, the samples were divided into two groups at the similarity level of 0.56, and the first group is the largest group, which can be divided into two subgroups. In the population structure analysis, the indicators of Observed number of alleles, Effective number of alleles, Nei's gene diversity and Shannon's Information index in populations and total population were calculated as 1.928, 1.641, 0.364 and 0.532, respectively. The total diversity, average intrapopulation diversity, level of population subdivision were also obtained as 0.380, 0.330 and 0.130 respectively. The maximum similarity was between the samples attributed to Darjeeling and selected Iranian samples. Conclusion: Based on the obtained data, it was determined that there are significant changes among the investigated samples based on the ISSR markers. The percentage of polymorphism and polymorphism information content of the used markers indicated that these markers have a high ability to identify diversity among tea genotypes. Also, the results of this study stated that tea genotypes in Iran have high genetic diversity because they are mostly sexually propagated. This level of variation found between samples suggests that tea from different companies or regions is of better quality, not entirely due to genotype, but rather the ecology in which the tea is grown in terms of climate and soil characteristics, as well as processing technology. At the same time, this genetic difference can be used in breeding studies. [ABSTRACT FROM AUTHOR]

Identifying isolated populations is a key step towards enacting effective conservation management. European lobsters (Homarus gammarus) from Oosterschelde in the Netherlands are subject to fishery pressure and have previously been reported as genetically differentiated. They are also putatively of transplanted origin and have subsequently endured recent bottlenecking and environmental change. We assessed Oosterschelde lobsters to evaluate their demographic independence and appraise potential founder effects and evolutionary responses to isolation. Using restriction-site associated DNA sequencing, we genotyped 6185 single nucleotide polymorphisms across 188 individuals from 27 sites across the Atlantic range of H. gammarus to investigate population genetic diversity, structure, and potential adaptation. Our results show that Oosterschelde lobsters are genetically divergent from other stocks. We evidence extensive differentiation via both neutral and outlier loci, indicative of strong biophysical and demographic isolation, and detect signatures of reduced genetic diversity that may reflect weak founder effects or subsequent population contractions. Among outlier loci, we identify candidates for range-wide local adaptation via variants in genes of important biological functionality and link a private allele of Oosterschelde to a locus potentially conveying adaptive tolerance to environmental hypoxia. Given our findings, we advise proactive monitoring of Oosterschelde lobsters to explore whether existing management measures effectively conserve this discrete, self-recruiting population. [ABSTRACT FROM AUTHOR]

Summary: Scots pine is the foundation species of diverse forested ecosystems across Eurasia and displays remarkable ecological breadth, occurring in environments ranging from temperate rainforests to arid tundra margins. Such expansive distributions can be favored by various demographic and adaptive processes and the interactions between them.To understand the impact of neutral and selective forces on genetic structure in Scots pine, we conducted range‐wide population genetic analyses on 2321 trees from 202 populations using genotyping‐by‐sequencing, reconstructed the recent demography of the species and examined signals of genetic adaptation.We found a high and uniform genetic diversity across the entire range (global FST 0.048), no increased genetic load in expanding populations and minor impact of the last glacial maximum on historical population sizes. Genetic‐environmental associations identified only a handful of single‐nucleotide polymorphisms significantly linked to environmental gradients.The results suggest that extensive gene flow is predominantly responsible for the observed genetic patterns in Scots pine. The apparent missing signal of genetic adaptation is likely attributed to the intricate genetic architecture controlling adaptation to multi‐dimensional environments. The panmixia metapopulation of Scots pine offers a good study system for further exploration into how genetic adaptation and plasticity evolve under gene flow and changing environment. See also the Commentary on this article by Duffy, 243: 830–832. [ABSTRACT FROM AUTHOR]

Aim: The factors that influence the diversity of Yungas Andean forest remain unexplored. Our study seeks to investigate the impact of key isolating factors on the genetic structure of multiple taxa, testing for four hypotheses: isolation by distance (IBD), isolation by resistance due to topography (IBRtopo), isolation by resistance due to habitat suitability (IBRsuit) and isolation by environmental dissimilarity (IBE). Location: Yungas Andean forest. Taxon: Tetrapoda. Methods: We analysed a dataset consisting of 477 Cyt‐b sequences from 138 localities, encompassing 13 species. Through multiple matrix regression, Moran Spectral Randomization of Mantel and GDM analyses, we tested the impact of each extrinsic predictor on observed genetic variation and determined the effect size of environmental variation on genetic divergence. Additionally, we investigated the spatial distribution of lineages within the study species. Results: The genetic variation within the Yungas exhibited varied responses that correspond to the regional landscape heterogeneity. We identified different isolating factors as the main predictor for specific species: IBD for Akodon spegazzinii; IBRtopo for certain small mammals' species; IBE for Thylamys cinderella and Oligoryzomys brendae; and IBRsuit for Calomys fecundus, Oreobates barituensis and Melanophryniscus rubriventris with some considerations. Furthermore, our results support the presence of a latitudinal pattern in the distribution of genetic lineages. Main Conclusions: The heterogeneous landscape of the Yungas Andean forest posed varied effects on genetic variation. The effect of topography and continuity of suitable habitats over vertebrate dispersal shapes the genetic diversity, in particular topography acts either as a barrier or as corridor, while habitat suitability resistance mainly shapes endemism genetic structure; local climate represents a strong genetic promoter in transition zones; and the effect of geographic distance is less evident when considering other landscape promoter of genetic divergence. This reinforces the understanding that the complex interplay of environmental and historical factors contributes to the observed patterns of genetic diversity in this region. [ABSTRACT FROM AUTHOR]

Octopus insularis is a shallow‐water octopus distributed throughout the western Atlantic, the Gulf of Mexico and the Caribbean. To evaluate its phylogeographic pattern, mitochondrial markers (16S rRNA and COIII) and genome‐wide nuclear markers (SNP's) were analyzed in individuals from artisanal fishing in different locations of the Colombian Caribbean coast. Mitochondrial analyzes displayed novel haplotypes (16S = H2, H3 and H4; COIII = H2–H7) and haplotypes shared with distant geographic areas (16S = H1 COIII = H1). The COIII gene did not show genetic differentiation between the analyzed localities, while the 16S gene showed significant differences between Santa Marta and Isla Fuerte. COIII's demographic analysis indicated that the species' effective population size has remained constant. Inferences were made from next‐generation genomic data with restriction site‐associated DNA (ddRAD‐seq) and 6769 polymorphic loci. The pairwise FST test indicated that there are low but significant differences between localities; however, the general molecular analysis of variance (AMOVA) and the principal coordinate analysis showed a lack of spatial structure in the populations analyzed. The Mantel test found no correlation between genetic distance and geographic distance, and the genetic structure analyses showed the presence of one genetic stock. The information obtained in this study indicates the genetic connectivity of O. insularis in the southwestern Caribbean, the absence of putative biogeographic barriers that affect its gene flow, and the crucial role played by life history strategies (planktonic paralarvae) and oceanographic factors to define the current distribution of its genetic diversity in this region. [ABSTRACT FROM AUTHOR]

The Human Genome Project was an enormous accomplishment, providing a foundation for countless explorations into the genetics and genomics of the human species. Yet for many years, the human genome reference sequence remained incomplete and lacked representation of human genetic diversity. Recently, two major advances have emerged to address these shortcomings: complete gap-free human genome sequences, such as the one developed by the Telomere-to-Telomere Consortium, and high-quality pangenomes, such as the one developed by the Human Pangenome Reference Consortium. Facilitated by advances in long-read DNA sequencing and genome assembly algorithms, complete human genome sequences resolve regions that have been historically difficult to sequence, including centromeres, telomeres, and segmental duplications. In parallel, pangenomes capture the extensive genetic diversity across populations worldwide. Together, these advances usher in a new era of genomics research, enhancing the accuracy of genomic analysis, paving the path for precision medicine, and contributing to deeper insights into human biology. [ABSTRACT FROM AUTHOR]

Aporcelaimellus obtusicaudatus was recovered from mustard and sugarcane fields of Uttar Pradesh and Uttarakhand, India. The present species was identified through morphology, molecular and phylogenetic analysis. The Indian populations are characterized by having females with a body length (1.7–3.4 mm), lip region (4.9–8.8 µm), Amphids 6–9 µm, odontostyle length (15.7–26.4 µm), neck length (374.6–745.1 µm), pharyngeal expansion occupying 45–60% of neck length, simple uterus (67.4–124.3 µm), V = 49.1–58.7, female tail (32–44.9 µm, c = 41.1–105, c' = 0.5–1.3) with short, conoid, rounded terminus to convex conical. The molecular phylogenetic analysis based on 18S and 28S rDNA revealed A. obtusicaudatus as a paraphyly. The present populations of Indian A. obtusicaudatus (OM269524; OP020675) placed close to deposited Indian sequence (OP048816; OP048823) and Slovakian populations of A. obtusicaudatus (MH206119). The result of 28S rDNA phylogeny showed that the present population (OM258706) placed close to other populations of the same species from India (OM418794) with 0.55 posterior probability supports. The haplotype analysis based on 28S rDNA revealed 6 haplotypes, which displayed low nucleotide (π = 0.013) diversity. In contrast, haplotype diversity (Hd) was 1.00, and the number of segregating sites (S) was 14. The phylogenetic analysis grouped the various populations into two clades, and the result showed German populations placed into two clades, which showed high variability in haplotype supported by the haplotype network. Tajima (D) and Fu's Fs were found to be negative (P > 0.05), whereas the overall FST value was 0.31040 (P = 0.118). In conclusion, genetic analysis revealed 31.04% variation among groups/populations and 68.95 within populations, indicating a low genetic variation between the same populations of A. obtusicaudatus belonging to the same country. [ABSTRACT FROM AUTHOR]

The population of the Northwest Pre-Caspian saiga (Saiga tatarica tatarica) numbered about 800 000 individuals in the middle of the last century. There was a dramatic decline at the end of the 20th century, and by 2015 the numbers of this saiga population reached about five thousand animals. The results of microsatellite loci and of mtDNA control region analysis obtained for museum saiga samples from the Northwest Pre-Caspian population, collected at the peak of their numbers in the 1950s, are presented. We compared these data with our previous results for the samples collected during the population depression in the years 1999–2016. There were no noticeable differences in the mtDNA control region diversity between the museum and modern saiga samples. The most vivid genetic consequence of the severe decline in population numbers was a significant increase of the inbreeding coefficient (Fis) calculated from the microsatellite loci. [ABSTRACT FROM AUTHOR]

• Modern varieties are derived from wild progenitors through crop domestication. • Limited genetic diversity is a constraint of crop improvement programs to keep pace with the challenges of climate change. • Crop wild relatives and their rich reservoir of gene pool provide the armor against crop stresses. • Genome editing tools are used to explore the germplasm of popular crops for domestication and climate-resilient genes. • Crop domestication is accelerated by Cis-regulating mutation, CRISPR-Cas-, and multiplex editing. Crop domestication is one of the oldest crop improvement methods, significantly impacting socioeconomic conditions globally. Modern varieties are derived from wild progenitors through crop domestication. These varieties are generated by crossing compatible genotypes to obtain the desired phenotype-containing progenies. The uncertainties and stress conditions caused by climate change deeply impact the current agricultural scenario. However, limited genetic diversity is the major constraint of the present crop improvement programs in keeping pace with climate change and several resulting biotic and abiotic stresses. Therefore, using crop wild relative and their rich reservoir of resistant genes to biotic and abiotic stressors must provide the armors against the crop stresses. However, crop wild relatives are unsuitable for direct intensive cropping because of many undesirable agronomic traits and are incompatible for gene transfer with conventional breeding. With the dawn of new-generation sequencing techniques and genome editing tools, scientists are trying to explore the germplasm of popular crops for domestication and climate-resilient genes. Considering the above context, the present review discusses the genetics of crop domestication, different strategies for a targeted mutation to accelerate crop domestication, and the current status of various crops. Further, it will discuss current challenges and the future fate of crop domestication using advanced biotechnological tools. [ABSTRACT FROM AUTHOR]

Rice landraces from the fragile riverine ecosystems surrounding Majuli islands in Assam are pivotal for local livelihoods, as well as for their potential in developing flood tolerant varieties. We characterized 87 landraces from Majuli, Dhemaji, and North Lakhimpur districts in Assam by assessing 36 agro‐morphological traits, submergence tolerance, and microsatellite diversity. Multivariate analyses revealed that grain and leaf characteristics, plant height, and tillering are important traits differentiating the cultivar types. Sixty‐six SSR markers generated 271 alleles with an average of 4.1 alleles per marker with population structuring in two clusters having an allele frequency divergence of 0.124. The Bao or deep‐water landraces displayed the highest phenotypic and genetic diversity, with potential genetic links to the aus and wild species. Sali (winter rice) and bora (sticky rice) landraces were predominantly indica type. Nearly 47% of the germplasm exhibited tolerance to two‐week submergence at seedling stage. Surveying SUB1A and SNORKEL genes revealed the presence of SUB1A‐1 and SNORKEL genes in 64% and 57% of the tolerant accessions, respectively. This study highlights the untapped potential of rice landraces in a fragile ecological region, providing insights into their agronomical traits, submergence tolerance, and genetic diversity. The findings lay the foundation for improved germplasm management and developing flood‐resilient rice varieties, crucial for sustainable agriculture in riverine ecosystems. [ABSTRACT FROM AUTHOR]

The Changle goose (CLG), a Chinese indigenous breed, is celebrated for its adaptability, rapid growth, and premium meat quality. Despite its agricultural value, the exploration of its genomic attributes has been scant. Our study entailed whole‐genome resequencing of 303 geese across CLG and five other Chinese breeds, revealing distinct genetic diversity metrics. We discovered significant migration events from Xingguo gray goose to CLG and minor gene flow between them. We identified genomic regions through selective sweep analysis, correlating with CLG's unique traits. An elevated inbreeding coefficient in CLG, alongside reduced heterozygosity and rare single nucleotide polymorphisms (RSNPs), suggests a narrowed genetic diversity. Genomic regions related to reproduction, meat quality, and growth were identified, with the GATA3 gene showing strong selection signals for meat quality. A non‐synonymous mutation in the Sloc2a1 gene, which is associated with reproductive traits in the CLG, exhibited significant differences in allelic frequency. The roles of CD82, CDH8, and PRKAB1 in growth and development, alongside FABP4, FAF1, ESR1, and AKAP12 in reproduction, were highlighted. Additionally, Cdkal1 and Mfsd14a may influence meat quality. This comprehensive genetic analysis underpins the unique genetic makeup of CLG, providing a basis for its conservation and informed breeding strategies. [ABSTRACT FROM AUTHOR]

Fusarium stalk rot (FSR), caused by the Fusarium species complex, is an economic threat to maize cultivation all over the world. We investigated the population structure and genetic diversity of Fusarium species obtained from five major maize-growing regions in India. The Tef-1α locus was used for phylogenetic analysis of geographically distinct isolates of Fusarium verticillioides, F. andiyazi, F. proliferatum, F. nygamai, and F. acutatum causing FSR. A phylogenetic tree showed monophyletic, polyphyletic, and paraphyletic groupings reflecting the complex evolutionary history and genetic diversity within the genus. Monophyletic groupings depicting strong bootstrap support were shown to have a single common ancestor and genetic coherence with limited genetic divergence among sequences. Polyphyletic groupings also presented significant genetic differentiation within the F. verticillioides sequences from diverse ecological niches. Nucleotide diversity of moderate level 0.02471 reflected genetic variations within populations that were attributed to factors such as mutation, genetic drift, or varying selection pressures. The Fst value of 0.98205 is particularly indicative of high genetic differentiation, implying that most of the genetic variance is due to differences between populations rather than within them. F. verticillioides, with 57 sequences, showed low genetic diversity with three segregating sites and a low haplotype diversity of 0.19486, suggesting the founder effect, where a reduced population expands from a limited genetic pool. The total data estimates across all populations for haplotype analysis showed 72 sequences, 44 segregating sites, and 9 haplotypes with a haplotype diversity of 0.48513. The evolutionary dynamics showed genetic differentiations among Fusarium species causing FSR. AMOVA indicated high within-population variations, depicting a substantial genetic diversity within individual populations. The results offer a comprehensive framework for discussing the implications of genetic diversity in pathogen management and the evolutionary dynamics of the Fusarium species causing FSR in maize in the Indian subcontinent. [ABSTRACT FROM AUTHOR]

Background: Silkie is a traditional Chinese chicken breed characterized by its unique combination of specialized morphological traits. While previous studies have focused on the genetic basis of these traits, the overall genomic characteristics of the Silkie breed remain largely unexplored. In this study, we employed whole genome resequencing data to examine the genetic diversity, selective signals and demographic history of the Silkie breed through comparative analyses with seven other Chinese indigenous breeds (IDGBs), a commercial breed, and the wild ancestor Red Jungle Fowl. Results: In total, 20.8 million high-quality single nucleotide polymorphisms and 86 large structural variations were obtained. We discovered that Silkie exhibits a relatively high level of inbreeding and is genetically distinct from other IDGBs. Furthermore, our analysis indicated that Silkie has experienced a stronger historical population bottleneck and has a smaller effective population size compared with other IDGBs. We identified 45 putatively selected genes that are enriched in the melanogenesis pathway, which probably is related to the feather color. Among these genes, LMBR1 and PDSS2 have been previously associated with the extra toe and the hookless feathers, respectively. Six of the selected genes (KITLG, GSK3B, SOBP, CTBP1, ELMO2, SNRPN) are known to be associated with neurodevelopment and mental diseases in human, and are possibly related to the distinct behavior of Silkie. We further identified structural variants in Silkie and found previously reported variants linked to hyperpigmentation (END3), muff and beard (HOXB8), and Rose-comb phenotype (MNR2). Additionally, we found a 0.61 Mb inversion overlapping with the GMDS gene, which was previously linked to neurodevelopmental defects in zebrafish and humans. This may also be related to the behavior distinctiveness of Silkie. Conclusions: Our study revealed that Silkie is genetically distinct and relatively highly inbred compared to other IDGB chicken populations, possibly attributed to more prolong population bottlenecks and selective breeding practice. These results enhance our understanding of how domestication and selective breeding have shaped the genome of Silkie. These findings contribute to the broader field of domestication and avian genomics, and have implications for the future conservation and breeding efforts. [ABSTRACT FROM AUTHOR]

It is known that some endangered species have persisted for thousands of years despite their very small effective population sizes and low levels of genetic polymorphisms. To understand the genetic mechanisms of long-term persistence in threatened species, we determined the whole genome sequences of akame (Lates japonicus), which has survived for a long time with extremely low genetic variations. Genome-wide heterozygosity in akame was estimated to be 3.3 to 3.4 × 10−4/bp, one of the smallest values in teleost fishes. Analysis of demographic history revealed that the effective population size in akame was around 1,000 from 30,000 years ago to the recent past. The relatively high ratio of nonsynonymous to synonymous heterozygosity in akame indicated an increased genetic load. However, a detailed analysis of genetic diversity in the akame genome revealed that multiple genomic regions, including genes involved in immunity, synaptic development, and olfactory sensory systems, have retained relatively high nucleotide polymorphisms. This implies that the akame genome has preserved the functional genetic variations by balancing selection, to avoid a reduction in viability and loss of adaptive potential. Analysis of synonymous and nonsynonymous nucleotide substitution rates has detected signs of positive selection in many akame genes, suggesting adaptive evolution to temperate waters after the speciation of akame and its close relative, barramundi (Lates calcarifer). Our results indicate that the functional genetic diversity likely contributed to the long-term persistence of this species by avoiding the harmful effects of the population size reduction. [ABSTRACT FROM AUTHOR]

The ecological characteristics of the eight-barbel loach Lefua tokaiensis Ito, Hosoya, and Miyazaki were elucidated. Ecological field research was conducted at two localities: the montane stream of Houraiji and the Arao River of the Toyo River system in the Tokai region of Japan. The two localities showed high population density of L. tokaiensis, consisting of young-to-aged individuals. Loaches were likely to reproduce and migrate both upstream and downstream throughout year. Their lifespan was over 10 years, and loaches of more than ten generations simultaneously lived together. Growth rates slowed down strikingly with increasing age. The montane stream of Houraiji was suitable for the population of L. tokaiensis. The results of this study contribute to the protection of this endangered species. [ABSTRACT FROM AUTHOR]

Simple Summary: Genetic diversity plays a crucial role in determining the ability of populations to evolve. We investigated the genetic variation of the black-and-white snub-nosed monkey by integrating adaptive MHC genes and neutral microsatellites. We found that neutral loci exhibited high heterozygosity and a high degree of polymorphism, while MHC genes showed high heterozygosity and moderate polymorphism. Additionally, positive selection and trans-species evolution indicated that historical balancing selection might have sustained the MHC polymorphism. This study provides valuable scientific evidence and a reference for formulating or amending conservation strategies for black-and-white snub-nosed monkeys. Genetic diversity is an essential indicator that echoes the natural selection and environmental adaptation of a species. Isolated small populations are vulnerable to genetic drift, inbreeding, and limited gene flow; thus, assessing their genetic diversity is critical in conservation. In this study, we studied the genetic diversity of black-and-white snub-nosed monkeys (Rhinopithecus bieti) using neutral microsatellites and five adaptive major histocompatibility complex (MHC) genes. Two DQA1 alleles, two DQB1 alleles, two DRB1 alleles, two DRB5 alleles, and three DPB1 alleles were isolated from a population. The results indicate that neutral microsatellites demonstrate a high degree of heterozygosity and polymorphism, while adaptive MHC genes display a high degree of heterozygosity and moderate polymorphism. The results also show that balancing selection has prominently influenced the MHC diversity of the species during evolution: (1) significant positive selection is identified at several amino acid sites (primarily at and near antigen-binding sites) of the DRB1, DRB5, and DQB1 genes; (2) phylogenetic analyses display the patterns of trans-species evolution for all MHC loci. This study provides valuable genetic diversity insights into black-and-white snub-nosed monkeys, which dwell at the highest altitude and have experienced the harshest environmental selection of all primates globally since the Pleistocene. Such results provide valuable scientific evidence and a reference for making or amending conservation strategies for this endangered primate species. [ABSTRACT FROM AUTHOR]

Phaseolus vulgaris is a globally important legume cash crop, which can carry out symbiotic nitrogen fixation with rhizobia. The presence of suitable rhizobia in cultivating soils is crucial for legume cropping, especially in areas beyond the plant-host native range, where soils may lack efficient symbiotic partners. We analyzed the distribution patterns and traits of native rhizobia associated with P. vulgaris in soils of Yunnan, where the common bean experienced a recent expansion. A total of 608 rhizobial isolates were tracked from soils of fifteen sampling sites using two local varieties of P. vulgaris. The isolates were discriminated into 43 genotypes as defined by IGS PCR-RFLP. Multiple locus sequence analysis based on recA, atpD and rpoB of representative strains placed them into 11 rhizobial species of Rhizobium involving Rhizobium sophorae, Rhizobium acidisoli, Rhizobium ecuadorense, Rhizobium hidalgonense, Rhizobium vallis, Rhizobium sophoriradicis, Rhizobium croatiense, Rhizobium anhuiense, Rhizobium phaseoli, Rhizobium chutanense and Rhizobium etli, and five unknown Rhizobium species; Rhizobium genosp. I~V. R. phaseoli and R. anhuiense were the dominant species (28.0% and 28.8%) most widely distributed, followed by R. croatiense (14.8%). The other rhizobial species were less numerous or site-specific. Phylogenies of nodC and nifH markers, were divided into two specific symbiovars, sv. phaseoli regardless of the species affiliation and sv. viciae associated with R. vallis. Through symbiotic effect assessment, all the tested strains nodulated both P. vulgaris varieties, often resulting with a significant greenness index (91–98%). However, about half of them exhibited better plant biomass performance, at least on one common bean variety, and two isolates (CYAH-6 and BLYH-15) showed a better symbiotic efficiency score. Representative strains revealed diverse abiotic stress tolerance to NaCl, acidity, alkalinity, temperature, drought and glyphosate. One strain efficient on both varieties and exhibiting stress abiotic tolerance (BLYH-15) belonged to R. genosp. IV sv. phaseoli, a species first found as a legume symbiont. [ABSTRACT FROM AUTHOR]

Similar to species richness, genotypic richness of plants plays a pivotal role in the structure and function of ecosystems. While the contribution of intraspecific variability to ecosystem function has been well-established, the mechanisms underlying the effect of genotypic richness on nitrogen (N) uptake patten remain poorly understood. We established experimental populations consisting of 1, 4, or 8 genotypes of the clonal plant Hydrocotyle verticillata in microcosms and conducted 15N-labeling to quantify plant N uptake. NH4+-N uptake rate of the populations with 8 genotypes was significantly higher than that of the populations with 1- and 4-genotypes, while genotypic richness did not influence NO3−-N uptake rate. Increasing genotypic richness also enhanced NH4+-N uptake preference and reduced NO3−-N uptake preference. Additionally, increasing genotypic richness facilitated the transformation of the soil nitrogen pool, resulting in a reduction of total soil N content and an increase in soil NH4+-N, thereby causing a shift in population N uptake preference. Our findings highlight the importance of genotypic richness on both N uptake and N form preference of plant populations. Such intraspecific variability in N uptake and N form preference may further influence population dynamics and ecosystem function. [ABSTRACT FROM AUTHOR]

At least 1–2% of DNA sequences annotated as Blastocystis in GenBank represent organisms other than Blastocystis or sequence artefacts. As well as being biologically incorrect, such practice can lead to overestimates of genetic diversity, underestimated host specificity, and incorrect classification of samples tested for Blastocystis using DNA-based methods. [ABSTRACT FROM AUTHOR]

Soybean is an important agricultural crop known for its high protein and oil content, contributing to essential nutritional and health benefits for humans. Domesticated in China over 5,000 years ago, soybean has since adapted to diverse environments and spread worldwide. This study aimed to investigate the genomic characteristics and population structures of 2,317 publicly available soybean whole-genome sequences from diverse geographical regions, including China, Korea, Japan, Europe, North America, and South America. We used large-scale whole-genome sequencing data to perform high-resolution analyses to reveal the genetic characteristics of soybean accessions. Soybean accessions from China and Korea exhibited landrace characteristics, indicating higher genetic diversity and adaptation to local environments. On the other hand, soybean accessions from Japan, the European Union, and South America were found to have low genetic diversity due to artificial selection and breeding for agronomic traits. We also identified key variants and genes associated with the ability to adapt to different environments. In Korean soybean accessions, we observed strong selection signals for isoflavone synthesis, an adaptive trait critical for improving soybean adaptability, survival, and reproductive success by mitigating environmental stress. Identifying specific genomic regions showing unique patterns of selective sweeps for genes such as HIDH, CYP73A11, IFS1, and CYP81E11 associated with isoflavone synthesis provided valuable insights into potential adaptation mechanisms. Our research has significantly improved our understanding of soybean diversity at the genetic level. We have identified key genetic variants and genes influencing adaptability, laying the foundation for future advances in genomics-based breeding programs and crop improvement efforts. [ABSTRACT FROM AUTHOR]

The inconsistency between traditional morphological taxonomy and molecular phylogenetic data is a major issue that puzzles the study of fish classification and evolution. Although mitochondrial genes are commonly used in phylogenetic analyses to compare fish species, the mitochondrial evolution and diversity of Schistura are still not well understood. To better understand the evolution of Schistura, we sequenced the mitochondrial genome of Schistura fasciolata and compared it with other species of Schistura. A 16,588 bp circular mitochondrial genome of S. fasciolata was obtained and it contains 13 protein-coding, 22 transfer RNA, and two ribosomal RNA genes, and a non-coding control region. The gene arrangement in the mitochondrial genomes of all Schistura species was consistent. However, we also found that S. fasciolata was not monophyletic. Although mitochondrial genes can be effectively used for Schistura species identification, they may not be suitable for inferring the evolutionary process of Schistura species. These results provide support for the use of mitochondrial genes in identifying Schistura species, and also serve as a warning against mistakenly using them to evaluate the evolution process of Schistura species. [ABSTRACT FROM AUTHOR]

The mite, Dermatophagoides farinae, is an allergen source that triggers allergy symptoms in humans. We studied how different habitats affect the genetic structure of D. farinae populations. We used 12 microsatellite loci to analyse the genetic structure of six D. farinae populations collected from four habitats: flour mill (FM), dormitory (DM), cotton mill (CM), and pillow (PL). The CM population had the highest genetic diversity (He = 0.641) while the FM population had less genetic diversity. AMOVA analysis showed 81% intrapopulation genetic variation and 19% interpopulation variation. The overall FST value of the six populations was 0.18531, indicating significant population genetic differentiation. Significant genetic differentiation occurred between the FM population and the other three habitat populations. Bayesian clustering analysis showed that the FM population was divided into two clusters. UPGMA tree and PCoA data supported the above results and indicated that the D. farinae populations from CM, PL, and DM1 had similar genetic ancestors. It was speculated that D. farinae could spread through the cotton-pillow-dormitory route. This study showed that D. farinae may have undergone habitat-associated differentiation and provides measures for preventing the dispersal of D. farinae. [ABSTRACT FROM AUTHOR]

Introduction: Bats are a diverse group of mammals that have unique features allowing them to act as reservoir hosts for several zoonotic pathogens such as Leptospira. Leptospires have been classified into pathogenic, intermediate, and saprophytic groups and more recently into clades P1, P2, S1, and S2, being all the most important pathogenic species related to leptospirosis included within the P1/pathogenic clade. Leptospira has been detected from bats in several regions worldwide; however, the diversity of leptospires harboured by bats is still unknown. Aim: The aim of the present study was to determine the genetic diversity of Leptospira spp. harboured by bats worldwide. Methods: A systematic review was conducted on four databases to retrieve studies in which Leptospira was detected from bats. All studies were screened to retrieve all available Leptospira spp. 16S rRNA sequences from the GenBank database and data regarding their origin. Sequences obtained were compared with each other and reference sequences of Leptospira species and analysed through phylogenetic analysis. Results: A total of 418 Leptospira spp. 16S rRNA sequences isolated from 55 bat species from 14 countries were retrieved from 15 selected manuscripts. From these, 417 sequences clustered within the P1/pathogenic group, and only one sequence clustered within the P2/intermediate group. Six major clades of P1/pathogenic Leptospira spp. were identified, three of them composed exclusively of sequences obtained from bats. Conclusion: We identified that bats harbour a great genetic diversity of Leptospira spp. that form part of the P1/pathogenic clade, some of which are closely related to leptospirosis‐associated species. This finding contributes to the knowledge of the diversity of leptospires hosted by bats worldwide and reinforces the role of bats as reservoirs of P1/pathogenic Leptospira spp. [ABSTRACT FROM AUTHOR]

In this study, 38 elite breeding pepper lines were genetically analyzed using SRAP markers and tested for resistance to PVY, TSWV, and PMMoV viruses using molecular markers. In the virus resistance tests, 1 line (37-H–D-6) from the Three-lobs population was found to be resistant to all 3 viruses tested. The 19 SRAP primer combinations used for genetic diversity yielded a total of 85 bands, 57 of which were polymorphic among pepper lines. While 2–8 bands per primer were obtained, the number of polymorphic bands ranged from 1 to 6. The average polymorphism rate of the primers was 66.44%. The PIC values ranged from 0.06 to 0.40 (with a mean of 0.18). In addition, the average gene diversity, effective allele number, and Shannon information index values of the primers were 0.21, 1.34, and 0.31, respectively. STRUCTURE analysis showed that the pepper lines were grouped into 4 clusters. PCoA and Q-matrix plots supported the cluster distribution. Some lines of the Sivri and Three-lobs pepper populations were observed as outliers in the plots. Kapia and Three-lobs were more similar to each other. This study showed that SRAP markers can be successfully used for genetic diversity of pepper breeding lines. [ABSTRACT FROM AUTHOR]

Animal genetic resources are crucial for ensuring global food security. However, in recent years, a noticeable decline in the genetic diversity of livestock has occurred worldwide. This decline is pronounced in developing countries, where the management of these resources is insufficient. In the current study, we performed whole genome sequencing for 20 Wuxue (WX) and five Guizhou White (GW) goats. Additionally, we utilized the published genomes of 131 samples representing five different goat breeds from various regions in China. We investigated and compared the genetic diversity and selection signatures of WX goats. Whole genome sequencing analysis of the WX and GW populations yielded 120 425 063 SNPs, which resided primarily in intergenic and intron regions. Population genetic structure revealed that WX exhibited genetic resemblance to GW, Chengdu Brown, and Jintang Black and significant differentiation from the other goat breeds. In addition, three methods (nucleotide diversity, linkage disequilibrium decay, and runs of homozygosity) showed moderate genetic diversity in WX goats. We used nucleotide diversity and composite likelihood ratio methods to identify within‐breed signatures of positive selection in WX goats. A total of 369 genes were identified using both detection methods, including genes related to reproduction (GRID2, ZNF276, TCF25, and SPIRE2), growth (HMGA2 and GJA3), and immunity (IRF3 and SRSF3). Overall, this study explored the adaptability of WX goats, shedding light on their genetic richness and potential to thrive in challenges posed by climatic changes and diseases. Further investigations are warranted to harness these insights to enhance more efficient and sustainable goat breeding initiatives. [ABSTRACT FROM AUTHOR]

The mitochondrial cytochrome c oxidase subunit I (COI) genes of six endangered goose breeds (Xupu, Yangjiang, Yan, Wuzong, Baizi, and Lingxian) were sequenced and compared to assess the genetic diversity of endangered goose breeds. By constructing phylogenetic trees and evolutionary maps of genetic relationships, the affinities and degrees of genetic variations among the six different breeds were revealed. A total of 92 polymorphic sites were detected in the 741 bp sequence of the mtDNA COI gene after shear correction, and the GC content of the processed sequence (51.11%) was higher than that of the AT content (48.89%). The polymorphic loci within the populations of five of the six breeds (Xupu, Yangjiang, Yan, Baizi, and Lingxian) were more than 10, the haplotype diversity > 0.5, and the nucleotide diversity (Pi) > 0.005, with the Baizi geese being the exception. A total of 35 haplotypes were detected based on nucleotide variation among sequences, and the goose breed haplotypes showed a central star-shaped dispersion; the FST values were −0.03781 to 0.02645, The greatest genetic differentiation (FST = 0.02645) was observed in Yan and Wuzong breeds. The most frequent genetic exchange (Nm > 15.00) was between the Wuzong and Yangjiang geese. An analysis of molecular variance showed that the population genetic variation mainly came from within the population; the base mismatch differential distribution analysis of the goose breeds and the Tajima's D and Fu's Fs neutral detection of the historical occurrence dynamics of their populations were negative (p > 0.10). The distribution curve of the base mismatches showed a multimodal peak, which indicated that the population tended to be stabilised. These results provide important genetic information for the conservation and management of endangered goose breeds and a scientific basis for the development of effective conservation strategies. [ABSTRACT FROM AUTHOR]

1. The Kaijiang duck is a native Chinese breed known for its excellent egg laying performance, killing-out percentage (88.57%), and disease resistance. The assessment of population genetic structure is the basis for understanding the genetics of indigenous breeds and for their protection and management. 2. In this study, whole-genome sequencing was performed on 60 Kaijiang ducks to identify genetic variations and investigate the population structure. Homozygosity (ROH) analysis was conducted to assess inbreeding levels in the population. 3. The study revealed a moderate level of inbreeding, indicated by an average inbreeding coefficient of 0.1043. This may impact the overall genetic diversity. 4. Genomic Regions of Interest identified included 168 genomic regions exhibiting high levels of autozygosity. These regions were associated with processes including muscle growth, pigmentation, neuromodulation, and growth and reproduction. 5. The significance of these pathways indicated their potential role in shaping the desirable traits of the Kaijiang duck. These findings provide insights into the genetic basis of the Kaijiang duck's desirable traits and can inform future breeding and conservation efforts. [ABSTRACT FROM AUTHOR]

Understanding the genetic diversity and origin of plantations will support the genetic monitoring and provenance selection in restoration projects and help to enhance the adaptation and resilience of plantation forests under climate change. However, information on the origin and genetic variation for plantations with native tree species is inadequate. Taiwania cryptomerioides Hayata is a threatened tree species and has been used as an important tree species for plantation in montane areas of South China. Information on the genetic diversity and origin of the existing Taiwania plantations is needed to facilitate their further development. In this study, using 12 nuclear microsatellite markers, the genetic diversity and structure were investigated in seven previously assumed natural populations and 19 plantation populations of T. cryptomerioides in South China. The Taiwania plantations showed lower genetic diversity and closer genetic distance than natural populations, indicating that most plantations were established with a narrow genetic basis. The results revealed that the majority of Taiwania plantations originated from two areas of the species' natural distribution: northwestern Yunnan and southeastern Guizhou. Interestingly, we found that part of plantations in western Yunnan might represent unique genetic resources. Finally, conservation strategies of germplasm resources and genetic guidelines for seed sourcing of T. cryptomerioides are recommended. This study could facilitate the sustainable development of Taiwania plantations and also serve as a valuable reference for plantation management in China and elsewhere. We suggest that genetic monitoring of plantation forests should be considered in future restoration programs. [ABSTRACT FROM AUTHOR]

Taxus baccata L. is a highly valuable species with wide distribution but scattered and locally rare occurrence. Human intervention, including forest management practices and fragmentation, can significantly impact the species' genetic diversity, structure, and dynamics. In this study, we investigated these factors within T. baccata populations in the Bavarian Forest National Park (NP) in Germany and their implications for conservation. We used 13 EST-SSRs to assess the genetic diversity and structure of the population. Our analysis revealed a scarcity of small-diameter trees, indicating limited natural regeneration over time. However, conservation efforts, like selectively removing competitor species and using protective fencing, have improved growth conditions and promoted seedling emergence. The NP's natural zone has no active management, which is confined to the development and management zones. Genetic diversity assessments revealed high genetic diversity (He: 0.612 and 0.614 for seedlings and adults, respectively) compared to other studies in Taxus baccata, dispelling concerns of significant inbreeding and showcasing a stable genetic structure. However, significant spatial clustering of related individuals (family structures) in both cohorts and low effective population size in the progeny hints at restricted gene flow, necessitating conservation efforts prioritizing safeguarding and promoting natural regeneration in development and management zones. Limited natural regeneration and the recent decrease in effective population size in the NP populations indicate habitat fragmentation and human interventions. Effective population size estimates emphasize the need for diverse conservation strategies. Conservation efforts should prioritize protecting natural regeneration and enhancing gene flow by actively promoting European yew, e.g., by shelterwood cutting, to ensure the long-term viability of T. baccata in the region outside the NP. [ABSTRACT FROM AUTHOR]

Hemicentrotus pulcherrimus is an important commercial aquatic species. However, wild stocks have dramatically decreased in recent decades, and the gonads of H.pulcherrimus of different sexes showed significant differences in gonad index, gonad color, and flavour. Understanding the population genetic structure and sex-differentiation/determination mechanism can provide vital information for genetic conservation and improvement. In the present study, the SuperGBS method was used to identify genome-wide SNPs from a collection of 80 individuals consisting of four geographical populations covering the natural habitats of H. pulcherrimus in China seas. A total of 5785 high-quality SNPs were detected by using SuperGBS technology. The genetic diversity index showed that all populations had similar patterns with high Fis and low Ne, suggesting that it is necessary to carry out the conservation of H. pulcherrimus in China. Low genetic differentiation among the four geographical populations was detected by pairwise Fst, PCA, and admixture analysis. In addition, three sex-related SNPs located on three scaffolds were identified, suggesting a ZW-ZZ sex determination system in H. pulcherrimus. However, no sex-specific marker was identified in this study. Therefore, larger sample sizes and marker numbers need to be implemented to investigate the sex-associated markers and genes of H. pulcherrimus. In general, this study provides a molecular basis for population genetic structure and sex-differentiation/determination mechanism of H. pulcherrimus. [ABSTRACT FROM AUTHOR]

Genetic diversity in Sclerotium rolfsii is useful for understanding its population structure, identifying different mycelial compatibility groups (MCGs), and developing targeted strategies for disease management in affected crops. In our study, a comprehensive genetic analysis was conducted on 50 isolates of S. rolfsii, collected from various geographic regions and host plants. Two specific genes, TEF1α and RPB2, were utilized to assess the genetic diversity and relationships among these isolates. Notably, out of 1225 pairings examined, only 154 exhibited a compatible reaction, while the majority displayed antagonistic reactions, resulting in the formation of a barrier zone. The isolates were grouped into 10 distinct MCGs. These MCGs were further characterized using genetic sequencing. TEF1α sequences distinguished the isolates into 17 distinct clusters, and RPB2 sequences classified them into 20 clusters. Some MCGs shared identical gene sequences within each gene, while others exhibited unique sequences. Intriguingly, when both TEF1α and RPB2 sequences were combined, all 10 MCGs were effectively differentiated, even those that appeared identical with single-gene analysis. This combined approach provided a comprehensive understanding of the genetic diversity and relationships among the S. rolfsii isolates, allowing for precise discrimination between different MCGs. The results shed light on the population structure and genetic variability within this plant pathogenic fungus, providing valuable insights for disease management and control strategies. This study highlights the significance of comprehending the varied virulence characteristics within S. rolfsii isolates, categorizing them into specific virulence groups based on disease severity index (DSI) values. The association with MCGs provides additional insights into the genetic underpinnings of virulence in this pathogen. Furthermore, the identification of geographical patterns in virulence implies the influence of region-specific factors, with potential implications for disease control and crop protection strategies. [ABSTRACT FROM AUTHOR]

Plasmodium vivax variant interspersed repeats (vir) refer to the key protein used for escaping the host immune system. Knowledge in the genetic variation of vir genes can be used for the development of vaccines or diagnostic methods. Therefore, we evaluated the genetic diversity of the vir genes of P. vivax populations of several Asian countries, including Pakistan, which is a malaria-endemic country experiencing a significant rise in malaria cases in recent years. We analyzed the genetic diversity and population structure of 4 vir genes (vir 4, vir 12, vir 21, and vir 27) in the Pakistan P. vivax population and compared these features to those of the corresponding vir genes in other Asian countries. In Pakistan, vir 4 (S=198, H=9, Hd=0.889, Tajima's D value=1.12321) was the most genetically heterogenous, while the features of vir 21 (S=8, H=7, Hd=0.664, Tajima's D value=−0.63763) and vir 27 (S=25, H=11, Hd=0.682, Tajima's D value=−2.10836) were relatively conserved. Additionally, vir 4 was the most genetically diverse among Asian P. vivax populations, although within population diversity was low. Meanwhile, vir 21 and vir 27 among all Asian populations were closely related genetically. Our findings on the genetic diversity of vir genes and its relationships between populations in diverse geographical locations contribute toward a better understanding of the genetic characteristics of vir. The high level of genetic diversity of vir 4 suggests that this gene can be a useful genetic marker for understanding the P. vivax population structure. Longitudinal genetic diversity studies of vir genes in P. vivax isolates obtained from more diverse geographical areas are needed to better understand the function of vir genes and their use for the development of malaria control measures, such as vaccines. [ABSTRACT FROM AUTHOR]

Plasmodium falciparum apical membrane antigen-1 (PfAMA-1) is a major candidate for the blood-stage malaria vaccine. Genetic polymorphisms of global pfama-1suggest that the genetic diversity of the gene can disturb effective vaccine development targeting this antigen. This study was conducted to explore the genetic diversity and gene structure of pfama-1 among P. falciparum isolates collected in the Khyber Pakhtunkhwa (KP) province of Pakistan. A total of 19 full-length pfama-1 sequences were obtained from KP-Pakistan P. falciparum isolates, and genetic polymorphism and natural selection were investigated. KP-Pakistan pfama-1 exhibited genetic diversity, wherein 58 amino acid changes were identified, most of which were located in ectodomains, and domains I, II, and III. The amino acid changes commonly found in the ectodomain of global pfama-1 were also detected in KP-Pakistan pfama-1. Interestingly, 13 novel amino acid changes not reported in the global population were identified in KP-Pakistan pfama-1. KP-Pakistan pfama-1 shared similar levels of genetic diversity with global pfama-1. Evidence of natural selection and recombination events were also detected in KP-Pakistan pfama-1. [ABSTRACT FROM AUTHOR]

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