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Large wild mammals are extremely important in their respective ecological communities and are frequently considered to be emblematic. This is the case of the different tapir species, the largest terrestrial mammals from the Neotropics. Despite their large size and being objects of interest for many naturalists, the field still lacks critical genetics and systematics information about tapir species. In the current work, we analyzed four molecular datasets (mitogenomes, and three nuclear genes, RAG 1-2, IRBP, and BRCA1) of two South American tapirs: the Andean tapir (Tapirus pinchaque) and the alleged new species of tapir, Tapirus kabomani. We derived four main findings. (1) Our molecular phylogenetic analyses showed T. pinchaque as the youngest tapir branch in Neotropics and a sister species of Tapirus terrestris. This contradicts the traditional morphological observations of renowned zoologists and paleontologists, who considered T. pinchaque as the oldest Neotropical tapir. (2) Our data does not support that the alleged T. kabomani is a full species. Rather, it is a specific group within T. terrestris. (3) T. pinchaque is the Neotropical tapir species which yielded the lowest levels of genetic diversity (both for mitochondrial and nuclear data). (4) The spatial genetic structure for T. pinchaque shows differences depending on the type of molecular marker used. With mitogenomes, the spatial structure is relatively weak, whereas with two nuclear genes (RAG 1-2 and IRBP), the spatial structure is highly significant. Curiously, for the other nuclear gene (BRCA1), the spatial structure is practically nonexistent. In any case, the northernmost population of T. pinchaque we studied (Los Nevados National Park in Colombia) was in a peripatric situation and was the most genetically differentiated. This is important for the adequate conservation of this population. (5) T. pinchaque showed clear evidence of population expansion during the last part of the Pleistocene, a period during which the dryness and glacial cold extinguished many large mammals in the Americas. However, T. pinchaque survived and spread throughout the Northern Andes. [ABSTRACT FROM AUTHOR]

Lablab is a regionally important multipurpose legume crop used for human consumption, animal feed, and soil conservation. Despite these qualities, the potential value of this crop has not been fully utilized, and very little research attention has been given to it. The main objective of the study was molecular genetic diversity analysis of Lablab collections using 15 SSR markers. The molecular genetic diversity study of 91 Lablab collections revealed a total of 225 alleles with an average of 14.80 alleles per locus. All markers across the entire population were found to be highly polymorphic and informative with PIC values ranging from 0.78 to 0.92 with a mean value of 0.85. The average expected heterozygosity and gene diversity were 0.75 and 0.86 respectively, indicating a high level of diversity. Analysis of molecular variance showed that 94% of the total genetic variation was attributed to within populations, while only 6% was attributed to among populations. The fixation index value (0.061) recorded indicates the presence of moderate population differentiation as a result of high gene flow (Nm = 3.820) among populations. Due to high gene flow, Cluster, PCoA, and structure analysis did not exactly categorize the populations into genetic groups corresponding to their geographic origin. The observed relatively higher genetic diversity in Konso and West Wellega populations among the eight populations indicates that these areas could be considered hot-spots for genetic diversity and possible germplasm evaluation. Generally, genetic diversity obtained from this study provides inputs for Lablab conservation and improvement in Ethiopia. [ABSTRACT FROM AUTHOR]

Wheat is one of the most important staple food crops in Ethiopia and elsewhere in the world. Knowledge of its genetic diversity provides breeders a chance to develop new, improved cultivars with desirable traits. In this research the genetic diversity and population structure of 180 bread wheat germplasms representing eight populations was analyzed using 10 Inter simple sequence repeat (ISSR) markers used. Based on diversity indices all the ISSR markers were polymorphic and highly informative. High within-populations genetic diversity with a mean allele values of 1.47, effective alleles of 1.33, Shannon's Information index of 0.29, Nei's gene diversity of 0.19, and percent polymorphic loci of 80.5% were obtained in this research. Among the populations, those from the International Septoria Observation Nursery (ISEPTON) showed relatively, the highest observed number of alleles (1.47), effective number of alleles (1.33), Shannon's Information index (0.4) and Nei's gene diversity (0.19). Thus, the ISEPTON lines could be a good source of useful alleles to be used in wheat improvement programs. Analysis of molecular variance revealed that 95% of the total genetic variation resides within populations, while the remaining 5% is accounted to among populations. Clustering using unweighted pair group method with arithmetic mean, principal coordinate analysis and population structure analysis did not group the wheat populations into genetically distinct clusters following their breeding objectives. In the present research adequate polymorphism and reproducible fingerprint profiles were explored from of the genetic structure analysis in the wheat germplasms. The information obtained could thus be useful in future bread wheat breeding programs as well it its sustainable use. [ABSTRACT FROM AUTHOR]

Abstract Mumps is a vaccine-preventable disease with high contagious capability. Its incidence declined rapidly since one dose of mumps vaccine was introduced into Expanded Program of Immunization (EPI) in 2008 in China. Nonetheless, the outbreaks of mumps remain frequent in China. Here we aim to assess herd immunity level followed by one-dose mumps ingredient vaccine and to elucidate the genetic characteristics of mumps viruses circulating in the post vaccine era in Jiangsu province of China. The complete sequences of mumps virus small hydrophobic(SH) gene were amplified and sequenced; coalescent-based Bayesian method was used to perform phylogenetic analysis with BEAST 1.84 software. Commercially available indirect enzyme-linked immune-sorbent IgG assay was used for the quantitative detection of IgG antibody against mumps virus. Our results show that genotype F was the predominant mumps viruses and belonged to indigenous spread, and most of Jiangsu sequences clustered together and formed a monophyly. The prevalence of mumps reached a peak in 2012 and subsequently declined, which presented an obvious different trajectory with virus circulating in other regions of China. The gene diversity of viruses circulating in Jiangsu province was far less than those in China. The antibody prevalence reached 70.42% in the general population during 2018 to 2020. The rising trend of antibody level was also observed. Although mumps antibody prevalence does not reach expected level, mumps virus faces higher pressure in Jiangsu province than the whole of China. To reduce further the prevalence of mumps viruses, two doses of mumps vaccine should be involved into EPI.

Abstract Background Fleas, considered to be the main transmission vectors of Bartonella, are highly prevalent and show great diversity. To date, no investigations have focused on Bartonella vectors in Southeast China. The aim of this study was to investigate the epidemiological and molecular characteristics of Bartonella in fleas in Southeast China. Methods From 2016 to 2022, flea samples (n = 1119) were collected from 863 rodent individuals in seven inland and coastal cities in Southeast China. Flea species, region, gender, host species and habitat were recorded. The DNA samples from each individual flea were screened by real-time PCR for the Bartonella ssrA gene. All positive samples were confirmed by PCR based on the presence of the gltA gene and sequenced. The factors associated with Bartonella infection were analyzed by the Chi-square test and Fisher's exact test. ANOVA and the t-test were used to compare Bartonella DNA load. Results Bartonella DNA was detected in 26.2% (293/1119) of the flea samples, including in 27.1% (284/1047) of Xenopsylla cheopis samples, 13.2% (5/38) of Monopsyllus anisus samples, 8.3% (2/24) of Leptopsylla segnis samples and 20.0% (2/10) of other fleas (Nosopsyllus nicanus, Ctenocephalides felis, Stivalius klossi bispiniformis and Neopsylla dispar fukienensis). There was a significant difference in the prevalence of Bartonella among flea species, sex, hosts, regions and habitats. Five species of Bartonella fleas were identified based on sequencing and phylogenetic analyses targeting the gltA gene: B. tribocorum, B. queenslandensis, B. elizabethae, B. rochalimae and B. coopersplainsensis. Conclusions There is a high prevalence and diversity of Bartonella infection in the seven species of fleas collected in Southeast China. The detection of zoonotic Bartonella species in this study, including B. tribocorum, B. elizabethae and B. rochalimae, raises public health concerns. Graphical Abstract

Mumps is a vaccine-preventable disease with high contagious capability. Its incidence declined rapidly since one dose of mumps vaccine was introduced into Expanded Program of Immunization (EPI) in 2008 in China. Nonetheless, the outbreaks of mumps remain frequent in China. Here we aim to assess herd immunity level followed by one-dose mumps ingredient vaccine and to elucidate the genetic characteristics of mumps viruses circulating in the post vaccine era in Jiangsu province of China. The complete sequences of mumps virus small hydrophobic(SH) gene were amplified and sequenced; coalescent-based Bayesian method was used to perform phylogenetic analysis with BEAST 1.84 software. Commercially available indirect enzyme-linked immune-sorbent IgG assay was used for the quantitative detection of IgG antibody against mumps virus. Our results show that genotype F was the predominant mumps viruses and belonged to indigenous spread, and most of Jiangsu sequences clustered together and formed a monophyly. The prevalence of mumps reached a peak in 2012 and subsequently declined, which presented an obvious different trajectory with virus circulating in other regions of China. The gene diversity of viruses circulating in Jiangsu province was far less than those in China. The antibody prevalence reached 70.42% in the general population during 2018 to 2020. The rising trend of antibody level was also observed. Although mumps antibody prevalence does not reach expected level, mumps virus faces higher pressure in Jiangsu province than the whole of China. To reduce further the prevalence of mumps viruses, two doses of mumps vaccine should be involved into EPI. [ABSTRACT FROM AUTHOR]

Cownose rays Rhinoptera bonasus and R. brasiliensis, are species distributed along the coastal waters from eastern United States, Gulf of Mexico to Brazil. This study represents the most extensive evaluation to date of the genetic diversity and population genetic structure of R. bonasus across its distribution, and it is the first to investigate the population genetics of R. brasiliensis. We analyzed sequences of COI and Cytb genes for Rhinoptera bonasus (COI: 230, Cytb: 108) and R. brasiliensis (COI: 181, Cytb: 105) to investigate the genetic diversity and their relationship with environmental variables, genetic structure, as well as demographic parameters. We found that benthic temperature and current velocity were the most important environmental variables in genetic diversity. The global population structure reveals the presence of significant population genetic structure in both species. Bayesian clusters in BAPS were consistent with the segregation pattern observed for haplotype networks based on COI and Cytb markers for both species, which may respond to philopatry and temperature. These results will further improve management and conservation efforts for these species of ecological and economic importance. [ABSTRACT FROM AUTHOR]

Background: Fleas, considered to be the main transmission vectors of Bartonella, are highly prevalent and show great diversity. To date, no investigations have focused on Bartonella vectors in Southeast China. The aim of this study was to investigate the epidemiological and molecular characteristics of Bartonella in fleas in Southeast China. Methods: From 2016 to 2022, flea samples (n = 1119) were collected from 863 rodent individuals in seven inland and coastal cities in Southeast China. Flea species, region, gender, host species and habitat were recorded. The DNA samples from each individual flea were screened by real-time PCR for the Bartonella ssrA gene. All positive samples were confirmed by PCR based on the presence of the gltA gene and sequenced. The factors associated with Bartonella infection were analyzed by the Chi-square test and Fisher's exact test. ANOVA and the t-test were used to compare Bartonella DNA load. Results: Bartonella DNA was detected in 26.2% (293/1119) of the flea samples, including in 27.1% (284/1047) of Xenopsylla cheopis samples, 13.2% (5/38) of Monopsyllus anisus samples, 8.3% (2/24) of Leptopsylla segnis samples and 20.0% (2/10) of other fleas (Nosopsyllus nicanus, Ctenocephalides felis, Stivalius klossi bispiniformis and Neopsylla dispar fukienensis). There was a significant difference in the prevalence of Bartonella among flea species, sex, hosts, regions and habitats. Five species of Bartonella fleas were identified based on sequencing and phylogenetic analyses targeting the gltA gene: B. tribocorum, B. queenslandensis, B. elizabethae, B. rochalimae and B. coopersplainsensis. Conclusions: There is a high prevalence and diversity of Bartonella infection in the seven species of fleas collected in Southeast China. The detection of zoonotic Bartonella species in this study, including B. tribocorum, B. elizabethae and B. rochalimae, raises public health concerns. [ABSTRACT FROM AUTHOR]

Shiga toxin-producing Escherichia coli (STEC) infection can cause a broad spectrum of symptoms spanning from asymptomatic shedding to mild and bloody diarrhea (BD) and even life-threatening hemolytic-uremic syndrome (HUS). As a member of the serine protease autotransporters of Enterobacteriaceae (SPATE) family, EspP has the ability to degrade human coagulation factor V, leading to mucosal bleeding, and also plays a role in bacteria adhesion to the surface of host cells. Here, we investigated the prevalence and genetic diversity of espP among clinical STEC isolates from patients with mild diarrhea, BD, and HUS, as well as from asymptomatic individuals, and assessed the presence of espP and its subtypes in correlation to disease severity. We found that 130 out of 239 (54.4%) clinical STEC strains were espP positive, and the presence of espP was significantly associated with BD, HUS, and O157:H7 serotype. Eighteen unique espP genotypes (GTs) were identified and categorized into four espP subtypes, i.e., espPα (119, 91.5%), espPγ (5, 3.8%), espPδ (4, 3.1%), and espPε (2, 1.5%). espPα was widely distributed, especially in strains from patients with BD and HUS, and correlated with serotype O157:H7. Serogroup O26, O145, O121, and O103 strains carried espPα only. Ten GTs were identified in espPα, and espPα/GT2 was significantly associated with severe disease, i.e., BD and HUS. Additionally, espP was strongly linked to the presence of eae gene, and the coexistence of espPα and stx2/stx2a + stx2c was closely related to HUS status. To sum up, our data demonstrated a high prevalence and genetic diversity of the espP gene in clinical STEC strains in Sweden and revealed an association between the presence of espP, espP subtypes, and disease severity. espP, particularly the espPα subtype, was prone to be present in more virulent STEC strains, e.g., "top-six" serotypes strains. [ABSTRACT FROM AUTHOR]

Strategies to improve a crop depend on a better understanding of its genetic architecture. In the era of genomics, it is important to develop new efficient genomic resources for orphan crops, considering the growing demand for the crop. Dolichos bean, a high-potential, nutrient-rich orphan legume crop, is gaining importance in many parts of the world. Hence, accelerating breeding activity with marker-assisted approaches is much needed. We developed a total of 670 simple sequence repeat (SSR) markers from the genome sequence information as new genomic resources for the crop. In order to assess the effectiveness of markers to use in genetic research, ensuring the informativeness of new genomic resources is a prerequisite. Hence, new markers were assayed on 96 diverse accessions and examined for their potential to explain population genomics. These new markers consisted of both di- and tri-nucleotide repeats in equal proportions. The population genetic parameters estimated with this marker information proved their efficiency in delineating genetic variations in the population. Results reinforced the relationships between the effective number of alleles, gene diversity, and polymorphic information content, thereby suggesting the informativeness of new markers as genomic resources. Population structure and gene flow information generated will be useful to understand the population dynamics of the dolichos bean. The classification of genotypes into clusters using marker information and the comparison of cluster phenotypes indicated the effectiveness of marker alleles in assessing genome diversity. At the outset, the results of the present study strongly prove the effectiveness of new genomic SSR markers to utilize in genomics-assisted breeding in dolichos bean. [ABSTRACT FROM AUTHOR]

Cownose rays Rhinoptera bonasus and R. brasiliensis, are species distributed along the coastal waters from eastern United States, Gulf of Mexico to Brazil. This study represents the most extensive evaluation to date of the genetic diversity and population genetic structure of R. bonasus across its distribution, and it is the first to investigate the population genetics of R. brasiliensis. We analyzed sequences of COI and Cytb genes for Rhinoptera bonasus (COI: 230, Cytb: 108) and R. brasiliensis (COI: 181, Cytb: 105) to investigate the genetic diversity and their relationship with environmental variables, genetic structure, as well as demographic parameters. We found that benthic temperature and current velocity were the most important environmental variables in genetic diversity. The global population structure reveals the presence of significant population genetic structure in both species. Bayesian clusters in BAPS were consistent with the segregation pattern observed for haplotype networks based on COI and Cytb markers for both species, which may respond to philopatry and temperature. These results will further improve management and conservation efforts for theses species of ecological and economic importance.

Key message Forest tree breeding must undergo significant revisions to adapt to the evolving challenges posed by climate change. Addressing the shifts in environmental conditions requires a comprehensive multidisciplinary approach that includes theoretical work and practical application. Specifically, there is a need to focus on developing new breeding strategies that are theoretically sound and practically feasible, considering the economic constraints of actual tree breeding programs. We present a novel concept utilizing genetic evaluation of multiple traits in forest stands of successive ages across wide ecological ranges. Incorporating genomics allows for detailed genetic evaluation, making use of high-density SNP markers and sophisticated algorithms like GBLUP for genetic parameter estimates. High-throughput phenotyping is conducted using drone-borne lidar technology to capture tree height and survival data across various forest stands. Assisted migration is considered to strategically position genotypes across predicted environmental climatic gradients, thereby accommodating the dynamic nature of ecological shifts. Mathematical optimization acts as an essential component for logistics, guiding the spatial allocation and timely substitution of genotypes to ensure a continually adaptive breeding program. The concept replaces distinct breeding cycles with continuous evaluation and selection, enhancing the rate of genetic response over time.

The study presents the status and diversity of major histocompatibility complex (MHC) class I genes in the Far Eastern leopard (Panthera pardus orientalis). 20 alleles of MHC genes were obtained from 11 samples in total, 19 alleles were described for the first time for the species. A high diversity of alleles is shown at the level of individuals as well as at the population level. Comparison of MHC gene polymorphism in leopard subspecies showed that the genetic diversity of the Far Eastern leopard is not lower and even possibly higher, than observed of the African and Indian subspecies. The high allelic diversity of the Far Eastern leopard genes is supported by the positive selection affecting on the antigen-binding region of the protein product they encrypt. It is concluded that the low abundance of the Far Eastern leopard has not yet led to irreparable losses in the genetic potential of the population. [ABSTRACT FROM AUTHOR]

Key message: Forest tree breeding must undergo significant revisions to adapt to the evolving challenges posed by climate change. Addressing the shifts in environmental conditions requires a comprehensive multidisciplinary approach that includes theoretical work and practical application. Specifically, there is a need to focus on developing new breeding strategies that are theoretically sound and practically feasible, considering the economic constraints of actual tree breeding programs. We present a novel concept utilizing genetic evaluation of multiple traits in forest stands of successive ages across wide ecological ranges. Incorporating genomics allows for detailed genetic evaluation, making use of high-density SNP markers and sophisticated algorithms like GBLUP for genetic parameter estimates. High-throughput phenotyping is conducted using drone-borne lidar technology to capture tree height and survival data across various forest stands. Assisted migration is considered to strategically position genotypes across predicted environmental climatic gradients, thereby accommodating the dynamic nature of ecological shifts. Mathematical optimization acts as an essential component for logistics, guiding the spatial allocation and timely substitution of genotypes to ensure a continually adaptive breeding program. The concept replaces distinct breeding cycles with continuous evaluation and selection, enhancing the rate of genetic response over time. [ABSTRACT FROM AUTHOR]

Wheat genotypes should be improved through available germplasm genetic diversity to ensure food security. This study investigated the molecular diversity and population structure of a set of Türkiye bread wheat genotypes using 120 microsatellite markers. Based on the results, 651 polymorphic alleles were evaluated to determine genetic diversity and population structure. The number of alleles ranged from 2 to 19, with an average of 5.44 alleles per locus. Polymorphic information content (PIC) ranged from 0.031 to 0.915 with a mean of 0.43. In addition, the gene diversity index ranged from 0.03 to 0.92 with an average of 0.46. The expected heterozygosity ranged from 0.00 to 0.359 with a mean of 0.124. The unbiased expected heterozygosity ranged from 0.00 to 0.319 with an average of 0.112. The mean values of the number of effective alleles (Ne), genetic diversity of Nei (H) and Shannon's information index (I) were estimated at 1.190, 1.049 and 0.168, respectively. The highest genetic diversity (GD) was estimated between genotypes G1 and G27. In the UPGMA dendrogram, the 63 genotypes were grouped into three clusters. The three main coordinates were able to explain 12.64, 6.38 and 4.90% of genetic diversity, respectively. AMOVA revealed diversity within populations at 78% and between populations at 22%. The current populations were found to be highly structured. Model-based cluster analyses classified the 63 genotypes studied into three subpopulations. The values of F-statistic (Fst) for the identified subpopulations were 0.253, 0.330 and 0.244, respectively. In addition, the expected values of heterozygosity (He) for these sub-populations were recorded as 0.45, 0.46 and 0.44, respectively. Therefore, SSR markers can be useful not only in genetic diversity and association analysis of wheat but also in its germplasm for various agronomic traits or mechanisms of tolerance to environmental stresses. [ABSTRACT FROM AUTHOR]

Shiga toxin-producing Escherichia coli (STEC) infection can cause a broad spectrum of symptoms spanning from asymptomatic shedding to mild and bloody diarrhea (BD) and even life-threatening hemolytic-uremic syndrome (HUS). As a member of the serine protease autotransporters of Enterobacteriaceae (SPATE) family, EspP has the ability to degrade human coagulation factor V, leading to mucosal bleeding, and also plays a role in bacteria adhesion to the surface of host cells. Here, we investigated the prevalence and genetic diversity of espP among clinical STEC isolates from patients with mild diarrhea, BD, and HUS, as well as from asymptomatic individuals, and assessed the presence of espP and its subtypes in correlation to disease severity. We found that 130 out of 239 (54.4%) clinical STEC strains were espP positive, and the presence of espP was significantly associated with BD, HUS, and O157:H7 serotype. Eighteen unique espP genotypes (GTs) were identified and categorized into four espP subtypes, i.e., espPα (119, 91.5%), espPγ (5, 3.8%), espPδ (4, 3.1%), and espPε (2, 1.5%). espPα was widely distributed, especially in strains from patients with BD and HUS, and correlated with serotype O157:H7. Serogroup O26, O145, O121, and O103 strains carried espPα only. Ten GTs were identified in espPα, and espPα/GT2 was significantly associated with severe disease, i.e., BD and HUS. Additionally, espP was strongly linked to the presence of eae gene, and the coexistence of espPα and stx2/stx2a + stx2c was closely related to HUS status. To sum up, our data demonstrated a high prevalence and genetic diversity of the espP gene in clinical STEC strains in Sweden and revealed an association between the presence of espP, espP subtypes, and disease severity. espP, particularly the espPα subtype, was prone to be present in more virulent STEC strains, e.g., “top-six” serotypes strains.

Abstract Background Excessive fat and protein in food can cause diarrhea by disturbing the intestinal microecology. Lactase is a functional enzyme strongly associated with diarrhea, while lactase bacteria in the intestine are an important source of microbial lactase. Therefore, we reconnoiter the relationship between diarrhea induced by a high-fat and high-protein diet (HFHPD) and intestinal mucosal lactase bacteria from the perspective of functional genes. Result Operational Taxonomic Units (OTUs) were 23 and 31 in the normal group (NM) and model group (MD), respectively, and 11 of these were identical. The Chao1 and Observed specie indexes in the MD were higher than those in the NM, but this was not significant (P > 0.05). Meanwhile, the Principal coordinate analysis (PCoA) and Adonis test showed that the community structures of lactase bacteria in NM and MD were significantly different (P

ObjectiveThe objectives of this research were the study genetic diversity in Iranian and foreign pistachio cultivars using CBDP markers and the efficiency of these markers in the differentiation and grouping of cultivars. Materials and methodsIn this research, the genetic diversity of 73 cultivars (63 Iranian and 10 foreign cultivars) was evaluated using 25 CBPD primers. ResultsThe results showed that the bands’ polymorphism for Iranian and foreign cultivars was 77.56% and 67.80%, respectively. The PIC mean for CBPD markers was 0.76 and all CBDP primers had a high ability to separate pistachio cultivars. The MI mean for CBDP primers was 2.65 and the CAAT2 primer showed the highest MI (8.52) value. Analysis of molecular variance determined 4% inter-group diversity and 96% intra-group diversity for studied genotypes. Gst value 0.04 verified low inter-group diversity as well. Nm value 11.03 showed the gene flow between foreign and Iranian pistachio cultivars. Iranian cultivars had higher values than foreign cultivars in terms of both Nei and Shannon gene diversity indices as well. Cluster analysis using the Jaccard matrix and UPGMA method was performed and the results showed, the average similarity coefficient between cultivars was 0.68 and the pistachio cultivars were divided in three main groups, in which the main groups were subdivided into several subgroups. The principal coordinate analysis also confirmed the result of the cluster analysis. ConclusionsIn conclusion, the use of CBDP markers is suitable for studying the genetic diversity of pistachio cultivars. Also, the efficiency and differentiation power of CBDP primers was confirmed due to the high mean of PIC and MI.

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Antigen 43 (Ag43) expression induces aggregation and biofilm formation that has consequences for bacterial colonisation and infection. Ag43 is secreted through the Type 5 subtype "a" secretion system (T5aSS) and is a prototypical member of the family of self-associating autotransporters (SAATs). As a T5aSS protein, Ag43 has a modular architecture comprised of (i) a signal peptide, (ii) a passenger domain that can be subdivided into three subdomains (SL, EJ, and BL), (iii) an autochaperone (AC) domain, and (iv) an outer membrane translocator. The cell-surface SL subdomain is directly involved in the "Velcro-handshake" mechanism resulting in bacterial autoaggregation. Ag43 is considered to have a ubiquitous distribution in E. coli genomes and many strains harbour multiple agn43 genes. However, recent phylogenetic analyses indicated the existence of four distinct Ag43 classes exhibiting different propensities for autoaggregation and interactions. Given the knowledge of the diversity and distribution of Ag43 in E. coli genomes is incomplete, we have performed a thorough in silico investigation across bacterial genomes. Our comprehensive analyses indicate that Ag43 passenger domains cluster in six phylogenetic classes associated with different SL subdomains. The diversity of Ag43 passenger domains is a result of the association of the SL subtypes with two different EJ-BL-AC modules. We reveal that agn43 is almost exclusively present among bacterial species of the Enterobacteriaceae family and essentially in the Escherichia genus (99.6%) but that it is not ubiquitous in E. coli. The gene is typically present as a single copy but up to five copies of agn43 with different combinations of classes can be observed. The presence of agn43 as well as its different classes appeared to differ between Escherichia phylogroups. Strikingly, agn43 is present in 90% of E. coli from E phylogroup. Our results shed light on Ag43 diversity and provide a rational framework for investigating its role in E. coli ecophysiology and physiopathology. [ABSTRACT FROM AUTHOR]

The study of gene diversity in interspecies contributes to our understanding of the environmental adaptation, evolutionary history, origin, and stability of biodiversity. Crabs are the main component of the macrobenthos community; therefore, how crabs adapt to different environments can be a guide to understand how to maintain community diversity. Previous studies on environmental adaptation have focused on differences in morphology, organ structure, and function, but there is a lack of research that explores this topic from the perspective of gene diversity in benthonic crabs. In this study, the leucosiid crab was selected for transcriptome assembly and was analyzed as this superfamily is one of the main clades in brachyuran crabs. Their transcriptome data were used to understand the gene diversity, phylogeny, and divergence time estimations. Subsequently, candidate gene families for depth adaptation were found in eight species that live in habitats with different depths. The results indicated that the number of total unigene sequences was between 65,617 (Philyra malefactrix) and 98,279 (Arcania heptacantha) in eight species. The total length of the genes was counted to be between 48,006,211 and 95,471,088 bp. The age of the superfamily Leucosioidea is over 150 Ma, dating back to at least the Jurassic geological period. The divergence of the family Leucosiidae would have occurred in the middle Cretaceous (around 100 Ma). After dividing into groups of three depth types, which carried the gene families, it was found that the three groups shared the solute carrier family, whereas bile acid secretion, organic solute transporter subunit alpha-like, and solute carrier organic anion transporter families only existed in the shallow group. This result shown that the gene function of ion concentration regulation might one of the candidate gene families related to the environmental adaptation of the leucosiid crab. Hence, these gene families will be analyzed in future studies to understand the mechanism of depth adaptation regulation in crabs. [ABSTRACT FROM AUTHOR]

In this paper, the genetic diversities of 12 rice genotypes (Oryza sativa L.), representing Indica, Japonica, and Indica–Japonica varieties, were assessed using twelve ISSR and five SSR markers. In addition, the rice genotypes were evaluated for 11 agro-morphological traits in a two-year trial. Association mapping was performed to detect any association between the DNA markers and the agro-morphological traits. An association analysis was conducted considering the relative kinship among the genotypes and accounting for the population structure using the unified mixed-model approach to avoid possible false-positive associations. Seventy-three alleles were collectively produced by ISSRs and SSRs, with an average of 6.3 and 2.8 alleles per locus, respectively. Both marker systems were informative, and the average polymorphism information content (PIC) was 0.222 and 0.352 for ISSRs and SSRs, respectively. The average expected heterozygosity (Hexp) was 0.264 for ISSRs compared to 0.457 for SSRs. After using the false discovery rate (FDR) method, the association analysis revealed a total of 12 significant marker–trait associations with six agro-morphological traits, including the no. of unfiled grains panicle−1, panicle length, panicle weight, the no. of panicles plant−1, the no. of tillers plant−1, and 1000-grain weight. ISSRs showed seven significant associations with five markers, while SSRs showed three significant associations with three markers. The phenotypic variance (R2) explained by each marker ranged between 29.2% for the ISSR marker HB11 (associated with 1000-grain weight) and 49.3% for the ISSR marker HB8 (associated with the no. of tillers plant−1). The identified marker–trait associations reported herein may improve the expected gain of future molecular-based rice-breeding programs, particularly those designed for improving grain-related or harvest-related traits. [ABSTRACT FROM AUTHOR]

Brown trout populations living in the limit of the distribution of the species face challenging environmental conditions. In islands, this vulnerable situation is exacerbated by geographical isolation. Sicilian trout persist only in the south-eastern part of the island and, based on their morphological characteristics, they have been recognized as a distinct species named Salmo cettii. We present the most extensive genetic study on Sicilian trout, based on 213 individuals from nine different streams in four basins. Sequencing of the mitochondrial control region and genotyping of the LDH-C* locus and eight microsatellite markers were carried out to evaluate hatchery introgression from past stocking practices in natural populations and to estimate the gene diversity distribution in populations. Results showed that only trout from the Tellesimo River remained free of hatchery introgression. Gene diversity was low in this native population, but increased in the rest of the samples, probably because of the introduction of hatchery genes. Despite the high level of introgression, the distribution of gene diversity depicted a clear natural pattern of population structure related to the hydrographic hierarchy. Because they represent long evolutionary histories, Sicilian trout populations should be considered of high conservation priority and managed according to at least four different genetic units. [ABSTRACT FROM AUTHOR]

ObjectiveThe objective of present study was to evaluate the genetic diversity within 23 genotypes of Freesia hybrida including 6 parents and their 17 F1 hybrids, using 10 ISSR primers in order to utilize such diversity in breeding program of this plant. Materials and methodsAfter extraction of genomic DNA from fresh leaves and amplification of marker regions by the PCR, followed by the electrophoresis, a matrix of binary data was created based on scoring of electrophoretic bands. Marker parameters including number of polymorphic loci, polymorphism information content, effective multiple ratio, resolution power index, and marker index as well as genetic variation indices including observed number of alleles, effective number of alleles, Nei's gene diversity index, and Shannon's information index were calculated by using the ISSR marker data. Principle components analysis based on the Jaccard similarity coefficient with UPGMA algorithm were done followed by the cluster analysis using Dice coefficient and based on Ward’s grouping method. ResultsOut of 110 amplified loci of the 10 ISSR markers, the mean of polymorphism percentage 94.7% within the used genotypes was estimated. Maker IS-HB11 showed maximum number of polymorphic loci (12), effective multiple ratio (7.93), resolution power index (7.83), and marker index (2.67) as well. Cluster analysis grouped genotypes into four clusters, which was confirmed by the result of principle component analysis. ConclusionsRelative high value of the polymorphism information content (0.368), showed that the ISSR makers utilized in present study were genetically well informative regarding to the number of identified alleles and their distribution in the genome of Freesia. Based on the gene diversity indices, there was no significant difference between the parental genotypes and the F1 hybrids in terms of genetic variation. However, the level of this variation was acceptable and is capable to be utilized for breeding program in this plant.

BACKGROUND: To improve production efficiency, positive alleles corresponding to yield‐related attributes must be accumulated in a single elite background. We designed and used cgSSR markers, which are superior to random SSR markers in genome‐wide association study, to identify genomic regions that contribute to panicle characters and grain yield in this study. RESULTS: As evidenced by the high polymorphic information content value and gene diversity coefficient, the new cgSSR markers were determined to be highly informative. These cgSSR markers were employed to generate genotype data for an association panel evaluated for four panicle characters and grain yield over three seasons. For five traits, 17 significant marker–trait associations on six chromosomes were discovered. The percentage of phenotypic variance that could be explained ranged from 4% to 13%. Unrelated gene‐derived markers had a strong association with target traits as well. CONCLUSION: Trait‐associated cgSSR markers derived from corresponding or related genes ensure their utility in direct allele selection, while other linked markers aid in allele selection indirectly by altering the phenotype of interest. Through a marker‐assisted breeding approach, these marker–trait associations can be leveraged to accumulate favourable alleles for yield enhancement in rice. © 2022 Society of Chemical Industry. [ABSTRACT FROM AUTHOR]

In 2003, Kandelia obovata was identified as a new mangrove species differentiated from Kandelia candel. However, little is known about their chloroplast (cp) genome differences and their possible ecological significance. In this study, 25 whole cp genomes, with seven samples of K. candel from Malaysia, Thailand, and Bangladesh and 18 samples of K. obovata from China, were sequenced for comparison. The cp genomes of both species encoded 128 genes, namely 83 protein-coding genes, 37 tRNA genes, and eight rRNA genes, but the cp genome size of K. obovata was ~2 kb larger than that of K. candle due to the presence of more and longer repeat sequences. Of these, tandem repeats and simple sequence repeats exhibited great differences. Principal component analysis based on indels, and phylogenetic tree analyses constructed with homologous protein genes from the singlecopy genes, as well as 38 homologous pair genes among 13 mangrove species, gave strong support to the separation of the two species within the Kandelia genus. Homologous genes ndhD and atpA showed intraspecific consistency and interspecific differences. Molecular dynamics simulations of their corresponding proteins, NAD(P)H dehydrogenase chain 4 (NDH-D) and ATP synthase subunit alpha (ATP-A), predicted them to be significantly different in the functions of photosynthetic electron transport and ATP generation in the two species. These results suggest that the energy requirement was a pivotal factor in their adaptation to differential environments geographically separated by the South China Sea. Our results also provide clues for future research on their physiological and molecular adaptation mechanisms to light and temperature. [ABSTRACT FROM AUTHOR]

We compared the genetic diversity and relative abundance of eukaryotic plankton in Daya Bay using two genetic markers(18S rRNA V4 and V9 regions) to amplify the eDNA and high-throughput sequencing technology. 56 classes, 101 orders of zooplankton and 52 classes, 69 orders of phytoplankton were detected using 18S rDNA V4 markers. And 47 classes, 81 orders of zooplankton and 56 classes, 101 orders of phytoplankton were detected using 18S rDNA V9 markers. Both 18S rDNA V4 and V9 regions results performed well to coverage communities and provided similar eukaryotic plankton distribution patterns at class taxonomic level. Maxillopoda is the dominant group of zooplankton, while Dinophyceae, Coscinodiscophyceae and Mamiellophyceae are the dominant groups of phytoplankton. Especially, two genetic markers amplification results present the similar diversity and relative abundance of Dinophyceae at order taxonomic level. The results of 18S rDNA V9 region presented higher abundance of Coscinodiscophyceae than that of V4. The results showed that the diversity of zooplankton amplification by 18S rDNA V4 primers was higher than that of 18S rDNA V9 primers, while that of phytoplankton amplification by 18S rDNA V9 primers was higher than that of 18S rDNA V4 primers. In this study, we first report high abundance parasitic Syndiniales and Mamiellales in Daya Bay [ABSTRACT FROM AUTHOR]

Parvalbumins (PVALBs) are low molecular weight calcium-binding proteins. In addition to their role in many biological processes, PVALBs play an important role in regulating Ca2+ switching in muscles with fast-twitch fibres in addition to their role in many biological processes. The PVALB gene family is divided into two gene types, alpha (α) and beta (β), with the β gene further divided into two gene types, beta1 (β1) and beta2 (β2), carrying traces of whole genome duplication. A large variety of commonly consumed fish species contain PVALB proteins which are known to cause fish allergies. More than 95% of all fish-induced food allergies are caused by PVALB proteins. The authentication of fish species has become increasingly important as the seafood industry continues to grow and the growth brings with it many cases of food fraud. Since the PVALB gene plays an important role in the initiation of allergic reactions, it has been used for decades to develop alternate assays for fish identification. A brief review of the significance of the fish PVALB genes is presented in this article, which covers evolutionary diversity, allergic properties, and potential use as a forensic marker. [ABSTRACT FROM AUTHOR]

Ideally, a panel of Y short tandem repeats (Y-STRs) should include markers with gene diversity (GD) ≥ 0.70 to guarantee a highly accurate and precise individual identification in all forensic situations where Y loci analysis is necessary to support the findings obtained with autosomal STRs. Since not all markers in a multiplex set reach the optimal GD value, to achieve a greater discrimination capacity (DC), the number of Y-STRs has been gradually expanded also with the addition of rapidly mutating Y-STRs (RM Y-STRs). The present study has tried to assess, based on the genetic diversity of each Y-STR and the cumulative haplotype diversity provided by the single Y-STR panels tested, whether to increase in the number of Y-STRs is effective. For this purpose, three commercially available forensic kits - the PowerPlex® Y23 System, the Yfiler™ Plus PCR Amplification Kit, and the ForenSeq™ DNA Signature Prep Kit - that allow for the simultaneous analysis of 22–25 Y chromosome markers (including Y-STRs and RM Y-STRs) have been used for typing 115 unrelated male individuals from North-East Italy employing two capillary electrophoresis (Applied Biosystems® 3130 Genetic Analyzer and SeqStudio Genetic Analyzer for HID) and one massively parallel sequencing (MiSeq FGx™ Forensic Genomics System) systems. Forensic parameters, such as gene diversity, cumulative haplotype diversity (cHD), and discrimination capacity, were determined for the three Y-STRs kits and the virtual pool of 30 Y-STRs obtained by the overall combination of the Y-loci of the three kits. From the findings, it emerges that twelve markers in the virtual panel of 30 Y-STRs, are characterized by a value of GD ≥ 0.70, and of these, eleven included in the Yfiler™ Plus kit seem to be sufficient to ensure the achievement of haplotype resolution. In light of this, it does not appear necessary to expand the number of Y-STRs in the currently available kits. [ABSTRACT FROM AUTHOR]

Botulinum neurotoxins (BoNT) are the most potent toxins in the world. They are produced by a few dozens of strains within several clostridial species. The toxin that they produce can cause botulism, a flaccid paralysis in humans and other animals. With seven established serologically different types and over 40 subtypes, BoNTs are among the most diverse known toxins. The toxin, its structure, its function and its physiological effects on the neural cell and animal hosts along with its diversity have been the subjects of numerous studies. However, many gaps remain in our knowledge about the BoNT toxin and the species that produce them. One of these gaps involves the distribution and extent of variability along the full length of the gene and the protein as well as its domains and subdomains. In this study, we performed an extensive analysis of all of the available 143 unique BoNT-encoding genes and their products, and we investigated their diversity and evolution. Our results indicate that while the nucleotide variability is almost uniformly distributed along the entire length of the gene, the amino acid variability is not. We found that most of the differences were concentrated along the protein's light chain (LC) domain and especially, the C-terminus of the receptor-binding domain (HCC). These two regions of the protein are thus identified as the main source of the toxin type differentiation, and consequently, this toxin's versatility to bind different receptors and their isoforms and act upon different substrates, thus infecting different hosts. [ABSTRACT FROM AUTHOR]

Background: Excessive fat and protein in food can cause diarrhea by disturbing the intestinal microecology. Lactase is a functional enzyme strongly associated with diarrhea, while lactase bacteria in the intestine are an important source of microbial lactase. Therefore, we reconnoiter the relationship between diarrhea induced by a high-fat and high-protein diet (HFHPD) and intestinal mucosal lactase bacteria from the perspective of functional genes. Result: Operational Taxonomic Units (OTUs) were 23 and 31 in the normal group (NM) and model group (MD), respectively, and 11 of these were identical. The Chao1 and Observed specie indexes in the MD were higher than those in the NM, but this was not significant (P > 0.05). Meanwhile, the Principal coordinate analysis (PCoA) and Adonis test showed that the community structures of lactase bacteria in NM and MD were significantly different (P < 0.05). In taxonomic composition, lactase bacteria on the intestinal mucosa were sourced from Actinobacteria and Proteobacteria. Where Actinobacteria were higher in NM, and Proteobacteria were higher in MD. At the genus level, Bifidobacterium was the dominant genus (over 90% of the total). Compared to NM, the abundance of Bifidobacterium were lower in MD, while MD added sources for lactase bacteria of Rhizobium, Amycolatopsis, and Cedecea. Conclusions: Our data demonstrate that HFHPD altered the community structure of lactase bacteria in the intestinal mucosa, decreased the abundance of the critical lactase bacteria, and promoted the occurrence of diarrhea. [ABSTRACT FROM AUTHOR]

Objective: The objectives of this research were the study genetic diversity in Iranian and foreign pistachio cultivars using CBDP markers and the efficiency of these markers in the differentiation and grouping of cultivars. Materials and methods: In this research, the genetic diversity of 73 cultivars (63 Iranian and 10 foreign cultivars) was evaluated using 25 CBPD primers. Results: The results showed that the bands' polymorphism for Iranian and foreign cultivars was 77.56% and 67.80%, respectively. The PIC mean for CBPD markers was 0.76 and all CBDP primers had a high ability to separate pistachio cultivars. The MI mean for CBDP primers was 2.65 and the CAAT2 primer showed the highest MI (8.52) value. Analysis of molecular variance determined 4% inter-group diversity and 96% intra-group diversity for studied genotypes. Gst value 0.04 verified low inter-group diversity as well. Nm value 11.03 showed the gene flow between foreign and Iranian pistachio cultivars. Iranian cultivars had higher values than foreign cultivars in terms of both Nei and Shannon gene diversity indices as well. Cluster analysis using the Jaccard matrix and UPGMA method was performed and the results showed, the average similarity coefficient between cultivars was 0.68 and the pistachio cultivars were divided in three main groups, in which the main groups were subdivided into several subgroups. The principal coordinate analysis also confirmed the result of the cluster analysis. Conclusions: In conclusion, the use of CBDP markers is suitable for studying the genetic diversity of pistachio cultivars. Also, the efficiency and differentiation power of CBDP primers was confirmed due to the high mean of PIC and MI. [ABSTRACT FROM AUTHOR]

The population genetic structure and female philopatry to nursery grounds of the scalloped hammerhead shark (Sphyrna lewini) were studied in different mangrove estuaries along the Mexican Pacific coast containing putative nurseries. These nurseries were grouped into northern (Sinaloa-Nayarit), central (Jalisco), and southern (Oaxaca-Chiapas) regions. Neonates and young of the year were collected near estuaries or river inlets, and their genetic variation was compared based on mitochondrial DNA (mtDNA) genome sequences and 11 nuclear microsatellite loci. The mtDNA analysis showed significant differences between the abovementioned regions, accompanied by genetic homogeneity of microsatellites. Based on the genetic divergence of mtDNA and the lack of differences in nuclear markers, our results are congruent with female philopatry to nursery areas, as observed in other shark species. The parentage analysis applied to the microsatellite data showed moderate levels of relatedness among individuals within nurseries, suggesting philopatry as a cause of the observed results. The pattern of nursery grounds of the scalloped hammerhead shark in the Mexican Pacific seems to be regional, as no differences were observed between neighboring estuaries within each studied region. These findings are relevant for delineating conservation plans to preserve key populations and minimize the effects of commercial fisheries. [ABSTRACT FROM AUTHOR]

Abstract Background Mung bean is a pulse crop principally grown in the tropic and subtropic parts of the world for its nutrient-rich seeds. Seven mung beans accessions from Eastern Kenya were evaluated using thirteen phenotypic traits. In addition, 10 SSR markers were used to determine their genetic diversity and population structure. This aimed at enhancing germplasm utilization for subsequent mung bean breeding programs. Results Analysis of variance for most of the phenology traits showed significant variation, with the yield traits recording the highest. The first three principal components (PC) explained 83.4% of the overall phenotypic variation, with the highest (PC1) being due to variation of majority of the traits studied such as pod length, plant height, and seeds per pod. The dendogram revealed that the improved genotypes had common ancestry with the local landraces. The seven mung beans were also genotyped using 10 microsatellite markers, eight of which showed clear and consistent amplification profiles with scorable polymorphisms in all the studied genotypes. Genetic diversity, allele number, and polymorphic information content (PIC) were determined using powermarker (version 3.25) and phylogenetic tree constructed using DARWIN version 6.0.12. Analysis of molecular variance (AMOVA) was calculated using GenALEx version 6.5. A total of 23 alleles were detected from the seven genotypes on all the chromosomes studied with an average of 2.875 across the loci. The PIC values ranged from 0.1224 (CEDG056) to 0.5918 (CEDG092) with a mean of 0.3724. Among the markers, CEDG092 was highly informative while the rest were reasonably informative except CEDG056, which was less informative. Gene diversity ranged from 0.1836 (CEDG050) to 0.5102 (CDED088) with an average of 0.3534. The Jaccards dissimilarity matrix indicated that genotypes VC614850 and N26 had the highest level of dissimilarity while VC637245 and N26 had lowest dissimilarity index. The phylogenetic tree grouped the genotypes into three clusters as revealed by population structure analysis (K = 3), with cluster III having one unique genotype (VC6137B) only. AMOVA indicated that the highest variation (99%) was between individual genotype. In addition, marker traits association analysis revealed 18 significant associations (P < 0.05). Conclusion These findings indicate sufficient variation among the studied genotypes that can be considered for germplasm breeding programs.

Hypothesis: The anthropogenic effects can be manifested in a decrease in genetic diversity and the population differentiation, and increase in the frequencies of rare and/or private alleles. Materials and methods: We have selected a collection of primers for B. inermis, consisting of 21 microsatellite loci from B. sterilis, B. tectorum and Triticum aestivum. Results: Only 38% of SSR primers showed good transferability and were used for B. inermis population studies from technogenic pollution areas. We revealed 42 alleles at eight loci, and the number of alleles per locus varied from one to 13 per populations. The percentage of polymorphic loci in B. inermis populations was 48.44%. A total of 22 rare, 14 private and 9 both rare and private alleles were reported. There were no correlations between geographic and genetic distances. Only 6.8% of the genetic variability was distributed among B. inermis populations. Conclusion: There was no decrease in genetic diversity found in B. inermis populations growing under anthropogenic stress. No significant differences in the number of rare and private alleles in the background and impact populations of B. inermis were found. The smooth brome is characterized by low differentiation of the populations. Possible reasons for this phenomenon are discussed. [ABSTRACT FROM AUTHOR]

Tillering is one of the most important agronomic traits for sugarcane which is a vegetatively propagated economic crop. Mining these genes related to tillering trait and utilizing them form an ideal architecture are important to effectively increase cane yield of sugarcane varieties. In this study, qRT-PCR technology was used to explore the expression characteristics of a homologue of HTD2 related to rice tillering, which was named ScHTD2 previously obtained from sugarcane. The polymorphism of ScHTD2 gene in sugarcane germplasm resource population was analyzed, and the correlation between variation sites and tillering trait were also detected. The results showed that relative expression of this gene was tissue specific and highest in leaves. During the germination and development of axillary, the relative expression was the highest in the dormant buds. With the germination of sugar buds, the relative expression level first was significantly down-regulated, and the germination and development of sugar buds were negatively regulated. Treatments of phytokinin, auxin and strigolactone can significantly induce its expression in germinating axillary buds and tiller buds of seedling. By combining with the phenotypic changes after hormone treatment, the high expression of this gene induced auxin and strigolactone could inhibit the continued development of germinating axillary buds and delay the occurrence of tillers, but this inhibitory effect did not occur in the high expression of this gene induced by phytokines. Gene polymorphism analysis on 520 cloned sequences of HTD2 genomic DNA from 26 sugarcane germplasm resources showed that the genome sequence structure of this gene contained two exons and one intron, and the variation was the most abundant in the intron region, followed by the exon 1 region. Much higher nucleotide diversity in intron region was detected in main sugarcane variety population, while the origin species parent population had the higher nucleotide diversity in exon 1 and 2 regions. In terms of haplotype diversity in the coding region, the origin species parent population possessed the most abundant haplotype diversity, followed by the main variety population. In the genetic selectivity test, the original species parent population was subjected to positive selection, with high selection pressure and rapid gene evolution, while the backbone parents population and the main variety populations are subject to negative selection toward purification. Two haplotypes of code region located at radiating center of haplotype evolution map, indicating that they belonged to primitive types. The dose effect of mutation type from 23 SNP sites and 5 InDel sites in the code region was significantly related to the tillering rate of sugarcane germplasm resources, so more attention should be paid to the dose effect of mutation types in sugarcane molecular assisted-breeding plan in future. The present study lays a foundation for further analyzing the biological meaning of tillering related to key genes and the development of functional markers in sugarcane. [ABSTRACT FROM AUTHOR]

Napier (Pennisetum purpureum) fodder is an important fodder supporting livestock systems in Bangladesh. Using gamma irradiation, we developed 48 Napier fodder mutants which were analyzed through morpho-molecular characterization. Among 48 Napier fodder mutants, 41 mutants were originated by applying radiation (20Gy, 30Gy, 40Gy and 50Gy) on them. The Napier mutants showed variations in survival rate and fresh weight. The survival rate (0-75%) was observed, 20Gy treated plants produced higher fresh weight in Napier-2, Napier-3, Rokona, Markiron grasses; whereas 30Gy treated plants produced higher fresh weight in Napier-1, Napier-4 and Pakchong. The total of the alleles found in molecular characterization were 17 and the mean number of allele per locus was 3.4. The PIC value ranged from 0.3047 to 0.6587 having an average of 0.4704 per locus. The highest gene diversity (0.7101) was observed in primer Xipes0093, and the lowest gene diversity (0.3750) was observed in primer PSMP2255, having an average diversity of 0.5286. Pair wise genetic distance values ranged (0.0-1.0) with highest between Napier-2 40Gy vs (Napier-1control, Napier-2 20Gy Napier-2 30Gy), Napier -3 control, vs (Napier-1control, Napier-2 20Gy Napier-2 30Gy), Napier-3 20Gy vs (Napier-1control, Napier-2 20Gy Napier-2 30Gy), (Napier-3 20Gy, Napier-3 30Gy Napier-1 20Gy, Napier-3 50Gy) vs (Napier -2 20Gy, Napier-3 control, Napier-3 20Gy) etc. The UPGMA displayed five major clusters including sub-clusters. Cluster 5 included the highest number of genotypes (21) and cluster 3 included the lowest number of genotypes (2). The results may be useful for future breeding program for Napier fodder development. [ABSTRACT FROM AUTHOR]

Eleusine coracana (L.) Gaertn., commonly known as finger millet, is a multipurpose crop used for food and feed. Genomic tools are required for the characterization of crop gene pools and their genomics-led breeding. High-throughput sequencing-based characterization of finger millet germplasm representing diverse agro-ecologies was considered an effective method for determining its genetic diversity, thereby suggesting potential candidates for breeding. In this study, the genotyping-by-sequencing (GBS) method was used to simultaneously identify novel single nucleotide polymorphism (SNP) markers and genotype 288 finger millet accessions collected from Ethiopia and Zimbabwe. The accessions were characterized at individual and group levels using 5,226 bi-allelic SNPs, with a minimum allele frequency (MAF) of above 0.05, distributed across 2,500 scaffolds of the finger millet reference genome. The polymorphism information content (PIC) of the SNPs was 0.23 on average, and a quarter of them have PIC values over 0.32, making them highly informative. The grouping of the 288 accessions into seven populations based on geographic proximity and the potential for germplasm exchange revealed a narrow range of observed heterozygosity (Ho; 0.09–0.11) and expected heterozygosity (He) that ranged over twofold, from 0.11 to 0.26. Alleles unique to the different groups were also identified, which merit further investigation for their potential association with desirable traits. The analysis of molecular variance (AMOVA) revealed a highly significant genetic differentiation among groups of accessions classified based on the geographic region, country of origin, days to flowering, panicle type, and Al tolerance (p < 0.01). The high genetic differentiation between Ethiopian and Zimbabwean accessions was evident in the AMOVA, cluster, principal coordinate, and population structure analyses. The level of genetic diversity of finger millet accessions varies moderately among locations within Ethiopia, with accessions from the northern region having the lowest level. In the neighbor-joining cluster analysis, most of the improved cultivars included in this study were closely clustered, probably because they were developed using genetically less diverse germplasm and/or selected for similar traits, such as grain yield. The recombination of alleles via crossbreeding genetically distinct accessions from different regions of the two countries can potentially lead to the development of superior cultivars. [ABSTRACT FROM AUTHOR]

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Grass pea (Lathyrus sativus L.) is a legume crop known to be an excellent source of protein, tolerant to drought, waterlogging, and salinity. The crop is used as an alternative source of protein to reduce malnutrition for resource-poor people and farmers leaving in marginal areas. However, due to the presence of a neurotoxin that causes lathyrism in the crop, it has been neglected and underutilized. As a necessary first step towards, therefore, this investigation was undertaken to assess the genetic diversity and population structure that existed within grass pea accessions collected from North-West Ethiopia using simple sequence repeat markers. Twenty-five grass pea accessions collected from the Ethiopian Biodiversity Institute were planted at the College of Agricultural Science, Ebonyi State University, Nigeria. The genomic DNA was extracted using Quick-DNA™ ZR Plant/Seed Miniprep Kit and amplified in an ABI Veriti PCR machine with 10 pairs of SSR markers in IITA, Ibadan, Nigeria. Out of 10 SSR primers, only eight primers were polymorphic. A total of 41 alleles were detected with an average of 5.13. The Polymorphism Information Content and Gene Diversity values ranged from 0.074 to 0.944 with a mean of 0.474 and 0.536 respectively. The largest pairwise genetic distance (0.365) was detected between North Gondar and East Gojjam populations. The ФPT (analog of FST test) estimated through AMOVA were 0.24, 0.20, and 0.05 for within accessions, among regions, and population within regions respectively. The highest genetic differentiation value (76%) resides within accessions followed by 20% among regions. Both the population structure and cluster analyses grouped the 25 grass pea accessions into two distinct subgroups. This grouping pattern indicates the presence of gene flow among geographic regions. In general, the findings of this study indicate that despite few numbers of SSR markers it was possible to detect genetic diversity among grass pea accessions indicating the power of the SSR marker in picking up the existing genetic diversity within the studied accessions. [ABSTRACT FROM AUTHOR]

Forty five natural populations of Drosophila ananassae, collected from entire geo-climatic regions of the India were analyzed to determine the distribution of genetic diversity relative to different eco-geographic factors. Quantitative data on the frequencies of three cosmopolitan inversions in the sampled populations were utilized to deduce Nei’s gene diversity estimates. Populations were grouped according to the time of collection (years and month); collection-regions like coastal and mainland regions, and collection-seasons. Further, data was subjected to network analysis to detect community structure in the populations and Modularity analysis to quantify the strength in community structure. Gene-diversity statistics revealed the presence of significant variability in the Indian natural populations of D.ananassae. Off all the parameters used to group the populations, geographical attributes seems to have maximum, while the time of collection and seasons have minimum influence on the genetic variability in Indian natural populations of D.ananassae. The results clearly link the association of genetic variability with environmental heterogeneity, elucidating the role of environment specific natural selection. The homogenizing effects could be due to genetic hitchhiking and canalization.

Eleusine coracana (L.) Gaertn., commonly known as finger millet, is a multipurpose crop used for food and feed. Genomic tools are required for the characterization of crop gene pools and their genomics-led breeding. High-throughput sequencing-based characterization of finger millet germplasm representing diverse agro-ecologies was considered an effective method for determining its genetic diversity, thereby suggesting potential candidates for breeding. In this study, the genotyping-by-sequencing (GBS) method was used to simultaneously identify novel single nucleotide polymorphism (SNP) markers and genotype 288 finger millet accessions collected from Ethiopia and Zimbabwe. The accessions were characterized at individual and group levels using 5,226 bi-allelic SNPs, with a minimum allele frequency (MAF) of above 0.05, distributed across 2,500 scaffolds of the finger millet reference genome. The polymorphism information content (PIC) of the SNPs was 0.23 on average, and a quarter of them have PIC values over 0.32, making them highly informative. The grouping of the 288 accessions into seven populations based on geographic proximity and the potential for germplasm exchange revealed a narrow range of observed heterozygosity (Ho; 0.09–0.11) and expected heterozygosity (He) that ranged over twofold, from 0.11 to 0.26. Alleles unique to the different groups were also identified, which merit further investigation for their potential association with desirable traits. The analysis of molecular variance (AMOVA) revealed a highly significant genetic differentiation among groups of accessions classified based on the geographic region, country of origin, days to flowering, panicle type, and Al tolerance (p < 0.01). The high genetic differentiation between Ethiopian and Zimbabwean accessions was evident in the AMOVA, cluster, principal coordinate, and population structure analyses. The level of genetic diversity of finger millet accessions varies moderately among locations within Ethiopia, with accessions from the northern region having the lowest level. In the neighbor-joining cluster analysis, most of the improved cultivars included in this study were closely clustered, probably because they were developed using genetically less diverse germplasm and/or selected for similar traits, such as grain yield. The recombination of alleles via crossbreeding genetically distinct accessions from different regions of the two countries can potentially lead to the development of superior cultivars.

Research of the population structure and genetic diversity has guiding significance to soybean improvement. In this study, 105 cultivar soybean accessions bred from Huang-Huai-Hai and Southern region of China were collected to detect their population structure and genetic diversity by using 99 SSR polymorphic primer pairs. The results showed that a total of 1142 alleles were detected at 99 loci with 11.54 average number of alleles per locus ranging from 5 to 24. The whole population was divided into 4 subgroups according to breeding period. The range of Nei's gene diversity was 0.628-0.839 with an average of 0.774. The polymorphism information content ranged from 0.562-0.820 with an average of 0.742. The genetic distance between subgroups ranged from 0.387 to 0.197 with an average of 0.297. Ninety-nine percentage of total variation was explained within the subgroups, and 1% of total variation was explained among subgroups based on the molecular variation analysis, which indicated that there were frequent gene exchanges in subgroups. The principal coordinate analysis showed that the first, second, and third principal factors explained 4.12%, 3.61%, and 2.90% of the total variation respectively. These soybean germplasm could be divided into 3 subgroups based on STRUCTURE analysis and unweighted pair group method with arithmetic average (UPGMA) cluster. Further comparison showed that the UPGMA subgroups and STRUCTURE subgroups displayed a highly consistent correlation with these pedigrees and the genetic base of each period. The genetic diversity had period characteristics and showed an increasing trend in this study. [ABSTRACT FROM AUTHOR]

Background: Mung bean is a pulse crop principally grown in the tropic and subtropic parts of the world for its nutrient-rich seeds. Seven mung beans accessions from Eastern Kenya were evaluated using thirteen phenotypic traits. In addition, 10 SSR markers were used to determine their genetic diversity and population structure. This aimed at enhancing germplasm utilization for subsequent mung bean breeding programs. Results: Analysis of variance for most of the phenology traits showed significant variation, with the yield traits recording the highest. The first three principal components (PC) explained 83.4% of the overall phenotypic variation, with the highest (PC1) being due to variation of majority of the traits studied such as pod length, plant height, and seeds per pod. The dendogram revealed that the improved genotypes had common ancestry with the local landraces. The seven mung beans were also genotyped using 10 microsatellite markers, eight of which showed clear and consistent amplification profiles with scorable polymorphisms in all the studied genotypes. Genetic diversity, allele number, and polymorphic information content (PIC) were determined using powermarker (version 3.25) and phylogenetic tree constructed using DARWIN version 6.0.12. Analysis of molecular variance (AMOVA) was calculated using GenALEx version 6.5. A total of 23 alleles were detected from the seven genotypes on all the chromosomes studied with an average of 2.875 across the loci. The PIC values ranged from 0.1224 (CEDG056) to 0.5918 (CEDG092) with a mean of 0.3724. Among the markers, CEDG092 was highly informative while the rest were reasonably informative except CEDG056, which was less informative. Gene diversity ranged from 0.1836 (CEDG050) to 0.5102 (CDED088) with an average of 0.3534. The Jaccards dissimilarity matrix indicated that genotypes VC614850 and N26 had the highest level of dissimilarity while VC637245 and N26 had lowest dissimilarity index. The phylogenetic tree grouped the genotypes into three clusters as revealed by population structure analysis (K = 3), with cluster III having one unique genotype (VC6137B) only. AMOVA indicated that the highest variation (99%) was between individual genotype. In addition, marker traits association analysis revealed 18 significant associations (P < 0.05). Conclusion: These findings indicate sufficient variation among the studied genotypes that can be considered for germplasm breeding programs. [ABSTRACT FROM AUTHOR]