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The complete chloroplast genome of a Chinese endemic species Hemiboea subacaulis var. jiangxiensis was reported and characterized. The length of chloroplast genome is 153,311 bp, with 37.6% GC content. It has a typical quadripartite structure, including a large single-copy region (LSC, 84,287 bp), a small single-copy region (SSC, 18,094 bp) and a pair of inverted repeats (IRs, 25,465 bp). Totally, 133 unique genes were predicted, including 88 protein-coding genes, 37 tRNA genes and eight rRNA genes. Phylogenetic analysis and genetic distance revealed this species is sister to its typic H. subacaulis var. subacaulis. This study offers novel genetic data for the molecular identification and phylogenetic analysis of the Hemiboea.

Acanthocephalans in the polymorphid genus Bolbosoma Porta, 1908 utilize marine mammals and seabirds as the definitive host, and marine fish as the paratenic host. As in many other groups of acanthocephalans, morphology-based species identification at the cystacanth stage of Bolbosoma is challenging; at present, DNA barcoding is the most reliable approach for larval identification. However, sequence data currently available for Bolbosoma are scarce. In this study, we report the morphology and DNA sequence information (cytochrome c oxidase subunit I and 18S rRNA genes) of Bolbosoma cystacanths from six marine fish species collected in Japan.

Combining ability and heterosis were estimated in 45 rice hybrids generated by mating 10 parents, comprising both land races and advance breeding lines, in half diallel fashion. Hayman’s graphical analysis showed that all the twelve morphological traits studied had significant positive dominance variance. Narrow sense heritability was high for Days to fifty percentage flowering, Plant height, Panicle length and Test weight (> 30 %), and low for Grain yield per plant. According to the VrWr graph, traits like GYPP, PL, PH, TN and plot yield showed partial dominance, whereas traits like Blast disease index showed overdominance. A significant improvement over check was observed for heterosis and the crosses Mynri x CAUS103, Joha x CAUS107, CAUS 126 x CAUS107 and CAUS103 x CP, exhibited significantly positive standard heterosis for GYPP (>80 %) and PY (>100 %). Genetic distance based on fourteen markers revealed significant positive association with mid parent and better parent heterosis for Spikelet’s per plant, Filled grains per plant, Harvest index, Grain yield per plant, Panicle number and Plot yield. Therefore, it is evident that crosses with larger genetic distance between the parents gave hybrids with higher heterosis.

The objective of this research was to describe the variation in breeding practices in the population of Arabian horses in Algeria in relation to the population size drop observed in the 2000s, due to an increase in the cost of food and a change in interest in racing, related to the black decade. As a result, the breeders had to face two opposite constraints: enhancing reproduction to counter the population decline and preventing the loss of genetic diversity. The aim of the study was to evaluate the genetic consequences of the decisions taken over a period of 30 years, starting from 1988 to 2018. The study was based on the analyses of the stud-book and on 11 microsatellite markers in a group of 943 horses, distributed into 13 age classes. Between 2004 and 2008, the breeders purchased foreign sires and dams, allowing a relative stability in unbiased heterozygosity of about 71%, due to the high genetic distances between foreign and local horses. As these importations stopped from 2009 on, there was a decrease in allele numbers of about 20%. Moreover, from 2010 on, we observe an excess of inbreeding and an increase in genetic drift relative to the starting population, due to population size decline. From the analysis of genetic distances between local individuals, it seems that the only constraint for sires and dams allowed to mate was a null coefficient of inbreeding.

Abstract Background Maternal genetic risk of type 2 diabetes (T2D) has been associated with fetal growth, but the influence of genetic ancestry is not yet fully understood. We aimed to investigate the influence of genetic distance (GD) and genetic ancestry proportion (GAP) on the association of maternal genetic risk score of T2D (GRST2D) with fetal weight and birthweight. Methods Multi-ancestral pregnant women (n = 1,837) from the NICHD Fetal Growth Studies – Singletons cohort were included in the current analyses. Fetal weight (in grams, g) was estimated from ultrasound measurements of fetal biometry, and birthweight (g) was measured at delivery. GRS T2D was calculated using T2D-associated variants identified in the latest trans-ancestral genome-wide association study and was categorized into quartiles. GD and GAP were estimated using genotype data of four reference populations. GD was categorized into closest, middle, and farthest tertiles, and GAP was categorized as highest, medium, and lowest. Linear regression analyses were performed to test the association of GRST2D with fetal weight and birthweight, adjusted for covariates, in each GD and GAP category. Results Among women with the closest GD from African and Amerindigenous ancestries, the fourth and third GRS T2D quartile was significantly associated with 5.18 to 7.48 g (weeks 17–20) and 6.83 to 25.44 g (weeks 19–27) larger fetal weight compared to the first quartile, respectively. Among women with middle GD from European ancestry, the fourth GRS T2D quartile was significantly associated with 5.73 to 21.21 g (weeks 18–26) larger fetal weight. Furthermore, among women with middle GD from European and African ancestries, the fourth and second GRS T2D quartiles were significantly associated with 117.04 g (95% CI = 23.88–210.20, p = 0.014) and 95.05 g (95% CI = 4.73–185.36, p = 0.039) larger birthweight compared to the first quartile, respectively. The absence of significant association among women with the closest GD from East Asian ancestry was complemented by a positive significant association among women with the highest East Asian GAP. Conclusions The association between maternal GRS T2D and fetal growth began in early-second trimester and was influenced by GD and GAP. The results suggest the use of genetic GD and GAP could improve the generalizability of GRS.

Abstract Background Although RNA-seq data are traditionally used for quantifying gene expression levels, the same data could be useful in an integrated approach to compute genetic distances as well. Challenges to using mRNA sequences for computing genetic distances include the relatively high conservation of coding sequences and the presence of paralogous and, in some species, homeologous genes. Results We developed a new computational method, RNA-clique, for calculating genetic distances using assembled RNA-seq data and assessed the efficacy of the method using biological and simulated data. The method employs reciprocal BLASTn followed by graph-based filtering to ensure that only orthologous genes are compared. Each vertex in the graph constructed for filtering represents a gene in a specific sample under comparison, and an edge connects a pair of vertices if the genes they represent are best matches for each other in their respective samples. The distance computation is a function of the BLAST alignment statistics and the constructed graph and incorporates only those genes that are present in some complete connected component of this graph. As a biological testbed we used RNA-seq data of tall fescue (Lolium arundinaceum), an allohexaploid plant ( $$2n = 14\text { Gb}$$ 2 n = 14 Gb ), and bluehead wrasse (Thalassoma bifasciatum), a teleost fish. RNA-clique reliably distinguished individual tall fescue plants by genotype and distinguished bluehead wrasse RNA-seq samples by individual. In tests with simulated RNA-seq data, the ground truth phylogeny was accurately recovered from the computed distances. Moreover, tests of the algorithm parameters indicated that, even with stringent filtering for orthologs, sufficient sequence data were retained for the distance computations. Although comparisons with an alternative method revealed that RNA-clique has relatively high time and memory requirements, the comparisons also showed that RNA-clique’s results were at least as reliable as the alternative’s for tall fescue data and were much more reliable for the bluehead wrasse data. Conclusion Results of this work indicate that RNA-clique works well as a way of deriving genetic distances from RNA-seq data, thus providing a methodological integration of functional and genetic diversity studies.

ABSTRACT: This study focuses on estimation of the inter and intra population genetic variability of 6 duck populations. Microsatellite loci were used to assess the genetic variation and population structure of 6 duck populations under a conservation program in Poland. DNA polymorphism was assessed using 24 microsatellite markers and 50 individuals from each population. Polymorphism information content (PIC), heterozygosity with 2 estimators of genetic differentiation (FST and GST), and Nei's standard genetic distance were calculated. The results showed that these 6 endangered duck populations showed high genetic polymorphism. Observed heterozygosity within populations ranged from 0.14 to 0.83, with the average value of 0.58. PIC within populations ranged from 0.038 (P-8 and P-9 lines) to 0.89 (LsA line). Average number of alleles in the studied populations ranged from 4.5 (KhO-1 line) to 7.3 (LsA line). Based on the results, the pairs of lines LsA: P-33 and P-8: P-9 were found to be the most related; and the most genetically distant group was KhO-1 line, which originated as a cross between Khaki Campbell with Orpington duck.

Rhadinorhynchus Lühe, 1911 consists of acanthocephalans parasitizing migratory fishes. Of about 50 congeners currently assigned in this genus, 10 named and six unidentified species have previously been studied in molecular phylogenetic works; the intrageneric phylogeny and molecular diversity are thus still incompletely understood. In this study, we examined the phylogenetic positions of the two species R. seriolae (Yamaguti, 1963) and R. laterospinosus Amin, Heckmann, and Ha, 2011 based on the cytochrome c oxidase subunit I and 18S rRNA genes determined from material found in the intestines of the Pacific bluefin tuna Thunnus orientalis (Temminck and Schlegel, 1844) (new host) and the frigate tuna Auxis thazard (Lacepède, 1800), respectively. This is the first record of R. laterospinosus from Japan.

ABSTRACT Kale is one of the most widely cultivated leafy vegetables in Brazil, but its breeding genetic is still limited. Therefore, it is crucial to develop research that explores the genetic diversity of the available germplasms, aiming to establish promising crosses in the studied populations. The present study aimed to evaluate the genetic divergence between half-sibling progenies of kale, obtained through recurrent selection, using multivariate methods to select the most promising progenies for forming a recombinant population. The plants obtained from the seeds of 25 pre-selected half-sibling progenies and three commercial cultivars were evaluated as treatment groups. These seeds were produced in 2018 by subjecting the clones of the progenies to recombination, followed by the selection of appropriate seeds from plants with superior agronomic performance. In the present study, plants in each plot were evaluated for twelve quantitative and fifteen qualitative traits. Genetic divergence was studied based on canonical variables to obtain quantitative data. The UPGMA method was applied to the quantitative, qualitative, and combined data, and Mahalanobis genetic distance was adopted. The first three canonical variables explained 73.75% of the total cumulative variation compared to the commercial cultivars and 55.29% when considering the half-sibling progenies exclusively. The half-sibling progenies P1, P2, P3, P4, P5, P9, P11, P15, P16, P18, P20, P22, P23, P24, and P25 were the most divergent and should, therefore, be prioritized when composing the recombinant population for the third cycle of recurrent selection because, in addition to genetic variation, these progenies also present characteristics of interest to the kale genetic breeding program. The commercial cultivars exhibited the most divergent genotypes and should, therefore, be included in the next recombination cycle.

Mitochondrial genomes serve as valuable markers for phylogenetic and evolutionary studies across diverse invertebrate taxa, but their application within Annelida remains limited. In this study, we report the mitochondrial genomes of seven species from four genera of Chaetopteridae (Annelida), obtained by high-throughput sequencing. Phylogenetic analysis was performed using cox1, 18S, 28S and all mitochondrial genes. Our results reveal Chaetopterus and Mesochaetopterus as well-supported monophyletic sister clades, while Phyllochaetopterus and Spiochaetopterus appear paraphyletic, with species from both genera in a mixed clade sister to Chaetopterus + Mesochaetopterus. While mitochondrial gene orders remain conserved within Chaetopteridae, they appear substantially different from those of the ancestral patterns in Annelida. All 13 protein-coding genes found in Chaetopteridae evolved under strong purification selection, although Phyllochaetopterus exhibited the highest base-substitution rate for most of them, suggesting a more relaxed purified selection. Overall, our study provides molecular resources for phylogenetic studies of Chaetopteridae, highlighting the necessity for a comprehensive revision of the family, particularly dealing with the paraphyletic Phyllochaetopterus and Spiochaetopterus.

Understanding the combining ability effects, heterosis, and genetic relationships between parental lines would be helpful in the maize breeding program to develop high-yielding and genetically stable maize varieties for various contrasting environments. Hence, the objective of this study was to estimate combining ability effects, heterosis, genetic distance (GD) and associations for grain yield and other agronomic traits. Forty-five F1 diallel crosses, four commercial checks, and ten inbred lines were evaluated at Bako and Jima Agricultural Research Centers, Ethiopia. Significant differences were observed among environments, genotypes and genotype by environment interaction for grain yield and almost all studied agronomic traits. Combining ability analysis showed both additive and non-additive gene effects significantly controlled grain yield and all other studied traits. The preponderance of general combining ability (GCA) effects indicates the importance of additive gene action inheriting most agronomic traits. Lines L2, L7, and L9 were the best combiners for grain yield, whereas lines L3 and L4 had desirable GCA values to improve days to flowering and plant height. Among the top ten crosses, L6 × L9, L6 × L7 and L4 × L9 were good specific combiners and had 18.8 %, 17.2 % and 16.2 % grain yield advantage over the best check, BH546. These hybrids also had high mid and better-parent heterosis compared with other crosses. The associations of GD with mean of F1 and SCA effects were positive and highly significant for grain yield and some other traits. In contrast, correlations of GD with mid and better parent heterosis were non-significant for grain yield and most other traits. The results of this study are particularly useful for breeders who envisage combining conventional and molecular methods.

The poultry red mite, Dermanyssus gallinae (De Geer, 1778), is widely regarded as the significant ectoparasite of egg-laying hens worldwide. Since many molecular studies on poultry red mites have focused on analyzing COI and ITS1-2 genes, the present study aimed to identify 16S rDNA and the relatively understudied nuclear 18S rDNA genes of Turkish D. gallinae populations. Twenty-eight different D. gallinae populations were collected from henhouses throughout Türkiye, and the target genes were amplified using conventional PCR after morphological analysis. Haplotype analyses of the 16S rDNA sequences revealed 14 different haplotypes, with Turkish D. gallinae grouped into two of these haplotypes. The intra-species genetic variation of the 18S rDNA and 16S rDNA sequences examined in the present study and the available sequences in public GeneBank were determined as 0.17% and 0.53%, respectively. The obtained sequences belonging to D. gallinae from Türkiye were submitted to GenBank for the first time. Given the importance of identifying genetic diversity within and between species across different geographical regions, the obtained data may contribute substantially to the genetic knowledge of the PRMs.

IntroductionHIV molecular network based on genetic distance (GD) has been extensively utilized. However, the GD threshold for the non-B subtype differs from that of subtype B. This study aimed to optimize the GD threshold for inferring the CRF01_AE molecular network.MethodsNext-generation sequencing data of partial CRF01_AE pol sequences were obtained for 59 samples from 12 transmission pairs enrolled from a high-risk cohort during 2009 and 2014. The paired GD was calculated using the Tamura-Nei 93 model to infer a GD threshold range for HIV molecular networks.Results2,019 CRF01_AE pol sequences and information on recent HIV infection (RHI) from newly diagnosed individuals in Shenyang from 2016 to 2019 were collected to construct molecular networks to assess the ability of the inferred GD thresholds to predict recent transmission events. When HIV transmission occurs within a span of 1-4 years, the mean paired GD between the sequences of the donor and recipient within the same transmission pair were as follow: 0.008, 0.011, 0.013, and 0.023 substitutions/site. Using these four GD thresholds, it was found that 98.9%, 96.0%, 88.2%, and 40.4% of all randomly paired GD values from 12 transmission pairs were correctly identified as originating from the same transmission pairs. In the real world, as the GD threshold increased from 0.001 to 0.02 substitutions/site, the proportion of RHI within the molecular network gradually increased from 16.6% to 92.3%. Meanwhile, the proportion of links with RHI gradually decreased from 87.0% to 48.2%. The two curves intersected at a GD of 0.008 substitutions/site.DiscussionA suitable range of GD thresholds, 0.008-0.013 substitutions/site, was identified to infer the CRF01_AE molecular transmission network and identify HIV transmission events that occurred within the past three years. This finding provides valuable data for selecting an appropriate GD thresholds in constructing molecular networks for non-B subtypes.

ABSTRACT The objective of this study was to estimate the genetic parameters and predict selection of genetic gains and genetic diversity of 12 Andropogon lateralis ecotypes collected in the State of Rio Grande do Sul, Brazil. To estimate genetic parameters and predict selection gains, the REML/BLUP technique was applied. Genetic diversity among the ecotypes was evaluated by two clustering methods (optimization and hierarchical) and principal component (PC) analysis, the latter method also used to discard variables. The genetic parameters studied showed high potential for selection of important agronomic forage traits for livestock production. Results showed that the 12 A. lateralis Nees ecotypes exhibited high genetic variability for the studied forage characters and indicated parental prosperity for crosses within the genetic breeding program. Principal component analysis showed that number of total vegetative tillers, leaf:stem ratio, number of reproductive tillers, and leaf dry matter yield accounted for 80.6% of the observed variation in PC1. These variables are important characteristics for quantifying the dry matter production and nutritional value of forage plants, and they can help to discriminate amongst ecotypes. Ecotypes sourced from the Pelotas, Piratini, Passo Fundo, Bagé, and Montenegro regions showed superior forage production when evaluated by the BLUP methodology. Therefore, this group was identified as the most suitable for selection and crossing purposes. Tocher’s cluster analysis grouped the ecotypes into five divergent groups. Principal component and UPGMA hierarchical methods were also efficient at separating the ecotypes.

Extended Abstract Introduction and Objective: The study of genetic diversity with the help of molecular markers is the main precondition and an important step in the improvement of vegetable plants, including tomato and is the basis for the effective use of heterosis and the protection of genetic pools. Several studies have been conducted using molecular markers between different tomato lines, but there is little studies in Iran. Based on this, the present study intends to estimate the genetic distance between a numbers of tomato lines using ISSR molecular markers. Materials and Methods: In the present study, 12 tomato lines were investigated using microsatellite primers (ISSR) at Sari University of Agricultural Sciences and Natural Resources. Polymerase chain reaction (PCR) was performed by ISSR primers and PCR products fractioned on 1.5% using agarose gel electrophoresis then the bands were analysed. Results: The primers used showed acceptable polymorphism (85.28) and suitable score able banding patterns. The highest and lowest polymorphism information content (PIC) with values of 0.40 and 0.22 were related to ISSR2 and ISSR10 primers, respectively. The ISSR2 primer was more efficient than other primers in identifying and classifying the studied lines. The degree of genetic similarity varied from 0.23 to 0.95 between the studied lines and lines Fanal and Harlekyn had the most similarity and lines CP with Bibor and after that SP with Bibor showed greatest genetic distances. Results of cluster analysis and evaluation of quantitative characterestics of studied lines showed that genotypes 4, 5, 6 and 8 placed in first group had better yield and earliness comparing other genotypes. Conclusion: Lines CP, SP and Bibor had a great genetic distance from each other and hybridization between CP and SP with Bibor as well as utilizing of selected genotypes in first group is recommended for next breeding programs in tomato. The ISSR2 primer has useful information in distinguishing the studied lines than other primers and its useful in breeding programs of tomato.

Objective To carry out a comprehensive production planning of the existing Rongchang pig population from both environmental and genetic aspects, and to establish a closed population with stable genetic diversity and strict pathogen control, it is necessary to fully understand the genetic background of the population. Methods We genotyped 54 specific pathogen free (SPF) Rongchang pigs using the Zhongxin-1 Porcine Breeding Array PLUS, calculated their genetic diversity parameters and constructed their families. In addition, we also counted the runs of homozygosity (ROH) of each individual and calculated the value of inbreeding coefficient based on ROH for each individual. Results Firstly, the results of genetic diversity analysis showed that the effective population size (Ne) of this population was 3.2, proportion of polymorphic markers (PN) was 0.515, desired heterozygosity (He) and observed heterozygosity (Ho) were 0.315 and 0.335. Ho was higher than He, indicating that the heterozygosity of all the selected loci was high. Secondly, combining the results of genomic relatedness analysis and cluster analysis, it was found that the existing Rongchang pig population could be divided into four families. Finally, we also counted the ROH of each individual and calculated the inbreeding coefficient value accordingly, whose mean value was 0.09. Conclusion Due to the limitation of population size and other factors, the genetic diversity of this Rongchang pig population is low. The results of this study can provide basic data to support the development of Rongchang pig breeding program, the establishment of SPF Rongchang pig closed herd and its experimental utilization.

Abstract Background Y-STR polymorphisms are useful in tracing genealogy and understanding human origins and migration history. This study aimed to fill a knowledge gap in the genetic diversity, structure, and haplogroup distribution of the Han and Manchu populations from the three northeastern provinces in China (Liaoning, Jilin, and Heilongjiang). Methods A total of 1,048 blood samples were collected from unrelated males residing in Dalian. Genotyping was performed using the AGCU Y37 + 5 Amplification Kit, and the genotype data were analyzed to determine allele and haplotype frequencies, genetic and haplotype diversity, discrimination capacity, and haplotype match probability. Population pairwise genetic distances (F st ) were calculated to compare the genetic relationships among Han and Manchu populations from Northeast China and other 23 populations using 27 Yfiler Plus loci set. Multi-dimensional scaling and phylogenetic analysis were employed to visualize the genetic relationships among the 27 populations. Moreover, haplogroups were predicted based on 27 Yfiler Plus loci set. Results The Han populations from Northeast China exhibited genetic affinities with both Han populations from the Central Plain and the Sichuan Qiang population, despite considerable geographical distances. Conversely, the Manchu population displayed a relatively large genetic distance from other populations. The haplogroup analysis revealed the prevalence of haplogroups E1b1b, O1b, O2, and Q in the studied populations, with variations observed among different ethnic groups. Conclusion The study contributes to our understanding of genetic diversity and history of the Han and Manchu populations in Northeast China, the genetic relationships between populations, and the intricate processes of migration, intermarriage, and cultural integration that have shaped the region’s genetic landscape.

The objective of the present study was to analyze the genetic diversity, individual-based assessment of population structure, and admixture in the Dülmen wild horse population in comparison to warmblood, coldblood, and primitive horse populations. The Dülmen wild horse is kept as a unique horse population in the Merfelder Bruch near Dülmen in Westphalia, Germany, and since 1856 has been managed by the Dukes of Croÿ. The Dülmen wild horse population is exposed to the natural conditions of the Merfelder Bruch all year round without human interventions for feeding and veterinary care. In the present study, genetic diversity was estimated for 101 Dülmen wild horses using multilocus genotypic information from a set of 29 autosomal microsatellites and compared with 587 horses from 17 different horse populations. Dülmen wild horses maintained a high degree of genetic diversity, with an average observed heterozygosity of 0.68, a mean number of 6.17 alleles, and heterozygote deficit of −0.035. Pairwise genetic distances (FST, Nei’s standard, and Cavalli-Sforza distances) were closest to German coldblood breeds, Polish Konik, and Icelandic horses and most divergent from Sorraia and Przewalski’s horses. Neighbor joining dendrogram and PCA plots showed a clear distinction of Dülmen wild horses from other populations, particularly from Przewalski horses. Posterior Bayesian analysis confirmed clear differentiation from other horse populations without an admixture pattern and a high membership index (0.92). It was possible to distinguish Dülmen wild horses from Dülmen and Polish Konik horses. In conclusion, Dülmen wild horses show a notable separation from other German horse breeds and primitive horse populations and may serve as a resource to study evolution of equine domestication.

Although a combination of immunoprophylaxis and antiviral therapy can effectively prevent mother-to-child transmission (MTCT) of hepatitis B virus (HBV), a considerable number of infants born to highly viremic mothers still develop occult HBV infection (OBI). To uncover the virological factor and risk predictor for OBI in infants, we found that the diversity and complexity of maternal HBV quasispecies in the case group were lower than those in the control group. Mutations with significant differences between the two groups were most enriched in the NTCPbd and PreC regions. Genetic distance at the amino-acid level of the PreC region, especially the combination of three amino-acid mutations in the PreC region, could strongly predict the risk of OBI in infants. HBV quasispecies in OBI infants were highly complex, and the non-synonymous substitutions were mainly found in the RT and HBsAg regions. The sK47E (rtQ55R) and sP49L mutations in OBI infants might contribute to OBI through inhibiting the production of HBV DNA and HBsAg, respectively. This study found the potential virological factors and risk predictors for OBI in infants born to highly viremic mothers, which might be helpful for controlling OBI in infants.

Human noroviruses (HuNoVs) are highly contagious pathogens responsible of norovirus-associated acute gastroenteritis (AGE). GII.4 is the prevailing HuNoV genotype worldwide. Currently there are no studies on the molecular monitoring and phylogenetic analysis of HuNoVs in the territory of the Sverdlovsk region; therefore, it is not possible to objectively assess their genetic diversity. The aim of the study is to carry out genotyping and phylogenetic analysis of HuNoVs in the Sverdlovsk region from 2022 to 2023. Fecal samples (n = 510) were collected from children suffering from HuNoV-AGE in municipalities of the Sverdlovsk region and the capsid genotype was determined by amplifying the ORF1/ORF2 junction. Of the 196 HuNoVs typed, which represent 38% of the studied samples, the largest share of HuNoV genotypes belong to the GII genogroup—86%, followed by the GI genogroup—14%. Noroviruses GII.4 and GII.17 were the co-dominant capsid genotypes (33.2% each). Phylogenetic analysis demonstrates that the identified sequences on the territory of the Sverdlovsk region have the smallest genetic distance, which gives grounds for their unification into a common cluster. Routine monitoring and phylogenetic analysis of circulating norovirus pathogens spectrum will enable timely tracking of HuNoVs genetic diversity and evolutionary events. This will lead to the development of more effective anti-epidemic measures, ultimately reducing the burden of infectious diseases.

Phalaenopsis was the genus with the highest ornamental and commercial values among orchids. Phalaenopsis with fragrance were rarely distributed in the market due to selection constraints, such as affinity, ploidy and breeding age. Therefore, research on transferring aroma traits into commercial Phalaenopsis are of great significance to the breeding of Phalaenopsis. In order to investigate the key aroma-causing components among different varieties of Phalaenopsis, the floral fragrance components of the eight new hybrid varieties in full blooming period were examined by headspace solid-phase microextraction and gas chromatography-mass spectrometry. The principal components, clustering and aroma quality analysis were performed based on the identification of floral substance components. The results were as follows: (1) 96 substances were detected in eight varieties of Phalaenopsis, mainly divided into eight categories of terpenes, aldehydes, esters, alcohols, ketones, ethers, phenols and aromatic compounds, among which terpenes were dominant in quantity and content and were the main volatile substances of Phalaenopsis. (2) Principal component analysis showed that eight varieties were divided into three quadrants, F2 had the most volatile components and the most quantity, terpenes were mainly 1,8-cineole, α-bergamotene, linalool and (+)-calarene; F1, F4, F5 and F8 were divided into a group without ketones, ethers or phenols, and they had the least volatile components and terpenes were mainly linalool; F3, F6 and F7 were divided into a group with more volatile components and the terpenes were mainly α-bergamotene. (3) The results of cluster analysis were consistent with the principal component analysis, and the eight varieties were clustered into three categories, F1, F4, F5 and F8 were more closely related to each other as floral odor types; F3, F6 and F7 were more closely related to each other as woody floral quality; F2 showed a long genetic distance from the other seven varieties, with complex floral components and relatively average contribution of volatile substances, and both woody, minty and fruity types. This study shows that floral fragrance substances can be used as potential trait markers to distinguish between groups of varieties with different fragrance characteristics and provide a theoretical basis for further development and utilization research through cross selection to achieve specific floral fragrance Phalaenopsis selection and product processing and production.

IntroductionNIR spectroscopy combined with chemometric algorithms has been widely used for seed authenticity detection. However, the study of seed genetic distance, an internal feature that affects the discriminative performance of classification models, has rarely been reported.MethodsTherefore, maize seed samples of different genotypes were selected to investigate the effect of genetic distance on the authenticity of single seeds detected by NIR spectroscopy. Firstly, the Support vector machine (SVM) model was established using spectral information combined with a preprocessing algorithm, and then the DNA of the samples was extracted to study the correlation between genetic and relative spectral distances, the model identification performance, and finally to compare the similarities and differences between the results of genetic clustering and relative spectral clustering.ResultsThe results were as follows: the average accuracy of the models was 93.6% (inbred lines) and 93.7% (hybrids), respectively; Genetic distance and correlation spectral distance exhibited positive correlation significantly (inbred lines: r=0.177, p

Species of the genus Pimelodella (Eigenmann & Eigenmann, 1988) present many similar morphological characteristics, which makes taxonomic identification difficult. Some species present morphological distinction and reproduce normally, while others present reproductive isolation without morphological distinction. Taking that into consideration, we used starch-gel electrophoresis of enzymes to compare two species of the genus Pimelodella collected in Paraná, Ivaí and Pirapó rivers of the Upper Paraná River basin. We analyzed the liver and muscle tissue of 82 Pimelodella avanhandavae and 29 Pimelodella gracilis individuals, which revealed few genetic differences between species. In addition, we carried out an experimental design based on the separation of four populations: P. avanhandavae, Parana River (n = 37); P. avanhandavae, Ivaí River (n = 6); P. gracilis, Ivaí River (n = 29); P. avanhandavae, Pirapó River (n = 39). The high proportions of polymorphic loci as well as the expected heterozygosity suggest that both species have high genetic variability. Nei’s genetic identity values and Wright's fixation indices revealed a large genetic proximity between the samples collected in Ivaí and Pirapó rivers, regardless of the species analyzed. The presence of fixed alleles at one hundred percent for two loci showed that P. avanhandavae individuals collected in the Parana River are genetically distant from all remaining populations. Data indicated that P. avanhandavae, collected in this river, constitutes a distinguished species from those collected in Ivaí and Pirapó rivers. Therefore, we suggest, that more studies with molecular markers be carried out with the genus, as well as a review of the diagnostic morphological characteristics used to separate P. avanhandavae from P. gracilis.

The taxonomic identification of mantis shrimp Lysiosquilla maculata was performed through DNA barcoding analysis of specimens collected from the Kasimedu fishing port, Chennai coast, Tamil Nadu, India. The mitochondrial cytochrome oxidase subunit I (mtCOI) gene with a region of 650 bp was sequenced for phylogenetic analysis. In the present record, mitochondrial gene sequences were used to identify the mantis shrimp. This is the first confirmed DNA barcoding record from Indian waters, whose mtCOI sequence was deposited in GenBank. The Neighbor-joining method was used for phylogenetic analysis. The calculated pairwise genetic distance with five closely related species ranged from 0.01 to 0.094%. The morphological and molecular analysis confirm that the specimens collected correspond to L. maculata.

Mitochondrial genomes are playing an increasingly important role in molluscan taxonomy, germplasm, and evolution studies. The first complete mitochondrial genome of the commercial big brown mactra clam, Mactra grandis, was characterized using Illumina next-generation sequencing in this study. The 17,289 bp circular genome has a typical gene organization of 13 protein-coding genes (PCGs), 2 rRNAs, and 22 tRNAs, with an obvious (A + T)-bias of 64.54%. All PCGs exhibited a homogeneous bias in nucleotide composition with a (A + T)-bias, a positive GC skew, and a negative AT skew. Results of phylogenetic analysis showed that Mactra grandis was most closely related to Mactra cygnus. The functional gene arrangement of the two species was identical but different from other Mactra species. The congeneric relationships among Mactra species were demonstrated by genetic distance analysis. Additionally, the selective pressure analysis suggested that cox1 was highly efficient for discriminating closely related species in genus Mactra, while nad2 was the most appropriate marker for population genetic analysis.

Abstract This study presents the first complete mitogenome of the Brazilian Atlantic bushmaster Lachesis with insights into snake evolution. The total length was 17,177 bp, consisting of 13 PCGs, 22 tRNAs, two rRNAs and a duplicate control region (CRs). Almost all genes were encoded by the heavy-strand, except for the ND6 gene and eight tRNAs (tRNA-Gln, Ala, Asn, Cys, Tyr, Ser[TGA anticodon], Glu, Pro). Only ATG, ATA, and ATC were starting codons for protein-coding sequences. Stop codons mainly were TAA, AGA, AGG, and TAG; whereas ND1, ND3, and CYTB terminated with incomplete stop codons. Phylogeny retrieved Lachesis within the Crotalinae as the sister group of Agkistrodon; and the Lachesis+Agkistrodon clade as the sister group of (Sistrurus+Crotalus)+Bothrops. The tree supports Crotalinae, Viperinae, and Azemiopinae in the Viperidae family, being sister taxa of Colubridae+(Elapidae+Psammophiidae). The mean genetic distance across 15 snake families and 57 nucleotide sequences was 0.37. The overall mean value of genetic distance across the Crotalinae was 0.23, with Lachesis muta exhibiting the shortest distance of 0.2 with Agkistrodon piscivorus, Protobothrops dabieshanensis and P. flavoviridis and the greatest 0.25 with Gloydius blomhoffii, Trimeresurus albolabris, S. miliarius, and Deinagkistrodon acutus. The complete Atlantic L. muta mitogenome presented herein is only the third annotated mitogenome from more than 430 described Brazilian snake species.

ABSTRACT Cacao fruits are agronomically important and show wide variability for several morphological descriptors. The present study aimed to characterize the genetic distance of 51 genotypes of Theobroma cacao L. in the cocoa-producing region of Southern Bahia (Brazil) based on morpho-agronomic descriptors. The inference of genetic similarity was performed from the phenotypic data derived simultaneously from qualitative and quantitative variables, using the Ward-MLM procedure (Modified Location Model) with the SAS® software. The distance matrix was obtained using the Gower logarithmic function. For this, 28 descriptors were evaluated, five qualitative and 23 quantitative. Furthermore, using the likelihood function procedure, the optimal number of groups was five indicating wide variability. Of 23 quantitative descriptors evaluated by fruits and leaves, 95% showed significant differences. The exception was seed width. Groups 1 and 5 were the most distant, while groups 2, 3, and 4 were closest to each other. The greatest difference between increments was 35.32 for the fifth group. The analysis of the first two canonical axes revealed that both represented 81.88% of the variation, with CAN1 and CAN2 responsible for 53.66% and 28.22% of the variation. The most promising genotypes for breeding programs belong to group 5 due to their superior performance for almost all characteristics analyzed.

Objective: To investigate 38 Y-chromosome short tandem repeat (Y-STR) genetic polymorphisms in Beijing Han and analyze the genetic distance with neighboring or linguistically similar populations. Materials and Methods: In the study, we selected 531 unrelated male individuals of Beijing Han, and the results were statistically analyzed by testing with GSTAR™ 41Y reagents. Results: The allele peak heights were balanced among the Y loci, the amplified fragment ranged from 100 to 500 bps. A total of 531 haplotypes were detected in 531 samples. Eight null genotypes were observed on locus DYS448. One and three double alleles were observed on single-copy locus DYS576 and DYS19, respectively. DYS385 a/b, DYF387S1 a/b, and DYS527 a/b were more common in double copies, but 3, 13, and 11 triple alleles were detected, respectively. The gene diversity values of Y-STRs except DYS391, DYS438, and DYS645 were >0.5. Twenty-seven Y-STRs of Beijing Han population were selected for genetic distance comparison with 17 populations including Changchun Han, with Rst values ranging from 0.0002 to 0.1703. Conclusion: The 38 Y-STRs in this study have strong male lineage identification ability and have great potential for individual identification, kinship identification, Y-STR database construction, and genetic relationship research.

ObjectiveTo investigate the genetic information of 57 autosomal InDel loci （A-InDels） included in AGCU InDel 60 fluorescence detection kit in the Beichuan Qiang population of Sichuan Province and evaluate its application value in forensic medicine.MethodsA total of 200 unrelated healthy individuals from Beichuan Qiang population of Sichuan Province were typing detected by AGCU InDel 60 fluorescence detection kit. Allele frequencies and population genetic parameters of the 57 A-InDels were statistically analyzed and compared with the available data of 26 populations.ResultsAfter Bonferroni correction, there was no linkage disequilibrium between the 57 A-InDels, and all loci were in Hardy-Weinberg equilibrium. Except for rs66595817 and rs72085595, the minor allele frequencies of 55 A-InDels were above 0.3. PIC ranged from 0.298 3 to 0.375 0, CDP was 1-2.974 8×10-24, CPEduo was 0.999 062 660, and CPEtrio was 0.999 999 999. The calculation of the genetic distance showed that Beichuan Qiang population had the closest genetic distances with Beijing Han and South China Han populations, but far away from African populations.ConclusionThe 57 A-InDels in AGCU InDel 60 fluorescence detection kit have a good genetic polymorphism in Beichuan Qiang population of Sichuan Province, which can be used as effective supplemental for individual identification and paternity identification in forensic medicine.

ObjectiveTo investigate the genetic polymorphism of InDel loci in SifalnDel 45plex system in the Han population in Jiangsu Province and the Mongolian population in Inner Mongolia, and to evaluate the effectiveness of the system in forensic medicine.MethodsSifaInDel 45plex system was used for genotyping in blood samples of 398 unrelated individuals from the above two populations, and allele frequencies and population genetic parameters of the two populations were calculated respectively. Eight intercontinental populations in the gnomAD database were used as reference populations. The genetic distances between the two studied populations and eight reference populations were calculated based on the allele frequencies of 27 autosomal-InDels （A-InDels）. The phylogenetic trees and multidimensional scaling （MDS） analysis diagrams were constructed accordingly.ResultsAmong two studied populations, the 27 A-InDels and 16 X-InDels showed no linkage disequilibrium between each other and the allele frequency distributions were in Hardy-Weinberg equilibrium. The CDP of the 27 A-InDels in two studied populations were all higher than 0.999 999 999 9, and the CPEtrio were all less than 0.999 9. The CDP of the 16 X-InDels in Han in Jiangsu and Mongolian in Inner Mongolia female and male samples were 0.999 997 962, 0.999 998 389, and 0.999 818 940, 0.999 856 063, respectively. The CMECtrio were all less than 0.999 9. The results of population genetics showed that the Jiangsu Han nationality, Inner Mongolia Mongolian nationality and East Asian population clustered into one branch, showing closer genetic relationship. The other 7 intercontinental populations clustered into another group. And the above 3 populations displayed distant genetic relationships with the other 7 intercontinental populations.ConclusionThe InDels in the SifaInDel 45plex system have good genetic polymorphism in the two studied populations, which can be used for forensic individual identification or as an effective complement for paternity identification, and to distinguish different intercontinental populations.

Abstract Background The family Capillariidae is a group of thread-like nematodes of 27 genera and over 300 species that infect a great variety of hosts including humans. Among these, some taxa such as the genus Aonchotheca have remained controversial regarding their systematic status for decades. The aim of the current study was to verify Aonchotheca’s systemic status and to further determine whether it is a distinct genus from Capillaria using molecular and phylogenetic analyses. Results We sequenced the mitochondrial (mt) genome and nuclear small subunit (18S) rRNA gene of Aonchotheca putorii, a representative species of the genus, and investigated its systematic status in Trichinellida using maximum likelihood and Bayesian inference. The differences in amino acid sequences of 13 protein-coding genes were 12.69–67.35% among Aonchotheca, Capillaria, Eucoleus, and Pseudocapillaria with cox1 (12.69%) and atp8 (67.35%) as the most and the least conserved gene, respectively, and the difference of two mt rRNAs was 18.61–34.15%. Phylogenetic analyses of the complete mt genome and 18S rRNAs unequivocally showed that Aonchotheca was a distinct genus from Capillaria. Conclusions Large difference exists among Aonchotheca, Capillaria, Eucoleus, and Pseudocapillarias. Aonchotheca putorii is the first species in the genus Aonchotheca for which a complete mitogenome has been sequenced. These data are useful for phylogenetics, systematics and the evolution of Capillariidae. Graphical Abstract

The Marbled Eel (Anguilla marmorata) has a widespread distribution with a complex migration life cycle There were 350 individuals of sizes from 120 to 1137 mm were analysed on characteristic morphology at 4 developing stages: juvenile, fingerling, pre-adulthood and adulthood. Morphological indicators: total length (TL), head length (HL), dorsal fin origin (PD), anal fin origin (PA), distance from dorsal to anal fin (AD), distance from pectoral fins to dorsal fin (PDH), body length (TR), eye diameter (E), tail length (T) and eye distance (IO), colour characteristics and 10 characters were standardized against the LT or LH ratios determine 95.664% of morphological differences between individuals in the study population based on principal component analysis and hierarchical cluster analysis tools. Phylogenetic tree with five morphological clusters with distance > 2.0 built a high genetic diversity. The difference of clusters is related to the morphology at different stages. Cluster 1 corresponds to the morphological characteristics at the fingerling stage (TL = 260–552.0 mm); cluster 3 is the pre-adult stage (TL = 324.6–533.9); cluster 4 is the juvenile stage (TL = 120.0–255.0); and clusters 2 and 5 for pre-adult and adult at reproductive migration (TL > 400).

IntroductionThis study explored the molecular characterization of 14 eggplant (brinjal) genotypes to evaluate their genetic diversity and the impact of heterosis. As eggplant is a vital horticultural crop with substantial economic and nutritional value, a comprehensive understanding of its genetic makeup and heterosis effects is essential for effective breeding strategies. Our aim was not only to dissect the genetic diversity among these genotypes but also to determine how genetic distance impacts heterotic patterns, which could ultimately help improve hybrid breeding programs.MethodsGenetic diversity was assessed using 20 SSR markers, and the parental lines were grouped into five clusters based on the Unweighted Pair Group Method of Arithmetic Means (UPGMA). Heterosis was examined through yield and yield-related traits among parents and hybrids.ResultsPolymorphisms were detected in eight out of the twenty SSR markers across the parental lines. Notably, a high genetic distance was observed between some parents. The analysis of yield and yield-related traits demonstrated significant heterosis over mid, superior, and standard parents, particularly in fruit yield per plant. Two crosses (RKML-26 X PPC and RKML1 X PPC) displayed substantial heterosis over mid and better parents, respectively. However, the positive correlation between genetic distance and heterosis was only up to a certain threshold; moderate genetic distance often resulted in higher heterosis compared to very high genetic distance.DiscussionThese findings emphasize the critical role of parental selection in hybrid breeding programs. The results contribute to the understanding of the relationship between genetic distance and heterosis, and it is suggested that future research should delve into the genetic mechanisms that drive heterosis and the effect of genetic distance variance on heterosis. The insights drawn from this study can be harnessed to enhance crop yield and economic value in breeding programs.

Data described in this article refer to molecular characterization and assessment of genetic diversity within a wide collection of pomegranate genotypes including both selections and cultivars from different geographical origin/disseminations by using microsatellite (SSR, Simple Sequence Repeats) markers. Supplied datasets refer to a set of 63 genotypes including 55 accessions (landraces) from Italy, Turkmenistan, Japan, and USA and 8 cultivars from Israel, established at the pomegranate repository of the Fruit Tree Unit of the Department of Soil, Plant and Food Science at University of Bari “Aldo Moro”, Italy. Pomegranate accessions differed for end-use purpose (edible, ornamental) and some morpho-pomological traits including juice taste, inner tegmen hardness, and skin/seed color. Molecular data were opportunely employed to build a similarity matrix to establish phylogenetic relationships (genetic similarity and distances) among pomegranate accessions and compare genetic clustering to morpho-pomological classification.The present data article provides detailed information and methodological protocols on SSR markers, PCR amplification and banding profiling aimed to molecular characterization of pomegranate collection. This latter was conducted by amplifying a set of informative polymorphic SSR markers on the genomic DNA of each pomegranate accession, and then comparing the different molecular profiles by capillary electrophoresis. The banding patterns obtained from microsatellite markers were used to build a binary matrix containing the scores for each individual SSR fragment, which was transformed into a similarity matrix and finally used for cluster analysis and dendrogram building based on the UPGMA algorithm. This paper supplies data potentially useful for the identification of polymorphic markers suitable for varietal identification and traceability, or discrimination between tightly related pomegranate accessions with very high morphological similarity and/or geographical identity.Data described in this paper support the published original research article titled “Exploiting DNA-based molecular tools to assess genetic diversity in pomegranate (Punica granatum L.) selections and cultivars” [1].

Subgroup K avian leukosis virus (ALV-K) is a new subgroup of avian leukosis virus (ALV) that was first defined in 2012 and has been become prevalent in Chinese native chickens in recent years. An in-depth analysis of the genetic diversity of ALV-K was performed in the study. By Blast analysis, the env gene and the sequences of the 25 ALV-K isolates we isolated were found to be closely related to the isolates from Guangdong, Hebei, Jiangsu, and Hubei provinces, China. Further eighty-nine sequences of the gp85 gene of ALV-K strains available were used in the phylogenetic and genetic distance analyses for the classification. ALV-K was divided into two second-order clades (Clades 1.1 and 1.2) and three third-order clades (Clades 1.2.1, 1.2.2, and 1.2.3), indicating that not only 1.1 and 1.2.3, the two old clades which are prevalent in Japan, but also two new clades (1.2.1, 1.2.2), are co-prevalent in China. The representative strains of each clade were defined for the first time. Notably, Clade 1.2.2 was found to have a deletion of an amino acid residue in the gp85 gene, which was obviously different from Clades 1.1, 1.2.1, and 1.2.3. The proposed classification method will facilitate future studies of ALV-K epidemiology and the comparison of sequences obtained across the world. The first global comprehensive molecular epidemiological analysis was accomplished on the emerging ALV-K.

Assessment of genetic distance between parents and selection of diverse parents are extensively used in many crops. Current study focuses the importance of genetic distance assessed through SSR markers (GDMOL) and morphological traits (GDMOR) in 28 fodder maize inbred lines and its impact on heterotic expression in resultant 195 single cross fodder maize hybrids. While comparing the mean green fodder yield in top performing hybrids synthesised with parents of higher GDMOL and GDMOR, it is understood that the genetic distance had definite impact on yielding heterotic hybrids with superior green fodder yield. It is evident from identification of a single cross UMI 1200 X GETM 25 with parents of greater GDMOL and GDMOR and a cross N 66 X DM 12-4 with parents of higher GDMOR recorded greater green fodder yield and superior standard heterosis (20.88%). The correlation studies revealed significant positive association between higher GDMOL of parents and heterotic performance of hybrids for crude protein and desirable negative association with crude fibre, ADF and NDF.

Several members of family Urticaceae are mainly found in the temperate and subtropical zones of the Northern Hemisphere and are important medicinal plants. Among them, Urtica dioica L. (Urticaceae) is an annual or perennial herb that has been used for feeding and medicinal purposes since long time and is the most exploited species of Urticaceae. Recently, it has received attention to be used as animal feed, as its fresh leaves fed to animals in moderate, dried, and other forms. This review details the advantages of U. dioica as an alternative feed in terms of germplasm specificity, nutritional composition, and feed application status. Its roots, stems, leaves, and seeds are rich in active ingredients. It has also been found to have anticancer effects through antioxidant action and promotion of apoptosis of cancer cells. In shady conditions, U. dioica is highly adaptable while under stressful conditions of drought; it also reduces light absorption and ensures carbon assimilation through light energy conversion efficiency. Therefore, it can be added to animal diets as a suitable feed to reduce costs and improve economic efficiency. This paper investigates the feasibility of using U. dioica as a feed and systematically presents the progress of research and exploitation of U. dioica.

Abstract Background The Souss, located in southern Morocco, is one of the oldest areas of human settlement in North Africa. Despite this historical relevance, the Souss has not received sufficient attention in terms of population genetic studies. Methods In this study, we utilized the AmpFlSTR Identifiler PCR amplification system to establish the allelic frequencies and statistical parameters of 15 autosomal STRs (Short Tandem Repeats) in 150 healthy unrelated Berber‐speaking individuals from the Souss. We explored the genetic relationships between Souss and other reference populations based on our dataset as well as previously published population data. Results A total of 210 alleles were detected with corresponding allele frequencies ranging from 0.003 to 0.367. The most polymorphic locus was D18S51 with 23 alleles which was also the most discriminating locus as expected. The phylogenetic analysis clustered the Souss closer to the Azrou and southern Moroccan populations. The population comparison showed affinity between the Souss and most North African populations, as well as with Middle Easterners and Europeans. Conclusion Historical events and geographical proximity have contributed to the affinity between the Souss and surrounding North African, Southern European, and Middle Eastern populations. Overall, this study highlights the reliability of the 15 STRs for identifying individuals and assessing paternity in the Souss population.

ObjectiveTo study the genetic polymorphism and population genetic parameters of 16 X-STR loci in Xinjiang Uygur population.MethodsThe Goldeneye® DNA identification system 17X was used to amplify 16 X-STR loci in 502 unrelated individuals （251 females and 251 males）. The amplified products were detected by 3130xl genetic analyzer. Allele frequencies and population genetic parameters were analyzed statistically. The genetic distances between Uygur and other 8 populations were calculated. Multidimensional scaling and phylogenetic tree were constructed based on genetic distance.ResultsIn the 16 X-STR loci, a total of 67 alleles were detected in 502 Xinjiang Uygur unrelated individuals. The allele frequencies ranged from 0.001 3 to 0.572 4. PIC ranged from 0.568 8 to 0.855 3. The cumulative discrimination power in females and males were 0.999 999 999 999 999 and 0.999 999 999 743 071, respectively. The cumulative mean paternity exclusion chance in trios and in duos were 0.999 999 997 791 859 and 0.999 998 989 000 730, respectively. The genetic distance between Uygur population and Kazakh population was closer, and the genetic distance between Uygur and Han population was farther.ConclusionThe 16 X-STR loci are highly polymorphic and suitable for identification in Uygur population, which can provide a powerful supplement for the study of individual identification, paternity identification and population genetics.

The stingless bee Melipona (Michmelia) seminigra Friese is a polytypic species widely distributed in Brazilian Amazon and Bolivia. Seven subspecies are recognized, four are described, which inhabit mutually exclusive areas in the Amazon basin, although zones of hybridization are recorded. The three other subspecies, despite being recognized by taxonomists are undescribed. Melipona seminigra is a good honey-producer and an important pollinator of native flora and crops. Partial DNA sequence of cytochrome c oxidase subunit 1 (COI) mitochondrial gene (526 bp) was used to identify the four described subspecies of M. seminigra (M. s. abunensis, M. s. merrillae, M. s. pernigra, M. s. seminigra) and two other possible subspecies (M. s. ssp1 and M. s. ssp2). We added public data (sequences of ten other Melipona species) of the same subgenera and carried out phylogenetic analyses. The aim was to evaluate if subspecies in the M. seminigra complex could be delimited using COI and measure the genetic distances between them. Our results revealed that the genetic distances between subspecies of M. seminigra ranged from 0.4 to 2.7% (average 1.80 ± 0.47) and among Melipona species from 0.2 to 2.9% (average 2.13 ± 0.5). The average haplotype diversity was 0.8770 ± 0.0140 and average nucleotide diversity 0.0166 ± 0.0004. Phylogenetic and clustering analysis revealed well delimited clusters for subspecies of M. seminigra and that the inter subspecies divergences are similar to inter species divergence. Our findings indicate that the COI gene can be used for delimiting subspecies of M. seminigra.

Abstract Background The Vietnamese Mekong Delta (VMD) is the granary for the whole country, providing animal and plant resources, especially fish. Among the fish species, the genus Glossogobius are the majority. Until now, research for this species has been solely relied on fish morphology for identification. Hence, the present study aimed to describe the morphological variations of the morphologically identified gobies and to validate them at the molecular level through the sequencing of the barcode region, the mitochondrial cytochrome C oxidase subunit I (COI) gene to preliminary provide fundamental information for conservation. Results The mitochondrial cytochrome C oxidase subunit I genes were amplified successfully with an approximate size of 650-680 bp. Their morphometries were quite different, and the genetic distance (p-value) among groups and within groups ranged from 0.00 to 0.12. The similarity of the COI gene sequences between the analyzed samples and in the NCBI database was from 87.01 to 100%. The specimens of G. aureus, G. giuris and G. sparsipapillus were interspersed in small branches of the phylogenetic tree with a low genetic distance highlighting that the genetic diversity of COI gene was low among species. Therefore, it is recommended that a combination of morphological method and mtCOI DNA barcoding is required for accurate classification. Conclusion This study helps determine three distinct lineages of Glossogobius species, so an appropriate strategy can be proposed for exploitation and conservation.

ABSTRACT This work was carried out in Antioquia, Colombia, in a collection of the Furcraea and Agave genera, important in the country for manufacturing strings, sacks, geotextiles, and handicrafts Currently, to enhance its use, applications have been developed in textiles, biodegradable materials and thermo-acoustic insulation, among others. The aim of this study was to characterize phenotypically and agronomically 94 accessions. The variables were weighted according to the degree of discrimination; a dissimilarity dendrogram was constructed using UPGMA based on Gower's distance, and the cophenetic correlation coefficient was determined. Six groups were identified; on the one hand, the accessions of the Agave genus formed groups A and B, with and without spines, respectively, showing the highest elongation values. On the other hand, the Furcraea accessions formed groups C to F, with the highest average values of fiber per plant, allowing a first approach to identify promising clones for their use per se or utilized in plant breeding programs. This study represents an approach to knowing the morphological and agronomic variability of the collection and highlights the importance of maintaining the germplasm bank for ex situ conservation.

The relationship between parental genetic differences and the quality and yield of japonica hybrid rice strongly influences japonica hybrid rice breeding. In this study, 137 parental lines of japonica hybrid rice were genotyped using 8K rice SNP-Chips to characterize their genetic diversity, population structure, and indica-genotype proportion. The genetic diversity of total parental lines averaged 0.264, with values of 0.287 for restorer lines and 0.148 for the sterile lines. The introduction of indica lineage increased the genetic diversity of restorer lines relative to that of sterile lines. By model-based population structure analysis, the 137 lines were divided into 14 groups. According to the grouping results, eight restorer lines and five sterile lines were selected from different groups for cross breeding, yielding 40 japonica hybrid rice combinations (F1). Investigation of the yield and quality of these combinations showed that high-yield combinations could be obtained by increasing parental genetic distance to 0.8–0.9, a result accomplished largely by the introduction of indica genomic components of restorer lines. To further improve grain quality, the genetic distance between parents should be reduced to 0.4–0.5, suggesting an indica-genotype proportion of 30%–40% for restorer lines. This study may provide a reference for breeding of japonica hybrid rice.

The Glossogobius species play an essential role in food supply and are distributed widely from the marine to freshwater, especially in the Mekong Delta, Vietnam (VMD). Some of their morphometrics and meristics are observed to vary with species and sampling sites. Therefore, the present study aims to verify if their mitochondrial Cytochrome b (Cytb) gene, one of the popular gene sequences used in fish phylogenic variation assessment, varies with species and sampling sites in the VMD. The Cytb gene size was 1300 bp for GcytbH/GcytbL primer pair and 1045 bp for GluMuq1-F/Mixcyto937-2R. The genetic distances within and among these three fish species groups were 0–11%. The Cytb gene sequences’ similarity between this study and the NCBI database was 85.84–100%. The Glossogobius specimens were observed to disperse in small branches of the phylogenetic tree with a low K2P value, suggesting that the Cytb genetic diversity may be low among species.

Abstract Background Freshwater planarians of the genus Dugesia (Platyhelminthes, Tricladida, Dugesiidae) are distributed in a major part of the Old World and Australia, although until recently only very few species were known from China. Results Two new species of Dugesia from Southern China are described on the basis of an integrative taxonomic approach. BI and ML phylogenetic trees based on the independent genes and on the concatenated dataset had similar topologies, only differing in some nodes that were weakly supported. Phylogenetic trees based on the concatenated dataset revealed that D. adunca Chen & Sluys, sp. nov. and D. tumida Chen & Sluys, sp. nov. are not closely related and belong to different clades. The two new species occupy separate long branches with high support values and, thus, are well-differentiated from their congeners. Separate species status of D. adunca and D. tumida is supported also by the genetic distances between the species included in our analysis, albeit that COI distances varied greatly among species. Dugesia adunca from Guangxi Province is characterized by the following features: living mature animals rather small; asymmetrical openings of the oviducts into the bursal canal; penis papilla with shape of an aquiline bill, albeit with a blunt tip; asymmetrical penis papilla, with a large antero-dorsal lip and a much smaller ventro-posterior lip; very large seminal vesicle, provided with trabeculae; small diaphragm; mixoploid karyotype with diploid complements of 2n = 2x = 16 and triploid complements of 2n = 3x = 24, with all chromosomes being metacentric. Dugesia tumida from Guangdong Province is characterized by a penis papilla provided with a large, symmetrical penial valve from the middle of which arises the small, distal section of the papilla; a duct intercalated between the seminal vesicle and the small diaphragm; ventrally displaced ejaculatory duct curving upwards before opening to the exterior; penis papilla highly asymmetrical, having a slim and long ventral portion and a short and stubby dorsal part; vasa deferentia separately opening into antero-dorsal portion of seminal vesicle; oviducts openings symmetrically into ventral portion of the bursal canal, near its opening into the atrium; mixoploid karyotype, with diploid chromosome portraits of 2n = 2x = 16, and triploid complements of 2n = 3x = 24, with all chromosomes being metacentric. In the context of the various kinds of mixoploidy and the sexualization of specimens, reproductive modalities within the genus Dugesia are shortly discussed. Conclusion Molecular, morphological, and karyological markers show that the two populations examined represent members of the genus Dugesia and constitute two new, distinct species.

Introduction Barberry is one of the native plants of Iran and tolerates environmental stresses, especially drought. This species can play a special role in the future development of horticulture in Iran. This species is drought tolerant and can be used in the development of rain-fed gardens. The Barberry family contains 15 genera and 650 species, most of which are distributed in the temperate regions of the Northern Hemisphere. The most important genus in the barberry family is Berberis. This genus has 500 species, some of which, including Zalzalaki, Zarafshani, Khorasani, Rastkhoshe, common and Japanese barberry, exist in Iran (i.e., Berberis vulgaris, B. orthobotrys, B. crataegina, B. integerrima, and B. khorasanica, respectively). This plant is widely distributed in Iran. Various wild species of barberry are distributed in the southern and northern slopes of Alborz from Firoozkooh, Taleghaneh, Miyaneh to Amarlu of Gilan. This genus grows on large areas of the Zagros at an altitude of 1000 to 2500 meters above sea level. Iran is the largest producer of seedless barberry in the world with a cultivated area of ​​18341 hectares and production of 21181 tons of dried barberry. This species can play a special role in the future development of horticulture in the country and reduce the pressure on water resources, especially in rain-fed horticulture.Materials and Methods In this study, 25 genotypes were evaluated from three regions: west of Alborz province (Taleghan region), north of Alborz province (Chalus road and Khuzenkola, Arangeh, Asara to Dizin heights) and northeast of Tehran (Lavasanat). Morphological evaluation was performed according to UPOV instruction (TG 68/3). 32 quantitative and qualitative morphological and horticultural traits were evaluated according to UPOV (TG 3.68). Of which, 11 quantifiable traits including leaf length and width, fruit length and width, pedicel length, Berries per raceme, cluster length, spines length, vitamin C, TA (Titratable Acidity) and TSS (Total Soluble Solid) were analyzed.Results and Discussion The results of analysis of variance showed significant differences between genotypes for all quantative traits evaluated at the level of 1% and for the number of berries per cluster at the level of 5%. The high coefficient of variation indicates high variability for the desired trait, which allows the breeder to have more choices for selecting desired genotypes. The number of fruits per cluster with 45.55, spines length with 28.67 and titratable acid with 26.58 percent malic acid, had the highest range of changes. Qualitative traits included Foliage secondary color, Leaf curvature and Leaf margin, Leaf glossiness, Color of lower side, Fruit tip, Fruit waxiness, Foliage persistence, and Shoot color in spring among the genotypes were uniform and without variance. The lowest coefficient of variation among quantitative traits was related to Brix (7. a16 percent) and fruit length (13.14 percent). The highest number of fruits was belonged to Lavasan genotype (AD8) giving an average of 25 fruits per cluster, which was substantially different from other genotypes. The highest and lowest fruit length and width are related to Taleghan 5 (11.59 mm) and Chalus 7 (3.26 mm) genotypes, respectively. In a study, the average length and width of barberry fruit were 7.69 and 3.32 mm, respectively. Vitamin C is one of the nutritional values of fruits and has direct effects on human health. Wild barberry genotypes possessing the least vitamin C content (4.7 mg/per 100 gram) of fresh fruit (Asara I genotype) and also the fruits containing the highest values (i.e., 10.57 (Taleghan 4), 9.63 (Chalous 8) and 9.4 (Taleghan 8)) yielded more than even temperate fruits such as stone and pome fruits (The mean amount of vitamin C in apples, grapes and black cherries is 4.6, 4, 10 mg/100 g FW, respectively). This value in strawberries as an indicator plant is reported between 10 and 100 and an average of 58.8 and the value for lemons is 53 mg/100 g FW. Khayat and Mahmoud Abadi (2010) reported the amount of vitamin C in seedless barberry treated by fertilizers varied from 4 to 9 mg per 100 g of fresh fruit.The highest values of total soluble solids or Brix˚ were related to Chalus 8 genotypes with value of 24.83% and Chalus 1 with value of 23.23% and the lowest amount was related to Asara 2 genotype with 18.1%. Khayat and Mahmoud Abadi (2010) reported the total soluble solids ranged between 18.3 to 33.06 percent in seedless barberry, which is much higher than our experiment. The highest titratable acidity were observed in Taleghan 4, Taleghan 8 and Taleghan 2 genotypes, with 2.66, 2.65 and 2.41 mg/ml malic acid respectively, and the lowest titratable acid was observed in Chalus 9 genotype with 1.12 mg/ml malic acid. This value has been reported in domestic barberry is between 1.07 and 2.95. The highest mean leaf lengths were observed in Chalus cultivars 3 and 5. Among the genotypes, Taleghan 7 has the longest Pedicel length.ConclusionThe selected genotypes for breeding programs were the Oshan (AD8) genotypes with an average of 25 fruits per cluster. Regarding vitamin C content the prominent genotypes were the Taleghan 4 (10.57), Chalus 8 (9.63) and Taleghan 8 (9.4) mg/100 g F.W. The highest genotypes for total soluble solids were Chalus 8 genotypes with 24.83 and Chalus 1 with 23.23 percent.

Abstract Background Salicornia is a halophyte plant capable of being irrigated with seawater, which can be used as an alternative food. Given this, it is necessary to study the potentials of this plant’s morphological diversity in the natural environment. In this study, 33 wild populations of Salicornia were collected from different geographical areas around Urmia Lake during the flowering stage, and 55 morphological traits and 25 ISSR loci of the plant were analyzed. Based on morphological and molecular traits and the cluster analysis, Salicornia populations were divided into four and two groups, respectively. Results Overall, the high percentage of polymorphic loci (65.69%), the average number of effective alleles per locus (1.63), and the Shannon data index (0.540) indicate that ISSR markers was used to identify genetic diversity. Molecular data cluster analysis divided the studied populations into two main groups, which included 12.12% and 87.88% of the populations, respectively. Based on the effective analysis of the population’s genetic structure and the precise classification of individuals into suitable sub-populations, the value of K=2 was calculated. Conclusions The research findings indicated that the populations of Salicornia have a considerable diversity in morphological traits. Furthermore, markers UBC823, B, A7, and K, as well as markers with the Shannon index, effective allele, and large heterozygosis values, are the most effective markers in comparison with other markers used in this study. The findings of this study will aid in parental selection studies for breeding programs of Salicornia in future.

The application of information-entropy analysis on real data is shown: 84 bulls of Jersey (n = 10), Ayrshire (n = 10), red Danish (n = 10), red Swedish (n = 9) breeds and Holstein ecotypes of German (n = 13), Dutch (n = 17) and North American (n = 15) breeding genotyped by 11 microsatellite loci. The Shannon information index for the combined breed samples was 1.695, the weighted average for the samples was 1.325, the inter-sample component (SHAP) was 0.370 nits or 21.8 % (all calculations according to GenAlEx 6.502). The total absolute diversity of Shannon was 5.45, averaged by samples – 3.76 effective alleles per locus, between breeds – 1.45 effective samples. The relative estimate of the differentiation of breed samples (D'β) was 36.2 % and was close to the «traditional» estimates for Hedrick, Jost and Ciao. The influence of within samples heterozygosity on SHAP estimates has not been established, but a positive trend of D'β-estimates has been noted. The matrix of paired genetic distances by breeds (D'β) and its 2D projection had a high correspondence with those by GST(NEI)-, FST(W&C)-, G"ST(HED)-, F'ST(W&C)-, DJOST-, DCHAO-measures (RMantel ≥ 0,94). Fixation indices (GST(NEI) and FST(W&C)) should be used to study the evolutionary stories of subdivided populations. To analyze the current structure of the genetic diversity of (sub)populations with an emphasis on dominant allele measures based on heterozygosity (G'ST(HED), F'ST(W&C), DJOST and DCHAO), if necessary, take into account all alleles – the Shannon measure (D'β). In conclusion, a family of Hill power measures of order q = 0, 1, 2 is considered for constructing diversity profiles containing all information about the distribution of alleles in a population.

【Objective】Plum (Prunus salicina L.) is a tree species with great economic prospect in northeast China, and it has important social and economic values. Genetic linkage maps of plum were constructed by molecular markers to provide a theoretical basis for breeding new plum varieties.【Method】Jilin 6 and Longyuan Qiuli were used as the mapping parents. The authenticity of F1 progeny was identified by SSR primers. 14 ISSR and 16 SRAP primers were selected to construct the genetic linkage map of plum by using Join Map 4.0 software and "double pseudo-testcross" theory.【Result】In this study, 72 authentic F1 progeny were obtained. ISSR and SRAP primers produced 5 segregation patterns and 120 marker loci in this F1 population. A genetic linkage map with 16 linkage groups and 38 marker loci with a total length of 528.5 cM was constructed by software analysis. The groups ranged in size from 9.6-71.1 cM, and the average size was 13.9 cM. The marker had a maximum genetic distance of 52.8 cM and a minimum genetic distance of 1.4 cM.【Conclusion】The construction of genetic linkage maps enriched the genetic research basis of plum in cold region, and contributed to the study of QTL mapping, marker-assisted breeding and gene mapping.

Abstract Background The 16S mitochondrial rRNA gene is the most widely sequenced molecular marker in amphibian systematic studies, making it comparable to the universal CO1 barcode that is more commonly used in other animal groups. However, studies employ different primer combinations that target different lengths/regions of the 16S gene ranging from complete gene sequences (~ 1500 bp) to short fragments (~ 500 bp), the latter of which is the most ubiquitously used. Sequences of different lengths are often concatenated, compared, and/or jointly analyzed to infer phylogenetic relationships, estimate genetic divergence (p-distances), and justify the recognition of new species (species delimitation), making the 16S gene region, by far, the most influential molecular marker in amphibian systematics. Despite their ubiquitous and multifarious use, no studies have ever been conducted to evaluate the congruence and performance among the different fragment lengths. Results Using empirical data derived from both Sanger-based and genomic approaches, we show that full-length 16S sequences recover the most accurate phylogenetic relationships, highest branch support, lowest variation in genetic distances (pairwise p-distances), and best-scoring species delimitation partitions. In contrast, widely used short fragments produce inaccurate phylogenetic reconstructions, lower and more variable branch support, erratic genetic distances, and low-scoring species delimitation partitions, the numbers of which are vastly overestimated. The relatively poor performance of short 16S fragments is likely due to insufficient phylogenetic information content. Conclusions Taken together, our results demonstrate that short 16S fragments are unable to match the efficacy achieved by full-length sequences in terms of topological accuracy, heuristic branch support, genetic divergences, and species delimitation partitions, and thus, phylogenetic and taxonomic inferences that are predicated on short 16S fragments should be interpreted with caution. However, short 16S fragments can still be useful for species identification, rapid assessments, or definitively coupling complex life stages in natural history studies and faunal inventories. While the full 16S sequence performs best, it requires the use of several primer pairs that increases cost, time, and effort. As a compromise, our results demonstrate that practitioners should utilize medium-length primers in favor of the short-fragment primers because they have the potential to markedly improve phylogenetic inference and species delimitation without additional cost.