Number Of Alleles Research Articles

Genome-wide association study implicates the role of TBXAS1 in the pathogenesis of depressive symptoms among the Korean population

Although depression is an emerging disorder affecting many people worldwide, most genetic studies have been performed in European descent populations. Herein, a genome-wide association study (GWAS) was conducted in Korean population to elucidate the genomic loci associated with depressive symptoms. Two independent cohorts were used as discovery datasets, which consisted of 6474 (1484 cases and 4990 controls) and 1654 (557 cases and 1097 controls) Korean participants, respectively. The participants were divided into case and control groups based on the Beck Depression Inventory (BDI). Meta-analysis using the two cohorts revealed that rs6945590 was significantly associated with the risk of depressive symptoms [P = 2.83 × 10−8; odds ratio (OR) = 1.23; 95% confidence interval (CI): 1.15–1.33]. This association was validated in other independent cohorts which were another Korean cohort (258 cases and 1757 controls) and the East Asian study of the Psychiatric Genomics Consortium (PGC) (12,455 cases and 85,548 controls). The predicted expression levels of thromboxane A synthase 1 gene (TBXAS1), which encodes the enzyme thromboxane A synthase 1 and participates in the arachidonic acid (AA) cascade, was significantly decreased in the whole blood tissues of the participants with depressive symptoms. Furthermore, Mendelian randomization (MR) analysis showed a causal association between TBXAS1 expression and the risk of depressive symptoms. In conclusion, as the number of risk alleles (A) of rs6945590 increased, TBXAS1 expression decreased, which subsequently caused an increase in the risk of depressive symptoms.

Capturing and managing genetic diversity in ex situ collections of threatened tropical trees: A case study in Karomia gigas.

Although ex situ collections of threatened plants are most useful when they contain maximal genetic variation, the conservation and maintenance of genetic diversity in collections are often poorly known. We present a case study using population genomic analyses of an ex situ collection of Karomia gigas, a critically endangered tropical tree from Tanzania. Only ~43 individuals are known in two wild populations, and ex situ collections containing 34 individuals were established in two sites from wild-collected seed. The study aimed to understand how much diversity is represented in the collection, analyze the parentage of ex situ individuals, and identify efficient strategies to capture and maintain genetic diversity. We genotyped all known individuals using a 2b-RADseq approach, compared genetic diversity in wild populations and ex situ collections, and conducted parentage analysis of the collections. Wild populations were found to have greater levels of genetic diversity than ex situ populations as measured by number of private alleles, number of polymorphic sites, observed and expected heterozygosity, nucleotide diversity, and allelic richness. In addition, only 32.6% of wild individuals are represented ex situ and many individuals were found to be the product of selfing by a single wild individual. Population genomic analyses provided important insights into the conservation of genetic diversity in K. gigas, identifying gaps and inefficiencies, but also highlighting strategies to conserve genetic diversity ex situ. Genomic analyses provide essential information to ensure that collections effectively conserve genetic diversity in threatened tropical trees.

Molecular Characterisation of Traditional Cashew (Anacardium occidentale L.) Populations from Nachingwea and Newala Districts in Tanzania

This study assessed the genetic diversity of 120 selected cashew plants from Nachingwea and Newala traditional cashew populations, comprising of 60 cashew plants from each population. Eight Simple Sequence Repeats (SSR) makers were used to ascertain the extent of genetic variation within and between the two traditional cashew populations. Genomic DNA extraction and Polymerase Chain Reaction (PCR) were performed using standard protocols. The results showed that all SSR markers were polymorphic. Average Polymorphic Information Content (PIC), heterozygosity, number of alleles per locus, allelic frequency and Shannon’s Index were 0.540, 0.721, 3.391, 0.666 and 0.649, respectively. Analysis of molecular variance results showed that genetic variation within populations was 88% while genetic variation between populations was 12%, implying gene flow between the populations. The results further showed that the two cashew populations are genetically diverse and that Nachingwea traditional cashew population was genetically more diverse than Newala population. High genetic variation observed in the cashew populations shows that they are suitable for use in cashew breeding programmes. Thus, conservation of traditional cashew populations is recommended

Revealing Genetic Diversity and Population Structure in Türkiye’s Wheat Germplasm Using iPBS-Retrotransposon Markers

Investigating the genetic diversity and population structure of wheat germplasm is crucial for understanding the underlying variability essential for breeding programs and germplasm preservation. This research aims to contribute novel insights with respect to the genetic makeup and relationships among these wheat genotypes, shedding light on the diversity present within the Turkish wheat germplasm. In this study, iPBS-retrotransposon markers were employed to analyze 58 wheat genotypes, encompassing 54 landraces and 4 cultivars sourced from Türkiye. These markers serve as genetic indicators that can be used to evaluate genetic variation, build genealogical trees, and comprehend evolutionary connections. The PCR products were visualized on agarose gel, and bands were scored as present/absent. The ten iPBS primers collectively yielded an average of 16.3 alleles, generating a total of 163 polymorphic bands. The number of alleles produced by individual markers ranged from 4 (iPBS-2386) to 29 (iPBS-2219). The genetic parameters were calculated using the popgen and powermarker programs. The genetic relationships and population structures were assessed using the ntsys and structure programs. Polymorphism information content (PIC) per marker varied from 0.13 (iPBS-2390) to 0.29 (iPBS-2386), with an average value of 0.22. Shannon’s information index (I) was calculated as 1.48, while the number of effective alleles (Ne) and Nei’s genetic diversity (H) were determined to be 0.26 and 0.31, respectively. Genotype numbers 3 (Triticum dicoccum) and 10 (Triticum monococcum) exhibited the maximum genetic distance of 0.1292, signifying the highest genetic disparity. Population structure analysis revealed the segregation of genotypes into three distinct subpopulations. Notably, a substantial portion of genotypes clustered within populations correlated with the wheat species. This population structure result was consistent with the categorization of genotypes based on wheat species. The comprehensive assessment revealed noteworthy insights with respect to allele distribution, polymorphism content, and population differentiation, offering valuable implications for wheat breeding strategies and germplasm conservation efforts. In addition, the iPBS markers and wheat genotypes employed in this study hold significant potential for applications in wheat breeding research and germplasm preservation.

Genetic diversity of three consecutive selective breeding generations in Pseudobagrus vachellii (Actinopterygii: Siluriformes: Bagridae)

Pseudobagrus vachellii (Richardson, 1846) is a commercially important freshwater fish species in China. To understand the effects of artificial breeding on the genetic diversity of three consecutive P. vachellii breeding populations (F1, F2, and F3) since 2012, a genetic analysis was conducted using polymorphic microsatellite markers. The mean allele number, expected heterozygosity, observed heterozygosity, and the polymorphic information content from generation F1 to F3 decreased from 7.75 to 5.63, from 0.77 to 0.63, from 0.83 to 0.77, and from 0.72 to 0.58, respectively. Analysis of molecular variance showed greater genetic divergence within the three generations (93.67%) than that among the generations (6.33%), and the overall differentiation level was moderate. Additionally, the lowest genetic differentiation was between F2 and F3 (Fst = 0.0484), and the highest was between F1 and F3 (Fst = 0.12864). Inbreeding occurred in each generation and was the highest in generation F3. Structural analysis showed that the three P. vachellii generations were most likely divided into two different genetic clusters. Although genetic diversity declined slightly in the mass selection lines after three breeding generations, overall genetic diversity was maintained at a relatively high level. To minimize the loss of genetic diversity and inbreeding in the subsequent breeding process, a moderate number of parents can be used for each generation. Information regarding the genetic diversity and structure of the selective P. vachellii breeding generations obtained in this study will be useful for future broodstock management and selective breeding programs.

Investigation of genetic diversity among autochthonous grape cultivars grown in Türkiye using molecular primers

AbstractGrape is a type of fruit widely grown globally and in Türkiye thanks to its importance in human nutrition and diversity of usage areas. Türkiye has a long history of grape cultivation, and the genetic diversity of local grapes grown in some regions has still not been revealed. This study showed the genetic diversity between 60 local grape genotypes selected from north Central Anatolia and nine reference grape cultivars;10 inter simple sequence repeats (ISSR) and 7 inter-primer binding site (IPBS) retrotransposon primers were used. The mean values of genetic diversity indices in ISSR and IPBS retrotransposon primers were calculated as expected allelic frequency (p) 0.476/0.195, observed allelic frequency (q) 0.524/0.805, number of effective alleles (Ne) 1.326/1.378, Shannon’s information index (I) 0.308/0.367, expected heterozygosity (He) 0.199/0.232 and unbiased expected heterozygosity (uHe) 0.201/0.234, respectively. Unweighted pair group method with arithmetic mean (UPGMA) and model-based STRUCTURE analysis divided the studied germplasm into two groups. However, local genotypes were not grouped per the regions where they grew. As a result of the analysis of molecular variance (AMOVA) analysis, the inter-population variation was determined to be 11%, and the intra-population variation was determined to be 89%. The mean genetic differentiation value (Fst) between populations was 0.303. The results showed that ISSR and IPBS retrotransposon primers effectively explained the genetic diversity.

Genetic Diversity and Population Structure Analysis of Excellent Sugar Beet (Beta vulgaris L.) Germplasm Resources

This study analyzed the genetic diversity, population structure, and cluster analysis of 129 sugar beet germplasm resources to screen superior germplasms for breeding using the 27 simple sequence repeat (SSR) and 33 pairs of insertion–deletion (InDel) molecular markers. After integrating the phenotypic variation of 16 descriptive and 4 qualitative phenotypic variables, the genetic variation levels of the 129 sugar beet germplasms’ phenotypic traits were analyzed using the principal component analysis (PCA), correlation analysis, and analysis of variance methods. The genetic diversity examination of molecular markers showed a polymorphism information content (PIC) of 0.419–0.773 (mean = 0.610). Moreover, the mean number of effective alleles detected via the SSR and InDel markers was 3.054 and 2.298, respectively. Meanwhile, the PIC ranged from 0.130 to 0.602 (mean = 0.462). The population structure analysis revealed the most appropriate K-value, indicating three populations (K = 3). The genetic distances of the 129 germplasm resources ranged from 0.099 to 0.466 (mean = 0.283). The cluster analysis results demonstrated that the germplasms were grouped into three primary classes. Based on the analysis of variance, the two qualitative features with the highest coefficients of variation were petiole width (16.64%) and length (17.11%). The descriptive trait root length index (1.395) exhibited the greatest genetic diversity. The PCA reduced the 20 phenotypic traits into five principal components, contributing 51.151%. The results of this study provide a theoretical foundation for the future selection and breeding of superior sugar beet germplasm resources.

Genetic diversity analysis and fingerprinting of 175 Chimonanthus praecox germplasm based on SSR molecular marker

The elucidation of resources pertaining to the Chimonanthus praecox varieties and the establishment of a fingerprint serve as crucial underpinnings for advancing scientific inquiry and industrial progress in relation to C. praecox. Employing the SSR molecular marker technology, an exploration of the genetic diversity of 175 C. praecox varieties (lines) in the Yanling region was conducted, and an analysis of the genetic diversity among these varieties was carried out using the UPDM clustering method in NTSYSpc 2.1 software. We analyzed the genetic structure of 175 germplasm using Structure v2.3.3 software based on a Bayesian model. General linear model (GLM) association was utilized to analyze traits and markers. The genetic diversity analysis revealed a mean number of alleles (Na) of 6.857, a mean expected heterozygosity (He) of 0.496 3, a mean observed heterozygosity (Ho) of 0.503 7, a mean genetic diversity index of Nei՚s of 0.494 9, and a mean Shannon information index of 0.995 8. These results suggest that the C. praecox population in Yanling exhibits a rich genetic diversity. Additionally, the population structure and the UPDM clustering were examined. In the GLM model, a total of fifteen marker loci exhibited significant (P < 0.05) association with eight phenotypic traits, with the explained phenotypic variation ranging from 14.90% to 36.03%. The construction of fingerprints for C. praecox varieties (lines) was accomplished by utilizing eleven primer pairs with the highest polymorphic information content, resulting in the analysis of 175 SSR markers. The present study offers a thorough examination of the genetic diversity and SSR molecular markers of C. praecox in Yanling, and establishes a fundamental germplasm repository of C. praecox, thereby furnishing theoretical underpinnings for the selection and cultivation of novel and superior C. praecox varieties, varietal identification, and resource preservation and exploitation.

Cross-Species Transferability of Specific SSR Markers from Carex curvula (Cyperaceae) to Other Carex Species

Microsatellites are codominant markers that, due to their high polymorphism, are a common choice for detecting genetic variability in various organisms, including fungi, plants, and animals. However, the process of developing these markers is both costly and time-consuming. As a result, the cross-species amplification has become a more rapid and more affordable alternative in biological studies. The objective of this study was to assess the applicability of 13 SSR markers, originally designed for Carex curvula, in other 14 species belonging to different sections of the genus. All the markers were successfully transferred with a mean of 90.76%, and 100% transferability was reached in two species (C. baldensis and C. rupestris). The lowest transferability was registered in the G165 marker, which did not produce amplification in six species. Together, the microsatellites amplified a total of 183 alleles, ranging from 10 to 19 alleles per locus, with an average of 14.07. The mean number of different alleles ranged from 0.846 to a maximum of 2.077 per locus. No significant departures from the Hardy–Weinberg equilibrium were detected in polymorphic loci. The transferability of the 13 SSR markers proved highly successful in various Carex species, across different clades and sections of the genus.

Polymorphism of serum blood proteins of herd horses (&lt;i&gt;Equus ferus caballus&lt;/i&gt;) of the transbaikal breed

The results of a study of the genetic diversity of the Transbaikal horse breed based on the polymorphism of whey proteins TF, Es, and ALB in four herds of the Transbaikal region are presented. The Transbaikal horse belongs to the ancient aboriginal breeds and is most adapted to the local climatic conditions of dry, hot summers and frosty winters with little snow. It is unpretentious, hardy, and has a strong constitution. Research is aimed at preserving the breed’s genetic diversity by studying polymorphic variants of whey proteins, which are reliable genetic markers due to their codominant inheritance and comprehensive polymorphism. In the albumin locus, two alleles and three genotypes were identified. In the esterase locus, there are six alleles and 13 genotypes. In the transferrin locus - 7 alleles and 18 genotypes occur with different frequencies in the studied herds, which makes it possible to characterise their genotypic characteristics. Rarely encountered genotypes of the transferrin locus (less than 10 %) include eight genotypes: TFDD, TFDH, TFDI, TFDR, TFFI, TFFM, TFOR, TFR; esterase locus – 6 genotypes: EsGI, EsHH, EsHI, EsHO, EsII, EsGI. Based on the frequency of genotypes and alleles, homozygosity was calculated for each whey protein system and for the entire sample from the herd, the level of which ranges from 7.87 to 12.25 %. The overall homozygosity rate varies from 34.35 to 43.36 %, and the number of effective alleles (Na) in all herds is almost the same (2.30–2.91). Genetic variability ranges from 56.96–63.74 %. The index of gene similarity between herds is at the level of 0.8439–0.9058. The analysed herds form two subclusters: the first includes horses from the APC (Agricultural Production Cooperative) Livestock Breeding Farm named after. Kalinin and SPK “Rassvet”. In the second - animals from APC (Agricultural Production Cooperative) “Livestock Breeding Farm “Rodina” and AC (Agricultural Cooperative) “Taptanay”.

Microsatellites reveal high levels of genetic admixture in the natural populations of Laurus azorica, Lauraceae

Laurus (Lauraceae) species are currently restricted to isolated refugia in the southern Black Sea, Mediterranean Basin, southern Morocco, and Macaronesian archipelagos. One to three species of Laurus has been recognized: the Azorean endemic Laurus azorica, L. nobilis from the Mediterranean, and L. novocanariensis from Madeira and the Canary Islands. This study aims to determine the population structure, genetic diversity, and associated patterns of gene flow within and between Azorean populations, using eight existing SSR markers. We also included plant material from L. nobilis populations found in the Azores, for comparison. Amplification was performed in 212 samples of L. azorica and in 30 samples of L. nobilis. For L. azorica, 78 alleles were amplified (average 9.75 alleles per loci). Bayesian analysis with STRUCTURE unveiled five genetic groups for the Azorean accessions, with high level of genetic admixture. Genetic diversity was generally high, with moderate levels of genetic differentiation among L. azorica populations. Moreover, high gene flow levels, likely mediated by past human translocations and naturally, by birds, might have contributed to the high level of genetic admixture observed possibly reflecting hybridization events between L. nobilis and L. azorica. Conservation measures should be applied to some populations of São Miguel, Santa Maria, and Flores Islands, based on the number of private alleles, and further, ad hoc translocation events should be avoided. Conservation in situ and the preservation of laurel forest remains are recommended. The study of this species’ taxonomy, genetics, and population dynamics in the Macaronesian region should be continued.

Genetic Variation among Aeluropus lagopoides Populations Growing in Different Saline Regions

Aeluropus lagopoides is a halophytic grass growing in different sabkhas of Saudi Arabia. In this study, 14 inter-simple sequence repeat (ISSR) and 15 sequence-related amplified polymorphism (SRAP) molecular markers were selected to investigate the genetic diversity within and among five natural populations of A. Lagopiodes. The genetic diversity varied within and among populations. ISSR markers were slightly more efficient than SRAP markers in evaluating genetic diversity. Average polymorphism information content, effective number of alleles, Nei’s genetic diversity, and Shannon’s information index values of ISSR markers were higher than SRAP. Analysis of molecular variance revealed about 40% genetic variation among the population and 60% within the population. Overall, the genetic diversity was lowest in Jouf (40%), while the Qaseem populations were the highest (60%). Jizan populations were highly dissimilar to other regions. A Mantel test indicated a positive correlation between geographic and genetic distance. The cluster analysis showed three groups; the first group comprises Jouf and Salwa populations, the second group comprises Qareenah and Qaseem, and the third group comprises the Jizan population. This observation matched the geographic distribution of the species. These findings can help in the conservation of a diverse population of A. lagopoides in saline regions as well as rehabilitation of these degraded unique habitats.

Genetic Relatedness in Elite Cultivars of Moth Bean using Morpho-agronomic and Molecular Markers

Background: Moth bean is a very nutritive and hardy crop, especially for resource poor-arid agriculture. The limited use of cultivars in moth bean breeding resulted into narrow genetic base. This study aimed to diversify the conical genetic base and developimproved cultivars, through molecular (RAPD) and morpho-agronomic characterization of commercially elite moth bean cultivars. Methods: Elite moth bean cultivars (15) were evaluated for 11 morpho-agronomic traits. Eleven RAPD markers were used to amplify genomic DNA and perform molecular characterization.Clustering approach was used for grouping of the cultivars. Result: RAPD markers revealed high polymorphism in 15 elite moth bean cultivars. The polymorphism information content (PIC) values varied within the range of 0.45 to 0.88, with an average of 0.77. The number of alleles at different loci ranged from 4 to 16, with an average of 10 alleles per locus. When employing UPGMA-based cluster analysis, utilizing 11 morpho-agronomic traits, the cultivars were grouped into four clusters. However, when RAPD markers were used, the cultivars were grouped into five clusters. The Jaccard’s similarity coefficient and Manhattan dissimilarity coefficient fell within the ranges of 0.18 to 0.70 and 0.02 to 0.42, respectively. These values signify the degree of genetic variability within the cultivars. Furthermore, a Mantel test was conducted to examine the correlation between agronomic traits and the RAPD-based matrix. The results showed a negative correlation, but it was not statistically significant.The high PIC values and the successful amplification of multiple loci demonstrate the efficacy of RAPD markers in assessing genetic diversity in moth beans. The study revealed enormous genetic variation among cultivars and crosses can be attempted between cultivars of different groups to create better recombinants in moth bean breeding programmes.

Genetic diversity and population structure of Anatolian Hair goats, an ancient breed

Abstract. This study aimed to investigate the genetic characterization and diversity of Hair goats from 10 regions using 20 microsatellite markers. A total of 522 alleles were observed. The INRA0023 locus exhibited the greatest number of alleles (48), while the DRBP1 locus had the highest effective allele number (16.27), and the BM1818 and DRBP1 loci had the highest polymorphic information content value (0.94). The expected heterozygosity value ranged from 0.85 (ILSTS011) to 0.94 (BM1818, SRCRSP15, and DRBP1). The Hair goat populations in Konya and Hatay displayed the lowest and highest allele numbers, with values of 10.40 and 16.25, respectively. The fixation index (FIS) values are significant in defining population structures and determining the extent of heterozygosity losses. The FIS values exhibited a range of 0.031 in Muǧla to 0.226 in Burdur. A total of 107 unique alleles were identified in Hair goat populations. However, it is noteworthy that, out of all the alleles, only 25 had a frequency exceeding 5 %. The results indicate that the microsatellite markers utilized demonstrate sufficient levels of polymorphism, making them appropriate for efficiently investigating the genetic variability of Hair goat populations.

Characteristic of allele pool of sheep of the southern meat breed using microsatellite markers

Purpose: to characterize the allele pool of sheep of the southern beef breed using microsatellites.Materials and methods. The biomaterial was ear’s plucks from 80 sheep of the southern meat breed, selected from the Ladozhsky Breeding Plant. 20 East Friesian sheep, 33 Dorset sheep and 63 Romanov sheep were used for comparison. Nine microsatellite loci (INRA005, SPS113, INRA23, MAF65, McM527, OarCP49, HSC, OarAE129, MAF214) were selected as DNA markers. Microsatellite variability was analyzed using the ABI3130x1 Genetic Analyzer. The results were processed in the GenAIEx 6.503 program, with the help of which the main indicators characterizing the state of the allele pool and genetic diversity were calculated.Results. Analysis of the population genetic parameters of sheep of the southern meat breed showed that the average number of alleles per locus (Na) and the effective number of alleles per locus (Ne) exceed the sample average by 1,72 and 0,58 alleles, respectively. The expected heterozygosity (He) was 0,766, while the observed heterozygosity (Ho) was 0,741. The coefficient of inbreeding (Fis) was 0,03. The analysis of the principal components, carried out for the studied breeds in the planes of the first and third principal components, did not fundamentally change the nature of the spatial clustering of the studied groups of sheep. Analysis of the principal coordinates, performed on the basis of calculation of pairwise Fst values, showed that the southern meat breed is located in the upper left quadrant and is isolated from other breeds. The values of the Fst indicator indicate that there is moderate genetic differentiation between the southern meat and dorset breeds (Fst=0,116), and significant genetic differentiation between the southern meat and romanov breeds (Fst=0,161).Conclusion. An analysis of the population genetic parameters of sheep of the southern meat breed, in comparison with the east friesian, dorset and romanov breeds, showed that, in general, in terms of the total number of alleles per locus and the number of effective alleles per locus, it is characterized by a high level of genetic diversity. The presence of a tendency towards a deficiency of heterozygotes is probably explained by the limited population, represented by the only relict gene pool in Russia.

Exploring the extents of genetic diversity and population structure of enset [Ensete ventricosum (Welw.) cheesman] from southern Ethiopia using simple sequence repeat markers: Implications for crop improvement and conservation

Enset (Ensete ventricosum) is a multi-use perennial herbaceous crop used as a staple food for over 20 million people in Ethiopia. Despite its high use values, very few studies have been conducted to improve this crop, particularly using molecular marker systems. In this context, the study aimed at evaluating the magnitude of genetic diversity and population structure of enset germplasm collections from four major enset growing zones in southern Ethiopia using 12 simple sequence repeat (SSR) markers. A total of 147 individual leaf samples were collected from the entire enset populations and gave 289 alleles, ranging from 12 to 41 alleles per locus, with a mean of 24.5. The polymorphism information content for each locus varied from 0.86 to 0.95, with a mean of 0.91. The number of effective alleles ranged from 5.13 to 11.79 with a mean of 8.27. The expected and observed heterozygosity showed average values of 0.85 and 0.84, respectively. The greatest genetic distance (1.16) was between Gurage and wild populations, while the shortest (0.37) was between Gurage and Silte. Among the six populations, the wild had the highest percentage of polymorphic loci (100%). AMOVA attributed 89% of the genetic variation to intra-population and only 11% to among populations. The whole set of germplasm indicates low genetic differentiation and high gene flow (Nm). The UPGMA and principal coordinates largely correspond to each other and indicate three major groups. Overall, the information gained from this study would be useful for enset improvements and conservation strategies.

Genetic diversity analysis of different geographic populations of black carp (Mylopharyngodon piceus) based on whole genome SNP markers

Black carp, Mylopharyngodon piceus, is one of the major farmed fish in China, generating a considerable amount of economic value annually. To investigate the genetic variation of black carp germplasm resources in China, this study was the first to use the whole genome SNPs of black carp for analysis. A total of 139 samples of nine black carp populations in the Yangtze River and Pearl River Systems of China were collected, and 53,322 high-quality SNP loci were obtained after GBS sequencing and filtering. Genetic diversity parameters were calculated for nine populations of black carp based on these genetic data. All 7 populations from the Yangtze River system and 2 populations from the Pearl River system showed high level of genetic diversity. For each population, the nucleotide diversity (π) varied from 0.283 to 0.308, the observed heterozygosity (Ho) from 0.271 to 0.317, the expected heterozygosity (He) from 0.273 to 0.292，the number of effective alleles (Ne) from 1.440 to 1.475, and the polymorphism information content (PIC) from 0.224 to 0.239. The fixation index (Fst) between populations ranged from 0.036 to 0.133, remaining at low and medium differentiation. Phylogenetic tree analysis, principal component analysis (PCA) and population genetic structure analysis revealed that the nine populations could be divided into three ancestral populations. The seven populations of the Yangtze River system comprised two primary ancestral groups, with a small amount of gene flow between populations. The internal genetic structure of populations within the Pearl River system was homogeneous, with one common ancestral source as the dominant component. In conclusion, the data and results generated from this study will provide a useful addition to the genetic resources of black carp and will provide reference information for further germplasm conservation and genetic improvement of black carp.

Development and validation of genome-wide SSR molecular markers of Tapes dorsatus.

Tapes dorsatus is an economically important benthic animal in the Beibu Gulf of China. However, the deficiency of microsatellite markers has hindered the study of its genetics. The development of microsatellite markers will provide useful tools for genetic improvement, variety identification, phylogenetic analysis and resource conservation. Within the genome sequence, 145,008 simple sequence repeats (SSRs) were identified, and 29,691 primer pairs were designed successfully. A total of 100 primer pairs were randomly synthesized for testing, and 93 primers yielded products. Sixty highly polymorphic primers were used to reveal the genetic diversity of 50 T. dorsatus individuals. The average number of alleles (Na) of the population was 10.40; the average number of effective alleleswas 6.16, the average expected heterozygosity (He) was 0.82, and the average polymorphic information contentwas 0.80. The genetic structure of the population was detected, by which the population could be divided into three subpopulations. We identified 145,008 SSRs in the genome of T. dorsatus and designed 29,691 primer pairs in this study. Of 100 synthesized primers, 60 were highly polymorphic and used to reveal the genetic diversity and structure of the population. The SSR markers identified here will provide useful tools and a foundation for genetic diversity, linkage mapping and molecular marker-aided breeding in T. dorsatus.

Dissecting the associations of KCNH2 genetic polymorphisms with various types of cardiac arrhythmias

BackgroundCardiac arrhythmia, a common cardiovascular disease, is closely related to genetic polymorphisms. However, the associations between polymorphisms in KCNH2 and various arrhythmias remain inadequately explored. MethodsGuided by the assumption that KCNH2 genetic polymorphisms significantly contribute to the development of arrhythmias, we thoroughly explored the associations between 85 KCNH2 genetic variations and 16 cardiac arrhythmias in a sample obtained from the UK Biobank (UKBB, N = 307,473). The illnesses documented in the electronic medical records of the sample were mapped to a phecode system for a more accurate representation of distinct phenotypes. Survival analysis was used to test the effect of KCNH2 variants on arrhythmia incidence, and a phenotype-wide association study (PheWAS) was performed to investigate the effect of KCNH2 polymorphisms on 102 traits, including physical measurements, biomarkers, and hematological indicators. ResultsNovel associations of variants rs2269001 and rs7789585 in KCNH2 with paroxysmal tachycardia (PT) and atrial fibrillation/flutter (AF/AFL), respectively, were identified. Moreover, with an increase in the number of minor alleles of these two variants, the incidence rates of PT and AF/AFL decreased. In addition, the PheWAS results suggested that these two single nucleotide polymorphisms were associated with multiple parameters in physical measurements and neutrophil percentage. ConclusionThe multiple novel associations observed in this study illustrate the importance of KCNH2 genetic variations in the pathogenesis of arrhythmia.

Diversity and genetic structure of yellow passion fruit in Boyacá-Colombia using microsatellite DNA markers.

The Yellow passion fruit belongs to the Passifloraceae family with great economic, nutritional and social importance in Colombia. It presents a great phenotypic and genotypic diversity, which has not yet been explored or used in genetic improvement programs. The objective of this study was to evaluate the genetic diversity of 84 cultivars of Passiflora edulis f. flavicarpa from nine farms in the municipality of Miraflores, Boyacá, using eight microsatellite markers (SSR). On the basis of this information, estimates of genetic diversity parameters, molecular variance analysis (AMOVA), genetic distances, and cluster of cultivars were obtained. Low levels of genetic differentiation between cultivars were observed in the Bayesian analysis using Structure software, as well as the absence of correlation between genetic and geographic distances. The observed heterozygosity (0.50) was greater than the expected heterozygosity (0.43), suggesting a significant number of heterozygous individuals. The number of alleles per locus varied from 2 to 4, with a mean 2.88. In general, SSR were classified as informative (0.36). The average value of the Shannon Index was 0.71, which shows moderate variability in this cultivar. AMOVA showed higher diversity within cultivars (98%). The gene flow (Nm=28.4) was moderate, this can be explained by the flow of pollen between the different cultivars, the reproduction system of the species, self-incompatibility and the introduction of genotypes from other sites by farmers. The genetic diversity identified in this study is sufficient to initiate breeding programs aimed at identifying cultivars with higher yields.