Effective Number Of Alleles Research Articles

Analysis of the genetic variability of camel populations in Kazakhstan using ISSR-PCR markers

In this study, we analyzed the genetic characteristics of camel populations of Kazakhstan using ISSR-PCR markers. As a result, fragments of the following sizes were identified using the (AG)9C primer: 200, 320, 370, 430, 580, and 700 bp. Based on the (GA)9C primer, the length of the amplicons was 300, 350, and 430 bp. An analysis of the genetic differences of camels in the populations was carried out using ISSR-PCR markers. As a result, the number of allelic indices of polymorphic loci of the (AG)9С primer and related polymorphic loci in the population of the Shymkent population was equal to 77.78%, the allelic index of polymorphic loci of camels in the Taraz population - 33.3%, Kyzylorda and Atyrau populations - 44,44%. In camels selected for the study, the number of observed alleles (Na) averaged 1.27, the effective number of alleles (Ne) was equal to 1.37, the genetic diversity (h) according to Nei was equal to 0.21 and the Shannon index (I) was equal to 0.30. The average allelic score for polymorphic loci was 50.0% across four populations. Based on our results, the two markers used in the work were informative in assessing the genetic diversity of camel populations.

Morphological and molecular diversity of eggplant accessions (Solanum melongena L) using Simple Sequence Repeats (SSR) markers

The evaluation of various desirable characteristics in eggplant genotypes has facilitated the efficient process of selecting and improving their traits. Morphological parameters have proven to be valuable in assessing the similarities or differences among different accessions, while molecular data have been used to support the conclusions drawn from the morphological analysis. This study was conducted to evaluate the performance of 42 eggplant genotypes collected from Malaysia, China, and Thailand. Data for growth, yield, and related traits were collected and subjected to analysis of variance (ANOVA) using SAS 9.4. The field trial experiment was designed as a completely randomized block design with three replications. Analysis of variance (ANOVA) showed that the traits under study were highly significant (p ≤ 0.01). MV18 (5.97 kg) and TV17 (5.59 kg) were observed to have high yields per plant. The SSR markers used exhibited moderate average values for the number of alleles (2.53). The major allele frequency displayed a high average value (0.53) and a moderate average number of effective alleles (2.31). Additionally, the observed Shannon's information index, expected heterozygosity, and PIC were high (0.84, 0.54, and 0.45, respectively). 42 accessions were grouped into five major clusters based on similarities using the unweighted pair-group method with arithmetic averages based on similarity matrices UPGMA Dendrogram and the EIGEN module. The findings of this study indicate that the use of simple sequence repeat (SSR) markers can effectively estimate genetic diversity and analyze phylogenetic relationships. Moreover, these markers can assist eggplant breeders in selecting desirable quantitative traits within their breeding program.

Impact of genetic background as a risk factor for atherosclerotic cardiovascular disease: A protocol for a nationwide genetic case-control (CV-GENES) study in Brazil.

Atherosclerotic Cardiovascular Disease (ASCVD) represents the leading cause of death worldwide, and individual screening should be based on behavioral, metabolic, and genetic profile derived from data collected in large population-based studies. Due to the polygenic nature of ASCVD, we aimed to assess the association of genomics with ASCVD risk and its impact on the occurrence of acute myocardial infarction, stroke, or peripheral artery thrombotic-ischemic events at population level. CardioVascular Genes (CV-GENES) is a nationwide, multicenter, 1:1 case-control study of 3,734 patients in Brazil. Inclusion criterion for cases is the first occurrence of one of the ASCVD events. Individuals without known ASCVD will be eligible as controls. A core lab will perform the genetic analyses through low-pass whole genome sequencing and whole exome sequencing. In order to estimate the independent association between genetic polymorphisms and ASCVD, a polygenic risk score (PRS) will be built through a hybrid approach including effect size of each Single Nucleotide Polymorphism (SNP), number of effect alleles observed, sample ploidy, total number of SNPs included in the PRS, and number of non-missing SNPs in the sample. In addition, the presence of pathogenic or likely pathogenic variants will be screened in 8 genes (ABCG5, ABCG8, APOB, APOE, LDLR, LDLRAP1, LIPA, PCSK9) associated with atherosclerosis. Multiple logistic regression will be applied to estimate adjusted odds ratios (OR) and 95% confidence intervals (CI), and population attributable risks will be calculated. Clinical trial registration: This study is registered in clinicaltrials.gov (NCT05515653).

Correlation of 20 Single-Nucleotide Polymorphisms with Weight and Wool Traits in Alpine Merino Sheep.

SNPs associated with important traits of fine-wool sheep that were previously obtained through genome-wide association analysis screening were verified and analyzed. A total of 20 SNPs related to birth weight, bundle strength, cleaning rate, and fiber diameter were screened using whole-genome resequencing, and the SNPshot assay was used to detect and analyze polymorphisms. This study found that, among the 20 SNPs associated with important traits in Alpine Merino sheep, 8 were monomorphic and 12 were polymorphic, of which 6 showed moderate polymorphisms and 6 showed low polymorphisms. The heterozygosity of the 12 polymorphic loci ranged from 0.10 to 0.49, the effective number of alleles ranged from 1.11 to 1.98, and the polymorphic information content ranged from 0.09 to 0.37. The chi-square test showed that only RHPN2:g.42678119T>G and RALYL:g.90030866A>G were in Hardy-Weinberg disequilibrium (p < 0.05); the other loci were in equilibrium (p > 0.05). These SNPs associated with important traits in Alpine Merino sheep provide a theoretical basis for genomic selection and molecular design breeding.

Genetic aspects in working with the kholmogory cattle breed in the arkhangelsk region

Monitoring of the genetic structure of cattle breeds allows conducting studies that provide information about the cross-section in the timeline by the frequencies of genotypes of blood groups. In particular, the study was carried out on 10 time intervals of observations in herds for the Kholmogorsky breed of breeding plants of the Arkhangelsk region (n = 10983). The dynamics is shown by the decrease and increase in the frequencies of individual alleles. The genetic structure of the herd becomes more homozygous, as the loss of alleles goes on. A similar situation has developed in the samples of cows of the first and ninth generations, their genetic structures are sharply different. According to the results of the research, it was found that the quantitative and qualitative composition of the allelofund of the Kholmogorsky cattle of the Arkhangelsk region has changed under the influence of breeding processes. It was found that the degree of homozygosity (theoretical) tends to decrease from 10.5% (3rd generation) to 6.5% (9th, 10th generation) in the context of the analyzed generations of females, and the number of effective alleles, respectively, increases from 9.4% to 15.4%. At the same time, it was revealed that the breeding stock of the herds of breeding plants of the Arkhangelsk region was heterogeneous according to the genetic panel of the EAV locus. The greatest genetic distance is shown by purebred cows of the Kholmogorsky breed of cattle of the 1-2 observation intervals with Holstein in the 9-10 intervals. Breeding work and assessment of genetic variability is a tool for successful breeding in cattle herds of breeding plants by generations. The event to create new and improve existing factory lines using genetic markers of breed affiliation is promising. This will reduce the negative consequences of related mating of parent pairs, as well as avoid an increase in the level of homozygosity in the controlled herds of the Arkhangelsk population of the Kholmogorsky cattle breed.

Towards the Conservation of Monumental Taxus baccata L. Trees of Thasos Island: Genetic Insights

Taxus baccata L. is a tertiary relict, long-lived, wind-pollinated dioecious tree species found throughout Europe. In the rocky mountains of Thasos island, monumental old trees create a unique area of natural beauty. In recent times, the need to implement conservation measures for key endangered species such as Taxus baccata has intensified. Exploring the genetic diversity of the species is a prerequisite for successful forest management decisions aimed at conservation. In this study, 28 monumental trees from two natural populations of Thasos were investigated using eight Simple Sequence Repeat markers in order to assess the levels of genetic diversity and genetic differentiation within the individuals, to estimate the degree of inbreeding and the effective population size of each population, and to discuss the impact this study has on conservation efforts for the species. Although the population size was small (14 individuals per population), the results showed moderate to high genetic diversity parameters. The mean expected heterozygosity was He = 0.649 and the number of effective alleles was Ne = 3.270 for both populations. Moreover, allelic richness (AR = 3.395) was high, indicating a variable genetic pool which is probably a result of a past established expansion of the species in the area. The results of the present study present a unique genetic pool harbored by specific trees, which is an important advantage for ensuring their conservation and resistance against biotic and abiotic threats. Our study paves the way towards conservation measures, which can be prioritized as follows: (a) in situ conservation, (b) seed bank establishment, and (c) in vitro propagation in order to secure future resilience and sustainability of the species.

ИЗУЧЕНИЕ ПОЛИМОРФИЗМА МИКРОСАТЕЛЛИТНЫХ ЛОКУСОВ ОБРАЗЦОВ ВИНОГРАДА С НЕИДЕНТИФИЦИРОВАННОЙ СОРТОВОЙ ПРИНАДЛЕЖНОСТЬЮ АМПЕЛОГРАФИЧЕСКОЙ КОЛЛЕКЦИИ «МАГАРАЧ» С ИСПОЛЬЗОВАНИЕМ МОЛЕКУЛЯРНЫХ МАРКЕРОВ

The paper presents the results of DNA profiling of 28 grape samples with unidentified varietal affiliation, selected from the Magarach Ampelographic Collection, and provides polymorphism assessment of their microsatellite loci. Genotyping was performed using 9 nuclear (VVMD5, VVMD7, VVMD25, VVMD27, VVMD28, VVMD32, VrZAG62, VrZAG79, VVS2) and 3 chloroplast (ccmp3, ccmp5, ccmp10) SSR markers. For nuclear loci, 105 alleles were identified, the average number of alleles per locus (na) was 11.7; the average effective number of alleles (ne) is 7.23; Shannon information index (I) for the studied batch of samples was 2.13. The highest allele frequency was observed in samples with VVS2133 and VVS2135 (p = 0.250), VVMD5238 (p = 0.232), VVMD7247 (p = 0.232), VVMD25239 (p = 0.250), VVMD27180 (p = 0.232), VVMD28236 (p = 0.143), VVMD32272 (p = 0.304), VrZAG62188 (p = 0.179), VrZAG79251 (p = 0.232) alleles. The average value of actual heterozygosity Heto was 0.8333, expected heterozygosity Hetе was 0.8712. For chloroplast loci, 7 alleles were identified: ccmp3106, ccmp3107, ccmp5104, ccmp5105, ccmp10114, ccmp10115, ccmp10116. Also 4 chlorotypes were identified: A (1 sample), B (9), C (13), D (5). A dendrogram of genetic similarity was constructed using the UPGMA method, which showed the presence of three clusters containing, respectively, 11, 11 and 6 samples. There was a uniform distribution of chlorotypes B and D over three clusters, and chlorotype C – over two clusters. It is concluded that the results can be used to assess the genetic diversity of Magarach Ampelographic Collection.

Analysis of the genetic diversity and population structures of black locust (Robinia pseudoacacia L.) stands in Poland based on simple sequence repeat markers

Abstract Black locust (Robinia pseudoacacia L.) was introduced in Poland over 200 years ago, and its distribution area now covers the whole country, with the highest concentration of occurrence in the western part. Breeding of this species has been started in Poland for about 20 years, albeit on a limited scale, and two selected seed stands, 34 plus trees and two seed orchards have been registered. So far, selection efforts have not been coupled with the recognition of variation in the genetic structure of local populations. To fill the knowledge gap on genetic diversity, we selected the seven qualitatively best populations of R. pseudoacacia for our study. To clarify the origin of the Polish population of R. pseudoacacia, a sample from a seed stand in eastern Germany and from a seed orchard with Hungarian clones from the Oborniki Śląskie Forest District was added. In this study, three microsatellites were used to evaluate genotypes: Rops15, Rops16 and Rops18, with the Rops15 locus (motif AG) showing hypermutability. Moderate or high variability was observed in all microsatellite loci examined, with a total of 27 alleles identified. In all stands, the average observed number of alleles per locus was higher than the average effective number of alleles per locus. Three main clusters have been identified in the genetic structure of the population, one of which is represented by the population from the Regional Directorate of State Forests in Zielona Góra. The second group comprised the populations from Mieszkowice, the populations Pińczów and Wołów, and the population from Germany. The last one included population from Strzelce and Oborniki Śląskie, where the population from Hungary is represented. This may be of great importance for practice. Perhaps it is worth postulating the separation of two seed regions. Under most scenarios, climate change is projected to change the distribution of forest types and tree species in all biomes. It can be assumed that the importance of black locust in times of climate change is likely to increase.

Improving DNA mixtures analysis using compound markers composed of InDels and SNPs screened from the whole genome with next-generation sequencing.

Next-generation sequencing (NGS) allows for better identification of insertion and deletion polymorphisms (InDels) and their combination with adjacent single nucleotide polymorphisms (SNPs) to form compound markers. These markers can improve the polymorphism of microhaplotypes (MHs) within the same length range, and thus, boost the efficiency of DNA mixture analysis. In this study, we screened InDels and SNPs across the whole genome and selected highly polymorphic markers composed of InDels and/or SNPs within 300bp. Further, we successfully developed and evaluated an NGS-based panel comprising 55 loci, of which 24 were composed of both SNPs and InDels. Analysis of 124 unrelated Southern Han Chinese revealed an average effective number of alleles (Ae ) of 7.52 for this panel. The cumulative power of discrimination and cumulative probability of exclusion values of the 55 loci were 1-2.37×10-73 and 1-1.19×10-28 , respectively. Additionally, this panel exhibited high allele detection rates of over 97% in each of the 21 artificial mixtures involving from two to six contributors at different mixing ratios. We used EuroForMix to calculate the likelihood ratio (LR) and evaluate the evidence strength provided by this panel, and it could assess evidence strength with LR, distinguishing real and noncontributors. In conclusion, our panel holds great potential for detecting and analyzing DNA mixtures in forensic applications, with the capability to enhance routine mixture analysis.

Genetic diversity, population structure, and DNA fingerprinting of Ailanthus altissima var. erythrocarpa based on EST-SSR markers

Ailanthus altissima var. erythrocarpa is an A. altissima variety with high economic, ecological and ornamental value, but there have been no reports on the development of SSR primers for it. According to the SSR primer information provided by the transcriptome of A. altissima var. erythrocarpa, 120 individuals with different redness levels were used to screen polymorphic primers. Transcriptomic analysis revealed 10,681 SSR loci, of which mononucleotide repeats were dominant (58.3%), followed by dinucleotide and trinucleotide repeats (16.6%, 15.1%) and pentanucleotide repeats (0.2%). Among 140 pairs of randomly selected primers, nineteen pairs of core primers with high polymorphism were obtained. The average number of alleles (Na), average number of effective alleles (Ne), average Shannon’s diversity index (I), average observed heterozygosity (Ho), average expected heterozygosity (He), fixation index (F) and polymorphic information content (PIC) were 11.623, 4.098, 1.626, 0.516, 0.696, 0.232 and 0.671, respectively. Nineteen EST-SSR markers were used to study the genetic diversity and population structure of A. altissima var. erythrocarpa. The phylogenetic tree, PCoA, and structure analysis all divided the tested resources into two categories, clearly showing the genetic variation between individuals. The population showed high genetic diversity, mainly derived from intraspecific variation. Among nineteen pairs of primers, 4 pairs (p33, p15, p46, p92) could effectively distinguish and be used for fingerprinting of the tested materials. This study is of great significance for genetic diversity analysis and molecular-assisted breeding of A. altissima var. erythrocarpa.

Genetic diversity of bonytongue fish Heterotis niloticus (Cuvier, 1829) in Cameroon, Central Africa

The African bonytongue (Heterotis niloticus) fish is the only species of the Osteoglossidae family in Africa. The characterization of this fish was carried out from January to June 2020 in Cameroon where this fish is distributed in native zones. This study aimed at contributing to the genetic characterization of Heterotis niloticus population in Cameroon. A total of 96 Heterotis niloticus were sampled from five regions namely Centre, South, Littoral, North and Far North. Caudal fins where randomly collected for genomic DNA (gDNA) extraction. Following standard procedures for simple sequence repeat markers available for this species, seven microsatellites were used for genotyping through Polymerase Chain Reaction (PCR) and electrophoresis. Genetic parameters were scored using the GenAlex 6.503 software and the population structure of Heterotis niloticus was assessed under STRUCTURE Version 2.3.4 software. The results showed that the local population of Heterotis niloticus in North-Cameroon has a higher number of allele (Na=6.00) and effective number of allele (Ne=3.66) while the highest Observed Heterozygosity (Ho) was observed for the population of Heterotis niloticus in the Far-North. The highest genetic distance is observed between the population of Far North and Centre, Far-North and South, Far-North and North. In general, similarity within the sub-population of Heterotis niloticus is higher than 65%. Genetically, the population of Heterotis niloticus in Cameroon was grouped into three genetic sub-populations based on microsatellites appraisal. Further investigations are suggested for analysis concerning productive traits for domestication and aquaculture purposes.

Parentage verification and genetic diversity of the Arabian and Thoroughbred horse populations in Türkiye using microsatellite analysis.

This study aimed to determine the effectiveness of parentage verification in Arabian and Thoroughbred horses in Türkiye using microsatellite markers. A total of 813 Arabian and 959 Thoroughbred horses were genotyped using a total of 17 microsatellite markers. The mean effective number of alleles was 3,34 and the mean number of alleles was 7,41 in Arabian horses. It was calculated that the mean He and Ho values in Arabian horses were 0,677 and 0,680, respectively. The mean effective number of alleles was 3,55 and the mean number of alleles was 6,59 in Thoroughbred horses. It was calculated that the mean Ho and He values in Thoroughbred horses were 0,697 and 0,684, respectively. When the studied Arabian and Thoroughbred horse populations are considered as a single population, the mean FIT, FST and FIS values were found to be 0,063, 0,074 and, - 0,011, respectively. Also, 4 loci in Arabian horses and 3 loci in Thoroughbred horses significantly deviated from HWE. The mean PIC value was 0,63 in Arabian horses and 0,64 in Thoroughbred horses. As a result; the microsatellites including the most informative 15 and 9 loci had a total value of > 0,9999 (11 and 7 loci > 0,999) in each population for PE - 1 and PE - 3, respectively. It has been concluded that parentage verification and genetic identification can be made successfully in the Arabian and Thoroughbred horse populations by using the microsatellite markers panel.

Exploring the Genetic Diversity and Population Structure of Daphnia cucullata Sars, 1862 in Boreal Lakes (Latvian Lakeland) Based on Microsatellites

We have used Daphnia cucullata (Crustacea: Cladocera) as a model organism for the first time in the four deepest Latvian lakes from the Boreal biogeographical region in order to find the genetic diversity of these populations. During the research, we detected the most appropriate microsatellite markers for future genetic studies of Daphnia cucullata populations of lakes Svente, Riča, Dridzis and Geraņimovas-Ilzas in the Boreal biogeographical region. Based on these microsatellite markers, we determined the genetic diversity of these populations. The loci Dgm105 and Dgm101 had the maximum number of alleles and the maximum number of private alleles. The specific locus Dgm105 had five private alleles (62% of all detected alleles), and locus Dgm101 had four private alleles (57% of all detected alleles) in these loci. We determined the observed heterozygosity (Hobs) and the expected heterozygosity (Hexp) level (via Hardy–Weinberg equilibrium), the number of polymorphic loci, the number of detected alleles in each analyzed microsatellite locus, the average number of alleles at the locus (Na), the average effective number of alleles at the locus (Ne), the FST of the population’s genetic differentiation, the genetic distance (D) (following Nei) and the significance (χ2-test) of differences between the levels of observed and expected heterozygosity. It was shown that Daphnia cucullata populations from lakes with a low number of zooplankton taxa (Riča and Geraņimovas-Ilzas) have a higher genetic diversity compared to lakes with a high number of zooplankton taxa (Dridzis and Svente). It was found that Daphnia cucullata populations from lakes Dridzis and Svente have the least genetic distance, and these populations form a single genetic group, as confirmed via clustering.

Analysis of Genetic Diversity and Construction of a Core Collection of Ginkgo biloba Germplasm Using EST-SSR Markers

Understanding genetic diversity and population structure is essential for the conservation and utilization of germplasm. Ginkgo biloba L. is a medicinal, edible and ornamental tree species. Detailed knowledge of genetic variability and diversity in different Ginkgo germplasm resources is still scarce. In this study, a total of 173,160 Expressed Sequence Tag Simple Sequences Repeat (EST-SSR) loci were derived from 43,073 Unigenes of the Ginkgo genome. A total of 43,731 pairs of specific primers were designed for the EST-SSR loci, with sequence lengths &gt;20 bp, and 100 of the SSR primers were randomly selected. Among these, 20 EST-SSR markers were verified and used to assess the genetic diversity of 101 Ginkgo individuals collected from different regions. The average values for Shannon’s diversity index (I, 0.993), expected heterozygosity (0.566) and Nei’s genetic diversity index (H, 0.563) indicate a high level of genetic diversity of Ginkgo populations. Based on the EST-SSR markers, a core collection of Ginkgo germplasm comprising 27 genetic resources was constructed. The retention rates of the number of resources, the number of alleles, the number of effective alleles, the I index, the H index and the percentage of polymorphic loci of the constructed core collection are 26.73%, 95.29%, 103.43%, 102.25%, 102.91% and 100.00%, respectively. The molecular markers developed in this study are an effective tool for Ginkgo genetic diversity analysis and will facilitate the future breeding of this species.

Polymorphism of allelic variants of milk protein genes

The polymorphism of allelic variants of milk productivity genes (alpha-lactoglobulin, beta-casein, kappa-casein, prolactin, somatotropin) in cattle of the yaroslavl breed was studied in conjunction with an assessment of the genetic diversity of the studied population. The distribution of frequencies of occurrence of genotypes in the genes of the studied herds (0.1...0.716049) was determined. Based on the calculations of the average values ??of the genetic diversity indices, the effective number of alleles (1.679...1.994), the Shannon information index (0.594...0.692), the observed heterozygosity (0.087...0.716), the expected heterozygosity (0.404...0.498), fixation index (-0.498...0.823).The coefficient of inbreeding of subpopulations in the studied genes relative to the entire population indicates a weak differentiation of different herds (-0.023 ... -0.002). According to the analysis of the equilibrium distribution of genotypes according to the Hardy-Weinberg law, it is noted that the largest part of the herds has an equilibrium distribution of genotypes. The exception is yaroslavka breeding Plant JSC for the A1A2 beta-casein gene (20.095) and Agromir LLC (Mikhailovskoe branch) for the beta-casein gene (15.581).

Association Analysis of Tiller-Related Traits with EST-SSR Markers in Psathyrostachys juncea.

Psathyrostachys juncea is a long-lived perennial Gramineae grass with dense basal tillers and soft leaves. It is used widely in cold and dry areas of Eurasia and North America to establish grazing pasture and is even used as an ideal plant for revegetation and ecological restoration. Plant architecture, especially tillering traits, is critical for bunch grasses in breeding programs, and these traits in plants are mostly quantitative traits. In this study, the genetic diversity, population structure, and linkage disequilibrium of 480 individual lines were analyzed using 127 pairs of the EST-SSR marker, and a significant association between ten plant-architecture-related traits of P. juncea and molecular markers was found. The results of the genetic diversity analysis showed that the number of observed alleles was 1.957, the number of effective alleles was 1.682, Shannon's information index was 0.554, observed heterozygosity was 0.353, expected heterozygosity was 0.379, and the polymorphism information content was 0.300. A total of 480 individual lines were clustered into five groups based on population genetic structure, principal coordinate analysis, and unweighted pair group method with arithmetic mean analysis (UPGMA). The linkage disequilibrium coefficient (r2) was between 0.00 and 0.68, with an average of 0.04, which indicated a relatively low level of linkage disequilibrium among loci. The results of the association analysis revealed 55 significant marker-trait associations (MTA). Moreover, nine SSR markers were associated with multiple traits. This study provides tools with promising applications in the molecular selection and breeding of P. juncea germplasm.

Establishment of AA-NAT, SCD, PROP1, and IGFBP3 gene frequency distributions in Karacabey Merino and Kivircik Sheep Breeds

Thus, the aim of the current study was to investigate the genotypic dispersion of AA-NAT, SCD, PROP1, and IGFBP3 genes in the target population. Primarily, the genomic DNA was isolated from blood samples by the phenol/chloroform method. The genomic analyses were performed on a total of 160 Karacabey Merino (KM) sheep (n=80) and Kivircik (n=80). The PCR-RFLP method was used to determine the genotype of the SNPs. Deviation from Hardy–Weinberg equilibrium (HWE) and population genetic assays such as observed (Ho) and expected (He) heterozygosities, effective allele numbers (Ne), and the polymorphism information content (PIC) were calculated for each gene in the population. As a result, there was no deviation from HWE was determined except SCD and PROP1 gene in KM. The most frequent genotypes were found AA (66,25% and 87,50%) for AA-NAT gene, CC (93,75% and 91,25%) for SCD gene and CC genotype (70,00% and 56,25%) for PROP1 gene in KM and Kivircik sheep. All breeds were detected monomorphic in terms of the IGFBP3 gene. In conclusion, the other regions of the IGFBP3 gene which were determined as monomorphic in the studied flock could be researched. Moreover, further studies should be necessary for defining the effects of investigated genes on related traits in KM and Kivircik sheep in terms of polymorphic genes specified.

A proof-of-principle study: The potential application of MiniHap biomarkers in ancestry inference based on the QNome nanopore sequencing

Haplotyped SNPs convey forensic-related information, and microhaplotypes (MHs), as the most representative of this kind of marker, have proved the potential value for human forensics. In recent years, nanopore sequencing technology has developed rapidly, with its outstanding ability to sequence long continuous DNA fragments and obtain phase information, making the detection of longer haplotype marker possible. In this proof-of-principle study, we proposed a new type of forensic marker, MiniHap, based on five or more SNPs within a molecular distance less than 800 bp, and investigated the haplotype data of 56 selected MiniHaps in five Chinese populations using the QNome nanopore sequencing. The sequencing performance, allele (haplotype) frequencies, forensic parameters, effective number of alleles (Ae), and informativeness (In) were subsequently calculated. In addition, we performed principal component analysis (PCA), phylogenetic tree, and structure analysis to investigate the population genetic relationships and ancestry components among the five investigated populations and 26 worldwide populations. MiniHap-04 exhibited remarkable forensic efficacy, with 148 haplotypes reported and the Ae was 66.9268. In addition, the power of discrimination (PD) was 0.9934, the probability of exclusion (PE) was 0.9898, and the In value was 0.7893. Of the 56 loci, 85.71% had PD values above 0.85, 66.07% had PE values above 0.54, 67.86% had Ae values over 7.0%, and 55.36% were with In values above 0.2 across all samples, indicating that most of the MiniHaps are suitable for individual identification, paternity testing, mixture deconvolution, and ancestry inference. Moreover, the results of PCA, phylogenetic tree and structure analysis demonstrated that this MiniHap panel had the competency in continental population ancestry inference, but the differentiation within intracontinental/linguistically restricted subpopulations was not ideal. Such findings suggested that the QNome device for MiniHap detection was feasible and this novel marker has the potential in ancestry inference. Yet, the establishment of a more comprehensive database with sufficient reference population data remains necessary to screen more suitable MiniHaps.

Induction of Synthetic Polyploids of Porang (&lt;i&gt;Amorphophallus muelerri&lt;/i&gt; Blume) and Assessment of Its Genetic Variability Using Morphological Data and RAPD Molecular Marker

This study uses morphological characteristics and RAPD markers to evaluate the polyploidization of synthetic porang. Seeds of triploid porang (2n=2x=26) were soaked in the different colchicine concentrations for 24 hours. After colchicine treatment, the porang seeds were planted to an MS medium that contained 2.2 µM of 6-benzylaminopurine (BAP), then, 40 days after planting in the MS media, the morphology and molecular of synthetic polyploid porang were characterized. For DNA extraction, a total of 100 mg of young leaves of porang plantlet was collected. One way Anova followed by the Duncan test (95%) was performed for phenotypic characterization. The number of different alleles, number of effective alleles, Shannon's information index, diversity, and unbiased diversity were assessed for genetic diversity. Synthetic polyploid porang has a higher total shoot, root, and wider leaves than normal porang. Polyploidy induction also successfully increased the genetic diversity of porang, and the genetic diversity will increase porang adaptability and sustainability of porang cultivation.

Construction of the core germplasm of yellowhorn (Xanthoceras sorbifolium Bunge) using physiological traits and SSR markers

Yellowhorn (Xanthoceras sorbifolium Bunge) is an important ecological, economic, and ornamental plant species native to China. However, the physiological diversity, genetic variation, and core germplasms have not been revealed, which hindered the breeding process of yellowhorn. Here, we evaluated the genetic diversity of 155 yellowhorn germplasms using five physiological traits. The content of flavonoids varied significantly in different germplasms, and it was positively correlated with soluble sugar content (P < 0.01). A total of 253, 336 candidate SSR were identified from the whole genome of yellowhorn. A moderate genetic diversity was found in yellowhorn based on the mean values of the number of effective alleles (Ne = 2.307), expected heterozygosity (He = 0.527), and observed heterozygosity (Ho = 0.317) with 30 pairs of polymorphic SSR markers. Population structure, Neighbor-Joining phylogeny, and principal coordinates analyses divided all genotypes into two major groups with few admixtures. Meanwhile, we extracted 34 (21.94 %) core yellowhorn germplasms based on the variation in physiological traits (14 germplasms) and genetic diversity (23 germplasms). After multiple different analyses including genetic diversity parameters, coincidence rate of range, variance difference percentage, and coefficient of variation rate of change, there was no obvious difference between core and original germplasm, which indicated that the core germplasm could represent the original germplasm well. Our study will lay a solid foundation for future conservation and management of yellowhorn germplasms and the core collection will be valuable in molecular breeding programs.