Number Of Alleles Research Articles

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.

Characterization of the Northwestern Population of <i>Puccinia striiformis</i> f. sp. <i>tritici</i> on the Basis of Virulence and Representation of Invasive <i>PstS1</i> and <i>PstS2</i> Races

The expansion of the area of significance of yellow rust was observed in the last years. Until recently, in the conditions of the North-West, the disease occurred sporadically. However, in recent years, its strong development has been observed on wheat samples studied on the collection fields of scientific research institutes and State variety plots, as well as on some commercial fields in the Leningrad region. The aim of this work is to study the virulence and racial composition of the yellow rust pathogen in the Northwest and to conduct a molecular analysis of population samples for the presence of invasive races PstS1 and PstS2. Leaves of common wheat samples with of Puccinia striiformis urediniopustules were collected on commercial fields, State variety plots and experimental fields of the Research Institutes in 2020–2022. Near isogenic Avocet lines (Av NIL) with genes Yr1, Yr5, Yr6, Yr7, Yr8, Yr9, Yr10, Yr15, Yr17, Yr18, Yr24, Yr26, YrSp, Yr27 and differential varieties from international [Chinese 166 (Yr1), Lee (Yr7, Yr+), Heines Kolben (Yr6, Yr+), Vilmorin 23 (Yr3), Moro (Yr10, YrMor), Strubes Dickkopf (YrSD, Yr25, Yr+), Suwon 92/Omar) (YrSu, Yr+)] and European [Hybrid 46 (Yr4, Yr+), Reichersberg 42 (Yr7, Yr+), Heines Peko (Yr2, Yr6, Yr25, Yr+), Nord Desprez (Yr3, YrND, Yr+), Compair (Yr8, Yr19), Carstens V (Yr32, Yr25, Yr+), Spaldings Prolific (YrSP, Yr+), Heines VII (Yr2, Yr25, Yr+)] sets used for characteristic of pathogen virulence. Set of SCAR markers (SCP19M24a1, SCP19M24a2, SCP19M26a1, SCP19M26a2) used for identification of invasive races. A total 92 isolates were studied. High effectiveness at the seedling stage had genes Yr5, Yr10, Yr15, Yr24, Yr26. Isolates virulent to differential varieties Moro (Yr10, YrMor) and Nord Desprez (Yr3, YrND, Yr+) was not determined. Virulence to wheat genotypes with Yr17 gene was rare. Twenty-four virulence phenotypes identified using 29 virulence testers. The number of virulence alleles varied from 7 to 21. At the same time, differences between the phenotypes of P. striiformis on the studied common wheat varieties were insignificant. Most of them have united in a common group. Two groups of isolates slightly differentiated from them. The first included isolates from varieties characterized by a smaller number of virulence alleles, the second – with the maximum number of virulence alleles. Molecular analysis of the northwestern po-pulation revealed isolates belonging to the invasive PstS2 group in 2020 and 2022. Their virulence did not differ significantly from other northwestern phenotypes. The high evolutionary potential predetermines the need for annual monitoring of pathogen populations based on virulence and representation of invasive races.

6 Pulse Pressure and APOE ε4 Dose Interact to Affect Cerebral Blood Flow in Older Adults Without Dementia

Objective:Alterations in cerebral blood flow (CBF) are associated with risk of cognitive decline and Alzheimer’s disease (AD). Although apolipoprotein E (APOE) ε4 and greater vascular risk burden have both been linked to reduced CBF in older adults, less is known about how APOE ε4 status and vascular risk may interact to influence CBF. We aimed to determine whether the effect of vascular risk on CBF varies by gene dose of APOE ε4 alleles (i.e., number of e4 alleles) in older adults without dementia.Participants and Methods:144 older adults without dementia from the Alzheimer’s Disease Neuroimaging Initiative (ADNI) underwent arterial spin labeling (ASL) and T1-weighted MRI, APOE genotyping, fluorodeoxyglucose positron emission tomography (FDG-PET), lumbar puncture, and blood pressure assessment. Vascular risk was assessed using pulse pressure (systolic blood pressure -diastolic blood pressure), which is thought to be a proxy for arterial stiffening. Participants were classified by number of APOE ε4 alleles (n0 alleles = 87, m allele = 46, n2 alleles = 11). CBF in six FreeSurfer-derived a priori regions of interest (ROIs) vulnerable to AD were examined: entorhinal cortex, hippocampus, inferior temporal cortex, inferior parietal cortex, rostral middle frontal gyrus, and medial orbitofrontal cortex. Linear regression models tested the interaction between categorical APOE ε4 dose (0, 1, or 2 alleles) and continuous pulse pressure on CBF in each ROI, adjusting for age, sex, cognitive diagnosis (cognitively unimpaired vs. mild cognitive impairment), antihypertensive medication use, cerebral metabolism (FDG-PET composite), reference CBF region (precentral gyrus), and AD biomarker positivity defined using the ADNI-optimized phosphorylated tau/ß-amyloid ratio cut-off of > 0.0251 pg/ml.Results:A significant pulse pressure X APOE ε4 dose interaction was found on CBF in the entorhinal cortex, hippocampus, and inferior parietal cortex (ps < .005). Among participants with two e4 alleles, higher pulse pressure was significantly associated with lower CBF (ps < .001). However, among participants with zero or one ε4 allele, there was no significant association between pulse pressure and CBF (ps > .234). No significant pulse pressure X APOE ε4 dose interaction was found in the inferior temporal cortex, rostral middle frontal gyrus, or medial orbitofrontal cortex (ps > .109). Results remained unchanged when additionally controlling for general vascular risk assessed via the modified Hachinski Ischemic Scale.Conclusions:These findings demonstrate that the cross-sectional association between pulse pressure and region-specific CBF differs by APOE ε4 dose. In particular, a detrimental effect of elevated pulse pressure on CBF in AD-vulnerable regions was found only among participants with the e4/e4 genotype. Our findings suggest that pulse pressure may play a mechanistic role in neurovascular unit dysregulation for those genetically at greater risk for AD. Given that pulse pressure is just one of many potentially modifiable vascular risk factors for AD, future studies should seek to examine how these other factors (e.g., diabetes, high cholesterol) may interact with APOE genotype to affect cerebrovascular dysfunction.

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.

History of traumatic brain injury does not alter course of neurocognitive decline in older adults with and without cognitive impairment.

Traumatic brain injury (TBI) history is associated with dementia risk, but it is unclear whether TBI history significantly hastens neurocognitive decline in older adults. Data were derived from the National Alzheimer's Coordinating Center (NACC) data set. Participants with a history of TBI (TBI +; n = 1,467) were matched to individuals without a history of TBI (TBI-; n = 1,467) based on age (50-97, M = 71.61, SD = 8.40), sex, education, race, ethnicity, cognitive diagnosis, functional decline, number of Apolipoprotein ε4 (APOE ε4) alleles, and number of annual visits (3-6). Mixed linear models were used to assess longitudinal neuropsychological test composite scores of executive functioning/attention/speed, language, and memory in TBI + and TBI- participants. Interactions between TBI and demographics, APOE ε4 status, and cognitive diagnosis were also examined. Longitudinal neuropsychological functioning did not differ between TBI groups (p's > .001). There was a significant three-way interaction (age, TBI history, time) in language (F[20, 5750.1] = 3.133, p < .001) and memory performance (F[20, 6580.8] = 3.386, p < .001), but post hoc analyses revealed TBI history was not driving this relationship (all p's > .096). No significant interactions were observed between TBI history and sex, education, race/ethnicity, number of APOE ε4 alleles, or cognitive diagnosis (p's > .001). Findings suggest TBI history, regardless of demographic factors, APOE ε4 status, or cognitive diagnosis, does not alter the course of neurocognitive functioning later-in-life in older adults with or without cognitive impairment. Future clinicopathological longitudinal studies that well-characterize head injuries and the associated clinical course are needed to help clarify the mechanism in which TBI may increase dementia risk. (PsycInfo Database Record (c) 2023 APA, all rights reserved).

87 Not Normal but not MCI: Course of Memory over time

Objective:A diagnosis of mild cognitive impairment (MCI) requires memory complaint and objective memory impairment. However, some individuals report subjective memory complaints (SMC) despite having intact memory performance, while others demonstrate subtle impairment on memory testing but have no memory complaints; neither case would meet criteria for MCI. This study aimed to compare memory performances over time in individuals who do not meet traditional MCI criteria to those with normal cognition and those who converted to MCI.Participants and Methods:Diagnoses for a longitudinal sample from the Texas Alzheimer’s Research and Care Consortium were reviewed by a consensus panel of neuropsychologists and neurologists and reclassified at time of last visit. Diagnostic categories included SMC (i.e., memory complaint but no impairment on testing), objective cognitive impairment but no complaint (Impaired but not MCI), normal control (NC), MCI, and dementia. In this study, 827 participants were divided into 4 groups: 1) NC over 5 visits (n=511, 71% female; 42% Latinx/Hispanic), 2) baseline NC to amnestic MCI (n=62; 63% female; 57% Latinx/Hispanic), 3) SMC at last visit (n=133; 58% female; 70% Latinx/Hispanic), and 4) impaired but not MCI at last visit (n=121; 71% female; 60% Latinx/Hispanic). A memory composite (z-score) was created from the CERAD list-learning task (immediate, delayed, and recognition-discrimination) and Wechsler Memory Scale (Immediate and Delayed Logical Memory and Visual Reproduction) to evaluate memory performance over time. A linear mixed-model adjusting for age, education, sex, ethnicity, and number of APOE e4 alleles evaluated memory performance across 5 visits for the groups. To assess if depression followed a similar course, a linear mixed-model evaluated Geriatric Depression Scale (GDS) scores over time.Results:At baseline, groups differed by age (F=22.82; p&lt;.001), education (F=8.60; p&lt;.001), MMSE scores (F=9.38; p&lt;.001), GDS-30 scores (F=3.56; p=.015), and memory composites (F=24.29; p&lt;.001). A significant group X time interaction was observed (F=4.83, p&lt;.001). Memory performance improved in both the SMC and the NC groups, remained stable in the impaired but not MCI group, and declined (as expected) in those who converted to amnestic MCI. Depression scores also showed a significant group X time interaction (F=2.43; p=.004), in which the NC to MCI group endorsed slightly more depression symptoms over time, while other groups declined or remained stable.Conclusions:Memory trajectories in this diverse sample differed across groups. Individuals with SMC but without objective memory impairment and normal controls showed some improvement in memory over time, presumably due to practice effects. Those with subtle memory impairments but no complaint (i.e., did not meet MCI criteria) remained stable and those who converted to amnestic MCI had worse memory across time. The stability of memory performances in the impaired not MCI group suggests these subtle memory inefficiencies may be longstanding or unperceived. However, because our sample achieved retrospective diagnoses of SMC and impaired not MCI, it will be important for future studies to prospectively follow these groups to determine which risk factors may predict progression to MCI and what impact ethnicity may have on these trajectories.

Genetic Variation among Three Species of Genus &lt;i&gt;Erythroculter&lt;/i&gt;

The genus Erythroculter (Cypriniformes, Cyprinidae, Abramidinae) is one of the most commercially important freshwater fish species inhabiting China. However, very limited information is available regarding genetic variation among Erythroculter species, therefore hindering their effective management. In this regard, microsatellite markers and sequences of mitochondrial COII and D-loop were analyzed to investigate the genetic variation among three species of genus Erythroculter. Results demonstrated that 11 microsatellite loci were amplified effectually, and the size of allele was 110–350, 94–338 and 86–384 bps in E. ilishaeformis, E. dabryi and E. mongolicus respectively. Average number of allele was 5.82, 5.73 and 6.45 per locus for E. ilishaeformis, E. dabryi and E. mongolicus respectively. Fragments of COII and D-loop was 675 and 929 bps respectively. On the basis of Shannon’s information index, heterozygosity, polymorphic information content and nucleotide diversity index (P), the microsatellite and nucleotide diversity of E. ilishaeformis was most abundant, and that of E. mongolicus was least abundant. Based on the haplotype distribution of D-loop or the allele size in microsatellite loci of EI19 or HWB05, it could be distinguished perfectly among E. ilishaeformis, E. dabryi and E. mongolicus. Some historical and environmental elements might result in the high genetic divergence and promote the speciation of E. ilishaeformis, E. dabryi and E. mongolicus. These results would be of avail in the conservation and sustainable utilization of these three species.

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 locus estimates of allelic diversity of STR markers in a sample of breeding bulls

Genotypes of the 11 DNA microsatellite loci of 84 bulls of seven breeds were used to evaluate 14 indicators of allelic diversity/differentiation. Traditional and multidimensional statistical methods were applied to the data matrices from the original and transformed estimates (11×14). Estimates of heterozygosity had coefficients of variability of 8-14 %, the number of alleles per locus and indicators of differentiation of breeds at the level of 20-26 %, fixation indices – 38-44 %. Statistically significant Kendall correlations (0.8-1.0) between indicators of allelic richness and heterozygosity, fixation indices, and differentiation indicators were established. The variability of the transformed estimates of diversity/differentiation indicators by loci was in the range of 6-32 %. Including by loci Eth3, Tgla122, Eth225, Bm2113 – 6-12 %, loci Inra23, Tgla126, Eth10 – 15-20 %, loci Tgla227, Sps115, Tgla53, Bm1824 – 28-32 %. The nonparametric Mann-Whitney-Wilcoxon test showed statistically significant differences in the medians of the Eth3 locus with the Bm2113 locus, the Tgla126 locus with the Eth3, Inra23, Tgla122, Eth225, Bm2113, Bm1824, Eth10 loci. The principal component analysis (PCA) identified two components with a total information content of 95,2 %. The first one took into account 59.4 % of the total variance, had the highest loads in intra-breed diversity data and was defined as an «alpha component». The second accounted for 35.8 % of the total variance, had the highest loads in inter-breed differentiation data and was defined as a «beta component». 2D-PCA-ordination showed that a characteristic grouping of loci took place for the analyzed breeds (samples), loci and measures of diversity. Loci Tgla227 and Tgla53 formed group A, group B – loci Tgla122, Eth225, Eth10, group C – loci Inra23, Bm2113 and Bm1824. The loci of the conditional group D (Eth3, Tgla126, Sps115) were defined as «untypical». Validation of ordination was confirmed by calculations on reduced data (dimension 11×7) and the method of non-metric multidimensional scaling (nMDS). The consistency of ordinations according to the Procrust test was 96 % (pperm &lt;0.001). A similar classification of loci was obtained by cluster analysis (UPGMA) with butstrap probabilities of cluster: A – 73, B – 100, C – 73, D – 47 %. The distances and similarity indicators (S) between the profiles of loci and the «true» summary estimates for 11 loci were calculated. Loci Tgla126 and Sps115 had S ≈ 40 %, loci Tgla53 and Bm1824 – at the level of 60 %, loci Inra23, Tgla227 and Bm2113 – 70-75 %, loci Eth3, Tgla122, Eth225 and Eth10 – 84-88 %. The average absolute deviation of the estimates of diversity indicators for the four loci with S≥84 % from the «true» estimates was 3.4 %, for the four loci with S≤60 % – 12.4 %. According to component scores, a general diversity index, γLV, was calculated for each locus. Its correlation with the estimates of the Shannon/Sherwin′s γ-diversity with a 95 % probability value was in the range of 0.73-0.98, Kendall's rank correlation was 0.67 (pvalue = 0.005). The conducted research makes a certain contribution to the expansion of tools for processing molecular genetic data in the analysis of allelic diversity in subdivided populations.

Microsatellite-based diversity analysis and the development of core-set germplasm in Pakistani barley lines.

Illustrating the population structure and genetic diversity in selected germplasm resources (after three year multi locations trials) plays a key role which directly utilize the selection of lines in a population for accumulative trait breeding in crops. In order to further understand, the structure of population and genetic variability, we explored 100 selected lines, cultivated for three consecutive years (2016-2019) in swat, University of Malakand, Khyber Pakhtunkhwa Pakistan and Provinces of China (Chongqing and Beijing) with 33 mapped SSR markers. The integrated population structure analysis in a core of hundred germplasm with Pakistani origin with three approved commercial barley cultivars have strong stratification that allowed their division into four major subpopulations (i.e. PI, PII, PIII and PIV) and an admixture subpopulation, with 52, 9, 15 and 27 germplasm respectively. A total of 133 alleles were identified with mean value of 0.80 Polymorphic information content. The number of alleles detected by the system varied from two alleles amplified to as six with an average of 4.03 per SSR marker pair. The gene diversity ranged from 0.56 to 0.98 with an average of 0.82 in selected germplasm resources. Based on the SSR data, the 100 selected germplasm with three cultivars were classified into four main phylogenetic Linages (LI, LII, LIII and LIV) which corresponded to the phylogenic grouping in genotypes. We assembled a core set of 20 barley genotypes (~1/5 of original population size) to sustain sufficient mapping of SSR marker with Phenotype, in which we proposed four SSR markers, Bmac0040, Bmac0134, Bmag0125 and Bmag0211 for malt gene and marker (Bmac0399) for tolerance to salinity gene, which will be applicable for marker assisted breeding in barley gene resources.

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.

Genetic and phenotypic diversity of native potatoes (Solanum spp.) from the Central Andes of Peru

The diversity of native potatoes cultivated above 3500 masl in the Pasco region (Central Andes of Peru) has not been fully characterized. It is currently subject to constant genetic erosion caused by biotic and abiotic factors. The research aimed to characterize phenotypically and genotypically 40 native potato landraces representative of 4 Solanum species. Twenty phenotypic descriptors and 10 microsatellites were used for genetic evaluation. Likewise, the ploidy level was evaluated based on the number of chloroplasts in the stomata. The clustering analysis was performed using the Infostat software and the R program with the Adegenet and Polysat libraries. The phenotypic characterization allowed to obtain five groups with a distance coefficient of 9.5. The molecular characterization found seven groups and 58 alleles in total. The average number of alleles per microsatellite was 5.5. 13.2 % of duplicates were identified. The microsatellites STG001, STM1106, ST0032, and STM5127 with an average He of 0.8 and a polymorphism information content (PIC) of 0.5 - 0.8 were the most informative. Finally, the ploidy results were 13 % diploid, 35 % triploid, and 52 % tetraploid. It was evidenced low diversity when using a set of 10 SSR markers, which indicates limited applicability for studying the genetic diversity of local potato landraces. It is necessary to involve a broader range of markers and a more diverse set of genotypes from the Pasco region for further studies.

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).

Detection of in silico SSR Markers Specific to Uzun and Kırmızı Cultivars in Pistachio

In the current paper, it was aimed to detect the SSR markers that can be used in the prevention of confusion that may occur in breeding or nurseries, and directly genetically separating Uzun and Kırmızı pistachio cultivars from other commercial cultivars. A total of genotypes of 16 Pistacia vera species, one P. atlantica, one P. eurycarpa and two P. terebinthus species were obtained from the farmer's orchard in Nizip district of Gaziantep province for genetic characterization. Genetic diversity and clustering analyzes were performed with UPGMA (Unweighted Pair Group Method with Arithmetic Average) and STRUCTURE 2.3.4 programs using the scored SSR loci. Genetic relationship and population structure of genotypes were defined using common and distinct polymorphic PCR fragments. Cultivar-specific markers to be used in identifying and distinguishing the genetic structure of Uzun and Kırmızı cultivars were carried out in the current research. CUPOhBa2127 marker has the highest allele number (Na=10). In addition, 11 out of 25 SSR markers were explained as cultivar-specific SSRs that can distinguish Uzun and Kırmızı cultivars. These markers can be used directly by breeders and geneticists without any preliminary screnning of the markers. A quite serious providence will be achieved in the cost and time that will occur with the preliminary analysis, and thus, the confusion that may occur in large scale orchard establishments or nurseries will be reduced to pretty low levels with DNA analysis.

Development of polymorphic simple sequence repeat markers in Agastache rugosa and their application in genetic evaluation and cross-taxon transferability of Agastache species

Agastache is a genus of perennial herbaceous plants belonging to the mint family, Lamiaceae. Several Agastache species are commercially cultivated and used as medicinal, culinary, and ornamental plants. However, information on the genetic diversity and population structure of the species remains unclear. In the present study, genetic diversity within Agastache species was analyzed using simple sequence repeat (SSR) markers. In this study, 249,746 SSRs were identified in the A. rugosa genome and primer pairs were designed for 56,675 SSRs. The majority of SSR repeat types were dinucleotides (60.65%), followed by trinucleotides (12.38%), and pentanucleotides (12.10%). PCR conditions were established for 250 primer pairs, 111 of which were found to be polymorphic in A. rugosa germplasm. The number of alleles (NA) ranged from 2 to 19, major allele frequency (MAF) ranged from 0.11 to 0.95, observed heterozygosity (HO) ranged from 0 to 0.89, and polymorphic information content (PIC) ranged from 0.09 to 0.92. Cross-species amplification of SSRs markers in other Agastache species showed amplification rates of 82.6% for A. foeniculum and 78.1% in A. urticifolia, with an average of 80.37%. Cluster analysis of the 19 A. rugosa accessions using SSRs markers revealed four major clusters, and population STRUCTURE analysis using 79 SSRs markers revealed three groups and three subgroups among the A. rugosa populations. The SSRs markers developed can contribute to applications such as varietal identification, genetic diversity analysis, and population structure analysis of A. rugosa germplasm.

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.

Alphabet cardinality and adaptive evolution

One of the most fundamental characteristics of a fitness landscape is its dimensionality, which is defined by genotype length and alphabet cardinality—the number of alleles per locus. Prior work has shown that increasing landscape dimensionality can promote adaptation by forming new ‘uphill’ mutational paths to the global fitness peak, but can also frustrate adaptation by increasing landscape ruggedness. How these two topographical changes interact to influence adaptation is an open question. Here, we address this question in the context of alphabet cardinality, using theoretical fitness landscapes with tuneable fitness correlations, as well as three empirical fitness landscapes for proteins. We find that the primary effect of increasing alphabet cardinality is the introduction of a new global fitness peak. Controlling for this effect, we find that increasing alphabet cardinality promotes adaptation on uncorrelated fitness landscapes, but frustrates adaptation on correlated fitness landscapes. The primary explanation is that the increased ruggedness that accompanies alphabet expansion is characterized by an increase in mean peak height on uncorrelated fitness landscapes, but a decrease in mean peak height in correlated fitness landscapes. Moreover, in two of the empirical fitness landscapes we observe no effect of increasing alphabet cardinality on adaptation, despite an increase in the number of peaks and a decrease in mean peak height, calling into question the utility of these common measures of landscape ruggedness as indicators of evolutionary outcomes.

Genome-wide in silico characterization, validation, and cross-species transferability of microsatellite markers in Mallard and Muscovy ducks

BackgroundMicrosatellites are important markers for livestock including ducks. The development of microsatellites is expensive and labor-intensive. Meanwhile, the in silico approach for mining for microsatellites became a practicable alternative. Therefore, the current study aimed at comparing whole-genome and chromosome-wise microsatellite mining approaches in Muscovy and Mallard ducks and testing the transferability of markers between them. The GMATA software was used for the in silico study, and validation was performed using 26 primers. ResultsThe total number of the detected microsatellites using chromosome-wise was 250,053 and 226,417 loci compared to 260,059 and 238,462 loci using whole genome in Mallards and Muscovies. The frequencies of different motifs had similar patterns using the two approaches. Dinucleotide motifs were predominant (> 50%) in both Mallards and Muscovies. The amplification of the genomes revealed an average number of alleles of 5.08 and 4.96 in Mallards and Muscovies. One locus was monographic in Mallards, and two were monomorphic in Muscovies. The average expected heterozygosity was higher in Muscovy than in Mallards (0.45 vs. 0.43) with no significant difference between the two primer sets, which indicated the usefulness of cross-species amplification of different primers. ConclusionThe current study developed a whole-genome SSR panel for ducks for the first time, and the results could prove that using chromosome-wise mining did not generate different results compared to the whole-genome approach.

Changes in Allele Frequencies and Genetic Diversity in Red Clover after Selection for Cold Tolerance Using SSR Markers

The selection of red clover (Trifolium pratense L.) populations adapted to extreme environmental conditions is of great importance due to continuing climate change. The plant material analyzed with simple sequence repeat (SSR) markers included two parent populations, P1 (cultivar ‘Reichersberger’) and P3 (cultivar ‘Croatia’) and their reselections, which were created after one cycle of selection under cold temperature conditions. The reselections PS1 and PS3 were produced by intercrossing 38 surviving plants of parent populations P1 and P3, respectively. A total of 48 plants from each cultivar and each reselection were randomly selected for SSR analysis. Sixteen SSR primer pairs were selected, taking into account the presence of loci on all seven pairs of red clover chromosomes. An increase in the average frequency of alleles from the initial populations to the populations after one cycle of selection was observed, followed by a decrease in the number of alleles. Out of a total of 16 loci, the Waples neutrality test revealed significant frequency changes at 12 loci from P1 to PS1 and 9 loci from P3 to PS3 populations. The genetic diversity in the studied populations did not change significantly after selection, leaving enough genetic variability as a prerequisite for the success of future selection.

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.