The interacting effects of genetic variation in Geranium subg. Geranium (Geraniaceae) using scot molecular markers

One of the most crucial aspects of biological diversity for conservation strategies is genetic diversity, particularly in rare and narrow endemic species. Our study is the first attempt to utilize SCoT markers to check the genetic diversity in Iran. We used 115 plant samples. Our objectives were 1) to check genetic diversity among Geranium species 2) Genetic structure of the Geranium 3) Do the Geranium species exchange genes? 4) To detect isolation by distance among the Geranium species. We used traditional morphological and molecular methods to assess genetic diversity and genetic structure in the Geranium species. A total of 129 amplified polymorphic bands were generated across 13 Geranium species. The size of the amplified fragments ranged from 150 to 3000 bp. G. stepporum showed the highest values for the effective number of alleles (Ne = 1.30) and Shannon information index (I =0.35). Significant ANOVA results (P <0.01) showed differences in quantitative morphological characters in plant species. G. sylvaticum showed high genetic diversity. Mantel test showed a significant correlation (r = 0.17, p=0.0002) between genetic distance and geographical distance, so isolation by distance (IBD) occurred among the Geranium species. According to the SCoT markers analysis, G. kotschyi and G. dissectum had the lowest similarity, and the species of G. sylvaticum and G. pratense had the highest similarity. The present study revealed that a combination of morphological and SCoT methods could distinguish the species of Geranium.

GENETIC DIVERSITY OF THE HOLSTEIN CATTLE POPULATION IN THE YAROSLAVL REGION

В работе представлена генетическая структура популяции крупного рогатого скота голштинской породы 9-ти племенных хозяйств Ярославской области, основанная на иммуногенетических показателях групп крови по EAB-локусу. Было проанализировано 6343 головы крупного рогатого скота и выявлено 78 аллельных вариантов. Генотипирование животных по генетическим маркерам позволяет оценить динамику генетических процессов в породе и отдельных стадах. На основании расчета частот аллельных вариантов проведена клатеризация хозяйств методом k-means для выявления генетически близких групп. Популяция голштинской породы разделилась на несколько кластеров, имеющих различное генетическое происхождение и отличающихся уникальными аллельными вариантами групп крови. Доли дисперсии, объясняемые главными компонентами, имеют значения от 0,14 до 0,22, что свидетельствует о высокой степени отражения главными компонентами реальной дисперсии частот. Мера информационного полиморфизма (PIC) для всех хозяйств находится на уровне 0,022—0,024, что говорит о невысокой дискриминационной способности данного маркера. Разброс показателей среднего на локус индекса информации Шенона (I) составил 0,031±0,001—0,039±0,001 и генного разнообразия (Ht) — 0,022±0,005—0,024±0,005, что свидетельствует о более высоком селекционном потенциале животных отдельных хозяйств и об уменьшении вероятности внутрипородного инбридинга. Представленные методы анализа данных и параметры генетического разнообразия позволяют выявить группы скота внутри популяции и оценить его генный потенциал. Это даст возможность судить о генетических процессах, происходящих в стадах, и рекомендовать представленные методы для оценки эффективности и направленности селекционного процесса. The article presents the genetic structure of Holstein cattle population of 9 breeding farms in the Yaroslavl region, based on the immunogenetic parameters of blood types at the EAB-loci. 6343 heads of cattle and 78 allelic variants were analyzed and identified. Genotyping of animals by genetic markers makes it possible to assess the dynamics of genetic processes in the breed and individual herds. Based on the frequency calculations of allelic variants, we carried out the clustering of farms by the k-means method to identify genetically similar groups. The population of the Holstein cattle was divided into several clusters with different genetic origins and differing in unique allelic variants of blood types. The proportions of dispersion explained by the principal components have values from 0.14 to 0.22, which indicates a high degree of reflection by the principal components of the real frequency dispersion. The measure of information polymorphism (PIC) for all farms is at the level of 0.022—0.024, which indicates a low discriminatory ability of this marker. The scatter of the indices of the average per locus of the Shannon information index (I) was 0.031 ± 0.001—0.039 ± 0.001 and of genetic diversity (Ht) — 0.022 ± 0.005-0.024 ± 0.005, this indicates a higher breeding potential of animals on individual farms and a decrease in the probability of inbreeding. The presented methods of data analysis and parameters of genetic diversity make it possible to identify groups of livestock within a population and assess its genetic potential. This will make it possible to judge the genetic processes occurring in herds, and to recommend the presented methods for assessing the performance and direction of the breeding process.

Universal Rice Primer (URP) and Start Codon Target (SCoT) Markers in Studying Population Structures and Genetic Variation in Ferula AssafoetidaL. Accessions

Ferula assafoetidais an herbaceous, annual and monocarpic genus of the Apiaceae family. So far, there has been common usage of Ferula oleo resinous gum in food and herbal medicines.The origin of F.assafoetidais can be traced back into the steppes of Iran and some reigns of Afghanistan with an extended distribution. Despite the economic value and therapeutic importance of F.assafoetida, only a few studies have reported on the genetic capacity of this herb.The present study was carried out on a set of 90 individual plants belonging to different populations of Ferula assafoetida L. via the start codon target marker (SCoT) and the universal rice primer (URP) markers. Twelve SCoT and twelve URP primers generated 192 and 149 polymorphic fragments, while having 16 and 12.41 fragments respectively on average per primer. The Polymorphism information content (PIC) for URP primers and ScoT ranged from 0.31 to 0.43 and 0.34 to 0.44 respectively, which indicated a good efficiency forboth markers. The diversity indices including heterozygosity (He), percentage of polymorphic bands (PPB), Shannon’s information index (I) and marker index (MI) were calculated based on the SCoT and URP data.The results revealed that SCoT primers were more efficient than URP primers in identifying genetic diversity within populations. Neighbor joining (Nj), as a base for clustering, classified 90 accessions into 5 and 6 groups using SCoT and URP data respectively. Moreover, the combined data (SCoT+URP) succeeded in classifying all accessions into 6 groups, although this did not correspond with the geographical distribution of accessions. Structure analysis divided 90 genotypesinto 5 subpopulations using SCoT and URP markers, whereas the combined data (SCoT+URP) divided the accessions into 6 subpopulations, which confirmed the classification achieved by the Nj method. Principal coordinate analysis (PCoA) corroborated these conclusions. According to the analysis of molecular variance) AMOVA(, a high percentage of genetic diversity was found within the species, suggesting a rich diversity of germplasm for breeding plans. The assessment of population structure demonstrated a high rate of gene flow and the mixture of populations. Taken together, our findings suggest SCoT markers are more efficient than URP markers in assessing genetic diversity among F.assafoetida genotypes. All in all, genetic diversity could help the selection of appropriate markers and special genotypes for breeding plans.

Water Activity Prediction in Sugar and Polyol Systems Using Theoretical Molecular Descriptors

Water activity is a key factor in the development of pharmaceutical, cosmetic, and food products. In aqueous solutions of nonelectrolytes, the Norrish model provides a simple and effective way to evaluate this quantity. However, it contains a parameter, known as the Norrish constant, that must be estimated from experimental data. In this study, a new strategy is proposed for the prediction of water activity in the absence of experimental information, based on the use of theoretical molecular descriptors for characterizing the effects of a solute. This approach was applied to the evaluation of water activity in the presence of sugars (glucose, fructose, xylose, sucrose) and polyols (sorbitol, xylitol, glycerol, erythritol). The use of two descriptors related to the constitutional and connectivity properties of the solutes was first investigated. Subsequently, a new theoretical descriptor, named the global information index (G), was developed. By using this index, the water activity curves in the binary systems were reconstructed. The positive results obtained support the proposed strategy, as well as the possibility of including, in a single information index, the main molecular features of a solute that determine its effects on water activity.

Genetic Divergence among Populations of Invasive Alien Species Lantana camara L. from Selected Areas of Bangladesh

Lantana camara L., a well-known invasive alien species causing invasion and posing threat to native plant species community in different regions of Bangladesh. The present study aimed to investigate the genetic diversity of L. camara populations in different regions of Bangladesh. Eight RAPD markers were used in order to probe into its genetic variability. Total number of bands (202), polymorphic loci (104), per-centage of polymorphism (97.20%), average Shanon’s information index (0.3051±0.115), Nei’s gene diversity (0.4733±0.144) was found and in different populations and multiple divergent genetic clustering along with presence of unique alleles (4) for RAPD revealed high genetic diversity among the populations of L. camara in different regions of Bangladesh.

Inter-Simple Sequence Repeat (ISSR) Markers Revealed Genetic Diversity and Population Structure Among 9 Wild Species of Clematis L.

To analyze the genetic diversity of 9 species of Clematis from 31 different populations, we extracted DNA by the improved CTAB method, used ISSR-PCR for amplification, and then selected 9 primers with clear amplified bands from amongst 220 primers. A total of 127 clear bands were amplified, of which 126 were polymorphic bands, yielding a ratio of 99.2%. The polymorphism information index (PIC) of the primers ranged from 0.9326 to 0.9649. The Nei’s genetic diversity index (H) was 0.2750, the total gene diversity (Ht) was 0.2845, and the genetic differentiation coefficient (Gst) was 0.6696, indicating high genetic differentiation among populations of Clematis. After cluster analysis, the 31 Clematis populations were divided into 3 categories. Principal coordination analysis (PCoA) of 9 Clematis species then showed that the genetic relationship between samples of the same Clematis germplasms was closer than that of samples from the same region. The mantel test revealed a significant positive correlation between genetic distance and geographical distance among the populations. The population clustering results are broadly consistent with the clustering graphs of UPGMA and PCoA. We can conclude the polymorphism of the 9 primers is good, and that the genetic diversity of 31 Clematis populations is rich. Individual Clematis germplasms are closely related and will gather together preferentially.

Eficiența unor marcheri moleculari în discriminarea populațiilor de lupoaie originare din China

In this study, the effectiveness of different types of molecular markers in assessing genetic diversity of populations of O. cumana from China was determined. ISSR and SSR markers detected different levels of genetic variability among and within broomrape populations. SSR markers analysis showed high level of genetic variation within the populations as revealed by high average values of Nei's gene diversity (H=0,75) and Shannon's information index (I=1,44), while genotyping with ISSR markers showed greater ability to discriminate genotypes according to Resolving power (Rp=7,24). Thus, the combined use of ISSR and SSR markers allowed the detection of higher polymorphism than either set of marker alone.

Eco-Geographical, Morphological and Molecular Characterization of a Collection of the Perennial Endemic Species Medicago tunetana (Murb.) A.W. Hill (Fabaceae) from Tunisia

In order to characterize and conserve the endemic pastoral species Medicago tunetana, many prospecting missions were carried out in mountainous regions of the Tunisian ridge. Twenty-seven eco-geographical and morphological traits were studied for six M. tunetana accessions and followed by molecular analysis using seven Simple Sequence Repeat (SSR). Only five markers were polymorphic and reproductible in the six M. tunetana populations. A total of 54 alleles were observed with an average of 10.8 bands/primer/genotype. Mean Polymorphism Information Content (PIC), Nei gene diversity (h) Shannon’s information index (I) indicated the high level of polymorphism. The generated dendrogram with hierarchical UPGMA cluster analysis grouped accessions into two main groups with various degree of subclustring. All the studied accessions shared 57% of genetic similarity. Analysis of variance showed high significant difference between morphological traits among M. tunetana populations where MT3 from Kesra showed different morphological patterns regarding leaf, pod and seeds traits. Canonical correspondence analysis (CCA) showed two principal groups of M. tunetana populations based on potassium, total and active lime contents in soil. Our results suggest that SSR markers developed in M. truncatula could be a valuable tool to detect polymorphism in M. tunetana. Furthermore, the studied morphological markers showed a large genetic diversity among M. tunetana populations. This approach may be applicable for the analysis of intra specific variability in M. tunetana accessions. Our study could help in the implementation of an effective and integrated conservation programs of perennial endemic Medicago.

Assessing quality of family planning counseling and its determinants in Kenya: Analysis of health facility exit interviews

Background Available evidence suggests that provision of quality of care in family planning services is crucial to increasing uptake and continuation of use of contraception. Kenya achieved a modern contraceptive prevalence rate of 60% in 2018, surpassing its 2020 target of 58%. With the high prevalence, focus is geared towards improved quality of family planning services. The objective of this study is to examine the quality of family planning counseling and its associated factors in health facilities in Kenya. Methods We conducted a secondary analysis of the 2019 Kenya Performance Monitoring and Action, client exit data of women who had received family planning services. Quality of counseling was assessed using the Method Information Index Plus. We conducted a multivariable ordinal logistic regression analysis of data from 3,731 women to establish determinants of receiving quality family planning services. Results The Method Information Index Plus score for higher-quality counseling was 56.7%, lower-quality counseling 32.4%, and no counseling 10.9%. Women aged 15–24 years (aOR = 0.69, 95% CI = 0.56–0.86, p = 0.001) had lower odds of receiving better counseling compared to women aged 35 years and above. Those with no education (aOR = 0.52, 95% CI = 0.33–0.82, p = 0.005), primary (aOR = 0.56, 95% CI = 0.44–0.71, p<0.001) and secondary (aOR = 0.79, 95% CI = 0.65–0.98, p = 0.028) were less likely to receive better counseling compared to those with tertiary education. Women who received long acting and reversible contraception methods (aOR = 1.75, 95% CI = 1.42–2.17, p<0.001), and those who were method switchers (aOR = 1.24, 95% CI = 1.03–1.50, p = 0.027), had a higher likelihood of receiving better quality of counseling as compared to those on short-term methods and those who were continuers, respectively. Conclusion The quality of family planning counseling in Kenya is still sub-optimal considering that some women receive no form of counseling at service delivery point. There is need to review the existing FP guidelines and training packages to increase focus on the quality of counseling services offered by health providers. Social accountability strategies that empower women to demand quality services should be included in community-level family planning interventions.