Hardy-Weinberg Expectations Research Articles

Measuring local genetic variation in permethrin-resistant head lice (Phthiraptera: Pediculidae) from Buenos Aires, Argentina.

The cosmopolitan ectoparasite human head louse, Pediculus humanus capitis (De Geer)(Phthiraptera:Pediculidae), affects mostly school-aged children, with infestations reported every year mainly due to louse resistance to pyrethroids. One of the main resistance mechanisms of pyrethroids is the target site insensitivity (kdr), which is caused by single-nucleotide point mutations (SNPs) located in the voltage-sensitive sodium channel gene. In this study, we analyzed individual head lice toxicologically via the description of their susceptibility profile to permethrin and genetically through the genotypification of their kdr alleles as well as nuclear microsatellite loci. Lice were collected from 4 schools in the city of Buenos Aires, Argentina. The resistance ratios varied from 33.3% to 71.4%, with a frequency of the T917I kdr mutation of 87.31% and with 83.6% of the head lice being homozygous resistant to pyrethroids. Microsatellite data indicated that all the louse school populations had genotype proportions that deviated from Hardy-Weinberg expectations, with FIS > 0 reflecting a deficit of heterozygotes. Bottleneck analysis suggested that all louse school populations underwent a recent reduction in population sizes, while 3 of the 4 schools had gene flow values around 1, indicating ongoing gene flow among those schools. Our study suggests that school louse populations in the city of Buenos Aires may form a metapopulation, where each school represents a small population that undergoes extinction and recolonization processes under strong permethrin selection. This is the first multilevel analysis integrating toxicological, kdr-genotyping, and microsatellite data in human louse populations.

A DNA profiling system for conservation management of Kamchatka brown bear (Ursus arctos piscator); population data and system performance from 16 autosomal STRs

Despite the high density of brown bears (Ursus arctos piscator) on the Kamchatka peninsula their genetic variation has not been studied by STR analysis. Our aim was, therefore, to provide population data from the Kamchatka brown bear population applying a validated DNA profiling system. Twelve dinucleotide STRs commonly used in Western-European (WE) populations and four additional ones (G10C, G10J, G10O, G10X), were included. Template input ≥ 0.2 ng was successfully amplified. Measurements of precision, stutter and heterozygous balance showed that markers could be reliably genotyped applying the thresholds used for genotyping WE brown bears. However, locus G10X revealed an ancient allele-specific polymorphism that led to suboptimal amplification of all 174 bp alleles (Kamchatka and WE). Allele frequency estimates and forensic genetic parameters were obtained from 115 individuals successfully identified by genotyping 434 hair samples. All markers met the Hardy-Weinberg and linkage equilibrium expectations, and the power of discrimination ranged from 0.667 to 0.962. The total average probability of identity from the 15 STRs was 1.4 ×10−14 (FST = 0.05) while the total average probability of sibling identity was 6.0 ×10−6. Relationship tests revealed several parent-cub and full sibling pairs demonstrating that the marker set would be valuable for the study of family structures. The population data is the first of its kind from the Kamchatka brown bear population. Population pairwise FST`s revealed moderate genetic differentiation that mirrored the geographic distances to WE populations. The DNA profiling system, providing individual-specific profiles from non-invasive samples, will be useful for future monitoring and conservation purposes

The role of the CNTNAP2 gene in the development of autism spectrum disorder

Autism spectrum disorder (ASD) is a neurodevelopmental disorder in which genetic and environmental factors interact in its development. Research suggests that the contactin associated protein 2 (CNTNAP2) gene may play a role in ASD pathophysiology, yet more studies involving human participants and animal models of autism are needed. One such model may be the use of prenatal valproic acid (VPA) model to induce autism-like behaviors in offspring rats. The aim of this study was twofold: (1) to examine the association of the CNTNAP2 gene rs2710102 variant with ASD in children; and (2) to examine the effect of prenatal exposure to VPA on Cntnap2 gene expression in the rat brain. The study included 167 children of European ancestry—81 diagnosed with ASD (20 girls, 61 boys; age 4.9 ± 1.4 years) and 86 controls (44 girls, 42 boys; 5.1 ± 1.2 years). In vivo experiments were conducted in 80 rats (40 with the VPA model of autism), with Cntnap2 gene expression analysis in the amygdala, hippocampus, prefrontal cortex, and cerebellum. Results demonstrated that the frequency of the CNTNAP2 gene rs2710102 GG genotype was significantly higher in children with ASD when compared with controls (33.3 vs 19.8%; OR=2.03, 95%CI [1.004, 4.102], p = 0.035), although, potentially due to bias in cohort selection, in the ASD children this polymorphism did not meet Hardy-Weinberg expectations (χ2 =5.40, p = 0.02). In addition, Cntnap2 gene expression was significantly lower (p < 0.01) in the amygdala and hippocampus of VPA rats when compared with controls, regardless of sex. These results support previous research and provide evidence for the CNTNAP2 gene as a risk factor for ASD.

PyPop: a mature open-source software pipeline for population genomics.

Python for Population Genomics (PyPop) is a software package that processes genotype and allele data and performs large-scale population genetic analyses on highly polymorphic multi-locus genotype data. In particular, PyPop tests data conformity to Hardy-Weinberg equilibrium expectations, performs Ewens-Watterson tests for selection, estimates haplotype frequencies, measures linkage disequilibrium, and tests significance. Standardized means of performing these tests is key for contemporary studies of evolutionary biology and population genetics, and these tests are central to genetic studies of disease association as well. Here, we present PyPop 1.0.0, a new major release of the package, which implements new features using the more robust infrastructure of GitHub, and is distributed via the industry-standard Python Package Index. New features include implementation of the asymmetric linkage disequilibrium measures and, of particular interest to the immunogenetics research communities, support for modern nomenclature, including colon-delimited allele names, and improvements to meta-analysis features for aggregating outputs for multiple populations. Code available at: https://zenodo.org/records/10080668 and https://github.com/alexlancaster/pypop.

Characterization of the genetic diversity, structure, and admixture of 7 Chilean chicken breeds

The Mapuche fowl is an autochthonous breed raised in Chile and represents an important zoogenetic resource for the local economy. This study aimed at investigating the genetic diversity, relationship and population structure of 96 local Chilean chickens derived from 3 ecotype of Mapuche fowl (Kollonka, Ketro, and Kollonka de aretes), 2 ecotype Chilean (Trintre, Cogote pelado) and 2 breeds (Light Brahma and Barred Plymouth Rock) using 12 microsatellite markers. In total, 113 alleles were detected in all populations, with a mean of 7.6 alleles per population. In all population chicken breeds, the observed and expected heterozygosity ranged from 0.91 to 0.98 and from 0.69 to 0.79. Furthermore, all populations showed significant deviations from Hardy-Weinberg expectations. Across each population, the global heterozygosity deficit (FIT) was -0.174, population differentiation index (FST) was 0.073, and the global inbreeding of individuals within breed (FIS) was -0.267. The phylogenetic relationships of chickens were examined using neighbor-joining trees constructed at the level of population. The highest Nei's standard genetic distance value of 0.559 was observed between Barred Plymouth Rock and Light Brahma, whereas the minimum value (0.099) was found between Kollonka and Trintre. The neighbor-joining tree constructed at population level revealed 2 main clusters, with Light Brahma, Barred Plymouth Rock, Ketro and Kollonka de aretes in 1 cluster, and Kollonka, Trintre and Cogote pelado breeds in the second cluster. Based on the results of the STRUCTURE analysis, the most likely number of clustering of the population evaluated was at K=3, with Light Brahma and Barred Plymouth Rock breeds forming their own distinct clusters, while Kollonka, Ketro, Kollonka de aretes, Trintre and Cogote pelado breeds clustered together. This study represents the first report of genetic diversity in these populations in Chile. These results can be used as baseline genetic information for genetic conservation program, for instance, to control inbreeding and to implement further genetic studies in local Chilean chickens.

The Relationship between Complement Components C1R and C5 Gene Polymorphism and the Values of Blood Indices in Suckling Piglets.

The main mechanism of innate immunity is the complement system. Its components include the protein products of the C1R and C5 genes, which are involved in the classical activation pathway as well as the inflammatory and cytolytic immune responses, respectively. The aim of this study was to determine the relationship between PCR-restriction fragment length polymorphism in C1R (726T > C) and C5 (1044A > C) genes, and the values of hematological and biochemical blood indices in suckling crossbred (Polish Large White × Polish Landrace × Duroc × Pietrain) piglets (n = 473), considering their age (younger, 21 ± 3 days, n = 274; older, 35 ± 3 days, n = 199) and health status. The frequencies of the C5 genotypes deviated from the Hardy-Weinberg expectations. Younger piglets, healthy piglets, piglets that deviated from physiological norms and older piglets with the C1R TT genotype all had lower white and red blood cell indices. In piglets with the C5 CC genotype, younger piglets, piglets that deviated from physiological norms and older piglets, a greater number and/or percentage of monocytes were recorded in the blood. Older piglets also showed an increase in the number of leukocytes and granulocytes, along with a tendency for a decrease in the percentage of lymphocytes in their blood. We concluded that a polymorphism in the C1R gene may exhibit a functional association or genetic linkage with other genes involved in the process of erythropoiesis. Furthermore the relationship between the C5 gene polymorphism and the number and/or percentage of monocytes in the blood may modify the body's defense abilities. Piglets with the CC genotype, having an increased number/proportion of these cells in their blood, probably display a weakened immune response to pathogens or a chronic stimulation of the immune system.

Population Genetic Study on the European Flounder (Platichthys flesus) from the Southern Baltic Sea Using SNPs and Microsatellite Markers.

The European flounder (Platichthys flesus), which is closely related to the recently discovered Baltic flounder (Platichthys solemdali), is currently the third most commercially fished species in the Baltic Sea. According to the available data from the Polish Fisheries Monitoring Center and fishermen's observations, the body condition indices of the species in the Baltic Sea have declined in recent years. The aim of the present study was to obtain information on the current patterns of genetic variability and the population structure of the European flounder and to verify whether the Baltic flounder is present in the southern Baltic Sea. Moreover, we aimed to verify whether the observed decline in the body condition indices of the species in the Baltic Sea might be associated with adaptive alterations in its gene pool due to increased fishing pressure. For this purpose, 190 fish were collected from four locations along the central coastline of Poland, i.e., Mechelinki, Władysławowo, the Vistula Lagoon in 2018, and the Słupsk Bank in 2020. The fish were morphologically analyzed and then genetically screened by the application of nineteen microsatellite DNA and two diagnostic SNP markers. The examined European flounder specimens displayed a high level of genetic diversity (PIC = 0.832-0.903, I = 2.579-2.768). A lack of significant genetic differentiation (Fst = 0.004, p > 0.05) was observed in all the examined fish, indicating that the European flounder in the sampled area constitutes a single genetic cluster. A significant deficiency in heterozygotes (Fis = 0.093, p < 0.05) and overall deviations from Hardy-Weinberg expectations (H-WE) were only detected in fish sampled from the Słupsk Bank. The estimated effective population size (Ne) among the sampled fish groups varied from 712 (Słupsk Bank) to 10,115 (Władysławowo and Mechelinki). However, the recorded values of the Garza-Williamson indicator (M = 0.574-0.600) and the lack of significant (p > 0.05) differences in Heq > He under the SMM model did not support the species' population size changes in the past. The applied SNP markers did not detect the presence of the Baltic flounder among the fish sampled from the studied area. The analysis of an association between biological traits and patterns of genetic diversity did not detect any signs of directional selection or density-dependent adaptive changes in the gene pool of the examined fish that might be caused by increased fishing pressure.

Genetic monitoring on the world’s first MSC eco-labeled common octopus (O. vulgaris) fishery in western Asturias, Spain

Octopus vulgaris (Cuvier, 1797) is a cephalopod species with great economic value. In western Asturias (northwest of Spain), O. vulgaris artisanal fisheries are relatively well monitored and conditionally eco-labeled by the Marine Stewardship Council (MSC). Despite this, the Asturian octopus stocks have not been genetically assessed so far. In order to improve the current fishery plan and contrast the octopus eco-label validity in Asturias, 539 individuals from five regions of the O. vulgaris geographic distribution, including temporal samplings in Asturias, were collected and genotyped at thirteen microsatellite loci. All the samples under analysis were in agreement with Hardy–Weinberg expectations. Spatial levels of genetic differentiation were estimated using F-statistics, multidimensional scaling, and Bayesian analyses. Results suggested that the O. vulgaris consists of at least four genetically different stocks coming from two ancestral lineages. In addition, temporal analyses showed stability in terms of genetic variation and high NE (> 50) for several generations in different localities within Asturias, pointing out to indeed sustainable fishery exploitation levels. Even though, the current Asturias fishery plan shows no significant genetic damages to the stocks, the regional-specific management plans need systematic genetic monitoring schemes as part of an efficient and preventive regional fishery regulation strategy.

ER22/23EK AND TTH111I POLYMORPHIC VARIANTS IN THE GLUCOCORTICOID RECEPTOR GENE IN PATIENTS WITH BRONCHIAL ASTHMA.

Aim: The objective of the study was to evaluate the frequency of the ER22/23EK and Tth111I polymorphic variants in the glucocorticoid receptor (GR) gene in patients with BA and to assess the risk of BA development with regard to these polymorphisms. Materials and Methods: We examined 553 BA patients and 95 apparently healthy individuals. BA was diagnosed according to the 2016 GINA recommendations and its later versions. The study was approved by the Bioethics Committee of the Medical Institute of Sumy State University. The ER22/23EK (rs 6189/6190) and Tth111I (rs10052957) polymorphisms in the GR gene were determined using polymerase chain reaction-restriction fragment length polymorphism analysis. Statistical analysis of obtained results was performed using SPSS-17 program. Results: The obtained distribution of genotypes for the ER22/23EK and Tth111I polymorphisms in the GR gene corresponded to the Hardy-Weinberg expectations (p > 0.05). We revealed no significant difference in the distribution of alleles and genotypes for the ER22/23EK polymorphism in the GR gene in patients with asthma and apparently healthy individuals (χ2 = 4.14; p = 0.126); apart from that, we found no statistically significant association with BA risk in any model of inheritance. A statistically significant difference was observed in the distribution of genotypes for the Tth111I polymorphism in the GR gene in patients with asthma and apparently healthy individuals (χ2 = 6.278; p = 0.043). BA risk was 2.69 times higher in the carriers of TT genotype for the Tth111I polymorphism in the GR gene vs. major allele carriers. No gender-specific difference was observed in the distribution of genotypes and alleles for the ER22/23EK and Tth111I polymorphisms in the GR gene. Conclusions: We found no gender-specific difference in the distribution of alleles and genotypes for the ER22/23EK and Tth111I polymorphisms in the GR gene; no difference in the distribution of alleles and genotypes for the ER22/23EK polymorphism in the GR gene in patients with asthma and apparently healthy individuals; and no statistically significant association with BA risk. A statistically significant difference was observed in the distribution of genotypes for the Tth111I polymorphism in the GR gene in patients with asthma and apparently healthy individuals; also, BA risk was 2.69 times higher in the minor allele homozygous patients vs. major allele carriers.

Testing of Hardy-Weinberg Equilibrium in Population of Two Nigerian Local Chicken Ecotypes Base on Location

Test of deviation from Hardy-Weinberg equilibrium expectation base on location of the Tiv and Fulani local chicken ecotypes of Nigeria was undertaken using eighty (80) matured birds (40 birds each for Tiv and Fulani ecotypes). Blood samples were collected from five locations each of the ecotype to determine their blood protein. Blood protein loci namely: haemoglobin, albumen, transferrin and carbonic anhydrase were determine using electrophoresis. Data collected were analyzed using popgene version 1.31. The result revealed significant deviations (P&lt;0.05) from Hardy-Weinberg expectations in the two ecotypes except in the Fulani ecotype were haemoglobin did not deviate significantly. Based on location, there were no significant (P&gt;0.05) deviation from Hardy-Weinberg expectations in the Fulani ecotype except in location 4 were Hb, Al and Ca as well as location 5 where Al and Ca were significant. Allelic frequencies of albumin showed significant (P&lt;0.05) deviation from Hardy-Weinberg expectations at locations 1 and 5 while allelic frequencies of transferrin deviated significantly (P&lt;0.05) from the Hardy-Weinberg frequency at location 5. In the Tiv ecotype, albumin showed the highest significant (P&lt;0.05) deviation from the Hardy-Weinberg expectations in all locations. The allelic frequencies of transferrin did not differ significantly (P&gt;0.05) from the Hardy-Weinberg expectations. From the finding of this research, it was concluded that the deviation from Hardy-Weinberg expectations at the four blood proteins loci of the two ecotypes indicated that the Tiv and the Fulani chicken populations are variable in their genome and that there are chances of genetic improvement when crossed between themselves across location or with exotic breeds. Generally, these findings provide the fundamental step in the direction of judicious decision-making before the development of genetic enhancement and preservation programmes without interfering with the uniqueness of the Tiv............

Evidence of mitochondrial capture in Australian glass shrimp (

Context The Australian glass shrimp (Paratya australiensis) has been identified as a cryptic species complex and several lineages occur sympatrically in eastern Australia. In south-eastern Queensland, the predominant lineages are ‘4’ and ‘6’, although the only known area of sympatry in the Conondale Range is the result of a translocation. Aim Our aim was to determine any evidence of natural sympatry between the two lineages in the Mary River catchment area using polymerase chain reatction–restriction fragment length polymorphism (PCR-RFLP) analysis. Methods Of six sites sampled, only one site showed sympatry between Lineage 4 and 6, so 39 individuals from this site were sequenced using fragment of the mtDNA COI gene and a neighbour joining tree revealed the existence of two lineages. Results On the basis of two sets of nuclear markers (allozymes and microsatellites), there was no evidence of two species, because all loci conformed to Hardy–Weinberg expectations and only Lineage 4 alleles were identified. Conclusion These results led to the inference that the existence of two mtDNA lineages could be due to mitochondrial capture. Implication The current situation in the Broken Bridge High site could be due to historical interbreeding between the two lineages reflected in the mtDNA data but not evident in the nuclear data.

Genetic variants of PON1, GSTM1, GSTT1, and locus 9p21.3, and the risk for premature coronary artery disease in Yucatan, Mexico.

Genetic variants of PON1, rs70587, rs662, rs854560, GSTM1, and GSTT1 and two single nucleotide polymorphisms (SNP) at 9p21.3 locus, rs1333049, and rs2383207; were evaluated in association with the risk for premature coronary artery disease (CAD) in a population of Yucatan, Mexico. These genes are involved in the inactivation of pro-oxidants and pro-inflammatory mediators, lipid and xenobiotic metabolism, detoxification of reactive oxygen species, and regulation of cellular proliferation playing key roles in the pathogenesis of atherosclerosis. We conducted a matched case-control study with 98 CAD cases and 101 healthy controls. Genotyping of PON1 and 9p21.2 SNP was performed by real time-PCR and for GSTM1 and GSTT1 with multiplex-PCR. Odds ratios (OR) were calculated to estimate association and generalized multifactor dimensionality reduction (GMDR) algorithm to identify gene-gene and gene-environment interactions. The distribution of all allele/genotype frequencies in controls was within Hardy-Weinberg expectations (p >.05) except for GSTM1. The allele/genotype frequencies of the GSTT1 null were significantly higher in CAD cases than in controls, suggesting association with higher risk for developing CAD. The other SNPs did not show any significant independent association with premature CAD. GMDR revealed a significant interaction between GSTT1 and LL55 genotype. Likewise, the body mass index (BMI) and smoking also showed an interaction with GSTT1. The GSTT1 null allele/genotype is associated with an increased risk of developing premature CAD, the effect of which is not modified by cardiovascular risk factors in the population of Yucatan.

Polymorphisms of the FCN2 Gene 3'UTR Region and Their Clinical Associations in Preterm Newborns.

Ficolin-2 is regarded as an important innate immunity factor endowed with both lectin (carbohydrate recognition) qualities and ability to induce complement activation. The aim of this study was to investigate the association of the FCN2 3’-untranslated region (3’UTR) polymorphisms with ficolin-2 expression and perinatal complications in preterm neonates. The sequencing analysis allowed us to identify six 3’UTR polymorphisms with minor allele frequency (MAF) >1%: rs4521835, rs73664188, rs11103564, rs11103565, rs6537958 and rs6537959. Except for rs4521835, all adhered to Hardy-Weinberg expectations. Moreover, rs6537958 and rs6537959 were shown to be in perfect linkage disequilibrium (LD) with nine other genetic polymorphisms: rs7040372, rs7046516, rs747422, rs7847431, rs6537957, rs6537960, rs6537962, rs11462298 and rs7860507 together stretched on a distance of 1242 bp and very high LD with rs11103565. The 3’UTR region was shown to bind nuclear extract proteins. The polymorphisms at rs4521835 and rs73664188 were found to influence serum ficolin-2 concentration significantly. All polymorphisms identified create (together with exon 8 polymorphism, rs7851696) two haplotype blocks. Among 49 diplotypes (D1-D49) created from rs7851696 (G>T), rs4521835 (T>G), rs73664188 (T>C), rs11103564 (T>C), rs11103565 (G>A) and rs6537959 (T>A), twenty two occurred with frequency >1%. Two diplotypes: D13 (GTTTGT/GGTCGT) and D10 (GTTTGT/GGTCGA), were significantly more frequent among preterm neonates with early onset of infection and pneumonia, compared with newborns with no infectious complications (OR 2.69 and 2.81, respectively; both p<0.05). The minor (C) allele at rs73664188 was associated with an increased risk of very low (≤1500 g) birthweight (OR=1.95, p=0.042) but was associated with the opposite effect at rs11103564 (OR=0.11, p=0.005).

Genetic diversity of Astronium graveolens Jacq. in Colombian seasonally dry tropical forest: support for the dry forest refugia hypothesis?

• The degradation of Colombian dry forest threatens tree species populations • We studied the genetic diversity of Astronium graveolens with nSSRs makers • The populations held healthy levels of genetic diversity • The genetic structure supports the dry forest refugia hypothesis • We identify priority areas for inclusive in situ conservation to support restoration Seasonally Dry Tropical Forest (SDTF) is one of the most threatened ecosystems worldwide and in Colombia it is considered critically endangered according to the national red list of ecosystems. Ongoing processes of fragmentation and degradation of SDTFs are expected to be accompanied by a loss of genetic diversity of the tree populations contained in it. Identifying remaining healthy tree populations is key for the implementation of conservation and restoration programs that embrace genetic diversity to enhance the capacity of populations to adapt to environmental changes. We studied the genetic diversity and structure of Astronium graveolens , one of the most ubiquitous species in Colombian SDTFs, across ten representative populations. We assess the relevance of the dry forest refugia hypothesis (DFRH) for explaining the observed genetic structures. We identified three genetic clusters which may have originated through prolonged isolation of populations. The most diverse cluster ranges from the Caribbean region to the Chicamocha river canyon which may reflect their connectedness during the last glacial period. A second cluster likely originated through isolation in a small area enclosed in the Caribbean region. The third cluster groups populations from the Cauca and Magdalena river valleys, suggesting cross-Andean expansion of populations at one point in time, thus corroborating similar findings for other species of SDTFs. Our results add to a growing number of studies providing support for the DFRH. All the populations sampled showed heterozygosity scores close to the Hardy-Weinberg expectations, suggesting populations might be relatively resistant to habitat fragmentation. However, our suitability modelling results suggest that climate change might imperil numerous areas in SDTFs where the species occurs today, including some that hold unique genetic diversity.

Genetic diversity and genetic structures of original plants of Viticis Fructus:an SSR markers-based analysis

The present study aimed to provide the protection strategies for wild germplasm resources of original plants of Viticis Fructus and a theoretical basis for the sustainable use of Viticis Fructus. The genetic diversity and genetic structures of the 232 indivi-duals in 19 populations of Vitex rotundifolia and V. trifolia were analyzed by eight SSR markers with tools such as Popgene32, GenAlex 6.502, and STRUCTURE. Bottleneck effect was detected for the population with more than 10 individuals. The results indicated that 42 and 26 alleles were detected from the populations of V. rotundifolia and V. trifolia, respectively, with average expected heterozygo-sities of 0.448 6 and 0.583 9, which are indicative of low genetic diversity. AMOVA revealed the obvious genetic variation of V. rotundifolia and V. trifolia within population(84.43%, P&lt;0.01; 60.37%, P&lt;0.01). Furthermore, in eight SSR loci, six from V. rotundifolia populations and two from V. trifolia populations failed to meet Hardy-Weinberg equilibrium expectations(P&lt;0.05), which confirmed that the populations experienced bottleneck effect. As assessed by Mantel test, geographical distance posed slight impacts on the genetic variation between the populations of V. rotundifolia and V. trifolia. Principal component analysis(PCA) and STRUCTURE analysis demonstrated evident introgression of genes among various populations. The original plants of Viticis Fructus were confirmed low in genetic diversity and genetic differentiation level. Therefore, the protection of wild resources of original plants of Viticis Fructus should be strengthened to ensure its sustainable use.

Self-Fertilization, Inbreeding, and Yield in Alfalfa Seed Production.

Selfing (self-pollination) is the ultimate form of inbreeding, or mating among close relatives. Selfing can create yield loss when inbreeding depression, defined as a lower survival and reproduction of inbred relative to outbred progeny, is present. To determine the impact of selfing in alfalfa (Medicago sativa L.), we quantified the selfing rate of 32 alfalfa seed production fields located in three regions, namely, the Pacific Northwest (PNW), the Central Valley of California (CEV), and the Imperial Valley of California (IMP). Selfing rates (the proportion of selfed seeds) varied between 5.3 and 30% with an average of 12.2% over the 32 seed production fields. In both the parents and their progeny, we observed an excess of heterozygotes relative to Hardy–Weinberg expectations. We detected notable levels of inbreeding in parents (0.231 ± 0.007 parental inbreeding coefficient) and progeny (0.229 ± 0.005). There were a 15% decrease in the number of seeds per stem (seed set) and a 13% decline in the number of seeds per pod in selfed relative to outcrossed stems, but negligible inbreeding depression for pods per raceme and seed weight. The number of racemes on selfed stems increased significantly in fields with greater selfing rates, supporting the presence of geitonogamous or among flower selfing. Despite the significant level of inbreeding depression, seed set did not decrease in fields with higher selfing rates, where the greater number of racemes on the selfed stems increased the seed set. The effects of the field selfing rate on the seed yield metrics were mostly indirect with direct effects of the number of racemes per stem. Available data indicate that the majority of selfing in alfalfa is pollinator-mediated, and thus, eliminating selfing in alfalfa seed production would require the selection of self-incompatible varieties, which, by eliminating inbreeding depression, would provide a 15% potential increase in seed yield and an increase in future hay yield.

Phenotypic and genotypic variability between two Nigerian indigenous goat population

In order to estimate the future breeding potential of a livestock breed, it is necessary to estimate the level of genetic diversity within the breed. Thus, this study was conducted to determine the phenotypic and genotypic variability within the West African dwarf (WAD) goats and a non-descript goat population. The WAD goats were obtained from Bodija market Ibadan, Oyo state, while the non-descript goats were obtained from the Animal Science Departmental Farm in Zaria, Kaduna State. Random collection of tissue samples was carried out on each goat population using an all flex ear punch tissue sample collector and aliquoted into plastic tubes containing the all flex preservative. DNA extraction, amplification and sequencing were carried out at the International Livestock Research Institute (ILRI), Nairobi, Kenya. DNA was extracted from the tissue cells using the Pure Link™ Genomic DNA-minikit according to the manufacturer's specifications and protocol and 25 microsatellite markers as recommended by FAO/ISAG were used for genotyping. Twenty three of the 25 microsatellite markers used in this analysis had four or more alleles. The mean Shannon index (I), observed (Ho) and expected heterozygosity (He) and inbreeding coefficient (Fis) for the WAD goats were 1.568, 0.584, 0.679 and 0.167, respectively. For the non-descript goats, the mean Shannon index, observed and expected heterozygosity and inbreeding coefficient (Fis) were 1.607, 0.678, 0.721 and 0.041, respectively. The microsatellite markers used in this study showed their suitability for analysis of genetic variability in this population as demonstrated by the high mean Shannon index. This study has shown that these two goat populations are significantly different phenotypically and genetically. Also, both populations showed significant deviations (P&lt;0.01) from Hardy-Weinberg expectations.&#x0D;

Genomic signatures of recombination in a natural population of the bdelloid rotifer Adineta vaga

Sexual reproduction is almost ubiquitous among extant eukaryotes. As most asexual lineages are short-lived, abandoning sex is commonly regarded as an evolutionary dead end. Still, putative anciently asexual lineages challenge this view. One of the most striking examples are bdelloid rotifers, microscopic freshwater invertebrates believed to have completely abandoned sexual reproduction tens of Myr ago. Here, we compare whole genomes of 11 wild-caught individuals of the bdelloid rotifer Adineta vaga and present evidence that some patterns in its genetic variation are incompatible with strict clonality and lack of genetic exchange. These patterns include genotype proportions close to Hardy-Weinberg expectations within loci, lack of linkage disequilibrium between distant loci, incongruent haplotype phylogenies across the genome, and evidence for hybridization between divergent lineages. Analysis of triallelic sites independently corroborates these findings. Our results provide evidence for interindividual genetic exchange and recombination in A. vaga, a species previously thought to be anciently asexual.

Characterization of a New Set of Microsatellite Markers Suggests Polygyny and Polyandry in Atta cephalotes (Hymenoptera: Formicidae).

The leaf-cutting ant, Atta cephalotes L. (1758), is a major herbivore with great economic impact in the Neotropics. Because of its broad range and human-mediated dissemination, the ecology of this ant has received considerable attention; however, questions concerning its population genetics, dispersal, and social structure remain unexplored. Here, we aimed to identify and provide information on molecular and statistical performance of a suite of polymorphic microsatellite markers for A. cephalotes while demonstrating their utility for further genetic studies. We designed primer sequences targeting thousands of microsatellite loci and then screened 30 of these for amplification and polymorphism. Fifteen of these loci were selected and used to evaluate their polymorphism using 74 ants sampled from 15 different nests of the same location. This set of 15 loci exhibited variation of 2-20 alleles, with a mean heterozygosity of 0.57. All loci followed Hardy-Weinberg expectations with no evidence of linkage disequilibrium, while two loci showed evidence of null alleles. Our preliminary analysis suggested substantial nest differentiation with no population viscosity within the sampled location, as well as colonies with multiple queens (polygyny) and paternity (polyandry). Our newly identified microsatellites have proven to be highly informative to investigate gene flow, social structure and reproduction of this key agricultural pest.

Structuration of multilocus genotypes associated with insecticide resistance of the peach potato aphid, Myzus persicae (Sulzer), in potato fields in southern Belgium.

The peach potato aphid, Myzus persicae, has developed resistance to many insecticides. In Belgium, M. persicae is one of the most common aphids in potato fields and one of the most effective virus vectors. We monitored resistance mutations to pyrethroids, carbamates and neonicotinoids and related these results to microsatellite genotyping to provide information to support the choice of management tactics. Most of the 254 aphids tested (97.6%) displayed at least one mutation conferring resistance to pyrethroids (L1014F, M918L and M918T) and 36.2% additionally carried the modified acetylcholinesterase (MACE) carbamates resistance making them resistant to two insecticide action modes. Ten mutation combinations were detected, two of which were frequent and a strong linkage was found between MACE and M918L mutations. The R81T mutation conferring resistance to neonicotinoids was not detected. Microsatellites highlighted a moderate genetic diversity [69 multilocus genotypes (MLG) detected], severe deviations from Hardy-Weinberg expectations, a highly significant excess of heterozygotes and linkage disequilibrium between all pairs of loci. A structuration of MLGs in association with the mutation combinations was observed. Genetic differentiation was mainly not significant between sampling locations and most MLGs were geographically widespread. These results suggest the likely coexistence of parthenogenesis (obligatory or facultative) and sexual reproduction, and the existence of 'old' parthenogenetic overwintering asexual lineages. The results of this monitoring at a regional scale provide useful information on insecticide resistance, genetic diversity and reproductive modes, and highlight the need to reduce the insecticide selection pressure and to implement mitigating techniques.