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Conservation of animal genetic resources requires regular monitoring and interventions to maintain population size and manage genetic variability. This study uses genealogical information to evaluate the impact of conservation measures in Europe, using (i) data from the Domestic Animal Diversity Information System (DAD-IS) and (ii) a posteriori assessment of the impact of various conservation measures on the genetic variability of 17 at-risk breeds with a wide range of interventions. Analysis of data from DAD-IS showed that 68% of national breed populations reported to receive financial support showed increasing demographic trends, v. 51% for those that did not. The majority of the 17 at-risk breeds have increased their numbers of registered animals over the last 20 years, but the changes in genetic variability per breed have not always matched the trend in population size. These differences in trends observed in the different metrics might be explained by the tensions between interventions to maintain genetic variability, and development initiatives which lead to intensification of selection.
Conservation of animal genetic resources is considered as one of the main challenges of today's breeding. Every breed of livestock is a valuable element of the world's animal genetic diversity. Over the last few decades, considerable reductions in the number of local breeds and their sizes have been registered. This trend caused the need to implement conservation programmes for endangered goose species. Poland has a number of local goose breeds which are the achievements of many generations of breeders. The objective of this review was to present the current status of the realised conservation programmes for 14 goose breeds in Poland by analysing population and molecular parameters. The conservation status of these populations has been presented including the effective population sizes, hypothetical inbreeding level, trends in performance traits as well as parameters estimated on the basis of genetic markers. In all the cases population sizes were well over 100 individuals, which is the minimum recommended by the FAO for conservation flocks. The effective population size ranged from 179 to 452, affecting a relatively low inbreeding level from 0.1 to 0.74%. The estimated correlations between hypothetical inbreeding rates and reproduction traits were negative. The heterozygosity coefficients varied from 0.27 (Biłgorajska breed) to 0.55 (Garbonosa breed). Generally, the parameters for goose breeds in Poland were compatible with the recommendations of the FAO.
Decreased reliance on pesticides can be achieved through a clever use of eco-evolutionary knowledge via intercropping economically valuable crops with companion plants that can hamper pest outbreaks. We created a greenhouse multi-layered microcosm system to test two potato peach aphid clones, performing alone or in competition, on mixes of genetically variable cultivars of cabbage, with and without onion. The onion acted as a nuisance/disturbance for the pest, which was generally for the benefit of the cabbage albeit both plants sharing space and nutrients. The onion effect was context-specific and differed by aphid genotype. Onion variable nuisance negatively affected the numbers of one aphid genotype (green) across all contexts, while the other genotype (pink) numbers were decreased in two contexts only. However, the green performed better than the pink on all cases of cabbage di-mixes despite its numbers being capped when the onion was present. Further, there was also a general aphid propensity to wander off the plant along with a differential production of winged morphs to escape the onion-affected environments. Moreover, through a comparative increase in dry mass, which was subject to onion and aphid effects, a diversity effect was found where the cabbages of fully genetically variable microcosms sustained similar final dry mass compared with non-infested microcosms. Our findings provide fresh insights into the use of multi-layered contextual designs that not only allow disentangling the relative effects of genetic variation and modes of interaction, but also help integrate their benefits into pest management in view of companion planting.
The aim of this study was to estimate genetic parameters for environmental sensitivities in milk yield and composition of Iranian Holstein cows using the double hierarchical generalized linear model (DHGLM) method. Data set included test-day productive records of cows which were provided by the Animal Breeding Center and Promotion of Animal Products of Iran during 1983 to 2014. In the DHGLM method, a random regression model was fitted which included two parts of mean and residual variance. A random regression model (mean model) and a residual variance model were used to study the genetic variation of micro-environmental sensitivities. In order to consider macro-environmental sensitivities, DHGLM was extended using a reaction norm model, and a sire model was applied. Based on the mean model, additive genetic variances for the mean were 38.25 for milk yield, 0.23 for fat yield and 0.03 for protein yield in the first lactation, respectively. Based on the residual variance model, additive genetic variances for residual variance were 0.039 for milk yield, 0.030 for fat yield and 0.020 for protein yield in the first lactation, respectively. Estimates of genetic correlation between milk yield and macro- and micro-environmental sensitivities were 0.660 and 0.597 in the first lactation, respectively. The results of this study indicated that macro- and micro-environmental sensitivities were present for milk production traits of Iranian Holsteins. High genetic coefficient of variation for micro-environmental sensitivities indicated the possibility of reducing environmental variation and increase in uniformity via selection.
Breast cancer (BC) is one of the most complex, diverse and leading cause of death in women worldwide. The present investigation aims to explore genes panel associated with BC in different African regions, and compare them to those studied worldwide.
We extracted relevant information from 43 studies performed in Africa using the following criteria: case-control study, association between genetic variations and BC risk. Data were provided on mutations and polymorphisms associated with BC without fixing a specific date. Case-only studies and clinical trials were excluded.
Our study revealed that the majority of African BC genetic studies remain restricted to the investigation of BRCA1 and BRCA2 genes and differences in their mutations spectrum. Therefore, it is necessary to encourage African researchers to characterize more genes involved in BC using methods generating global information such as next-generation sequencing in order to guide specific and more effective therapeutic strategies for the African community.
Cystic echinococcosis (CE) is a severe parasitic disease caused by the species complex Echinococcus granulosus sensu lato. Human infections are most commonly associated with E. granulosus sensu stricto (s.s.), comprising genotypes G1 and G3. The objective of the current study was to provide first insight into the genetic diversity and phylogeography of genotype G3. Despite the epidemiological importance of the genotype, it has remained poorly explored due to the ambiguity in the definition of the genotype. However, it was recently demonstrated that long sequences of mitochondrial DNA (mtDNA) provide a reliable method to discriminate G1 and G3 from each other. Therefore, we sequenced near-complete mtDNA of 39 G3 samples, covering most of the known distribution range and host spectra of the genotype. The phylogenetic network revealed high genetic variation within E. granulosus s.s. G3 and while G3 is significantly less prevalent worldwide than G1, the genetic diversity of both of the genotypes is equally high. We also present the results of the Bayesian phylogeographic analysis, which yielded several well-supported diffusion routes of genotype G3 originating from Turkey and Iran, suggesting the Middle East as the origin of the genotype.
Iron deficiency chlorosis (IDC) is common among groundnut grown in calcareous and alkaline soils in India, China and Pakistan and causes considerable reduction in pod yield. To identify genetically diverse IDC tolerant accessions, the mini-core collection of groundnut representing geographical diversity was evaluated for IDC response over 2 years in iron-deficient calcareous soils. Enormous genetic variability was evident in the mini-core collection for IDC tolerance-related traits such as a visual chlorotic rating (VCR) and SPAD chlorophyll meter reading (SCMR) across five growth stages. Several IDC tolerant sources belonging to different botanical varieties such as hypogaea bunch (ICG # 5051, 6766, 5286, 6667, 4538, 14008, 5663, 9842, 11855), hypogaea runner (ICG 10479), fastigiata (ICG 10890) and vulgaris (ICG # 11651, 118) were identified. Among the six botanical varieties of groundnut, hypogaea bunch types were found most tolerant to IDC and this is the first report in groundnut. The IDC tolerant sources identified were irrespective of their country of origin. The principal component analysis based on VCR, SCMR, pod yield and its related traits revealed five major principal components that explained 80% of the total variation. The biplot generated using PC1 and PC2 revealed a distinct separation of IDC tolerant genotypes from the susceptible ones. The hierarchical clustering using five major principal components revealed seven major clusters that were mainly based on IDC response of the accessions.
Livestock guarding dogs are a valuable adjunct to the pastoral community. Having been traditionally selected for their working ability, they fulfil their function with minimal interaction or command from their human owners. In this study, the population structure and the genetic differentiation of three Italian livestock guardian breeds (Sila’s Dog, Maremma and Abruzzese Sheepdog and Mannara’s Dog) and three functionally and physically similar breeds (Cane Corso, Central Asian Shepherd Dog and Caucasian Shepherd Dog), totalling 179 dogs unrelated at the second generation, were investigated with 18 autosomal microsatellite markers. Values for the number of alleles per locus, observed and expected heterozygosity, Hardy–Weinberg Equilibrium, F stats, Nei’s and Reynold’s genetic distances, clustering and sub-population formation abilities and individual genetic structures were calculated. Our results show clear breed differentiation, whereby all the considered breeds show reasonable genetic variability despite small population sizes and variable selection schemes. These results provide meaningful data to stakeholders in specific breed and environmental conservation programmes.
Genomic and genetic variation among six Italian chicken native breeds (Livornese, Mericanel della Brianza, Milanino, Bionda Piemontese, Bianca di Saluzzo and Siciliana) were studied using single nucleotide polymorphism (SNP) and copy number variants (CNV) as markers. A total of 94 DNA samples genotyped with Axiom® Genome-Wide Chicken Genotyping Array (Affymetrix) were used in the analyses. The results showed the genetic and genomic variability occurring among the six Italian chicken breeds. The genetic relationship among animals was established with a principal component analysis. The genetic diversity within breeds was calculated using heterozygosity values (expected and observed) and with Wright’s F-statistics. The individual-based CNV calling, based on log R ratio and B-allele frequency values, was done by the Hidden–Markov Model (HMM) of PennCNV software on autosomes. A hierarchical agglomerative clustering was applied in each population according to the absence or presence of definite CNV regions (CNV were grouped by overlapping of at least 1 bp). The CNV map was built on a total of 1003 CNV found in individual samples, after grouping by overlaps, resulting in 564 unique CNV regions (344 gains, 213 losses and 7 complex), for a total of 9.43 Mb of sequence and 1.03% of the chicken assembly autosome. All the approaches using SNP data showed that the Siciliana breed clearly differentiate from other populations, the Livornese breed separates into two distinct groups according to the feather colour (i.e. white and black) and the Bionda Piemontese and Bianca di Saluzzo breeds are closely related. The genetic variability found using SNP is comparable with that found by other authors in the same breeds using microsatellite markers. The CNV markers analysis clearly confirmed the SNP results.
Gene survival in a population which increases without density dependence is considered using a generalization of the Moran model for haploid individuals in which we have differential reproductive rates. It is shown under very mild conditions that ultimate fixation is certain. This provides some mathematical support for the phenomenon of reduced genetic variability in isolated populations established from founder groups.
In India 14 seagrass species can be found with monospecific genera (Enhalus, Thalassia and Syringodium), Cymodocea with two species and Halophila and Halodule represented by more than two taxonomically complex species. Considering this, the present study was made to understand the level and pattern of genetic variability among these species collected from Tamilnadu coast, India. Random amplified polymorphic DNA (RAPD) analysis was used to evaluate the level of polymorphism existing between the species. Out of the 12 primers tested, 10 primers amplified 415 DNA fragments with an average of 41.5 fragments per primer. Of the total 415 amplified fragments only 123 (29.7%) were monomorphic and the remaining 292 (70.3%) were polymorphic for Indian seagrass species. Among the 10 primers used four are identified as the key primers capable of distinguishing all the Indian seagrasses with a high degree of polymorphism and bringing representative polymorphic alleles in all the tested seagrasses. From the present investigation, this study shows that the RAPD marker technique can be used not only as a tool to analyse genetic diversity but also to resolve the taxonomic uncertainties existing in the Indian seagrasses. The efficiency of these primers in bringing out the genetic polymorphism or homogeneity among different populations of the Halophila and Halodule complex still has to be tested before recommending these primers as an identification tool for Indian seagrasses.
Fungal blast disease is one of the major constraints in finger millet production. Breeding for disease resistance in finger millet, needs characterization of genetic polymorphism among and between the resistant and susceptible genotypes. In total, 67 finger millet genotypes, which are resistant or susceptible to fungal blast disease, were analysed using sequence-related amplified polymorphism (SRAP) and simple sequence repeat (SSR) markers to assess genetic variations and select diverse parents. Twelve each of SRAP and SSR primers produced 95.1 and 93.1% polymorphic bands and grouped them into unweighted pair-group method with arithmetic average clusters. Two of the finger millet genotypes, IE 4709 (blast resistant) and INDAF 7 (susceptible) were distinguished as most diverse genotypes as parents. Several genotype-specific bands observed with SSR primers are potential in developing genotype-specific markers. A high genetic diversity within the resistant and susceptible genotypes, rather than between them, was revealed through Nei's gene diversity (h) index and analysis of molecular variance. The finding helps us to understand the extent of genetic polymorphism between blast disease resistant and susceptible finger millet genotypes to exploit in resistance breeding programs.
Lasioderma serricorne (F.) is a small cosmopolitan beetle regarded as a destructive pest of several stored products such as grains, flour, spices, dried fruit and tobacco. Chemical insecticides are one of the measures used against the pest. However, intensive insecticide use has resulted in the appearance of resistant insect populations. Therefore, for the elaboration of more effective control programs, it is necessary to know the biological aspects of L. serricorne. Among these aspects, the genetic variability knowledge is very important and may help in the development of new control methods. The objective of this study was to evaluate the genetic variability of 11 natural populations of L. serricorne collected respectively in three and four towns in the states of Paraná and São Paulo, Brazil, using 20 primers random amplified polymorphic DNA (RAPD) and polymorphisms of esterases. These primers produced 352 polymorphic bands. Electrophoretic analysis of esterases allowed the identification of four polymorphic loci (Est-2, Est-4, Est-5 and Est-6) and 18 alleles. Results show that populations are genetically differentiated and there is a high level of genetic variability within populations. The high degree of genetic differentiation is not directly correlated to geographical distance. Thus, our data indicate that movement of infested commodities may contribute to the dissemination of L. serricorne, facilitating gene flow.
Fasciola hepatica is the causative agent of fasciolosis, a zoonosis with significant impact both in human and animal health. Understanding the basic processes of parasite biology, especially those related to interactions with its host, will contribute to control F. hepatica infections and hence liver pathology. Mucins have been described as important mediators for parasite establishment within its host, due to their key roles in immune evasion. In F. hepatica, mucin expression is upregulated in the mammalian invasive newly excysted juvenile (NEJ) stage in comparison with the adult stage. Here, we performed sequencing of mucin cDNAs prepared from NEJ RNA, resulting in six different cDNAs clusters. The differences are due to the presence of a tandem repeated sequence of 66 bp encoded by different exons. Two groups of apomucins one with three and the other with four repeats, with 459 and 393 bp respectively, were identified. These cDNAs have open reading frames encoding Ser-Thr enriched proteins with an N-terminal signal peptide, characteristic of apomucin backbone. We cloned a 4470 bp gene comprising eight exons and seven introns that encodes all the cDNA variants identified in NEJs. By real time polymerase chain reaction and high-resolution melting approaches of individual flukes we infer that fhemuc-1 is a single-copy gene, with at least two different alleles. Our data suggest that both gene polymorphism and alternative splicing might account for apomucin variability in the fhemuc-1 gene that is upregulated in NEJ invasive stage. The relevance of this variation in host–parasite interplay is discussed.
Inter-simple sequence repeats markers were used to determinate the genetic variability of Fasciola hepatica populations recovered from sheep and cattle from Spain (Sp1, Sp2, Sp3 and Sp4), UK (Eng), Ireland (Ir) and Mexico (Mex). Twenty five primers were tested but only five produced 39 reproducible bands, being 71·79% polymorphic bands. This percentage ranged from 10·26% in Sp4 to 48·72% in Sp1, and per host between 28·21 and 48·72% in sheep and between 10·26 and 38·46% in cattle. This relatively low range of genetic diversity within populations, with a mean of 34·40%, implies that a large proportion of variation resided among populations. The population differentiation (Gst = 0·547) indicated that 54·7% of variation is due to differences between populations and 45·3% due to differences within population. The Nei's distance ranged between 0·091 and 0·230 in sheep and between 0·150 and 0·337 in cattle. The genetic relationships between populations and individuals were shown by a UPGMA dendrogram and a principal coordinate analysis; both grouped all populations separately from Sp4, a population of from the Midwest of Spain with the lowest level of diversity. Small genetic distances were observed between Eng and Ir, on the one hand, and Sp1, Sp2, Sp3, from the Northwest of Spain, together with Mex, on the other.
In the absence to date of studies on genetic variability in the Creole cattle of the Southern Region of Ecuador, the analysis and characterization of this population was carried out in order to provide the technical information needed for the planning and development of measures aimed at the population's conservation and sustainable use in the harsh ecosystem these animals inhabit. For this purpose, 46 adult animals, out of a population of 114 Creole cattle, were genetically analysed; on the basis of phaneroptical traits, they were classified into four groups known locally as Negro Lojano (15 animals), Encerado (15), Colorado (9) and Pintado or Cajamarca (7). The analysis of the intra-population genetic variability brought out a Na of 228, an average number of alleles per locus of 8.14 and a PIC of 0.70 ± 0.10. All 28 markers analyzed were polymorphic and highly informative. The He and Ho amounted to 0.74 ± 0.0178 and 0.676 ± 0.013, which is an indication of a high molecular diversity in the population studied. The HWE determines that 32 per cent of the alleles are not in equilibrium. The Gst amounted to 4.5 ± 2.8 per cent and the Fst was 0.08 per cent, which corroborates that there is no genetic differentiation among the four groups of this population. The average values for Fit and Fis were 8.89 and 8.92 percent, respectively. The degrees of genetic distance between this Creole population and 18 cattle and zebu breeds were also determined. The distance exceeded 0.10 for all populations, with the lowest distances being those between Ec:BC (0.1031), Ec:PAJ (0.1132), Ec:NAN (0.1302), Ec:VCA (0.1326) and Ec:FRI (0.1362). The greatest distances were observed between Ec:GUZ (0.4725) and Ec:NEL (0.4624). These values show that the Creole cattle of the Southern Region of Ecuador are very distant from the zebu breeds, and therefore their ancestors would be more likely to have originated from Iberian populations. The results concerning variability and genetic distance will enable strategies to be devised for managing and conserving the Creole breed of the Southern Region of Ecuador. These results also suggest that the four groups with phaneroptical differences should be managed independently at the different altitudes of the Andean Region of Ecuador.
The presence of excessive phytic acids in foods exerts undesirable antinutritional effects while their agricultural product is utilized as food for humans and as fodder for animals. In this study, 40 cultivated groundnut genotypes were grown in two years and used to estimate the phytic acid phosphorus (PAP) and inorganic phosphorus (InP) contents. The PAP content differed significantly (P= 0.01) among the genotypes and ranged from 149.3 to 315.0 mg PAP/100 g seed with an average of 227.6 mg PAP/100 g seed. The genotypes TG 17 and TG 67 had the highest (315 mg) and the lowest (149.3 mg) PAP content, respectively. The InP content ranged from 58.7 mg/100 g seed in the SG 99 genotype to 102.6 mg/100 g seed in the TG 40 genotype, with a mean of 82.6 mg/100 g seed. The ratio of InP to PAP varied from 0.24 to 0.56. A significantly higher InP:PAP ratio was found in the genotypes TKG 19A, TAG 24, TG 37A, TBG 39 (TDG 39), TG 51, TG 67 and GG 7, which was due to either an increase in InP content or a decrease in PAP content.
Energy digestibility in the growing pig increases with BW increase and may differ between breeds of pigs or between lines selected on criteria other than digestion. However, little is known about the variability in energy digestibility within a line or a breed of pigs, especially when fibrous diets are fed. For this purpose, 20 Large White castrated male growing pigs originating from four boars (five per boar), and three to four sows per boar, were fed a high dietary fibre (DF) diet (18% NDF) and measured over 10 consecutive weeks (30 to 95 kg BW range) for their apparent faecal energy, nitrogen and organic matter digestibility. Each week, faeces were totally collected over 5 days and the feed dry matter intake over the same days was recorded. All digestibility coefficients increased regularly (P < 0.001) over the experimental periods or with BW increase (+0.6 point/10 kg BW increase for energy); this rate of increase was not affected by boar origin (no interaction; P > 0.05). The digestibility coefficients were affected by boar origin (P < 0.005 for energy), with about 2 points for energy between the extremes (81.7% v. 79.5%), and there was no marked interaction between boar origin and period. These preliminary results suggest the possibility of selecting growing pigs for an increased digestive efficiency when fed high DF diets.
Using several clonal lineages of Simocephalus vetulus (Cladocera, Daphniidae) as a random sample, we investigated the genetic component of the halotolerance of one brackish and two freshwater populations of this littoral filter feeder. We hypothesized that genotypes from the brackish population were more tolerant than freshwater ones, via adaptation to local environmental conditions. Clonal identity was established by a cost-effective molecular fingerprinting technique (microsatellite-primed polymerase chain reaction (MSP-PCR)). Two distinct methodologies were used to assess cladoceran sensitivity to synthetic-grade sodium chloride (NaCl): (i) standard 48-h acute assays and (ii) 12-h survival time (ST) trials. No correlation was found between acute EC50 and ST values. The sensitivity of brackish and freshwater clones was comparable in terms of acute EC50 (varied from 2.28 to 3.83 g.L−1). On the contrary, genetically determined differential tolerance to NaCl among populations was found for ST: all brackish genotypes, except one, were more resilient (ST>120 min) than freshwater clones (ST<120 min). Bearing in mind that these results were obtained with isolates from the extant population, it is surprising that the range of acute sensitivity of the freshwater and brackish genotypes was similar, and that the only difference between them was the ability of brackish clones to survive longer under high salinity stress (6 g.L−1, in ST trials). We must conclude that the effect of salinity (original environment context) on the selection of genotypes was weaker than we had expected and than other authors have shown for other stressors.
Thrips are small insects (0.5–3.0 mm) with distinct habits and life histories characterized by haplodiploid sex determination. In general, low levels of genetic diversity have been reported in haplodiploid insects, although most reports focus on the order Hymenoptera. Therefore, we used RAPD markers to evaluate the structure and both inter- and intra-population genetic variability of Gynaikothrips uzeli (Thysanoptera: Phlaeothripidae). Six populations, three from Paraná state, southern Brazil, and three from Bahia, northeastern Brazil, were studied. Similarly to other haplodiploid insects, the genetic diversity of G. uzeli was reduced. This result is putatively related to the haplodiploid sex determination system, which yields little genetic variation, and to ecological traits of the studied species, such as the low dispersal abilities and life mode in leaf galls. All individuals were homogeneously clustered in their respective collection sites, forming two main groups in which populations from similar environments were more closely related. The analyzed populations were highly structured, and the genetic variation was higher among than within populations.