Polydactyl Pigs: There’s More to the Story Than Just Extra Toes

Several pigs expressing a polydactyl (extra toes) phenotype were identified in the ISU purebred Yorkshire herd. Sires, dams, and littermate sibs to the polydactyl pigs were retained in the herd and planned matings were designed to enlarge the population. In addition to creating 12 pigs with either extra toes or dewclaws, the population also had an extremely high number of stillborn and mummified pigs. Furthermore, this population also showed differences in growth and reproduction. Multiple genes have been implicated in causing extra digits in several other species. Using comparative genomics as a guide many of these genes were expected to map on pig chromosome 18. Pig chromosome 18 is the smallest pig autosome on which there has been limited research. Candidate genes on pig chromosome 18 were mapped to ensure their location using Iowa State University’s Berkshire by Yorkshire resource population. Once chromosomal locations were confirmed for each candidate gene, genotypes were obtained for each gene on all pigs in the polydactyl population and were used by a complex statistical method (Elston-Stewart algorithm) to calculate the likelihood that the gene caused the polydactyl phenotype

Cover plants with potential to reduce two-spotted spider mite population in soybean

O objetivo deste trabalho foi avaliar o potencial de plantas de cobertura na redução da população do ácaro-rajado, Tetranychus urticae, em soja. Foram avaliadas sete plantas hospedeiras – algodão (Gossypium hirsutum), braquiária (Urochloa ruziziensis), crotalária (Crotalaria juncea), milho (Zea mays), rabanete (Raphanus sativus), soja (Glycine max) e sorgo (Sorghum bicolor) – quanto ao seu efeito nos parâmetros biológicos (oviposição, estágios de desenvolvimento e sobrevivência) e na preferência por odores voláteis (com uso de olfatômetro em forma de Y) de T. urticae. Tetranychus urticae preferiu o algodão e apresentou taxa de crescimento populacional mais alta nesta planta hospedeira. A sobrevivência e a oviposição de T. urticae foram prolongadas nas plantas de rabanete e crotalária, enquanto os juvenis não completaram seu desenvolvimento imaturo nas folhas de braquiária. Nenhuma preferência foi observada entre os odores voláteis de braquiária, rabanete e crotalária. A braquiária pode reduzir as populações de T. urticae em soja.The objective of this work was to evaluate the potential of cover plants in reducing the population of the two-spotted spider mite, Tetranychus urticae, in soybean. Seven host plants – cotton (Gossypium hirsutum), Urochloa ruziziensis, crotalaria (Crotalaria juncea), corn (Zea mays), radish (Raphanus sativus), soybean (Glycine max), and sorghum (Sorghum bicolor) – were evaluated for their effect on T. urticae biological parameters (oviposition, development stages, and survival) and preference for volatile odors (using a Y-tube olfactometer). Tetranychus urticae preferred cotton and showed a higher population growth rate on this host plant. The survival and oviposition of T. urticae was prolonged in radish and crotalaria plants, whereas juveniles did not complete their immature development on U. ruziziensis leaves. No preference was observed between the volatile odors of U. ruziziensis, radish, and crotalaria. Urochloa ruziziensis can reduce T. urticae populations in soybean plants

Searching for mutations in pigs using the human genome

In humans, mice, rats, primates and pigs, it has been observed that some genes contain a high number of mutations, while others contain no mutations at all. It has not been determined whether a relationship exists across species for the variability of mutation number (i.e. a gene with a large number of mutations in one species will also have a large number of mutations in a closely related species). Here, the number of mutations in regions of genes that code for proteins were compared across pig, human and mouse. For the comparison, the pig mutations were obtained using computational methods that sorted through gene sequences to find differences. The mutations in humans and mice were real mutations from studies of individuals/animals. A high human-pig correlation and a lesser human-mouse correlation were found after comparing mutation number in genes. This is the first evidence of similarity across species in the variability of mutation number in genes. It indicates that discovery of mutations in pigs could be increased by searching in pig genes that are similar to human genes previously shown to have a large number of mutations in their protein coding regions. Some of these newly discovered mutations will change the protein that is produced by the gene, which can affect the protein’s function, and result in changes in economically important traits such as growth, meat quality and reproduction. These mutations can then be used to select animals that are genetically superior

The identification of runs of homozygosity give a focus on the genetic diversity and the adaptation of the "Charolais de Cuba" cattle

Altres ajuts: CERCA Programme/Generalitat de Catalunya.Inbreeding and effective population size (Ne) are fundamental indicators for the management and conservation of genetic diversity in populations. Genomic inbreeding gives accurate estimates of inbreeding, and the Ne determines the rate of the loss of genetic variation. The objective of this work was to study the distribution of runs of homozygosity (ROHs) in order to estimate genomic inbreeding (FROH) and an effective population size using 38,789 Single Nucleotide Polymorphisms (SNPs) from the Illumina Bovine 50K BeadChip in 86 samples from populations of Charolais de Cuba (n = 40) cattle and to compare this information with French (n = 20) and British Charolais (n = 26) populations. In the Cuban, French, and British Charolais populations, the average estimated genomic inbreeding values using the FROH statistics were 5.7%, 3.4%, and 4%, respectively. The dispersion measured by variation coefficient was high at 43.9%, 37.0%, and 54.2%, respectively. The effective population size experienced a very similar decline during the last century in Charolais de Cuba (from 139 to 23 individuals), in French Charolais (from 142 to 12), and in British Charolais (from 145 to 14) for the ~20 last generations. However, the high variability found in the ROH indicators and FROH reveals an opportunity for maintaining the genetic diversity of this breed with an adequate mating strategy, which can be favored with the use of molecular markers. Moreover, the detected ROH were compared to previous results obtained on the detection of signatures of selection in the same breed. Some of the observed signatures were confirmed by the ROHs, emphasizing the process of adaptation to tropical climate experienced by the Charolais de Cuba population

The Identification of Runs of Homozygosity Gives a Focus on the Genetic Diversity and Adaptation of the “Charolais de Cuba” Cattle

Inbreeding and effective population size (Ne) are fundamental indicators for the management and conservation of genetic diversity in populations. Genomic inbreeding gives accurate estimates of inbreeding, and the Ne determines the rate of the loss of genetic variation. The objective of this work was to study the distribution of runs of homozygosity (ROHs) in order to estimate genomic inbreeding (FROH) and an effective population size using 38,789 Single Nucleotide Polymorphisms (SNPs) from the Illumina Bovine 50K BeadChip in 86 samples from populations of Charolais de Cuba (n = 40) cattle and to compare this information with French (n = 20) and British Charolais (n = 26) populations. In the Cuban, French, and British Charolais populations, the average estimated genomic inbreeding values using the FROH statistics were 5.7%, 3.4%, and 4%, respectively. The dispersion measured by variation coefficient was high at 43.9%, 37.0%, and 54.2%, respectively. The effective population size experienced a very similar decline during the last century in Charolais de Cuba (from 139 to 23 individuals), in French Charolais (from 142 to 12), and in British Charolais (from 145 to 14) for the ~20 last generations. However, the high variability found in the ROH indicators and FROH reveals an opportunity for maintaining the genetic diversity of this breed with an adequate mating strategy, which can be favored with the use of molecular markers. Moreover, the detected ROH were compared to previous results obtained on the detection of signatures of selection in the same breed. Some of the observed signatures were confirmed by the ROHs, emphasizing the process of adaptation to tropical climate experienced by the Charolais de Cuba population.info:eu-repo/semantics/publishedVersio

Novel Insights into the Bovine Polled Phenotype and Horn Ontogenesis in Bovidae

Despite massive research efforts, the molecular etiology of bovine polledness and the developmental pathways involved in horn ontogenesis are still poorly understood. In a recent article, we provided evidence for the existence of at least two different alleles at the Polled locus and identified candidate mutations for each of them. None of these mutations was located in known coding or regulatory regions, thus adding to the complexity of understanding the molecular basis of polledness. We confirm previous results here and exhaustively identify the causative mutation for the Celtic allele (PC) and four candidate mutations for the Friesian allele (PF). We describe a previously unreported eyelash-and-eyelid phenotype associated with regular polledness, and present unique histological and gene expression data on bovine horn bud differentiation in fetuses affected by three different horn defect syndromes, as well as in wild-type controls. We propose the ectopic expression of a lincRNA in PC/p horn buds as a probable cause of horn bud agenesis. In addition, we provide evidence for an involvement of OLIG2, FOXL2 and RXFP2 in horn bud differentiation, and draw a first link between bovine, ovine and caprine Polled loci. Our results represent a first and important step in understanding the genetic pathways and key process involved in horn bud differentiation in Bovidae

Evaluation of Antiplasmodial activity of extracts and constituents from Ampelozizyphus amazonicus

PMID: 26664012 WOS: 000362879000003BACKGROUND: Ampelozizyphus amazonicus Ducke, a plant that is widely used by the population of the Amazonian region to prevent and treat malaria, was investigated in this work, which describes, for the first time, the antiplasmodial activity of its extracts and associates this activity with its isolated constituents. METHODS: Different extracts with solvents of increasing polarity (hexane, chloroform, ethanol, and water) were obtained of the root bark. This procedure resulted in extracts that were characterized for their constituents. The cytotoxicity and activity of the extracts against Plasmodium berghei (schizontocidal activity, liver stage) and Plasmodium falciparum (3D7 and Dd2 strains, erythrocyte stage) were assessed in vitro. RESULTS: Of the four extracts assayed against P. berghei, the chloroform extract showed the greatest activity, with an inhibitory concentration 50% (IC50) value of 30.1 µg/mL, followed by the aqueous extract (IC50 = 39.9 µg/mL). The chloroform extract exhibited the highest antiplasmodial activity in the erythrocyte stage of P. falciparum, with an IC50 value lower than 15 µg/mL. Fractionation of this more active extract led to the isolation and elucidation of pentacyclic triterpenes, lupeol, betulin and betulinic acid, which showed antiplasmodial activities with IC50 values ranging from 5.6 to 80.30 µM. The most active of these, betulinic acid, was further quantified in the extracts by high-performance liquid chromatography-photodiode array detector analyzes. The higher amount was found in the chloroform extract, which was the most active one against P. falciparum. CONCLUSION: The results obtained in this work may partly explain the popular intake of A. amazonicusas an antimalarial remedy in the Amazon region.publishersversionpublishe

Small and mighty: adaptation of superphylum Patescibacteria to groundwater environment drives their genome simplicity.

BackgroundThe newly defined superphylum Patescibacteria such as Parcubacteria (OD1) and Microgenomates (OP11) has been found to be prevalent in groundwater, sediment, lake, and other aquifer environments. Recently increasing attention has been paid to this diverse superphylum including > 20 candidate phyla (a large part of the candidate phylum radiation, CPR) because it refreshed our view of the tree of life. However, adaptive traits contributing to its prevalence are still not well known.ResultsHere, we investigated the genomic features and metabolic pathways of Patescibacteria in groundwater through genome-resolved metagenomics analysis of > 600 Gbp sequence data. We observed that, while the members of Patescibacteria have reduced genomes (~ 1 Mbp) exclusively, functions essential to growth and reproduction such as genetic information processing were retained. Surprisingly, they have sharply reduced redundant and nonessential functions, including specific metabolic activities and stress response systems. The Patescibacteria have ultra-small cells and simplified membrane structures, including flagellar assembly, transporters, and two-component systems. Despite the lack of CRISPR viral defense, the bacteria may evade predation through deletion of common membrane phage receptors and other alternative strategies, which may explain the low representation of prophage proteins in their genomes and lack of CRISPR. By establishing the linkages between bacterial features and the groundwater environmental conditions, our results provide important insights into the functions and evolution of this CPR group.ConclusionsWe found that Patescibacteria has streamlined many functions while acquiring advantages such as avoiding phage invasion, to adapt to the groundwater environment. The unique features of small genome size, ultra-small cell size, and lacking CRISPR of this large lineage are bringing new understandings on life of Bacteria. Our results provide important insights into the mechanisms for adaptation of the superphylum in the groundwater environments, and demonstrate a case where less is more, and small is mighty

Whole-genome sequencing reveals insights into the adaptation of French Charolais cattle to Cuban tropical conditions

In the early 20th century, Cuban farmers imported Charolais cattle (CHFR) directly from France. These animals are now known as Chacuba (CHCU) and have become adapted to the rough environmental tropical conditions in Cuba. These conditions include long periods of drought and food shortage with extreme temperatures that European taurine cattle have difficulty coping with. In this study, we used whole-genome sequence data from 12 CHCU individuals together with 60 whole-genome sequences from six additional taurine, indicus and crossed breeds to estimate the genetic diversity, structure and accurate ancestral origin of the CHCU animals. Although CHCU animals are assumed to form a closed population, the results of our admixture analysis indicate a limited introgression of Bos indicus. We used the extended haplotype homozygosity (EHH) approach to identify regions in the genome that may have had an important role in the adaptation of CHCU to tropical conditions. Putative selection events occurred in genomic regions with a high proportion of Bos indicus, but they were not sufficient to explain adaptation of CHCU to tropical conditions by Bos indicus introgression only. EHH suggested signals of potential adaptation in genomic windows that include genes of taurine origin involved in thermogenesis (ATP9A, GABBR1, PGR, PTPN1 and UCP1) and hair development (CCHCR1 and CDSN). Within these genes, we identified single nucleotide polymorphisms (SNPs) that may have a functional impact and contribute to some of the observed phenotypic differences between CHCU and CHFR animals. Whole-genome data confirm that CHCU cattle are closely related to Charolais from France (CHFR) and Canada, but also reveal a limited introgression of Bos indicus genes in CHCU. We observed possible signals of recent adaptation to tropical conditions between CHCU and CHFR founder populations, which were largely independent of the Bos indicus introgression. Finally, we report candidate genes and variants that may have a functional impact and explain some of the phenotypic differences observed between CHCU and CHFR cattle