Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1178124 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Fennoscandian Shield genomic database (FSGD)
| PRJNA627556 | ENA
Project description:In the breeding programs with local breeds, it is crucial to balance the selection for genetic gain and the maintaining of genetic diversity. These two objectives are often conflicting, and finding the optimal point of the trade-off has been a challenge for breeders. Genomic selection (GS) provides a revolutionary tool for the genetic improvement of farm animals. At the same time, it can increase inbreeding and produce a more rapid depletion of genetic variability of the selected traits in future generations. Optimum-contribution selection (OCS) represents an approach to maximize genetic gain while constraining inbreeding within a targeted range. In the present study, 515 Ningxiang pigs were genotyped with the Illumina Porcine SNP60 array or the GeneSeek Genomic Profiler Porcine 50K array. The Ningxiang pigs were found to be highly inbred at the genomic level. Average locus-wise inbreeding coefficients were 0.41 and 0.37 for the two SNP arrays used, whereas genomic inbreeding coefficients based on runs of homozygosity were 0.24 and 0.25, respectively. Simulated phenotypic data were used to assess the utility of genomic OCS (GOCS) in comparison with GS without inbreeding control. GOCS was conducted under two scenarios, selecting sires only (GOCS_S) or selecting sires and dams (GOCS_SD), while kinships were constrained on selected parents. The genetic gain for average daily body weight gain (ADG) per generation was between 18.99 and 20.55 g with GOCS_S, and between 23.20 and 28.92 with GOCS_SD, and it varied from 25.38 to 48.38 g under GS without controlling inbreeding. While the rate of genetic gain per generation obtained using GS was substantially larger than that obtained by the two scenarios of genomic OCS in the beginning generations of selection, the difference in the genetic gain of ADG between GS and GOCS reduced quickly in latter generations. At generation ten, the difference in the realized rates of genetic gain between GS and GOCS_SD diminished and ended up with even a slightly higher genetic gain with GOCS_SD, due to the rapid loss of genetic variance with GS and fixation of causative genes. The rate of inbreeding was mostly maintained below 5% per generation with genomic OCS, whereas it increased to between 10.5% and 15.3% per generation with GS. Therefore, genomic OCS appears to be a sustainable strategy for the genetic improvement of local breeds such as Ningxiang pigs, but keeping mind that a variety of GOCS methods exist and the optimal forms remain to be exploited further.
2020-08-01 | E-MTAB-8933 | biostudies-arrayexpress
Project description:The genomic causes of inbreeding depression are poorly known. Several studies have found widespread transcriptomic alterations in inbred organisms, but it remains unclear which of these alterations are causes of the depression and which are mere responses to the ensuing physiological stress. We made a c-DNA microarray analysis in Drosophila melanogaster attempting to differentiate causes from responses of inbreeding depression. The rationale of the experiment was that, while depression is a general phenomenon producing similar consequences in different inbred lines, its first genetic causes would be different for each inbred line, as they are expected to be caused by the fixation of rare deleterious genes. Many changes in expression were common to all sets, but fourteen genes, grouped in four expression clusters, showed strong set-specific changes, and were therefore candidates to be sources of the inbreeding depression observed.
2013-05-31 | GSE47176 | GEO
Project description:Whole Genome Sequencing of the Wolverine Gulo gulo
| PRJEB10674 | ENA
Project description:Gulo gulo luscus (isolate FN33715) Genome sequencing and assembly
| PRJNA675847 | ENA
Project description:The ability to synthesize essential molecules is sometimes lost in evolution. A classic example is ascorbate (Vitamin C), which is synthesized in most animals by L-Gulonolactone Oxidase (GULO), an enzyme lost multiple independent times in animal evolution. This event is thought to be evolutionarily neutral, however, GULO-deficient animals including humans need to obtain ascorbate from their diet and are prone to ascorbate deficiency and scurvy. We therefore hypothesized that this disadvantage of GULO loss is offset by physiological benefits. Here we show that ascorbate deficiency benefits mice infected with schistosome parasites, which cause schistosomiasis, a debilitating parasitic disease that afflicts 250 million people. Schistosoma mansoni worms required host ascorbate to produce eggs in vivo. Consequently, ascorbate-deficient mice were protected from schistosomiasis pathologies and transmission. Intermittent ascorbate deficiency protected Gulo-deficient mice from both scurvy and schistosomiasis mortality. The effects of ascorbate on schistosome reproduction were mediated by ascorbate-dependent histone demethylation which promoted vitellocyte development in female schistosomes. We propose that vitamin deficiencies are not always detrimental but can protect animals from pathogens which need to obtain vitamins from their host.
2025-11-20 | GSE310725 | GEO