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Background: Imputation from genotyping array to whole-genome sequence variants using resequencing of representative reference populations enhances our ability to map genetic factors affecting complex phenotypes in livestock species. The accumulation of knowledge about gene function in human and laboratory animals can provide substantial advantage for genomic research in livestock species.
Results: In this study, 201,388 pigs from three commercial Danish breeds genotyped with low to medium (8.5k to 70k) SNP arrays were imputed to whole genome sequence variants using a two-step approach. Both imputation steps achieved high accuracies, and in total this yielded 26,447,434 markers on 18 autosomes. The average estimated imputation accuracy of markers with minor allele frequency ≥ 0.05 was 0.94. To overcome the memory consumption of running genome-wide association study (GWAS) for each breed, we performed within-breed subpopulation GWAS then within-breed meta-analysis for average daily weight gain (ADG), followed by a multi-breed meta-analysis of GWAS summary statistics. We identified 15 quantitative trait loci (QTL). Our post-GWAS analysis strategy to prioritize of candidate genes including information like gene ontology, mammalian phenotype database, differential expression gene analysis of high and low feed efficiency pig and human GWAS catalog for height, obesity, and body mass index, we proposed MRAP2, LEPROT, PMAIP1, ENSSSCG00000036234, BMP2, ELFN1, LIG4 and FAM155A as the candidate genes with biological support for ADG in pigs.
Conclusion: Our post-GWAS analysis strategy helped to identify candidate genes not just by distance to the lead SNP but also by multiple sources of biological evidence. Besides, the identified QTL overlap with genes which are known for their association with human growth-related traits. The GWAS with this large data set showed the power to map the genetic factors associated with ADG in pigs and have added to our understanding of the genetics of growth across mammalian species.
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http://dx.doi.org/10.1186/s12864-022-08373-3 | DOI Listing |
Nucleic Acids Res
December 2024
Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) OT Gatersleben, Corrensstr 3, 06466 Seeland, Germany.
In eukaryotes, accurate chromosome segregation during cell division relies on the centromeric histone H3 variant, CENH3. Our previous work identified KINETOCHORE NULL2 (αKNL2) as a plant CENH3 assembly factor, which contains a centromere-targeting motif, CENPC-k, analogous to the CENPC motif found in CENP-C. We also demonstrated that αKNL2 can bind DNA in vitro in a sequence-independent manner, without the involvement of its CENPC-k motif.
View Article and Find Full Text PDFVopr Kurortol Fizioter Lech Fiz Kult
December 2024
Saint-Petersburg State Pediatric Medical University, Saint-Petersburg, Russia.
Unlabelled: Dystrophinopathies - a group of hereditary X-linked neuromuscular diseases characterized by worsening fibrofatty degeneration of skeletal muscles, muscular weakness, low exercise tolerance, as well as orthopedic, cardiovascular and respiratory complications. Study of the effectiveness of physical medical rehabilitation in patients with neuromuscular diseases, evaluation of the influence of external and internal factors on functional capabilities and effectiveness of the conducted rehabilitation are highly relevant.
Objective: To evaluate the effectiveness of physical medical rehabilitation of patients with dystrophinopathies at the outpatient stages of the disease's course and the influence of anthropometric characteristics and functional status of patients' motor capabilities.
ACS Appl Bio Mater
December 2024
Polymers & Functional Materials Division, CSIR- Indian Institute of Chemical Technology, Hyderabad 500007, India.
Neurological disorders impact global health by affecting both central and peripheral nervous systems. Understanding the neurogenic processes, i.e.
View Article and Find Full Text PDFTissue Eng Part A
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Department of Orthopedics, Municipal Hospital Affiliated to Taizhou University, Taizhou City, China.
Senescence and osteogenic differentiation potential loss limited bone nonunion treatment effects of bone marrow-derived mesenchymal stem cells (BMSCs). MiR-100-5p/Lysine(K)-specific demethylase 6B (KDM6B) can inhibit osteogenesis, but their effects on bone union remain unclear. This study aims to investigate the effects of miR-100-5p/KDM6B on osteogenic differentiation and bone defects.
View Article and Find Full Text PDFMol Hum Reprod
December 2024
Center for Reproductive Medicine and Obstetrics and Gynecology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China.
Endometrial collagen I undergoes dynamic degradation and remodelling in response to endometrial stromal cell (ESC) decidualization and embryo implantation. However, excessive collagen I deposition in the endometrium during the implantation window may impair decidualization, causing embryo implantation failure in patients with endometriosis (EMS). We found that endometrial collagen I expression during the mid-secretory phase was increased in the EMS group of patients.
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