Genetic and genomic analyses of embryo production in dairy cattle

2020 ◽  
Vol 32 (2) ◽  
pp. 50
Author(s):  
C. Jaton ◽  
F. S. Schenkel ◽  
T. C. S. Chud ◽  
F. Malchiodi ◽  
M. Sargolzaei ◽  
...  
Keyword(s):  
Genome Wide Association Study ◽  
Assisted Reproductive Technologies ◽  
Bovine Genome ◽  
Genetic Correlations ◽  
Genetic Selection ◽  
Dairy Industry ◽  
Reproductive Technologies ◽  
Chromosome 11 ◽  
Embryo Production ◽  
A Genome

The Canadian dairy industry has been using invivo and invitro assisted reproductive technologies to produce embryos. Technological improvements have helped increase the number and quality of embryos produced, but genetic and genomic tools for improving these traits have yet to be assessed for the Canadian Holstein population. Genetic parameters and a genome-wide association study were performed in Canadian Holstein for the total number of embryos (NE) and the number of viable embryos (VE). Results showed potential for genetic selection for both NE and VE, with heritability estimates (± s.e.) of approximately 0.15±0.01. Genetic correlations between the number of embryos produced using different procedures (invivo and invitro) suggested that a similar number of embryos should be expected from a donor regardless of the procedure used. A region on chromosome 11 of the bovine genome was found to be significantly associated with the number of embryos, indicating a potential regulatory role of this region on embryo production. Overall, these findings are of interest for the Canadian dairy industry because they provide useful information for breeders that are interested in producing embryos from the elite donors in their herds or in the population using assisted reproductive technologies.

scholarly journals Genetic basis and identification of candidate genes for wooden breast and white striping in commercial broiler chickens

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Juniper A. Lake ◽  
Jack C. M. Dekkers ◽  
Behnam Abasht
Keyword(s):  
Candidate Genes ◽  
Broiler Chickens ◽  
Genetic Basis ◽  
Genome Wide Association Study ◽  
Specific Protein ◽  
Chromosome 11 ◽  
A Genome ◽  
White Striping ◽  
Commercial Broiler ◽  
Wooden Breast

AbstractWooden breast (WB) and white striping (WS) are highly prevalent and economically damaging muscle disorders of modern commercial broiler chickens characterized respectively by palpable firmness and fatty white striations running parallel to the muscle fiber. High feed efficiency and rapid growth, especially of the breast muscle, are believed to contribute to development of such muscle defects; however, their etiology remains poorly understood. To gain insight into the genetic basis of these myopathies, a genome-wide association study was conducted using a commercial crossbred broiler population (n = 1193). Heritability was estimated at 0.5 for WB and WS with high genetic correlation between them (0.88). GWAS revealed 28 quantitative trait loci (QTL) on five chromosomes for WB and 6 QTL on one chromosome for WS, with the majority of QTL for both myopathies located in a ~ 8 Mb region of chromosome 5. This region has highly conserved synteny with a portion of human chromosome 11 containing a cluster of imprinted genes associated with growth and metabolic disorders such as type 2 diabetes and Beckwith-Wiedemann syndrome. Candidate genes include potassium voltage-gated channel subfamily Q member 1 (KCNQ1), involved in insulin secretion and cardiac electrical activity, lymphocyte-specific protein 1 (LSP1), involved in inflammation and immune response.

Searching for Disease Modifiers Genes in Thalassemia.

Blood ◽  
2005 ◽  
Vol 106 (11) ◽  
pp. 3642-3642
Author(s):  
Suthat Fucharoen ◽  
Orapan Sripichai ◽  
Pranee Winichagoon ◽  
Kenneth Abel ◽  
Andreas Braun
Keyword(s):  
Disease Severity ◽  
Dna Analysis ◽  
Genome Wide Association Study ◽  
Globin Gene ◽  
Fetal Hemoglobin ◽  
Nucleotide Polymorphisms ◽  
Genetic Modifiers ◽  
Chromosome 11 ◽  
Genotype Frequencies ◽  
A Genome

Abstract β0-thalassemia/HbE disease is one of the most common thalassemias in Southeast Asia. Patients with compound heterozygote for HbE and β0 mutant alleles display remarkable variability in clinical expression, ranging from nearly asymptomatic to severe, transfusion-dependent disease. It is believed that additional genetic factors modifying disease severity may account for this variability. A universal platform technology (MassARRAY) based on mass spectrometry for analyzing nucleic acids at a high level of precision and accuracy has been developed. To identify genetic modifiers influencing severity among 1060 β0-thalassemia/HbE patients, we are utilizing this technology to conduct a genome-wide association study involving approximately 110,000 gene-based single nucleotide polymorphisms (SNPs). This assay panel corresponds to SNPs with a median spacing of 10.4 kilobases, in approximately 99% of all known and predicted human genes. DNAs from approximately 200 regionally matched patients representing the extremes of mild and severe cases were included in each DNA pool. Allele frequencies for all SNPs were estimated in both pools, and those showing suggestive significant differences (p values <0.02) were selected for verification by repeated pooled DNA analysis. Approximately one-fourth of these showed reproducible allelic differences at p<0.05, and more than 600 were selected for genotyping the individual patient DNAs in order to determine precise allele and genotype frequencies. A number of SNPs showed evidence for association with disease severity, including several in reported quantitative trait loci (QTLs) associated with fetal hemoglobin HbF levels. However the most strongly associated SNPs were within a region on chromosome 11 distinct from the beta globin gene cluster, within which most analysis to date has focused.

scholarly journals Analysis of genotype by environment interactions in a maize mapping population

2021 ◽  
Author(s):  
Asher I Hudson ◽  
Sarah G Odell ◽  
Pierre Dubreuil ◽  
Marie-Helene Tixier ◽  
Sebastien Praud ◽  
...  
Keyword(s):  
Genome Wide Association Study ◽  
Genetic Correlations ◽  
Genotype By Environment Interaction ◽  
Environment Interaction ◽  
Crop Breeding ◽  
Genotype By Environment Interactions ◽  
Genotype By Environment ◽  
Genome Wide ◽  
A Genome ◽  
Genetic Covariances

Genotype by environment interactions are a significant challenge for crop breeding as well as being important for understanding the genetic basis of environmental adaptation. In this study, we analyzed genotype by environment interaction in a maize multi-parent advanced generation intercross population grown across five environments. We found that genotype by environment interactions contributed as much as genotypic effects to the variation in some agronomically important traits. In order to understand how genetic correlations between traits change across environments, we estimated the genetic variance-covariance matrix in each environment. Changes in genetic covariances between traits across environments were common, even among traits that show low genotype by environment variance. We also performed a genome-wide association study to identify markers associated with genotype by environment interactions but found only a small number of significantly associated markers, possibly due to the highly polygenic nature of genotype by environment interactions in this population.

scholarly journals Genetic parameters and associated genomic regions for global immunocompetence and other health-related traits in pigs

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Maria Ballester ◽  
Yuliaxis Ramayo-Caldas ◽  
Olga González-Rodríguez ◽  
Mariam Pascual ◽  
Josep Reixach ◽  
...  
Keyword(s):  
Genome Wide Association Study ◽  
Genetic Correlations ◽  
Γδ T Cells ◽  
Phagocytic Capacity ◽  
Reactive Protein ◽  
A Genome ◽  
Effective Selection ◽  
Health Related ◽  
Genome Level ◽  
Genomic Regions

Abstract The inclusion of health-related traits, or functionally associated genetic markers, in pig breeding programs could contribute to produce more robust and disease resistant animals. The aim of the present work was to study the genetic determinism and genomic regions associated to global immunocompetence and health in a Duroc pig population. For this purpose, a set of 30 health-related traits covering immune (mainly innate), haematological, and stress parameters were measured in 432 healthy Duroc piglets aged 8 weeks. Moderate to high heritabilities were obtained for most traits and significant genetic correlations among them were observed. A genome wide association study pointed out 31 significantly associated SNPs at whole-genome level, located in six chromosomal regions on pig chromosomes SSC4, SSC6, SSC17 and SSCX, for IgG, γδ T-cells, C-reactive protein, lymphocytes phagocytic capacity, total number of lymphocytes, mean corpuscular volume and mean corpuscular haemoglobin. A total of 16 promising functionally-related candidate genes, including CRP, NFATC2, PRDX1, SLA, ST3GAL1, and VPS4A, have been proposed to explain the variation of immune and haematological traits. Our results enhance the knowledge of the genetic control of traits related with immunity and support the possibility of applying effective selection programs to improve immunocompetence in pigs.

scholarly journals 34 Reproductive management of beef females in tropical and sub-tropical environments

2019 ◽  
Vol 97 (Supplement_3) ◽  
pp. 37-37
Author(s):  
Nicola Oosthuizen ◽  
Pedro Levy Piza Fontes ◽  
G Cliff Lamb
Keyword(s):  
Assisted Reproductive Technologies ◽  
Bos Taurus ◽  
Management Strategies ◽  
Bos Indicus ◽  
The United States ◽  
Reproductive Technologies ◽  
Pregnancy Rates ◽  
Embryo Production ◽  
Reproductive Management

Abstract Bos indicus and Bos taurus cattle diverged from an evolutionary standpoint more than 110,000 years ago. Since then, Bos indicus cattle have undergone genetic adaptations beyond the commonly discussed increased thermo-tolerance and parasite resistance. Several physiological differences exist between Bos indicus and Bos taurus cattle, and it is important to consider these differences when establishing reproductive management strategies. It has been well described that Bos indicus cattle have a delayed onset of puberty and longer periods of postpartum anestrus, yet through the utilization of estrus synchronization protocols these challenges can be attenuated. However, when Bos indicus females are exposed to these protocols, they are known to have smaller dominant follicles, lower expression of estrus, and decreased pregnancy rates to artificial insemination (AI) when compared to Bos taurus females. These factors can be overcome through the utilization of estradiol and progesterone based synchronization protocols, which improve follicular dynamics and yield acceptable pregnancy rates to assisted reproductive technologies in cattle adapted to tropical or subtropical conditions. However, the use of estrogens for synchronization purposes is not permitted in the United States, and cattle producers need to rely on GnRH-based protocols. Another key difference between subspecies, is that Bos indicus females have greater antral follicle counts than Bos taurus females, which proves beneficial for in vitro embryo production. Therefore, an opportunity exists to explore the greater productivity of donors in embryo production in order to improve genetics in herds that utilize these breeds.

scholarly journals Genome-wide association study identifies RNF123 locus as associated with chronic widespread musculoskeletal pain

2021 ◽  
pp. annrheumdis-2020-219624
Author(s):  
Md Shafiqur Rahman ◽  
Bendik S Winsvold ◽  
Sergio O Chavez Chavez ◽  
Sigrid Børte ◽  
Yakov A Tsepilov ◽  
...  
Keyword(s):  
Association Study ◽  
Musculoskeletal Pain ◽  
Tissue Specificity ◽  
Genome Wide Association Study ◽  
Genetic Correlations ◽  
The Body ◽  
Genome Wide Association ◽  
Suggestive Association ◽  
Genome Wide ◽  
A Genome

Background and objectivesChronic widespread musculoskeletal pain (CWP) is a symptom of fibromyalgia and a complex trait with poorly understood pathogenesis. CWP is heritable (48%–54%), but its genetic architecture is unknown and candidate gene studies have produced inconsistent results. We conducted a genome-wide association study to get insight into the genetic background of CWP.MethodsNorthern Europeans from UK Biobank comprising 6914 cases reporting pain all over the body lasting >3 months and 242 929 controls were studied. Replication of three independent genome-wide significant single nucleotide polymorphisms was attempted in six independent European cohorts (n=43 080; cases=14 177). Genetic correlations with risk factors, tissue specificity and colocalisation were examined.ResultsThree genome-wide significant loci were identified (rs1491985, rs10490825, rs165599) residing within the genes Ring Finger Protein 123 (RNF123), ATPase secretory pathway Ca2+transporting 1 (ATP2C1) and catechol-O-methyltransferase (COMT). The RNF123 locus was replicated (meta-analysis p=0.0002), the ATP2C1 locus showed suggestive association (p=0.0227) and the COMT locus was not replicated. Partial genetic correlation between CWP and depressive symptoms, body mass index, age of first birth and years of schooling were identified. Tissue specificity and colocalisation analysis highlight the relevance of skeletal muscle in CWP.ConclusionsWe report a novel association of RNF123 locus and a suggestive association of ATP2C1 locus with CWP. Both loci are consistent with a role of calcium regulation in CWP. The association with COMT, one of the most studied genes in chronic pain field, was not confirmed in the replication analysis.

scholarly journals Genome-wide Association Study of Pulmonary Function in Europeans and Africans from the UK Biobank Identifies Distinct Variants

2022 ◽  
Author(s):  
Musalula Sinkala ◽  
Samar S. M. Elsheikh ◽  
Mamana Mbiyavanga ◽  
Joshua Cullinan ◽  
Nicola Mulder
Keyword(s):  
Pulmonary Function ◽  
Genome Wide Association Study ◽  
Well Being ◽  
Genome Wide Association ◽  
Significant Finding ◽  
Uk Biobank ◽  
Chromosome 11 ◽  
Genome Wide ◽  
A Genome ◽  
The Uk

Pulmonary function is an indicator of well-being, and pulmonary pathologies are the third major cause of death worldwide. FEV1, FVC, and PEF are quantitively used to assess pulmonary function. We conducted a genome-wide association analysis of pulmonary function in 383,471 individuals of European and 5,978 African descent represented in the UK Biobank. Here, we report 817 variants in Europeans and 3 in Africans associated (p-values < 5 x 10-8) with three pulmonary function parameters; FEV1, FVC and PEF. In addition to 377 variants in Europeans previously reported to be associated with phenotypes related to pulmonary function, we identified 330 novel loci, including an ISX intergenic variant rs369476290 on chromosome 22 in Africans and a KDM2A intron variant rs12790261 on chromosome 11 in Europeans. Remarkably, we find no shared variants among Africans and Europeans. Enrichment analyses of variants separately for each ancestry background revealed significant enrichment for terms related to pulmonary phenotypes in Europeans but not Africans. Further analysis of studies of pulmonary phenotypes revealed individuals of European background are disproportionally overrepresented in datasets compared to Africans, with the gap widening over the past five years. Our findings offer a better understanding of the different variants that modify pulmonary function in Africans and Europeans, a significant finding for future GWAS studies and medicine.

scholarly journals Genome-wide association study identifies two new loci associated with anti-NMDAR encephalitis

2021 ◽  
Author(s):  
Anja K Tietz ◽  
Klemens Angstwurm ◽  
Tobias Baumgartner ◽  
Kathrin Doppler ◽  
Katharina Eisenhut ◽  
...  
Keyword(s):  
Association Study ◽  
Genome Wide Association Study ◽  
Immune Cell ◽  
Genome Wide Association ◽  
Chromosome 11 ◽  
Genetic Determinants ◽  
Nmdar Encephalitis ◽  
Genome Wide ◽  
A Genome ◽  
Causal Genes

AbstractObjectiveTo investigate the genetic determinants of the most common type of antibody-mediated autoimmune encephalitis, anti-N-methyl-D-aspartate receptor (anti-NMDAR) encephalitis.MethodsWe performed a genome-wide association study in 178 patients with anti-NMDAR encephalitis and 590 healthy controls followed by a colocalization analysis to identify putatively causal genes.ResultsWe identified two independent risk loci harboring genome-wide significant variants (P < 5 × 10−8, OR ≤ 2.2), one on chromosome 15, harboring only the LRRK1 gene, and one on chromosome 11 centered on the ACP2 and NR1H3 genes in a larger region of high linkage-disequilibrium. Colocalization signals with expression quantitative trait loci (eQTL) for different brain regions and immune cell types suggested ACP2, NR1H3, MADD, DDB2, and C11orf49 as putatively causal genes. The best candidate genes in each region are LRRK1, encoding Leucine-Rich Repeat Kinase 1, a protein involved in B-cell development, and NR1H3 liver x receptor alpha, a transcription factor whose activation inhibits inflammatory processes.ConclusionThis study provides evidence for relevant genetic determinants of antibody-mediated autoimmune encephalitides outside the HLA-region. The results suggest that future studies with larger sample sizes will successfully identify additional genetic determinants and contribute to the elucidation of the pathomechanism.

123 LONG-TERM PRODUCTION OF IN VITRO-MATURED PORCINE OOCYTES AND EMBRYOS

2009 ◽  
Vol 21 (1) ◽  
pp. 161
Author(s):  
A. M. Paprocki ◽  
C. M. Syverson ◽  
R. W. Koppang ◽  
J. R. Dobrinsky
Keyword(s):  
Assisted Reproductive Technologies ◽  
Genetic Material ◽  
Reproductive Technologies ◽  
Scientific Data ◽  
Developmental Competence ◽  
Embryo Production ◽  
Pump System ◽  
Developmental Potential ◽  
Parthenogenetic Embryos

Although in vivo matured, ovulated, or both, oocytes provide the finest genetic material for use in assisted reproductive technologies (ART), their en masse production requires livestock production facilities, staff and associated overhead, is expensive and labor intensive, their harvest involves surgical or laparoscopic expertise, and large yields needed for en masse daily embryo production are cumbersome and very costly. In vitro-matured (IVM) oocytes have long been a practical gamete source for ART, including in vitro fertilization, ICSI and cloning. Rather than using conventional IVF to produce embryos, we employ in vitro oocyte activation for the production of diploidized parthenogenetic embryos, removing problems associated with variable embryo production due to polyspermic inseminations. In this way, we can produce a repeatable and consistent supply of mature oocytes, advanced embryos, or both, used in product testing, quality control, transgenic or cloned (or both) embryo production, in vitro development controls, as well as in-house culture control embryos for customer scientific data sharing. In this study, we observe mature oocyte and parthenogenetic embryo production over a complete year as control information for our laboratory. Additionally, colleagues may use these data for comparison in their own scientific mission. At least 3 times a month for 12 consecutive months, ovaries were collected from mature females at an abattoir and transported to our laboratory. Cumulus–oocyte complexes were aspirated from 4–6 mm follicles with an 18-gauge needle fixed to a vacuum pump system. Only COC surrounded by two or more layers of compact cumulus investment and containing oocytes of equal size were placed into a commercial TCM-199-based IVM system (Minitube of America Inc., Verona, WI, USA). After 42 h IVM, mature oocytes were isolated from their expanded cumulus and subjected to chemical (ionomycin/DMAP) parthenogenetic activation based on US Patent 5,496,720. Embryos were cultured 120 h in NCSU-23, then cultured for an additional 48 h in NCSU-23 (no BSA) supplemented with 10% FBS. A minimum of 1504 premium and 4604 standard oocytes (Minitube of America Inc.) were placed into IVM. Both premium (1364, 90.7%) and standard (4061, 88.2%; P > 0.05) oocytes are used to produce mature oocytes (MO). Of 781 premium MOs made into diploidized parthenogenetic embryos, 459 (58.8%) developed into blastocysts (61.3 cells/embryo). Of 2068 standard MO made into diploidized parthenogenetic embryos, 914 (44.2%; P < 0.05) developed into blastocysts (64.7 cells/embryo). En masse in vitro maturation of oocytes can supply a repeatable and consistent supply of mature oocytes for use in assisted reproductive technologies. These MO have the developmental potential to form blastocysts in vitro and enable scientists to infer developmental competence of in vitro-produced embryos for research and commercial use.

scholarly journals An Independent Locus Upstream of ASIP Controls Variation in the Shade of the Bay Coat Colour in Horses

Genes ◽  
2020 ◽  
Vol 11 (6) ◽  
pp. 606 ◽  
Author(s):  
Laura J. Corbin ◽  
Jessica Pope ◽  
Jacqueline Sanson ◽  
Douglas F. Antczak ◽  
Donald Miller ◽  
...  
Keyword(s):  
Genome Wide Association Study ◽  
Health Management ◽  
Relative Concentration ◽  
Regulatory Region ◽  
Genetic Selection ◽  
Coat Colour ◽  
The Body ◽  
Single Region ◽  
A Genome ◽  
Independent Locus

Novel coat colour phenotypes often emerge during domestication, and there is strong evidence of genetic selection for the two main genes that control base coat colour in horses—ASIP and MC1R. These genes direct the type of pigment produced, red pheomelanin (MC1R) or black eumelanin (ASIP), as well as the relative concentration and the temporal–spatial distribution of melanin pigment deposits in the skin and hair coat. Here, we describe a genome-wide association study (GWAS) to identify novel genic regions involved in the determination of the shade of bay. In total, 126 horses from five different breeds were ranked according to the extent of the distribution of eumelanin: spanning variation in phenotype from black colour restricted only to the extremities to the presence of some black pigment across nearly all the body surface. We identified a single region associated with the shade of bay ranking spanning approximately 0.5 MB on ECA22, just upstream of the ASIP gene (p = 9.76 × 10−15). This candidate region encompasses the distal 5′ end of the ASIP transcript (as predicted from other species) as well as the RALY gene. Both loci are viable candidates based on the presence of similar alleles in other species. These results contribute to the growing understanding of coat colour genetics in the horse and to the mapping of genetic determinants of pigmentation on a molecular level. Given pleiotropic phenotypes in behaviour and obesity for ASIP alleles, especially those in the 5′ regulatory region, improved understanding of this new Shade allele may have implications for health management in the horse.

Sign in / Sign up

Export Citation Format

Share Document