47 Genomic Studies of Reproductive Performance in American Mink

2021 ◽  
Vol 99 (Supplement_3) ◽  
pp. 26-27
Author(s):  
Shafagh Valipour ◽  
Karim Karimi ◽  
Younes Miar
Keyword(s):  
Genetic Correlation ◽  
Genomic Selection ◽  
Reproductive Performance ◽  
Genetic Parameters ◽  
Association Studies ◽  
American Mink ◽  
Reproductive Traits ◽  
Gestation Length ◽  
Genome Wide Association Studies ◽  
Breeding Programs

Abstract Improving reproductive efficiency is one of the main breeding goals in mink farming. Understanding the genetics of reproductive performance is essential for the development of effective breeding programs in mink. The objectives of this study are to 1) estimate the phenotypic and genetic parameters for litter sizes (LS), mortality rate at birth. (MB) and gestation-length (GL) traits; 2) perform genome-wide association studies (GWAS) for these reproductive traits; 3) implement GWAS results in the selection of mink for reproductive performance; 4) explore the potential for genomic selection in mink. The detailed reproductive performance on 3,500 female mink has been collected at the Canadian Center for Fur Animal Research at Dalhousie University (Truro, NS, Canada), in which, 1,000 of them will be genotyped with Affymetrix 50k SNP panel. A series of univariate and bivariate analyses were implemented in ASREML software to estimate the genetic and phenotypic parameters. Heritability estimates (±SE) were low-to-moderate, ranged from 0.06±0.02 for total number born to 0.23±0.03 for GL. High positive genetic correlations (±SE) were observed between LS traits, ranged from 0.59±0.18 to 0.85±0.11. There was a moderate genetic correlation (±SE) between MB and total number of kits born (0.46±0.15). However, MB had a favorable strong negative genetic correlation (±SE) with the number of weaned kits (–0.75±0.16). These estimated genetic parameters can be incorporated into Canadian mink breeding programs. Considering the low-to-moderate heritability of reproduction traits, the availability of the mink reference genome and genotyping panel will provide opportunities to accelerate mink breeding through genomics. The results of this project will contribute significantly to the current genetic knowledge of reproductive traits and identify the opportunities for genetic improvement through the application of genomics. The overall project aim is to develop a cost-effective, low-density panel of markers for the implementation of genomic selection for reproductive performance in mink.

scholarly journals Impaired Reproductive Function in Equines: From Genetics to Genomics

Animals ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 393
Author(s):  
Nora Laseca ◽  
Gabriel Anaya ◽  
Zahira Peña ◽  
Yamila Pirosanto ◽  
Antonio Molina ◽  
...  
Keyword(s):  
Reproductive Performance ◽  
Chromosomal Abnormalities ◽  
Association Studies ◽  
Copy Number Variants ◽  
Point Mutations ◽  
Reproductive Function ◽  
Reproductive Traits ◽  
Genome Wide Association Studies ◽  
Sequencing Technologies ◽  
Fertility Traits

Fertility is one of the key factors in the economic and productive success of the equine industry. Despite this, studies on the genetic causes affecting reproductive performance are scarce, especially in mares, where the genetic architecture of the reproductive traits is extremely complex. Today, with the increasing availability of new genomic methodologies for this species, we are presented with an interesting opportunity to understand the genetic basis of equine reproductive disorders. These include, among others, novel techniques for detecting chromosomal abnormalities, whose association with infertility in horses was established over 50 years ago; new sequencing technologies permitting an accurate detection of point mutations influencing fertility, as well as the study of inbreeding and molecular homozygosity, which has been widely suggested as one of the main causes of low reproductive performance in horses. Finally, over the last few years, reproductive performance has also been associated with copy number variants and candidate genes detected by genome-wide association studies on fertility traits. However, such studies are still scarce, probably because they depend on the existence of large and accurate phenotypic datasets of reproductive and/or fertility traits, which are still difficult to obtain in equines.

scholarly journals Molecular advances on agricultural crop improvement to meet current cultivating demands

2019 ◽  
Vol 12 (2) ◽  
pp. 39-60
Author(s):  
T. Margaritopoulou ◽  
D. Milioni
Keyword(s):  
Genomic Selection ◽  
Quantitative Traits ◽  
Seed Quality ◽  
Association Studies ◽  
Crop Improvement ◽  
Genome Wide Association Studies ◽  
Whole Genome ◽  
Agricultural Crop ◽  
Marker Assisted Breeding ◽  
Breeding Programs

Abstract Sunflower, maize and potato are among the world’s principal crops. In order to improve various traits, these crops have been genetically engineered to a great extent. Even though molecular markers for simple traits such as, fertility, herbicide tolerance or specific pathogen resistance have been successfully used in marker-assisted breeding programs for years, agronomical important complex quantitative traits like yield, biotic and abiotic stress resistance and seed quality content are challenging and require whole genome approaches. Collections of genetic resources for these crops are conserved worldwide and represent valuable resources to study complex traits. Nowadays technological advances and the availability of genome sequence have made novel approaches on the whole genome level possible. Molecular breeding, including both transgenic approach and marker-assisted breeding have facilitated the production of large amounts of markers for high density maps and allowed genome-wide association studies and genomic selection in sunflower, maize and potato. Marker-assisted selection related to hybrid performance has shown that genomic selection is a successful approach to address complex quantitative traits and to facilitate speeding up breeding programs in these crops in the future.

scholarly journals Genome-wide association studies for growth traits in broilers

2022 ◽  
Vol 23 (1) ◽  
Author(s):  
Dachang Dou ◽  
Linyong Shen ◽  
Jiamei Zhou ◽  
Zhiping Cao ◽  
Peng Luan ◽  
...  
Keyword(s):  
Genomic Selection ◽  
Candidate Genes ◽  
Rapid Growth ◽  
Genetic Parameters ◽  
Growth Traits ◽  
Association Studies ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Multiple Methods ◽  
Genome Wide

Abstract Background The identification of markers and genes for growth traits may not only benefit for marker assist selection /genomic selection but also provide important information for understanding the genetic foundation of growth traits in broilers. Results In the current study, we estimated the genetic parameters of eight growth traits in broilers and carried out the genome-wide association studies for these growth traits. A total of 113 QTNs discovered by multiple methods together, and some genes, including ACTA1, IGF2BP1, TAPT1, LDB2, PRKCA, TGFBR2, GLI3, SLC16A7, INHBA, BAMBI, APCDD1, GPR39, and GATA4, were identified as important candidate genes for rapid growth in broilers. Conclusions The results of this study will provide important information for understanding the genetic foundation of growth traits in broilers.

scholarly journals 27 Genomic relationship between antibody response to porcine reproductive and respiratory syndrome virus vaccination and reproductive performance in commercial sows

2020 ◽  
Vol 98 (Supplement_4) ◽  
pp. 20-21
Author(s):  
Leticia P Sanglard ◽  
Rohan Fernando ◽  
Kent A Gray ◽  
Daniel C Linhares ◽  
Jack C Dekkers ◽  
...  
Keyword(s):  
Antibody Response ◽  
Reproductive Performance ◽  
Association Studies ◽  
Genetic Correlations ◽  
Reproductive Traits ◽  
Respiratory Syndrome Virus ◽  
Genome Wide Association Studies ◽  
Prrs Virus ◽  
Positive Ratio ◽  
Commercial Farms

Abstract Antibody response, measured as sample-to-positive ratio (S/P), to porcine reproductive and respiratory syndrome (PRRS) after PRRS outbreaks has been proposed as an indicator trait to improve reproductive performance in PRRS-infected sows. However, waiting for a PRRS outbreak to occur and having different relationships in healthy pigs may limit the use of this trait. Thus, we proposed to investigate if this relationship also occurs between S/P to PRRS vaccination and reproductive performance in sows without exposure to PRRS. Nine hundred six F1 replacement gilts (139□17 days old) from two commercial farms were vaccinated with a commercial modified live PRRS virus vaccine. Blood samples were collected at 52 days after vaccination to measure S/P to PRRS and SNP genotyping. Reproductive performance included: number born alive (NBA), number of piglets weaned, number born mummified (MUM), number stillborn (NSB), and pre-weaning mortality (PWM) at parities (P) 1 to 3. Average performance was calculated for each trait per sow per year (PSY). Farrowing rate and age at first service were also analyzed. BayesC0 was used to estimate genetic correlations between S/P and reproductive performance. Bivariate genome-wide association studies of antibody response and reproductive traits were performed using BayesB. High genetic correlations between S/P and farrowing performance were identified for NBA_P1 (0.61±0.16), PWM_P2 (-0.64±0.15), PWM_P2 (-0.63±0.20), NSB_P3 (-0.84±0.05), MUM_P3 (-0.83±0.11), and NSB_PSY (-0.90±0.05). A QTL was identified on chromosome 7 (MHC region) for these reproductive traits and for S/P, explaining from 1.2% (PWM_P2) to 22.4% (S/P) of the genetic variance. SNP H3GA0020505 explained most of the variance in this region for these traits. Heterozygote animals for this SNP had overall better performance: greater S/P (P = 0.001), greater (P = 0.06) NBA_P1, and lesser (P = 0.06) MUM_P3 than other genotypes. These results suggest that antibody response to PRRS vaccination may be used as a genetic indicator to improve reproductive performance in commercial pigs.

scholarly journals PSV-15 Genomic basis of reproductive performance in PRRSV-infected sows

2020 ◽  
Vol 98 (Supplement_3) ◽  
pp. 162-163
Author(s):  
Felipe Hickmann ◽  
José Braccini Neto ◽  
Luke Kramer ◽  
Kent Gray ◽  
Yijian Huang ◽  
...  
Keyword(s):  
Reproductive Performance ◽  
Association Studies ◽  
Random Effect ◽  
Model Fitting ◽  
Reproductive Traits ◽  
Fixed Effect ◽  
Genomic Relationship Matrix ◽  
Relationship Matrix ◽  
Genome Wide Association Studies ◽  
Genomic Basis

Abstract Previous studies have shown that reproductive traits in sows during porcine reproductive and respiratory syndrome (PRRS) outbreaks are lowly heritable. However, little is known about the genomic basis of reproductive performance in PRRS virus (PRRSV)-infected sows. Thus, the objective of this work was to evaluate the genomic basis of reproductive performance in PRRSV-infected sows. Farrowing data from 475 Duroc and 405 Landrace sows that experienced a PRRS outbreak were used. Heritability and genome-wide association studies (GWAS) based on ~30K SNP genotypes were performed for each breed separately, for number of piglets born alive (NBA), stillborn piglets (NSB), mummified piglets (NM), piglets born dead (NBD; NSB+NM), total number of piglets born (TNB; NBA+NBD), and piglets weaned (NW). Heritabilities were estimated with ASReml using a model with the fixed-effect of parity and an animal random-effect, using a genomic-relationship matrix. GWAS was performed using Bayes-B in GenSel with a model fitting parity as fixed-effect and SNP effects as random. Heritability estimates (± standard error) for NBA, NSB, NM, NBD, TNB, and NW were 0.07±0.07, 0.02±0.11, 0.04±0.10, 0.08±0.08, 0.08±0.07, 0.06±0.04, respectively, for Duroc, and 0.09±0.07, 0.10±0.07, 0.10±0.08, 0.11±0.07, 0.07±0.08, 0.07±0.08, respectively, for Landrace. For Duroc, GWAS identified a quantitative trait locus (QTL) on chromosome (chr) 3 [114-120 megabases (Mb)] explaining 3.9% of the genetic variance (GV) for NBA, on chr 13 (189-193 Mb) explaining 2.7% GV for NBD, and on chr 5 (36-41 Mb) explaining 4.3% GV for TNB. For Landrace, GWAS identified a QTL on chr 13 (154-162 Mb) explaining 12.8% GV for NBA, on chr 14 (59-69 Mb) explaining 2.5% GV for NBD, and on chr 10 (7-9 Mb) explaining 4.1% GV for NW. These results indicate that reproductive traits are lowly heritable during a PRRS outbreak with few QTL identified in Duroc and Landrace sows.

166 Livestock Resiliency: Concepts and Approaches

2021 ◽  
Vol 99 (Supplement_3) ◽  
pp. 89-90
Author(s):  
Christine F Baes ◽  
Filippo Miglior ◽  
Flavio S Schenkel ◽  
Ellen Goddard ◽  
Gerrit Kistemaker ◽  
...  
Keyword(s):  
Genomic Selection ◽  
Large Scale ◽  
Association Studies ◽  
Genetic Correlations ◽  
Performance Testing ◽  
Breeding Value ◽  
Estimation Methods ◽  
Genome Wide Association Studies ◽  
Breeding Programs ◽  
Fertility Traits

Abstract Genetic improvement of health, welfare, efficiency, and fertility traits is challenging due to expensive and fuzzy phenotypes, the polygenic nature of traits, antagonistic genetic correlations to production traits and low heritabilities. Nevertheless, many organizations have introduced large-scale genetic evaluations for such traits in routine selection indexes. Medium and high-density arrays can be applied in genomic selection strategies to improve breeding value accuracy, and also in genome-wide association studies (GWAS) to identify causative mutations responsible for economically important traits. Genomic information is particularly helpful when traits have low heritability. The objective here is to provide a framework for including health, welfare, efficiency, and fertility traits taken from large-scale genetic and genomic analyses and identifying areas of potential improvement in terms of trait definition and performance testing. General tendencies between trait groups confirmed that a number of moderate unfavourable correlations (+/-0.20 or higher) exist between economically important trait complexes and health, welfare, and fertility traits. A number of trait complexes were identified in which “closer-to-biology” phenotypes could provide clear improvements to routine genetic and genomic selection programs. Here we outline development of these phenotypes and describe their collection. While conventional variance component estimation methods have underpinned the genomic component of some traits of economic interest, performance testing for health, welfare, efficiency, and fertility traits remains an elusive goal for breeding programs. Although our results are encouraging, there is much to be done in terms of trait definition and obtaining better measures of physiological parameters for wide-scale application in breeding programs. Close collaboration between veterinarians, physiologists, and geneticists is necessary to attain meaningful advancement in such areas. We would like to acknowledge the support and funding from all national and international partners involved in the RDGP project through the Large Scale Applied Research Project program from Genome Canada

Genetic parameters for reproductive performance of breeding cows and carcass traits of fattening animals in Japanese Black (Wagyu) cattle

2004 ◽  
Vol 78 (2) ◽  
pp. 195-201 ◽  
Author(s):  
K. Oyama ◽  
T. Katsuta ◽  
K. Anada ◽  
F. Mukai
Keyword(s):  
Reproductive Performance ◽  
Genetic Parameters ◽  
Genetic Relationships ◽  
Carcass Traits ◽  
Genetic Correlations ◽  
Subcutaneous Fat ◽  
Reproductive Traits ◽  
Gestation Length ◽  
Marbling Score ◽  
Selection For

AbstractReproductive performance is receiving increased attention from beef cattle producers. There are concerns that intensive selection for carcass traits might reduce the reproductive performance of females. Genetic parameters among six carcass traits and, age at first calving (AFC), gestation length (GL), days open (DO) and calving interval (CI) under year-round artificial insemination were estimated. Reproductive traits were extracted from 174005 calving records of Japanese Black cows and were analysed with 31364 carcass records. The restricted maximum likelihood procedure under animal models was used to estimate the parameters. Heritabilities of AFC, GL, DO and CI were estimated to be 0.20, 0.40, 0.05 and 0.05, respectively, and those of carcass traits were higher, ranging from 0.38 to 0.56. Genetic correlations of CI with AFC and GL were 0.25 and 0.16, respectively, while no relationship was observed between AFC and GL. Correlations among carcass traits were generally favourable and a slightly negative estimate was obtained between subcutaneous fat thickness and marbling score. Genetic correlations for AFC were -0.27 with carcass weight and -0.24 with marbling score. In contrast, GL, DO and CI were genetically independent of carcass traits. Genetic relationships between reproductive and carcass traits were generally low, and therefore serious antagonism was not observed. The results suggested that selection for carcass traits would not compromise genetic progress in reproductive traits.

scholarly journals Genomic Analysis, Progress and Future Perspectives in Dairy Cattle Selection: A Review

Animals ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 599
Author(s):  
Miguel A. Gutierrez-Reinoso ◽  
Pedro M. Aponte ◽  
Manuel Garcia-Herreros
Keyword(s):  
Dairy Cattle ◽  
Production Efficiency ◽  
Association Studies ◽  
Phenotypic Traits ◽  
Progeny Testing ◽  
Genome Wide Association Studies ◽  
Genetic Progress ◽  
Breeding Programs ◽  
Increased Risk ◽  
Selection Of

Genomics comprises a set of current and valuable technologies implemented as selection tools in dairy cattle commercial breeding programs. The intensive progeny testing for production and reproductive traits based on genomic breeding values (GEBVs) has been crucial to increasing dairy cattle productivity. The knowledge of key genes and haplotypes, including their regulation mechanisms, as markers for productivity traits, may improve the strategies on the present and future for dairy cattle selection. Genome-wide association studies (GWAS) such as quantitative trait loci (QTL), single nucleotide polymorphisms (SNPs), or single-step genomic best linear unbiased prediction (ssGBLUP) methods have already been included in global dairy programs for the estimation of marker-assisted selection-derived effects. The increase in genetic progress based on genomic predicting accuracy has also contributed to the understanding of genetic effects in dairy cattle offspring. However, the crossing within inbred-lines critically increased homozygosis with accumulated negative effects of inbreeding like a decline in reproductive performance. Thus, inaccurate-biased estimations based on empirical-conventional models of dairy production systems face an increased risk of providing suboptimal results derived from errors in the selection of candidates of high genetic merit-based just on low-heritability phenotypic traits. This extends the generation intervals and increases costs due to the significant reduction of genetic gains. The remarkable progress of genomic prediction increases the accurate selection of superior candidates. The scope of the present review is to summarize and discuss the advances and challenges of genomic tools for dairy cattle selection for optimizing breeding programs and controlling negative inbreeding depression effects on productivity and consequently, achieving economic-effective advances in food production efficiency. Particular attention is given to the potential genomic selection-derived results to facilitate precision management on modern dairy farms, including an overview of novel genome editing methodologies as perspectives toward the future.

scholarly journals PSVIII-38 Late-Breaking Abstract: Estimating genetic parameters of feed efficiency traits in American mink

2020 ◽  
Vol 98 (Supplement_4) ◽  
pp. 347-347
Author(s):  
Pourya Davoudi ◽  
Duy Ngoc Do ◽  
Guoyu Hu ◽  
Siavash Salek Ardestani ◽  
Younes Miar
Keyword(s):  
Body Weight ◽  
Genetic Correlation ◽  
Feed Intake ◽  
Feed Efficiency ◽  
Fixed Effects ◽  
Genetic Parameters ◽  
American Mink ◽  
Genetic Correlations ◽  
Final Body Weight ◽  
Selection For

Abstract Feed cost is the major input cost in the mink industry and thus improvement of feed efficiency through selection for high feed efficient mink is necessary for the mink farmers. The objective of this study was to estimate the heritability, phenotypic and genetic correlations for different feed efficiency measures, including final body weight (FBW), daily feed intake (DFI), average daily gain (ADG), feed conversion ratio (FCR) and residual feed intake (RFI). For this purpose, 1,088 American mink from the Canadian Center for Fur Animal Research at Dalhousie Faculty of Agriculture were recorded for daily feed intake and body weight from August 1 to November 14 in 2018 and 2019. The univariate models were used to test the significance of sex, birth year and color as fixed effects, and dam as a random effect. Genetic parameters were estimated via bivariate models using ASReml-R version 4. Estimates of heritabilities (±SE) were 0.41±0.10, 0.37±0.11, 0.33±0.14, 0.24±0.09 and 0.22±0.09 for FBW, DFI, ADG, FCR and RFI, respectively. The genetic correlation (±SE) was moderate to high between FCR and RFI (0.68±0.15) and between FCR and ADG (-0.86±0.06). In addition, RFI had low non-significant (P > 0.05) genetic correlations with ADG (0.04 ± 0.26) and BW (0.16 ± 0.24) but significant (P < 0.05) high genetic correlation with DFI (0.74 ± 0.11) indicating that selection for lower RFI will reduce feed intake without adverse effects on the animal size and growth rate. The results suggested that RFI can be implemented in genetic/genomic selection programs to reduce feed intake in the mink production system.

scholarly journals Investigating genetic correlations and causal effects between caffeine consumption and sleep behaviours

2017 ◽  
Author(s):  
Jorien L. Treur ◽  
Mark Gibson ◽  
Amy E Taylor ◽  
Peter J Rogers ◽  
Marcus R Munafò
Keyword(s):  
Genetic Correlation ◽  
Sleep Duration ◽  
Genetic Variants ◽  
Mendelian Randomization ◽  
Association Studies ◽  
Genetic Correlations ◽  
Causal Effects ◽  
Genome Wide Association Studies ◽  
Caffeine Consumption ◽  
Insomnia Complaints

AbstractStudy Objectives:Higher caffeine consumption has been linked to poorer sleep and insomnia complaints. We investigated whether these observational associations are the result of genetic risk factors influencing both caffeine consumption and poorer sleep, and/or whether they reflect (possibly bidirectional) causal effects.Methods:Summary-level data were available from genome-wide association studies (GWAS) on caffeine consumption (n=91,462), sleep duration, and chronotype (i.e., being a ‘morning’ versus an ‘evening’ person) (both n=128,266), and insomnia complaints (n=113,006). Linkage disequilibrium (LD) score regression was used to calculate genetic correlations, reflecting the extent to which genetic variants influencing caffeine consumption and sleep behaviours overlap. Causal effects were tested with bidirectional, two-sample Mendelian randomization (MR), an instrumental variable approach that utilizes genetic variants robustly associated with an exposure variable as an instrument to test causal effects. Estimates from individual genetic variants were combined using inverse-variance weighted meta-analysis, weighted median regression and MR Egger regression methods.Results:There was no clear evidence for genetic correlation between caffeine consumption and sleep duration (rg=0.000,p=0.998), chronotype (rg=0.086,p=0.192) or insomnia (rg=-0.034,p=0.700). Two-sample Mendelian randomization analyses did not support causal effects from caffeine consumption to sleep behaviours, or the other way around.Conclusions:We found no evidence in support of genetic correlation or causal effects between caffeine consumption and sleep. While caffeine may have acute effects on sleep when taken shortly before habitual bedtime, our findings suggest that a more sustained pattern of high caffeine consumption is likely associated with poorer sleep through shared environmental factors.

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