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S. Geerts - One of the best experts on this subject based on the ideXlab platform.
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Susceptibility of West African Dwarf goats and WAD × Saanen crosses to experimental infection with Trypanosoma congolense
Veterinary Parasitology, 2005Co-Authors: S. Dhollander, J.f.f.p. Bos, S. Kora, M. Sanneh, M. Gaye, S. Leak, D. Berkvens, S. GeertsAbstract:West African Dwarf goats (WADs) and their Saanen crosses were experimentally infected with Trypanosoma congolense. No significant differences were found between trypanosome parasitaemia and antibody response of the crossbred and WAD goats. Neither the WAD goats nor the Saanen crosses were able to control the drop in PCV following trypanosome infection. The level of anaemia caused by the trypanosome infection was similar in the two breeds during the trial. Based on these findings, no difference in tolerance or susceptibility to T. congolense could be demonstrated between the WAD goats and their Saanen crosses. Although the weight of all goats increased during the trial, the crosses gained significantly more weight than the WAD goats. The trypanosome infection reduced the growth rate of both breeds, but this reduction was not statistically significant. Crossbreeding trypanotolerant WADs with trypanosusceptible Saanen goats might, therefore, be an effective means of increasing productivity.
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Susceptibility of West African Dwarf goats and WAD x Saanen crosses to experimental infection with Trypanosoma congolense.
Veterinary parasitology, 2005Co-Authors: S. Dhollander, S. Kora, M. Sanneh, M. Gaye, S. Leak, D. Berkvens, J Bos, S. GeertsAbstract:West African Dwarf goats (WADs) and their Saanen crosses were experimentally infected with Trypanosoma congolense. No significant differences were found between trypanosome parasitaemia and antibody response of the crossbred and WAD goats. Neither the WAD goats nor the Saanen crosses were able to control the drop in PCV following trypanosome infection. The level of anaemia caused by the trypanosome infection was similar in the two breeds during the trial. Based on these findings, no difference in tolerance or susceptibility to T. congolense could be demonstrated between the WAD goats and their Saanen crosses. Although the weight of all goats increased during the trial, the crosses gained significantly more weight than the WAD goats. The trypanosome infection reduced the growth rate of both breeds, but this reduction was not statistically significant. Crossbreeding trypanotolerant WADs with trypanosusceptible Saanen goats might, therefore, be an effective means of increasing productivity.
S. Dhollander - One of the best experts on this subject based on the ideXlab platform.
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Susceptibility of West African Dwarf goats and WAD × Saanen crosses to experimental infection with Trypanosoma congolense
Veterinary Parasitology, 2005Co-Authors: S. Dhollander, J.f.f.p. Bos, S. Kora, M. Sanneh, M. Gaye, S. Leak, D. Berkvens, S. GeertsAbstract:West African Dwarf goats (WADs) and their Saanen crosses were experimentally infected with Trypanosoma congolense. No significant differences were found between trypanosome parasitaemia and antibody response of the crossbred and WAD goats. Neither the WAD goats nor the Saanen crosses were able to control the drop in PCV following trypanosome infection. The level of anaemia caused by the trypanosome infection was similar in the two breeds during the trial. Based on these findings, no difference in tolerance or susceptibility to T. congolense could be demonstrated between the WAD goats and their Saanen crosses. Although the weight of all goats increased during the trial, the crosses gained significantly more weight than the WAD goats. The trypanosome infection reduced the growth rate of both breeds, but this reduction was not statistically significant. Crossbreeding trypanotolerant WADs with trypanosusceptible Saanen goats might, therefore, be an effective means of increasing productivity.
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Susceptibility of West African Dwarf goats and WAD x Saanen crosses to experimental infection with Trypanosoma congolense.
Veterinary parasitology, 2005Co-Authors: S. Dhollander, S. Kora, M. Sanneh, M. Gaye, S. Leak, D. Berkvens, J Bos, S. GeertsAbstract:West African Dwarf goats (WADs) and their Saanen crosses were experimentally infected with Trypanosoma congolense. No significant differences were found between trypanosome parasitaemia and antibody response of the crossbred and WAD goats. Neither the WAD goats nor the Saanen crosses were able to control the drop in PCV following trypanosome infection. The level of anaemia caused by the trypanosome infection was similar in the two breeds during the trial. Based on these findings, no difference in tolerance or susceptibility to T. congolense could be demonstrated between the WAD goats and their Saanen crosses. Although the weight of all goats increased during the trial, the crosses gained significantly more weight than the WAD goats. The trypanosome infection reduced the growth rate of both breeds, but this reduction was not statistically significant. Crossbreeding trypanotolerant WADs with trypanosusceptible Saanen goats might, therefore, be an effective means of increasing productivity.
Rachel Rupp - One of the best experts on this subject based on the ideXlab platform.
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Genome wide association analysis on semen volume and milk yield using different strategies of imputation to whole genome sequence in French dairy goats
BMC Genetics, 2020Co-Authors: Estelle Talouarn, Rachel Rupp, Philippe Bardou, Isabelle Palhiere, Claire Oget, Virginie Clément, Gwenola Tosser-klopp, Christèle Robert GraniéAbstract:Background Goats were domesticated 10,500 years ago to supply humans with useful resources. Since then, specialized breeds that are adapted to their local environment have been developed and display specific genetic profiles. The VarGoats project is a 1000 genomes resequencing program designed to cover the genetic diversity of the Capra genus. In this study, our main objective was to assess the use of sequence data to detect genomic regions associated with traits of interest in French Alpine and Saanen breeds. Results Direct imputation from the GoatSNP50 BeadChip genotypes to sequence level was investigated in these breeds using FImpute and different reference panels: within-breed, all Capra hircus sequenced individuals, European goats and French mainland goats. The best results were obtained with the French goat panel with allele and genotype concordance rates reaching 0.86 and 0.75 in the Alpine and 0.86 and 0.73 in the Saanen breed respectively. Mean correlations tended to be low in both breeds due to the high proportion of variants with low frequencies. For association analysis, imputation was performed using FImpute for 1129 French Alpine and Saanen males using within-breed and French panels on 23,338,436 filtered variants. The association results of both imputation scenarios were then compared. In Saanen goats, a large region on chromosome 19 was significantly linked to semen volume and milk yield in both scenarios. Significant variants for milk yield were annotated for 91 genes on chromosome 19 in Saanen goats. For semen volume, the annotated genes include YBOX2 which is related to azoospermia or oligospermia in other species. New signals for milk yield were detected on chromosome 2 in Alpine goats and on chromosome 5 in Saanen goats when using a multi-breed panel. Conclusion Even with very small reference populations, an acceptable imputation quality can be achieved in French dairy goats. GWAS on imputed sequences confirmed the existence of QTLs and identified new regions of interest in dairy goats. Adding identified candidates to a genotyping array and sequencing more individuals might corroborate the involvement of identified regions while removing potential imputation errors.
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Using sequence data to refine QTL mapping in French dairy goats
2019Co-Authors: Estelle Talouarn, Rachel Rupp, Philippe Bardou, Gwenola Tosser-klopp, Christèle Robert GraniéAbstract:Goats were domesticated 10,500 years ago with the aim of supplying milk, meat and fibres. Since then, breeds have specialized and adapted to their local environment developing specific genetic profiles. The VarGoats project is an international resequencing program, which aims at covering at best the genetic diversity of the Capra species. To date the sequence data 829 Capra hircus of various breeds and geographical origins. Variant calling led to the identification of a total of 110,193,942 variants on the 29 autosomal chromosomes. Quality checks were applied to sequence variants using various indicators: quality, depth, minor allele frequency and position. For French Alpine and Saanen breeds the concordance with 50k genotypes (CaprineSNP50 BeadChip) was checked. Mean concordance rate was 98.22% and ranged from 94.00 to 99.96% among individuals. Imputation was tested on the 23,338,436 filtered variants using FImpute software. Pedigree was provided and imputation was performed in a within-breed leaveone-out scenario. Imputation quality was checked for 4 individuals on all chromosomes and for every sequenced animal on chromosome 29. Mean concordance rate for chromosome 29 ranged from 73.49 to 85.71% and from 72.72 to 79.27% in Alpine and Saanen breeds respectively. On all chromosomes, average correlation between true and imputed sequence were 0.77 and 0.76 in Alpine and Saanen respectively. Imputation was then applied to a population of 1,129 French Alpine and Saanen males with at least 10 daughters phenotypes. Association analysis was performed on production and functional traits using polygenic models with the GCTA software. Using genotype data imputed to sequence level allowed to improve the significance of QTL previously identified with 50k SNP-chip only. In Saanen breed, 1.6 Mb region on chromosome 19 was identified as significantly linked to 4 conformation traits, 3 semen production traits, somatic cell count, milk yield and protein and fat contents. These researches provided insights on how to implement a quality check, imputation that will ensure the quality of subsequent analyses, and on new SNPs to be added to the 50k SNP-chip.
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Imputation from CaprineSNP50 BeadChip to sequence : a case-study in French Alpine and Saanen data from the VarGoats project
2019Co-Authors: Estelle Talouarn, Rachel Rupp, Philippe Bardou, Gwenola Tosser, Christèle Robert GraniéAbstract:Goats were domesticated 10,500 years ago with the aim of supplying milk, meat and fibers. Since then, breeds have specialized and adapted to their local environment developing specific genetic profiles. The VarGoats project is an international resequencing program which aims at covering at best the genetic diversity of the Capra species. To date the sequence data available include 16 wild types and 578 Capra hircus of 65 different breeds. Variant calling led to the identification of a total of 105,772,894 variants on the 29 autosomal chromosomes. For French Alpine and Saanen individuals the concordance with 50k genotypes was checked. Mean concordance rate was 97.74% and ranged from 90.16% to 99.96%. Quality checks were applied to sequence variants using various indicators: QUAL, GQ, DP, MAF and position. Imputation was tested on the 5,926,620 filtered variants using FImpute software. Pedigree was provided and different reference populations were compared in a leave-one-out scenario. Mean concordance rate ranged from 90.6 to 92.5% and from 89.7 to 91.7% in Alpine and Saanen breeds respectively. Correlation between true and imputed sequence ranged from 0.78 to 0.83 and from 0.76 to 0.81 in Alpine and Saanen respectively. Imputation will be applied to a population of 3,618 French Alpine and Saanen goats genotyped with the CaprineSNP50 BeadChip. The next step will be to compare association studies using 50K data or SNPs imputed from the sequence data. This research provides insights on how to implement a solid quality check, and imputation that will ensure the quality of subsequent analyses.
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Genome-wide study finds a QTL with pleotropic effects on semen and production traits in Saanen goats
2018Co-Authors: Claire Oget, Isabelle Palhiere, Virginie Clément, Gwenola Tosser-klopp, Stéphane Fabre, Rachel RuppAbstract:Economic sustainability of dairy ruminant farms mainly relies on production, reproduction, and health of livestock. In this study, we investigated the genomic regions controlling seventeen production traits (eleven type traits, milk yield, four milk composition traits and lifespan of livestock trait), five reproduction traits (semen production and quality), and one trait related to health (Somatic Cell Score, as a proxy for mastitis resistance). Daughter yield deviation values were computed for 597 (672) Alpine and 460 (519) Saanen AI rams from Capgènes testing station for production traits, mastitis (and reproduction). For lifespan, only the oldest rams had yield deviations to allow large progeny and good accuracy, i.e. 341 Alpine and 298 Saanen. All AI rams were genotyped with the Illumina GoatSNP50 Bead Chip. We conducted genome wide association studies using polygenic mixed models and genomic relatedness matrix with the GEMMA software. The two breeds were analysed separately. Results showed a highly significant QTL on CHI 19 (22.8-28.9 Mb) in the Saanen breed for 12 of 23 studied traits. The most significant traits were udder floor position (P=7.31e-24), volume of semen production (P=8.43e-21) and protein yield (P=6.64e-17). We did not find this QTL in the Alpine breed suggesting a breed-specific control. Analyses of sequencing data of 11 Alpine and 9 Saanen rams highlighted a candidate causal mutation in the Sex Hormone Binding Globulin (SHBG) gene. We will determine whether these pleiotropic relationships are further supported by one single mutation or resolved into closely linked loci. Altogether, these results identify a major pleiotropic QTL in the Saanen breed. They will be helpful for goat selection in the future. They indicate that a within-breed genomic selection should be favoured for those traits and that including QTL information might prove useful. The study further pave the way for the addition of reproduction traits in the French goat breeding programs.
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Genome Wide Association Study Identifies New Loci Associated with Undesired Coat Color Phenotypes in Saanen Goats
PLoS ONE, 2016Co-Authors: Pauline Martin, Gwenola Tosser-klopp, Isabelle Palhiere, Anne Ricard, Rachel RuppAbstract:This paper reports a quantitative genetics and genomic analysis of undesirable coat color patterns in goats. Two undesirable coat colors have routinely been recorded for the past 15 years in French Saanen goats. One fifth of Saanen females have been phenotyped "pink" (8.0%) or "pink neck" (11.5%) and consequently have not been included in the breeding program as elite animals. Heritability of the binary "pink" and "pink neck" phenotype, estimated from 103,443 females was 0.26 for "pink" and 0.21 for "pink neck". Genome wide association studies (using haplotypes or single SNPs) were implemented using a daughter design of 810 Saanen goats sired by 9 Artificial Insemination bucks genotyped with the goatSNP50 chip. A highly significant signal (-log10pvalue = 10.2) was associated with the "pink neck" phenotype on chromosome 11, suggesting the presence of a major gene. Highly significant signals for the "pink" phenotype were found on chromosomes 5 and 13 (-log10p values of 7.2 and, 7.7 respectively). The most significant SNP on chromosome 13 was in the ASIP gene region, well known for its association with coat color phenotypes. Nine significant signals were also found for both traits. The highest signal for each trait was detected by both single SNP and haplotype approaches, whereas the smaller signals were not consistently detected by the two methods. Altogether these results demonstrated a strong genetic control of the "pink" and "pink neck" phenotypes in French Saanen goats suggesting that SNP information could be used to identify and remove undesired colored animals from the breeding program.
S. Kora - One of the best experts on this subject based on the ideXlab platform.
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Susceptibility of West African Dwarf goats and WAD × Saanen crosses to experimental infection with Trypanosoma congolense
Veterinary Parasitology, 2005Co-Authors: S. Dhollander, J.f.f.p. Bos, S. Kora, M. Sanneh, M. Gaye, S. Leak, D. Berkvens, S. GeertsAbstract:West African Dwarf goats (WADs) and their Saanen crosses were experimentally infected with Trypanosoma congolense. No significant differences were found between trypanosome parasitaemia and antibody response of the crossbred and WAD goats. Neither the WAD goats nor the Saanen crosses were able to control the drop in PCV following trypanosome infection. The level of anaemia caused by the trypanosome infection was similar in the two breeds during the trial. Based on these findings, no difference in tolerance or susceptibility to T. congolense could be demonstrated between the WAD goats and their Saanen crosses. Although the weight of all goats increased during the trial, the crosses gained significantly more weight than the WAD goats. The trypanosome infection reduced the growth rate of both breeds, but this reduction was not statistically significant. Crossbreeding trypanotolerant WADs with trypanosusceptible Saanen goats might, therefore, be an effective means of increasing productivity.
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Susceptibility of West African Dwarf goats and WAD x Saanen crosses to experimental infection with Trypanosoma congolense.
Veterinary parasitology, 2005Co-Authors: S. Dhollander, S. Kora, M. Sanneh, M. Gaye, S. Leak, D. Berkvens, J Bos, S. GeertsAbstract:West African Dwarf goats (WADs) and their Saanen crosses were experimentally infected with Trypanosoma congolense. No significant differences were found between trypanosome parasitaemia and antibody response of the crossbred and WAD goats. Neither the WAD goats nor the Saanen crosses were able to control the drop in PCV following trypanosome infection. The level of anaemia caused by the trypanosome infection was similar in the two breeds during the trial. Based on these findings, no difference in tolerance or susceptibility to T. congolense could be demonstrated between the WAD goats and their Saanen crosses. Although the weight of all goats increased during the trial, the crosses gained significantly more weight than the WAD goats. The trypanosome infection reduced the growth rate of both breeds, but this reduction was not statistically significant. Crossbreeding trypanotolerant WADs with trypanosusceptible Saanen goats might, therefore, be an effective means of increasing productivity.
M. Sanneh - One of the best experts on this subject based on the ideXlab platform.
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Susceptibility of West African Dwarf goats and WAD × Saanen crosses to experimental infection with Trypanosoma congolense
Veterinary Parasitology, 2005Co-Authors: S. Dhollander, J.f.f.p. Bos, S. Kora, M. Sanneh, M. Gaye, S. Leak, D. Berkvens, S. GeertsAbstract:West African Dwarf goats (WADs) and their Saanen crosses were experimentally infected with Trypanosoma congolense. No significant differences were found between trypanosome parasitaemia and antibody response of the crossbred and WAD goats. Neither the WAD goats nor the Saanen crosses were able to control the drop in PCV following trypanosome infection. The level of anaemia caused by the trypanosome infection was similar in the two breeds during the trial. Based on these findings, no difference in tolerance or susceptibility to T. congolense could be demonstrated between the WAD goats and their Saanen crosses. Although the weight of all goats increased during the trial, the crosses gained significantly more weight than the WAD goats. The trypanosome infection reduced the growth rate of both breeds, but this reduction was not statistically significant. Crossbreeding trypanotolerant WADs with trypanosusceptible Saanen goats might, therefore, be an effective means of increasing productivity.
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Susceptibility of West African Dwarf goats and WAD x Saanen crosses to experimental infection with Trypanosoma congolense.
Veterinary parasitology, 2005Co-Authors: S. Dhollander, S. Kora, M. Sanneh, M. Gaye, S. Leak, D. Berkvens, J Bos, S. GeertsAbstract:West African Dwarf goats (WADs) and their Saanen crosses were experimentally infected with Trypanosoma congolense. No significant differences were found between trypanosome parasitaemia and antibody response of the crossbred and WAD goats. Neither the WAD goats nor the Saanen crosses were able to control the drop in PCV following trypanosome infection. The level of anaemia caused by the trypanosome infection was similar in the two breeds during the trial. Based on these findings, no difference in tolerance or susceptibility to T. congolense could be demonstrated between the WAD goats and their Saanen crosses. Although the weight of all goats increased during the trial, the crosses gained significantly more weight than the WAD goats. The trypanosome infection reduced the growth rate of both breeds, but this reduction was not statistically significant. Crossbreeding trypanotolerant WADs with trypanosusceptible Saanen goats might, therefore, be an effective means of increasing productivity.
