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See detailGenetic diversity, Population structure, parentage analysis, and construction of core collections in the French apple germplasm based on SSR markers
Lassois, Ludivine ULg; Denancé, Caroline; Ravon, Elisa et al

in Plant Molecular Biology Reporter (2016)

In-depth characterization of apple genetic resources is a prerequisite for genetic improvement and for germplasm management. In this study, we fingerprinted a very large French collection of 2163 ... [more ▼]

In-depth characterization of apple genetic resources is a prerequisite for genetic improvement and for germplasm management. In this study, we fingerprinted a very large French collection of 2163 accessions with 24 SSR markers in order to evaluate its genetic diversity, population structure and genetic relationships, to link these features with cultivar selection date or usage (old or modern, dessert or cider cultivars), and to construct core collections. Most markers were highly discriminating and powerful for varietal identification, with a probability of identity P(ID) over the 21 retained SSR loci close to 10-28. Pairwise comparisons revealed 34% redundancy and 18.5% putative triploids. The results showed that the germplasm is highly diverse with an expected heterozygosity He of 0.82 and observed heterozygosity Ho of 0.83. A Bayesian model-based clustering approach revealed a weak but significant structure in three subgroups (FST = 0.014-0.048) corresponding, albeit approximately, to the three subpopulations defined beforehand (Old Dessert, Old Cider and Moderncultivars). Parentage analyses established already known and yet unknown relationships, notably between old cultivars, with the frequent occurrence of cultivars such as ‘King of Pippin’ and ‘Calville Rouge d’Hiver’ as founders. Finally, core collections based on allelic diversity were constructed. A large dessert core collection of 278 cultivars contained 90% of the total dessert allelic diversity, whereas a dessert sub-core collection of 48 cultivars contained 71% of diversity. For cider apples, a 48-cultivars core collection contained 83% of the total cider allelic diversity. [less ▲]

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See detailGenetic diversity, structure and parentage analysis within several European apple germplasm collections assessed by microsatellite markers
Durel, Charles-Eric; Denancé, Caroline; Ravon, Elisa et al

Conference (2014, June)

Detailed reference viewed: 75 (2 ULg)
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See detailGenetic effects of heat stress on milk yield and MIR predicted methane emissions of Holstein cows
Vanrobays, Marie-Laure ULg; Gengler, Nicolas ULg; Kandel, Purna Bhadra ULg et al

Conference (2013, August 28)

Dairy cows both contribute to and are affected by climate change. Breeding for heat tolerance and reduced methane (CH4) emissions is a key requirement to mitigate interactions between dairy cows and ... [more ▼]

Dairy cows both contribute to and are affected by climate change. Breeding for heat tolerance and reduced methane (CH4) emissions is a key requirement to mitigate interactions between dairy cows and climate change. This study was aimed to estimate genetic variation of milk yield and CH4 emissions over the whole trajectory of temperature humidity index (THI) using a reaction norm approach. A total of 257,635 milk test-day (TD) records and milk mid-infrared (MIR) spectra from 51,782 Holstein cows were used. Data were collected between January 2007 and December 2010 in 983 herds by the Walloon Breeding Association (Ciney, Belgium). The calibration equation developed by Vanlierde et al. (Abstract submitted to EAAP 2013; R² of cross-validation=0.70) was applied on the spectral data in order to predict CH4 emissions values (g CH4/d). These values were divided by fat and protein corrected milk yield (FPCM) defining a new CH4 trait (g CH4/kg of FPCM). Daily THI values were calculated using the mean of daily values of dry bulb temperature and relative humidity from meteorological data. Mean daily THI of the previous 3 days before each TD record was used as the THI of reference for that TD. Bivariate (milk yield and a CH4 trait) random regression TD mixed models with random linear regressions on THI values were used. Estimated average daily heritability for milk yield was 0.17 and decreased slightly at extreme THI values. However, heritabilities of MIR CH4 traits increased as THI values increase: from 0.10 (THI=28) to 0.14 (THI=75) for MIR CH4 (g/d) and from 0.14 (THI=28) to 0.21 (THI=75) for MIR CH4 (g/kg of FCPM). Genetic correlations between milk yield and MIR CH4 (g/d) ranged from -0.09 (THI=28) to -0.12 (THI=75) and those between milk yield and MIR CH4 (g/kg of FPCM) from -0.75 (THI=28) to -0.71 (THI=75). These results showed that milk production and CH4 emissions of dairy cows seemed to be influenced by THI. [less ▲]

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See detailGenetic effects of heat stress on milk yield and MIR predicted methane emissions of Holstein cows
Vanrobays, Marie-Laure ULg; Gengler, Nicolas ULg; Kandel, Purna Bhadra ULg et al

in Book of Abstracts of the 64th Annual Meeting of the European Federation of Animal Science (2013, August)

Dairy cows both contribute to and are affected by climate change. Breeding for heat tolerance and reduced methane (CH4) emissions is a key requirement to mitigate interactions between dairy cows and ... [more ▼]

Dairy cows both contribute to and are affected by climate change. Breeding for heat tolerance and reduced methane (CH4) emissions is a key requirement to mitigate interactions between dairy cows and climate change. This study was aimed to estimate genetic variation of milk yield and CH4 emissions over the whole trajectory of temperature humidity index (THI) using a reaction norm approach. A total of 257,635 milk test-day (TD) records and milk mid-infrared (MIR) spectra from 51,782 Holstein cows were used. Data were collected between January 2007 and December 2010 in 983 herds by the Walloon Breeding Association (Ciney, Belgium). The calibration equation developed by Vanlierde et al. (Abstract submitted to EAAP 2013; R² of cross-validation=0.70) was applied on the spectral data in order to predict CH4 emissions values (g CH4/d). These values were divided by fat and protein corrected milk yield (FPCM) defining a new CH4 trait (g CH4/kg of FPCM). Daily THI values were calculated using the mean of daily values of dry bulb temperature and relative humidity from meteorological data. Mean daily THI of the previous 3 days before each TD record was used as the THI of reference for that TD. Bivariate (milk yield and a CH4 trait) random regression TD mixed models with random linear regressions on THI values were used. Estimated average daily heritability for milk yield was 0.17 and decreased slightly at extreme THI values. However, heritabilities of MIR CH4 traits increased as THI values increase: from 0.10 (THI=28) to 0.14 (THI=75) for MIR CH4 (g/d) and from 0.14 (THI=28) to 0.21 (THI=75) for MIR CH4 (g/kg of FCPM). Genetic correlations between milk yield and MIR CH4 (g/d) ranged from -0.09 (THI=28) to -0.12 (THI=75) and those between milk yield and MIR CH4 (g/kg of FPCM) from -0.75 (THI=28) to -0.71 (THI=75). These results showed that milk production and CH4 emissions of dairy cows seemed to be influenced by THI. [less ▲]

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See detailGenetic engineering of the beta-oxydation pathway in the yeast Yarrowia lipolytica to increase the production of aroma compounds
Waché, Y.; Groguenin, A.; Escamilla Garcia, E. et al

in Chemické Listy (2003, June), 97

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See detailGenetic engineering of the β-oxidation pathway in the yeast Yarrowia lipolytica to increase the production of aroma compounds
Groguenin, A.; Waché, Y.; Garcia, E. E. et al

in Journal of Molecular Catalysis B : Enzymatic (2004), 28(2-3), 75-79

The yeast Yarrowia lipolytica possesses five acyl-CoA oxidases (Aox1p to 5), the enzyme catalysing the first reaction of β-oxidation. The understanding of the specific role of each acyl-CoA oxidase is ... [more ▼]

The yeast Yarrowia lipolytica possesses five acyl-CoA oxidases (Aox1p to 5), the enzyme catalysing the first reaction of β-oxidation. The understanding of the specific role of each acyl-CoA oxidase is important to construct a yeast strain growing at a good rate and able to produce without degrading the aroma compound γ-decalactone. In this study we observed that Aox4p exhibits a slight activity on a broad spectrum of substrates and that it is involved in lactone degradation. We constructed a strain lacking this activity. Its growth was only slightly altered and it produced 10 times more lactone than the wild type in 48h. © 2004 Elsevier B.V. All rights reserved. [less ▲]

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See detailGenetic evaluation considering phenotypic data and limited molecular information using a novel equivalent model: Case study using effect of the mh locus on milk production in the dual-purpose Belgian Blue breed
Colinet, Frédéric ULg; Gengler, Nicolas ULg

in Book of Abstracts of the 60th Annual Meeting of the European Association for Animal Production (2009, August)

The introduction of molecular information into genetic evaluation systems is currently under research. Based on an equivalent method, we developed from existing theory a new alternative strategy for the ... [more ▼]

The introduction of molecular information into genetic evaluation systems is currently under research. Based on an equivalent method, we developed from existing theory a new alternative strategy for the prediction of gene effects and especially their smooth integration into genetic evaluations. Underlying hypothesis were based on the idea that knowledge of genotypes will not affect overall additive genetic variance but only change expected values of genetic effects for animals with known genotypes. However, all animals could not be genotyped. Thus, the developed equations were modified to allow the integration of the known genotype for a portion of the population. This strategy was tested for the mh locus (responsible for the double-muscling phenotype) in dual-purpose Belgian Blue cattle. The genotype was determined for 123 bulls and 1940 cows (+/+ 19.5, mh/+ 39.3 and mh/mh 41.2%). These animals had 11,150 daughters with test-day (TD) records. The genotypes were incorporated into a modified genetic evaluation based on the current routine multi-trait multibreed test-day model used in the Walloon Region (Belgium). Data used included 12,829,309 TD records for 689,057 dairy cows in production. The pedigree file contained 1,606,024 animals (cows with TD records and ancestors). Computation of the modified mixed model equations was done solving iteratively two systems of equations, one for the polygenic effects and one for the gene effect until the relative differences in the gene solutions were below 10-5. A linear extrapolation was also used to speed up the convergence of gene effects. As expected, the mh locus exerts negative effects on milk production traits. For the first three lactations, the average estimated allelic substitution effects were -158.7 kg milk, -8.93 kg fat and -5.64 kg protein per lactation (305 days). [less ▲]

Detailed reference viewed: 39 (16 ULg)
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See detailGenetic evaluation considering phenotypic data and limited molecular information using a novel equivalent model: Case study using effect of the mh locus on milk production in the dual-purpose Belgian Blue breed
Colinet, Frédéric ULg; Gengler, Nicolas ULg

Conference (2009, August)

The introduction of molecular information into genetic evaluation systems is currently under research. Based on an equivalent method, we developed from existing theory a new alternative strategy for the ... [more ▼]

The introduction of molecular information into genetic evaluation systems is currently under research. Based on an equivalent method, we developed from existing theory a new alternative strategy for the prediction of gene effects and especially their smooth integration into genetic evaluations. Underlying hypothesis were based on the idea that knowledge of genotypes will not affect overall additive genetic variance but only change expected values of genetic effects for animals with known genotypes. However, all animals could not be genotyped. Thus, the developed equations were modified to allow the integration of the known genotype for a portion of the population. This strategy was tested for the mh locus (responsible for the double-muscling phenotype) in dual-purpose Belgian Blue cattle. The genotype was determined for 123 bulls and 1940 cows (+/+ 19.5, mh/+ 39.3 and mh/mh 41.2%). These animals had 11,150 daughters with test-day (TD) records. The genotypes were incorporated into a modified genetic evaluation based on the current routine multi-trait multibreed test-day model used in the Walloon Region (Belgium). Data used included 12,829,309 TD records for 689,057 dairy cows in production. The pedigree file contained 1,606,024 animals (cows with TD records and ancestors). Computation of the modified mixed model equations was done solving iteratively two systems of equations, one for the polygenic effects and one for the gene effect until the relative differences in the gene solutions were below 10-5. A linear extrapolation was also used to speed up the convergence of gene effects. As expected, the mh locus exerts negative effects on milk production traits. For the first three lactations, the average estimated allelic substitution effects were -158.7 kg milk, -8.93 kg fat and -5.64 kg protein per lactation (305 days). [less ▲]

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See detailGenetic evaluation for body condition score in the Walloon region of Belgium
Bastin, Catherine ULg; Gillon, Alain ULg; Massart, Xavier et al

in Interbull Bulletin (2010), 42

Detailed reference viewed: 36 (10 ULg)
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See detailGenetic evaluation for body condition score in the Walloon Region of Belgium
Bastin, Catherine ULg; Gillon, Alain ULg; Massart, Xavier et al

Conference (2010, June 02)

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See detailGenetic evaluation of calving ease for Walloon Holstein dairy cattle
Vanderick, Sylvie ULg; Troch, Thibault ULg; Gillon, Alain et al

Conference (2013, August 25)

Calving complications have an incidence on the economic profitability of dairy herds. In the Walloon Region of Belgium, calving ease data recording is being done on voluntary basis since 2000. This allows ... [more ▼]

Calving complications have an incidence on the economic profitability of dairy herds. In the Walloon Region of Belgium, calving ease data recording is being done on voluntary basis since 2000. This allows now the implementation of a genetic evaluation of Holstein dairy cattle addressing the need of dairy breeders to select bulls in order to reduce frequency of calving problems. Calving ease scores were analyzed using univariate animal linear models, which were fitted with the genetic correlation between direct and maternal additive genetic effects either estimated or constrained to zero. Variance components and related genetic parameters were estimated from a dataset including 33,155 calving records. Included in the models were fixed season effects, fixed herd effects and fixed sex of calf*age of dam classes*group of calvings interaction effects, random herd*year of calving effects, random maternal permanent environment effects, and random animal direct and maternal additive genetic effects. For both models, direct and maternal heritabilities for calving ease were about 8% and about 2%, respectively. Genetic correlation between direct and maternal additive effects was found to be non-significantly different from zero. So, an animal linear model with genetic correlation between direct and maternal effects constrained to zero was adopted for the routine genetic evaluation of calving ease for Walloon Holstein dairy cattle. This model was validated by Interbull in January 2013 and, since April 2013, the Walloon Region of Belgium has officially participated to the international MACE evaluation for calving traits. [less ▲]

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See detailGenetic evaluation of calving ease for Walloon Holstein dairy cattle.
Vanderick, Sylvie ULg; Troch, Thibault ULg; Gillon, Alain et al

in Interbull Bulletin (2013), 47

Calving complications have an incidence on the economic profitability of dairy herds. In the Walloon Region of Belgium, calving ease data recording is being done on voluntary basis since 2000. This allows ... [more ▼]

Calving complications have an incidence on the economic profitability of dairy herds. In the Walloon Region of Belgium, calving ease data recording is being done on voluntary basis since 2000. This allows now the implementation of a genetic evaluation of Holstein dairy cattle addressing the need of dairy breeders to select bulls in order to reduce frequency of calving problems. Calving ease scores were analyzed using univariate animal linear models, which were fitted with the genetic correlation between direct and maternal additive genetic effects either estimated or constrained to zero. Variance components and related genetic parameters were estimated from a dataset including 33,155 calving records. Included in the models were fixed season effects, fixed herd effects and fixed sex of calf*age of dam classes*group of calvings interaction effects, random herd*year of calving effects, random maternal permanent environment effects, and random animal direct and maternal additive genetic effects. For both models, direct and maternal heritabilities for calving ease were about 8% and about 2%, respectively. Genetic correlation between direct and maternal additive effects was found to be non-significantly different from zero. So, an animal linear model with genetic correlation between direct and maternal effects constrained to zero was adopted for the routine genetic evaluation of calving ease for Walloon Holstein dairy cattle. This model was validated by Interbull in January 2013 and, since April 2013, the Walloon Region of Belgium has officially participated to the international MACE evaluation for calving traits. [less ▲]

Detailed reference viewed: 39 (16 ULg)
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See detailGenetic evaluation of cow survival using a lactation random regression model
Gengler, Nicolas ULg; Vanderick, Sylvie ULg; Mayeres, Patrick et al

in INTERBULL Bulletin (2005), 33

Detailed reference viewed: 13 (3 ULg)
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See detailGenetic evaluation of female fertility for Walloon dairy and dual purpose cows using a parity random regression model: first results
Mayeres, Patrick; Vanderick, Sylvie ULg; Croquet, Coraline et al

in INTERBULL Bulletin (2006), 34

Detailed reference viewed: 25 (6 ULg)
Peer Reviewed
See detailGenetic evaluation of type traits in Northern part of Belgium
Detilleux, Johann ULg; Volckaert, D.; Leroy, Pascal ULg

(1996)

Detailed reference viewed: 8 (1 ULg)
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See detailGenetic evidence for a TatC dimer at the core of the Escherichia coli twin arginine (Tat) protein translocase
Maldonado-Larrosa, Barbara Maria ULg

in Journal of Molecular Microbiology & Biotechnology (2011)

Detailed reference viewed: 17 (5 ULg)
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See detailGenetic evidence from Indian red jungle fowl corroborates multiple domestication of modern day chicken.
Kanginakudru, Sriramana; Metta, Muralidhar ULg; Jakati, R. D. et al

in BMC Evolutionary Biology (2008), 8

BACKGROUND: Domestication of chicken is believed to have occurred in Southeast Asia, especially in Indus valley. However, non-inclusion of Indian red jungle fowl (RJF), Gallus gallus murghi in previous ... [more ▼]

BACKGROUND: Domestication of chicken is believed to have occurred in Southeast Asia, especially in Indus valley. However, non-inclusion of Indian red jungle fowl (RJF), Gallus gallus murghi in previous studies has left a big gap in understanding the relationship of this major group of birds. In the present study, we addressed this issue by analyzing 76 Indian birds that included 56 G. g. murghi (RJF), 16 G. g. domesticus (domestic chicken) and 4 G. sonneratii (Grey JF) using both microsatellite markers and mitochondrial D-loop sequences. We also compared the D-loop sequences of Indian birds with those of 779 birds obtained from GenBank. RESULTS: Microsatellite marker analyses of Indian birds indicated an average FST of 0.126 within G. g. murghi, and 0.154 within G. g. domesticus while it was more than 0.2 between the two groups. The microsatellite-based phylogenetic trees showed a clear separation of G. g. domesticus from G. g. murghi, and G. sonneratii. Mitochondrial DNA based mismatch distribution analyses showed a lower Harpending's raggedness index in both G. g. murghi (0.001515) and in Indian G. g. domesticus (0.0149) birds indicating population expansion. When meta analysis of global populations of 855 birds was carried out using median joining haplotype network, 43 Indian birds of G. g. domesticus (19 haplotypes) were distributed throughout the network sharing haplotypes with the RJFs of different origins. CONCLUSION: Our results suggest that the domestication of chicken has occurred independently in different locations of Asia including India. We found evidence for domestication of Indian birds from G. g. spadiceus and G. g. gallus as well as from G. g. murghi, corroborating multiple domestication of Indian and other domestic chicken. In contrast to the commonly held view that RJF and domestic birds hybridize in nature, the present study shows that G. g. murghi is relatively pure. Further, the study also suggested that the chicken populations have undergone population expansion, especially in the Indus valley. [less ▲]

Detailed reference viewed: 45 (0 ULg)