Background Increasing resilience is a priority in modern pig breeding.Recent research shows that general resilience can be quantified via variability in longitudinal data.The collection of such longitudinal data on we...Background Increasing resilience is a priority in modern pig breeding.Recent research shows that general resilience can be quantified via variability in longitudinal data.The collection of such longitudinal data on weight,feed intake and feeding behaviour in pigs has been facilitated by the development of technologies such as automated feeding stations.The goal of this study was to investigate resilience traits,which were estimated as deviations from longitudinal weight,feed intake and feeding behaviour data during the finishing phase.A dataset with 324,207 records between the age of 95 and 155 days on 5,939 Pietrain pigs with known pedigree and genomic information was used.We provided guidelines for a rigid quality control of longitudinal body weight data,as we found that outliers can significantly affect results.Gompertz growth curve analysis,linear modelling and trajectory analyses were used for quantifying resilience traits.Results To our knowledge,this is the first study comparing resilience traits from longitudinal body weight,feed intake and feeding behaviour data in pigs.We demonstrated that the resilience traits are lowly to moderately heritable for deviations in body weight(h2=2.9%–20.2%),in feed intake(9.4%–23.3%)and in feeding behaviour(16.2%–28.3%).Additionally,these traits have good predictive abilities in cross-validation analyses.Deviations in individual body weight and feed intake trajectories are highly correlated(rg=0.78)with low to moderate favourable genetic correlations with feed conversion ratio(rg=0.39–0.49).Lastly,we showed that some resilience traits,such as the natural logarithm of variances of observed versus predicted body weights(lnvarweight),are more robust to lower observation frequencies and are repeatable over three different time periods of the finishing phase.Conclusions Our results will help future studies investigating resilience traits and resilience-related traits.Moreover,our study provides first results on standardization of quality control and efficient data sampling from automated feeding station data.Our findings will be valuable for breeding organizations as they offer evidence that pigs’general resilience can be selected on with good accuracy.Moreover,this methodology might be extended to other species to quantify resilience based on longitudinal data.展开更多
Quantitative trait loci(QTL)mapping approaches rely on the correct ordering of molecular markers along the chromosomes,which can be obtained from genetic linkage maps or a reference genome sequence.For apple(Malus dom...Quantitative trait loci(QTL)mapping approaches rely on the correct ordering of molecular markers along the chromosomes,which can be obtained from genetic linkage maps or a reference genome sequence.For apple(Malus domestica Borkh),the genome sequence v1 and v2 could not meet this need;therefore,a novel approach was devised to develop a dense genetic linkage map,providing the most reliable marker-loci order for the highest possible number of markers.The approach was based on four strategies:(i)the use of multiple full-sib families,(ii)the reduction of missing information through the use of HaploBlocks and alternative calling procedures for single-nucleotide polymorphism(SNP)markers,(iii)the construction of a single backcross-type data set including all families,and(iv)a two-step map generation procedure based on the sequential inclusion of markers.The map comprises 15417 SNP markers,clustered in 3 K HaploBlock markers spanning 1267 cM,with an average distance between adjacent markers of 0.37 cM and a maximum distance of 3.29 cM.Moreover,chromosome 5 was oriented according to its homoeologous chromosome 10.This map was useful to improve the apple genome sequence,design the Axiom Apple 480 K SNP array and perform multifamily-based QTL studies.Its collinearity with the genome sequences v1 and v3 are reported.To our knowledge,this is the shortest published SNP map in apple,while including the largest number of markers,families and individuals.This result validates our methodology,proving its value for the construction of integrated linkage maps for any outbreeding species.展开更多
Despite the availability of whole genome sequences of apple and peach,there has been a considerable gap between genomics and breeding.To bridge the gap,the European Union funded the FruitBreedomics project(March 2011 ...Despite the availability of whole genome sequences of apple and peach,there has been a considerable gap between genomics and breeding.To bridge the gap,the European Union funded the FruitBreedomics project(March 2011 to August 2015)involving 28 research institutes and private companies.Three complementary approaches were pursued:(i)tool and software development,(ii)deciphering genetic control of main horticultural traits taking into account allelic diversity and(iii)developing plant materials,tools and methodologies for breeders.Decisive breakthroughs were made including the making available of ready-to-go DNA diagnostic tests for Marker Assisted Breeding,development of new,dense SNP arrays in apple and peach,new phenotypic methods for some complex traits,software for gene/QTL discovery on breeding germplasm via Pedigree Based Analysis(PBA).This resulted in the discovery of highly predictive molecular markers for traits of horticultural interest via PBA and via Genome Wide Association Studies(GWAS)on several European genebank collections.FruitBreedomics also developed pre-breeding plant materials in which multiple sources of resistance were pyramided and software that can support breeders in their selection activities.Through FruitBreedomics,significant progresses were made in the field of apple and peach breeding,genetics,genomics and bioinformatics of which advantage will be made by breeders,germplasm curators and scientists.A major part of the data collected during the project has been stored in the FruitBreedomics database and has been made available to the public.This review covers the scientific discoveries made in this major endeavour,and perspective in the apple and peach breeding and genomics in Europe and beyond.展开更多
Background:The pork industry faces unprecedented challenges from disease,which increases cost of production and use of antibiotics,and reduces production efficiency,carcass quality,and animal wellbeing.One solution is...Background:The pork industry faces unprecedented challenges from disease,which increases cost of production and use of antibiotics,and reduces production efficiency,carcass quality,and animal wellbeing.One solution is to improve the overall resilience of pigs to a broad array of common diseases through genetic selection.Behavioral changes in feeding and drinking are usually the very first clinical signs when animals are exposed to stressors such as disease.Changes in feeding and drinking behaviors in diseased pigs may reflect the way they cope with the challenge and,thus,could be used as indicator traits to select for disease resilience.The objectives of this study were to estimate genetic parameters of feeding and drinking traits for wean-to-finish pigs in a natural polymicrobial disease challenge model,to estimate genetic correlations of feeding and drinking traits with growth rate and clinical disease traits,and to develop indicator traits to select for disease resilience.Results:In general,drinking traits had moderate to high estimates of heritability,especially average daily water dispensed,duration,and number of visits(0.44 to 0.58).Similar estimates were observed for corresponding feeding traits(0.35 to 0.51).Most genetic correlation estimates among drinking traits were moderate to high(0.30 to 0.92)and higher than among feeding traits(0 to 0.11).Compared to other drinking traits,water intake duration and number of visits had relatively stronger negative genetic correlation estimates with treatment rate and mortality,especially across the challenge nursery and finisher(−0.39 and−0.45 for treatment rate;−0.20 and−0.19 for mortality).Conclusion:Most of the recorded drinking and feeding traits under a severe disease challenge had moderate to high estimates of heritability,especially for feed or water intake duration and number of visits.Phenotypic and genetic correlations among the recorded feeding traits under disease were generally low but drinking traits showed high correlations with each other.Water intake duration and number of visits are potential indicator traits to select for disease resilience because of their high heritability and had moderate genetic correlations with treatment and mortality rates under severe disease.展开更多
基金This study was partially funded by an FR PhD fellowship(1104320N,WG)two SB PhD fellowships(1S05818N(CW)and 1S37119N(RM))of the Research Foundation Flanders(FWO)+1 种基金Moreover,RM and LC were also partly funded by a KU Leuven C2 project(C24/18/036)KH was funded by the UNIPIG project of VLAIO(HBC.2019.2866).
文摘Background Increasing resilience is a priority in modern pig breeding.Recent research shows that general resilience can be quantified via variability in longitudinal data.The collection of such longitudinal data on weight,feed intake and feeding behaviour in pigs has been facilitated by the development of technologies such as automated feeding stations.The goal of this study was to investigate resilience traits,which were estimated as deviations from longitudinal weight,feed intake and feeding behaviour data during the finishing phase.A dataset with 324,207 records between the age of 95 and 155 days on 5,939 Pietrain pigs with known pedigree and genomic information was used.We provided guidelines for a rigid quality control of longitudinal body weight data,as we found that outliers can significantly affect results.Gompertz growth curve analysis,linear modelling and trajectory analyses were used for quantifying resilience traits.Results To our knowledge,this is the first study comparing resilience traits from longitudinal body weight,feed intake and feeding behaviour data in pigs.We demonstrated that the resilience traits are lowly to moderately heritable for deviations in body weight(h2=2.9%–20.2%),in feed intake(9.4%–23.3%)and in feeding behaviour(16.2%–28.3%).Additionally,these traits have good predictive abilities in cross-validation analyses.Deviations in individual body weight and feed intake trajectories are highly correlated(rg=0.78)with low to moderate favourable genetic correlations with feed conversion ratio(rg=0.39–0.49).Lastly,we showed that some resilience traits,such as the natural logarithm of variances of observed versus predicted body weights(lnvarweight),are more robust to lower observation frequencies and are repeatable over three different time periods of the finishing phase.Conclusions Our results will help future studies investigating resilience traits and resilience-related traits.Moreover,our study provides first results on standardization of quality control and efficient data sampling from automated feeding station data.Our findings will be valuable for breeding organizations as they offer evidence that pigs’general resilience can be selected on with good accuracy.Moreover,this methodology might be extended to other species to quantify resilience based on longitudinal data.
基金We thank Yolanda Noordijk for the isolation of DNA from all samples at Wageningen-UR and Elisa Banchi for her work on the genotyping of these samples with the 20 K Infinium SNP array at the Fondazione Edmund MachThis work has been co-funded by the EU seventh Framework Programme by the FruitBreedomics project N°.265582:Integrated Approach for increasing breeding efficiency in fruit tree crops(www.FruitBreedomics.com).
文摘Quantitative trait loci(QTL)mapping approaches rely on the correct ordering of molecular markers along the chromosomes,which can be obtained from genetic linkage maps or a reference genome sequence.For apple(Malus domestica Borkh),the genome sequence v1 and v2 could not meet this need;therefore,a novel approach was devised to develop a dense genetic linkage map,providing the most reliable marker-loci order for the highest possible number of markers.The approach was based on four strategies:(i)the use of multiple full-sib families,(ii)the reduction of missing information through the use of HaploBlocks and alternative calling procedures for single-nucleotide polymorphism(SNP)markers,(iii)the construction of a single backcross-type data set including all families,and(iv)a two-step map generation procedure based on the sequential inclusion of markers.The map comprises 15417 SNP markers,clustered in 3 K HaploBlock markers spanning 1267 cM,with an average distance between adjacent markers of 0.37 cM and a maximum distance of 3.29 cM.Moreover,chromosome 5 was oriented according to its homoeologous chromosome 10.This map was useful to improve the apple genome sequence,design the Axiom Apple 480 K SNP array and perform multifamily-based QTL studies.Its collinearity with the genome sequences v1 and v3 are reported.To our knowledge,this is the shortest published SNP map in apple,while including the largest number of markers,families and individuals.This result validates our methodology,proving its value for the construction of integrated linkage maps for any outbreeding species.
基金This work has been funded under the EU seventh Framework Programme by the FruitBreedomics project No.265582:Integrated Approach for increasing breeding efficiency in fruit tree crops(http://www.fruitbreedomics.com/).
文摘Despite the availability of whole genome sequences of apple and peach,there has been a considerable gap between genomics and breeding.To bridge the gap,the European Union funded the FruitBreedomics project(March 2011 to August 2015)involving 28 research institutes and private companies.Three complementary approaches were pursued:(i)tool and software development,(ii)deciphering genetic control of main horticultural traits taking into account allelic diversity and(iii)developing plant materials,tools and methodologies for breeders.Decisive breakthroughs were made including the making available of ready-to-go DNA diagnostic tests for Marker Assisted Breeding,development of new,dense SNP arrays in apple and peach,new phenotypic methods for some complex traits,software for gene/QTL discovery on breeding germplasm via Pedigree Based Analysis(PBA).This resulted in the discovery of highly predictive molecular markers for traits of horticultural interest via PBA and via Genome Wide Association Studies(GWAS)on several European genebank collections.FruitBreedomics also developed pre-breeding plant materials in which multiple sources of resistance were pyramided and software that can support breeders in their selection activities.Through FruitBreedomics,significant progresses were made in the field of apple and peach breeding,genetics,genomics and bioinformatics of which advantage will be made by breeders,germplasm curators and scientists.A major part of the data collected during the project has been stored in the FruitBreedomics database and has been made available to the public.This review covers the scientific discoveries made in this major endeavour,and perspective in the apple and peach breeding and genomics in Europe and beyond.
基金funded by Genome Canada,Genome Alberta,and PigGen Canada.JC was funded in part by USDA-NIFA grant#2017-67007-26144.
文摘Background:The pork industry faces unprecedented challenges from disease,which increases cost of production and use of antibiotics,and reduces production efficiency,carcass quality,and animal wellbeing.One solution is to improve the overall resilience of pigs to a broad array of common diseases through genetic selection.Behavioral changes in feeding and drinking are usually the very first clinical signs when animals are exposed to stressors such as disease.Changes in feeding and drinking behaviors in diseased pigs may reflect the way they cope with the challenge and,thus,could be used as indicator traits to select for disease resilience.The objectives of this study were to estimate genetic parameters of feeding and drinking traits for wean-to-finish pigs in a natural polymicrobial disease challenge model,to estimate genetic correlations of feeding and drinking traits with growth rate and clinical disease traits,and to develop indicator traits to select for disease resilience.Results:In general,drinking traits had moderate to high estimates of heritability,especially average daily water dispensed,duration,and number of visits(0.44 to 0.58).Similar estimates were observed for corresponding feeding traits(0.35 to 0.51).Most genetic correlation estimates among drinking traits were moderate to high(0.30 to 0.92)and higher than among feeding traits(0 to 0.11).Compared to other drinking traits,water intake duration and number of visits had relatively stronger negative genetic correlation estimates with treatment rate and mortality,especially across the challenge nursery and finisher(−0.39 and−0.45 for treatment rate;−0.20 and−0.19 for mortality).Conclusion:Most of the recorded drinking and feeding traits under a severe disease challenge had moderate to high estimates of heritability,especially for feed or water intake duration and number of visits.Phenotypic and genetic correlations among the recorded feeding traits under disease were generally low but drinking traits showed high correlations with each other.Water intake duration and number of visits are potential indicator traits to select for disease resilience because of their high heritability and had moderate genetic correlations with treatment and mortality rates under severe disease.
