| 1. |
- Berg, Lotta, et al.
(author)
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Djurskydd inom grisuppfödning
- 2020
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Reports (other academic/artistic)abstract
- I Sverige tillåts idag generellt avvänjning av smågrisar i praktiken vid en individuell ålder om tidigast 28 dagar. Detta skiljer från EUs grisdirektiv där avvänjning tillåts från 21 dagars ålder. En digivningsperiod på 21 dagar ger en högre produktion eftersom medeltalet kullar per sugga och år teoretiskt då kan öka med 4,5 % (från 2,2 till 2,3 kullar per år). Det har även föreslagits att en kortare digivningsperiod skulle innebära mindre påfrestningar på suggorna, och därigenom medföra förbättrad välfärd för dessa. Rådet finner att det finns mycket få studier som jämför avvänjning vid just 21 och 28 dagar. De vetenskapliga studier som studerar detta mer i detalj är i de flesta fall genomförda i alternativa system, så som grupphållnings-system eller så kallade ”getaway pens” där suggan kan gå ifrån sina smågrisar. Resultat från dessa studier går därmed inte att generalisera till konventionella system där suggor med smågrisar hålls individuellt med små möjligheter för suggan att reglera t.ex. digivning eller födosöksbeteende. Trots bristen på vetenskapligt granskade rapporter konstaterades att en avvänjning vid 28 dagars ålder var att föredra sett ur smågrisens perspektiv, eftersom matsmältningsapparat och immunsystem är mer utvecklade den fjärde levnadsveckan. Det förefaller dock finnas en ganska tydlig skillnad i fysiologisk mognad mellan grisar som är yngre (<19-21 dagar) respektive äldre (28 dagar), men där grisar som är 25 dagar och äldre skiljer sig mindre från grisar som är 28 dagar gamla än grisar som är 23 dagar och yngre. Diperiodens belastning på den domesticerade suggan i modern grisproduktion överstiger den hos frilevande suggor eftersom antalet överlevande kultingar är högre, samt att suggan inte heller genom att styra digivningen kan skydda sig från kullens ökande krav på att dia. De ökande kullstorlekarna kan teoretiskt innebära påfrestningar på suggan, och tidig avvänjning skulle därmed kunna bidra till att minska påfrestningarna på suggan. Det finns dock inga vetenskapliga studier som stödjer en sådan slutsats. Det kan dock konstateras att en svensk sugga under slutet av diperioden i medeltal ger di till 13 kultingar som vardera väger cirka 10 kg, vilka tillsammans dagligen kräver 108 MJ omsättbar energi (25 800 kcal) varav huvuddelen kommer från suggans mjölk. I dagens svenska grisproduktion med omgångsuppfödning kan det skilja 4-7 dagar mellan de först födda och de sist födda i gruppen. För att samla sugg-gruppen inför nästa grisning avvänjs alla suggor samma dag och vid en lägsta individuell avvänjningsålder av 28 dagar blir medelåldern vid avvänjning därför i praktiken cirka 32 dagar. Om lantbruken fortsätter att fokusera på avvänjning så nära 28 dagars ålder som möjligt kommer ”manöverutrymmet” för att synkronisera suggorna vid avvänjning att försvinna. Suggor med fysiologiskt längre dräktighet än genomsnittet riskerar då att förskjutas i grisningstid jämfört med medelsuggorna. Vid en förlängning med tre dagar mellan två grisningstillfällen kan en sugga redan som tredjegrisare vara så pass avvikande vad gäller grisningsdag att hon kommer att slås ut (slaktas) i förtid om det inte ges möjlighet att synkronisera gruppen vid avvänjning. Vid en bedömning av lämpligaste dagen för avvänjning bör såväl smågrisens som suggans situation beaktas. Det vetenskapliga underlaget för detta är mycket begränsat, men det ska beaktas att inhysning och skötsel har större betydelse för såväl smågrisars som suggors hälsa och välfärd än den exakta avvänjningsåldern. Vid en samlad bedömning ansågs därför att en avvänjning vid 28 dagar i genomsnitt förefaller acceptabel, under förutsättning att avvänjningsåldern i inget enskilt fall understiger 25 dagar.
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| 2. |
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| 3. |
- Berg, Lotta, et al.
(author)
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Minkhållning i Sverige
- 2020
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Reports (other academic/artistic)abstract
- Den här rapporten är framtagen av SLUs vetenskapliga råd för djurskydd i syfte att utvärdera djurvälfärden hos minkar inom svensk pälsdjursproduktion och bedöma om den vetenskapliga litteraturen ger stöd för att produktionen, så som den bedrivs i dag, ger djuren möjlighet att bete sig naturligt. Minkar som föds upp för pälsproduktion i Sverige måste hållas och skötas enligt Statens jordbruksverks föreskrifter och allmänna råd (SJVFS 2012:14) om uppfödning och hållande av pälsdjur. Rapporten har tagits fram på uppdrag av Jordbruksverket som en del i ett regeringsuppdrag om minkhållning. Den beskriver minkens ursprung och domesticering, naturligt beteende hos vild mink, inhysning och skötsel vid pälsuppfödning, onormalt beteende, miljöberikningar, smittskydd, förekommande sjukdomar och avlivningsmetoder. I rapporten ges rekommendationer baserat på tillgänglig vetenskaplig litteratur, och behov av framtida forskning identifieras.Minken är en opportunistisk köttätare som behöver äta relativt ofta. I pälsdjursproduktionen tillämpas i princip fri tillgång på foder till digivande honor och växande valpar men inför parningssäsongen innebär den fria tillgången ökad risk för komplikationer vid valpningen på grund av övervikt hos honan. Fodringen behöver därför anpassas under vintern för att minska risken för feta honor och därmed ökad dödlighet vid valpningen. Neddragen fodertillgång kan orsaka frustration som då visar sig i beteendestörningar. Olika aspekter på utfodring bör därför beaktas i framtida forskning. Den vilda minken lever solitärt under stora delar av året, dock kan en till flera honor leva inom en hanes revir. I pälsdjursproduktionen bör därför vuxna minkar hållas individuellt, undantaget är växande ungminkar som med fördel kan hållas tillsammans. Att hålla två minkar tillsammans är det vanligaste, dock fungerar det att hålla tre ungminkar i etagebur om de ges extra foder och god tillsyn. Grupper med fler än tre djur bör undvikas då riskerna för aggression ökar. En lya fastsatt utanpå buren är viktigt för alla minkar året runt då de naturligt vilar mycket i sina bohål, samt även för att minkhonan ska kunna ta hand om de outvecklade ungarna första tiden efter födelsen. I fångenskap används halm för att skapa ett varmt bo under den kalla årstiden samt för att bygga ett bo för ungarna under uppfödningsperioden.Systematisk genetisk selektion för önskat beteende (temperament) förbättrar välfärden hos minken. Systemet tillämpas på svenska gårdar genom att minkar som uppvisar rädsla eller stress selekteras bort vid avelsurvalet. Urvalet av avelsdjur görs kontinuerligt från det att valparna föds, då reproduktion, valpöverlevnad och temperament registreras tidigt och är viktiga parametrar att ta hänsyn till i urvalet. Det slutliga urvalen sker på hösten då längd, vikt och pälsegenskaper graderas. Ju tidigare dessa urval görs desto tidigare kan utfodringen anpassas för att undvika att avelsdjuren blir överviktiga under hösten. Det är viktigt att aveln inte resulterar i för stora djur, då detta kan leda till välfärdsproblem i framtiden.Mink i vilt tillstånd använder vatten i sin jakt på bytesdjur, men är inget vattenlevande djur, per se. Badvatten till mink bedöms däremot vara en positiv berikning, dock inte vetenskapligt belagt, som ett grundläggande beteendebehov. Forskning visar att beteendestörningar kan förebyggas genom att minkarna ges fri tillgång på foder, hålls i etageburar med bolåda, hyllor, strömedel och berikningar som byts ut regelbundet. I svenska djurskyddsföreskrifter ingår dessa som krav för hållande av mink för pälsdjursproduktion. Mer kunskap behövs för hur ofta berikningar bör skiftas.Djurvälfärd i samband med livdjurstransport och avlivning av mink lyfts fram som angelägna forskningsområden. En snabb avlivning vid hemmaburen bedöms vara det bästa ur djurvälfärdssynpunkt. För att minska risken för spridning av sjukdomar bör importerade minkar hållas i karantän och hög biosäkerhet tillämpas på gården.
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| 4. |
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| 5. |
- Berg, Lotta, et al.
(author)
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Yttrande från SLUs vetenskapliga råd för djurskydd om djurskydd inom grisuppfödning
- 2019
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Other publication (other academic/artistic)abstract
- Detta yttrande svarar på följande fråga av Djurskyddet Sverige, Svenska Djurskyddsföreningen, Djurens Rätt, World Animal Protection Sverige, Compassion in World Farming Sverige och Vi Konsumenter, som vänt sig till det vetenskapliga rådet med anledning av Jordbruksverkets ändring av djurskyddsbestämmelserna för gris, Statens jordbruksverks föreskrifter och allmänna råd m ( SJVFS 2017:25) om grishållning inom lantbruket m.m., saknr. L 106: Är det förenat med bättre, likvärdig eller sämre djurvälfärd, vid en sammantagen bedömning av såväl smågrisens välfärd som suggans, om smågrisar avvänjs från suggan vid 21 dagars ålder i stället för vid 28 dagars ålder? Rådet ombads att belysa frågan utifrån ett brett perspektiv innefattande såväl psykisk som fysisk hälsa och välbefinnande.
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| 6. |
- Berg, Lotta, et al.
(author)
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Yttrande från SLUs vetenskapliga råd för djurskydd om hållande av hund och katt
- 2018
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Other publication (other academic/artistic)abstract
- Detta yttrande är skrivet på uppdrag av Jordbruksverket i samband med verkets översyn av föreskrifterna för hund och katt. För att Jordbruksverkets föreskrifter ska vara väl förankrade i den senaste forskningen önskar verket inhämta underlag från det vetenskapliga rådet för djurskydd vid Sveriges lantbruksuniversitet, specifikt gällande områdena rörelsebehov, social kontakt och avvänjning.
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| 7. |
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| 8. |
- Amuzu, Esinam, et al.
(author)
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Predicting heterosis for egg production traits in crossbred offspring of individual White Leghorn sires using genome-wide SNP data
- 2015
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In: Genetics Selection Evolution. - : Springer Science and Business Media LLC. - 0999-193X .- 1297-9686. ; 47
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Journal article (peer-reviewed)abstract
- Background: The development of a reliable method to predict heterosis would greatly improve the efficiency of commercial crossbreeding schemes. Extending heterosis prediction from the line level to the individual sire level would take advantage of variation between sires from the same pure line, and further increase the use of heterosis in crossbreeding schemes. We aimed at deriving the theoretical expectation for heterosis due to dominance in the crossbred offspring of individual sires, and investigating how much extra variance in heterosis can be explained by predicting heterosis at the individual sire level rather than at the line level. We used 53 421 SNP (single nucleotide polymorphism) genotypes of 3427 White Leghorn sires, allele frequencies of six White Leghorn dam-lines and cage-based records on egg number and egg weight of ~210 000 crossbred hens. Results: We derived the expected heterosis for the offspring of individual sires as the between- and within-line genome-wide heterozygosity excess in the offspring of a sire relative to the mean heterozygosity of the pure lines. Next, we predicted heterosis by regressing offspring performance on the heterozygosity excess. Predicted heterosis ranged from 7.6 to 16.7 for egg number, and from 1.1 to 2.3 grams for egg weight. Between-line differences accounted for 99.0% of the total variance in predicted heterosis, while within-line differences among sires accounted for 0.7%. Conclusions: We show that it is possible to predict heterosis at the sire level, thus to distinguish between sires within the same pure line with offspring that show different levels of heterosis. However, based on our data, variation in genome-wide predicted heterosis between sires from the same pure line was small; most differences were observed between lines. We hypothesise that this method may work better if predictions are based on SNPs with identified dominance effects.
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| 9. |
- Amuzu, Esinam, et al.
(author)
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Prediction of Heterosis in White Leghorn Crossbreds using Paternal 60K SNP Genotypes
- 2014
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Other publication (other academic/artistic)abstract
- Predicting heterosis for crossbred offspring of individual sires would harness variation between sires from the same pure-line, and can increase the utilization of heterosis in crossbreeding schemes. We aimed to derive the theoretical expectation for heterosis in crossbred offspring of individual sires, and then predict heterosis for these offspring. We used 60K SNP-genotypes from 3427 sires, allele frequencies from 9 pure-lines, and egg number records from 16 crosses between those lines, representing ~210,000 crossbred hens. Results show that it is possible to predict heterosis at the sire level, thereby distinguishing between sires within the same pure-line whose offspring will show higher heterosis. However, variation in predicted heterosis between sires within a line was low in our data; most differences were seen between lines. A potential improvement of the method would be to base predictions on a subset of SNPs with identified effects on heterosis.
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| 10. |
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| 11. |
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| 12. |
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| 13. |
- Chalkias, Helena, et al.
(author)
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Identification of novel candidate genes for the inverted teat defect in sows using a genome-wide marker panel
- 2017
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In: Journal of Applied Genetics. - : Springer Science and Business Media LLC. - 1234-1983 .- 2190-3883. ; 58, s. 249-259
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Journal article (peer-reviewed)abstract
- The number of functional teats is an important selection criterion in pig breeding. Inherited defects of the udder, such as the inverted teat, do have a considerable negative impact on the nursing ability of the sow. To investigate the genetic background of this defect and the number of functional teats in Swedish maternal lines, samples from 230 Yorkshire pigs were selected for genotyping using the PorcineSNP60K BeadChip (Illumina Inc.), each pig with at least one inverted teat was matched with one non-affected pig (fullsib or pairs with matching herd and gender). A genome-wide association study on these 230 pigs was performed using the two-step approach implemented in GenABEL using 46,652 single nucleotide polymorphisms across all autosomes and the X chromosome. A number of significant regions were identified for the inverted teat defect on chromosomes 2, 10, and 18. Many of the regions associated with the number of functional teats were located in the same or close regions, except two associated markers on the X chromosome and one on chromosome 3. We identified some of the regions on chromosomes previously reported in one linkage and one gene expression study. We conclude, despite being able to suggest new candidate genes, that further studies are needed to better understand the biologic background of the teat development. Despite the in-depth comparison of identified regions for the inverted teat defect done here, more studies are required to allow a clear identification of genetic regions relevant for this defect across many pig populations.
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| 14. |
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| 15. |
- Cordero, Juan, et al.
(author)
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Genome-wide association study identifies loci influencing natural antibody titers in milk of Dutch Holstein-Friesian cattle
- 2019
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In: Journal of Dairy Science. - : American Dairy Science Association. - 0022-0302 .- 1525-3198. ; 102, s. 11092-11103
-
Journal article (peer-reviewed)abstract
- Natural antibodies (NAb) are produced without any antigenic stimulation as a part of the innate immune system and provide a first line of defense against pathogens. Hence, they may be a useful trait when estimating an animal's potential immune competence and in selection for disease resistance. The aim of this study was to identify genomic regions associated with different NAb traits in milk and potentially describe candidate genes. Milk samples from 1,695 first-lactation Holstein Friesian cows with titer measurements for keyhole limpet hemocyanin, lipopolysaccharide, lipoteichoic acid, and peptidoglycan-binding total NAb and isotypes IgG(1), IgM, and IgA were used. Genome-wide association study analyses were performed using imputed 777K SNP genotypes, accounting for relationships using pedigree information. Functional enrichment analysis was performed on the significantly associated genomic regions to look for candidate genes. For IgM NAb, significant associations (false discovery rate <0.05) were found on Bos taurus autosonie (BTA) 17, 18, and 21 with candidate genies related to immunoglobulin structure and early B cell development. For IgG(1), associations were found on BTA3, and we confirmed a quantitative trait loci on BTA21 previously reported for IgG NAb in serum. Our results provide new insights into the regulation of milk NAb that will help unravel the complex relationship between milk immunoglobulins and disease resistance in dairy cattle.
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| 16. |
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| 17. |
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| 18. |
- Crooks, Lucy, et al.
(author)
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Comparison of analyses of the QTLMAS XII common dataset. II : genome-wide association and fine mapping.
- 2009
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In: BMC Proceedings. - 1753-6561. ; 3 Suppl 1
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Journal article (peer-reviewed)abstract
- As part of the QTLMAS XII workshop, a simulated dataset was distributed and participants were invited to submit analyses of the data based on genome-wide association, fine mapping and genomic selection. We have evaluated the findings from the groups that reported fine mapping and genome-wide association (GWA) efforts to map quantitative trait loci (QTL). Generally the power to detect QTL was high and the Type 1 error was low. Estimates of QTL locations were generally very accurate. Some methods were much better than others at estimating QTL effects, and with some the accuracy depended on simulated effect size or minor allele frequency. There were also indications of bias in the effect estimates. No epistasis was simulated, but the two studies that included searches for epistasis reported several interacting loci, indicating a problem with controlling the Type I error rate in these analyses. Although this study is based on a single dataset, it indicates that there is a need to improve fine mapping and GWA methods with respect to estimation of genetic effects, appropriate choice of significance thresholds and analysis of epistasis.
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| 19. |
- De Koning, Dirk-Jan
(author)
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A 0.5‑Mbp deletion on bovine chromosome 23 is a strong candidate for stillbirth in Nordic Red cattle
- 2016
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In: Genetics Selection Evolution. - : Springer Science and Business Media LLC. - 0999-193X .- 1297-9686. ; 48
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Journal article (peer-reviewed)abstract
- Background: A whole-genome association study of 4631 progeny-tested Nordic Red dairy cattle bulls using imputed next-generation sequencing data revealed a major quantitative trait locus (QTL) that affects birth index (BI) on Bos taurus autosome (BTA)23. We analyzed this QTL to identify which of the component traits of BI are affected and understand its molecular basis. Results: A genome-wide scan of BI in Nordic Red dairy cattle detected major QTL on BTA6, 14 and 23. The strongest associated single nucleotide polymorphism (SNP) on BTA23 was located at 13,313,896 bp with -log10(p) = 50.63. Analyses of component traits showed that the QTL had a large effect on stillbirth. Based on the 10 most strongly associated SNPs with stillbirth, we constructed a haplotype. Among this haplotype's alleles, HAPQTL had a large negative effect on stillbirth. No animals were found to be homozygous for HAPQTL. Analysis of stillbirth records that were categorized by carrier status for HAPQTL of the sire and maternal grandsire suggested that this haplotype had a recessive mode of inheritance. Illumina BovineHD BeadChip genotypes and genotype intensity data indicated a chromosomal deletion between 12.28 and 12.81 Mbp on BTA23. An independent set of Illumina Bovine50k BeadChip genotypes identified a recessive lethal haplotype that spanned the deleted region. Conclusions: A deleted region of approximately 500 kb that spans three genes on BTA23 was identified and is a strong candidate QTL with a large effect on BI by increasing stillbirth.
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| 20. |
- De Koning, Dirk-Jan
(author)
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Accuracy of genomic prediction using low-density marker panels
- 2011
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In: Journal of Dairy Science. - : American Dairy Science Association. - 0022-0302 .- 1525-3198. ; 94, s. 3642-3650
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Journal article (peer-reviewed)abstract
- Genomic selection has been widely implemented in national and international genetic evaluation in the dairy cattle industry, because of its potential advantages over traditional selection methods and the availability of commercial high-density (HD) single nucleotide polymorphism (SNP) panels. However, this method may not be cost-effective for cow selection and for other livestock species, because the cost of HD SNP panels is still relatively high. One possible solution that can enable other species to benefit from this promising method is genomic selection with low-density (LD) SNP panels. In this simulation study, LD SNP panels designed with different strategies and different SNP densities were compared. The effects of number of quantitative trait loci, heritability, and effective population size were evaluated in the framework of genomic selection with LD SNP panels. Methodologies of Bayesian variable selection; BLUP with a trait-specific, marker-derived relationship matrix; and BLUP with a realized relationship matrix were employed to predict genomic estimated breeding values with both HD and LD SNP panels. Up to 95% of accuracy obtained by using an HD panel can be obtained by using only a small proportion of markers. The LD panel with markers selected on the basis of their effects always performs better than the LD panel with evenly spaced markers. Both the genetic architecture of the trait and the effective population size have a significant effect on the performance of the LD panels. We concluded that, to implement genomic selection with LD panels, a training population of sufficient size and genotyped with an HD panel is necessary. The trade-off between the LD panels with evenly spaced markers and selected markers must be considered, which depends on the number of target traits in a breeding program and the genetic architecture of these traits. Genomic selection with LD panels could be feasible and cost-effective, though before implementation, a further detailed genetic and economic analysis is recommended.
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| 21. |
- De Koning, Dirk-Jan
(author)
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An eQTL in the cystathionine beta synthase gene is linked to osteoporosis in laying hens
- 2020
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In: Genetics Selection Evolution. - : Springer Science and Business Media LLC. - 0999-193X .- 1297-9686. ; 52
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Journal article (peer-reviewed)abstract
- Background Skeletal damage is a challenge for laying hens because the physiological adaptations required for egg laying make them susceptible to osteoporosis. Previously, we showed that genetic factors explain 40% of the variation in end of lay bone quality and we detected a quantitative trait locus (QTL) of large effect on chicken chromosome 1. The aim of this study was to combine data from the commercial founder White Leghorn population and the F2 mapping population to fine-map this QTL and understand its function in terms of gene expression and physiology. Results Several single nucleotide polymorphisms on chromosome 1 between 104 and 110 Mb (galGal6) had highly significant associations with tibial breaking strength. The alternative genotypes of markers of large effect that flanked the region had tibial breaking strengths of 200.4 vs. 218.1 Newton (P < 0.002) and, in a subsequent founder generation, the higher breaking strength genotype was again associated with higher breaking strength. In a subsequent generation, cortical bone density and volume were increased in individuals with the better bone genotype but with significantly reduced medullary bone quality. The effects on cortical bone density were confirmed in a further generation and was accompanied by increased mineral maturity of the cortical bone as measured by infrared spectrometry and there was evidence of better collagen cross-linking in the cortical bone. Comparing the transcriptome of the tibia from individuals with good or poor bone quality genotypes indicated four differentially-expressed genes at the locus, one gene, cystathionine beta synthase (CBS), having a nine-fold higher expression in the genotype for low bone quality. The mechanism was cis-acting and although there was an amino-acid difference in the CBS protein between the genotypes, there was no difference in the activity of the enzyme. Plasma homocysteine concentration, the substrate of CBS, was higher in the poor bone quality genotype. Conclusions Validated markers that predict bone strength have been defined for selective breeding and a gene was identified that may suggest alternative ways to improve bone health in addition to genetic selection. The identification of how genetic variants affect different aspects of bone turnover shows potential for translational medicine.
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| 22. |
- De Koning, Dirk-Jan
(author)
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An Expression QTL of Closely Linked Candidate Genes Affects pH of Meat in Chickens
- 2014
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In: Genetics. - : Oxford University Press (OUP). - 0016-6731 .- 1943-2631. ; 196, s. 867-874
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Journal article (peer-reviewed)abstract
- Genetical genomics has been suggested as a powerful approach to study the genotype-phenotype gap. However, the relatively low power of these experiments (usually related to the high cost) has hindered fulfillment of its promise, especially for loci (QTL) of moderate effects.One strategy with which to overcome the issue is to use a targeted approach. It has two clear advantages: (i) it reduces the problem to a simple comparison between different genotypic groups at the QTL and (ii) it is a good starting point from which to investigate downstream effects of the QTL. In this study, from 698 F2 birds used for QTL mapping, gene expression profiles of 24 birds with divergent homozygous QTL genotypes were investigated. The targeted QTL was on chromosome 1 and affected initial pH of breast muscle. The biological mechanisms controlling this trait can be similar to those affecting malignant hyperthermia or muscle fatigue in humans. The gene expression study identified 10 strong local signals that were markedly more significant compared to any genes on the rest of the genome. The differentially expressed genes all mapped to a region <1 Mb, suggesting a remarkable reduction of the QTL interval. These results, combined with analysis of downstream effect of the QTL using gene network analysis, suggest that the QTL is controlling pH by governing oxidative stress. The results were reproducible with use of as few as four microarrays on pooled samples (with lower significance level). The results demonstrate that this cost-effective approach is promising for characterization of QTL.
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| 23. |
- De Koning, Dirk-Jan
(author)
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Analysis of the genetics of boar taint reveals both single SNPs and regional effects
- 2014
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In: BMC Genomics. - : Springer Science and Business Media LLC. - 1471-2164. ; 15
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Journal article (peer-reviewed)abstract
- Background: Boar taint is an offensive urine or faecal-like odour, affecting the smell and taste of cooked pork from some mature non-castrated male pigs. Androstenone and skatole in fat are the molecules responsible. In most pig production systems, males, which are not required for breeding, are castrated shortly after birth to reduce the risk of boar taint. There is evidence for genetic variation in the predisposition to boar taint. A genome-wide association study (GWAS) was performed to identify loci with effects on boar taint. Five hundred Danish Landrace boars with high levels of skatole in fat (>0.3 μg/g), were each matched with a litter mate with low levels of skatole and measured for androstenone. DNA from these 1,000 non-castrated boars was genotyped using the Illumina PorcineSNP60 Beadchip. After quality control, tests for SNPs associated with boar taint were performed on 938 phenotyped individuals and 44,648 SNPs. Empirical significance thresholds were set by permutation (100,000). For androstenone, a ‘regional heritability approach' combining information from multiple SNPs was used to estimate the genetic variation attributable to individual autosomes. Results: A highly significant association was found between variation in skatole levels and SNPs within the CYP2E1 gene on chromosome 14 (SSC14), which encodes an enzyme involved in degradation of skatole. Nominal significance was found for effects on skatole associated with 4 other SNPs including a region of SSC6 reported previously. Genome-wide significance was found for an association between SNPs on SSC5 and androstenone levels and nominal significance for associations with SNPs on SSC13 and SSC17. The regional analyses confirmed large effects on SSC5 for androstenone and suggest that SSC5 explains 23% of the genetic variation in androstenone. The autosomal heritability analyses also suggest that there is a large effect associated with androstenone on SSC2, not detected using GWAS. Conclusions: Significant SNP associations were found for skatole on SSC14 and for androstenone on SSC5 in Landrace pigs. The study agrees with evidence that the CYP2E1 gene has effects on skatole breakdown in the liver. Autosomal heritability estimates can uncover clusters of smaller genetic effects that individually do not exceed the threshold for GWAS significance.
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| 26. |
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| 27. |
- de Koning, Dirk-Jan
(author)
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Efficacy of Lactobacillus plantarum and Saccharomyces cerevisiae on growth improvement of hybrid Nile and Rufiji tilapia populations
- 2021
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In: Western Indian Ocean Journal of Marine Science. - : African Journals Online (AJOL). - 0856-860X .- 2683-6416. ; 20, s. 35-45
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Journal article (peer-reviewed)abstract
- An investigation of the role of Lactobacillus plantarum and Saccharomyces cerevisiae on growth performance of hybrids from Oreochromis niloticus and Oreochromis urolepis urolepis was carried out in plastic tanks at 10 fish/m3 density and a salinity of 25 units. The probiotic treatments were 2, 4 and 6 g/kg feed while the control feed did not include any probiotics. Growth parameters were measured fortnightly and water quality parameters monitored every day. Survival rate and water quality factors revealed non-significant variations (p > 0.05). Final weight differed significantly among the treatments (p < 0.05). Furthermore, Food Conversion Ratio (FCR), Specific Growth Rates (SGR), and weight gain did not differ significantly (p > 0.05) between the control and 2 g/kg treatments. However, the 4 and 6 g/ kg feed treatments showed significant differences (p < 0.05) from the control diet and 2 g/kg for both L. plantarum and S. cerevisiae. The condition factor did not show any significant difference (p > 0.05) among the treatments. Results of this study indicate that increasing the quantity of commercial probiotics in feeds improved growth rates. Condition factor observed in the treatments could be due to the role of the tested probiotics in improving the water quality of tanks. Therefore, probiotics could potentially be used to enhance coastal aquaculture development.
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| 28. |
- De Koning, Dirk-Jan
(author)
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Efficiency of genomic prediction for boar taint reduction in Danish Landrace pigs
- 2015
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In: Animal Genetics. - : Wiley. - 0268-9146 .- 1365-2052. ; 46, s. 607-616
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Journal article (peer-reviewed)abstract
- Genetic selection against boar taint, which is caused by high skatole and androstenone concentrations in fat, is a more acceptable alternative than is the current practice of castration. Genomic predictors offer an opportunity to overcome the limitations of such selection caused by the phenotype being expressed only in males at slaughter, and this study evaluated different approaches to obtain such predictors. Samples from 1000 pigs were included in a design which was dominated by 421 sib pairs, each pair having one animal with high and one with low skatole concentration (0.3g/g). All samples were measured for both skatole and androstenone and genotyped using the Illumina SNP60 porcine BeadChip for 62153 single nucleotide polymorphisms. The accuracy of predicting phenotypes was assessed by cross-validation using six different genomic evaluation methods: genomic best linear unbiased prediction (GBLUP) and five Bayesian regression methods. In addition, this was compared to the accuracy of predictions using only QTL that showed genome-wide significance. The range of accuracies obtained by different prediction methods was narrow for androstenone, between 0.29 (Bayes Lasso) and 0.31 (Bayes B), and wider for skatole, between 0.21 (GBLUP) and 0.26 (Bayes SSVS). Relative accuracies, corrected for h(2), were 0.54-0.56 and 0.75-0.94 for androstenone and skatole respectively. The whole-genome evaluation methods gave greater accuracy than using only the QTL detected in the data. The results demonstrate that GBLUP for androstenone is the simplest genomic technology to implement and was also close to the most accurate method. More specialised models may be preferable for skatole.
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| 29. |
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| 30. |
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| 31. |
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| 32. |
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| 33. |
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| 34. |
- De Koning, Dirk-Jan
(author)
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Genome-wide Association Studies in Pedigreed Populations
- 2014
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In: Molecular and Quantitative Animal Genetics. - 9781118677407 ; , s. 155-162
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Book chapter (peer-reviewed)abstract
- Animal genetics is a central topic in upper-level animal science programs. Filling a void in existing literature on animal science, Animal Genetics introduces genetic principles and presents their application in production and companion animals. The book details population and quantitative genetics, epigenetics, biotechnology, and breeding among other topics. Useful in upper-level studies, Animal Genetics is an irreplaceable educational resource.
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| 35. |
- De Koning, Dirk-Jan
(author)
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Genome-wide associations for investigating time-dependent genetic effects for milk production traits in dairy cattle
- 2012
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In: Animal Genetics. - : Wiley. - 0268-9146 .- 1365-2052. ; 43, s. 375-382
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Journal article (peer-reviewed)abstract
- Phenotypic variation in milk production traits has been described over the course of a lactation as well as between different parities. The objective of this study was to investigate whether variation in production is affected by different loci across lactations. A genome-wide association study (GWAS) using a 50-k SNP chip was conducted in 152 divergent German Holstein Friesian cows to test for association with milk production traits over different lactations. The first four lactations were analysed regarding milk yield, fat, protein, lactose, milk urea nitrogen yield and content as well as somatic cell score. Two approaches were used: (i) Wilmink curve parameters were used to assess the genetic effects over the course of a lactation and (ii) test-day yield deviations (YD) were used as a normative approach for a GWAS. The significant effects were largest for markers affecting curve parameters for which there was a statistical power <0.8 of detection even in this small design. While significant markers for YDs were detected in this study, the power to detect effects of a similar magnitude was only 0.11, suggesting that many loci may have been missed with this approach in the present design. Furthermore, all significant effects were specific for a single lactation, leading to the conclusion that the variance explained by a certain locus changes from lactation to lactation. We confirm the common evidence that most production traits vary in the degree of persistency after the peak as a result of genetic influence.
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| 36. |
- De Koning, Dirk-Jan
(author)
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Genome-wide mapping of large deletions and their population-genetic properties in dairy cattle
- 2018
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In: DNA Research. - : Oxford University Press (OUP). - 1340-2838 .- 1756-1663. ; 25, s. 49-59
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Journal article (peer-reviewed)abstract
- Large genomic deletions are potential candidate for loss-of-function, which could be lethal as homozygote. Analysing whole genome data of 175 cattle, we report 8,480 large deletions (199 bp-773 KB) with an overall false discovery rate of 8.8%; 82% of which are novel compared with deletions in the dbVar database. Breakpoint sequence analyses revealed that majority (24 of 29 tested) of the deletions contain microhomology/homology at breakpoint, and therefore, most likely generated by microhomology-mediated end joining. We observed higher differentiation among breeds for deletions in some genic-regions, such as ABCA12, TTC1, VWA3B, TSHR, DST/BPAG1, and CD1D. The genes overlapping deletions are on average evolutionarily less conserved compared with known mouse lethal genes (P-value = 2.3 x 10(-6)). We report 167 natural gene knockouts in cattle that are apparently nonessential as live homozygote individuals are observed. These genes are functionally enriched for immunoglobulin domains, olfactory receptors, and MHC classes (FDR = 2.06 x 10(-22), 2.06 x 10(-22), 7.01 x 10(-6), respectively). We also demonstrate that deletions are enriched for health and fertility related quantitative trait loci (2- and 1.5-fold enrichment, Fisher's P-value = 8.91 x 10(-10) and 7.4 x 10(-11), respectively). Finally, we identified and confirmed the breakpoint of a similar to 525 KB deletion on Chr23: 12,291,761-12,817,087 (overlapping BTBD9, GLO1 and DNAH8), causing stillbirth in Nordic Red Cattle.
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| 37. |
- De Koning, Dirk-Jan
(author)
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Genomic Selection and Genome-wide Association Study for Feed-Efficiency Traits in a Farmed Nile Tilapia (Oreochromis niloticus) Population
- 2021
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In: Frontiers in Genetics. - : Frontiers Media SA. - 1664-8021. ; 12
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Journal article (peer-reviewed)abstract
- Nile tilapia is a key aquaculture species with one of the highest production volumes globally. Genetic improvement of feed efficiency via selective breeding is an important goal, and genomic selection may expedite this process. The aims of this study were to 1) dissect the genetic architecture of feed-efficiency traits in a Nile tilapia breeding population, 2) map the genomic regions associated with these traits and identify candidate genes, 3) evaluate the accuracy of breeding value prediction using genomic data, and 4) assess the impact of the genetic marker density on genomic prediction accuracies. Using an experimental video recording trial, feed conversion ratio (FCR), body weight gain (BWG), residual feed intake (RFI) and feed intake (FI) traits were recorded in 40 full-sibling families from the GIFT (Genetically Improved Farmed Tilapia) Nile tilapia breeding population. Fish were genotyped with a ThermoFisher Axiom 65 K Nile tilapia SNP array. Significant heritabilities, ranging from 0.12 to 0.22, were estimated for all the assessed traits using the genomic relationship matrix. A negative but favourable genetic correlation was found between BWG and the feed-efficiency related traits; -0.60 and -0.63 for FCR and RFI, respectively. While the genome-wide association analyses suggested a polygenic genetic architecture for all the measured traits, there were significant QTL identified for BWG and FI on chromosomes seven and five respectively. Candidate genes previously found to be associated with feed-efficiency traits were located in these QTL regions, including ntrk3a, ghrh and eif4e3. The accuracy of breeding value prediction using the genomic data was up to 34% higher than using pedigree records. A SNP density of approximately 5,000 SNPs was sufficient to achieve similar prediction accuracy as the full genotype data set. Our results highlight the potential of genomic selection to improve feed efficiency traits in Nile tilapia breeding programmes.
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| 38. |
- De Koning, Dirk-Jan, et al.
(author)
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Genomic selection needs to be carefully assessed to meet specific requirements in livestock breeding programs
- 2015
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In: Frontiers in Genetics. - : Frontiers Media SA. - 1664-8021. ; 6
-
Research review (peer-reviewed)abstract
- Genomic selection is a promising development in agriculture, aiming improved production by exploiting molecular genetic markers to design novel breeding programs and to develop new markers-based models for genetic evaluation. It opens opportunities for research, as novel algorithms and lab methodologies are developed. Genomic selection can be applied in many breeds and species. Further research on the implementation of genomic selection (GS) in breeding programs is highly desirable not only for the common good, but also the private sector (breeding companies). It has been projected that this approach will improve selection routines, especially in species with long reproduction cycles, late or sex-limited or expensive trait recording and for complex traits. The task of integrating GS into existing breeding programs is, however, not straightforward. Despite successful integration into breeding programs for dairy cattle, it has yet to be shown how much emphasis can be given to the genomic information and how much additional phenotypic information is needed from new selection candidates. Genomic selection is already part of future planning in many breeding companies of pigs and beef cattle among others, but further research is needed to fully estimate how effective the use of genomic information will be for the prediction of the performance of future breeding stock. Genomic prediction of production in crossbreeding and across-breed schemes, costs and choice of individuals for genotyping are reasons for a reluctance to fully rely on genomic information for selection decisions. Breeding objectives are highly dependent on the industry and the additional gain when using genomic information has to be considered carefully. This review synthesizes some of the suggested approaches in selected livestock species including cattle, pig, chicken, and fish. It outlines tasks to help understanding possible consequences when applying genomic information in breeding scenarios.
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| 39. |
- De Koning, Dirk-Jan, et al.
(author)
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Growth performance of five different strains of Nile tilapia (Oreochromis niloticus) introduced to Tanzania reared in fresh and brackish waters
- 2021
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In: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 11
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Journal article (peer-reviewed)abstract
- Five introduced strains of Nile tilapia (Oreochromis niloticus) were tested for growth performance both in fresh- and brackish-water (2 salinity units) environments for 56 days. The BIG NIN, GIFT, Chitralada, "Ruvu Farm" and Silver YY strains with initial mean average weight (+/- standard error) of 96.4 +/- 6.90 g, 104.1 +/- 7.19 g, 137.2 +/- 7.21 g, 53.2 +/- 6.98 g and 95.3 +/- 7.11 g, respectively were used. Individuals were tagged and pooled in hapas (12 mx8.5 mx2 m each), aligned into different ponds (20 mx20 m each). Stocking density of 5 fish/m(2) and 350 g/kg crude protein diet were used. Overall, the average weight gain for GIFT strain was 7.5%, 32%, 45% and 86.5% higher than BIG NIN, Chitralada, "Ruvu Farm" and Silver YY strains, respectively, across both environments. All strains performed significantly better (p<0.05) when reared in brackish-water than their respective counterparts in freshwater, except for the BIG NIN strain. The morphometric correlations for all strains in both environments ranged from moderate (0.50) to strong positive (0.92). The GIFT strain demonstrated superior growth and genotype by environment interaction was weak and not important to be prioritized in breeding programs.
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| 40. |
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| 41. |
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| 42. |
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| 43. |
- De Koning, Dirk-Jan
(author)
-
Meuwissen et al. on Genomic Selection
- 2016
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In: Genetics. - : Oxford University Press (OUP). - 0016-6731 .- 1943-2631. ; 203, s. 5-7
-
Other publication (other academic/artistic)
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| 44. |
- De Koning, Dirk-Jan
(author)
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No evidence that selection for egg production persistency causes loss of bone quality in laying hens
- 2021
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In: Genetics Selection Evolution. - : Springer Science and Business Media LLC. - 0999-193X .- 1297-9686. ; 53
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Journal article (peer-reviewed)abstract
- Background The physiological adaptations that have evolved for egg laying make hens susceptible to bone fractures and keel bone damage. In modern laying hen breeds, longer periods of egg laying could result in a greater risk of poor bone quality, and selection for increased egg production has frequently been stated to be a cause. However, the existing literature does not support this hypothesis. To test the hypothesis that egg production is associated with quality, breaking strength and density of bone, genetic correlations between these traits were estimated in White Leghorn and Rhode Island Red breeds. Genetic correlations of cortical and medullary bone material chemical properties with bone quality were also estimated, in order to identify methods to improve bone quality with appropriately targeted measurement of key traits. Results Estimates of heritability for bone quality traits were moderate (0.19-0.59) for both White Leghorn and Rhode Island Red breeds, except for the keel bone trait, which had a heritability estimate equal to zero. There was no evidence for genetic or phenotypic relationships between post-peak egg production and bone quality. In the White Leghorn breed, the estimate of the genetic correlation between pre-peak production/age at first egg and bone quality was significant and negative (- 0.7 to - 0.4). Estimates of heritability of thermogravimetric measurements of tibial medullary bone mineralisation were significant (0.18-0.41), as were estimates of their genetic correlations with tibia breaking strength and density (0.6-0.9). Conclusions The low genetic correlation of post-peak egg production with bone quality suggests that selection for increased persistency of egg production may not adversely affect bone quality. Onset of puberty and mineralisation of the medullary bone, which is a specialised adaptation for egg laying, were identified as important factors associated with the quality of the skeleton later during egg production. These are traits for which genetic, as well as environmental and management factors can positively impact the overall quality of the skeleton of laying hens.
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| 45. |
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| 46. |
- De Koning, Dirk-Jan
(author)
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Predicted optimum ambient temperatures for broiler chickens to dissipate metabolic heat do not affect performance or improve breast muscle quality
- 2016
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In: British Poultry Science. - : Informa UK Limited. - 0007-1668 .- 1466-1799. ; 57, s. 134-141
-
Journal article (peer-reviewed)abstract
- 1. An experiment was conducted to test the hypothesis that muscle damage in fast-growing broiler chickens is associated with an ambient temperature that does not permit the birds to lose metabolic heat resulting in physiological heat stress and a reduction in meat quality. 2. The experiment was performed in 4 climate chambers and was repeated in 2 trials using a total of 200 male broiler chickens. Two treatments compared the recommended temperature profile and a cool regimen. The cool regimen was defined by a theoretical model that determined the environmental temperature that would enable heat generated by the bird to be lost to the environment. 3. There were no differences in growth rate or feed intake between the two treatments. Breast muscles from birds on the recommended temperature regimen were lighter, less red and more yellow than those from the cool temperature regimen. There were no differences in moisture loss or shear strength but stiffness was greater in breast muscle from birds housed in the cool compared to the recommended regimen. 4. Histopathological changes in the breast muscle were similar in both treatments and were characterised by mild to severe myofibre degeneration and necrosis with regeneration, fibrosis and adipocyte infiltration. There was no difference in plasma creatine kinase activity, a measure of muscle cell damage, between the two treatments consistent with the absence of differences in muscle pathology. 5. It was concluded that breast muscle damage in fast-growing broiler chickens was not the result of an inability to lose metabolic heat at recommended ambient temperatures. The results suggest that muscle cell damage and breast meat quality concerns in modern broiler chickens are related to genetic selection for muscle yields and that genetic selection to address breast muscle integrity in a balanced breeding programme is imperative.
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| 47. |
- De Koning, Dirk-Jan
(author)
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QTL affecting morphometric traits and stress response in the gilthead seabream (Sparus aurata)
- 2011
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In: Aquaculture. - : Elsevier BV. - 0044-8486 .- 1873-5622. ; 319, s. 58-66
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Journal article (peer-reviewed)abstract
- The gilthead seabream (Sparus aurata) is an important aquaculture species that has only been subject to an incipient selective breeding programme. This study, which examined the genetic architecture of seabream morphology and stress response to confinement, takes a step toward the use of marker assisted selection in this species. Major loci affecting these traits were mapped, using data from 460 offspring derived from seven paternal and 73 maternal half-sib families. Fish were killed following a four-hour confinement experiment to induce stress, after which 15 morphometric measurements were collected and blood was sampled for DNA extraction and plasma cortisol level determination. Heritabilities for the morphometric traits were moderate to high (0.24-0.58), with genetic and phenotypic correlations between the traits generally very high. However, the heritability of plasma cortisol level was not significantly different from zero.A population-specific genetic linkage map was built for 56 microsatellite markers. comprising 16 linkage groups (LG) and ten unlinked markers. Half-sib and variance components QTL analyses detected a single genome-wide significant QTL (SaimbcF7b), a single unlinked marker explaining 13-23% of the phenotypic variance in the majority of the morphometric traits. Several other putative QTL were identified for morphometric traits (on LG 4a, 7, 9, 18, A, C, F and I), along with two other QTL (LG10 and B) that were suggestive for stress response. Fitting body weight as a covariate for the morphometric traits resulted in three genome-wide significant QTL affecting aspects of body shape independent of overall body size. For stress response we only identified suggestive evidence for QTL. These findings contribute to understanding the genetic regulation of important economic traits in seabream. Crown Copyright (C) 2011 Published by Elsevier B.V. All rights reserved.
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| 49. |
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| 50. |
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