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Mixture models detect large effect QTL better than GBLUP and result in more accurate and persistent predictions

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journal of Animal Science and Biotechnology 2016年第4期7卷 468-473页

作者： Anna Wolc jesus Arango Petek Settar janet E.Fulton Neil P.O'Sullivan jack C.M.Dekkers Rohan Fernando dorian j.garrick Department of Animal Science Iowa State University Hy-Line International Dallas Center

Background： Accurate evaluation of SNP effects is important for genome wide association studies and for genomic prediction. The genetic architecture of quantitative traits differs widely, with some traits exhibiting few if any quantitative trait loci （QTL） with large effects, while other traits have one or several easily detectable QTL with large effects. Methods： Body weight in broilers and egg weight in layers are two examples of traits that have QTL of large effect A commonly used method for genome wide association studies is to fit a mixture model such as BayesB that assumes some known proportion of SNP effects are zero. In contrast, the most commonly used method for genomic prediction is known as GBLUP, which involves fitting an animal model to phenotypic data with the variance-covariance or genomic relationship matrix among the animals being determined by genome wide SNP genotypes. Genotypes at each SNP are typically weighted equally in determining the genomic relationship matrix for GBLUP. We used the equivalent marker effects model formulation of GBLUP for this study. We compare these two classes of models using egg weight data collected over 8 generations from 2,324 animals genotyped with a 42 K SNP ***： Using data from the first 7 generations, both BayesB and GBLUP found the largest QTL in a similar well-recognized QTL region, but this QTL was estimated to account for 24 % of genetic variation with BayesB and less than 1% with GBLUP. When predicting phenotypes in generation 8 BayesB accounted for 36 % of the phenotypic variation and GBLUP for 25 %. When using only data from any one generation, the same QTL was identified with BayesB in all but one generation but never with GBLUP. Predictions of phenotypes in generations 2 to 7 based on only 295 animals from generation 1 accounted for 10 % phenotypic variation with BayesB but only 6 % with GBLUP. Predicting phenotype using only the marker effects in the 1 Mb region that accounted for the largest e

关键词： Bayesian methods Bias QTL

Comparison of methods for deriving phenotypes from incomplete observation data with an application to age at puberty in dairy cattle

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journal of Animal Science and Biotechnology 2024年第2期15卷 535-545页

作者： Melissa A.Stephen Chris R.Burke jennie E.Pryce Nicole M.Steele Peter R.Amer Susanne Meier Claire V.C.Phyn dorian j.garrick DairyNZ Ltd 605 Ruakura RoadHamilton 3240New Zealand AL Rae Centre for Genetics and Breeding-Massey University RuakuraHamilton 3214New Zealand Agriculture Victoria Research AgriBioCentre for AgriBioscienceBundooraVictoria 3083Australia School of Applied Systems Biology La Trobe UniversityBundooraVictoria 3083Australia AbacusBio DunedinNew Zealand

Background Many phenotypes in animal breeding are derived from incomplete measures,especially if they are challenging or expensive to measure *** include time-dependent traits such as reproductive status,or *** measures for these traits result in phenotypes that are subject to left-,interval-and rightcensoring,where phenotypes are only known to fall below an upper bound,between a lower and upper bound,or above a lower bound *** we compare three methods for deriving phenotypes from incomplete data using age at first elevation(>1 ng/mL)in blood plasma progesterone(AGEP4),which generally coincides with onset of puberty,as an example *** We produced AGEP4 phenotypes from three blood samples collected at about 30-day intervals from approximately 5,000 Holstein–Friesian or Holstein–Friesian×jersey cross-bred dairy heifers managed in 54 seasonal-calving,pasture-based herds in New *** used these actual data to simulate 7 different visit scenarios,increasing the extent of censoring by disregarding data from one or two of the three *** methods for deriving phenotypes from these data were explored:1)ordinal categorical variables which were analysed using categorical threshold analysis;2)continuous variables,with a penalty of 31 d assigned to right-censored phenotypes;and 3)continuous variables,sampled from within a lower and upper bound using a data augmentation *** Credibility intervals for heritability estimations overlapped across all methods and visit scenarios,but estimated heritabilities tended to be higher when left censoring was *** sires with at least 5 daughters,the correlations between estimated breeding values(EBVs)from our three-visit scenario and each reduced data scenario varied by method,ranging from 0.65 to *** estimated breed effects also varied by method,but breed differences were smaller as phenotype censoring *** Our results indicate that using

关键词： Cattle Gibbs sampler Markov-chain Monte Carlo(MCMC) Puberty

Identification of recombination hotspots and quantitative trait loci for recombination rate in layer chickens

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journal of Animal Science and Biotechnology 2019年第2期10卷 314-326页

作者： Ziqing Weng Anna Wolc Hailin Su Rohan L.FernANDo jack C.M.Dekkers jesus Arango Petek Settar janet E.Fulton Neil P.O’Sullivan dorian j.garrick Department of Animal Science Iowa State UniversityAmesIA 50010USA Hy-Line International Dallas CenterIA 50063USA AL Rae Centre for Genetics and Breeding Massey UniversityPalmerston North 4442New Zealand.

Background: The frequency of recombination events varies across the genome and between individuals, which may be related to some genomic features. The objective of this study was to assess the frequency of recombination events and to identify QTL(quantitative trait loci) for recombination rate in two purebred layer chicken ***: A total of 1200 white-egg layers(WL) were genotyped with 580 K SNPs and 5108 brown-egg layers(BL)were genotyped with 42 K SNPs(single nucleotide polymorphisms). Recombination events were identified within half-sib families and both the number of recombination events and the recombination rate was calculated within each0.5 Mb window of the genome. The 10% of windows with the highest recombination rate on each chromosome were considered to be recombination hotspots. A BayesB model was used separately for each line to identify genomic regions associated with the genome-wide number of recombination event per meiosis. Regions that explained more than 0.8% of genetic variance of recombination rate were considered to harbor ***: Heritability of recombination rate was estimated at 0.17 in WL and 0.16 in BL. On average, 11.3 and 23.2 recombination events were detected per individual across the genome in 1301 and 9292 meioses in the WL and BL,respectively. The estimated recombination rates differed significantly between the lines, which could be due to differences in inbreeding levels, and haplotype structures. Dams had about 5% to 20% higher recombination rates per meiosis than sires in both lines. Recombination rate per 0.5 Mb window had a strong negative correlation with chromosome size and a strong positive correlation with GC content and with CpG island density across the genome in both lines. Different QTL for recombination rate were identified in the two lines. There were 190 and 199 non-overlapping recombination hotspots detected in WL and BL respectively, 28 of which were common to both ***: Differences in the r

关键词： Layer chicken QTL Recombination SNP

Fine mapping of genomic regions associated with female fertility in Nellore beef cattle based on sequence variants from segregating sires

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journal of Animal Science and Biotechnology 2020年第2期11卷 303-315页

作者： Gerson A.Oliveira júnior Daniel j.A.Santos Aline S.M.Cesar Solomon A.Boison Ricardo V.Ventura Bruno C.Perez joséF.Garcia joséBento S.Ferraz dorian j.garrick Department of Veterinary Medicine University of São Paulo(USP)Faculty of Animal Science and Food EngineerPirassunungaSPBrazil Department of Animal Bioscience Center for Genetic Improvement of LivestockUniversity of GuelphGuelphONCanada Department of Animal and Avian Sciences University of MarylandCollege ParkMarylandUSA Department of Animal Science University of São Paulo(USP)PiracicabaSPBrazil Department of Sustainable Agricultural Systems University of Natural Resources and Life SciencesViennaAustria Department of Animal Nutrition and Production School of Veterinary Medicine and Animal ScienceUniversity of São Paulo(USP)PirassunungaBrazil Department of Support Production and Animal HealthSchool of Veterinary MedicineSão Paulo State University(Unesp)AraçatubaSPBrazil School of Agriculture Massey UniversityRuakura Ag CentreHamiltonNew Zealand

Background:Impaired fertility in cattle limits the efficiency of livestock production *** the genetic architecture of fertility traits would facilitate their improvement by *** this study,we characterized SNP chip haplotypes at QTL blocks then used whole-genome sequencing to fine map genomic regions associated with reproduction in a population of Nellore(Bos indicus)***:The dataset comprised of 1337 heifers genotyped using a GeneSeek®Genomic Profiler panel(74677 SNPs),representing the daughters from 78 *** performing marker quality control,64800 SNPs were *** carried by each sire at six previously identified QTL on BTAs 5,14 and 18 for heifer pregnancy and BTAs 8,11 and 22 for antral follicle count were constructed using findhap *** significance of the contrasts between the effects of every two paternally-inherited haplotype alleles were used to identify sires that were heterozygous at each ***-genome sequencing data localized to the haplotypes from six sires and 20 other ancestors were used to identify sequence variants that were concordant with the haplotype *** analyses were applied to these variants using KEGG and MeSH ***:A total of six(BTA 5),six(BTA 14)and five(BTA 18)sires were heterozygous for heifer pregnancy QTL whereas six(BTA 8),fourteen(BTA 11),and five(BTA 22)sires were heterozygous for number of antral follicles’*** to inadequate representation of many haplotype alleles in the sequenced animals,fine mapping analysis could only be reliably performed for the QTL on BTA 5 and 14,which had 641 and 3733 concordant candidate sequence variants,*** KEGG“Circadian rhythm”and“Neurotrophin signaling pathway”were significantly associated with the genes in the QTL on BTA 5 whereas 32 MeSH terms were associated with the QTL on BTA *** the concordant sequence variants,0.2%and 0.3%were classified as missense variants for BTAs 5 and 14,respe

关键词： Antral follicles Causal variants Haplotype Heifer pregnancy WGS

Estimates of genomic inbreeding and identification of candidate regions that differ between Chinese indigenous sheep breeds

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journal of Animal Science and Biotechnology 2022年第1期13卷 52-65页

作者： jiaxin Liu Liangyu Shi Yang Li Liang Chen dorian garrick Lixian Wang Fuping Zhao Key Laboratory of Animal Genetics Breeding and Reproduction(Poultry)of Ministry of AgricultureInstitute of Animal SciencesChinese Academy of Agricultural SciencesBeijing 100193China The Affiliated High School of Peking University Beijing 100192China A.L.Rae Centre of Genetics and Breeding Massey UniversityHamilton 3240New Zealand

Background:A run of homozygosity(ROH)is a consecutive tract of homozygous genotypes in an individual that indicates it has inherited the same ancestral haplotype from both *** inbreeding can be quantified based on *** regions enriched with ROH may be indicative of selection sweeps and are known as ROH *** carried out ROH analyses in five Chinese indigenous sheep breeds;Altay sheep(n=50 individuals),Large-tailed Han sheep(n=50),Hulun Buir sheep(n=150),Short-tailed grassland sheep(n=150),and Tibetan sheep(n=50),using genotypes from an Ovine Infinium HD SNP ***:A total of 18,288 ROH were *** average number of ROH per individual across the five sheep breeds ranged from 39(Hulun Buir sheep)to 78(Large-tailed Han sheep)and the average length of ROH ranged from 0.929 Mb(Hulun Buir sheep)to 2.544 Mb(Large-tailed Han sheep).The effective population size(Ne)of Altay sheep,Large-tailed Han sheep,Hulun Buir sheep,Short-tailed grassland sheep and Tibetan sheep were estimated to be 81,78,253,238 and 70 five generations *** highest ROH-based inbreeding estimate(FROH)was 0.0808 in Large-tailed Han sheep,whereas the lowest F_(ROH)was 0.0148 in Hulun Buir ***,the highest proportion of long ROH fragments(>5 Mb)was observed in the Large-tailed Han sheep breed which indicated recent *** total,49 ROH islands(the top 0.1% of the SNPs most commonly observed in ROH)were identified in the five sheep *** ROH islands were common to all the five sheep breeds,and were located on OAR2:12.2-12.3 Mb,OAR12:78.4-79.1 Mb and OAR13:53.0-53.6 *** breed-specific ROH islands were observed in Altay sheep(OAR15:3.4-3.8 Mb),Large-tailed Han sheep(ORA17:53.5-53.8 Mb)and Tibetan sheep(ORA5:19.8-20.2 Mb).Collectively,the ROH islands harbored 78 unique genes,including 19 genes that have been documented as having associations with tail types,adaptation,growth,body size,reproduction or immune ***:Different

关键词： Candidate genes Genomic inbreeding coefficient ROH islands Runs of homozygosity Sheep

Genetic gain and inbreeding from simulation of different genomic mating schemes for pig improvement

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journal of Animal Science and Biotechnology 2023年第4期14卷 1363-1376页

作者： Fuping Zhao Pengfei Zhang Xiaoqing Wang Deniz Akdemir dorian garrick jun He Lixian Wang Key Laboratory of Animal Genetics Breeding and Reproduction(Poultry)of Ministry of Agriculture and Rural AffairsInstitute of Animal ScienceChinese Academy of Agricultural SciencesBeijing 100193China Center for Blood and Marrow Transplant Research MinneapolisMNUSA. AL Rae Centre for Genetics and Breeding Massey UniversityHamilton 3240New Zealand College of Animal Science and Biotechnology Hunnan Agricultural UniversityChangsha 410128China

Background Genomic selection involves choosing as parents those elite individuals with the higher genomic estimated breeding values(GEBV)to accelerate the speed of genetic improvement in domestic *** after multi-generation selection,the rate of inbreeding and the occurrence of homozygous harmful alleles might increase,which would reduce performance and genetic *** mitigate the above problems,we can utilize genomic mating(GM)based upon optimal mate allocation to construct the best genotypic combinations in the next *** this study,we used stochastic simulation to investigate the impact of various factors on the efficiencies of GM to optimize pairing combinations after genomic selection of candidates in a pig *** factors included:the algorithm used to derive inbreeding coefficients;the trait heritability(0.1,0.3 or 0.5);the kind of GM scheme(focused average GEBV or inbreeding);the approach for computing the genomic relationship matrix(by SNP or runs of homozygosity(ROH)).The outcomes were compared to three traditional mating schemes(random,positive assortative or negative assortative matings).In addition,the performance of the GM approach was tested on real datasets obtained from a Large White pig breeding *** Genomic mating outperforms other approaches in limiting the inbreeding accumulation for the same expected genetic *** use of ROH-based genealogical relatedness in GM achieved faster genetic gains than using relatedness based on individual *** GROH-based GM schemes with the maximum genetic gain resulted in 0.9%-2.6%higher rates of genetic gainΔG,and 13%-83.3%lowerΔF than positive assortative mating regardless of *** rates of inbreeding were always the fastest with positive assortative *** from a purebred Large White pig population,confirmed that GM with ROH-based GRM was more efficient than traditional mating *** Compared with traditional mating schemes,genomic

关键词： Genetic gain Genomic mating Genomic selection Inbreeding Pig

Genome-wide association studies of lactation yields of milk, fat, protein and somatic cell score in New Zealand dairy goats

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journal of Animal Science and Biotechnology 2020年第4期11卷 937-949页

作者： Megan Scholtens Andrew jiang Ashley Smith Mathew Littlejohn Klaus Lehnert Russell Snell Nicolas Lopez-Villalobos dorian garrick Hugh Blair AL Rae Centre for Genetics and Breeding School of AgricultureMassey UniversityPalmerston NorthNew Zealand Applied Translational Genetics Group School of Biological SciencesThe University of AucklandAucklandNew Zealand Research and Development Livestock Improvement CorporationRuakura RoadHamiltonNew Zealand.

Background: Identifying associations between genetic markers and traits of economic importance will provide practical benefits for the dairy goat industry, enabling genomic prediction of the breeding value of individuals, and facilitating discovery of the underlying genes and mutations. Genome-wide association studies were implemented to detect genetic regions that are significantly associated with effects on lactation yields of milk(MY), fat(FY),protein(PY) and somatic cell score(SCS) in New Zealand dairy ***: A total of 4,840 goats were genotyped with the Caprine 50 K SNP chip(Illumina Inc., San Diego, CA).After quality filtering, 3,732 animals and 41,989 SNPs were analysed assuming an additive linear model. Four GWAS models were performed, a single-SNP additive linear model and three multi-SNP Bayes C models. For the single-SNP GWAS, SNPs were fitted individually as fixed covariates, while the Bayes C models fit all SNPs simultaneously as random effects. A cluster of significant SNPs were used to define a haplotype block whose alleles were fitted as covariates in a Bayesian model. The corresponding diplotypes of the haplotype block were then fit as class variables in another Bayesian ***: Across all four traits, a total of 43 genome-wide significant SNPs were detected from the SNP GWAS. At a genome-wide significance level, the single-SNP analysis identified a cluster of variants on chromosome 19 associated with MY, FY, PY, and another cluster on chromosome 29 associated with SCS. Significant SNPs mapped in introns of candidate genes(45%), in intergenic regions(36%), were 0–5 kb upstream or downstream of the closest gene(14%) or were synonymous substitutions(5%). The most significant genomic window was located on chromosome 19 explaining up to 9.6% of the phenotypic variation for MY, 8.1% for FY, 9.1% for PY and 1% for ***: The quantitative trait loci for yield traits on chromosome 19 confirms reported findings in other dairy goat p

关键词： Dairy goat GWAS Milk production New Zealand QTL

The evolving role of Fourier-transform midinfrared spectroscopy in genetic improvement of dairy cattle

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journal of Animal Science and Biotechnology 2020年第3期11卷 626-638页

作者： K.M.Tiplady T.j.Lopdell M.D.Littlejohn D.j.garrick research and development livestock improvement corporationprivate bag 3016hamilton 3240new zealand school of agriculture massey universityruakurahamilton 3240new zealand

Over the last 100 years,significant advances have been made in the characterisation of milk composition for dairy cattle improvement *** progress has enabled a shift from labour intensive,on-farm collection and processing of samples that assess yield and fat levels in milk,to large-scale processing of samples through centralised laboratories,with the scope extended to include quantification of other ***-transform midinfrared(FT-MIR)spectroscopy has had a significant role in the transformation of milk composition phenotyping,with spectral-based predictions of major milk components already being widely used in milk payment and animal evaluation systems ***,there is interest in analysing the individual FT-MIR wavenumbers,and in utilising the FT-MIR data to predict other novel traits of importance to breeding *** includes traits related to the nutritional value of milk,the processability of milk into products such as cheese,and traits relevant to animal health and the *** ability to successfully incorporate these traits into breeding programs is dependent on the heritability of the FT-MIR predicted traits,and the genetic correlations between the FT-MIR predicted and actual trait *** FT-MIR predicted traits to the underlying mutations responsible for their variation can be difficult because the phenotypic expression of these traits are a function of a diverse range of molecular and biological mechanisms that can obscure their genetic *** individual FT-MIR wavenumbers give insights into the chemical composition of milk and provide an additional layer of granularity that may assist with establishing causal links between the genome and observed ***,there are other molecular phenotypes such as those related to the metabolome,chromatin accessibility,and RNA editing that could improve our understanding of the underlying biological systems controlling traits of ***

关键词： Bovine milk Cattle breeding genetics Fourier-transform infrared spectroscopy Trait prediction

Enhancement of hydroxyapatite dissolution through structure modification by Krypton ion irradiation

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journal of Materials Science & Technology 2020年第3期38卷 148-158页

作者： Hui Zhu Dagang Guo Hang Zang dorian AHHanaor Sen Yu Franziska Schmidt Kewei Xu State Key Laboratory for Mechanical Behavior of Materials School of Material Science and EngineeringXi’an Jiaotong UniversityXi’an710049China School of Nuclear Science and Technology Xi’an Jiaotong UniversityXi’an710049China Fachgebiet Keramische Werkstoffe/Chair of Advanced Ceramic Materials Institut für Werkstoffwissenschaften und-TechnologienTechnische Universit?t BerlinHardenbergstra?e 4010623BerlinGermany Shaanxi Key Laboratory of biomedical metal materials Northwest Institute for Non-ferrous Metal ResearchXi’an710016China

Hydroxyapatite(HA)synthesized by a wet chemical route was subjected to heavy ion irradiation,using4 Me V Krypton ion(Kr17+)with ion fluence ranging from 1×1013 to 1×1015 ions/*** incidence X-ray diffraction(GIXRD)results confirmed the phase purity of irradiated HA with a moderate contraction in lattice parameters,and further indicated the irradiation-induced structural disorder,evidenced by broadening of the diffraction ***-resolution transmission electron microscopy(HRTEM)observations indicated that the applied Kr irradiation induced significant damage in the hydroxyapatite ***,cavities were observed with their diameter and density varying with the irradiation fluences,while a radiation-induced crystalline-to-amorphous transition with increasing ion dose was *** and X-ray photoelectron spectroscopy(XPS)analysis further indicated the presence of irradiationinduced *** release from pristine and irradiated materials following immersion in Tris(p H 7.4,37?)buffer showed that dissolution in vitro was enhanced by irradiation,reaching a peak at 0.1 *** examined the effects of irradiation on the early stages of the mouse osteoblast-like cells(MC3 T3-E)response.A cell counting kit-8 assay(CCK-8 test)was carried out to investigate the cytotoxicity of samples,and viable cells can be observed on the irradiated materials.

关键词： High energy heavy ion irradiation Hydroxyapatite HRTEM Crystal defects In vitro dissolution Cell compatibility