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United States Department of Agriculture

Agricultural Research Service

Animal Selection & Heterosis
item Explorations in genome-wide association studies and network analyses with dairy cattle fertility traits (Aug 2016)
item Sexed-semen usage for Holstein AI in the United States (Jul 2016)
item Exploring the feasibility of using copy number variants as genetic markers through large-scale whole genome sequencing experiments (Jul 2016)
item Use of a threshold animal model to estimate calving ease and stillbirth (co)variance components for US Holsteins (Jul 2016)
item Improving fertility of dairy cattle using translational genomics (Jul 2016)
item Strategy for incorporating newly discovered causative genetic variants into genomic evaluations (Jul 2016)
item Breed base representation in dairy animals of 5 breeds (Jul 2016)
item Single-step GBLUP using APY inverse for protein yield in US Holstein with a large number of genotyped animals (Jul 2016)
item Genetic solutions to infertility caused by heat stress (Jul 2016)
item Genetic analysis of superovulation and embryo transfer traits in Holstein cattle (Jul 2016)
item Selection of sequence variants to improve dairy cattle genomic predictions (Jul 2016)
item Genomic analysis of lactation persistency in four breeds of dairy cattle (Jul 2016)
item Identifying and calling insertions, deletions, and single-base mutations efficiently from sequence data (Jul 2016)
item Genetic evaluation of dairy cow livability (Jul 2016)
item Genetic architecture of feed efficiency in mid-lactation Holstein dairy cows (Jul 2016)
item Reducing animal sequencing redundancy by preferentially selecting animals with low-frequency haplotypes (Jul 2016)
item Genomic evaluation, breed identification, and population structure of Guernsey cattle in North America, Great Britain, and the Isle of Guernsey (Jul 2016)
item Across-breed EPD tables for the year 2016 adjusted to breed differences for birth year of 2014 (Jun 2016)
item Mean EPDs reported by different breeds (Jun 2016)
item Selection enhanced estimates of marker effects on means and variances of beef tenderness (Jun 2016)
item Performance of selected eastern oyster lines across northeastern US estuaries (Jun 2016)
item Successful production of Nile and blue tilapia fry - findings based on degree days and demonstrated for earthen ponds in subtropical climates (Jun 2016)
item The channel catfish genome sequenc provides insights into the evolution of scale formation in teleosts (Jun 2016)
item Sharing reference data and including cows in the reference population improve genomic predictions in Danish Jersey (Jun 2016)
item Use of single nucleotide polymorphisms in candidate genes associated with daughter pregnancy rate for prediction of genetic merit for reproduction in Holstein cows (Jun 2016)
item Increasing the number of single nucleotide polymorphisms used in genomic evaluation of dairy cattle (Jun 2016)
item Functional characterization of the turkey macrophage migration inhibitory factor (Jun 2016)
item Draft genome sequence of Aeromonas hydrophila TN97-08 (May 2016)
item Genome sequence of the fish pathogen Flavobacterium columnare genomovar II strain 94-081 (May 2016)
item Breed effects and genetic parameter estimates for calving difficulty and birth weight in a multi-breed population (May 2016)
item Genomic selection in multi-breed dairy cattle populations (Apr 2016)
item An integrated genetic linkage map and comparative genome analysis for the estuarine Atlantic killifish, Fundulus heteroclitus (Mar 2016)
item Vaccination of full-sib channel catfish families against enteric septicemia of catfish with an oral live attenuated Edwardsiella ictaluri vaccine (Mar 2016)
item Low-intensity, stocker-based channel catfish culture (Mar 2016)
item A non-lethal means to identify spermiating D&B strain of blue catfish, Ictalurus furcatus (Mar 2016)
item Influence of fertilizing water pH on the hatching success of stripped channel catfish eggs on channel x blue hybrid catfish embryo production in hatcheries (Mar 2016)
item Biofloc production technology promising in temperate zones – Channel catfish perform during winter months (Mar 2016)
item Estimates of epistatic and pleiotropic effects of casein alpha s1 (CSN1S1) and thyroglobulin (TG) genetic markers on beef heifer performance traits enhanced by selection (Mar 2016)
item Practical implications for genetic modeling in the genomics era (Mar 2016)
item Using genomics to enhance selection of novel traits in North American dairy cattle (Mar 2016)
item Ultrasound use for body composition and carcass quality assessment in cattle and lambs (Feb 2016)
item Influence of strain of sire on channel x blue F1 hybrid catfish embryo production and fingerling performance under commercial farm conditions. (Feb 2016)
item Effects of vitamin C on percent neurulation, hatch, growth, and survival of hybrid catfish challenged with virulent Edwardsiella ictaluri (Feb 2016)
item Potency of blue catfish, Ictalurus furcatus (individual vs pooled) sperm to fertilize stripped channel catfish, I. punctatus eggs on the production and performance of progeny (Feb 2016)
item Benchmarking dairy herd health status using routinely recorded herd summary data (Feb 2016)
item Improving the goat long-read assembly with optical mapping (Jan 2016)
item Dissecting non-additive genetic effects for production and reproductive traits in dairy cattle (Jan 2016)
item Effect of sex, age, and breed on genetic recombination features in cattle (Jan 2016)
item Fast single-pass alignment and variant calling using sequencing data (Jan 2016)
item A sensitive method for detecting and genotyping Cryptosporidium parvum oocysts (Dec 2015)
item Genetics | Selection: Evaluation and Methods (Dec 2015)
item A simple strategy for managing many recessive disorders in a dairy cattle breeding program (Nov 2015)
item Optimizing fish meal-free commercial diets for Nile Tilapia, Oreochromis niloticus (Nov 2015)
item Cattle sex-specific recombination and genetic control from a very large pedigree (Nov 2015)
item Accounting for discovery bias in genomic EPD (Nov 2015)
item Measuring feed intake and BRD susceptibility:BIF guidelines (Nov 2015)
item Early innate immune response of immune proteins in juvenile channel catfish Ictalurus punctatus (Nov 2015)
item Complete genome sequence of an Edwardsiella piscicida-like species recovered from tilapia in the United States (Sep 2015)
item Tet-mediated imprinting erasure in H19 locus following reprogramming of spermatogonial stem cells to induced pluripotent stem cells (Sep 2015)
item Comparison of domestic and foreign genotypes by country and continent (Aug 2015)
item Re-examination of service-sire conception rates in the United States (Aug 2015)
item Strategies to choose from millions of imputed sequence variants (Aug 2015)
item Genomic evaluations and breed composition for crossbred U.S. dairy cattle (Aug 2015)
item Revisiting the “a posteriori” granddaughter design (Aug 2015)
item Recent improvements in catfish hatcheries not only changed the type of catfish to be raised but also how they are raised (Aug 2015)
item Markers associated with disease resistance in Eastern oysters, Crassostrea virginica (Aug 2015)
item Characterization of phenotypic variation for dermo resistance among selectively-bred families of the Eastern oyster, Crassostrea virginica (Aug 2015)
item Single nucleotide polymorphisms associated with thermoregulation in lactating dairy cows exposed to heat stress (Jul 2015)
item Dietary nutrients, additives, and fish health (Jul 2015)
item Minerals (Jul 2015)
item Fast imputation using medium or low-coverage sequence data (Jul 2015)
item Identification of differentially regulated proteins of Edwardsiella ictaluri during iron restriction (Jul 2015)
item Genetic interactions for heat stress and production level: predicting foreign from domestic data (Jul 2015)
item Assignment of polled status using single nucleotide polymorphism genotypes and predicted gene content (Jul 2015)
item Effect of increasing the number of single-nucleotide polymorphisms from 60,000 to 85,000 in genomic evaluation of Holsteins (Jul 2015)
item Selection signature analysis in Holstein cattle identified genes known to affect reproduction (Jul 2015)
item Animal selection for whole genome sequencing by quantifying the unique contribution of homozygous haplotypes sequenced (Jul 2015)
item Single nucleotide polymorphisms in specific candidate genes are associated with phenotypic differences in days open for first lactation in Holstein cows (Jul 2015)
item Practical implications for genetic modeling in the genomics era for the dairy industry (Jul 2015)
item Identification of copy number variable gene families in Holstein and Jersey cattle (Jul 2015)
item Effects of maternal lines and mating systems on susceptibility to parasitism in a pasture-lambing, low-input production system (Jul 2015)
item Genome-wide association study of fertility traits in dairy cattle using high-density single nucleotide polymorphism marker panels (Jul 2015)
item Identification of gene networks underlying dystocia in dairy cattle (Jul 2015)
item Using routinely recorded herd data to predict and benchmark herd and cow health status (Jul 2015)
item Genomic evaluation, breed identification, and population structure of North American, English and Island Guernsey dairy cattle (Jul 2015)
item Genetic variance and covariance components for feed intake, average daily gain, and postweaning gain in growing beef cattle (Jul 2015)
item RAPTR-SV: a hybrid method for the detection of structural variants (Jun 2015)
item Complete genome sequence of Edwardsiella tarda (isolate FL95-01)recovered from channel catfish (Jun 2015)
item Innate immune responses of immune proteins in juvenile channel catfish (May 2015)
item Hydrolysates from scallop and squid processing byproducts as specialty aquafeed ingredients (May 2015)
item Expression of an antimicrobial peptide, digestive enzymes and nutrient transporters in the intestine of E. praecox-infected chickens (May 2015)
item The use of –omic tools in the study of disease processes in marine bivalves (May 2015)
item Developing tools for the study of molluscanimmunity: The sequencing of the genome of the eastern oyster, Crassostreavirginica (May 2015)
item Characterization of the Eimeria maxima sporozoite surface protein IMP1 (May 2015)
item Genomic prediction of disease occurrence using producer-recorded health data: A comparison of methods (May 2015)
item Effect of reference population size and available ancestor genotypes on imputation of Mexican Holstein genotypes (May 2015)
item Short communication: Improving accuracy of Jersey genomic evaluations in the United States and Denmark by sharing reference population bulls (May 2015)
item Complete genome sequence of Aeromonas hydrophila AL06-06 (Apr 2015)
item Short communication: Analysis of genomic predictor population for Holstein dairy cattle in the United States – Effects of sex and age (Apr 2015)
item Expression of digestive enzymes and nutrient transporters in Eimeria-challenged broilers (Mar 2015)
item Inhibition of CD23-mediated IgE transcytosis suppresses the initiation and development of airway allergic inflammation (Mar 2015)
item Impact of genomic collaboration and the need to continually improve methods (Mar 2015)
item Rapid calculation of genomic evaluations for new animals (Mar 2015)
item A genome-wide association study for clinical mastitis in first parity US Holstein cows using a single-step approach and a genomic matrix re-weighting procedure (Feb 2015)
item Dissection of genomic correlation matrices of US Holsteins using multivariate factor analysis (Feb 2015)
item Invited review: overview of new traits and phenotyping strategies in dairy cattle with a focus on functional traits (Feb 2015)
item Genetic effects on birth weight in reciprocal Brahman-Simmental crossbred calves (Feb 2015)
item Assessment of autozygosity in Nellore cows (Bos indicus) through high-density SNP genotypes (Jan 2015)
item Potential use of the invasive European green crab (Carcinus maenas) as an ingredient in Atlantic Salmon (Salmo salar) diets; a preliminary analysis (Jan 2015)
item Selection responses for caracass weight in four Atlantic Salmon year classes (Jan 2015)
item selectSNP – An R package for selecting SNPs optimal for genetic evaluation (Jan 2015)
item The use of PacBio and Hi-C data in denovo assembly of the goat genome (Jan 2015)
item Comparison of CNVs in Buffalo with other species (Jan 2015)
item Incidence of infection in 39-month-old ewes with TMEM154 diplotypes "1 1," "1 3," and "3 3" after natural exposure to ovine progressive pneumonia virus (Jan 2015)
item Estimation of breed-specific heterosis effects for birth, weaning, and yearling weight in cattle (Jan 2015)
item Genetic improvement of dairy cattle (Jan 2015)
item A rapid method for determining salinomycin and monensin sensitivity in Eimeria tenella (Dec 2014)
item ICAR guidelines for recording, evaluation and genetic improvement of female fertility in dairy cattle (Dec 2014)
item Use of robust multivariate linear mixed models for estimation of genetic parameters for carcass traits in beef cattle (Dec 2014)
item Comparison of single-trait to multi-trait national evaluations for yield, health, and fertility (Dec 2014)
item CAPN1, CAST, and DGAT1 genetic effects on preweaning performance, carcass quality traits, and residual variance of tenderness in a beef cattle population selected for haplotype and allele equalization (Dec 2014)
item Protection of non-immunized broiler chicks housed with immunized cohorts against infection with Eimeria maxima and E. acervulina (Nov 2014)
item Genetic base changes for December 2014 (Oct 2014)
item Evaluation of an experimental irradiated oocysts vaccine to protect broiler chicks against avian coccidosis (Oct 2014)
item Expression of nutrient transporters in duodenum, jejunum and ileum of Eimeria maxima- infected broiler chickens (Oct 2014)
item Net merit as a measure of lifetime profit: 2014 revision (Oct 2014)
item Use of ultrasound scanning and body condition score to evaluate composition traits in mature beef cows (Sep 2014)
item Beef cattle body temperature during climatic stress: a genome-wide association study (Aug 2014)
item Is there a genetic solution to bovine respiratory disease complex? (Aug 2014)
item Large effects on birth weight follow inheritance pattern consistent with gametic imprinting and X chromosome (Aug 2014)
item Selection enhanced estimates of µ-calpain, calpastatin, and dacylglycerol O-acyltransferase 1 genetic effects on pre-weaning performance, carcass quality traits, and residual variance of tenderness in composite ... cattle (Aug 2014)
item Including cow information in genomic prediction of Holstein dairy cattle in the US (Aug 2014)
item Using haplotypes to unravel the inheritance of Holstein coat color for a larger audience (Aug 2014)
item Increasing the number of single nucleotide polymorphisms used in genomic evaluations of dairy cattle (Aug 2014)
item Approximation of reliability of direct genomic breeding values (Aug 2014)
item Single nucleotide polymorphisms in candidate genes related to daughter pregnancy rate in Holstein cows (Aug 2014)
item The hunt for a functional mutation affecting conformation and calving traits on chromosome 18 in Holstein cattle (Aug 2014)
item Using the whole read: structural variant detection using NGS data (Aug 2014)
item Improving genomic prediction for Danish Jersey using a joint Danish-US reference population (Aug 2014)
item Fast imputation using medium- or low-coverage sequence data (Aug 2014)
item Impact of adding foreign genomic information on Mexican Holstein imputation (Aug 2014)
item Increasing predictive ability using dominance in genomic selection (Aug 2014)
item Improvement of prediction ability for genomic selection of dairy cattle by including dominance effects (Aug 2014)
item The development of genomics applied to dairy breeding (Aug 2014)
item Multi-trait, multi-breed conception rate evaluations (Jul 2014)
item Calculation and delivery of US genomic evaluations for dairy cattle (Jul 2014)
item Determination of single nucleotide polymorphisms associated with subclinical ketosis in Jersey cattle (Jul 2014)
item An updated version of lifetime net merit incorporating additional fertility traits and new economic values (Jul 2014)
item Systems biology approaches to understanding conceptus elongation and early pregnancy loss (Jul 2014)
item Development of a lifetime merit-based selection index for US dairy grazing systems (Jul 2014)
item Salinity effects on Atlantic sturgeon growth and osmoregulation (Jun 2014)
item Genomic evaluation, breed identification, and discovery of a haplotype affecting fertility for Ayrshire dairy cattle (Jun 2014)
item Genotypes are useful for more than genomic evaluation (May 2014)
item Genotypes are useful for more than genomic evaluation (May 2014)
item Expression of digestive enzymes and nutrient transporters in Eimeria acervulina-challenged layers and broilers (May 2014)
item Short communication: Use of young bulls in the United States (May 2014)
item A genome-wide association study of calf birth weight in Holstein cattle using single nucleotide polymorphisms and phenotypes predicted from auxiliary traits (May 2014)
item Genomic selection for producer-recorded health event data in US dairy cattle (May 2014)
item Application of the a posteriori granddaughter design to the Holstein genome (Apr 2014)
item Genetic evaluation of stillbirth in US Brown Swiss and Jersey cattle (Apr 2014)
item Accuracy of genomic predictions in Bos indicus (Nellore) cattle (Feb 2014)
item The challenges and importance of structural variation detection in livestock (Feb 2014)
item Increasing long-term response by selecting for favorable minor alleles (Feb 2014)
item µ-Calpain, calpastatin, and growth hormone receptor genetic effects on preweaning performance, carcass quality traits, and residual variance of tenderness in Angus cattle selected to increase minor haplotype ... frequencies (Feb 2014)
item The use of population-scale sequencing to identify CNVs impacting productive traits in different cattle breeds (Jan 2014)
item Candidate causative mutation on BTA18 associated with calving and conformation traits in Holstein bulls (Jan 2014)
item Mating programs including genomic relationships and dominance effects (Dec 2013)
item Effects of TMEM154 haplotypes 1 and 3 on susceptibility to ovine progressive pneumonia virus following natural exposure in sheep (Nov 2013)
item Modulation of the intestinal environment, innate immune response, and barrier function by dietary threonine and purified fiber during a coccidiosis challenge in broiler chicks (Nov 2013)
item Different susceptibilities of Eimeria acervulina, Eimeria maxima, and Eimeria tenella oocysts to dessication (Oct 2013)
item Increased efficacy of Eimeria oocysts delivery by gel beads or spray vaccination (Sep 2013)
item Increasing long term response by selecting for favorable minor alleles (Sep 2013)
item Measuring genomic pre-selection in theory and in practice (Sep 2013)
item Random forests approach for identifying additive and epistatic single nucleotide polymorphisms associated with residual feed intake in dairy cattle (Aug 2013)
item Application of a posteriori granddaughter and modified granddaughter designs to determine Holstein haplotype effects (Aug 2013)
item Single nucleotide polymorphisms in candidate genes associated with fertilizing ability of sperm and subsequent embryonic development in cattle (Jul 2013)
item Genome-wide association mapping for identification of quantitative trait loci for rectal temperature during heat stress in Holstein cattle (Jul 2013)
item Genetic relationships among milk production and teat and udder scores in cows sired by seven prominent beef cattle breeds (Jul 2013)
item CAPN1 and GDF8 genetic marker effects on heifer performance, reproduction, and first calf performance traits in beef cattle (Jul 2013)
item Heritability estimates of performance and health traits of Holstein calves (Jul 2013)
item Using 90,113 single nucleotide polymorphisms in genomic evaluation of dairy cattle (Jul 2013)
item Breeding for polled dairy cows versus dehorning: Preliminary cost assessments & discussion (Jul 2013)
item Application of a posteriori granddaughter and modified granddaughter designs to determine Holstein haplotype effects (Jul 2013)
item Analysis of health trait data from on-farm computer systems in the U.S. I: Pedigree and genomic variance components estimation (Jul 2013)
item Dissection of genomic correlation matrices using multivariate factor analysis in dairy and dual-purpose cattle breeds (Jul 2013)
item Mating programs including genomic relationships (Jul 2013)
item Trends in noncompliance with milk quality standards for Dairy Herd Improvement herds in the United States (Jul 2013)
item Genomic evaluation and identification of haplotype affecting fertility for Ayrshire dairy cattle (Jul 2013)
item Tools to exploit sequence data to find new markers and disease loci in dairy cattle (Jul 2013)
item Optimal age at first calving for U.S. dairy cattle (Jul 2013)
item Regression metamodels of an optimal genomic testing strategy in dairy cattle when selection intensity is low (Jul 2013)
item Analysis of health trait data from on-farm computer systems in the U.S. II: Comparison of genomic analyses including two-stage and single-step methods (Jul 2013)
item We are making inroads on health and fitness traits (Jul 2013)
item Discovery of single nucleotide polymorphisms in candidate genes associated with fertility and production traits in Holstein cattle (Jun 2013)
item The use of dual-energy X-ray absorptiometry (DEXA) to assess the impact of Eimeria infections in broiler chicks (Jun 2013)
item Genomic evaluation of health traits in dairy cattle (May 2013)
item Standardization of health data – ICAR guidelines including health key (May 2013)
item Challenges and opportunities for farmer-recorded data in health and welfare selection (May 2013)
item Mating programs including genomic relationships and dominance effects (Apr 2013)
item Open source tools to exploit DNA sequence data from livestock species (Apr 2013)
item Changes in expression of CWC15 during preimplantation development in the bovine embryo (Apr 2013)
item Estimation of genetic marker effects for CAPN1, CAST, and GHR on carcass quality traits in Angus cattle selected to increase minor marker frequencies (Mar 2013)
item Development and applications of low-cost, high-throughput genotyping (Mar 2013)
item Systems Biology in Animal Breeding: Identifying relationships among markers, genes, and phenotypes (Feb 2013)
item Low density marker assays (LDMA) for high throughput, highly multiplexed detection, CNV, methylation, and expression assays (Jan 2013)
item Low-cost genotyping by next generation sequencing: Next generation genotyping (Jan 2013)
item Development of low-cost, high-throughput genotyping to complement SNP discovery by individual animal whole-genome sequencing (Jan 2013)
item Molecular characterization and immunological roles of avian IL-22 and its soluble receptor IL-22 binding protein (Sep 2012)
Last Modified: 9/20/2013
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