G.R. Wiggans

G.R. Wiggans
Council on Dairy Cattle Breeding

About

280
Publications
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Introduction
Skills and Expertise

Publications

Publications (280)
Article
Full-text available
The present study aimed to estimate covariance components of milk fatty acids (FA) and to compare the genomic estimated breeding values under general and heat-stress effects. Data consisted of 38,762 test-day records from 6,344 Holstein cows obtained from May 2012 through January 2018 on 4 dairy herds from Brazil. Single-trait repeatability test-da...
Article
Genomic evaluations are useful for crossbred as well as purebred populations when selection is applied to commercial herds. Dairy farmers had already spent more than $1 million to genotype over 32,000 crossbred animals before US genomic evaluations became available for those animals. Thus, new tools were needed to provide accurate genomic predictio...
Article
Advances in the molecular area of selection have expanded knowledge of the genetic architecture of complex traits through genome-wide association studies (GWAS). Several GWAS have been performed so far, but confirming these results is not always possible due to several factors, including environmental conditions. Thus, our objective was to identify...
Article
Genealogical information is an essential tool for carrying out any genetic improvement program. The objective of this study was to determine the accuracy of pedigree information in the Mexican registered Holstein population using genomic data available in Mexico and for the US Holstein population. The study included 7,508 animals (158 sires and 7,3...
Article
Experimental designs that exploit family information can provide substantial predictive power in quantitative trait nucleotide discovery projects. Concordance between quantitative trait locus genotype as determined by the a posteriori granddaughter design and marker genotype was determined for 30 trait-by-chromosomal segment effects segregating in...
Article
The objective of this study was to identify genomic regions and candidate genes associated with feed efficiency in lactating Holstein cows. In total, 4,916 cows with actual or imputed genotypes for 60,671 single nucleotide polymorphisms having individual feed intake, milk yield, milk composition, and body weight records were used in this study. Cow...
Chapter
This article describes the procedures used for collecting and analyzing data for genetic improvement of dairy cattle. Methods of identification and milk recording are presented. Selection traits include production (milk, fat, and protein yields and component percentages), conformation (final score and linear type traits), fitness (mastitis, longevi...
Article
Full-text available
Genomic selection has revolutionized dairy cattle breeding. Since 2000, assays have been developed to genotype large numbers of single-nucleotide polymorphisms (SNPs) at relatively low cost. The first commercial SNP genotyping chip was released with a set of 54,001 SNPs in December 2007. Over 15,000 genotypes were used to determine which SNPs shoul...
Article
Full-text available
This study compares how different cow genotyping strategies increase the accuracy of genomic estimated breeding values (EBV) in dairy cattle breeds with low numbers. In these breeds, few sires have progeny records, and genotyping cows can improve the accuracy of genomic EBV. The Guernsey breed is a small dairy cattle breed with approximately 14,000...
Article
Full-text available
Low-density (LD) single nucleotide polymorphism (SNP) arrays provide a cost-effective solution for genomic prediction and selection, but algorithms and computational tools are needed for the optimal design of LD SNP chips. A multiple-objective, local optimization (MOLO) algorithm was developed for design of optimal LD SNP chips that can be imputed...
Data
selectSNP Vignette V1.1 This is the vignette for the selectSNP package (trial version 1.1). (PDF)
Data
Imputation accuracy from three sets of 6K SNP genotypes to 80K genotypes in U.S. Holstein animals. The reference population for imputation consisted of 7,012 Holstein animals, each genotyped by GGPHD 80K SNPs and the validation set had 2,639 Holstein animals also with 80K genotypes. For the purpose of evaluation imputation error, only selected 6K g...
Data
Composition (i.e., number of SNPs) of the common-variant 24K bovine SNP chip for seven cattle breeds. Holstein is a dairy cattle breed, and the remaining six are all beef breeds. The base and the backbone consisted of SNPs common to the seven cattle breeds. The number of SNPs selected for each category is listed by its category name (e.g., Limousin...
Data
Summary of maps for the 50K vs. 24K bovine SNP chips. The column names are nLoci (number of SNPs on each chromosome), Length (physical map length, in base pairs, of each chromosome), max.bw (maximum gap, in base pairs, on each chromosome). Chromosome 30 stands for X Chromosome. (DOCX)
Data
Summary of the GGPHD 80K bovine SNP chip. The column names are N (number of SNPs per chromosome), and mean, SD (standard deviation), Min (minimum value), and Max (maximum value) of SNP spacing, where SNP spacing is defined as the map distance in base pairs between two adjacent SNPs on each chromosome. (DOCX)
Data
Genomic prediction accuracy using three subsets of 6K SNP genotypes, imputed 80K genotypes, and original 80K genotypes, respectively, in 2,639 U.S. Holstein animals. SNP effects for genomic prediction were estimated on original 80K SNP genotypes in the reference population of 7,012 Holstein animals. Genomic prediction accuracy for three quantitativ...
Data
Percentages of SNP variance on the three traits for the three 6K SNP panels. The three quantitative traits were daughter pregnancy rate (DPR), fat yield (FY) and milk yield (MY). Of the three LD 6K SNP panels, the 6KA panel consisted of 5,260 unique SNPs pooled from each of the 2,000 SNPs with the largest SNP variances for each trait. The 6KB panel...
Data
Map view of two LD 6K SNP panels. The 6KA panel consisted of 5,260 unique SNPs pooled from each of the 2,000 SNPs with the largest SNP variances for each trait. The 6KB panel included all the SNPs in the 6KA panel, plus additional 740 SNPs which were optimally selected by the selectSNP package. These SNPs were located on 30 chromosomes, of which Ch...
Data
selectSNP Manual V1.1 This is an users? manual for the selectSNP package (trial version 1.1). (PDF)
Data
Summary statistics of predicted transmitting ability (PTA) for daughter pregnancy rate (DPR), fat yield (FY), and milk yield (MY) in a U.S. Holstein population. The column names are N (sample size), and Min (minimum value), Q1 (25% quantile), Q3 (75% quantile), Max (maximum value), and Mean and SD (standard) deviation) of PTA. (DOCX)
Article
Seven years after the introduction of genomic selection in the United States, it is now possible to evaluate the impact of this technology on the population. Selection differential(s) (SD) and generation interval(s) (GI) were characterized in a four-path selection model that included sire(s) of bulls (SB), sire(s) of cows (SC), dam(s) of bulls (DB)...
Article
Full-text available
As of December 2015, 2,376 Guernsey bulls and cows had genotypes from collaboration between the United States, Canada, the United Kingdom, and the Isle of Guernsey. Of those, 439 bulls and 504 cows had traditional US evaluations, which provided sufficient data to justify investigation of the possible benefits of genomic evaluation for the Guernsey...
Article
Information about genetic parameters is essential for selection decisions and genetic evaluation. These estimates are population specific; however, there are few studies with dairy cattle populations reared under tropical and sub-tropical conditions. Thus, the aim was to obtain estimates of heritability and genetic correlations for milk yield and q...
Article
GeneSeek (Neogen Corp., Lexington, KY) designed a new version of the GeneSeek Genomic Profiler HD BeadChip for Dairy Cattle, which originally had >77,000 single nucleotide polymorphisms (SNP). A set of >140,000 SNP was selected that included all SNP on the existing GeneSeek chip, all SNP used in US national genomic evaluations, SNP that were possib...
Article
The objectives of this paper were to briefly review progress in the genetic evaluation of novel traits in Canada and the United States, assess methods to predict selection accuracy based on cow reference populations, and illustrate how the use of indicator traits could increase genomic selection accuracy. Traits reviewed are grouped into the follow...
Article
Genomic evaluations of dairy cattle became official in the United States in January 2009 for Holsteins and Jerseys, and later for Brown Swiss, Ayrshires, and Guernseys. Up to 33 yield, fitness, calving, and conformation traits are evaluated, and the fertility traits included daughter pregnancy rate and heifer and cow conception rates. Additional fe...
Article
Full-text available
Meiotic recombination is an essential biological process that generates genetic diversity and ensures proper segregation of chromosomes during meiosis. From a large USDA dairy cattle pedigree with over half a million genotyped animals, we extracted 186,927 three-generation families, identified over 8.5 million maternal and paternal recombination ev...
Conference Paper
Full-text available
An updated search for quantitative trait loci (QTLs) in the Holstein genome was conducted using the a posteriori granddaughter design. The number of Holstein sires with ³100 genotyped and progeny-tested sons has increased from the previous 52 to 71 for a total of 14 246 sons. The bovine genome was divided into 621 segments of ~100 markers each. The...
Conference Paper
Full-text available
The use of genomic information has improved the accuracy of estimated breeding values, allowing the selection of young animals with high reliability. This way, the generation interval was reduced and, consequently, the genetic gain was increased. These advantages are particularly applicable for dairy cattle production because of its long generation...
Article
Full-text available
Small reference populations limit the accuracy of genomic prediction in numerically small breeds, such like Danish Jersey. The objective of this study was to investigate two approaches to improve genomic prediction by increasing size of reference population in Danish Jersey. The first approach was to include North American Jersey bulls in Danish Je...
Article
Full-text available
Inbreeding is often an inevitable outcome of strong directional artificial selection but on average it reduces population fitness with increased frequency of recessive deleterious alleles. Runs of homozygosity (ROH) representing genomic autozygosity that occur from mating between selected and genomically related individuals may be able to reveal th...
Article
The effect on prediction accuracy for Jersey genomic evaluations of Danish and US bulls from using a larger reference population was assessed. Each country contributed genotypes from 1,157 Jersey bulls to the reference population of the other. Data were separated into reference (US only, Danish only, and combined US-Danish) and validation (US only...
Article
The effects of reference population size and the availability of information from genotyped ancestors on the accuracy of imputation of single nucleotide polymorphisms (SNP) were investigated for Mexican Holstein cattle. Three scenarios for reference population size were examined: (1) a local population of 2,011 genotyped Mexican Holsteins, (2) anim...
Article
Increased computing time for the ever-growing predictor population and linkage decay between the ancestral population and current animals have become concerns for genomic evaluation systems. The effects on reliability of US genomic evaluations from including cows and bulls in the Holstein predictor population and also from excluding older bulls fro...
Book
Genetic improvement of dairy cattle . Chapter 15
Article
A method was developed to calculate preliminary genomic evaluations daily or weekly before the release of official monthly evaluations by processing only newly genotyped animals using estimates of single nucleotide polymorphism effects from the previous official evaluation. To minimize computing time, reliabilities and genomic inbreeding are not ca...
Conference Paper
Abstract Text: The number of females genotyped in the US has increased to 12,650 per month comprising 74% of the total genotypes received in 2013. The objective of this study was to evaluate the accuracy of cow and bull traditional information in the genomic evaluation system. Cutoff studies to determine gains in reliability due to the addition o...
Conference Paper
Full-text available
Two methods to efficiently approximate theoretical genomic reliabilities are presented. The first relies on the direct inverse of the left hand side (LHS) of mixed model equations. It uses the genomic relationship matrix for a small subset of individuals with the highest genomic relationship with the individual of interest. The second is a ridge-re...
Conference Paper
Abstract Text: This study assessed the gain of genomic prediction accuracy when including US Jersey bulls in the Danish Jersey reference population. The data included 1,262 Danish progeny-tested bulls and 1,157 US progeny-tested bulls. Genomic breeding values (GEBV) were predicted using a GBLUP model from the Danish reference and the joint Danish...
Conference Paper
Full-text available
Abstract Text: ABSTRACT: The genetic architecture of residual feed intake (RFI) and related traits was evaluated using a dataset of 2,894 cows. A Bayesian analysis estimated that markers accounted for 14% of the variance in RFI, and RFI had considerable genetic variation. Effects of marker windows were small, but QTL peaks were identified. Six of...
Conference Paper
Abstract Text: The impact of adding US and Canada genomic information to the imputation of Mexican Holstein genotypes was measured by comparing 3 scenarios: 1) 2,018 Mexican genotyped animals; 2) animals from scenario 1 plus 886 related North American animals; and 3) animals from scenario 1 and all North American genotyped animals (338,073). Four...
Conference Paper
Abstract Text: Subclinical ketosis is a fresh cow disorder that is costly in terms of lost milk production and treatment cost. Although treatment and prevention strategies are available, prevention requires targeting animals that are likely to develop the disease. Whole-herd genotyping is becoming more common with commercial dairies, and identifi...
Article
Full-text available
An a posteriori granddaughter design was applied to estimate quantitative trait loci genotypes of sires with many sons in the US Holstein population. The results of this analysis can be used to determine concordance between specific polymorphisms and segregating quantitative trait loci. Determination of the actual polymorphisms responsible for obse...
Article
Genomic evaluations of dairy cattle in the United States have been available for Brown Swiss, Holsteins, and Jerseys since 2009. As of January 2013, 1,023 Ayrshires had genotypes in the North American database. Evaluation accuracy was assessed using genomic evaluations based on 646 bulls with 2008 traditional evaluations to predict daughter perform...
Article
Full-text available
The recent discovery of bovine haplotypes with negative effects on fertility in the Brown Swiss, Holstein, and Jersey breeds has allowed producers to identify carrier animals using commercial single nucleotide polymorphism (SNP) genotyping assays. This study was devised to identify the causative mutations underlying defective bovine embryo developm...
Article
Full-text available
The intensive selection programs for milk made possible by mass artificial insemination increased the similarity among the genomes of North American (NA) Holsteins tremendously since the 1960s. This migration of elite alleles has caused certain regions of the genome to have runs of homozygosity (ROH) occasionally spanning millions of continuous bas...
Article
Full-text available
To assist cattle producers transition from microsatellite (MS) to single nucleotide polymorphism (SNP) genotyping for parental verification we previously devised an effective and inexpensive method to impute MS alleles from SNP haplotypes. While the reported method was verified with only a limited data set (N = 479) from Brown Swiss, Guernsey, Hols...
Article
A posteriori and modified granddaughter designs were applied to determine haplotype effects for Holstein bulls and cows with BovineSNP50 [~50,000 single nucleotide polymorphisms (SNP); Illumina Inc., San Diego, CA] genotypes. The a posteriori granddaughter design was applied to 52 sire families, each with ≥100 genotyped sons with genetic evaluation...
Article
Full-text available
Bovine Progressive Degenerative Myeloencephalopathy (Weaver Syndrome) is a recessive neurological disease that has been observed in the Brown Swiss cattle breed since the 1970's in North America and Europe. Bilateral hind leg weakness and ataxia appear in afflicted animals at 6 to 18 months of age, and slowly progresses to total loss of hind limb c...
Data
Target SNP interactions and filter information. (XLSX)
Data
140 SNP Weaver Haplotype. (XLSX)
Data
Predicted effect of filtered sequence variations. (XLSX)
Data
Target SNP genotpyes and pedigree information. (XLSX)
Data
Weaver 50K+Target SNP Haplotypes. (XLSX)
Article
Call rates on both a single nucleotide polymorphism (SNP) basis and an animal basis are used as measures of data quality and as screening tools for genomic studies and evaluations of dairy cattle. To investigate the relationship of SNP call rate and genotype accuracy for individual SNP, the correlation between percentages of missing genotypes and p...
Article
Selection, mating, and improvement of dairy animals have required accurate pedigrees. Genomic tools allow paternal ancestors to be easily confirmed or discovered because most sires are genotyped for many markers, but maternal ancestors are more difficult to discover because most female ancestors are not genotyped. Three methods to discover maternal...
Article
Genetic parameters were estimated for mobility score and 16 linear type traits of Brown Swiss dairy cattle. Mobility is an overall assessment trait that measures a cow's ability to move, as well as the structure of her feet, pasterns, and legs. Scores from 50 to 99 were assigned by appraisers for the Brown Swiss Cattle Breeders' Association of the...
Article
The GeneSeek Genomic Profiler (GGP) BeadChip (GeneSeek, Lincoln, NE), which became available commercially in February 2012, is based on the Illumina BovineLD Genotyping BeadChip (Illumina Inc., San Diego, CA), with 1,745 additional single nucleotide polymorphisms (SNP) for genomic evaluation and SNP for proprietary single-gene tests. The BovineLD c...
Article
Full-text available
Genomic evaluations for 161,341 Holsteins were computed by using 311,725 of 777,962 markers on the Illumina BovineHD Genotyping BeadChip (HD). Initial edits with 1,741 HD genotypes from 5 breeds revealed that 636,967 markers were usable but that half were redundant. Holstein genotypes were from 1,510 animals with HD markers, 82,358 animals with 45,...
Article
Full-text available
Background Artificial insemination and genetic selection are major factors contributing to population stratification in dairy cattle. In this study, we analyzed the effect of sample stratification and the effect of stratification correction on results of a dairy genome-wide association study (GWAS). Three methods for stratification correction were...
Data
Full-text available
Figure S6. Global view of P-values of 45,878 SNP effects per trait for 31 production, health, reproduction and body conformation traits by three methods for stratification correction. MY, milk yield; FY, fat yield; PY, protein yield; FPC, fat percentage; PPC, protein percentage; PL, productive life; SCS, somatic cell score; DPR, daughter pregnancy...
Data
Full-text available
Figure S2. Pedigree of the 1,654 contemporary cows tracing back to ancestors born in 1930’s (approximately 10–15 generations). Circles in gold color are the 1,654 cows used in the genome-wide association analysis. The pedigree shows that all 1,654 cows are related.
Data
Table S4. (Excel file) Overlap between top 100 effects per trait for 31 dairy traits from methods for stratification correction and the top 100 effects from the analysis without stratification correction. A1_elite160: frequency of allele 1 in the elite cluster of 160 cows; A1_1494: frequency of allele 1 in the remaining 1,494 cows excluding the eli...
Data
Full-text available
Figure S1. Multidimensional scaling (MDS) plots of SNP genotypes of 1,654 contemporary Holstein cows by chromosome. C1 = dimension 1, C2 = dimension 2. Left column: C1 and C2 values were calculated using 1,654 contemporary cows. Right column: C1 and C2 values were calculated using 2,366 Holstein cattle, including the University of Minnesota Holstei...
Data
Figure S7. Manhattan plots of the AIPL effect distribution, and results from three sets of analysis: 1) LS, GLS, EMMAX-IBS using the full data set of 1,654 cows; 2) adding PCA to GLS and EMMAX-IBS using 1,654 cows; and 3) LS, GLS and EMMAX using 1,494 cows by removing the 160 elite cows. Red triangle indicates confirmation between effect size and s...
Article
Full-text available
Microsatellite (MS) markers have recently been used for parental verification and are still the international standard despite higher cost, error rate, and turnaround time compared with Single Nucleotide Polymorphisms (SNP)-based assays. Despite domestic and international interest from producers and research communities, no viable means currently e...