Joel Ira Weller

Joel Ira Weller
Agricultural Research Organization ARO | aro · Institute of Animal Science

Ph. D.

About

191
Publications
12,730
Reads
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6,675
Citations
Introduction
Statistical genetics, quantitative genetics, analysis of quantitative trait loci, animal breeding, dairy cattle, economic aspects of animal breeding, genetic evaluation
Additional affiliations
October 2012 - February 2013
United States Department of Agriculture, ARS
Position
  • Visiting Research Scientist
September 1999 - July 2000
September 1993 - July 1994
United States Department of Agriculture
Position
  • Visiting Research Scientist

Publications

Publications (191)
Article
Full-text available
Flathead gray mullet (Mugil cephalus) is a cosmopolitan mugilid species popular in fishery and aquaculture with an economic preference for all-female population. However, it displays neither sexual dimorphisms nor heteromorphic sex chromosomes. We have previously presented a microsatellite-based linkage map for this species locating a single sex de...
Article
Our objective was to combine the methods of geometric morphometrics and multivariate quantitative genetics to genetic evaluation of the size and shape of lactation curves of milk of 3,492 Israeli first-parity Holstein cattle. Lactation records were treated as morphological data, for which 2 different lactation shape functions were evaluated, one de...
Article
Full-text available
Effective farming of tilapia requires all-male culture, characterized by uniformity and high growth rate. Males of O. aureus (Oa) and females of O. niloticus (On) produce all-male offspring, but there is a behavioral reproductive barrier between the two species that prevents mass production. In crosses between Oa and On broodstocks, few hybrid fema...
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...
Conference Paper
Routinely, genetic evaluations are based on 305-d lactations, which represent the size or magnitude of lactation curve but ignore the shape, an inherently multidimensional feature. We combined the methods of quantitative genetics and the geometric morphometrics (GM) to evaluate the heritability and genetic correlations of size and shape of lactatio...
Article
Full-text available
The Lake Tiberias (Sea of Galilee) grey mullet (Mugil cephalus) population originates from translocated wild-caught, or hatchery-reared, fish. The aim of the study was to identify the taxonomic status and stock origin of a sample of 32 mullet individuals caught in the Sea of Galilee, based on the mitochondrial Cytochrome Oxidase I (COI) sequence an...
Article
For countries without large-scale genotyping, it is a challenge to implement an effective genomic evaluation system. Breeding company CRV has merged its bull training population with two such countries to build a training population of significance, and provide genomic software. Results show 6-20 times increase in training population adding the CRV...
Article
Genomic evaluation has been successfully implemented in the United States, Canada, Great Britain, Ireland, New Zealand, Australia, France, the Netherlands, Germany, and the Scandinavian countries. Adoption of this technology in the major dairy producing countries has led to significant changes in the worldwide dairy industry. Gradual elimination of...
Conference Paper
Concerns have been raised in the past about the Dairy Herd Improvement Association recording frequency, because the interval between samples, about 4 weeks, may not capture the peak production for cows with shorter lactation (less than 10 mo), which have led to the conclusion that these cows have an atypical lactation curve shape. This may be due t...
Article
Although it now standard practice to genotype thousands of female calves, genotyping of bull calves is generally limited to progeny of elite cows. In addition to genotyping costs, increasing the pool of candidate sires requires purchase, isolation, and identification of calves until selection decisions are made. We economically optimized via simula...
Article
Full-text available
In accordance with their tropical origin, the optimal water temperature for most tilapia species is between 25 and 28 °C. The lethal temperature varies as a function of environmental effects, individual fish histories and genetic effects; however, the genetic basis of cold tolerance in tilapia has not been investigated in detail. Blue tilapia (Oreo...
Article
The objective was to test the hypothesis that more frequent but less accurately analyzed milk components may give a more representative measure of a cow's total lactation production. Daily records for milk production and fat and protein concentration collected by the AfiLab recording system (Afimilk, Kibbutz Afikim, Israel) from January 2014 to Jan...
Article
Full-text available
Elucidation of the sex-determination mechanism in flathead grey mullet (Mugil cephalus) is required to exploit its economic potential by production of genetically determined monosex populations and application of hormonal treatment to parents rather than to the marketed progeny. Our objective was to construct a first-generation linkage map of the M...
Article
Full-text available
A total of 1922 first generation crossbred cows born between 2005 and 2012 produced by inseminating purebred Israeli Holstein cows with Norwegian Red semen, and 7487 purebred Israeli Holstein cows of the same age in the same 50 herds were analyzed for production, calving traits, fertility, calving diseases, body condition score, abortion rate and s...
Book
The field of whole genome selection has quickly developed into the breeding methodology of the future. As efforts to map a wide variety of animal genomes have matured and full animal genomes are now available for many animal scientists and breeders are looking to apply these techniques to livestock production. Providing a comprehensive, forward-loo...
Chapter
This chapter describes in general terms the main statistical methodologies used for estimation of parameters, or fixed variables. Least squares parameter estimation (LSE) is based on deriving the parameter estimates that minimize the expectation of the sum of squared errors. Although least squares is used almost exclusively to estimate parameters,...
Chapter
This chapter focuses on the methods to estimate linkage disequilibrium (LD) between markers. It reviews the studies that estimate the extent of LD in animal populations. The chapter also considers basic principles of LD QTL mapping. It then focuses on joint linkage and LD mapping of QTL as applied to the granddaughter design, and describes multitra...
Chapter
This chapter presents methods to estimate the parameters for the mixed model equations, chiefly variance components (VC), by maximum likelihood (ML), restricted maximum likelihood (REML), and Gibbs sampling (GS). For mixed models, the likelihood function is the joint density function integrated over the random effects. The main interest in simple M...
Chapter
Methods to compute genomic genetic evaluations can be divided into two groups, denoted single step methods and multistep methods. In single-step methods actual records are analyzed, and the effects of markers and the additive genetic variation not included in the marker effects are estimated. In multistep methods, genetic evaluations are first comp...
Chapter
Current mid density single nucleotide polymorphism (SNP) chips generally include over 50,000 genetic markers. This chapter considers the basic question related to genomic evaluation. For genomic evaluations the multiple comparison problem considered previously becomes more acute. A second problem is that most markers will have no measurable effect...
Chapter
This chapter discusses the types of markers that were used for marker-assisted selection and the markers currently used for genomic selection has been included, as the characteristics of these markers affect the methodologies that have been developed for marker-assisted and genomic selection. It then briefly reviews the current state of complete ge...
Chapter
All animal breeding programs are based on the principles of quantitative genetics. Advanced animal breeding programs can be divided into two groups: within-breed selection and programs based on crossbreeding among different breeds. Breeding programs based on crossbreeding are the norms for beef cattle, poultry, and swine. Crossbreeding programs can...
Chapter
This chapter reviews the landmark breakthroughs that lead to genomic selection. First the chapter reviews the milestones in the synthesis of Mendelian and quantitative genetics. Then it reviews the early experiments of quantitative trait locus (QTL) detection using morphological and biochemical markers, beginning with Sax's landmark experiment with...
Chapter
Generally genomic selection breeding programs have been evaluated merely in terms of the increase in accuracy of genomic evaluations, as compared to genetic evaluations based on phenotypic records and pedigree. In economic evaluation of any enterprise, both returns and costs should be considered. This chapter describes the basic principles of econo...
Chapter
This chapter summarizes the literature dealing with marker-assisted selection (MAS) prior to the introduction of high-density marker panels including tens of thousands of markers. It first reviews the situations in which selection index is inefficient, and presents the general considerations for MAS within a breed. The chapter also considers the sp...
Chapter
This chapter reviews methods to detect segregating quantitative trait nucleotides (QTL) in animal populations based on genome wide association studies (GWAS). It then considers strategies for QTL determination and validation. The chapter also considers the question of what gains can be expected by QTN determination and finally reviews the current s...
Chapter
Linkage disequilibrium (LD) mapping was first proposed in 1989 based on maximum likelihood (ML) methodology for crosses between inbred lines. This chapter derives some methods such as backcross (BC) design, interval mapping for daughter and granddaughter designs to estimate parameters of quantitative trait locus (QTL) effects for most experimental...
Chapter
This chapter presents different algorithms that have been proposed for imputation and explain why different strategies have been proposed for humans and farm animals. It then compares these methods on actual cattle data, based on accuracy and speed. Finally the chapter focuses on how imputation affects genomic evaluation of farm animals. There are...
Chapter
This chapter reviews the application of genetic markers to pedigree validation and determination. Pedigree mistakes lower rates of genetic gain. Confirmation and correction of pedigrees can be considered a by-product of genomic evaluation obtained at virtually no extra cost. As genotyping costs decrease, the gains obtained directly from pedigree co...
Chapter
All studies have assumed that the basis for comparison of genomic evaluations is the parent average (PA) of genetic evaluations derived by standard mixed model methodology. The main criteria for comparison are accuracy and bias of the evaluations. In addition to analyses of simulated populations, this chapter describes studies that have analyzed ac...
Chapter
This chapter presents likelihood equations for two QTL estimation designs that require inclusion of random polygenic effects in the analysis model: the “daughter” and “granddaughter” designs. It then considers Bayesian estimation of the parameters of the granddaughter design, based on assumptions with respect to the prior distributions of the QTL p...
Chapter
A number of studies have used stochastic simulations to evaluate marker-assisted selection (MAS) or genomic selection. This chapter reviews the mathematical models that have been used to describe the polygenic variance, and then presents formulas to calculate the effective number of quantitative trait locus (QTL) for a trait. It presents results fr...
Chapter
This chapter describes single-step methods to compute genomic genetic evaluations in detail. In these methodologies, the phenotypic records are the dependent variables, and the analysis model includes the polygenic effect, the effects of the individual markers, and all fixed effects, such as herd-year-season. The major difficulties with application...
Chapter
Genomic evaluation is still a highly dynamic field, and additional discoveries and new ideas will probably transform the discipline in the next few years. In the next few years complete genome sequencing costs will probably be in the range of a thousand dollars per individual. In the United States and other advanced countries, genotyping of cows fo...
Chapter
In genetic evaluation based on field records, it will also be necessary to include other effects, such as herd or block, in the model. These “nuisance” effects will generally be considered fixed. Therefore, analysis models will include both fixed and random effects in addition to the residual. This chapter focuses on the selection index theory, ass...
Chapter
The traditional approach to deal with multiple comparisons is to control the family-wise (or experiment-wise) error rate (FWER), instead of controlling the nominal or comparison wise error rate (CWER). The FWER is controlled by setting the rejection threshold sufficiently strict, so that the probability that any of the null hypotheses tested are er...
Article
Five alternative models were applied for analysis of dystocia and stillbirth in first and second parities. Models 1 and 2 were included only to estimate the parameters required for model 4, and models 3 and 5 are included only as comparisons to the model 4 estimates. Variance components were estimated by multi-trait REML, including cows with valid...
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...
Article
The objectives were to investigate the accuracy of genomic evaluations obtained for a small dairy cattle population (Israeli Holsteins) via joint evaluation with a larger population (Dutch Holsteins), and to evaluate the use of pedigree data from foreign bulls computed by Interbull without daughter records in Israel. The training population include...
Article
The objectives were to investigate the effects of various environmental factors that may affect herd-life of Israeli Holsteins, including first-calving age and season, calving ease, number of progeny born, and service sire for first calving in complete and truncated records; and to estimate heritabilities and genetic correlations between herd-life...
Article
Full-text available
Background The probable influence of genes and the environment on sex determination in Nile tilapia suggests that it should be regarded as a complex trait. Detection of sex determination genes in tilapia has both scientific and commercial importance. The main objective was to detect genes and microRNAs that were differentially expressed by gender i...
Conference Paper
Abstract Text: Datasets of US and Israeli Holsteins, and pigs from PIC were used to evaluate the impact of different number of generations on ability to predict GEBV of young genotyped animals. The inclusion of only two generations of ancestors (A2) or all ancestors (Af) was also evaluated. A total of 34,506 US and 1,305 Israeli Holsteins bulls, an...
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
Full-text available
Data sets of US Holsteins, Israeli Holsteins, and pigs from PIC (a Genus company, Henderson, TN) were used to evaluate the effect of different numbers of generations on ability to predict genomic breeding values of young genotyped animals. The influence of including only 2 generations of ancestors (A2) or all ancestors (Af) was also investigated. A...
Article
Full-text available
Several studies have shown that computation of genomic estimated breeding values (GEBV) with accuracies significantly greater than parent average (PA) estimated breeding values (EBVs) requires genotyping of at least several thousand progeny-tested bulls. For all published analyses, GEBV computed from the selected samples of markers have lower or eq...
Article
Full-text available
Methods for genomic prediction were evaluated for an Israeli Holstein dairy population of 713,686 cows and 1,305 progeny-tested bulls with genotypes. Inclusion of genotypes of 343 elite cows in an evaluation method that considers pedigree, phenotypes, and genotypes simultaneously was also evaluated. Two data sets were available: a complete data set...
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
Based on pairwise identity-by-state (IBS) distances and whole-genome SNP data, kinship was investigated in the Israeli Holstein population. A total of 789 bulls, including most of the artificial insemination sires in service since 1987, were genotyped by the BovineSNP50 BeadChip. This sample included up to five generations. For each bull-by-bull co...
Article
Strong selection in the Israeli Holstein dairy cattle population over the last three decades should have left clear signatures of selection. Two experimental approaches were applied to detect evidence of contemporary selection based on the 54K BeadChip genotypes of ~1000 Israeli Holstein bulls: (i) the long-range haplotype test, which searches for...
Article
Full-text available
An efficient algorithm for genomic selection of moderately sized populations based on single nucleotide polymorphism chip technology is described. A total of 995 Israeli Holstein bulls with genetic evaluations based on daughter records were genotyped for either the BovineSNP50 BeadChip or the BovineSNP50 v2 BeadChip. Milk, fat, protein, somatic cel...
Article
Full-text available
Polymorphisms in mitochondrial DNA (mtDNA) protein- and tRNA-coding genes were shown to be associated with various diseases in humans as well as with production and reproduction traits in livestock. Alignment of full length mitochondria sequences from the 5 known ovine haplogroups: HA (n = 3), HB (n = 5), HC (n = 3), HD (n = 2), and HE (n = 2; GenB...
Article
Full-text available
Evidence supports that sex determination (SD) in tilapia is controlled by major genetic factors that may interact with minor genetic as well as environmental factors, thus implying that SD should be analyzed as a quantitative trait. Quantitative trait loci (QTL) for SD in Oreochromis niloticus were previously detected on linkage groups (LG) 1 and 2...
Article
Full-text available
A quantitative trait locus (QTL) affecting female fertility, scored as the inverse of the number of inseminations to conception, on Bos taurus chromosome 7 was detected by a daughter design analysis of the Israeli Holstein population (P < 0.0003). Sires of five of the 10 families analyzed were heterozygous for the QTL. The 95% confidence interval o...
Article
Full-text available
A single nucleotide polymorphism in the intergenic region upstream of the ZNF496 gene on Bos taurus chromosome 7 displayed significant population-wide linkage disequilibrium with milk protein percentage in the Israeli Holstein population. The frequency of the allele associated with increased protein concentration was 10%. This single nucleotide pol...
Article
Genome-wide association studies based on tens of thousands of single nucleotide polymorphisms have been completed for several dairy cattle populations. Methods have been proposed to directly incorporate genome scan data into breeding programs, chiefly by selection of young sires based on their genotypes for the genetic markers and pedigree without...
Data
Full-text available
Detailed mathematical solution for the trinomial expansion of the Hardy-Weinberg principle. Text in PDF format.
Data
Allele distribution, χ2 test, rl and rg values for SNPs of the Illumina BovineSNP50 BeadChip. Spread sheet in Excel format summarizing the genotypes obtained from the 912 sire samples for all 54,001 genetic markers on BovineSNP50.
Data
Gene ontology categories in Holstein CNV. Spread sheet in Excel format.
Data
Common CNVs. Spread sheet in Excel format summarizing the positions and gene content of copy losses (red background) and copy gains (blue background) that displayed significantly high frequency by both the HWE-based and SI-based methods. Previously reported common (frequency > 2.5%) cattle CNVs are also reported using yellow and no colour backgroun...
Article
Full-text available
Copy number variation (CNV) has been recently identified in human and other mammalian genomes, and there is a growing awareness of CNV's potential as a major source for heritable variation in complex traits. Genomic selection is a newly developed tool based on the estimation of breeding values for quantitative traits through the use of genome-wide...
Article
Genetic markers in tilapia species associated with loci affecting sex determination (SD), sex-specific mortality or both were mapped to linkage groups (LG) 1, 2, 3, 6 and 23. The objective of this study was to use these markers to fine-map the locus with the greatest effect on SD in Oreochromis niloticus. Our parental stock, full-sibs of Nile tilap...
Article
Summary The phenomenon of chimaerism occurs in the majority of cattle twin pregnancies. The objectives of this study were to develop a powerful diagnostic test for chimaerism in bovine male and female co-twins using X and Y chromosome-linked markers and to determine the extent of chimaerism in twins, triplets and quadruplets. We developed a multipl...
Article
Incorrect paternity assignment in cattle can have a major effect on rates of genetic gain. Of the 576 Israeli Holstein bulls genotyped by the BovineSNP50 BeadChip, there were 204 bulls for which the father was also genotyped. The results of 38 828 valid single nucleotide polymorphisms (SNPs) were used to validate paternity, determine the genotyping...
Article
Full-text available
Single nucleotide polymorphisms (SNPs) are amenable to automation and therefore have become the marker of choice for DNA profiling. SNaPshot, a primer extension-based method, was used to multiplex 25 SNPs that have been previously validated as useful for identity control. Detection of extended products was based on four different fluorochromes and...
Article
Full-text available
The method of Israel and Weller (Estimation of candidate gene effects in dairy cattle populations. Journal of Dairy Science 1998, 81, 1653-1662) to estimate quantitative trait locus (QTL) effects when only a small fraction of the population was genotyped was investigated by simulation. The QTL effect was underestimated in all cases, but bias was gr...
Article
Full-text available
Weight of male and female Israeli Holstein calves and yearling gain were analyzed on 285 800 records from 105 935 animals from 458 herds recorded between 1994 and 2007. The difference between the sexes increased until around 400 days, at which point the difference between males and females was 110 kg. Yearling gain, defined as 365 × (weight - 35)/a...
Article
An efficient algorithm is described for marker-assisted selection appropriate for large populations, even though only a small fraction of the population is genotyped. Genotype probabilities for specific loci are computed for all animals without genotypes. Effects of the quantitative trait loci (QTL) are then estimated by a "cow model" and the appro...
Article
Formulae were developed to compute exclusion probabilities for parentage confirmation for any number of diallelic markers under the assumption that the minor allele frequency (MAF) varied among markers, but has a uniform distribution. Three scenarios were analysed: a progeny with (1) a single putative parent; (2) two putative parents; and (3) one a...
Article
Twinning rate was analyzed in the Israeli Holstein dairy cattle population by the multiple-trait animal model, and a daughter design genome scan for quantitative trait loci was performed. Each parity was considered a separate trait. Heritabilities of twinning rate were very low, but increased by parity from 0.01 in first parity to 0.03 in fifth par...
Article
A total of 5,459 Israeli Holstein cows, daughters of 11 sires, were genotyped for 29 microsatellites spanning chromosome 7 and analyzed by the daughter design for 9 economic traits: milk, fat, and protein yield, fat and protein percentage, somatic cell score, female fertility, herd life, and milk persistency. Quantitative trait loci at chromosome-w...
Article
Many quantitative trait loci (QTL) affecting economic traits in livestock have now been identified. However, the confidence interval (CI) of individual QTL as determined by linkage analysis often spans tens of map units, containing hundreds of genes. Linkage disequilibrium (LD) mapping can reduce the CI to individual map units, but this reduced int...
Article
Full-text available
Many studies have proposed that rates of genetic gain in dairy cattle can be increased by direct selection on the individual quantitative loci responsible for the genetic variation in these traits, or selection on linked genetic markers. The development of DNA-level genetic markers has made detection of QTL nearly routine in all major livestock spe...
Article
Full-text available
Many studies have found segregating quantitative trait loci (QTL) for milk production traits in different dairy cattle populations. However, even for relatively large effects with a saturated marker map the confidence interval for QTL location by linkage analysis spans tens of map units, or hundreds of genes. Combining mapping and arraying has been...
Article
A single nucleotide change (A/C) in exon 14 is capable of encoding a substitution of tyrosine-581 to serine (Y581S) in the ABCG2 (ATP binding cassette, subfamily G, member 2) gene and affects milk production traits. The ABCG2(A) allele decreases milk yield and increases protein and fat concentration. The allele frequencies were determined in 32 Bos...
Article
Full-text available
Investment in breeding is unique because genetic gains are eternal and cumulative. They are never "used up", and never "wear out". However, nearly all of the gain is transferred to the national economy. Very little stays with farmers or commercial breeders. Unlike genetic gains, costs are not cumulative. With a profit horizon of 20 years and a disc...