Comparing sire and dam estimates of heritability: jackknife and likelihood approaches

Three estimates of heritability are available from the half-sib pedigree design: the sire, dam and genotypic estimates. Because of its significantly smaller standard error, the genotypic estimate is preferred provided that there are no non-additive effects that inflate the estimate. I present two methods to test for such effects: these are a t-test of the paired sire and dam pseudovalues from the jackknife procedure and the likelihood ratio test from the animal model. Both methods are shown to be valid tests for significant dominance and/or maternal effects. SPLUS coding for the implementation of the jackknife method is provided. Unless sample sizes are very large, the power of the tests is low and hence caution is advised in the use of the genotypic estimate following a nonsignificant test. An approximate power analysis can be done using the data from the jackknife method but the estimated power is typically a substantial underestimate of the true power and its use is not recommended.     

Estimation of genetic associations between reproduction and production traits based on a sire and dam line with common ancestry

Genetic parameters for survival, reproduction and production traits were estimated for a sire and dam line, originating from one Large White breed separated more than 25 years ago. The change in parameters due to different selection pressure on reproduction and production traits in both lines was also examined. Data collected between 1990 and 2007 were available for the analysis of reproduction traits in 4713 litters (sire line) and 14836 litters (dam line) and for the production traits in 58329 pigs (sire line) and 108912 pigs (dam line). Genetic parameters were estimated using a Bayesian approach. Average phenotypic differences between lines were substantial with 1.5 more piglets born in the dam line and 1.7 mm less backfat thickness (BF) in the sire line. Based on a multiple trait analysis which included both reproduction and production traits, heritabilities for survival and litter size traits in the sire (or dam) line were estimated at 0.03 ± 0.01 (0.06 ± 0.01) for percentage of stillborn piglets (SB), 0.10 ± 0.03 (0.11 ± 0.01) for total number of piglets born (NBT) and 0.09 ± 0.03 (0.09 ± 0.01) for number of piglets born alive. Heritabilities for production traits were estimated at 0.29 ± 0.01 (0.29 ± 0.01) for average daily gain, 0.50 ± 0.01 (0.42 ± 0.01) for BF and 0.41 ± 0.01 for muscle depth. Selection pressure on litter size in the dam line resulted in a slightly unfavourable correlation for SB-NBT (0.21 ± 0.11), which was only marginally unfavourable in the sire line (0.06 ± 0.24). Selection pressure on BF in the sire line may have resulted in the moderately undesirable correlation with SB (-0.46 ± 0.15), which was not significant in the dam line (-0.08 ± 0.06). Changing the base population in the dam line to animals born since the year 2000 indicated that selection pressure on different traits has altered the heritabilities and correlations of the traits within the line. The undesirable correlations between survival at birth and reproduction traits or production traits were low so that simultaneous improvement of all traits can be achieved. Heritabilities for survival at birth and reproduction traits were low, but genetic variation was substantial and extensive pedigree information can be used to improve the accuracy of breeding values, so that genetic improvement is expected to be efficient.     

Testicular size at weaning in tropically-adapted beef bulls as influenced by breed of sire and dam

This study was conducted to evaluate testicular size at weaning for bulls representing diverse tropically-adapted genotypes. Calves from 2 locations were weighed and castrated at weaning. In one herd, calves were born to Brahman dams and Angus, Tuli, and Brahman sires. Body weights and paired testes weights were heavier (P < 0.01) for Angus x Brahman (AB) genotype than for Tuli x Brahman (TB) and purebred Brahman (BB) genotype calves. The testes:body weight ratio was greater (P < 0.01) for AB than for TB and BB calves. In a second herd, calves were born to Angus cows and Brahman, Tuli, and Senepol sires. Means were similar between Brahman- (BA), Tuli-(TA), and Senepol-sired (SA) calves for body weight and testes:body weight ratio. Paired testes weight was heavier (P < 0.05) for SA than BA calves. Across locations, paired testes weights were heavier (P < 0.01) for TA than TB calves but their body weights were similar. Within-herd deviations were greater (P < 0.01) for AB than BA calves for paired testes weight and testes:body weight ratio. The correlation between the proportion of Bos indicus genetic contribution and testes:body weight ratio was significantly negative. Tropically-adapted calves differed in testicular size at weaning due to breed of sire and dam effects.     

Genetic relatedness analysis: modern data and new challenges

Individuals who belong to the same family or the same population are related because of their shared ancestry. Population and quantitative genetics theory is built with parameters that describe relatedness, and the estimation of these parameters from genetic markers enables progress in fields as disparate as plant breeding, human disease gene mapping and forensic science. The large number of multiallelic microsatellite loci and biallelic SNPs that are now available have markedly increased the precision with which relationships can be estimated, although they have also revealed unexpected levels of genomic heterogeneity of relationship measures.     

Genetic analysis of biological pathway data through genomic randomization

Genome Wide Association Studies (GWAS) are a standard approach for large-scale common variation characterization and for identification of single loci predisposing to disease. However, due to issues of moderate sample sizes and particularly multiple testing correction, many variants of smaller effect size are not detected within a single allele analysis framework. Thus, small main effects and potential epistatic effects are not consistently observed in GWAS using standard analytical approaches that consider only single SNP alleles. Here, we propose unique methodology that aggregates variants of interest (for example, genes in a biological pathway) using GWAS results. Multiple testing and type I error concerns are minimized using empirical genomic randomization to estimate significance. Randomization corrects for common pathway-based analysis biases, such as SNP coverage and density, linkage disequilibrium, gene size and pathway size. Pathway Analysis by Randomization Incorporating Structure (PARIS) applies this randomization and in doing so directly accounts for linkage disequilibrium effects. PARIS is independent of association analysis method and is thus applicable to GWAS datasets of all study designs. Using the KEGG database as an example, we apply PARIS to the publicly available Autism Genetic Resource Exchange GWAS dataset, revealing pathways with a significant enrichment of positive association results.     

Conversion of capillary electrophoresis microchip genotyping data for analysis with Genetic Profiler software

The collection and conversion of 4-color fluorescent genotyping data from capillary array electrophoresis microchip devices and its conversion to a format easily and rapidly analyzed by Genetic Profiler genotyping software is presented. Microchip fluorescence intensity data are acquired and stored as 4-color tab-delimited text. These files are converted to electrophoretic signal data (ESD) files using a utility program (TEXT-to-ESD) written in C. TEXT-to-ESD generates an ESD file by converting text data to binary data and then appending a 632-byte ESD-file trailer. Up to 96 ESD files are then assembled into a run folder and imported into Genetic Profiler, where data are reduced to 4-color electropherograms and analyzed. In this manner, DNA fragment sizing data acquired with our high-speed electrophoretic microchip devices can be rapidly analyzed using robust commercial software. Additionally, the conversion program allows sizing of data with Genetic Profiler that have been preprocessed using other third-party software, such as BaseFinder.     

Genetic association analysis using data from triads and unrelated subjects

The selection of an appropriate control sample for use in association mapping requires serious deliberation. Unrelated controls are generally easy to collect, but the resulting analyses are susceptible to spurious association arising from population stratification. Parental controls are popular, since triads comprising a case and two parents can be used in analyses that are robust to this stratification. However, parental controls are often expensive and difficult to collect. In some situations, studies may have both parental and unrelated controls available for analysis. For example, a candidate-gene study may analyze triads but may have an additional sample of unrelated controls for examination of background linkage disequilibrium in genomic regions. Also, studies may collect a sample of triads to confirm results initially found using a traditional case-control study. Initial association studies also may collect each type of control, to provide insurance against the weaknesses of the other type. In these situations, resulting samples will consist of some triads, some unrelated controls, and, possibly, some unrelated cases. Rather than analyze the triads and unrelated subjects separately, we present a likelihood-based approach for combining their information in a single combined association analysis. Our approach allows for joint analysis of data from both triad and case-control study designs. Simulations indicate that our proposed approach is more powerful than association tests that are based on each separate sample. Our approach also allows for flexible modeling and estimation of allele effects, as well as for missing parental data. We illustrate the usefulness of our approach using SNP data from a candidate-gene study of psoriasis.     

Genetic diversity of carrion and jungle crows from RAPD-PCR analysis data

RAPD-PCR analysis of the genetic diversity of the carrion crow (Corvus corone) and jungle crow (C. macrorhynchos) living in the continental parts of their species ranges and on some Russian and Japanese Far Eastern islands has been performed. Taxon-specific molecular markers have been found for each species. The genetic diversity of the carrion crow is considerably less than that of the jungle crow at the same genetic distance (P95 = 68.2%, DN = 0.27 and P95 = 88.4%, DN = 0.24, respectively). In both species, the genetic polymorphism of island samples is almost two times greater than that of continental samples (62 and 31.8%, respectively, for C. corone and 81.5 and 47.2%, respectively, for C. macrorhynchos). In addition, differences in genetic diversity between males and females (P95 = 55.1 and P95 = 72.1, respectively) has been found in the carrion crow but not in the jungle crow. The gene diversity of C. macrorhynchos is greater than that of C. corone: the mean numbers of alleles per locus are 2 and 1.81, effective numbers of alleles are 1.62 and 1.43, and the mean expected heterozygosities are 0.39 and 0.30, respectively. The phenograms and phylograms significantly segregate the clusters of the carrion and jungle crows. The clustering patterns of carrion crows corresponds to the intraspecies taxonomic and geographic differentiation: subspecies C. c. corone and C.c. orientalis living in the western and eastern parts of the species range, respectively, form different subclusters. The cluster of the jungle crow does not exhibit differentiation into subspecies C. m. mandshuricus and C. m. japonensis; molecular genetic differences between them are small.     

Influence of the dam and sire on size at birth and subsequent growth, milk production and fertility in dairy heifers

Genetic selection has resulted in larger cows with high milk production potential but a tendency for poor fertility. In multiparous cows fetal development competes for nutrients with concurrent milk production. This study tested the hypotheses that (a) maternal age and milk yield during pregnancy alter calf birth size and (b) birth weight influences subsequent productivity and fertility. Concurrently born Holstein-Friesian heifers (n=65) with multiparous dams and three sires were monitored from birth to the end of their first lactation to assess effects of birth weight on growth, milk production and fertility. Calves were analyzed as three subgroups: low (L), average (A) and high (H) birth weight (BW) calves (n=21-22 per group). LBW calves were born 10 kg lighter than HBW calves and remained significantly lighter throughout the study. They were generally smaller in other measured indices (length, height, girth, ponderal index) between birth and 9 months and were more likely to have older dams (lactations 3-6) with higher peak yields (>42 kg/day). Milk production parameters were indistinguishable between the 3 birthweight groups and metabolic parameters (IGF-I, insulin, glucose) measured around first calving were unaffected. HBW offspring were more likely to have persistent corpora lutea following their first calving and other fertility parameters also tended to be worse. Sire influenced gestation length but not birth size. Sire heritability estimates showed that weight, IGF-I and insulin concentrations after first calving and fertility in the first lactation were all heritable. The results support the hypothesis that high milk production in the dam may predispose to birth of a smaller calf. Smaller birth size did not, however, have any subsequent adverse effects on productivity or fertility in the first lactation and sire was more influential at this stage.     

A theory of natural selection incorporating interaction among individuals. VII. Use of groups consisting of one sire and one dam

A previous study, (V), in this series dealt with the problem of interaction among individuals in a population by utilizing a conceptual life-history model that assumed the synchronization of fitness components (viability and fecundity) for members within groups of interacting individuals. The model also assumed that the group members were not differentiated in any way. It was shown that these assumptions of synchronization and homogeneity of group members resulted in overall symmetric fitness values, and that selection operating on these symmetric values produced optimum short- and long-term results.Since the idealized model of paper (V) yields optimum selection results, it is of interest to consider specific biological mechanisms which can be used to fulfill the conceptual assumptions involved. The solution adopted in this study is to, first, require survival to occur at the group level. This forces the viability parameters to be identical for all group members.Second, the group composition is restricted to a single pair mating. This forces the fecundity parameters to be identical for members (sire and dam) of the same group. However, this solution causes a complication. Since each individual is identified as belonging to one of the two sexual types, it is necessary to extend the previous analysis in paper (V), to accommodate differentiated group members. It is shown that this differentiation leads to a non-symmetric fitness matrix. However, it is further shown that the selection results can be obtained by use of a ‘combined’ fitness matrix that is symmetric. Therefore, the important result is demonstrated that selection involving differentiated sire-dam groups possesses all of the optimum short- and long-term properties inherent in the original non-differentiated selection procedure developed in paper (V). It is speculated that these results could be of some significance with regard to the evolution of a monogamous, pair-bonding family structure.     

Effects of sire and dam genotype for complex vertebral malformation (CVM) on risk of return-to-service in Holstein dairy cows and heifers

The emergence of a new hereditary disease, called "Complex vertebral malformation" (CVM), has been described in Holstein cattle population. This paper studied the incidence of mating concerning Holstein dairy cattle with CVM in Brittany and the possible influences of CVM status for sires and dams on return-to-service at different intervals post-service in cows and heifers. It was carried out based on a set of data for first and second inseminations between 1998 and 2001 in cows (n=530,538) and heifers (n=248,140). Incidence of matings between CVM gene carriers, between a carrier bull and a non-carrier cow and between a non-carrier bull and a carrier cow were estimated to be 1.4, 10.6 and 9%, respectively (1.1, 9.3 and 10.9%, respectively in heifers). Compared to CVM-free mating, the relative risk of return-to-service was increased when the sire was a CVM carrier and the dam was at risk of being a carrier, especially for late return (>25 days post-service). When the sire alone was a carrier, the relative risk was increased whenever the return occurred at a low but significant level. Following mating between a non-carrier bull and a dam at risk of being a carrier, the risk of return-to-service decreased at a low but significant level, whatever the interval in the heifers but only for 19-25 days intervals in the cows.     

Genetic and maternal determinants of effective dispersal: the effect of sire genotype and size at birth in side-blotched lizards

We assessed genetic factors on progeny dispersal due to sire color morph genotypes in a field pedigree and lab crosses, and we measured maternal effects by studying both natural and experimentally induced egg size variation. Progeny were released into nature upon hatching, but we recorded dispersal distance at maturity, which reflects effective dispersal after viability selection has run its course. Progeny dispersal was significantly affected by sire genotype. Progeny from orange sires dispersed the farthest. Progeny from blue sires dispersed intermediate distances. Progeny from yellow sires were the most philopatric. Sire genotype effects interacted with egg size. In particular, enlarged progeny from orange sires dispersed farther, while enlarged progeny from yellow sires were more philopatric. Progeny from blue sires were unaffected by egg size manipulations. Egg manipulations and natural variation generally had concordant effects indicative of causation. However, asymmetry of gigantization and miniaturization on progeny dispersal from some sire genotypes suggest the involvement of maternal factors besides egg size. Results of laboratory crosses with progeny released into nature confirmed key sire genotype effects and identified additional maternal effects that modulated dispersal as a function of progeny gender. We discuss the adaptive implications of progeny dispersal in the context of male (rock-paper-scissors) and female strategies (r- and K-density cycle) that are associated with color morphs.     

Unequivocal determination of sire allele origin for multiallelic microsatellites when only the sire and progeny are genotyped

The effect of a segregating economic trait locus (ETL) can be detected with the aid of a linked genetic marker, if specific alleles of each locus are in association among the individuals genotyped for the genetic marker. For dairy cattle this can be achieved by application of the ‘granddaughter design’. If only the sires and their sons are genotyped for the genetic markers, then the allele origin of sons having the same genotypes as their sires cannot be determined. Seven sires and 101 sons were genotyped for five microsatellites. The mean frequency of heterozygous sires was 77%. The mean number of alleles per locus was 8.2. Frequency of informative sons per locus ranged from 60% to 80% with a mean of 72%. With highly polymorphic microsatellites, at least 60% more grandsire families can be included in the analysis, and the number of sons assayed can be reduced by 40%, as compared to diallelic markers.     

Genetic correlation estimations between artificial insemination sire performances and their progeny beef traits both measured in test stations

In France, beef traits of artificial insemination (AI) beef bulls are improved through the sequential selection for their own performances and for their male progeny performances, both being recorded in test stations. The efficiency of such programmes mainly depends on the genetic correlations between sire performances and progeny beef traits. Such correlations were independently estimated, using the multivariate REML (restricted maximum likelihood) method in a Limousin and a Charolais programme. In both breeds, high genetic correlations were observed between sires and progeny analogous morphology scores (from 0.64 to 0.82). Genetic correlations estimated between sires and progeny growth (from 0.41 to 0.70) were lower probably due to the difference of diet in central and progeny stations. Correlations between sire muscling scores and progeny skeletal frames (and vice-versa) were negative (from -0.05 to -0.58). The genetic correlations of sire traits with progeny dressing percentage (DP_p) and carcass fatness score (CF_p) were only low to moderate. These results show that the selection of bulls at the end of performance testing in test stations may be efficient in improving progeny growth and morphology. However, such a selection is insufficient in improving their dressing percentage and carcass composition.     

Orthoptera of Montenegro: new faunistic data with new records for the country

Summary

Grasshoppers and crickets of Montenegro have never been systematically studied. In this paper we present new distribution records of 119 Orthoptera species from Montenegro, sampled at 116 localities in different parts of the country in the period between 2010 and 2017. We also present records of older material deposited in the collection of the Hungarian Natural History Museum, Budapest. Oecanthus dulcisonans Gorochov, 1993 is recorded for the first time in Montenegro. Most of the areas investigated in this paper were never studied before, so our data represent the first information on Orthoptera of these parts of Montenegro.     

Impact of candidate sire number and sire relatedness on DNA polymorphism-based measures of exclusion probability and probability of unambiguous parentage

Genetic paternity testing can provide sire identity data for offspring when females have been exposed to multiple males. However, correct paternity assignment can be influenced by factors determined in the laboratory and by size and genetic composition of breeding groups. In the present study, DNA samples from 26 commingled beef bulls and their calves from the Nebraska Reference Herd-1 (NRH1), along with previously reported Illinois Reference/Resource Families data, were used to estimate the impact of sire number and sire relatedness on microsatellite-based paternity testing. Assay performance was measured by exclusion probabilities and probabilities of unambiguous parentage (PUP) were derived. Proportion of calves with unambiguous parentage (PCUP) was also calculated to provide a readily understandable whole-herd measure of unambiguous paternity assignment. For NRH1, theoretical and observed PCUP values were in close agreement (85.3 and 85.8%, respectively) indicating good predictive value. While the qualitative effects on PUP values of altering sire number and sire relatedness were generally predictable, we demonstrate that the impacts of these variables, and their interaction effects, can be large, are non-linear, and are quantitatively distinct for different combinations of sire number and degree of sire relatedness. In view of the potentially complex dynamics and practical consequences of these relationships in both research and animal production settings, we suggest that a priori estimation of the quantitative impact of a given set of interacting breeding group-specific and assay-specific parameters on PUP may be indicated, particularly when candidate sire pools are large, sire relatedness may be high, and/or loci numbers or heterozygosity values may be limiting.     

Genetic association analysis using sibship data: a multilevel model approach

Family based association study (FBAS) has the advantages of controlling for population stratification and testing for linkage and association simultaneously. We propose a retrospective multilevel model (rMLM) approach to analyze sibship data by using genotypic information as the dependent variable. Simulated data sets were generated using the simulation of linkage and association (SIMLA) program. We compared rMLM to sib transmission/disequilibrium test (S-TDT), sibling disequilibrium test (SDT), conditional logistic regression (CLR) and generalized estimation equations (GEE) on the measures of power, type I error, estimation bias and standard error. The results indicated that rMLM was a valid test of association in the presence of linkage using sibship data. The advantages of rMLM became more evident when the data contained concordant sibships. Compared to GEE, rMLM had less underestimated odds ratio (OR). Our results support the application of rMLM to detect gene-disease associations using sibship data. However, the risk of increasing type I error rate should be cautioned when there is association without linkage between the disease locus and the genotyped marker.     

Genetic and environmental influences on alcohol use: DF analysis of NLSY kinship data

Research designs to study alcohol use and abuse have included twin, adoption and family history/high risk studies. Results have consistently implied a genetic factor in the aetiology of alcohol abuse. However, less research has been conducted in search of environmental factors. This study uses kinship structure in a large national dataset (the National Longitudinal Survey of Youth) to estimate (using DeFries-Fulker analysis) the extent of the shared genetic, non-shared genetic, shared environmental and non-shared environmental influences on alcohol use. The NLSY kinship sample contained 3890 pairs of cousins, half-siblings, full-siblings and twins between the ages of 14 and 21 in the initial year of the survey (1979). Estimates of heritability (h2) and shared environment (c2) were small to moderate for the entire dataset for both light drinking and heavy drinking behaviour, with h2 estimates slightly higher in each case. Non-shared genetic measures of self-esteem and locus of control accounted for a significant portion of the remaining variance in heavy drinking behaviour. Race and gender patterns showed c2 and h2 estimates that were also small to moderate for both light and heavy drinking behaviour. Significant non-shared effects were found for the White group for heavy drinking behaviour, and for male pairs for both heavy and light drinking behaviour. Additionally, implications and future directions are discussed.