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PubMed2006

An algorithm to compute optimal genetic contributions in selection programs with large numbers of candidates.

A novel algorithm, OCSELECT, is presented for the calculation of optimal genetic contributions with a restricted rate of inbreeding when the number of selection candidates is very large. The calculation of optimal genetic contributions requires the relationship matrix between the candidates and its inverse. The relationship matrix was written as: A = ZA(p)Z' + D, where A(p) is the relationship matrix of the parents, D is a diagonal matrix of Mendelian sampling variances, and Z contains genetic contributions from parents to offspring. Therefore, A(-1) = d(-1) - d(-1)Z(Z'd(-1)Z + A(P)(-1))(-1) Z'd(-1), requires only inversion of matrices of the size of the number of parents instead of the number of offspring. The new algorithm was compared with the software package GENCONT on a salmon data set containing 39,214 selection candidates and 45,846 pedigreed fish in total. Because GENCONT could not handle such a large data set, this data set was split into 19 smaller data sets. Both algorithms gave the same solution with respect to the genetic gain and very similar solutions with respect to the number of selected animals. The OCSELECT algorithm was able to calculate the optimal contributions for the complete data set of 39,214, and therefore no preselection of the 39,214 fish was necessary before entering the fish into the new optimal contribution selection procedure.

Algorithms↗
PubMed1983

Comparison of two- and three-way rotational crossing and synthetic variety production involving inbred lines of Hereford cattle: postweaning traits.

Data for this linecrossing study were the postweaning growth and weight records of calves born from 1967 through 1975. The records consisted of 264 bull (M) and 263 heifer (F) straightline (SL) calves; 108 M and 100 F two-line rotational cross (2W) calves; 130 M and 102 F three-line rotational cross (3W) calves and 58 M and 51 F synthetic variety (SV) calves, all in the Hereford breed. Average inbreeding percentages of calves and dams in Lines 1, 4, 6 and 10 were 24, 28, 34 and 28; respectively. The M calves were fed a growing-fattening diet for 196 d after a 14-d period of adjustment to postweaning environment. The F calves were fed to gain approximately .5 kg daily during winter from weaning to about 12 mo of age and were then grazed on native pasture until about 18 mo of age. For M, average percentage increases over SL by 2W, 3W and SV combined over three generations were respectively, 9.0, 11.0, 11.6 for initial weight; 5.9, 8.1, 8.8 for 140-d weight; 4.8, 7.2, 7.7 for final 196-d weight and 1.5, 4.2, 4.7 for 196-d gain. All above estimates of increased weight or gain over SL were significant except for 196-d gain in 2W. For F, average percentage increases over SL by 2W, 3W and SV, respectively, were 9.0, 10.9, 11.3 for initial weight; 8.2, 9.2, 8.4 for 12-mo weight; 7.5, 7.7, 9.1 for 18-mo weight; 5.2, 5.3, 5.7 for 18-mo score. All these estimated increases over SL were significant.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗
PubMed1983

Pituitary-ovarian relationships during the estrous cycle and the influence of parity in an inbred strain of miniature swine.

Pituitary-ovarian function was analyzed in a strain of miniature swine previously shown to produce a low ovulation rate resulting in the formation of only 8.6 corpora lutea (CL)/animal. Five multiparous (M) and four nulliparous (N) miniature pigs with a mean inbreeding coefficient of .39 were monitored for estrous behavior through four consecutive estrous cycles. Daily blood samples were collected from 5 d before to 5 d after the onset of the second, third and fourth estrus and at 48-h intervals during the remainder of the second and third estrous cycle. Laparoscopy was used to examine the ovaries 1 and 5 d after onset of the third estrus and 2 d after the beginning of the fourth estrus. For the entire group, temporal fluctuations among serum estradiol-17 beta, luteinizing hormone (LH) and progesterone concentrations and sexual behavior were similar to previously published data in standard swine breeds. Although the mean lengths of the estrous cycle were not different (P greater than .05) between parity subgroups (M, 23 +/- 1.3 vs N, 22 +/- .7 d), multiparous pigs were in estrus longer (P less than .05) than nulliparous females (M, 3.7 +/- .2 vs N, 2.2 +/- .4 d). Parity subgroups were similar with respect to the mean number of follicles forming CL (M, 8.8 +/- .7 vs N, 9.2 +/- .2). Although an average of 6.2 +/- 2.1 CL had formed by 24-h after onset of estrus in the nulliparous subgroup, no CL were detected in the multiparous subgroup at this time.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗
PubMed1985

Selection for weaning weight and postweaning gain in Hereford cattle. I. Population structure and selection applied.

Single trait selection was practiced in three lines of Hereford cattle derived from a common base population. Selection was practiced on males only within sire families for increased weaning weight (WW) in the WW line (WWL), for postweaning gain (PG) in the PG line (PGL) and at random in the control line (CTL). Females were culled on the basis of age or reproductive failure. Progeny of selected bulls were produced in two herds from 1970 through 1981. The data consisted of records on 2,467 progeny of 125 sires and 922 dams. Generations of selection to produce the 1981 calf crop were 1.96, 1.85 and 1.80 for WWL, PGL and CTL, respectively. For calves born in 1981, mean cumulative selection differentials (CSD) were 54.5 kg in WWL and 37.8 kg in PGL. Corresponding values in standard deviation units (SDU) were 2.31 and 1.68, respectively. Secondary selection differentials were 25 to 40% as large as selection differentials for the primary traits. Unintentional selection in the CTL in 1981 was 16.2 kg or .68 SDU for WW and .2 kg or .01 SDU for PG, respectively. Regressions of CSD on year were 4.1 kg or .17 SDU in WWL and 3.2 kg or .14 SDU in PGL. Realized selection differentials were approximately 88% of the potential selection differentials in both lines. Inbreeding coefficients of dam and calves in 1981 were 2.0 and 3.5% in WWL, 2.1 and 3.5% in PGL and 2.9 and 5.8% in CTL.

Animals↗
PubMed2006

Major advances in globalization and consolidation of the artificial insemination industry.

The artificial insemination (AI) industry in the United States has gone through many consolidations, mergers, and acquisitions over the past 25 yr. There are 5 major AI companies in the United States today: 3 large cooperatives, 1 private company, and 1 public company. The latter 2 have majority ownership outside of the United States. The AI industry in the United States progeny-tests more than 1,000 Holstein young sires per year. Because healthy, mature dairy bulls are capable of producing well over 100,000 straws of frozen semen per year, only a relatively small number of bulls are needed to breed the world's population of dairy cows. Most AI companies in the United States do not own many, if any, females and tend to utilize the same maternal families in their breeding programs. Little differences exist among the selection programs of the AI companies in the United States. The similarity of breeding programs and the extreme semen-production capabilities of bulls have contributed to difficulties the AI companies have had in developing genetically different product lines. Exports of North American Holstein genetics increased steadily from the 1970s into the 1990s because of the perceived superiority of North American Holsteins for dairy traits compared with European strains, especially for production. The breeding industry moved towards international genetic evaluations of bulls in the 1990s, with the International Bull Evaluation Service (Interbull) in Sweden coordinating the evaluations. The extensive exchange of elite genetics has led to a global dairy genetics industry with bulls that are closely related, and the average inbreeding level for the major dairy breeds continues to increase. Genetic markers have been used extensively and successfully by the industry for qualitative traits, especially for recessive genetic disorders, but markers have had limited impact for quantitative traits. Selection emphasis continues to migrate away from production traits and towards nonproduction traits, especially towards health and fitness traits. Specifically, fertility has arguably become the major breeding and management issue facing dairy farmers today. Some producers have implemented crossbreeding programs in an effort to capitalize on heterosis, and crossbreeding will almost certainly need to be a bigger part of the AI companies business in the years ahead.

Animals↗
PubMed1985

Potential genetic gains from producing bulls with only sires as parents.

Micromanipulation of sperm and ova has been suggested as a means to produce progeny of two sires instead of a sire and dam. Selection schemes taking advantage of this technology could produce genetic gains 1.5 to 2 times current gains. An optimum strategy both genetically and economically would be to breed 99% of the population to young sires and 1% to progeny-tested sires. The genetic pathway from sires to sons could become the only pathway affecting genetic gain; this would eliminate problems of cow evaluation and would give artificial insemination organizations more control over quality of young sires. Inbreeding would not be a problem, and few other technologies could offer superior rates of genetic gain.

Animals↗
PubMed1992

Approximate accuracy of genetic evaluation under a single-trait animal model.

A method to approximate breeding value accuracy under a single-trait animal model was developed. Meyer's method was extended to account explicitly for the covariance between contemporaries, the distribution of relatives across herds, exact relationships between animals, and some cases of close in-breeding. The procedure comprised five steps. The diagonal term of each animal in the mixed model equations was progressively adjusted for 1) the herd-year-season effect, 2) contemporaries, 3) progeny and contemporaries of progeny, 4) mates, and 5) parents and parents of contemporaries, before being inverted and expressed in term of repeatability. The efficiency of this method and Meyer's method was compared with two examples. The proposed method appeared to be more efficient, particularly when herds were small, progeny concentrated in a few herds, and animals inbred. Estimates of repeatability from both methods were biased upward and remained sensitive to the number of generations included in the analysis. However, because of its ease of use, Meyer's method, with simple adjustments for repeatability level and inbreeding, can be recommended.

Animals↗
PubMed1997

Application of canonical transformation with missing values to multitrait evaluation of Jersey type.

A multitrait animal model was used to calculate predicted transmitting ability and reliabilities for final score and 15 linear type traits of 225,632 US Jersey cows. Records were adjusted for age and stage of lactation before analysis. The model contained effects for interactions of herd and date scored; year scored, parity, and age; and herd and sire; effects of permanent environment and additive genetics were also included. Of the 381,511 records included, some observations were missing for final score (8%), body depth (43%), and teat length (33%). The evaluation system used a canonical transformation, included several random effects, and estimated missing values with each iteration. Inbreeding was considered in the computations. Convergence was achieved in approximately 50 rounds of iteration. Correlations between animal and sire model predicted transmitting ability ranged from 0.56 to 0.95 and generally were higher for bulls than for cows and for more recent birth years. Genetic trend was strongly positive for dairy form, final score, and rear udder traits (height and width) and negative for udder depth. For other traits, genetic trend was small. This methodology should improve the accuracy of genetic evaluations for type traits of US Jerseys.

Aging↗
PubMed1984

Differences in body fat of six inbred lines of white leghorns derived from a common base population.

Genetic differences in body fat, body weight, follicle number, and egg production were found among six inbred lines of White Leghorn hens derived from a common outbred base population. High positive genetic correlations of body fat with body weight were found between inbred lines as well as between inbred parents and line-cross progeny. Heterosis of fatness, body weight, egg production, egg weight, and liver weight were observed. Large follicles and liver weight were unaffected by inbreeding and crossing of lines.

Adipose Tissue↗
PubMed1991

Deoxyribonucleic acid fingerprint comparisons between selected populations of chickens.

A pair of lines of White Plymouth Rock chickens selected for high or low juvenile body weight, a pair of White Leghorn chickens selected for high or low antibody response to sheep erythrocytes, and an F1 cross between each pair of lines, were used to produce DNA fingerprints (DFP). These DFP were prepared by mixing equal amounts of DNA from several individuals of a particular population, resulting in a DFP characteristic of the population. The populations provided individuals of known genetic relationships and inbreeding levels to evaluate the sensitivity of the DFP technique with DNA mixing. Levels of band sharing between breeds were lowest, those between selected lines within a breed were intermediate, and those between the selected lines and their F1 crosses were highest. These results show that DFP analysis is sensitive to several levels of genetic relationship.

Animals↗
PubMed1999

Heritability of recurrent exertional rhabdomyolysis in Thoroughbred racehorses.

OBJECTIVE: To determine the likely mode of inheritance and identify probable foundation horses for recurrent exertional rhabdomyolysis (RER) in Thoroughbred (TB) racehorses. ANIMALS: 4 families of TB racehorses with a high prevalence of RER, consisting of 3 to 53 horses/family, were used to determine mode of inheritance. Sixty-two TB horses with RER and 34 control TB racehorses without RER were used to identify probable foundation horses for the RER trait. PROCEDURE: RER was diagnosed by a veterinarian and verified by detecting high serum creatine kinase activity. Pedigrees dating from 1930 for all horses were entered into a database. Pedigrees of horses in 4 families were visually inspected for a pattern of inheritance and used for calculation of foundation horse contributions and inbreeding coefficients. The Markov chain Monte Carlo technique was used to analyze pedigrees of the 62 affected and 34 control horses for the conditional probability of foundation genotypes. A dominant mode of inheritance with variable expression model was used. RESULTS: Pedigree analysis supported an autosomal dominant mode of inheritance with variable expression. All affected horses from the 4 families shared a common ancestor. This ancestor and 5 other stallions had a conditional probability of 1.00 for being affected. All 6 stallions shared a common male ancestor within 3 to 5 generations. CONCLUSIONS AND CLINICAL RELEVANCE: On the basis of this study, the RER trait has been in TB racehorses for more than 70 years and may be inherited as an autosomal dominant trait with variable expression.

Alleles↗
PubMed2000

Selected lines and inbred strains. Tools in the hunt for the genes involved in alcoholism.

In their quest to elucidate the genetic influences contributing to alcoholism, researchers have long used selected lines and inbred strains of rodents. Selected lines are obtained by repeatedly mating those animals within a population that show extremely high or low values of the desired trait. Inbred strains are generated by mating male and female siblings, irrespective of any particular trait, over several generations. Both of these approaches have provided researchers with extensive knowledge about the genetic and neurobiological mechanisms contributing to alcohol-related traits. However, the use of these models is associated with some limitations, mostly resulting from the inbreeding involved in generating such lines and strains. Nevertheless, these models can offer some advantages over other genetic approaches, such as the analysis of quantitative trait loci or the generation of transgenic and knockout mice.

Alcoholism↗
PubMed2001

Isonymy, consanguinity and repeated pairs of surnames in Aromun populations.

The Aromuns represent a small and almost unknown people that live scattered over the Balkan Peninsula. Due to their language, that is very similar to classical Latin, they are in a special position. The Aromuns settled only in more recent times. Until now they lived as shepherds, as caravan guides and merchants and lead a semi-nomadic life. We are currently carrying out studies to determine the genetic structure of this population. To facilitate the interpretation of these data, we are also trying to obtain other important parameters that pertain to migration processes and the genealogical structure of this populations. The data arise from three areas in Albania, the Republic of Macedonia and Romania. The inbreeding coefficient and the proportion of repeated pairs of surnames was calculated through the use of genealogies and the isonymy method. The difference between these three populations are due primarily to confounding by selection of mates and family composition.

Albania↗
PubMed2001

[Influences on the occurrence of abomasal displacements in German Holstein cows].

The objectives of this study were to analyse risk factors for the prevalence of abomasal displacement in German Holstein cows. In the period from 02/01/1999 to 01/31/2000 five veterinary surgeons in Northern Lower Saxony registered all cases of abomasal displacement in German Holstein cows being under the official milk recording scheme. In total, the investigation included 160 farms and 9315 cows. An abomasal displacement was registered in 151 German Holstein cows, corresponding to a frequency of 1.6%. More than 75% of the abomasal displacements appeared during the first 30 days after calving. The left abomasal displacement (74.8%) was recorded more often than the right abomasal displacement (25.2%). Milk recording and pedigree data were supplied by the VIT (Vereinigte Informationssystem Tierhaltung), Verden, and merged with the own recordings. The influences of the calving month, the lactation number, the age at calving, the inbreeding coefficient, calving performance, duration of pregnancy, breed of calf sire, calf sire and the breeding values for the milk performance did not explain a significant part of the variation of the frequency of the abomasal displacement. Significant effects of the sire, birth of twins or even more calves and the herd were obtained for the leftsided abomasal displacement. For the rightsided abomasal displacement and for all abomasal displacements the herd effect was not significant. Heritability estimates using bivariate linear REML models were h2 = 0.043 +/- 0.012 for the leftsided abomasal displacement, and h2 = 0.007 +/- 0.004 for the rightsided abomasal displacement, respectively. Using the threshold model the heritabilities yielded estimates of h2 = 0.51 for the left abomasal displacement, and for the right abomasal displacement of h2 = 0.19, respectively.

Abomasum↗
PubMed1975

[A medico-genetic study of the population of Western Pamir. VI. Local genetic differentiation in the populations of Western Pamir].

The article comprises the results on the analysis of the structure of the great Pamirs' population (of a higher rank) and of one of its parts, the subpopulation of the valley of the river Bartang. Wright's F coefficient was used for the statistical treatment of the data obtained in the course of the analysis. The FST estimates were obtained from the variances of the frequencies of the genes located in 5 loci (ABO, MN, P, Rh and P.T.C.) culculated for 23 samples of the great populations of the Pamirs and for 9 samples of the population of the Bartang river valley. The general inbreeding coefficient for the Pamirs FIT=0,0323, its random component FST=0,0017 and the non-random component FIS=0.0306.

Blood Group Antigens↗
PubMed1992

Genetic diversity of laboratory gray short-tailed opossums (Monodelphis domestica): effect of newly introduced wild-caught animals.

The colony of gray, short-tailed opossums (Monodelphis domestica) at the Southwest Foundation for Biomedical Research, the primary supplier of this species for research purposes, was founded with nine animals trapped in 1978 in the state of Pernambuco, Brazil. Since 1984, 14 newly acquired founders from the state of Paraiba, Brazil have contributed to the gene pool of the colony. The animals from Paraiba and their descendants are significantly larger than the founders from Pernambuco and their descendants. The two groups also differ significantly in several measurements of morphologic traits. The changes in proportional contribution of each founder to the colony, and changes in inbreeding coefficients during the colony's history, are evaluated. Using previously established markers and three newly identified markers (ACP2, APRT, and DIA1), we show that the Paraiba-derived animals differ significantly from the original founders in allele frequencies and heterozygosity. The genetic diversity of the colony has been substantially increased by acquisition of the new founders from Paraiba. The colony is highly polymorphic, with 22.2% of loci surveyed by protein electrophoresis being variable. We conclude that the genetic differences between populations and among projects within the colony should be considered in future colony management procedures and in selection of experimental subjects.

Alleles↗
PubMed1976

[Clinico-genetic features of epilepsy in isolates and a panmictic population with intra-pair, intra-isolate and inter-isolate analysis].

Clinico-genealogical investigation revealed certain specific clinico-genetic characteristics of epilepsy under the conditions of isolation (62 cases) as compared to a panmictic population (76 cases). Itra-pair inter-isolate (31 pairs) and intra-isolate (29pairs) comparison has shown a higher frequency of complete phenotypic similarity in cases of intraisolate (24,1%), than in cases of inter-isolate (9,7%) epilepsy. A more conspicuous interisolate (than intra-isolate) clinical polymorphism of epilepsy combined with an equal frequency of intra-pair inter- and intra-isolate similarity with respect to exogonia and with a distinct (two-fold) increase of the average inbreeding coefficient between the parents of the patients (F = 0,0285) as compared to the general population of the isolates affords the evidence of the genetic heterogeneity of the disease. One of the mechanisms of the hereditary heterogeneity is assumed to be the polylocularity (genocopying).

Epilepsy↗
PubMed2003

[Case report--polydactyly in a German holstein calf].

A female German Holstein twin calf showed polydactyly in both front limbs and in one of the hind limbs. In three limbs an additional medial toe was seen. No malformations of the limbs were present in the male twin partner and four maternal half sibs. The analysis of the pedigree revealed that the affected calf had common ancestors. The coefficient of inbreeding of the affected calf was 1.312%. As a monogenic or digenic inheritance was suspected in similar cases, it may be probable that the polydactyly observed here has a genetic background.

Animals↗