Genetic Evaluation

Although the theoretical relationship between population size, fitness, and genetic variation is well established, only a few studies have provided direct evidence that ties a decline in both genetic variation and fitness to a demographic bottleneck for a natural system. We report on a genetic comparison of four populations of the Greater Prairie Chicken (  Tympanuchus cupido) with different demographic histories. Specifically, we compared a population from Illinois that has suffered an extreme demographic contraction and an associated decline in population fitness (measured in terms of hatchability rates) with populations from Kansas, Nebraska, and Minnesota with no known history of bottlenecks or associated declines in fitness. Using the polymerase chain reaction, we amplified six microsatellite loci from which levels of heterozygosity, allelic diversity, and geographic differentiation (FST and RST   ) of the studied populations were estimated. Results of this analysis showed that...

Forest trees can occupy extensive geography and environmentally highly variable areas which result in high genetic variability in the direction of pressure from natural selection. At the same time, the majority of conifer species are wind-pollinated from both short and long distances, resulting in wide-spread gene flow, which can lead to maladaptation to local conditions. Quantitative analyses of provenance/progeny tests correct for genetic differences between populations to ensure unbiased genetic parameters are obtained. Commonly, the provenance effect is fitted as a fixed term or can be implemented as a contemporary group in the pedigree. The use of a provenance effect, either as a fixed term or as the same contemporary groups in both maternal and paternal sides of the pedigree, resulted in fairly similar precision of genetic parameters in our case. However, when we developed a phantom contemporary group for the paternal side of the pedigree that considered a different genetic quality of pollen compared with the maternal contribution from trees in the local environment, the model fit and accuracy of breeding values increased. Consideration of the mating dynamics and the vector of gene flow are important factors in modelling contemporary genetic groups, particularly when implementing pedigrees within a mixed model framework to obtain unbiased estimates of genetic parameters. This approach is especially important in traits involved in local adaptation.

Foram utilizados 263.390 registros de produção de leite no dia do controle (PDC) de 32.448 primeiras lactações de vacas da raça Holandesa com parto no período de 1991 a 2001, para estimar componentes de variância e parâmetros genéticos utilizando um modelo animal e a metodologia REML. Os dados de produção foram coletados pelo Serviço de Controle Leiteiro da Associação Brasileira de Criadores de Bovinos da Raça Holandesa e suas afiliadas estaduais e disponibilizados pela Embrapa Gado de Leite. O modelo para ajuste da produção de leite até 305 dias (P305) incluiu os efeitos fixos de rebanho-ano de parto, época do parto e idade da vaca ao parto, com termos linear e quadrático, e os efeitos aleatórios de animal e erro. Os mesmos efeitos foram incluídos no modelo para as produções de leite no dia do controle (PDC) tanto sob modelo uni- e bi-caráter como sob modelo de repetibilidade (MRS), exceto para o efeito fixo de grupo contemporâneo, definido por rebanho-ano-mês do controle. Alternat...

A total of 7622 cattle were measured for several weight and body composition traits in temperate and tropically adapted breeds. Traits included: liveweight, hip height, body fat score, muscle score, flight time, ultrasound scanned fatness, and eye muscle area. Measurements were taken at 3 stages during the project: post-weaning, start of finishing, and end of finishing (i.e. pre-slaughter). Animals were finished to 3 target market-weight end-points (220, 280, or 340 kg carcass weight), either on pasture or in a feedlot, and in 2 different geographic regions for tropically adapted breeds. These data were used to estimate genetic parameters for the traits at each stage, and also to estimate the effect of market weight and finishing regimes on the phenotypic and genetic expression of each trait measured at the end of finishing stage. Results showed, for all traits, that the magnitude of the phenotypic expression increased across the stages and market-weight end-points for the end of fi...

The objectives of this study were to examine the genetic control of survival in segregant families F3 of the common bean (Phaseolus vulgaris L.) in southern Brazil during the 2004-2005 growing season, to identify useful genotypes for the breeding program of this crop, and to determine the genetic association between survival and weight of 100 seeds (production trait; P100). A Bayesian approach was used to predict breeding values and to estimate variance components. Survival was recorded as a binary response: dead plant or live plant during harvest. The total population consisted of 11,520 individual plants. The difference in the magnitude between the best and the worst families was as high as 22%, and varied from 57 to 73%. Survival was found to be highly heritable, with an a posteriori heritability mean and Bayesian credible interval: H² = 53% (43-65%). The genetic advance by direct selection achieved a value of 18%, considering a selection intensity of 25%. Survival was not correl...

The aim of this study was to compare different scenarios for bull dam selection in a nucleus herd. A deterministic simulation study using selection index methodology was undertaken. In the scenarios studied, differing amounts of information on functional traits were available when bull dams were selected, and the resulting genetic responses in these traits were compared. Field-recorded fertility traits used in the scenarios were available as progeny test results of artificial insemination bulls: these included pregnant at first insemination (PFI), interval between calving and first insemination (CFI), and cases of reproductive disorders (RD). Similarly, field-recorded cases of clinical mastitis (CM), lactation somatic cell score (LSCS), and protein yield (PY) were included for pedigree selection. In the scenarios, heat intensity score and progesterone levels were treated as new indicator traits of fertility recorded in the nucleus herd. Traits CFI and LSCS were assumed to be better ...

Records of 18,770 Nelore animals, born from 1975 to 2002, in 8 herds participating in the Nelore Cattle Breeding Program, were analyzed to es- timate genetic parameters for mature BW. The mature BW were analyzed as a single BW taken closest to 4.5 yr of age for each cow in the data file, considering BW starting from 2 (W2Y_S), 3

The objective of this study was to estimate parameters required for genetic evaluation of Simmental carcass merit using carcass and live animal data. Carcass weight, fat thickness, longissimus muscle area, and marbling score were available from 5,750 steers and 1,504 heifers sired by Simmental bulls. Additionally, yearling ultrasound measurements of fat thickness, longissimus muscle area, and estimated percentage of intramuscular fat were available on Simmental bulls (n = 3,409) and heifers (n = 1,503). An extended pedigree was used to construct the relationship matrix (n = 23,968) linking bulls and heifers with ultrasound data to steers and heifers with carcass data. All data were obtained from the American Simmental Association. No animal had both ultrasound and carcass data. Using an animal model and treating corresponding ultrasound and carcass traits separately, genetic parameters were estimated using restricted maximum likelihood. Heritability estimates for carcass traits were...

An investigation was carried out with nineteen genotypes of cucumber to study the nature and magnitude of genetic variability among them by considering twenty one traits at the Vegetable Research Farm of Department of Horticulture, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi during Kharif 2016. High estimates of PCV and GCV were obtained for traits like number of node at which first pistillate flower appears, fruit yield (q/ha), fruit length while the moderate value was recorded for the traits like average fruit weight indicated a good deal of variability in those characters signifying the effectiveness of selection of desirable types for improvement of such characters will be rewarding. Heritability and genetic advance are important selection parameters and selection success is a reflectance of selection response. Heritability estimates along with genetic advance are normally more helpful in predicting the gain under selection than heritability estimates alone. High heritability coupled with high genetic advance as percentage of mean were observed for number of node at which first pistillate flower appears followed by fruit yield (q/ha), fruit length, average fruit weight, test weight, number of fruits per plant, number of nodes per vine, number of primary branches per vine, etc., indicating predominance of additive gene action for these characters. Hence, simple selection based on phenotypic performance of these characters would be more effective.

Adenocarcinoma in Barrett's esophagus is the second most rapidly increasing cancer in western society. The cause and pathogenesis are unknown. Although histological studies suggest that there is successive progression from metaplasia and dysplasia, with a high risk of subsequent invasive carcinoma, at present there is no direct evidence that metaplastic and dysplastic epithelia are clonal precursors of adenocarcinoma. We selected 12 esophagectomy specimens of Barrett's esophagus patients, which showed a spectrum of normal tissue, metaplasia, dysplasia, and invasive carcinoma in each individual biopsy. We applied the microdissection technique to selectively procure microscopic tissue samples from H&E-stained slides for genetic evaluation using polymorphic markers flanking the APC gene locus. Identical APC gene alterations were found in the dysplastic and adenocarcinoma foci of all informative cases. The same changes were observed even in some metaplastic foci adjacent to dysp...

Mastitis is associated with elevated somatic cell count in milk, inducing a positive correlation between milk somatic cell score (SCS) and the absence or pres- ence of the disease. In most countries, selection against mastitis has focused on selecting parents with genetic evaluations that have low SCS. Univariate or multivar- iate mixed linear models have been used for statistical description of SCS. However, an observation of SCS can be regarded as drawn from a 2- (or more) component mixturedefinedbythe(usually)unknownhealthstatus of a cow at the test-day on which SCS is recorded. A hierarchical 2-component mixture model was devel- oped, assuming that the health status affecting the re- cordedtest-daySCSiscompletelyspecifiedbyanunder- lying liability variable. Based on the observed SCS, inferences can be drawn about disease status and pa- rameters of both SCS andliability to mastitis. The prior probability of putative mastitis was allowed to vary between subgroups (e.g., herds, fam...

Background In aquaculture breeding, resistance against infectious diseases is commonly assessed as time until death under exposure to a pathogen. For some diseases, a fraction of the individuals may appear as "cured" (non-susceptible), and the resulting survival time may thus be a result of two confounded underlying traits, i.e., endurance (individual hazard) and susceptibility (whether at risk or not), which may be accounted for by fitting a cure survival model. We applied a cure model to survival data of Pacific white shrimp (Penaeus vannamei) challenged with the Taura syndrome virus, which is one of the major pathogens of Panaeid shrimp species. Methods In total, 15,261 individuals of 513 full-sib families from three generations were challenge-tested in 21 separate tests (tanks). All challenge-tests were run until mortality naturally ceased. Time-until-event data were analyzed with a mixed cure survival model using Gibbs sampling, treating susceptibility and endurance a...

Broadening the genetic base of upland cotton (Gossypium hirsutum L.) is essential for continu- ous genetic improvement of yield and fiber quality through breeding. The objectives of this study were to evaluate a species polycross (SP) popula- tion for phenotypic and genotypic variations in yield and fiber quality, investigate morphological variations among the SP lines, and analyze the interrelationships among

Summary In October 2008 the joint Nordic total merit index named Nordic Total Merit (NTM) for the Nordic Red breeds, Holstein and Jersey in Sweden, Finland and Denmark was published for the first time. The NTM-index is composed of joint Nordic EBV's for the different trait groups and was driven by a wish from Nordic Cattle Genetic Evaluation to get

The validity of national genetic evaluations depends on the quality of input data, on the model of analysis, and on the correctness of genetic evaluation software. A general strategy was developed to validate national breeding value prediction software: performances from a real data file were replaced with simulated ones, created from simulated fixed and random effects and residuals in such a way that BLUP estimates from the evaluation software must be equal to the simulated effects. This approach was implemented for a multiple-trait model and a random regression test-day model. An example was presented on test-day observations analyzed with a random regression animal model including a lactation curve described as a sum of fixed polynomial regression and fixed spline regression on days in milk, and with genetic and permanent environmental effects modeled by using Legendre polynomials of order 2. Residuals had heterogeneous variances, and phantom parent groups were included. This met...

The availability of genomic estimated breeding values (GEBV) allows for possible modifications to existing dairy cattle breeding programs. Selection index calculations including genomic and phenotypic observations as index sources were used to determine the optimal number of offspring per genotyped sire with a focus on functional traits and the design of cooperator herds, and to evaluate the importance of a central station test for genotyped bull dams. Evaluation criteria to compare different breeding strategies were correlations between index and aggregate genotype (r(TI)), and the relative selection response percentage (RSR) of an index without single nucleotide polymorphism information in relation to a single nucleotide polymorphism-based index. The number of required daughter records per sire to achieve a predefined r(TI) strongly depends on the accuracy of GEBV (r(mg)) and the heritability of the trait. For a desired r(TI) of 0.8, h(2) = 0.10, and r(mg) = 0.5, at least 57 addit...