Genome-wide association study for age at puberty and resumption of cyclicity in a crossbred dairy cattle population.

Fertility is of primary economic importance in dairy cattle and the most common reason for involuntary culling. However, standard fertility traits have very low heritability that renders genetic selection slow and difficult. In this study, we explored fertility from an endocrine standpoint.

Short communication: Methods to compute genomic inbreeding for ungenotyped individuals.

The genomic measure of inbreeding is closer to the actual inbreeding than the pedigree-based measure. However, it cannot be computed for ungenotyped animals. An estimate of genomic inbreeding comes from the diagonal of matrix H used in single-step methods.

A fast indirect method to compute functions of genomic relationships concerning genotyped and ungenotyped individuals, for diversity management.

Background: Pedigree-based management of genetic diversity in populations, e.g., using optimal contributions, involves computation of the [Formula: see text] type yielding elements (relationships) or functions (usually averages) of relationship matrices.

Optimizing selection with several constraints in poultry breeding.

Poultry breeding schemes permanently face the need to control the evolution of coancestry and some critical traits, while selecting for a main breeding objective. The main aims of this article are first to present an efficient selection algorithm adapted to this situation and then to measure how the severity of constraints impacted on the degree of loss for the main trait, compared to BLUP selection on the main trait, without any constraint. Broiler dam and sire line schemes were mimicked by simulation over 10 generations and selection was carried out on the main trait under constraints for coancestry and for another trait, antagonistic with the main trait.

Utility of reassessment after neoadjuvant therapy and difficulties in interpretation.

We describe the main tools for MR assessment of the response of rectal cancer tumors after chemotherapy, before surgery. In locally advanced cases of rectal and lower rectal cancer, MR is useful in allowing the treatment strategy to be adjusted, enabling conservative surgery to be performed if the patient responds well. The different types of response (fibrous, desmoplastic and colloid), their appearances and difficulties in MR interpretation are described.

MIM: an indirect method to assess inbreeding and coancestry in large incomplete pedigrees of selected dairy cattle.

In real data, inbreeding is usually underestimated because of missing pedigree information. A method adapted to the dairy cattle situation is presented to approximate inbreeding when the stored population pedigree is incomplete. Missing parents in incomplete pedigrees were given a dummy identification and assigned to groups (up to nine for a given birth date of progeny).

Optimized diffusion of buck semen for saving genetic variability in selected dairy goat populations.

Background: Current research on quantitative genetics has provided efficient guidelines for the sustainable management of selected populations: genetic gain is maximized while the loss of genetic diversity is maintained at a reasonable rate. However, actual selection schemes are complex, especially for large domestic species, and they have to take into account many operational constraints. This paper deals with the actual selection of dairy goats where the challenge is to optimize diffusion of buck semen on the field.

Reproductive technologies and genomic selection in cattle.

The recent development of genomic selection induces dramatic changes in the way genetic selection schemes are to be conducted. This review describes the new context and corresponding needs for genomic based selection schemes and how reproductive technologies can be used to meet those needs. Information brought by reproductive physiology will provide new markers and new improved phenotypes that will increase the efficiency of selection schemes for reproductive traits.

A mating method accounting for inbreeding and multi-trait selection in dairy cattle populations.

Selection in dairy cattle populations usually takes into account both the breed profiles for many traits and their overall estimated breeding values (EBV). This can result in effective contributions of breeding animals departing substantially from contributions optimised for saving future genetic variability. In this work, we propose a mating method that considers not only inbreeding but also the detailed EBV of progeny or the EBV of sires in reference to acceptance thresholds.

Optimized management of genetic variability in selected pig populations.

Controlling the increase of coancestry and inbreeding coefficients in selected populations is made possible through calculation of the optimal contributions allowed to breeding animals, given the current situation with regard to genetic diversity, and further, through optimal design of matings. The potential of such an approach for pig breeding was tested by retrospective optimization on the French Landrace population in reference to the matings actually carried out during a 21-week test period. The major constraint was that the average overall estimated breeding value (EBV) should be the same as the observed one, for not decreasing short-term genetic gain.

Sustainable long-term conservation of rare cattle breeds using rotational AI sires.

The development of inbreeding in rotation breeding schemes, sequentially using artificial insemination (AI) sires over generations, was investigated for a full AI scheme. Asymptotic prediction formulae of inbreeding coefficients were established when the first rotation list of AI sires (possibly related) was in use. Simulated annealing provided the optimal rotation order of sires within this list, when the sires were related.

A proximal decomposition of inbreeding, coancestry and contributions.

Wright's (1922) coalescence probabilistic method decomposes the average coancestry or the average inbreeding of the population of interest into contributions of ancestors who are directly responsible for coancestry. These ancestors are less numerous and younger than those given by Caballero & Toro's (2000) method. Then, Wright's method yields a more parsimonious representation of the origin of coancestry or inbreeding.

Pharmacologically active microcarriers releasing glial cell line - derived neurotrophic factor: Survival and differentiation of embryonic dopaminergic neurons after grafting in hemiparkinsonian rats.

To improve the outcome of foetal dopaminergic cell transplantation for the treatment of Parkinson's disease, pharmacologically active microcarriers (PAM) were developed. PAM are able to convey cells on their surface and release a growth factor to improve cell survival, differentiation and integration after brain implantation. Lysozyme-releasing PAM were first produced and characterized.

Estimation of genetic parameters for quantitative trait loci for dairy traits in the French Holstein population.

A marker-assisted selection program (MAS) has been implemented in dairy cattle in France. The efficiency of such a selection program depends on the use of correct genetic parameters for the marked quantitative trait loci (QTL). Therefore, the objective of this study was to estimate the proportion of genetic variance explained by 4 QTL described in previous studies (these QTL are segregating on chromosomes 6, 14, 20, and 26).

Efficient computation of the inverse of gametic relationship matrix for a marked QTL.

Best linear unbiased prediction of genetic merits for a marked quantitative trait locus (QTL) using mixed model methodology includes the inverse of conditional gametic relationship matrix (G-1) for a marked QTL. When accounting for inbreeding, the conditional gametic relationships between two parents of individuals for a marked QTL are necessary to build G-1 directly. Up to now, the tabular method and its adaptations have been used to compute these relationships.

A fast algorithm for computing inbreeding coefficients in large populations.

Inbreeding coefficients of animals are required in many genetic analyses of livestock records. A modification of Colleau's indirect algorithm to compute inbreeding coefficients in large populations is presented. With overlapping generations, the modified algorithm evaluated all progeny of each sire simultaneously in one back and forth exploration of a reduced pedigree.

A method for the dynamic management of genetic variability in dairy cattle.

According to the general approach developed in this paper, dynamic management of genetic variability in selected populations of dairy cattle is carried out for three simultaneous purposes: procreation of young bulls to be further progeny-tested, use of service bulls already selected and approval of recently progeny-tested bulls for use. At each step, the objective is to minimize the average pairwise relationship coefficient in the future population born from programmed matings and the existing population. As a common constraint, the average estimated breeding value of the new population, for a selection goal including many important traits, is set to a desired value.

Predicting observed and latent responses to BLUP selection involving logistic variates.

Multivariate BLUPs can be derived when data are a mixture of continuous traits and observed discrete traits controlled by logistic latent traits. Algorithms were developed for predicting discrete responses to BLUP selection, and latent responses when the selection process included additional culling on scores. These algorithms were Taylor expansions using well-known expressions such as the probabilities and the two first moments of the truncated multinormal distribution, after appropriate re-parametrizations.

An indirect approach to the extensive calculation of relationship coefficients.

A method was described for calculating population statistics on relationship coefficients without using corresponding individual data. It relied on the structure of the inverse of the numerator relationship matrix between individuals under investigation and ancestors. Computation times were observed on simulated populations and were compared to those incurred with a conventional direct approach.

Estimation of the genetic correlations between twisted legs and growth or conformation traits in broiler chickens.

Genetic correlations between two types of leg deformities, valgus and varus angulations, and some growth or conformation traits were estimated in two commercial broiler strains. 14 264 chickens of both sexes in line A were measured for leg defects at 6 weeks and body weight at 3 (BW3) or 6 (BW6) weeks. The same measures were taken in line B on 8 164 chickens, as well as breast angle (BRA) and breast meat yield (BRM) at 6 weeks on 70% of the male birds.

Marker-assisted selection for a sex-limited character in a nucleus breeding population.

The benefits of marker-assisted selection were examined by simulation of an adult multiple ovulation and embryo transfer nucleus breeding scheme. Animals were either typed for two polymorphic marker loci, 20 centimorgans apart, flanking a single biallelic quantitative trait locus and were evaluated using a model accounting for marker information, or animals were not typed but were evaluated by a conventional BLUP animal model. Selection was for a single trait measured on females, and each dam had 4 sons and 4 daughters.

Genetic steady-state under BLUP selection for an infinite and homogeneous population with discrete generations.

A matrix derivation is proposed to analytically calculate the asymptotic genetic variance-covariance matrix under BLUP selection according to the initial genetic parameters in a large population with discrete generations. The asymptotic genetic evolution of a homogeneous population with discrete generations is calculated for a selection operating on an index including all information (pedigree and records) from a non-inbred and unselected base population (BLUP selection) or on an index restricted to records of a few ancestral generations. Under the first hypothesis, the prediction error variance of the selection index is independent of selection and is calculated from the genetic parameters of the base population.

Marker assisted selection for genetic improvement of animal populations when a single QTL is marked.

A Monte Carlo simulation study to evaluate the benefits of marker assisted selection (MAS) in small populations with one marked bi-allelic quantitative trait locus (QTL) is described. In the base generation, linkage phase equilibrium between the markers, QTL and polygenes was assumed and frequencies of 0.5 for the two QTL alleles were used.

A simulation study of selection methods to improve mastitis resistance of dairy cows.

Mastitis problems were assumed to decrease profitability of dairy cows through milk price, treatment cost, and involuntary culling cost. Milk price decreased through a stepwise function of SCC (actual French conditions). A continuous latent variate was supposed to trigger other costs through appropriate thresholds.