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With the new opportunities from DNA technology, multitier breeding schemes have the potential to become more effective and more integrated. Integrated breeding schemes can also be better adapted to account for potential genotype by environment interactions (G × E) between tiers. In this case, phenotypic and genotype information from lower tiers becomes more valuable as it involves measurement of traits that directly represent the breeding objective. The objective of this study was to compare scenarios that represented different selection strategies and their economic effectiveness in fine-wool commercial sheep operations that exploit multitier breeding structures. Genomic selection (GS) applied in the multiplier and the commercial tier presented the largest additional revenue among all scenarios, as it resulted in the largest amount of genetic progress. The largest benefits from GS were outweighed by the genotyping costs, which made DNA parentage the most feasible strategy for the multiplier tier, resulting in the highest cumulative net present value (CNPV). The benefits of phenotypes and genotype information from the commercial environment were larger in the presence of G × E between the nucleus and the commercial tier. The CNPV was larger with a 50% reduction in genotyping costs, which increased the returns of GS scenarios by 2.7-fold on average. Higher selection intensity when selecting multiplier rams also resulted in larger benefits. In this case, returns for the breeding scheme were 3.5-fold higher when 33% of multiplier males were selected based on commercial information, compared to scenarios selecting 50% of the available multiplier rams. The benefits of collecting commercial phenotypes and genotypes were long term, which means that return on investment often took more than 10 years to be achieved, and were largely dependent on two-stage selection to reduce cost while maintaining selection efficiency and on the cost of a genotype test.

Residual feed intake (RFI) has been adopted in Australia for the purpose of genetic improvement in feed efficiency in beef cattle. RFI is the difference between the observed feed intake of an animal and the predicted feed intake based on its size and growth rate over a test period. Gene expression of eight candidate genes (AHSG, GHR, GSTM1, INHBA, PCDH19, S100A10, SERPINI2 and SOD3), previously identified as differentially expressed between divergent lines of high- and low-RFI animals, was measured in an unselected population of 60 steers from the Angus Society Elite Progeny Test Program using quantitative real-time PCR. Results showed that the levels of gene expression were significantly correlated with RFI. The genes explain around 33.2% of the phenotypic variance in RFI, and prediction equations using the expression data are reasonably accurate estimators of RFI. The association of these genes with economically important traits, such as other feed efficiency-related traits and fat, growth and carcass traits, was investigated as well. The expression of these candidate genes was significantly correlated with feed conversion ratio and daily feed intake, which are highly associated with RFI, suggesting a functional role for these genes in modulating feed utilisation. The expression of these genes did not show any association with average daily gain, eye muscle area and carcass composition.

Summary A genome-wide scan for quantitative trait loci (QTL) affecting gastrointestinal nematode resistance in sheep was completed using a double backcross population derived from Red Maasai and Dorper ewes bred to F1 rams. This design provided an opportunity to map potentially unique genetic variation associated with a parasite-tolerant breed like Red Maasai, a breed developed to survive East African grazing conditions. Parasite indicator phenotypes (blood packed cell volume – PCV and faecal egg count – FEC) were collected on a weekly basis from 1064 lambs during a single 3-month post-weaning grazing challenge on infected pastures. The averages of last measurements for FEC (AVFEC) and PCV (AVPCV), along with decline in PCV from challenge start to end (PCVD), were used to select lambs (N = 371) for genotyping that represented the tails (10% threshold) of the phenotypic distributions. Marker genotypes for 172 microsatellite loci covering 25 of 26 autosomes (1560.7 cm) were scored and corrected by Genoprob prior to qxpak analysis that included Box–Cox transformed AVFEC and arcsine transformed PCV statistics. Significant QTL for AVFEC and AVPCV were detected on four chromosomes, and this included a novel AVFEC QTL on chromosome 6 that would have remained undetected without Box–Cox transformation methods. The most significant P-values for AVFEC, AVPCV and PCVD overlapped the same marker interval on chromosome 22, suggesting the potential for a single causative mutation, which remains unknown. In all cases, the favourable QTL allele was always contributed from Red Maasai, providing support for the idea that future marker-assisted selection for genetic improvement of production in East Africa will rely on markers in linkage disequilibrium with these QTL.

SUMMARY Since the publication of the mouse genome, attention has focused on the strains that were selected for sequencing. In this paper we report the results of experiments that characterized the response to infection with the murine gastrointestinal nematode Heligmosomoides polygyrus of eight new strains (A/J, C57BL/6, C3H, DBA/2, BALB/c, NIH, SJL and 129/J), in addition to the well-characterized CBA (poor responder) and SWR (strong responder) as our controls. We employed the repeated infection protocol (consisting of 7 superimposed doses of 125L3 each administered at weekly intervals, faecal egg counts in weeks 2, 4 and 6 and assessment of worm burdens in week 6) that was used successfully to identify quantitative trait loci for genes involved in resistance to H. polygyrus . SWR, SJL and NIH mice performed indistinguishably and are confirmed as strong responder strains to H. polygyrus . CBA, C3H and A/J mice all tolerated heavy infections and are assessed as poor responders. In contrast, DBA/2, 129/J and BALB/c mice performed variably between experiments, some tolerating heavy worm burdens comparable to those in poor responders, and some showing evidence of resistance, although only in one experiment with female 129/J females and one with female BALB/c was the pattern and extent of worm loss much like that in SWR mice. Because the genetic relationships between six of the strains exploited in this study are now well-understood, our results should enable analysis through single nucleotide polymorphisms and thereby provide more insight into the role of the genes that control resistance to H. polygyrus.

Summary Microsatellite markers are commonly used for population genetic analyses of livestock. However, up to now, combinations of microsatellite data sets or comparison of population genetic parameters from different studies and breeds has proven difficult. Often different genotyping methods have been employed, preventing standardization of microsatellite allele calling. In other cases different sets of markers have been genotyped, providing differing estimates of population genetic parameters. Here, we address these issues and illustrate a general two-step regression approach in cattle using three different sets of microsatellite data, to combine population genetics estimates of diversity and admixture. This regression-based method is independent of the loci genotyped but requires common breeds in the data sets. We show that combining microsatellite data sets can provide new insights on the origin and geographical distribution of genetic diversity and admixture in cattle, which will facilitate global management of this livestock species.

To evaluate the Weitzman approach for assessing alternative conservation strategies for breed (population) diversity, we used genetic distance measures between 49 African cattle breeds divided into two groups of 26 taurine ( Bos taurus ) and sanga ( Bos taurusBos indicus ) breeds and 23 zebu ( Bos indicus ) and zenga (sangaBos indicus ) breeds. The derived maximum-likelihood trees clearly displayed the geo- graphic distribution and the zebu-taurine admixture of the breeds. We developed a novel scheme to estimate the extinction probability for each breed which considered total population size, change of population size over the last 10 years, distribution of the breed, risk of indiscriminate crossing, organization among farmers, establishment of conservation schemes, political situation of the countries, special traits, sociocultural impor- tance, and reliability of information. This scheme yielded reasonable estimates of extinction probabilities for the analyzed breeds, which were significantly influenced by the population size and its recent change, distri- bution of the breed, organization among farmers, establishment of conservation schemes, and reliability of information. The average extinction probability over all breeds and for each breed group was around 48%. Diversity in the zebu-zenga group was only half the diversity in the taurine-sanga group, mainly because of the lower number of breeds and their genetic origin. For both groups, the expected diversity after 20-50 years was about half the current diversity, and the coefficient of variation was about 20%. Our results suggest that the optimum conservation strategy is to give priority to those breeds with the highest marginal diversity, rather than to the most endangered breeds; thus, Madagascar Zebu and Muturu should be given conserva- tion priority in their respective groups. Our study demonstrates that efficient conservation of genetic diversity with limited funds has to take genetic and nongenetic factors into account. Nongenetic factors are accounted for within our scheme to derive extinction probabilities. Within-breed and within-population diversity are not accounted for. Extending Weitzman's basic approach accordingly could yield an effective methodology for determining conservation strategies under highly varying circumstances and for many species, including wild organisms.

This paper reports the results of a genome-wide search for quantitative trait loci (QTL) influencing immunological responses to infection with the gastro-intestinal nematode parasite Heligmosomoides polygyrus in an F2 population created by crossing the resistant SWR and the susceptible CBA inbred mouse strains. Following infections, intestinal granuloma score at post mortem, mucosal mast cell protease 1, and IgE and IgG1 titres were recorded. The susceptible CBA mice had significantly higher IgG1, but significantly lower IgE, mucosal mast cell protease 1 and granuloma scores than SWR mice. Significant QTL were mapped to chromosomes 4, 11, 13 and 17 for granuloma score; chromosomes 12 and 17 for IgE; chromosome 10, 17 and 18 for IgG1 and chromosomes 1, 9, 10, 11, 17 and 18 for mucosal mast cell protease 1. Chromosomes 10, 11, 17 and 18 had QTL affecting more than one trait, and these are most likely to represent single QTL with multiple effects rather than multiple QTL. Some of these QTL map to regions known to harbour genes responsible for the induction of immunological responses to intestinal worms.

The objective of this study was to evaluate whether the efficacy of marker assisted selection (MAS) could be improved by considering a confidence interval (CI) of QTL position. Specifically, MAS was applied for within-family selection in a stochastic simulation of a closed nucleus herd. The location and effect of the QTL were estimated by least squares interval mapping with a granddaughter design and marker information was then used in a top down scheme. Three approaches were used to select the best bull within full sibships of 3 or 40 bulls. All three were based on the probability of inheriting the favorable allele from the grandsire (PROB). The first method selected the sib with the highest PROB at the location with the highest F-ratio (MAX). The other two approaches were based on sums of estimated regression coefficients weighted by PROB at each cM within a 95% CI based on either bootstrapping (BOOT) or approximate LOD scores (LOD). Accounting for CI increased the relative genetic gain in all scenarios. The average breeding value (BV) of the selected bulls was increased by 2.00, 2.60 and 2.59% when MAS was applied using MAX, BOOT and LOD, respectively, compared to random selection (h2=0.30). Selected bulls carried the correct allele in 63.0, 68.5, 67.6 and 50.1% of the cases for MAX, BOOT, LOD and random selection, respectively. Beru;cksichtigung der Unsicherheit von QTL Positionen bei Marker-gestu;tzter Vorselektion von jungen Bullen vor der Nachkommenpru;fung Das Ziel dieser Studie war es zu prufen, ob die Effizienz von MAS (Marker gestutzte Selektion) durch Berucksichtigung des Konfidenzintervalls (CI) einer QTL Position verbessert werden kann. Es wurde MAS bei der Selektion innerhalb Familien in einer geschlossenen Nukleus Herde in einer stochastischen Simulation angewandt. Die Postition und der Effekt des QTL wurden in einem Granddaughter Design mit einer Least=Square Intervall Kartierung geschatzt. Die Marker Informationen wurden dann in einem top-down-Schema verwendet. Drei Ansatze fanden Verwendung, um den besten Bullen innerhalb von Vollgeschwistern von 3 oder 40 Bullen zu selektieren. Alle drei Ansatze basieren auf der Wahrscheinlichkeit, ein zu bevorzugendes Allel vom Grossvater zu erben (PROB). Bei der ersten Methode wurden die Geschwister mit der hochsten PROB an der Position mit dem hochsten F-Wert selektiert (MAX). Die beiden anderen Ansatze basierten auf den Summen der geschatzten Regressionskoeffizienten, gewichtet nach PROB an jedem cM innerhalb eines 95%igen CI, das entweder auf Bootstrapping (BOOT) oder approximativen LOD Scores (LOD) basiert. Die Berucksichtigung des CI vergrosserte den relativen genetischen Fortschritt in allen Szenarien. Bei Anwendung von MAS waren die durchschnittlichen Zuchtwerte der selektierten Bullen bei Verwendung von MAX, BOOT und LOD verglichen mit zufalliger Selektion (h2=0,30) um 2,00, 2,60 und 2,59% gestiegen. Die selektierten Bullen trugen das richtige Allel bei den entsprechenden Berechnungen MAX, BOOT, LOD und zufalliger Selektion in 63,0, 68,5, 67,6 und 50,1% der Falle.

Summary Stochastic simulation was used to study the effect on selection response of accounting for inbreeding versus ignoring it in the construction of the inverse of the relationship matrix used in mixed model equations (MME) to obtain BLUP of breeding values. Three different heritabilities of 0.10, 0.25, and 0.50 and two different family structures were used. Selection of replacement animals was based on best linear unbiased predictors (BLUP) of breeding values using an animal model. Average inbreeding coefficients (F) were in the range of 0.4–0.5 after 11 generations of selection. Even with such high inbreeding levels, no significant differences in selection responses were found between accounting or ignoring F in MME construction over the range of heritabilities and family structures. Zusammenfassung Die Einbeziehung von Inzuchtkoeffizienten bei der BLUP-Zuchtwertschatzungen und ihre Auswirkung auf den Selektionserfolg Um bei der Aufstellung der inversen Verwandtschaftsmatrix in Mischmodellgleichungen (MME) zur BLUP-Zuchtwertschatzung unter einem Tiermodell, den Effekt einer Einbeziehung bzw. Vernachlassigung von Inzucht auf den Selektionserfolg zu untersuchen, wurde eine stochastische Simulation durchgefuhrt. Drei verschiedene Heritabilitaten von 0.10, 0.25 and 0.50 und zwei verschiedene Familienstrukturen wurden verwendet. Die Selektion der Remonte erfolgte auf der Basis der ‘best linear unbiased prediction’ (BLUP) fur die Zuchtwerte unter einem Tiermodell. Die mittleren Inzuchtkoeffizienten (F) bewegten sich im Bereich 0.4–0.5 nach 11 Generationen der Selektion. Selbst unter so hohem Inzuchtniveau konnte kein signifikanter Unterschied im Selektionserfolg bei Beachtung oder Vernachlassigung des Inzuchtkoeffizienten F, bei der Konstruktion der MME, festgestellt werden. Das gilt sowohl fur die Bandbreite der Heritabilitaten als auch fur die Familienstrukturen.

A polymorphism in the igf2 gene of chickens was identified using NlaIII (GenBank accession number AF218827). In some embryos, the igf2 alleles were expressed monoallelically from either maternal or paternal alleles. These data demonstrate that genomic imprinting is not confined to mammalian vertebrates and suggest that genomic imprinting evolved at an early stage of vertebrate evolution. The observations that the igf2 gene is imprinted in a minority of embryos suggest that the imprinting in birds is unrelated to embryonic growth. Genome imprinting may provide opportunities for evolution of genes in a nonexpressed state. In poultry breeding, the presence of imprinted genes may make a major contribution to unequal performance in reciprocal matings between commercial lines. Mol. Reprod. Dev. 56:345–352, 2000. © 2000 Wiley-Liss, Inc.

Sequence analysis of PCR products of a 343-bp fragment from exon 29 of the porcine APOB gene of four Erhualian and four Landrace pigs revealed a missense G/C substitution at position of 6117 in this gene. Two allele-specific primers were designed to genotype this polymorphism using the Bi-PASA technique. Genotyping of 146 animals from Erhualian, Hampshire, Large White, Landrace and Duroc breeds revealed large breed differences in allele frequency. No association with fatness was observed within each of the four European breeds, where animals had been selected to be those with the highest and those with the lowest backfat depth at 100 kg liveweight from a large carcass dissection project.

Summary Deterministic methods were used to calculate the accuracy of evaluation, and the correlation of estimated breeding values (EBV) among sibs, when evaluation is based on phenotypic records of the individual and relatives, or on quantitative-trait-locus (QTL) information. An additive infinitesimal genetic model was assumed, with discrete generations of truncation selection on EBV, and random mating of selected parents in a hierarchical design. It was shown that the overlap of phenotypic data between the evaluations of relatives causes large increases in correlations of EBV with only modest increases in accuracy. This explains the disproportionate increases in inbreeding observed by other authors. By contrast, the use of major-locus information leads to low correlations of EBV among relatives, provided that functional loci are directly identified or there is complete linkage disequilibrium. Use of information from QTL should reduce EBV correlations and, hence, inbreeding, but use of information from markers may not be so useful, since errors of estimation of association with QTL will be shared by family members, leading to increased correlations of EBV. Zusammenfassung Genauigkeit und Korrelation der geschatzten Zuchtwerte von verwandten Tieren mit Information von Verwandten oder von identifizierten Genen Zur Kalkulation der Genauigkeit und Korrelation der geschatzten Zuchtwerte von Geschwistern sind deterministische Methoden angewandt worden fur die Situation, das die geschatzten Zuchtwerte auf phanotypischen Beobachtungen von einem Individuum und dessen Verwandten oder auf der Information von Loci, die quantitative Merkmale beeinflusen (QTL), basieren. Ein additiv-genetisches Infinitisimalmodell wurde unterstellt, nach diskreten Generationen mit Selektion nach geschatzten Zuchtwerten und Zufallspaarung der selektierten Eltern in einem hierarchischen Design. Es konnte gezeigt werden, das die Uberlappung der phanotypischen Daten bei der Zuchtwertschatzung von verwandten Tieren zu einer erheblichen Erhohung der Korrelation wischen geschatzten Zuchtwertenfuhrte, wahrend die Genauigkeit der Schatzwerte nur geringfugig erhoht war. Diese Ergebnisse konnen die unverhaltmassige Erhohung der Inzucht, die andere Autoren beobachtet haben, erklaren. Im Gegensatz dazu fuhrte die Verwendung der Information von QTL zu einer niedrigenen Korrelation der geschatzten Zuchtwerte von verwandten Tieren, vorausgesetzt die funktionellen QTL konnen direkt identifiziert werden oder es besteht ein vollstandiges Kopplungsungleichgewicht. Die Berucksichtigung der Information von QTL sollte die Korrelation der geschatzten Zuchtwerte reduzieren konnen und fuhrt deshalb zur Verminderung der inzucht. Die Verwendung von Markerinformation konnte weriger nutzlich sein, weil Fehler bei der Schatzung der Kopplung zwischen Marker und QTL fur alle Mitglieder einer Familie gemeinsam sind und deshalb zu erhohten Korrelationen zwischen geschatzten Zuchtwerten fuhren konnen. Resumen Precision de la Evaluacion y Correlacion de los Valores Reproductivos Entre Parientes con Evaluacion Basada en Informacion de Parientes o de Loci Conocido. Metodos deterministicos fueron usados para calcular la precision de evaluacion y la correlacion de los valores reproductivos estimados (EBV) entre hermanos cuando la evaluacion esta basada en informacion fenotipica de individuos y parientes o basada en informacion de loci en caracteristicas cuantitativas (QTL). Se asumio un modelo genetico infinitesimal con generaciones discretas de seleccion truncacional sobre los EBV y apareamiento aleatorio de padres seleccionados en un diseno jerarquico. Se demostro que la sobreposicion de informacion fenotipica entre las evaluaciones de los parientes causa un gran incremento en las correlaciones de los EBV con aumentos minimos de la precision de evaluacion. Esto explica los desproporcionados aumentos de endogamia observados por otros autores. En contraste el uso de informacion proveniente de QTL induce a bajas correlaciones de los EBV entre parientes, asumiendo que los loci funcionales estan directamente identificados o hay un complete ligamiento desequilibrado. El uso de la informacion de QTL deberia reducir las correlaciones de los EBV y por lo tanto la endogamia, pero el uso de informacion de marcadores puede no ser tan util debido a que los errores de estimacion de la asociacion con QTL seran comunes para los miembros de la familia, lo cual lleva al aumento de la correlacion entre los EBV.

The polymorphism at the PvuII recognition site in the ESR gene showed no statistically significant association with sow productivity traits in a Meishan x Large White F2 population. Estimates of the effect on litter size were, however, in the opposite direction and statistically different from previously published estimates. Taken together with results from other publications, results here indicate that this PvuII polymorphism displays different degrees of linkage disequilibrium with a gene or genes controlling litter size in different populations.

Multi-primer target polymerase chain reaction (MPT-PCR) is a rapid method for the identification of specific BoLA-DRB3 alleles. In a single PCR reaction, the presence of two alleles associated with increased risk, DRB3.2*23 (DRB3*2701-2703, 2705-2707) and decreased risk, DRB3.2*16 (DRB3*1501, 1502), of mastitis in Canadian Holstein can be detected. Two outer primers amplify exon 2 of DRB3. Simultaneously, two inner, allele-specific primers amplify individual alleles. Initially, 40 cows previously typed by PCR-restriction fragment length polymorphism (PCR-RFLP) were genotyped using the multi-primer approach. An additional 30 cows were first genotyped by multi-primer target PCR, then by PCR-RFLP. All animals were correctly identified and there were no false positives. This technique can readily be modified to identify other BoLA alleles of interest.

Data on the evolution of a polygenically determined resistance to dimethoate, in populations of houseflies on Danish farms, were examined in order to see whether useful information about the processes involved could be obtained. Examination of the variance of tolerances in samples of flies suggested that there was considerable genetic variability for resistance before dimethoate was first used, but provided no other information. Before examining estimates of log LD50 (LLD50), the relationship between LLD50 and the log weight of the flies assayed was investigated in an experiment in Denmark, and the standard error of LLD50 estimates was estimated. Examination of LLD50 estimates (adjusted for log weight) provided evidence of substantial migration of flies between farms, which produced large and unpredictable changes in tolerance levels on individual farms, and prevented extraction of further useful information from the data. However, it was concluded that even had migration been negligible, the data would not have provided information suitable for the construction of models of the evolution of this polygenically determined resistance. This conclusion is likely to hold for most existing data. Alternative approaches towards obtaining models of the evolution of polygenically determined resistances are suggested.