Application of differential display RT-PCR to identify porcine liver ESTs

Differential display banding patterns of liver and nine other tissues were produced in order to isolate porcine expressed sequence tags (ESTs), representing genes active in liver while avoiding redundant analysis of housekeeping genes. We cloned and sequenced those cDNA fragments that were unique to the liver banding pattern or that appeared in liver and a maximum of four other tissues. We analyzed 240 sequences that represent 200 distinct ESTs/genes and that make up the first list of liver ESTs in the pig. Ninety-one clones correspond to known genes and 109 clones showed no significant match with any gene or DNA sequence in GenBank and EMBL databases. Fifty-eight clones represent 18 distinct genes, the most abundant representing the albumin gene (13/240). The majority of genes that were represented by more than one clone code for proteins released by the liver into the plasma. We demonstrated the suitability of the differential display reverse transcription polymerase chain reaction approach for the detection of porcine liver ESTs. It is shown that this approach is appropriate to reduce redundant analysis of clones containing the same sequence.

Expression of homeobox-containing genes in cDNA libraries derived from cattle oocytes and preimplantation stage embryo

The homeobox-containing gene family plays a pivotal role in regulating, patterning, and axial morphogenesis in the developing embryo. But there is still very little known about the expression and function of these genes in mammalian oocytes and preimplantation stage embryos. In this study we have used degenerate primers corresponding to the highly conserved regions of Antennapedia class homeodomains as a rapid and an efficient method to survey bovine cDNA libraries derived from unfertilised oocytes, single 2-cell, 4-cell, 8-cell, morula, and blastocyst stage embryos for the presence of homeobox sequences. Our results provide, for the first time, evidence for the transcription of Hoxa3 and Hoxd1 in oocytes; Cdx1 and Cdx2 in the 2-cell; Cdx1, Hoxa1, Hoxd1, and Hoxd4 in the 4-cell; Cdx1, Hoxa1, and Hoxc9 in the 8-cell; Cdx2, Hoxb9, and Hoxc9 in the morula; Cdx2, Hoxb7, Hoxb9, and Hoxc9 in blastocyst stage cattle embryos. These are candidate genes for the developmental capacity of in vivo and in vitro produced bovine embryos.

Empirical evaluation of genetic clustering methods using multilocus genotypes from 20 chicken breeds

We tested the utility of genetic cluster analysis in ascertaining population structure of a large data set for which population structure was previously known. Each of 600 individuals representing 20 distinct chicken breeds was genotyped for 27 microsatellite loci, and individual multilocus genotypes were used to infer genetic clusters. Individuals from each breed were inferred to belong mostly to the same cluster. The clustering success rate, measuring the fraction of individuals that were properly inferred to belong to their correct breeds, was consistently approximately 98%. When markers of highest expected heterozygosity were used, genotypes that included at least 8-10 highly variable markers from among the 27 markers genotyped also achieved >95% clustering success. When 12-15 highly variable markers and only 15-20 of the 30 individuals per breed were used, clustering success was at least 90%. We suggest that in species for which population structure is of interest, databases of multilocus genotypes at highly variable markers should be compiled. These genotypes could then be used as training samples for genetic cluster analysis and to facilitate assignments of individuals of unknown origin to populations. The clustering algorithm has potential applications in defining the within-species genetic units that are useful in problems of conservation.

Genetic distinctness of African, Asian and South American local chickens

The genetic variability of various local chicken populations derived from Bolivia, India, Nigeria and Tanzania was evaluated with 22 microsatellites. Between two and 11 alleles per locus were detected. All populations showed high levels of heterozygosity with the lowest value of 45% for the population named Aseel from India and the highest value of 67% for Arusha from Tanzania. A dendrogram was constructed based on CHORD distance by upgMa analysis. Within this tree the populations were assorted according to their geographical origin. Bootstrapping values within the dendrogram were between 37 and 99%. The contribution of the determination of genetic variability with genetic markers to the decision on conservation and/or further use of the populations in crossbreeding programs designed to create genetic stocks with improved adaptability and productivity in tropical countries is discussed.

Maternal influences on litter size and growth in reciprocal crossed Miniature Pigs and Durocs

Abstract. In order to demonstrate the potential power of maternal effects on litter size and growth in pigs a reciprocal cross of Berlin Miniature Pigs and Durocs was carried out. The average body weight of the Duroc dams (151 kg) was more than three times higher than the weight of the Miniature Pig dams (48 kg). A considerable maternal effect on fertility, estimated from reciprocal crossbred differences in the litter size of 3.5 piglets was found. The least Squares means of birth weight were 1.18 kg and 0.75 kg for Fl animals bom from Duroc dams and Miniature Pig dams, respectively. This maternal caused disadvantage in body weight of crossbred offspring from Miniature Pig dams is compensated in the interval from weaning to the 13th week of age. The end weight estimated by means of Gompertz and Bertalanffy growth functions showed only minor differences between the reciprocal crossed groups in favour of Fl born from Duroc dams. Our data suggest that the uterine capacity of the dam could play an important role in the fertility of extreme breed crosses. Concerning growth performance the milk yield of the sow and the influence of the birthweight of the piglets were discussed.

Application of microsatellite analysis to group chicken according to their genetic similarity

Abstract. When estimating genetic variability of groups of local chicken from Nigeria we had to deal with the problem that the groups could not be regarded as distinct breeds or strains. The original sample groups obviously just represent individuals sampled in the same geographical region. The aim was to arrange these chicken in new groups according to their genetic similarity. Therefore 60 chicken from Nigeria and 10 Dahlem Reds (RIR) were genotyped at 20 microsatellite loci. In order to build up new groups "allele sharing" was calculated as the proportion of shared alleles between each pair of individuals and was used to construct a dendrogram of all individuals including Dahlem Reds as a reference group which represents a well defined line. All Dahlem Reds clustered in this dendrogram indicating that this is an adequate approach to group individuals according to their common genetic make-up. The Nigerian chicken were arranged in 7 new groups. CHORD genetic distances between these new groups ranged from 0.07 to 0.27 and were higher than the values revealed by the original local sample groups (0.05–0.16).

Evaluation of oligonucleotide probes for simple tandem repeats (STR) to produce informative DNA fingerprints of the chicken

1. DNA fingerprints of chickens from 2 commercial lines were used to identify oligonucleotide probes providing informative DNA fingerprints. 2. The oligonucleotides [CA]8, [CAC]5, [GGAT]4 and [GACA]4, producing a high number of bands of sufficient intensity and regular distribution, were chosen for further analysis out of 10 tested. 3. Analyses of banding patterns within families revealed Mendelian inheritance of the fragments detected. The DNA fingerprints obtained with the 4 chosen oligonucleotide probes showed about 40 scorable bands in total. 4. Comparison of banding patterns within and between the chicken lines for all 4 oligonucleotide probes revealed levels of bandsharing which did not differ significantly. The number of loci detected by these probes ranged from 25 to 30 each. 5. The probes [CA]8, [CAC]5, [GGAT]4 and [GACA]4 can be used to produce informative DNA fingerprints of chicken. These probes provide estimates of the genetic similarity/variability of individuals or of populations and provide a valid measure of the actual degree of genetic similarity/variability.

Evaluation of genetic variation within and between different chicken lines by DNA fingerprinting

A DNA fingerprinting technique was used to assess the extent of genetic variation within and between 12 lines of chickens of different origin. DNA fingerprints were obtained with the restriction endonucleases AluI and HinfI and with the oligonucleotide probes (CA)8, (CAC)5, (GGAT)4, and (GACA)4. Different methods that are based on band sharing and band frequency were tested to estimate genetic variation within and between populations. The genetic variability was significantly different within the populations. It was highest in a commercial broiler line and lowest in a White Leghorn inbred line. All three measures of genetic variation within populations provided results that were highly correlated (r = 0.89-0.97). A lower degree of correspondence was observed for the estimation of genetic variation between populations by three different methods. This is shown by differences of the phylogenetic trees and by coefficients of correlation between these measures ranging from r = 0.51-0.96.

Assessment of parental genomic proportions in crossbred chickens by DNA fingerprints

SUMMARY

Starting with the second crossbred generation, parental genomic-proportion lines in individuals deviate considerably from expectation. These individual variations offer the potential to increase the efficiency of crossbreeding programmes. DNA fingerprinting was established as an approach, to quantify the genomic contribution of the parental lines in individuals of two crossbred generations. For this purpose, line-specific bands were identified in representative banding patterns of pooled DNA from purebreds. The representative banding patterns obtained with eight combinations of restriction enzymes HinfI and AluI, and oligonucleotide probes [CA]8, [CAC]5, [GGAT]4, and [GACA]4, contained between nine and 14 line-specific bands. The estimation of the proportion was based on the relative proportion of line-specific bands of one parental line in banding patterns of crossbreds. This was first done in F1 individuals with a definite 50% genomic proportion of each parental line, to determine the accuracy of the approach. The mean value, 51.0 ± 0.34%, observed in 45 F1s using all eight combinations of enzymes and probes, of genomic contribution of one parental line, was close to the theoretical value of 50%. In 24 animals of the BC1, considerable shifting of the parental genomic proportion was observed. ZUSAMMENFASSUNG: Schätzung der Genomanteile bei Hühnern verschiedener Kreuzungsstufen durch DNA-Fingerprinting Von der ersten Rückkreuzungsgeneration an treten erhebliche, individuelle Verscheibungen in der Verteilung der Genomanteile der parentalen Ausganslinien vom Durchschnitt auf. Diese individuelle Variation stellt ein Potential zur Steigerung der Effektivität von Kreuzungszuchtprogrammen dar. Mit der vorliegenden Arbeit wird eine Untersuchungsmethode zur direkten Quantifizierung der Genombeiträge der parentalen Ausganslinien bei Individuen verschiedener Kreuzungsstufen durch DNA fingerprints vor gestellt. Dazu wurden in für die Ausgangslinien repräsentativen Bandenmustern aus DNA-Gemischen linienspezifische Banden identifiziert. Die repräsentativen Bandenmuster wurden mit den Restriktionsenzymen HinfI and AluI sowie den Oligonukleotidsonen [CA](8) , [CAC](5) , [GGAT](4) , und [GACA](4) erzeugt und enthielten 9-14 linienspezifische Banden. Die Bestimmung der parentalen Genomanteile beruhte auf der Identifizierung linienspezifischer Banden in den Bandmustern von Kreuzungsindividuen und der anschließenden Berechnung des relativen Anteils an für eine parentale Linie spezifischen Banden. Um die Genauigkeit der Untersuchungsmethode zu evaluieren, wurde sie zunächst bei F(1) Tieren angewandt, die einen Anteil von jeweils 50% der elterlichen Linien aufweisen müssen. Der Durchschnittswert berechnet über alle 45 F(1) Individuen und alle acht Kombinationen von Enzymen und Sonden betrug 51,0 ± 0,34% Genomanteil der einen parentalen Linie und lag somit nahe dem theoretischen Wert von 50%. Bei 24 Tieren der R1 konnte eine beachtliche Verschiebung der Genombeiträge der parentalen Ausgangslinien gezeigt werden.