Egg white polymorphisms and economic characters in the domestic fowl

The possible association between genes at 4 egg white loci, Ov, II, III, and Tf and 4 production characters were studied in 3 closed populations consisting of 2 flocks of White Leghorns, each of about 1000 hens, and a Light Sussex flock of 380 hens. The characters studied were: body weight at 5 different ages, egg weight at 3 different ages, age at sexual maturity and egg number at 2 ages. Only the last two characters were studied in the Light Sussex population. Three egg white loci had statistically significant effects on production traits. With body weight and egg weight, the Ov locus had an additive effect, the Ov^A allele being superior. The influence on body weight was significant only on adults, i.e., post‐sexual maturity weights. This was shown to be partly attributable to differences in age at maturity. Locus II was significantly overdominant with respect to egg number in 2 populations while the Tf locus heterozygotes were significantly inferior to the Tf^b/Tf^b homozygotes in the Light Sussex flock. In addition to these direct effects, complex interactions involving these loci were also present on egg number. The additive genetic variance controlled by these loci was also determined. The proportion of the variance attributable to these loci (as a fraction of the additive genetic variance of the trait) was not large enough for any single trait to be of practical importance in selection.     

A search for an association between maternal egg white protein polymorphisms and embryonic mortality in the domestic fowl

The possible association between the maternal genotype at two egg white loci and viability of their embryos was examined in two closed flocks of White Leghorn hens. One of the populations was polymorphic at the ovalbumin locus and locus II and the other at locus II only. Two generations of the first population comprising 536 hens and 9092 fertile eggs and one generation of the second comprising 83 hens and 1159 eggs were used in the study. Significant effects were observed with mortality at different stages of incubation but the results were not consistent for the two strains or for the 2 years studied.     

New SNPs in the IGF2 gene and association between this gene and backfat thickness and lean meat content in Large White pigs

IGF2‐in3‐G3072A is a causative mutation for paternally expressed quantitative trait loci on the p arm of porcine chromosome 2 with substantial effect on muscle growth and backfat thickness. The linkage disequilibrium between IGF2‐in3‐G3072A and IGF2‐in7‐G162C (IGF2‐NciI) in four breeds and associations between these polymorphisms and growth and meat performance in pigs of the Large White breed were analysed. A significant effect of these polymorphisms on backfat thickness and lean meat content was found. In addition, we identified two new single nucleotide polymorphisms (SNPs) in intron 7 of the gene. The existence of complete linkage disequilibrium between IGF2‐in3‐G3072A locus in the population under study where the locus segregated and SNPs in intron 7 of the IGF2 gene detectable with simple and reliable polymerase chain reaction–restriction fragment length polymorphism techniques (G162C, C179G and G186T) offer possibilities to use these SNPs for genotyping of quantitative trait nucleotide in Large White and Landrace breeds.     

Linkage analysis using direct and indirect counting and relative efficiencies for codominant and dominant loci

A method based on direct and indirect counting is developed for rapid and accurate linkage analysis for codominant and dominant loci. Methods for estimating gender-specific recombination frequencies are available for cases where at least one of the two loci is multiallelic and for biallelic loci with mixed parental linkage phases where at least one locus is codominant. Most of the estimates of gender-average and gender-specific recombination frequencies required iterative solutions. The new method makes use of the full data set, yields exact estimates of the recombination frequencies when the observed and expected genotypic frequencies are equal, and are computationally efficient. Relative efficiency of various data types is affected by the inheritance mode and by parental linkage phases of biallelic loci, but unaffected by the locus polymorphism when using the full data set for linkage analysis. The ability to determine parental linkage phases is affected by the locus polymorphism as well as inheritance mode. Intercross (or F-2 design) is more efficient for mapping codominant loci, whereas backcross is more efficient if dominance is involved. Mixed parental linkage phases of biallelic loci are less efficient than coupling or repulsion linkage phases. Ignoring noninformative offspring results in biased estimates of recombination frequency for biallelic loci only and reduced LOD scores for all cases.     

豫西脂尾羊血液蛋白的多态性研究

本研究利用聚丙烯酰胺凝胶电泳技术(PAGE)分析了河南豫西脂尾羊的血红蛋白(Hb)、转铁蛋白(Tf)、红细胞蛋白质(Ep)、前白蛋白(Pa)和血清酯酶(Es)的多态性。结果表明,在豫西脂尾羊群体中Hb存在3种基因型为HbAA、HbAB、HbBB,它们受Hb^A和Hb^B两个共显性等位基因控制,其中HbAA基因型频率为0.0571,HbAB为0.6286,HbBB为0.3143;Hb^A等位基因频率为0.3714,Hb^B为0.6286。Tf存在3种基因型为TfAA、TfAB、TfBB,它们受Tf^A和Tf^B两个共显性等位基因控制,其中TfAA基因型频率为0.2000,TfAB为0.2545,TfBB为0.5455;Tf^A等位基因频率为0.3273,Tf^B为0.6727。Ep有EpAA和EpAa共2种基因型,其中EpAA基因型频率为 0.4286,EpAa为0.5714;Ep^A基因频率为 0.7143,Ep^a为0.2857。Es基因座有2个等位基因即Es⁺和Es^-,而且Es⁺和Es^-的基因频率分别为0.5500和0.4500,有3种基因型Es⁺⁺、Es^+-、Es^--的频率分别为0.4250、0.2500和0.3250。Pa上未检测到多态性,它呈现单态。     

Pedal bone fractures

Fractures of the pedal bone are usually the result of direct trauma, and are relatively commonly encountered in equine practice. Either front or hind feet may be affected. Seven distinct fracture types are recognised. Type I fractures involve the palmar/plantar process and do not enter the distal interphalangeal (DIP) joint. Type II fractures are oblique or parasagittal fractures that are articular but are not on the midline. Type III fractures are midline articular fractures that bisect the pedal bone into 2 equal halves. Type IV fractures involve the extensor (pyramidal) process of the pedal bone. Type V fractures are comminuted and split the pedal bone into multiple fragments. Type VI fractures are solar margin fractures. Type VII fractures are exclusive to foals and are also fractures of the solar margin. In most cases the onset of clinical signs is acute. The diagnosis is usually achieved by radiography, although computed tomography or magnetic resonance imaging can be helpful in some cases. Treatment options include surgical and nonsurgical therapies. The prognosis for articular fractures (Types II and III) is worse than for nonarticular fractures (Types I, IV, VI and VII) because of the likelihood of osteoarthritis within the DIP joint. Nonarticular fractures carry a good prognosis if a long enough convalescence is undertaken. Comminuted fractures (Type V) carry a poor, but not hopeless, prognosis.     

PLAG1 and NCAPG‐LCORL in livestock

A recent progress on stature genetics has revealed simple genetic architecture in livestock animals in contrast to that in humans. PLAG1 and/or NCAPG‐LCORL, both of which are known as a locus for adult human height, have been detected for association with body weight/height in cattle and horses, and for selective sweep in dogs and pigs. The findings indicate a significant impact of these loci on mammalian growth or body size and usefulness of the natural variants for selective breeding. However, association with an unfavorable trait, such as late puberty or risk for a neuropathic disease, was also reported for the respective loci, indicating an importance to discriminate between causality and association. Here I review the recent findings on quantitative trait loci (QTL) for stature in livestock animals, mainly focusing on the PLAG1 and NCAPG‐LCORL loci. I also describe our recent efforts to identify the causative variation for the third major locus for carcass weight in Japanese Black cattle.     

Halothane Sensitivity,The H Blood Group System and Phosphohexose Isomerase (PHI) in Pigs: A Linkage Study Of Physiological Importance

Previous investigations have clearly shown the existence of associations between halothane sensitivity, the H blood group system and the PHI enzyme system in pigs (Rasmusen & Christian 1976, Jørgensen et al. 1976). These associations which have considerable practical interest are most probably linkage phenomenons (Jørgensen 1977, Andresen & Jensen 1977). The major recessive locus for halothane sensitivity (HAL) comprises the two alleles N and n, n being responsible for halothane sensitivity. The distances between this locus and the loci for H and PHI are still not known exactly. This communication aims at clarifying these problems.     

Genetic mapping of the prion protien gene (PRPN) on bovine chromosome 13

The bovine prion protein gene (PRNP) potentially plays a key role in the development of bovine spongiforme encephalopathy (BSE). In species other than cattle, expression of BSE is clearly dependent on polymorphisms in this gene. PRNP has previously been assigned to the bovine chromosome 13 (BTA13). The present study is an attempt to embed PRNP into a grid of published marker maps. A genetic mapping panel consisting of 266 animals has been genotyped with 19 microsatellites and a polymerase chain reaction‐amplified polymorphism within the PRNP coding region. The linear locus order and the relative distances of these loci are presented. Our linkage map spans 111.6c m of BTA13. The results suggest PRNP to be located telomeric of the microsatellite BMS1580 and centromeric of BM9248 with a log‐likelihood of 2. Our findings further characterize the vicinity of PRNP on BTA13.     

Basic characterization of avian β‐defensin genes in the Japanese quail,Coturnix japonica

In this study, we identified a cluster of 14 avian β‐defensins (AvBD; approximately 66 kbp) in the Japanese quail, Coturnix japonica. Except for AvBD12 (CjAvBD12) and ‐13, the CjAvBDs coding sequences exhibited greater than 78.0% similarity to the respective orthologous chicken AvBD genes (GgAvBD). The putative amino acid sequence encoded by each CjAvBD contained six cysteine residues and the GXC (X1‐2) motif considered essential for the β‐defensin family. Each CjAvBDs also formed a sub‐group with the respective orthologous genes of various bird species in a phylogenetic tree analysis. Synteny between the CjAvBD cluster and GgAvBD cluster was confirmed. The CjAvBD cluster was mapped on the long‐arm end of chromosome 3 by linkage analysis based on single nucleotide polymorphisms (SNPs) of CjAvBD1 and CjAvBD12 (approximately 46kbp), as well as GgAvBD cluster. We also confirmed that CjAvBD1, ‐4, ‐5, ‐9, and ‐10 are transcribed in 20 tissues, including immune and digestive tissues. However, our experimental data indicated that the CjAvBD cluster lacks the AvBD3 and ‐7 loci, whereas the CjAvBD101α, ‐101β, and ‐101θ loci arose from gene duplication of the AvBD6 orthologous locus in the CjAvBD cluster after differentiation between Coturnix ‐ Gallus.     

A test for linkage of the loci for dominant white and barring with loci controlling growth rate in the fowl 1

Females from a coloured inbred line of Leghorns (ii) were mated to three groups of males heterozygous for the dominant white gene (Ii). The parents transmitting the I gene to the three groups of males were respectively larger, smaller and of the same size as the parents transmitting the i gene. No differences were observed between the three types of crosses in the effect of colour genotype on body weight, providing no evidence for linkage between the dominant white locus and loci affecting body weight.

When comparisons were made between the colour genotype classes, pooled within full sib groups, the coloured genotype was larger in ten of the twelve test cross‐sex‐hatch combinations. Two of these differences, were statistically significant, but when the data were pooled over hatch, sex and test cross, no significant difference was found. The data thus offer meagre support for weight differences in favour of the coloured genotype, but the negative evidence of the pooled analysis raises considerable doubt that real differences in weights between the colour classes exist in these populations.

A similar comparison was made between the barred and non‐barred genotypes among the coloured female progeny in one test cross. The barred progeny were heavier in each hatch, in spite of the fact that the barring gene and sex chromosome were derived from the smaller grandparent. The differences were not statistically significant in either hatch or when the mean squares were pooled over hatches. It is concluded, therefore, that this experiment provides no evidence for any association between the barring locus and the genes for growth rate in this population.     

Linkage disequilibrium and genomic scan to detect selective loci in cattle populations adapted to different ecological conditions in Ethiopia

Despite the wide range of observed phenotypic diversities and adaptation to different ecological conditions, little has been studied regarding the genetics of adaptation in the genome of indigenous cattle breeds of developing countries. Here, we investigated the linkage disequilibrium (LD) and identified the subset of outlier loci that are highly differentiated among cattle populations adapted to different ecological conditions in Ethiopia. Specifically, we genotyped 47 unrelated animals sampled from high‐ versus low‐altitude environments using a Bovine 50K SNP BeadChip. Linkage disequilibrium was assessed using both D′ and r² between adjacent SNPs. We calculated F_ST and heterozygosity at different significance levels as measures of genetic differentiation for each locus between high‐ and low‐altitude populations following the hierarchical island model approach. We identified 816 loci (p < 0.01) showing selection signals and are associated with genes that might have roles in local adaptation. Some of them are associated with candidate genes that are involved in metabolism (ATP2A3, CA2, MYO18B, SIK3, INPP4A, and IREB2), hypoxia response (BDNF, TFRC, and PML) and heat stress (PRKDC, CDK1, and TFDC). Average r² and D′ values were 0.14 ± 0.21 and 0.57 ± 0.34, respectively, for a minor allele frequency (MAF) ≥ 0.05 and were found to increase with increasing MAF value. The outlier loci identified in the studied Ethiopian cattle populations indicate the presence of genetic variation produced/shaped by adaptation to different environmental conditions and provide a basis for further validation and functional analysis using a reasonable sample size and high‐density markers.     

Fine mapping of a QTL for intramuscular fat on porcine chromosome 6 using combined linkage and linkage disequilibrium mapping

In this study data from a commercial Norwegian slaughter pig cross was analysed to confirm a previous reported quantitative trait locus (QTL) affecting intramuscular fat (IMF) on porcine chromosome 6. The data consisted of an old experiment, in which the QTL was previously detected, and new experimental data from the Norwegian slaughter pig cross. The old and new experimental data were analysed separately and together. A previously described method combining linkage and linkage disequilibrium analysis (LDLA) was used for the analysis, but this method assumes that all animals are descendants from a common base population, which is not realistic in a cross between different breeds. An adjusted version of the method, able to distinguish between different breeds in the cross, is presented here. Using the LDLA method, we were not able to confirm the QTL in the old experimental data, because the genetic variance could be explained by the polygenic effect. Analysis from the new experimental data did however detect the QTL, and analysing the data from both experiments together gave highly significant results for a QTL (p < 0.001) between markers SW1355 and SW1823. The main conclusion is therefore that the previously reported QTL for IMF on porcine chromosome 6 was confirmed within a 8.7‐cM confidence interval.     

Further studies of linkage and mappings of the loci of genes in group 3 on chromosome 1 of the domestic fowl

1. Evidence is presented to confirm the placing of the extended black E‐locus in linkage Group 3 on chromosome 1, E being linked with peacomb P by 43 map units. P has been shown to be linked with dark‐brown Columbian Db and sleepy‐eye se by 32 and 45 map units, respectively, se being independent of E.

2. Evidence is also presented to demonstrate independence of E and Db; hence, Db and se have their loci on the same side of P, the gene order being E‐P‐Db‐se, thus contradicting published mappings which place P between Db and se.

3. An investigation into the deductive relationships on which published mappings are based led to the conclusion that insufficient evidence existed for the inclusion of the sub‐group comprising blood group Ea‐P, naked neck Na, silky feathering h and flightless El as part of Group 3.

4. Furthermore, it appears only 4 genes in Group 3 have actually had their loci mapped; blue egg O, P, the eumelanin extension charcoal cha and the feather growth restrictor tardy t.

5. No evidence appears to have been presented to establish on which arm of chromosome 1 any of the other genes in Group 3 have their loci. A revised map of chromosome 1 and a schematic arrangement to demonstrate the relative linkage distances of the loci of the unmapped genes in Group 3 are presented and explained.     

Studies of Transferrin Polymorphism in Swedish Cattle Using Agarose Gel Electrophoresis

The polymorphic transferrin picture in the sera from 894 Swedish cattle was investigated with an agarose gel electrophoresis technique. The serum transferrin bands in the electrophoresis pattern were first identified by labelling with ⁵⁹Fe. Six existing phenotypes based on the alleles Tf^A, Tf^D and Tf^E could be detected. The frequencies of transferrin types and transferrin alleles are presented, and it is concluded that there are great differences in the frequencies between the Swedish Red and White and the Swedish Friesian.     

Studies on Blood and Serum Types of the Icelandic Horses

By means of isoimmunizations and heteroimmunizations 10 equine blood typing reagents were isolated. The specific antibodies were complete agglutinins, which were used in the direct agglutination test in saline medium. The reagents were designated A₂, C, D, E, G, H, I, K, Da₁, and Da₂ reagent. Da₁ and Da₂ are preliminary designations.The data obtained from blood typing of a family material and a population material of Icelandic horses showed that the occurrence of each blood type factor is controlled by a single, dominant gene. The family data tended to show that the blood factors under investigation belonged to 8 blood type systems. The A system contained the antigens A₂ and Da₂. These antigens are related to each other through a linear subgroup relationship. The D system had the factors D and J. The G, E, G, I, K, and Da₁ systems are one-factor, two-allele blood type systems. The H factor was not observed in Icelandic horses. In connection with the establishment of the 8 blood type systems it must be emphasized that the problem of allelism or nonallelism of 2 genes can only be solved by means of relevant family data. Because of the rare occurrence of some of the blood factors in the Icelandic horse such data were in some cases not available. Thus some conclusions were based on results from two-by-two contingency tables with the use of population data. This was used particularly for the D and G systems, and additional family data are necessary for a definite establishment of these systems.Exceptions to the genetic theory, apparently caused by erroneous registration, were presented.Finally, estimates were given of gene frequencies of the causative genes among Icelandic horses.Starch gel electrophoresis of sera from Icelandic horses revealed the existence of 21 transferrin phenotypes. The data obtained supported the theory advanced, that transferrin polymorphism in horses is controlled by 6 autosomal codominant alleles: Tf^D, Tf^F, Tf^H, Tf^M, Tf^O, and Tf^H.925 randomly selected Icelandic horses were typed for serum transferrin and the gene frequencies were estimated.Starch gel electrophoresis of about 100 horse serum samples did hot reveal individual variation of the equine haptoglobin and ceruloplasmin. Studies on approximately 300 sera showed an identical serum amylase pattern.     

Genetic analysis of Ankamali pigs of India using microsatellite markers and their comparison with other domesticated Indian pig types

Ankamali pigs, the domesticated native pigs of Kerala province of India were genetically characterized using 23 FAO recommended microsatellite markers and were compared with other native Indian pig types and Large White pigs. Twenty‐six blood samples were collected from genetically unrelated animals from their breeding tract and DNA was isolated by standard procedure of phenol/chloroform. The genomic DNA was amplified by polymerase chain reaction (PCR) at these 23 microsatellite loci, which were also used earlier to characterize Desi (North Indian) and Gahuri (North‐East Indian) pigs, the other two native domesticated pig types of India. The PCR products were resolved by denaturing urea‐polyacrylamide gel electrophoresis and alleles were visualized after silver nitrate staining. The data were analysed for allele size range, number of alleles, allelic frequencies, heterozygosity and polymorphism information content for each locus. The allele size range varied between 92–108 bp at locus S0026 and 280–296 bp at locus IGF‐1. The total number of alleles varied between five (S0178 and S0386) and 11 (S0355). The mean observed and expected heterozygosities were found to be 0.74 ± 0.09 and 0.83 ± 0.03 respectively. In the neighbour‐joining dendrogram based on D_A genetic distances developed after 1000 bootstraps, the Ankamali pigs did not show genetic closeness either with other native Indian pig types or exotic Large White pigs with high bootstrap values indicating genetic distinctness of Ankamali pigs.     

Molecular typing of Brucella melitensis endemic strains and differentiation from the vaccine strain Rev-1

In the present study forty-four Greek endemic strains of Br. melitensis and three reference strains were genotyped by Multi locus Variable Number Tandem Repeat (ML-VNTR) analysis based on an eight-base pair tandem repeat sequence that was revealed in eight loci of Br. melitensis genome. The forty-four strains were discriminated from the vaccine strain Rev-1 by Restriction Fragment Length Polymorphism (RFLP) and Denaturant Gradient Gel Electrophoresis (DGGE). The ML-VNTR analysis revealed that endemic, reference and vaccine strains are genetically closely related, while most of the loci tested (1, 2, 4, 5 and 7) are highly polymorphic with Hunter-Gaston Genetic Diversity Index (HGDI) values in the range of 0.939 to 0.775. Analysis of ML-VNTRs loci stability through in vitro passages proved that loci 1 and 5 are non stable. Therefore, vaccine strain can be discriminated from endemic strains by allele’s clusters of loci 2, 4, 6 and 7. RFLP and DGGE were also employed to analyse omp2 gene and reveled different patterns among Rev-1 and endemic strains. In RFLP, Rev-1 revealed three fragments (282, 238 and 44 bp), while endemic strains two fragments (238 and 44 bp). As for DGGE, the electrophoretic mobility of Rev-1 is different from the endemic strains due to heterologous binding of DNA chains of omp2a and omp2b gene. Overall, our data show clearly that it is feasible to genotype endemic strains of Br. melitensis and differentiate them from vaccine strain Rev-1 with ML-VNTR, RFLP and DGGE techniques. These tools can be used for conventional investigations in brucellosis outbreaks.     

Application of bovine microsatellite markers for genetic diversity analysis of European bison (Bison bonasus)

In this study, the cross‐amplification of a commercial multiplex set of 11 cattle (Bos taurus) microsatellites was tested on a panel of 35 European bison (Bison bonasus) individuals. After polymerase chain reaction optimization, all loci cross‐amplified successfully in investigated bisons. Number of alleles and observed and expected heterozygosity per locus are in the range of 2–4, 0.086–0.629 and 0.288–0.621 respectively. The availability of a heterologous set of multiplexed microsatellite markers derived from cattle opens an avenue for collecting profound genetic data for efficient conservation management strategies of the European bison.