Duplex comb in the chicken: a multi-allelic trait

Allelism at the duplex comb locus was studied by means of crosses between the Sicilian Buttercup and La Flèche breeds of chickens and two single combed breeds. The horn V-shaped duplex comb of the La Flèche was shown to be inherited as an incomplete dominant when crossed with single comb birds, and it exhibited complete penetrance and a strong expression of duplex. The buttercup duplex comb of the Sicilian Buttercup in similar crosses was also shown to be inherited as an incompletely dominant trait, but with this type comb penetrance was reduced by 32% in females and its expression of duplex was greatly reduced when compared with the La Flèche. When the duplex comb types were crossed to each other, the V-shaped comb showed complete dominance over the buttercup comb. It is proposed that there are at least three alleles at the duplex locus: D (v-type) greater than Dc (buttercup type) greater than d+ (non-duplex type). The most dominant allele (Dv) causes both doubling of the comb and suppression of its tissue mass, while the less dominant allele (Dc) only causes doubling of the comb.     

A CIS-Acting Mutation within the MATa Locus of SACCHAROMYCES CEREVISIAE That Prevents Efficient Homothallic Mating-Type Switching

Homothallic strains of Saccharomyces cerevisiae are able to switch from one mating-type to the other as frequently as every cell division. We have identified a cis-dominant mutation of the MATa locus, designated MATa-inc, that can be converted to MATalpha at only about 5% of the normal efficiency. In homothallic MATa-inc/mata* diploids, the MATa-inc locus switched to MATalpha in only one of 30 cases, while the mata* locus switched to MATalpha in all 30 cases. The MATa-inc mutation can be "healed" by a series of switches, first to MATalpha and then to a normal allele of MATa. These data are consistent with the "cassette" model of Hicks, Strathern and Herskowitz (1977), in which mating conversions involve the transposition of wild-type copies of a or alpha information from silent genes elsewhere in the genome. The MATa-inc mutation appears to alter a DNA sequence necessary for the replacement of MATa by MATalpha. The MATa-inc mutation has no other effect on MATa functions. In beterothallic backgrounds, the mutation has no effect on the sensitivity to alpha-factor, synthesis of a-factor, expression of barrier phenotype or ability to mate or sporulate.--The MATa-inc allele does, however, exhibit one pleiotropic effect. About 1% of homothallic MATa-inc cells become completely unable to switch mating type because of mutations at HMa, the locus proposed to carry the silent copy of alpha information.--In addition, we have isolated a less efficient allele of the HO gene.     

Genetic heterogeneity and selection signature at the KIT gene in pigs showing different coat colours and patterns

Mutations in the porcine KIT gene (Dominant white locus) have been shown to affect coat colours and colour distribution in pigs. We analysed this gene in several pig breeds and populations (Sicilian black, completely black or with white patches; Cinta Senese; grey local population; Large White; Duroc; Hampshire; Pietrain; wild boar; Meishan) with different coat colours and patterns, genotyping a few polymorphisms. The 21 exons and parts of the intronic regions were sequenced in these pigs and 69 polymorphisms were identified. The grey-roan coat colour observed in a local grey population was completely associated with a 4-bp deletion of intron 18 in a single copy KIT gene, providing evidence that this mutation characterizes the I^d allele described in the early genetic literature. The white patches observed in black Sicilian pigs were not completely associated with the presence of a duplicated KIT allele (I^p), suggesting that genetic heterogeneity is a possible cause of different coat colours in this breed. Selection signature was evident at the KIT gene in two different belted pig breeds, Hampshire and Cinta Senese. The same mutation(s) may cause the belted phenotype in these breeds that originated in the 18th–19th centuries from English pigs (Hampshire) and in Tuscany (Italy) in the 14th century (Cinta Senese). Phylogenetic relationships of 28 inferred KIT haplotypes indicated two clades: one of Asian origin that included Meishan and a few Sicilian black haplotypes and another of European origin.     

Genetic diversity and admixture analysis of Sanfratellano and three other Italian horse breeds assessed by microsatellite markers

Sanfratellano is a native Sicilian horse breed, mainly reared in the north east of the Island, developed in the 19th century from local dams and sires with a restricted introgression of Oriental, African and, more recently, Maremmano stallions. In this study, the genetic relationships and admixture among Sanfratellano, the other two Sicilian autochthonous breeds and Maremmano breed were assessed using a set of microsatellites. The main goals were to infer the impact of Maremmano breed in the current Sanfratellano horse and to provide genetic information useful to improve the selection strategies of the Sanfratellano horse. The whole sample included 384 horses (238 Sanfratellano, 50 Sicilian Oriental Purebred, 30 Sicilian Indigenous and 66 Maremmano), chosen avoiding closely related animals. A total of 111 alleles from 11 microsatellite loci were detected, from four at HTG7 to 15 at ASB2 locus. The mean number of alleles was the lowest in Oriental Purebred (6.7), the highest in Sanfratellano (8.3). All the breeds showed a high level of gene diversity (He) ranging from 0.71 ± 0.04 in Sicilian Oriental Purebred to 0.81 ± 0.02 in Sicilian Indigenous. The genetic differentiation index was low; only about 6% of the diversity was found among breeds. Nei's standards (DS) and Reynolds' (DR) genetic distances reproduced the same population ranking. Individual genetic distances and admixture analysis revealed that: (a) nowadays Maremmano breed does not significantly influence the current Sanfratellano breed; (b) within Sanfratellano breed, it is possible to distinguish two well-defined groups with different proportions of Indigenous blood.     

Identifying the ptilopody (feathered shank) loci of the chicken.

A series of crosses was made involving lightly-, and heavily-, and non-feather-shanked chickens in an attempt to clear up the confusion in the literature concerning the inheritance of feathered shanks in chickens. The Langshan and Brahma breeds were both shown to possess the same single shank-feathering locus, but because of their differences in phenotype and penetrance in the genetic crosses it was suggested that they possessed different alleles at this locus. This locus was designated as Pti-1, with Pti-1L being the Langshan allele and Pti-1B the Brahma allele. The Brahma allele was shown to be dominant over the Langshan allele. Both the Sultan and Cochin breeds were shown to possess two shank-feathering loci, and the data suggested that one of the loci in the Sultan contained the Pti-1L allele. It is hypothesized that the comparable allele in the Cochin breed was Pti-1B. It is proposed that the second locus in both of these breeds is similar, and the symbol Pti-2 is suggested.     

Polymorphism of cattle prolactin gene: microsatellites, PSR-RFLP]

In the samples of Russian Ayrshire and Gorbatov Red cattle breeds, distribution of frequencies of prolactin (PRL) gene alleles generated due to the presence of polymorphic RsaI site in exon 3 were studied. In the breeds, the frequencies of the B allele of the PRL gene (with RsaI(+) site) detected by the PCR-RFLP method were 14.1 and 8.6%, respectively. In Black Pied, Ayrshire and Gorbatov Red cattle breeds, variation of the microsatellite dinucleotide repeat in the regulatory region of the gene PRL was also studied. Gorbatov Red breed was monomorphic at the microsatellite locus with the only allele 164 bp in length. Two alleles (164 bp and 162 bp) were detected in the other breeds studied. The frequencies of 164-bp allele of the microsatellite locus were 93.7 and 90.0% in Black Pied and Ayrshire breeds, respectively. In Gorbatov Red breed of dairy type with good beef qualities and low milk-fat yield, lower level of heterozygosity for PRL gene was demonstrated compared to Ayrshire and Black Pied breeds with high milk-fat yield. In three cattle breeds, higher mean estimate of polymorphism information content of PCR-RFLP in exon 3 (PIC = 0.21) was revealed compared with the same estimate (PIC = 0.09) for the microsatellite locus variability in the regulatory region of the PRL gene. Characteristics of allele B distribution of the PRL gene in the representatives of the Bovidae family are considered.     

Genetic polymorphism and close linkage of two plasma protein loci in dogs

By using a simple method of two-dimensional horizontal electrophoresis, phenotypes of an unidentified plasma protein (PA4) were determined in 967 dogs belonging to 43 different breeds. Two codominant, autosomal alleles (F and S) of PA4 were reported. While many of the breeds of middle and north-eastern Asia (akita inu, Alaskan malamute, chow chow, samoyed, Siberian husky and Tibetan terrier) showed a substantial frequency (0.1 to 0.6) of the S allele, a majority of the European breeds had only the F allele. Evidence was provided that the PA4 locus is closely linked to the plasma pretransferrin 1 locus (PRT1). No recombinant was observed in 45 informative offspring studied. In nearly all breeds, the PA4 S allele was almost always in coupling phase with the PRT1 F allele.     

Mutations in the melanocortin 1 receptor (MC1R) gene are associated with coat colours in the domestic rabbit (Oryctolagus cuniculus)

We sequenced almost the complete coding region of the MC1R gene in several domestic rabbits (Oryctolagus cuniculus) and identified four alleles: two wild-type alleles differing by two synonymous single nucleotide polymorphisms (c.333A>G;c.555T>C), one allele with a 30-nucleotide in-frame deletion (c.304_333del30) and one allele with a 6-nucleotide in-frame deletion (c.280_285del6). A polymerase chain reaction-based protocol was used to distinguish the wild-type alleles from the other two alleles in 263 rabbits belonging to 37 breeds or strains. All red/fawn/yellow rabbits were homozygous for the c.304_333del30 allele. This allele represents the recessive e allele at the extension locus identified through pioneering genetic studies in this species. All Californian, Checkered, Giant White and New Zealand White rabbits were homozygous for allele c.280_285del6, which was also observed in the heterozygous condition in a few other breeds. Black coat colour is part of the standard colour in Californian and Checkered breeds, in contrast to the two albino breeds, Giant White and New Zealand White. Following the nomenclature established for the rabbit extension locus, the c.280_285del6 allele, which is dominant over c.304_333del30, may be allele E(D) or allele E(S).     

Polymorphism at the ovine major histocompatibility complex class II loci

Southern hybridization analysis of the ovine major histocompatibility complex (MHC) ( MhcOvar ) class II region, using sheep-specific probes for the DQA1, DQA2, DQB and DRA loci, has revealed extensive polymorphism. DQA1 and DQAP had eight and 16 alleles respectively, DQB had six and DRA had three alleles. Little information was derived from the DRB locus owing to extensive cross-hybridization between the DRB probe and the DQB locus. Differences in allele frequency between breeds were revealed. At the DQA1 locus a null allele (DQA1-N) was observed with a frequency of between 27% and 45%, making this the most common DQA1 allele in all breeds examined. The frequency of DQA1-N homozygotes was between 11% and 18%, raising questions as to the functional significance of the DQA1 gene. Linkage analysis between the DQA1, DQA2, DQB and DRA loci did not reveal any recombination.     

Polymorphism of Bovine Prolactin Gene: Microsatellites,PCR–RFLP

In the samples of Russian Ayrshire and Gorbatov Red cattle breeds, distribution of frequencies of prolactin (PRL) gene alleles generated due to the presence of polymorphic RsaI site in exon 3 were studied. In the breeds, the frequencies of the Ballele of the PRLgene (with RsaI(+) site) detected by the PCR–RFLP method were 14.1 and 8.6%, respectively. In Black Pied, Ayrshire and Gorbatov Red cattle breeds, variation of the microsatellite dinucleotide repeat in the regulatory region of the gene PRLwas also studied. Gorbatov Red breed was monomorphic at the microsatellite locus with the only allele 164 bp in length. Two alleles (164 bp and 162 bp) were detected in the other breeds studied. The frequencies of 164-bp allele of the microsatellite locus were 93.7 and 90.0% in Black Pied and Ayrshire breeds, respectively. In Gorbatov Red breed of dairy type with good beef qualities and low milk-fat yield, lower level of heterozygosity for PRLgene was demonstrated compared to Ayrshire and Black Pied breeds that have high milk-fat yield. In three cattle breeds, higher mean estimate of polymorphism information content of PCR–RFLP in exon 3 (PIC = 0.21) was revealed compared with the same estimate (PIC = 0.09) for the microsatellite locus variability in the regulatory region of the PRLgene. Characteristics of allele Bdistribution of thePRLgene in the representatives of the Bovidae family are considered.     

Alpha and beta globin polymorphism in Italian islander sheep breeds

Previous investigations have highlighted the elevated haemoglobin polymorphism of Apulian native sheep. Thanks to the use of highly resolving analytical procedures (PAGIF, AUT-PAGE and RP-HPLC), the alpha globin genetic system (HBA) has been shown to exhibit both qualitative and quantitative variations (HBA1L, HBA1A, HBA1D, HBA2L, HBA2H, HBA3L, HBA3H, and HBA4H), while three allelic variants have been detected at the beta globin locus (HBBA, HBBB, and HBBI). The effect of a possibly adaptive response to the Apulian environmental conditions was suggested to account for both for the unusual presence of alpha haplotypes characterized by extra-numerary genes and the high frequency of the HBBB and HBBI alleles. Unfortunately, the few data in the literature regarding the HBA system polymorphism and the presence of the HBBI gene do not allow a comparison between Apulian sheep and those from other geographical areas. This work reports the results of a screening of Italian islander sheep breeds with a view to expanding the existing data set. A total of 465 blood samples were taken from 156 Comisana (C), 159 Sardinian (S) and 150 Valle del Belice (VdB) sheep belonging to 13 different flocks located in Apulia. Haemolysates were prepared from EDTA samples and analyzed by PAGIF, AUT-PAGE and RP-HPLC. Based on our results, the islander breeds exhibited slight differences in the HBA2H gene frequency compared to the HBA system of the Apulian native sheep; the most interesting finding was that though no HBA1D genes were recorded, the frequencies of triplicated haplotypes were very close, which supports the hypothesis that extra-numerary genes in Mediterranean environments may be an adaptive response to endemic tick borne parasites. Regarding the HBB locus, the results indicated that both Sicilian breeds exhibit an HBBI allele frequency of about 0.2, which is more than double that of previously reported data; this finding provided confirmatory evidence that HBBI is a rather common allele in Southern Italian sheep breed and suggested that an appropriate next step should be to investigate whether it presents the same frequency latitudinal cline as HBBB gene.     

Frequency and inheritance of A and B blood types in feline breeds of the United States

Using a simple hemagglutination assay to determine A and B blood types, we surveyed 1,072 domestic short- and longhair (DSH/DLH) cats and 1,100 purebred cats in the United States. Data from 234 matings with 552 offspring were consistent with the hypothesis that feline blood types A and B are due to the action of two different alleles at the same gene locus and that A is completely dominant over B. Neither an AB nor an O type cat was encountered. No type B cats were found in the Siamese and related breeds or in American Shorthair and Norwegian Forest cats. Among the breeds with type B blood, the proportion was lowest in DSH/DLH cats (0.0028) and variably higher in Abyssinian, Birman, British Shorthair, Devon Rex, Himalayan, Persian, Scottish Fold, and Somali, ranging from 0.15 to 0.59. Since all type B cats have strong, naturally occurring anti-A alloantibodies, fatal neonatal isoerythrolyses occur in type A offspring of type B mothers bred to type A males. The gene frequency of the B allele and the proportion of mating at risk of neonatal isoerythrolysis were estimated in a number of breeds. In most breeds, the frequency of the B allele was less than 0.5. Since the kittens at risk for neonatal isoerythrolysis always have the genotype AB, there is constant natural selection against heterozygotes. Heterozygote disadvantage in the cat AB system represents an unusual form of negative selection, similar to that in Rh blood group incompatibility in humans.     

Analysis of Genetic Variation at the Prolactin-RsaI (PRL-RsaI) Locus in Indian Native Cattle Breeds (Bos indicus)

This study assessed the distribution pattern of allelic variants at the prolactin-RsaI locus in 23 Indian native cattle breeds (Bos indicus). PCR-RFLP genotyping of a 156?bp fragment of prolactin (PRL) in exon 3 revealed the predominance of the heterozygous AB genotype (mean frequency 0.58) irrespective of utility type (dairy, dual, draft), geographic region (northern, central, southern), and coat color (red, gray) of the breeds analyzed. The overall frequencies of homozygous AA (0.22) and BB (0.20) genotypes were in a similar range. The PRL (A) and PRL (B) alleles exhibited similar gene frequencies (means 0.52 and 0.48, respectively). The existing profile of the PRL-RsaI gene locus in a large set of Indian native cattle breeds was different from that of Bos taurus and cattle breeds of other countries, where either the BB genotype and PRL (B) allele or the AA genotype and PRL (A) allele have been reported to be more prevalent.     

The evolution of recombination in permanent translocation heterozygotes

The evolution of a selectively neutral locus that controls the degree to which alleles at a single selected locus are linked with a particular set of chromosomes in a permanent translocation heterozygote is studied. With complete selfing and fitness overdominance a new allele at the modifying locus will increase in frequency if it increases the linkage of all alleles at the selected locus to a particular set of chromosomes. With random mating a new allele at the modifying locus will increase when rare if it increases the linkage of alleles at the selected locus to a particular set of chromosomes. In addition, a parameter analogous to the coefficient of linkage disequilibrium in usual two-locus models with random mating must be nonzero if a new allele at the modifying locus is to increase in frequency at a geometric rate when rare. With mixed selfing and random mating a new allele at the modifying locus will apparently increase when rare only if it increases the linkage of alleles at the selected locus to a particular set of chromosomes.     

Pleiotropic patterns of quantitative trait loci for 70 murine skeletal traits

Quantitative trait locus (QTL) studies of a skeletal trait or a few related skeletal components are becoming commonplace, but as yet there has been no investigation of pleiotropic patterns throughout the skeleton. We present a comprehensive survey of pleiotropic patterns affecting mouse skeletal morphology in an intercross of LG/J and SM/J inbred strains (N = 1040), using QTL analysis on 70 skeletal traits. We identify 798 single-trait QTL, coalescing to 105 loci that affect on average 7-8 traits each. The number of traits affected per locus ranges from only 1 trait to 30 traits. Individual traits average 11 QTL each, ranging from 4 to 20. Skeletal traits are affected by many, small-effect loci. Significant additive genotypic values average 0.23 standard deviation (SD) units. Fifty percent of loci show codominance with heterozygotes having intermediate phenotypic values. When dominance does occur, the LG/J allele tends to be dominant to the SM/J allele (30% vs. 8%). Over- and underdominance are relatively rare (12%). Approximately one-fifth of QTL are sex specific, including many for pelvic traits. Evaluating the pleiotropic relationships of skeletal traits is important in understanding the role of genetic variation in the growth and development of the skeleton.     

Economic implications of using Japanese Black sires carrying recessive genes associated with genetic defects

The objective of this study was to calculate cumulative discounted expressions (CDE) for Japanese Black sires carrying a single defective allele in a herd by applying the gene-flow method to investigate the expression pattern of homozygous recessive genotype and to evaluate the monetary loss of using these sires. A single biallelic locus was considered with A representing the dominant allele and a representing the recessive allele. The gene-flow method was modified to consider the fitness of homozygous recessive genotype. Input parameters representing a typical situation in a Japanese Black cattle herd were used to calculate the CDE and the loss of using carrier sires. The effects of initial allele frequency and fitness on the CDE were determined for Aa and AA sires. The CDE of Aa sires were larger than those of AA sires under all initial allele frequencies and fitness. The difference in the CDE between using Aa and AA sires was largest when fitness was 0 (lethal recessive condition). The differences in the loss between Aa and AA sires were larger with increasing initial allele frequencies in lethal recessive condition. Applying the method used in this study to defects reported in Japanese Black cattle and with a population size of 628 000, the difference in the loss between using Aa and AA sires was US$48 575 800 and US$74 418 000 in the case of Band-3 and Claudin-16 deficiencies, respectively. The approach used in this study could be applied to other genetic defects in different breeds and species.     

Definition and Estimation of Higher-Order Gene Fixation Indices

Fixation indices summarize the associations between genes that arise from the joint effects of inbreeding and selection. In this paper, fixation indices are derived for pairs, triplets and quadruplets of genes at a single multiallelic locus. The fixation indices are obtained by dividing cumulants by constants; the cumulants describe the statistical distribution of alleles and the constants are functions of gene frequency. The use of cumulants instead of moments is necessary only for four-gene indices, when the fourth cumulant is used. A second type of four-gene index is also required, and this index is based upon the covariation of second-order cumulants. At multiallelic loci, a large number of indices is possible. If alleles are selectively neutral, the number of indices is reduced and the relationship between gene identity and gene cumulants is shown.--Two-gene indices can always be estimated from genotypic frequency data at a single polymorphic locus. Three-gene indices are also estimable except when allele frequency equals one-half. Four-gene indices are not estimable unless selection is assumed to have an equal effect upon each allele (such as under selective neutrality) and the locus contains at least three alleles of unequal frequency. For diallelic or selected loci, an alternative four-gene fixation index is proposed. This index incorporates both types of four-gene associations but cannot be related to gene identity.     

The high grain protein content gene Gpc-B1 accelerates senescence and has pleiotropic effects on protein content in wheat

High grain protein content (GPC) is a frequent target of wheat breeding programmes because of its positive effect on bread and pasta quality. A wild wheat allele at the Gpc-B1 locus with a significant impact on this trait was identified previously. The precise mapping of several senescence-related traits in a set of tetraploid recombinant substitution lines (RSLs) segregating for Gpc-B1 is reported here. Flag leaf chlorophyll degradation, change in peduncle colour, and spike water content were completely linked to the Gpc-B1 locus and to the differences in GPC within a 0.3 cM interval corresponding to a physical distance of only 250 kb. The effect of Gpc-B1 was also examined in different environments and genetic backgrounds using a set of tetraploid and hexaploid pairs of isogenic lines. The results were consistent with those observed in the RSLs. The high GPC allele conferred a shorter duration of grain fill due to earlier flag leaf senescence and increased GPC in all four genetic backgrounds. The effect on grain size was more variable, depending on the genotype-environment combinations. These results are consistent with a model in which the wild-type allele of Gpc-B1 accelerates senescence in flag leaves producing pleiotropic effects on nitrogen remobilization, total GPC, and grain size.