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.     

鸡的血型研究 Ⅹ.我国11个地方鸡种的血型和血浆蛋白质多态分析

对我国11个地方鸡种1087羽鸡群进行了血型和血浆蛋白质多态7个位点22个等位基因的群体遗传学分析。结果表明,血型A、C位点,基因频率各鸡种存在显著差异,B位点则没有显著差异,血型和血浆蛋白质多态位点基因纯合系数普遍较低,血型因子分布在群体中较为分散,表明这些地方品种存在较大的选择潜力。血浆蛋白质多态位点,中国与外国的某些鸡种比较,存在着较大的相同或相异,可能意味着我国和外国鸡种起源上的同缘或品种起源、进化上的多样性。聚类分析表明,这11个地方鸡种可系统聚类成4个类群,其结果与目前人们对这些鸡种的表征分类不尽一致。     

Evaluation of genetic diversity in Chinese indigenous chicken breeds using microsatellite markers

China is rich in chicken genetic resources, and many indigenous breeds can be found throughout the country. Due to poor productive ability, some of them are threatened by the commercial varieties from domestic and foreign breeding companies. In a large-scale investigation into the current status of Chinese poultry genetic resources, 78 indigenous chicken breeds were surveyed and their blood samples collected. The genomes of these chickens were screened using microsatellite analysis. A total of 2740 individuals were genotyped for 27 microsatellite markers on 13 chromosomes. The number of alleles of the 27 markers ranged from 6 to 51 per locus with a mean of 18.74. Heterozygosity (H) values of the 78 chicken breeds were all more than 0.5. The average H value (0.622) and polymorphism information content (PIC, 0.573) of these breeds suggested that the Chinese indigenous chickens possessed more genetic diversity than that reported in many other countries. The fixation coefficients of subpopulations within the total population (F _ST) for the 27 loci varied from 0.065 (LEI0166) to 0.209 (MCW0078), with a mean of 0.106. For all detected microsatellite loci, only one (LEI0194) deviated from Hardy-Weinberg equilibrium (HWE) across all the populations. As genetic drift or non-random mating can occur in small populations, breeds kept on conservation farms such as Langshan chicken generally had lower H values, while those kept on large populations within conservation regions possessed higher polymorphisms. The high genetic diversity in Chinese indigenous breeds is in agreement with great phenotypic variation of these breeds. Using Nei’s genetic distance and the Neighbor-Joining method, the indigenous Chinese chickens were classified into six categories that were generally consistent with their geographic distributions. The molecular information of genetic diversity will play an important role in conservation, supervision, and utilization of the chicken resources.     

Evaluation of genetic diversity in Chinese indigenous chicken breeds using microsatellite markers

China is regarded as one of the domestication cen-ters for chickens and archaeological studies provided evidence of chicken domestication in northern Chinaas early as 6000 BC[1]. At present, China has the larg-est chicken population in the world, represen…     

Identification of genes controlling collagen-induced arthritis in mice: striking homology with susceptibility loci previously identified in the rat.

The susceptibility to collagen-induced arthritis in the highly susceptible DBA/1 mouse has earlier been shown to be partly controlled by the MHC class II gene Aq. To identify susceptibility loci outside of MHC, we have made crosses between DBA/1 and the less susceptible B10.Q strain, both expressing the MHC class II gene Aq. Analysis of 224 F2 intercross mice with 170 microsatellite markers in a genome-wide scan suggested 4 quantitative trait loci controlling arthritis susceptibility located on chromosomes 6, 7, 8, and 10. The locus on chromosome 6 (Cia6), which was associated with arthritis onset, yielded a logarithm of odds score of 4.7 in the F2 intercross experiment and was reproduced in serial backcross experiments. Surprisingly, the DBA/1 allele had a recessive effect leading to a delay in arthritis onset. The suggestive loci on chromosomes 7 and 10 were associated with arthritis severity rather than onset, and another suggestive locus on chromosome 8 was most closely associated with arthritis incidence. The loci on chromosomes 7, 8, and 10 all appeared to contain disease-promoting alleles derived from the DBA/1 strain. Interestingly, most of the identified loci were situated in chromosomal regions that are homologous to regions in the rat genome containing susceptibility genes for arthritis; the mouse Cia6 locus is homologous with the rat Cia3, Pia5, Pia2, and Aia3; the locus on chromosome 7 (Cia7) is homologous with the rat Cia2; and the locus on chromosome 10 (Cia8) is homologous with the rat Cia4.     

Evaluation of factors affecting individual assignment precision using microsatellite data from horse breeds and simulated breed crosses

Assignment tests have been utilized to investigate population classification, measure genetic diversity and to solve forensic questions. Using microsatellite data from 26 loci genotyped in eight horse breeds we examined how population differentiation, number of scored loci, number of scored animals per breed and loci variability affected individual assignment precision applying log likelihood methods. We found that both genetic differentiation and number of scored loci were highly important for recognizing the breed of origin. When comparing two and two breeds, a proportion of 95% of the most differentiated breeds (0.200 < or = FST < or = 0.259) could be identified scoring only three loci, while the corresponding number was six for the least differentiated breeds (0.080 < or = FST < or = 0.139). An identical proportion of simulated breed crosses, differentiated from their parental breeds by FST estimates in the range 0.050-0.069, was identified when scoring 12 loci. This level of source identification was not obtained for the less differentiated breed crosses. The current data further suggested that population sample size and locus variability were not critical for the assignment precision as long as moderately large sample sizes (> or = 20 animals per population) and fairly variable loci were used.     

我国地方鸡品种保种群微卫星多态性分析与分子标记档案的建立

利用20个微卫星标记对国家家禽品种资源基因库中保存的11个地方鸡品种保种群进行了遗传检测,计算各群体的等位基因频率、平均基因杂合度、平均多态信息含量及各群体间的遗传距离,并用类平均法进行聚类分析。研究结果表明：20个微卫星标记在11个地方鸡品种保种群共检测到176个等位基因,平均为8.8个,基因频率分布在0.013～0.838之间。检测到等位基因中,有45个等位基因为11个地方鸡品种所共有;11个地方鸡品种平均杂合度在0.6800～0.7432之间。其中藏鸡最高,为0.7432;狼山鸡最低,为0.6800;平均多态信息含量在0.6329～0.7023之间,均大于0.5,表现为高度多态性;11 个鸡品种聚为4类。丝羽乌骨鸡、茶花鸡、仙居鸡、藏鸡、萧山鸡聚为一类,鹿苑鸡、狼山鸡聚为一类,固始鸡、北京油鸡、大骨鸡聚为一类,河南斗鸡单独聚为一类;通过利用20个微卫星基因座检测不同世代群体中等位基因及其频率、群体基因平均杂合度和多态信息含量,建立地方鸡品种保种群微卫星标记档案,并分析世代间的差异,预期可以达到监测保种效果的目的。     

Comparison of renal ornithine transcarbamylase activities within different chicken breeds

Comparisons were made of the renal ornithine transcarbamylase (OTC) activities within different groups of chickens including Japanese native breeds. OTC activities varied markedly within these groups. The Cochin Bantam breed and White Leghorn B line had an especially high activity, about 400 units/g of kidney, in contrast to two Japanese native breeds, Japanese Game (white variety) and Banshuu Gashiwa, and the California Gray breed, which showed a very low activity, the values being almost undetectable. In crossing experiments using the California Gray breed as a tester strain, Cochin Bantam OTC represents a simple autosomal incompletely dominant trait similar to the White Leghorn B line OTC. Kinetic studies using partially purified OTC preparations from the White Leghorn B line and Cochin Bantam breed revealed that both enzymes were identical for a variety of enzymic characteristics. In light of these results, the physiological significance of chick kidney OTC is discussed.     

Some observations on high cavernous nostrils in the chicken

Wide high cavernous nostrils are characteristic of all chicken breeds of the V-shaped duplex comb type, whereas all other breeds have slit-type nostrils, including the Sicilian Buttercup breed that has the buttercup-type duplex comb. Crosses between the Sicilian Buttercup and La Flèche breeds and single comb breeds suggest that this trait is a pleiotropic effect of the Dv allele at the duplex locus and is inherited as a recessive when crosses are made to the wild type (d+). The buttercup allele (Dc) at this same locus does not influence nostril morphology by itself, but, when combined with the V-shape comb allele (Dv/Dc), it does allow a single Dv allele to produce mutant nostrils. In this case the inheritance appears dominant. It is proposed that cavernous nostrils are a pleiotropic effect of the comb-size-reducing ability of the Dv allele rather than its duplexing ability.     

An unusual heteromorphic incompatibility system

Summary By means of intra- and intermorph crosses it has been shown that the distyly in Anchusa officinalis L. is governed by a single diallelic locus with dominance. Presence of the dominant allele is reflected in the short-styled morph, while homozygous recessives become long-styled. Most of the short-styled plants are heterozygous, but homozygotes have been found among the raised progeny resulting from crossings. Diallel crosses have revealed that at least two incompatibility loci must exist. These and the morphological locus segregate independently. The type of incompatibility system is as yet unknown, though the great frequency of non-reciprocal incompatibility points to a sporophytic system.     

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.     

Variation of short tandem repeats within and between species belonging to the Canidae family

Frequency distribution and allele size in 20 canine microsatellite loci were analyzed in 33 flat-coated retrievers, 32 dachshunds, 10 red foxes, and 10 Arctic foxes. Overall, the major difference between the two dog breeds was the relative allele frequencies rather than the size ranges of alleles at the individual locus. The average heterozygosity within the two dog breeds was not significantly different. Since the average heterozygosity at several polymorphic loci is a relative measure of heterogeneity within the population, analysis of heterozygosity within microsatellite loci is suggested as a measure for the diversity of populations. Eighty percent (16 of 20) of the canine microsatellite primer pairs amplified corresponding loci in the two fox species. This reflects a very high sequence conservation within the Canidae family relative to findings in, for instance, the Muridae family. This indicates that it will be possible to utilize the well-characterized fox karyotype instead of the dog karyotype as a step towards physical mapping of the dog genome. Analysis of exclusion power and probabilities of genetic identity between unrelated animals by use of the seven most informative loci demonstrated that it will be possible to assemble a panel of microsatellite loci that is effective for parentage analysis in all breeds.     

利用微卫星技术分析中国部分地方鸡种的遗传结构

利用7个微卫星标记对鹿苑鸡、固始鸡、藏鸡、白耳鸡、仙居鸡、茶花鸡、大骨鸡、北京油鸡、狼山鸡、河南斗鸡、泰和乌骨鸡和萧山鸡等12个中国地方鸡种的等位基因频率、基因杂合度、平均基因杂合度、多态信息含量以及群体间的亲缘关系进行分析。研究结果表明,12个地方鸡种在7个微卫星座位上的基因频率存在一定的差异;鹿苑鸡的平均基因杂合度最高,为0．5929;茶花鸡的平均遗传杂合度最低,为0．3514。平均多态信息含量也出现了类似的结果,说明鹿苑鸡的遗传多样性最丰富。模糊聚类分析结果表明,12个地方鸡种间,泰和乌骨鸡与河南斗鸡的亲缘关系相对较近,而固始鸡与其他11个地方鸡种的亲缘关系相对较远。12个地方鸡种可以聚为3类：泰和乌骨鸡、河南斗鸡、狼山鸡、大骨鸡、萧山鸡、北京油鸡、鹿苑鸡聚为第1个类群;茶花鸡、藏鸡、仙居鸡、白耳鸡聚为第2类群;固始鸡为第3类群。     

Flesh color association with polymorphism of the tyrosinase gene in different Chinese chicken breeds

In order to study genetic variation of tyrosinase gene in four different flesh color chicken breeds selected from special districts including Guyuan, Wenchang, Tibetan and Hisex chicken, five loci of the TYR gene exon-1 and one locus of 5′ flanking region were analyzed in PCR-SSCP and DNA sequencing. The results indicated that there were polymorphisms only at TYR1 and TYR3 locus. At TYR1 locus located in exon-1, there were three genotypes (TT, CC, TC), respectively, in three Chinese chicken breeds, and Genotype CC had not been detected in Hisex chicken. At TYR3 locus located in 5′ flanking region, there were three genotypes (GG, AA and GA) in Chinese local chicken breeds and genotype AA had not been detected in Hisex chicken breed. It was concluded that there were many variations of TYR gene in Chinese local chicken breeds. DNA sequencing of PCR products for different genotypes showed that there were two mutation sites, respectively, C to T at TYR1 locus and G to A at TYR3 locus. Mutation at TYR1 locus did not cause any amino acid variation. The chi-square analysis revealed that there were significant statistical differences generally between flesh color and the two loci among four chicken populations (P < 0.01). Our results suggested that the flesh color was related to genotype of TYR gene in Chinese chicken breeds. This study provided original information for elucidating the possible roles of exon-1 of TYR gene and 5′ flanking region in chickens with different flesh color chicken.     

Plasma alpha-protease inhibitors in Norwegian Landrace and Czech Landrace pigs

The studies on alpha-protease inhibitors systems, controlled by four tightly linked loci, were performed within 159 families of Norwegian Landrace (NL) and 40 families of Czech Landrace (CL) pigs. Significant differences in allele and haplotype frequencies between the two breeds were shown. The SE-F and SSsS haplotypes (Pi1, Po1A, Po1B, Pi2 loci) appeared to be the most frequent haplotypes in NL and CL breeds respectively. This system of blood plasma proteins can be very useful for studying the relationship between breeds.     

Characterization of the genetic diversity, structure and admixture of British chicken breeds

The characterization of livestock genetic diversity can inform breed conservation initiatives. The genetic diversity and genetic structure were assessed in 685 individual genotypes sampled from 24 British chicken breeds. A total of 239 alleles were found across 30 microsatellite loci with a mean number of 7.97 alleles per locus. The breeds were highly differentiated, with an average F(ST) of 0.25, similar to that of European chicken breeds. The genetic diversity in British chicken breeds was comparable to that found in European chicken breeds, with an average number of alleles per locus of 3.59, ranging from 2.00 in Spanish to 4.40 in Maran, and an average expected heterozygosity of 0.49, ranging from 0.20 in Spanish to 0.62 in Araucana. However, the majority of breeds were not in Hardy-Weinberg Equilibrium, as indicated by heterozygote deficiency in the majority of breeds (average F(IS) of 0.20), with an average observed heterozygote frequency of 0.39, ranging from 0.15 in Spanish to 0.49 in Cochin. Individual-based clustering analyses revealed that most individuals clustered to breed origin. However, genetic subdivisions occurred in several breeds, and this was predominantly associated with flock supplier and occasionally by morphological type. The deficit of heterozygotes was likely owing to a Wahlund effect caused by sampling from different flocks, implying structure within breeds. It is proposed that gene flow amongst flocks within breeds should be enhanced to maintain the current levels of genetic diversity. Additionally, certain breeds had low levels of both genetic diversity and uniqueness. Consideration is required for the conservation and preservation of these potentially vulnerable breeds.     

Extensive genetic polymorphism of four plasma α-protease inhibitors in pigs and evidence for tight linkage between the structural loci of these inhibitors

Summary. Two-dimensional horizontal gel electrophoresis of pig plasma samples (under non-denaturing conditions) using Immobiline pH gradient gels 4.0–6.0 for the first dimension separation, resulted in clear resolution of the variants of four different α-protease inhibitors (protease inhibitor -1 and -2, P11 and P12; postalbumin -1A and -1B, PO1A and PO1B). All these variants were readily visualized by general protein staining. About 900 families each of Swedish Landrace (SL) and Yorkshire (SY) breeds were studied. The extensive inheritance data, including the recombinants encountered, indicated that each of these four inhibitors is controlled by a separate, autosomal locus and that the four loci are tightly linked (spread over a distance of 1–1.5 cM) with the order as Pil-Po1A-Po1B-Pi2 . The alleles observed were two of Pil, 14 of Po1A , 11 of Po1B and 8 of Pi2 . About 40 haplotypes were observed in each of the two breeds. The allele frequencies at Po1A, Po1B and Pi2 loci were remarkably different in the two breeds; the alleles at these three loci showed a very strong linkage disequilibrium (0.8–1.0). The females showed much higher recombination frequencies than the males in the Po1A-Pi2 interval, suggesting that gene conversion-like events may be occurring at these loci. This linkage in pigs and similar ones comprising some plasma α-protease inhibitor genes in humans and in rodents, reported recently in the literature, indicate evolutionary conservation of a homologous linkage group in these species.     

Genetics of ethylene biosynthesis and restriction fragment length polymorphisms (RFLPs) of ACC oxidase and synthase genes in melon ( Cucumis melo L.)

We investigated the genetics of ethylene biosynthesis and its linkage to the RFLPs of the ACC oxidase and synthase genes in melon ( Cucumis melo L.). The results suggested that the A(0) and B(0) fragments of RFLP-MEL1 of the ACC oxidase gene were two alleles from a single locus, as were the B and C fragments of RFLP-MEACS1 of the ACC synthase gene. The B(0) allele seemed to be partially dominant over the A(0) allele, whereas B and C alleles appeared to map to quantitative trait loci (QTLs), which most likely contributed to ethylene production. Both RFLPs were linked to ethylene production rates, but they were not linked to each other. The interaction effects of the ACC oxidase and synthase genes on ethylene production were revealed by segregation of RFLP-MEL1 and RFLP-MEACS1. The results of single-copy-reconstruction assays suggested that the ACC oxidase gene is a single copy, whereas the ACC synthase gene is a component of a multigene family in the melon genome. The abscission phenotype appeared to be controlled by an independent locus, with the abscission (full-slip) allele dominant over the non-abscission (not full-slip) allele. These results may facilitate efforts toward mapping the quantitative trait loci (QTLs) of ethylene production. The RFLPs may be used in marker-assisted selection in developing melons with a more-desirable low ethylene production rate for enhancing postharvest storage life.     

Characterization of porcine autism susceptibility candidate 2 as a candidate gene for the number of corpora lutea in pigs

In a previous study, we mapped two quantitative trait loci (QTL) approximately 50cM apart, both influencing the number of corpora lutea in pigs on chromosome 3. One locus included functional candidate genes for proteins related to specific aspects of fertility, such as the follicle-stimulating hormone receptor and the luteinizing hormone/choriogonadotropin receptor. However, specific genes related to the second locus have not yet been identified. This study aims to identify another candidate gene influencing the number of corpora lutea in pigs. Using 12 polymorphic markers, we fine-mapped a narrow region of pig chromosome 3 that had been shown to contain a QTL for corpora lutea. In the critical region, only 1 gene, autism susceptibility candidate 2 (AUTS2), was identified as a positional candidate. Our results demonstrate that the porcine AUTS2 gene consists of 19 exons with a complete open reading frame of 3768bp encoding an AUTS2 protein of 1256 amino acids. We screened the whole coding sequence and parts of the untranslated region for polymorphisms in an F(2) population of Duroc×Meishan crosses. We found 1 ins/del and 7 single nucleotide polymorphisms (SNP), including 2 nonsynonymous variants, c.943C>T in exon 7 and c.2828C>T in exon 19, resulting in P315S and A943V, respectively. The SNP c.943C>T within a proline-rich domain was genotyped in several breeds; the C allele occurred in all breeds, whereas the T allele occurred only in Meishan pigs. Using in situ hybridization, the mRNA expression of the AUTS2 gene was observed on granulosa cells in the porcine ovary and thus may be associated with hormone sensitivity.     

Fine‐mapping the POLL locus in Brahman cattle yields the diagnostic marker CSAFG29

The POLL locus has been mapped to the centromeric region of bovine chromosome 1 (BTA1) in both taurine breeds and taurine–indicine crosses in an interval of approximately 1 Mb. It has not yet been mapped in pure‐bred zebu cattle. Despite several efforts, neither causative mutations in candidate genes nor a singular diagnostic DNA marker has been identified. In this study, we genotyped a total of 68 Brahman cattle and 20 Hereford cattle informative for the POLL locus for 33 DNA microsatellites, 16 of which we identified de novo from the bovine genome sequence, mapping the POLL locus to the region of the genes IFNAR2 and SYNJ1. The 303‐bp allele of the new microsatellite, CSAFG29, showed strong association with the POLL allele. We then genotyped 855 Brahman cattle for CSAFG29 and confirmed the association between the 303‐bp allele and POLL. To determine whether the same association was found in taurine breeds, we genotyped 334 animals of the Angus, Hereford and Limousin breeds and 376 animals of the Brangus, Droughtmaster and Santa Gertrudis composite taurine–zebu breeds. The association between the 303‐bp allele and POLL was confirmed in these breeds; however, an additional allele (305 bp) was also associated but not fully predictive of POLL. Across the data, CSAFG29 was in sufficient linkage disequilibrium to the POLL allele in Australian Brahman cattle that it could potentially be used as a diagnostic marker in that breed, but this may not be the case in other breeds. Further, we provide confirmatory evidence that the scur phenotype generally occurs in animals that are heterozygous for the POLL allele.