An improved method for discriminating between Japanese Nagoya chickens and others

Recently, we reported a method for identifying the Nagoya, a Japanese chicken breed. Here we describe an improved method suitable for use in conventional laboratories. Five microsatellite markers fixed in the Nagoya breed were amplified by multiplex polymerase chain reaction (PCR). The PCR products were digested with CEL I nuclease and electrophoresed in a ready‐made gel. The fragment‐length polymorphisms of each marker were detected clearly in the gel, and the resultant exclusion probabilities were almost equal to that in our previous data. This method can be used in laboratories without a DNA sequencer for routinely discriminating between the Nagoya breed and other chickens.     

Differences in genetic structure assessed using Y‐chromosome and mitochondrial DNA markers do not shape the contributions to diversity in African sires

Up to 173 African sires belonging to 11 different subpopulations representative of four cattle groups were analysed for six Y‐specific microsatellite loci and a mitochondrial DNA fragment. Differences in Y‐chromosome and mtDNA haplotype structuring were assessed. In addition, the effect of such structuring on contributions to total genetic diversity was assessed. Thirty‐five Y‐chromosome and 71 mtDNA haplotypes were identified. Most Y‐chromosomes analysed (73.4%) were of zebu origin (11 haplotypes). Twenty‐two Y‐haplotypes (44 samples) belonged to the African taurine subfamily Y2a. All mtDNA haplotypes belonged to the “African” taurine T1 haplogroup with 16 samples and nine haplotypes belonging to a recently identified subhaplogroup (T1e). Median‐joining networks showed that Y‐chromosome phylogenies were highly reticulated with clear separation between zebu and taurine clusters. Mitochondrial haplotypes showed a clear star‐like shape with small number of mutations separating haplotypes. Mitochondrial‐based F_ST‐statistics computed between cattle groups tended to be statistically non‐significant (p > .05). Most F_ST values computed among groups and subpopulations using Y‐chromosome markers were statistically significant. AMOVA confirmed that divergence between cattle groups was only significant for Y‐chromosome markers (Φ_CT = 0.209). At the mitochondrial level, African sires resembled an undifferentiated population with individuals explaining 94.3% of the total variance. Whatever the markers considered, the highest contributions to total Nei's gene diversity and allelic richness were found in West African cattle. Genetic structuring had no effect on patterns of contributions to diversity.     

Association of three beta-defensin gene (AvBD4, AvBD5, AvBD14) polymorphisms with carrier-state susceptibility to salmonella in chickens

ABSTRACT

1. Chicken salmonellosis is a common zoonotic infectious disease transmitted both vertically and horizontally. Avian beta-defensins (gallinacins) play an important role in the innate defence of the host and provide broad-spectrum immunity against multiple pathogens.

2. To detect the relationship between immune genes and salmonella carrier status and susceptibility to salmonellosis in chickens, polymorphisms with carrier-state susceptibility to salmonella and, hence, developing salmonellosis, were investigated in three avian beta-defensin genes (AvBD4, AvBD5, and AvBD14) in a Chinese local chicken breed, based on a case-control study.

3. Fifteen, twenty and nineteen SNPs were found in AvBD4, AvBD5 and AvBD14, respectively. Among the 54 total SNPs, four resulted in non-synonymous substitution of amino acid changes. Five SNPs in AvBD5 and four SNPs in AvBD14 were significantly associated with salmonellosis susceptibility (P < 0.05). Using the PHASE program, thirteen, ten and twelve major haplotypes were constructed in AvBD4, AvBD5 and AvBD14. Logistic regression analysis revealed that five haplotypes in AvBD5 and six haplotypes in AvBD14 were significantly associated with salmonellosis susceptibility, but no significant haplotype in AvBD4 was detected. A total of six strongly susceptible haplotypes with odds ratio (OR) values greater than 2.0 and four strongly resistant haplotypes with OR value less than 0.5 were revealed in the three genes examined.

4. These results suggested that the AvBD5 and AvBD14 genes may play an important role in the susceptibility to salmonellosis in chickens.     

Influences of major histocompatibility complex class I haplotypes on avian influenza virus disease traits in Thai indigenous chickens

Natural infections with influenza viruses have been reported in a variety of animal species including humans, pigs, horses, sea mammals, mustelids and birds. Occasionally, devastating pandemics occur in domestic chickens (broiler and layers) and in humans. From November 2003 to March 2004 in many countries in Asia, there were outbreaks of H5N1 avian influenza virus, causing death of infected patients, and devastating the poultry industry. Some groups of Thai indigenous chickens survived and were therefore classified as resistant. These traits were related to immunogenetics, in particular, the major histocompatibility complex (MHC) class I and class II molecules. The chicken MHC class I were investigated as candidate genes for avian influenza virus disease resistance. Seven hundred and thirty Thai indigenous chickens from smallholder farms in the rural area of avian influenza virus disease outbreaks in the central part of Thailand were used in the present study. They were separated into two groups, 340 surviving chickens and 390 dead chickens (resistant and susceptible). Genomic DNA were precipitated from blood samples and feathers. The DNA were used to amplify the MHC class I gene. Data were analyzed using χ² analysis to test significant differences of influences of MHC class I haplotypes on avian influenza virus disease traits. The results represented nine MHC class I haplotypes: A1, B12, B13, B15, B19, B21, B2, B6, and BA12, and included 10 of their heterozygotes. The homozygous B21 from these collected samples had a 100% survival rate and they were the major survival group. In addition, the heterozygous B21 also had a high survival rate because of co‐dominant expression of these genes. In contrast, the homozygous B13 had a 100% mortality rate and they were the major mortality group. These results confirmed that MHC class I haplotypes influence avian influenza virus disease‐resistant traits in Thai indigenous chicken. The MHC genes can be used as genetic markers to improve disease‐resistant traits in chicken.     

四川常羽乌骨鸡群体遗传多样性分析

利用选自家禽基因组的10个微卫星标记,对四川常羽乌骨鸡5个群体(四川山地乌骨鸡白羽系、黑羽系;黄忠山地乌骨鸡;黄忠山地乌骨鸡绿壳蛋系;草科乌骨鸡)的遗传多样性进行了检测,计算了各群体的群体杂合度、群体间遗传距离,并根据遗传距离进行了聚类分析。结果表明所选择的微卫星标记在各群体中表现出较高的多态性;四川5个乌骨鸡群体遗传多样性比较丰富,群体平均杂合度为0.5383到0.6659;各群体间的遗传距离有一定的差异;聚类分析将5个群体聚为三类。     

Diversity of the Icelandic goat breed assessed using population data

Abstract

The Icelandic goat breed is a closed population consisting of around 700 animals kept in 45 herds. Several population bottlenecks are known to have occurred and the population has at least twice declined below 100 animals. Here the genetic diversity of the breed was estimated using pedigree information, D-loop sequencing and microsatellite markers. The annual rate of inbreeding was estimated as 3% and the effective population size as 5.1 animals. The effective population size based on molecular markers was estimated in the range of 4.1–8.8 individuals and mtDNA D-loop sequencing identified only three haplotypes. The results presented here show the population to be highly inbred, fragmented and the level of genetic variation among the lowest found in livestock. The results will be an important input into conservation planning for the Icelandic goat.     

Genetic association between GHSR1a 5′UTR‐microsatellite and nt‐7(C>A) loci and growth and carcass traits in Japanese Black cattle

We carried out a genetic association study between five nucleotide polymorphisms (5′UTR microsatellite ((TG)_n), nt‐7(C>A), L24V, DelR242 and Intron 1 microsatellite) of the GHSR1a gene and growth and carcass traits in 1285 steers sired by 117 Japanese Black bulls in a progeny testing program. We report herein, a significant association between the 5′UTR microsatellite and nt‐7(C>A) loci and growth and carcass traits. We also propose a translational hypothesis that the association is due to differences in the secondary structure of GHSR1b mRNA (the non‐spliced type with the 5′UTR microsatellite) among the GHSR1a gene haplotypes. Furthermore, we predicted the potential increase in profitability due to increased carcass weight in cow‐calf fattening enterprises through planned matings based on DNA testing of the 5′UTR microsatellite. Statistical analysis revealed that the 5′UTR microsatellite locus had a significant additive effect on carcass weight (CW) and average daily gain (ADG), but not on beef marbling score (BMS). One of the four major microsatellite alleles (19‐TG allele) with an allele frequency of 0.145, had a significantly (P < 0.0007) desirable effect on CW and ADG. We concluded that the 19‐TG allele could potentially be economically useful nucleotide markers for growth and carcass traits in Japanese Black cattle.     

Marker-assisted selection for forelimb-girdle muscular anomaly of Japanese Black cattle

Forelimb‐girdle muscular anomaly is a hereditary disorder of Japanese Black cattle characterized by tremors and astasia caused by hypoplasia of the forelimb‐girdle muscles. The locus responsible for this disorder has been mapped on a middle region of bovine chromosome 26. In this study, we applied marker‐assisted selection to identify the carriers of this disorder. Four microsatellite markers, DIK4440, BM4505, MOK2602 and IDVGA‐59, linked to the disorder locus were genotyped in 37 unaffected offspring of a carrier sire. Transmission of the mutant or wild‐type allele of the disorder locus of the sire to the 37 offspring was determined by examining the haplotypes of these markers. The results showed that nine and 18 of the 37 animals possessed the paternally transmitted mutant and wild‐type alleles, respectively, and therefore, the nine animals with the mutant allele were identified as carriers. We concluded that the marker‐assisted selection using these four markers can be applied for the identification of the carriers of forelimb‐girdle muscular anomaly of Japanese Black cattle.     

Single strand conformation polymorphism detection in alpha-lactalbumin gene of Indian Jakhrana milk goats

Abstract

Alpha-lactalbumin (α-LA) (ALA), one of the two major whey proteins, is strongly correlated with the nutritional value and the functional properties of whey and whey products. The genetic variations of ALA gene in Jakhrana Goat breed (Capra hircus) were investigated using an optimized non-radioactive polymerase chain reaction–single strand conformation polymorphism (PCR–SSCP) analysis of four amplified fragments covering all four exons of the gene. A total of eight SSCPs patterns were detected in three of these exons in a sample of 50 Jakhrana goats, indicating that this breed has high genetic variability in the ALA gene. This result opens interesting prospects for future breeding programs and conservation strategies. These ALA gene variants can be sequenced and screened in the entire population to develop single nucleotide polymorphisms for association studies with different productive and reproductive performances and marker assisted selection. In addition, our data show that PCR–SSCP is an appropriate tool for evaluating genetic variability.     

Heritage Finnish Landrace chickens are genetically diverse and geographically structured

ABSTRACT

The Finnish Landrace breed of chickens (in Finnish suomalainen maatiaiskana) traces its origins to almost 1,000 years ago. Today, remnant populations of phenotypically distinct lineages are maintained by a network of volunteer hobbyists in Finland, managed by Natural Resources Institute Finland (Luke). Guided by a prior Major Histocompatibility Complex B-locus haplotype study, we sought now to characterize genetically Finnish Landrace chickens using denser genomic sampling. A new panel of 101 selectively neutral SNP sites was used to interrogate genetic variation in 192 individuals sampled from 13 putatively distinctive population units. Individuals partitioned into K?=?11 genetic clusters characterized by high levels of genetic diversity, strong patterns of genetic structure and low levels of inbreeding. Evidence of an undocumented genetic lineage was also discovered. Facilitated by an inexpensive SNP assay, this study shows that the genetic integrity of the Finnish Landrace persists and represents a rich resource of natural (adaptive) genomic variation.     

Genetic diversity,structure and individual assignment of Casta Navarra cattle: a well‐differentiated fighting bull population

The Casta Navarra lineage was one of the populations used to establish the fighting bull (FB) breed, and it has also been reproductively isolated from the others FBs. A total of 1284 individuals from two generations of 16 Casta Navarra herds were sampled to analyse their diversity, their genetic structure and the ability of 28 microsatellite markers to assign individuals to closely related populations. These animals were compared with closely related phylogenetic (FB) or geographical (Pirenaica and Monchina) populations. Hardy–Weinberg equilibrium analysis showed that 82% of the loci had a significant heterozygote deficit as a consequence of the Wahlund effect. The average proportion of genetic variation explained by farm differences was 9% by Wright's F_ST index. A phylogenetic tree constructed with a neighbour‐joining method based on Reynolds genetic distances and a Bayesian Markov chain Monte Carlo clustering approach revealed clear differences between farm groups that generally corresponded to historical information and could unambiguously differentiate Casta Navarra cattle from the other populations. The percentage of animals correctly assigned to the Casta Navarra population was 91.78% for a q threshold of >0.9. Admixture was only detected in 4.45% (q < 0.8) of the cattle. These results are relevant for the maintenance and development of diversity and conservation in the Casta Navarra population.     

Homozygosity of single nucleotide polymorphisms in the 3′ region of the canine estrogen receptor 1 gene is greater in Toy Poodles than in Miniature Dachshunds and Chihuahuas

Differences in the distribution of single nucleotide polymorphisms (SNPs) and haplotypes in the estrogen receptor α gene (ESR1) were examined in Miniature Dachshunds (n = 48), Chihuahuas (n = 20) and Toy Poodles (n = 18). Five DNA fragments located in the 40‐kb region at the 3′ end of ESR1 were amplified by polymerase chain reaction and were directly sequenced. We compared allele, genotype and estimated haplotype frequencies at each SNP in the 3′ end of ESR1 for these three breeds of small dog. The frequency of the major allele and the genotype frequency of the major allele homozygotes, were significantly higher in Toy Poodles for five SNPs (SNP #5, #14–17) than in Miniature Dachshunds, and significantly higher in Toy Poodles than Chihuahuas for three SNPs (SNP #15–17). A common haplotype block was identified in an approximately 20‐kb region encompassing four SNPs (SNPs # 14–17). The frequencies of the most abundant estimated haplotype (GTTG) and GTTG homozygotes were significantly higher in Toy Poodles than in the other two breeds. These results imply that homozygosity for the allele, genotype and haplotype distribution within the block at the 3′ end of ESR1 is greater in Toy Poodles than in Miniature Dachshunds and Chihuahuas.     

Feeding status of free-range scavenging chickens in different agro-climatic regions of India

ABSTRACT

1. The aim of this study was to determine the nutritional status of backyard chickens reared under 4 different agro-climatic conditions (tropical, humid subtropical, cool-temperate and semi-arid) of India during different seasons of the year and to compare their nutritional status with those reared under confined feeding system (CFS). In each season, 15 adult and 15 grower chickens were slaughtered for collecting content of crop and gizzard to assess the nutritional status from different agro-climatic conditions.

2. The dry matter content of crop and gizzard was higher (P < 0.01) in chickens reared under backyard conditions compared to those reared under CFS.

3. Higher (P < 0.01) crop and gizzard contents were recorded during winter compared to the rainy season. The proportion of grains in the crop during summer and winter season was higher compared to rainy season. Further, there were more insects present in the crop during the rainy season and winter compared to summer.

4. The proportion of insects was higher in chickens reared in humid, subtropical and cool temperate regions compared to semi-arid conditions. The consumption of grasses was higher in cool-temperate regions as compared to those reared under other areas.

5. Crude protein (CP), Ca, P and gross energy (GE) content of the crop were higher in chickens reared under CFS compared to those reared in backyard systems and CP in the crop contents was lower in backyard chickens reared in humid subtropical and semi-arid regions compared to other areas. Similarly, lower (P < 0.01) Ca levels were seen in crop and gizzard contents from birds reared in semi-arid Rajasthan, and P and GE were lower in tropical wet and dry Telangana (TWT) compared to the chickens reared in the backyard conditions in other regions.

6. Based on the results, the nutrient intake for birds utilising the scavenging feed resource base (SFRB) in the TWT region was below the requirements of backyard chickens from the other regions selected in the present study. GE and CP were critically deficient in the SFRB of the TWT region. Therefore, evolving location-specific supplementary diets using locally available feed resources to meet nutrient requirement of backyard chickens is required for optimising production potential.     

Application of bovine microsatellite markers on Saola (Pseudoryx nghetinhensis)

The aim of the present study was to assess the applicability of bovine microsatellite markers on Saola (Pseudoryx nghetinhensis). A total of 127 microsatellite markers were tested on a male and a young female Saola. An efficient amplification was observed for 123 markers (96.8%), 73 markers (59.3%) were polymorphic. Four loci (BM2304, BMS1928, BMS779 and ILSTS006) on cattle chromosomes 1, 4, 7 and 8, respectively, failed to amplify in Saola. Two cattle Y‐chromosome‐specific microsatellite markers (INRA126 and BM861) were successfully amplified from both sexes in Saola. However, two additional markers (INRA124 and INRA189) on Y‐chromosome failed to amplify in the female animal. These results show that most of the bovine microsatellite markers are applicable in Saola and therefore they can be used to study the phylogenetic relationships and the genetic diversity of the Saola population.     

Genetic diversity of Bangladeshi native chickens based on complete sequence of mitochondrial DNA D-loop region

ABSTRACT

1. The aim of this study was to explore genetic diversity and possible origin of Bangladeshi (BD) native chickens. The complete mtDNA D-loop region was sequenced in 60 chickens representing five populations; naked neck, full feathered, Aseel, Hilly and autosomal dwarf. The 61 reference sequences representing different domestic chicken clades in China, India, Laos, Indonesia, Myanmar, and other Eurasian regions were included. The mtDNA D-loop sequence polymorphism and maternal origin of five BD populations were analysed.

2. A total of 35 polymorphic sites, and 21 haplotypes were detected in 60 mtDNA D-loop sequences. The haplotype and nucleotide diversity of the five populations were 0.921 ± 0.018 and 0.0061 ± 0.0019, respectively. Both mtDNA network and phylogenetic analysis indicated four clades (four haplogroups) in BD populations (21 haplotypes) along with 61 reference haplotypes. Clade E contained the most individuals (20) and haplotypes (11) of BD chickens, followed by clade D (17, 6), clade C (12, 2) and clade F (11, 2), respectively.

3. The higher number of unique haplotypes found in Yunnan, China, suggested that the origin of BD chickens was in this region. The haplotypes from different haplogroups were introduced in Bangladeshi chickens from India, China and Myanmar. The phylogenetic tree showed a close relationship of BD chickens with the clusters from India, China, Myanmar and Laos, and indicated the dispersion of BD chickens from these sources. The phylogenetic information revealed high genetic diversity of BD chickens because of their origin from different lineages with high genetic variation and distance, which was determined from four cluster and neighbour-joining trees.

4. In conclusion, BD populations had high genetic diversity. The mtDNA network profiles and phylogenetic trees showed multiple maternal origins of BD chickens from India, China, Myanmar and Laos.     

Y‐chromosomal variation of local goat breeds of Turkey close to the domestication centre

Genetic variations in chromosome Y are enabling researchers to identify paternal lineages, which are informative for introgressions and migrations. In this study, the male‐specific region markers, sex‐determining region‐Y (SRY), amelogenin (AMELY) and zinc finger (ZFY) were analysed in seven Turkish native goat breeds, Angora, Kilis, Hair, Honaml?, Norduz, Gürcü and Abaza. A SNP in the ZFY gene defined a new haplotype Y2C. All domestic haplogroups originate from Capra aegagrus, while the finding of Y1A, Y1B, Y2A and Y2C in 32, 4, 126 and 2 Turkish domestic goats, respectively, appears to indicate a predomestic origin of the major haplotypes. The occurrence of four haplotypes in the Hair goat and, in contrast, a frequency of 96% of Y1A in the Kilis breed illustrate that Y‐chromosomal variants have a more breed‐dependent distribution than mitochondrial or autosomal DNA. This probably reflects male founder effects, but a role in adaptation cannot be excluded.     

Shiga toxin-producing Escherichia coli O157:H7 from extensive cattle of the fighting bulls breed

Shiga toxin-producing Escherichia coli (STEC) O157:H7 represents a major public health concern worldwide, with cattle recognized as their main natural reservoir. The aim of this work was to determine the prevalence and the pheno-genotypic characteristics of STEC O157:H7 in a herd with 268 cattle of the fighting bulls breed (De Lidia breed) managed under extensive conditions in the South-West of Spain. Rectal-anal swabs of all animals were collected and examined for STEC O157:H7 by performing an immunomagnetic concentration and separation procedure combined with PCR, and the resulting isolates were characterized by both phenotypic and genotypic methods. Overall, STEC O157:H7 was isolated from seven animals (2.6%) in the herd. The PCR procedure indicated that all seven isolates displayed stx₂, eae-γ1, ehxA, O157 rfbE, and fliCh7 genes. They belonged to phage types 4 (one isolate) and 42 (two isolates), and four isolates reacted with typing phages but did not conform to a recognized pattern. Among the seven isolates there were five indistinguishable PFGE patterns and other two which differed only in ?2 restriction fragments, supporting the existence of horizontal transmission among animals in the herd. The present study demonstrates that cattle managed under extensive conditions in Spain can excrete STEC O157:H7 with their faeces. To our knowledge this is the first isolation of this pathogen from De Lidia cattle.     

Molecular characterization and differentiation of five horse breeds raised in Algeria using polymorphic microsatellite markers

In this study, genetic analyses of diversity and differentiation were performed on five horse breeds raised in Algeria (Barb, Arab‐Barb, Arabian, Thoroughbred and French Trotter). All microsatellite markers were highly polymorphic in all the breeds. A total of 123 alleles from 14 microsatellite loci were detected in 201 horses. The average number of alleles per locus was the highest in the Arab‐Barb horses (7.86) and lowest in the thoroughbred breed (5.71), whereas the observed and expected heterozygosities per breed ranged from 0.71 (Thoroughbred) to 0.752 (Barb) and 0.71 (Thoroughbred) to 0.77 (Arab‐Barb), respectively. The genetic differentiation between the breeds was significant (p < 0.01) based on the infinitesimal model (F_ST). Three different approaches for evaluating the genetic relationships were applied. Genetic distances, the factorial correspondence analysis and structure analysis showed that a significant amount of genetic variation is maintained in the native horse populations and the other breeds. The Barb and Arab‐Barb breeds seem to be the most genetically related and support the decision to consider the breeds as same population.     

Pinpointing the candidate region for muscular dystrophy in chickens with an abnormal muscle gene

Muscular dystrophies, a group of inherited diseases with the progressive weakness and degeneration of skeletal muscle, contain genetically variable diseases. Though chicken muscular dystrophy with abnormal muscle (AM) has long been known, the gene responsible has not yet been identified. In this study, a resource family for AM was established with 487 F2 individuals and 22 gene markers, including microsatellite and insertion–deletion markers, were developed. The haplotypes were analyzed with these markers for the candidate region of GGA2q described in a previous study. The candidate region was successfully narrowed down to approximately 1Mbp. The region included seven functional genes predicted as the most likely AM candidates.     

Genetic diversity of Forest and Savannah chicken populations of Ghana as estimated by microsatellite markers

The characterization of indigenous animal genetic resources is a requisite step in providing needed information for the conservation of useful genotypes against future needs. Thus, in this study, 22 microsatellite markers were used to genotype 114 local chickens from the Forest (n = 59) and Savannah (n = 55) eco‐zones of Ghana and the results compared to those of the ancestral red junglefowl (n = 15) and two European commercial chicken populations – a broiler (n = 25) and white leghorn (n = 25). A total of 171 alleles were observed, with an average of 7.8 alleles per locus. The local Ghanaian chickens showed higher diversity in terms of the observed number of alleles per locus (6.6) and observed heterozygosity (0.568) compared with the combined control populations (6.0 and 0.458, respectively). However, Wright's F‐statistics revealed negligible genetic differentiation (F_ST) in local Ghanaian chicken populations. In addition, 65% of the Savannah chickens were inferred to be more likely from the Forest, suggesting a south‐north dispersal of chickens from their probable original location in the Forest zone to the Savannah areas. It is concluded that the Forest and Savannah chickens of Ghana are a single, randomly mating unselected population, characterized by high genetic diversity and constitute a valuable resource for conservation and improvement.