Overview of Native Chicken Breeds in Italy: Small Scale Production and Marketing.
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ABSTRACT:
SUBMITTER: Franzoni A
PROVIDER: S-EPMC7996916 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:The most reared species of farm animal around the world is the chicken. However, the intensification of livestock systems has led to a gradual increase in the concentration of a limited number of breeds, resulting in substantial erosion to the genetic pool. The initial step of an 'animal conservation program' entails establishing the actual conservation statuses of the breeds concerned in a defined area; in this case, in Italy. To this end, a survey of breeds was performed by means of a census questionnaire divided into two parts. The first part collected information on breeds, breeders, housing facilities, and management aspects, the results of which are presented here. The second part of the questionnaire regarded chicken products and their markets, and these data will be reported in a second paper. The breed status of six chicken breeds was shown to be exceptionally worrying, with total numbers ranging from just 18 to 186 birds. Population sizes exceeding 1000 birds was identified for just four breeds, the maximum being 3400. Some improvements in status were noted in relation to breeds which had been the subject of conservation efforts in the past. The two most common breeds reported are the Bionda Piemontese, a double-purpose breed, and the Livorno egg-laying hen. Collo Nudo Italiano, Millefiori Piemontese, Pollo Trentino, and Tirolese chicken breeds and the Castano Precoce turkey breed were not listed by breeders at all. The most reported turkey breeds are the Bronzato Comune and the Ermellinato di Rovigo. The population sizes of native Italian poultry breeds were shown to be generally poor. Italian poultry farmers and the population at large are largely ignorant about indigenous poultry breeds. Thus, promoting the virtues of Italian breeds would help their conservation by encouraging breeders to rear these birds and consumers to buy their products. The identification of strategies to facilitate access to pure breed birds is essential, and will require the collaboration of university research centers, public entities, and breeders. The results presented in this paper constitute the initial part of a more complex conservation program.
| S-EPMC7917728 | biostudies-literature
Project description:Adaptive genetic variations have direct influences on the fitness traits of the animal. The major histocompatibility complex B (MHC-B) region is responsible for adaptive and innate immune responses in chickens. In native Korean chicken breeds, no information on serologically defined B haplotypes is available. We investigated the MHC-B diversity in 5 restored lines of Korean native chicken and Ogye chicken breeds using a recently described MHC-B single-nucleotide polymorphism (SNP) panel and the MHC-linked LEI0258 variable number of tandem repeat marker. High SNP haplotype diversity was observed in Korean native chicken breeds with an average of 9.7 MHC-B SNP haplotypes per line. The total number of haplotypes ranged from 6 to 12 per line, and population-specific haplotypes ranged from 3 to 4. A total of 41 BSNP haplotypes, including 26 novel population-specific haplotypes and 15 common haplotypes, were reported over all populations. The 15 common haplotypes included 7 novel and 8 previously reported standard haplotypes. Selection and breeding evidence supports the observation of common haplotypes between the Korean native chicken and exotic breeds. Similarly, the LEI0258 marker showed allele variation, between 193 bp and 474 bp having 5 to 8 alleles per population. Some of these alleles (193, 249, 309, and 443 bp) were shared and more frequently observed. Comparison between SNP haplotypes and LEI0258 allele sizes for the same samples showed that some LEI0258 allele sizes correspond to more than one BSNP haplotype. The use of the MHC-B SNP panel greatly enhances the identification of MHC diversity compared with the sole use of the LEI0258 marker in native chicken populations.
| S-EPMC7598131 | biostudies-literature
Project description:BackgroudMycoplasma synoviae (M. synoviae) is widely distributed around the world, and leads to serious economic losses in the world every year. Nevertheless, the incidence and epidemiology of M. synoviae infection in China have remained unclear.ResultsIn this study we demonstrate that over 9773 broiler chicken flocks in 16 Chinese provinces were affected by M. synoviae between 2010 and 2015. Our epidemiological study revealed that M. synoviae was widely prevalent in multi-aged Chinese native breeder chickens, and the prevalence of M. synoviae in embryos of breeders reached up to 16.29%. In addition, our data showed that chickens aged 14 days or younger carried simultaneously high levels of maternal antibody against M. synoviae and high M. synoviae infection (10%), and low M. synoviae antibody levels in breeders and high proportion of M. synoviae infection in embryos could increase the chances of incidence in the offspring. Finally, our results also indicated that 3- to 7-week-old chickens might be most the susceptible to M. synoviae and, therefore, might play a key role in the horizontal transmission of M. synoviae.ConclusionOur findings suggest that M. synoviae is widely circulating in Chinese native chickens, accordingly, effective control measures are urgently needed to control the spread.
| S-EPMC5405555 | biostudies-literature
Project description:Background: Detecting genetic variation is a critical step in elucidating the molecular mechanisms underlying phenotypic diversity. Until recently, such detection has mostly focused on single nucleotide polymorphisms (SNPs) because of the ease in screening complete genomes. Another type of variant, copy number variation (CNV), is emerging as a significant contributor to phenotypic variation in many species. Here we describe a genome-wide CNV study using array comparative genomic hybridization (aCGH) in a wide variety of chicken breeds. Results: We identified 3,154 CNVs, grouped into 1,556 CNV regions (CNVRs). Thirty percent of the CNVs were detected in at least 2 individuals. The average size of the CNVs detected was 46.3 kb with the largest CNV, located on GGAZ, being 4.3 Mb. Approximately 75% of the CNVs are copy number losses relatively to the Red Jungle Fowl reference genome. The genome coverage of CNVRs in this study is 60 Mb, which represents almost 5.4% of the chicken genome. In particular large gene families such as the keratin gene family and the MHC show extensive CNV. Conclusions: A relative large group of the CNVs are line-specific, several of which were previously shown to be related to the causative mutation for a number of phenotypic variants. The chance that inter-specific CNVs fall into CNVRs detected in chicken is related to the evolutionary distance between the species. Our results provide a valuable resource for the study of genetic and phenotypic variation in this phenotypically diverse species.
2013-08-21 | GSE47623 | GEO
Project description:BackgroundDetecting genetic variation is a critical step in elucidating the molecular mechanisms underlying phenotypic diversity. Until recently, such detection has mostly focused on single nucleotide polymorphisms (SNPs) because of the ease in screening complete genomes. Another type of variant, copy number variation (CNV), is emerging as a significant contributor to phenotypic variation in many species. Here we describe a genome-wide CNV study using array comparative genomic hybridization (aCGH) in a wide variety of chicken breeds.ResultsWe identified 3,154 CNVs, grouped into 1,556 CNV regions (CNVRs). Thirty percent of the CNVs were detected in at least 2 individuals. The average size of the CNVs detected was 46.3 kb with the largest CNV, located on GGAZ, being 4.3 Mb. Approximately 75% of the CNVs are copy number losses relatively to the Red Jungle Fowl reference genome. The genome coverage of CNVRs in this study is 60 Mb, which represents almost 5.4% of the chicken genome. In particular large gene families such as the keratin gene family and the MHC show extensive CNV.ConclusionsA relative large group of the CNVs are line-specific, several of which were previously shown to be related to the causative mutation for a number of phenotypic variants. The chance that inter-specific CNVs fall into CNVRs detected in chicken is related to the evolutionary distance between the species. Our results provide a valuable resource for the study of genetic and phenotypic variation in this phenotypically diverse species.
| S-EPMC3751642 | biostudies-literature
Project description:Background: Detecting genetic variation is a critical step in elucidating the molecular mechanisms underlying phenotypic diversity. Until recently, such detection has mostly focused on single nucleotide polymorphisms (SNPs) because of the ease in screening complete genomes. Another type of variant, copy number variation (CNV), is emerging as a significant contributor to phenotypic variation in many species. Here we describe a genome-wide CNV study using array comparative genomic hybridization (aCGH) in a wide variety of chicken breeds. Results: We identified 3,154 CNVs, grouped into 1,556 CNV regions (CNVRs). Thirty percent of the CNVs were detected in at least 2 individuals. The average size of the CNVs detected was 46.3 kb with the largest CNV, located on GGAZ, being 4.3 Mb. Approximately 75% of the CNVs are copy number losses relatively to the Red Jungle Fowl reference genome. The genome coverage of CNVRs in this study is 60 Mb, which represents almost 5.4% of the chicken genome. In particular large gene families such as the keratin gene family and the MHC show extensive CNV. Conclusions: A relative large group of the CNVs are line-specific, several of which were previously shown to be related to the causative mutation for a number of phenotypic variants. The chance that inter-specific CNVs fall into CNVRs detected in chicken is related to the evolutionary distance between the species. Our results provide a valuable resource for the study of genetic and phenotypic variation in this phenotypically diverse species. In total 62 chicken DNA samples (derived from 15 lines) were analyzed against the chicken reference animal UCD001 (the same induvidual that was used to generate the chicken genome reference sequence (ICGSC, 2004)
2013-08-21 | E-GEOD-47623 | biostudies-arrayexpress
Project description:The major histocompatibility complex (MHC) is a highly polymorphic gene region that regulates cellular communication in all specific immune responses. In this study, we investigated 11 microsatellite (MS) markers in the MHC-B region of chicken populations from four countries: Sri Lanka, Bangladesh, South Korea, and Nigeria. The MS markers were divided into two sets. Set 1 included five novel MS markers, which we assessed using 192 samples from 21 populations. Set 2 included six previously reported markers, which we assessed using 881 samples from 29 populations. The Set 1 MS markers had lower polymorphism (polymorphic information content (PIC) < 0.5) than the Set 2 markers (PIC = 0.4-0.9). In all populations, the LEI0258 marker was the most polymorphic, with a total of 38 alleles (PIC = 0.912, expected heterozygosity (He) = 0.918). Local populations from Sri Lanka, Bangladesh, and Nigeria had higher allele diversity and more haplotypes for Set 2 MS markers than Korean and commercial populations. The Sri Lankan Karuwalagaswewa village population had the highest MHC diversity (mean allele number = 8.17, He = 0.657), whereas the white leghorn population had the lowest (mean allele number = 2.33, He = 0.342). A total of 409 haplotypes (89 shared and 320 unique), with a range of 4 (Rhode Island red) to 46 (Karuwalagaswewa village (TA)), were identified. Among the shared haplotypes, the B21-like haplotype was identified in 15 populations. The genetic relationship observed in a neighbour-joining tree based on the DA distance agreed with the breeding histories and geographic separations. The results indicated high MHC diversity in the local chicken populations. The difference in the allelic pattern among populations presumably reflects the effects of different genotypes, environments, geographic variation, and breeding policies in each country. The selection of MHC allele in domestic poultry can vary due to intensification of poultry production. Preserved MHC diversity in local chicken provides a great opportunity for future studies that address the relationships between MHC polymorphisms and differential immune responses.
| S-EPMC7915948 | biostudies-literature
Project description:Small-scale farming of meat chicken flocks using local native breeds contributes to the economy of many rural livelihoods in Vietnam and many other low- and middle-income countries (LMICs). These systems are also the target of high levels of antimicrobial use (AMU); however, little is known about the profitability and sustainability of such systems. Since small-scale farms are commercial enterprises, this knowledge is essential to develop successful strategies to curb excessive AMU. Using longitudinal data from 203 small-scale (100-2,000 heads) native chicken flocks raised in 102 randomly selected farms in Dong Thap province (Mekong Delta, Vietnam), we investigated the financial and economic parameters of such systems and the main constraints to their sustainability. Feed accounted for the largest financial cost (flock median 49.5 % [Inter-quartile range (IQR) 41.5-61.8 %]) of total costs, followed by day-old-chicks (DOCs) (median 30.3 % [IQR 23.2-38.4 %]), non-antimicrobial health-supporting products (median 7.1 % [IQR 4.7-10.5 %]), vaccines (median 3.1 % [IQR 2.2-4.8 %]), equipment (median 1.9 % [IQR 0.0-4.9 %]) and antimicrobials (median 1.9 % [IQR 0.7-3.6 %]). Excluding labor costs, farmers achieved a positive return on investment (ROI) from 120 (59.1 %) flocks, the remainder generating a loss (median ROI 124 % [IQR 36-206 %]). Higher ROI was associated with higher flock size and low mortality. There was no statistical association between use of medicated feed and flock mortality or chicken bodyweight. The median daily income per person dedicated to raising chickens was 202,100 VND, lower than alternative rural labor activities in the Mekong Delta. In a large proportion of farms (33.4 %), farmers decided to stop raising chickens after completing one cycle. Farmers who dropped off chicken production purchased more expensive feed (in 1000 VND per kg): 11.1 [10.6-11.5] vs. 10.8 [10.4-11.3] for farms that continued production (p = 0.039), and experienced higher chicken mortality (28.5 % [12.0-79.0 %] vs. 16 [7.5-33.0 %]; p = 0.004). The rapid turnover of farmers raising chickens in such systems represents a challenge to the uptake of messages on appropriate AMU and chicken health. To ensure sustainability of small-scale commercial systems, advisory services need to be available to farmers as they initiate new flocks, and support them in the early stages to help overcome their limited experience and skills. This targeted approach would support profitability whilst reducing risk of emergence of AMR and infectious disease from these systems.
| S-EPMC8463836 | biostudies-literature
Project description:Salmonella is a common food-borne Gram-negative pathogen with multiple serotypes. Pullorum disease, caused by Salmonella Pullorum, seriously threatens the poultry industry. Many previous studies were focused on the epidemiological characteristics of Salmonella infections in conventional antibiotic use poultry. However, little is known about Salmonella infections in chicken flocks fed on antibiotic-free diets. Herein, we investigated and compared Salmonella infections in three Chinese native breeders fed on antibiotic-free diets, including the Luhua, Langya, and Qingjiaoma chickens, and one conventional breeder, the Bairi chicken, via analyzing 360 dead embryos in 2019. The results showed that the main Salmonella serotypes detected in a total of 155 isolates were S. Pullorum (82.6%) and S. Enteritidis (17.4%). Coinfection with two serotypes of Salmonella was specifically found in Bairi chicken. The sequence type (ST) in S. Pullorum was ST92 (n = 96) and ST2151 (n = 32), whereas only ST11 (n = 27) was found in S. Enteritidis. The Salmonella isolates from three breeder flocks fed on antibiotic-free diets exhibited phenotypic heterogeneity with a great variety of drug resistance spectrum. Most of the isolates among three chicken breeds Luhua (64.9%, 50/77), Langya (60%, 12/20) and Qingjiaoma (58.3%, 7/12) fed on antibiotic-free diets were resistant to only one antibiotic (erythromycin), whereas the rate of resistance to one antibiotic in conventional Bairi chicken isolates was only 4.3% (2/46). The multidrug-resistance rate in Salmonella isolates from layer flocks fed on antibiotic-free diets (20.2%, 22/109) was significantly (P < 0.0001) lower than that from chickens fed on conventional diets (93.5%, 43/46). However, high rate of resistance to erythromycin (97.4%~100%) and streptomycin (26%~41.7%) were also found among three breeder flocks fed on antibiotic-free diets, indicating resistance to these antibiotics likely spread before antibiotic-free feeding in poultry farms. The findings of this study supplement the epidemiological data of salmonellosis and provide an example of the characteristics of Salmonella in the chicken flocks without direct antibiotic selective pressure.
| S-EPMC8021795 | biostudies-literature
Project description:Investigation into the genetic diversity of certain endangered native breeds of domestic animals has been in common practice for several decades. The primary objective of these investigations has been to reveal the exceptional genetic value of such breeds, both for their conservation and also to gain insight into their current genetic status, as they have been undergoing a progressive decrease in population size and general diversity; this has been compounded by the general lack of an optimal breeding scheme. In this study, we have investigated changes in the genetic diversity of six Hungarian local chicken breeds based on 29 microsatellite loci over a period of 15 years. In terms of the basic diversity measures, populations sampled in 2017 generally exhibited a lower heterozygosity and mean number of alleles and thus, experienced a higher degree of inbreeding. Although the effective population size increased, the estimates of populations sampled over different periods indicated comparatively low values, suggesting overall lower genetic variance. Pairwise FST estimates were higher in the populations sampled in 2017, showing a larger genetic distance between them. Considerable differences exist between the populations of the same breeds, which can most likely be attributed to genetic drift. STRUCTURE results have shown a clear separation between the Hungarian populations, which is in agreement with the principal coordinate analysis. The most likely clustering was found at K = 6, classifying the populations of the same breed as one group. No considerable allele loss was found in the Hungarian indigenous chicken breeds after 15 years of conservation. In general terms, after 15 years, the level of inbreeding within the populations was, in fact, higher, although this could be effectively reduced through the use of an improved mating system. Consequently, the breed management applied in the case of Hungarian local chicken breeds was found to be effective at adequately conserving their genetic variability.
| S-EPMC7478839 | biostudies-literature