Polymorphisms in pattern recognition receptor genes of indigenous and White Leghorn breeds of chicken

Functional polymorphisms in pattern recognition receptors (PRRs) modulate innate immunity and play a crucial role in resistance or susceptibility to diseases. The present study was carried out to explore polymorphic patterns in the coding sequences of PRR genes TLR3, TLR1LA (TLRs), MDA5, LGP2 (RLRs) and NOD1 (NLR) in chicken breeds of India, namely Ghagus (GH), Nicobari (NB) and the exotic White Leghorn (WLH) breed. Out of 209 SNPs observed in five genes among three breeds, 117 were synonymous (Syn) and 92 were non-synonymous (NS) SNPs. In TLR genes the highest polymorphism was observed in NB (16, 28) compared to GH (14, 16) and WLH (13, 19) breeds. In the MDA5 gene the highest polymorphism was observed in GH (12) compared to NB (eight) and WLH (four) breeds. However, an almost similar level of polymorphism was observed in the LGP2 gene among the three breeds. In the NOD1 gene, the highest polymorphism was observed in NB (27), followed by WLH (11) and GH (10) breeds. The overall highest number of SNPs was observed in NB (90), followed by GH (62) and the WLH (57) breed. With regard to variation in polymorphism among different classes of PRRs, the study revealed the highest polymorphism in TLRs compared to NOD1 and the RLR class of PRRs. Further, the domain locations of various Syn and NS SNPs in each PRR among the three breeds were identified. In silico analysis of NS SNPs revealed that most of them had a neutral effect on protein function. However, two each in TLR1LA and LGP2 and one in the MDA5 gene were predicted to be deleterious to protein function. The present study unravelled extensive polymorphism in the coding sequences of the TLR and NLR class of PRR genes, and the polymorphism was higher in indigenous chicken breeds.</p

Genetic and phenotypic response in Vanaraja male line chicken under short term selection experiment

The genetic and phenotypic response for 6 weeks shank length (SL6) and correlated response for body weights at 2, 4 and 6 weeks of age were evaluated in short term selection experiment in Vanaraja male line (PD-1) utilizing the data collected for the last 6 generations in a pedigreed mating. The direct response in SL, the primary trait was 2.01±0.85 mm on genetic scale and 2.35±0.36 mm on phenotypic scale. The SL was 68.07±0.004 mm in first generation of study (S4) which gradually improved to 81.01±0.002 mm over the last 6 generations. The correlated genetic response in body weight at 2, 4 and 6 weeks of age was in positive direction though not significant. The body weights improved as correlated response to the primary trait. The phenotypic response in body weights was in positive direction and significant at 6 weeks of age; however at 2 and 4 weeks, it was not significant. The effective population size (Ne) ranged from 150 to 167, the selection intensity (i) between 0.24 to 1.09 and rate of inbreeding from 0.0029 to 0.0033 in the last 6 generations. The realized and estimated heritability estimates were 0.17 and 0.12 for 6 week shank length, respectively. The study concluded that, the genetic and phenotypic responses were positive over the generation with a gradual improvement in the primary trait as well as the juvenile body weights in PD-1 line. The improvement trend was also reflected in Vanaraja, a terminal cross produced for rural/backyard poultry using PD-1 as male line

Eimeria species occurrence varies between geographic regions and poultry production systems and may influence parasite genetic diversity

Coccidiosis is one of the biggest challenges faced by the global poultry industry. Recent studies have highlighted the ubiquitous distribution of all Eimeria species which can cause this disease in chickens, but intriguingly revealed a regional divide in genetic diversity and population structure for at least one species, Eimeria tenella. The drivers associated with such distinct geographic variation are unclear, but may impact on the occurrence and extent of resistance to anticoccidial drugs and future subunit vaccines. India is one of the largest poultry producers in the world and includes a transition between E. tenella populations defined by high and low genetic diversity. The aim of this study was to identify risk factors associated with the prevalence of Eimeria species defined by high and low pathogenicity in northern and southern states of India, and seek to understand factors which vary between the regions as possible drivers for differential genetic variation. Faecal samples and data relating to farm characteristics and management were collected from 107 farms from northern India and 133 farms from southern India. Faecal samples were analysed using microscopy and PCR to identify Eimeria occurrence. Multiple correspondence analysis was applied to transform correlated putative risk factors into a smaller number of synthetic uncorrelated factors. Hierarchical cluster analysis was used to identify poultry farm typologies, revealing three distinct clusters in the studied regions. The association between clusters and presence of Eimeria species was assessed by logistic regression. The study found that large-scale broiler farms in the north were at greatest risk of harbouring any Eimeria species and a larger proportion of such farms were positive for E. necatrix, the most pathogenic species. Comparison revealed a more even distribution for E. tenella across production systems in south India, but with a lower overall occurrence. Such a polarised region- and system-specific distribution may contribute to the different levels of genetic diversity observed previously in India and may influence parasite population structure across much of Asia and Africa. The findings of the study can be used to prioritise target farms to launch and optimise appropriate anticoccidial strategies for long-term control

Gene Expression Profiles of Chicken Embryo Fibroblasts in Response to Salmonella Enteritidis Infection

The response of chicken to non-typhoidal Salmonella infection is becoming well characterised but the role of particular cell types in this response is still far from being understood. Therefore, in this study we characterised the response of chicken embryo fibroblasts (CEFs) to infection with two different S. Enteritidis strains by microarray analysis. The expression of chicken genes identified as significantly up- or down-regulated (≥3-fold) by microarray analysis was verified by real-time PCR followed by functional classification of the genes and prediction of interactions between the proteins using Gene Ontology and STRING Database. Finally the expression of the newly identified genes was tested in HD11 macrophages and in vivo in chickens. Altogether 19 genes were induced in CEFs after S. Enteritidis infection. Twelve of them were also induced in HD11 macrophages and thirteen in the caecum of orally infected chickens. The majority of these genes were assigned different functions in the immune response, however five of them (LOC101750351, K123, BU460569, MOBKL2C and G0S2) have not been associated with the response of chicken to Salmonella infection so far. K123 and G0S2 were the only 'non-immune' genes inducible by S. Enteritidis in fibroblasts, HD11 macrophages and in the caecum after oral infection. The function of K123 is unknown but G0S2 is involved in lipid metabolism and in β-oxidation of fatty acids in mitochondria

Microbial diversity and community composition of caecal microbiota in commercial and indigenous Indian chickens determined using 16s rDNA amplicon sequencing

Different alpha diversity indices for each sample of university farm data estimated using QIIME for primer pair P2 data. OTUs were clustered at > 97% similarity. (XLSX 12 kb

The genomic architecture of resistance to Campylobacter jejuni intestinal colonisation in chickens

Campylobacter is the leading cause of foodborne diarrhoeal illness in humans and is mostly acquired from consumption or handling of contaminated poultry meat. In the absence of effective licensed vaccines and inhibitors, selection for chickens with increased resistance to Campylobacter could potentially reduce its subsequent entry into the food chain. Campylobacter intestinal colonisation levels are influenced by the host genetics of the chicken. In the present study, two chicken populations were used to investigate the genetic architecture of avian resistance to colonisation: (i) a back-cross of two White Leghorn derived inbred lines [(61 x N) x N] known to differ in resistance to Campylobacter colonisation and (ii) a 9th generation advanced intercross (61 x N) line

Poultry Production and Disease Management

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ICAR-DPR Annual Report

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Not AvailableNative chickens are the mainstay of backyard or free range systems of farming in India. They contributed about 11.5% to the total egg production ofthe country in the year 2019. Over the years their contribution to the total egg production is declining. Furthermore, they were neglected due to theirlow production potential and given least importance in the past. However, in recent years native chickens are gaining importance due to increasingdemand for their meat and eggs. Consumers are willing to pay higher price for meat and eggs of native chickens due to their perceived healthbenefits. A total of 19 breeds were recognized and registered as native chicken breeds at breed registry (ICAR-NBAGR). They are known to behardy, able to thrive under adverse climatic conditions and also reported to be resistant to bacterial and parasitic diseases. Studies on some of thesenative breeds carried out at intensive system indicated that there is high genetic diversity and they possess unique characteristics which are lacking inthe improved or commercial chickens. In this paper the status of native chicken production with respect to characterization for growth and productiontraits, immune competence/ disease resistance carcass and meat quality traits, nutrient requirements and improvement studies and challenges to thenative chicken production in the country are discussed. Authors believe this information could be useful for characterization and improvement of theperformance of native chicken breeds in India and other developing countries.Not Availabl

Livestock Research for Rural Development

Not AvailableNative chickens are the mainstay of backyard or free-range systems of farming in India. They contributed about 11.5% to the total egg production of the country in the year 2019. Over the years their contribution to the total egg production is declining. Furthermore, they were neglected due to their low production potential and given the least importance in the past. However, in recent years native chickens are gaining importance due to the increasing demand for their meat and eggs. Consumers are willing to pay a higher price for meat and eggs of native chickens due to their perceived health benefits. A total of 19 breeds were recognized and registered as native chicken breeds at the breed registry (ICAR-NBAGR). They are known to be hardy, able to thrive under adverse climatic conditions, and also reported to be resistant to bacterial and parasitic diseases. Studies on some of these native breeds carried out at intensive system indicated that there is high genetic diversity and they possess unique characteristics which are lacking in the improved or commercial chickens. In this paper, the status of native chicken production with respect to characterization for growth and production traits, immune competence/ disease resistance carcass and meat quality traits, nutrient requirements and improvement studies, and challenges to the native chicken production in the country are discussed. Authors believe this information could be useful for the characterization and improvement of the performance of native chicken breeds in India and other developing countries