Indian Chicken Research Articles

Mapping genome-wide diversity and population dynamics in Indian chicken breeds for targeted conservation and breeding

ABSTRACT 1. Genetic improvement and widespread use of artificial selection may have impacted the genetic make-up of Indian chicken breeds. The genetic architecture of contemporary chicken population of India needs to be assessed for future improvement and conservation programmes. This study utilised whole-genome sequences in 180 chicken samples from 16 indigenous breeds, along with the Red Jungle Fowl and the commercial White Leghorn. 2. A panel of 76 978 genome-wide single-nucleotide polymorphisms (SNP) was selected for comparative genome analysis after stringent screening. Breeds originating from the eastern regions of India exhibited higher genomic diversity, indicative of a rich repository of distinct germplasm. Conversely, the Uttara breed, from the northern hilly areas, display considerable genetic differentiation with diminished diversity compared to others, underscoring conservation concerns. The average coefficient (FIS) of 0.084 caution the need to mitigate risks associated with inbreeding. 3. The study revealed that the analysis of 76 978 genome-wide SNP will serve as a cornerstone in refining conservation strategies, to design interventions with greater precision. 4. The contribution of Red Jungle Fowl to the gene pool of all native breeds was supported by this study. Genetic structuring indicated a relationship among breeds based on geographical proximity, underscored by varying levels of admixture.

An Effective Supervised Machine Learning Approach for Indian Native Chicken’s Gender and Breed Classification

This study proposes a computer vision and machine learning (ML)-based approach to classify gender and breed in native chicken production industries with minimal human intervention. The supervised ML and feature extraction algorithms are utilized to classify eleven Indian chicken breeds, with 17,600 training samples and 4,400 testing samples (80:20 ratio). The gray-level co-occurrence matrix (GLCM) algorithm is applied for feature extraction, and the principle component analysis (PCA) algorithm is used for feature selection. Among the tested 27 classifiers, the FG-SVM, F-KNN, and W-KNN classifiers obtain more than 90% accuracy, with individual accuracies of 90.1%, 99.1%, and 99.1%. The BT classifier performs well in gender and breed classification work, achieving accuracy, precision, sensitivity, and F-scores of 99.3%, 90.2%, 99.4%, and 99.5%, respectively, and a mean absolute error of 0.7.

Immobilization of α-Amylase by Pseudomonas sp isolated from Indian Chicken

Immobilization of α-Amylase by Pseudomonas sp isolated from Indian Chicken

Genetic diversity among two native Indian chicken populations using cytochrome c oxidase subunit I and cytochrome b DNA barcodes.

Background and Aim:India has large varieties (recognized, unrecognized) of native chickens (Desi) scattered throughout the country, managed under scavenging system different from commercial chicken breeds. However, they are less investigated for genetic diversity they harbor. The present study was planned to evaluate genetic diversity among two native chicken populations of North Gujarat (proposed Aravali breed) and South Gujarat (Ankleshwar breed). Aravali chicken, a distinct population with unique characters different from the registered chicken breeds of India is under process to be registered as a new chicken breed of Gujarat, India.Materials and Methods:Two mitochondrial markers, namely, cytochrome oxidase c subunit I (COX I) and cytochrome b (Cyt b) genes were studied across 10 birds from each population. Methodology included sample collection (blood), DNA isolation (manual), polymerase chain reaction amplification of mitochondrial genes, Sanger sequencing, and purification followed by data analysis using various softwares.Results:Haplotype analysis of the COX I gene unveiled a total eight and three haplotypes from the Aravali and Ankleshwar populations, respectively, with haplotype diversity (Hd) of 92.70 % for the Aravali and 34.50% for the Ankleshwar breed. Haplotype analysis of the Cyt b gene revealed a total of four haplotypes from the Aravali population with 60% Hd and no polymorphism in Ankleshwar breed. The phylogenetic analysis uncovered Red Jungle Fowl and Gray Jungle Fowl as prime roots for both populations and all domestic chicken breeds.Conclusion:Study findings indicated high genetic variability in Aravali chicken populations with COX I mitochondrial marker being more informative for evaluating genetic diversity in chickens.

Quality Characteristics of Breast and Thigh Chicken Meat from Free- Range System: Comparative Antioxidant Profile of Indigenous and Improved Germplasm

Background: New chicken breeds are being evolved for backyard rural poultry production to overcome the slow growth, late sexual maturity and poor production of indigenous breeds. However, autochthonous poultry is epitomized for quality attributes of their products. With this in mind, the present study for the first time explored the antioxidant capacity of meat obtained from a unique Indian chicken, Kadaknath and a synthetic breed of poultry, Jabalpur colour (JBC). Methods: During the period 2018-2020, breast and thigh meat were collected from chickens (n=20/ group) at their commercial slaughter age (20 weeks). Meat extract was used for qualitative evaluation. Antioxidant activity was explored using five well established in vitro methods testing for different antioxidant mechanisms. Result: Both, Kadaknath and JBC meat was proteinaceous with higher protein concentration (g/100 g of wet weight) in the breast (Kadaknath, 25.21±0.31 and JBC, 25.65±0.39) than the thigh (Kadaknath, 19.98±0.29 and JBC, 19.04±0.23). Both the groups exhibited antioxidant capacity in all the assays. They showed good radical scavenging for ABTS and DPPH free radicals. Superiority of Kadaknath meat was ascertained unequivocally by the three assays viz. Ferric reducing antioxidant power (FRAP), lipid oxidation inhibition (TBARS) and metal chelating capacity. FRAP values (mM Fe2+/g of tissue) were 26.97±0.37 and 33.85±0.47 (Kadaknath) and 22.84±0.25 and 26.82±0.36 (JBC) for breast and thigh, respectively. Similarly, Kadaknath meat was more potent (% inhibition) iron chelator (breast, 62.71±0.99 and thigh, 75.07±0.98) in comparison to the JBC (breast, 46.30±2.36 and thigh, 63.12±1.87). Breast meat had better scavenging capacity than the thigh except in FRAP and metal chelating assays. Results provide insight into the antioxidant potential of backyard poultry germplasm thus, laying foundation for developing marketing strategies targeting consumers interested in nutritional quality, animal welfare and environmental sustainability. Furthermore, baseline data has been generated for studying medicinal properties attributed to the black chicken meat of Kadaknath.

Molecular and pathotypic characterization of fowl adenovirus associated with inclusion body hepatitis in Indian chickens

Inclusion body hepatitis (IBH) is a disease of chickens characterized by acute mortality with severe anemia caused by fowl adenoviruses (FAdV). IBH is one of the most important re-emerging diseases worldwide. In India earlier IBH/ Hydropericardium Syndrome (HPS) outbreaks were mainly due to (FAdV) type 4; however, in recent outbreaks, other serotypes are involved, despite regular vaccination in breeders and young chicks. The aim of the present study was isolation and molecular characterization of FAdV associated with IBH in India. A total of 193 liver samples of IBH suspected broiler chickens were collected from different regions of India. Liver samples were initially screened by histopathology and further, a total of 127 samples which microscopically showed basophilic, intra-nuclear inclusion bodies were processed for FAdV detection. A total of 69 samples were found to be positive for Hexon gene in PCR, of which 28 were sequenced. These samples showed more than 94% sequence homology with FAdV2 and 97% with FAdV11, which was confirmed by Restriction Enzyme Analysis (REA). Tissue Culture Infective Dose50 (TCID50) and Egg Infective Dose50 (EID50) titer of isolated FAdV was found to be 106.5/ml. Pathogenicity study in SPF chicks showed 100% mortality up to Post Infection Day (PID)-6. These findings conclude that the prevalence of FAdV-11 is currently causing IBH outbreaks India. However, further genetic and pathogenic analysis of FAdV is required, which would provide useful information for the development of the efficient commercial IBH vaccine.

Molecular Identification and Characterization of Chicken Parvovirus from Indian Chicken and Association with Runting and Stunting Syndrome

Background: Runting-stunting syndrome (RSS) in chickens is a worldwide problem, attributed with several etiological agents. The present study aimed to identify the association of enteric viruses with RSS in different chicken flocks. Methods: Intestinal samples from 14 flocks of chicken of different age and breed and with or without RSS were collected randomly from necropsy samples, isolated nucleic acids, and screened for major enteric viruses by Polymerised chain reaction (PCR), using species-specific primers. Result: Chicken Parvovirus (ChPV) was identified in 100% of the flocks with RSS, in two of which ChPV alone was detected. While in others it was associated with Avian nephritis virus, Avian Rotavirus, Chicken astrovirus, and Fowl adenovirus in 80%, 50%, 30% and 10% flocks, respectively. RSS was reproduced and isolated ChPV by chicken embryo inoculation using the samples from ChPV alone infected cases. Sequence analysis of ChPV revealed closer association with Ecuodor isolates than the Asian isolates. The results indicated the presence of ChPV in Indian chicken flocks and its close association with RSS.

The emergence of subclades A1 and A3 avipoxviruses in India.

During the years 2010-2018, avipoxvirus (APV) outbreaks were observed in the domestic chickens and pigeons present in the eastern Indian state of Odisha. Based on typical pox lesions, followed by molecular techniques, the overall morbidity was found to be 18%-19.23% and 16.92%-23% in chickens and pigeons, respectively. The cutaneous forms of the disease were observed with varied rates of mortality, being 47.36%-52.77% in chickens and 39.13%-92% in pigeons. PCR amplification targeting the viral P4b core protein-coding gene and the DNA polymerase gene confirmed the presence of APV strains in 10 birds. Subsequent phylogenetic analysis of these two genes confirmed that the circulating strains were members of APV clade A. The subclade analysis revealed the introduction of A1 and A3 subclades in Indian chickens and pigeons, respectively. This study is the first molecular record of APVs circulating in eastern Indian birds (Odisha) and involves the first use of the polymerase gene to reveal the circulating clades of Indian APVs.

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

BackgroundThe caecal microbiota plays a key role in chicken health and performance, influencing digestion and absorption of nutrients, and contributing to defence against colonisation by invading pathogens. Measures of productivity and resistance to pathogen colonisation are directly influenced by chicken genotype, but host driven variation in microbiome structure is also likely to exert a considerable indirect influence.MethodsHere, we define the caecal microbiome of indigenous Indian Aseel and Kadaknath chicken breeds and compare them with the global commercial broiler Cobb400 and Ross 308 lines using 16S rDNA V3-V4 hypervariable amplicon sequencing.ResultsEach caecal microbiome was dominated by the genera Bacteroides, unclassified bacteria, unclassified Clostridiales, Clostridium, Alistipes, Faecalibacterium, Eubacterium and Blautia. Geographic location (a measure recognised to include variation in environmental and climatic factors, but also likely to feature varied management practices) and chicken line/breed were both found to exert significant impacts (p < 0.05) on caecal microbiome composition. Linear discriminant analysis effect size (LEfSe) revealed 42 breed-specific biomarkers in the chicken lines reared under controlled conditions at two different locations.ConclusionChicken breed-specific variation in bacterial occurrence, correlation between genera and clustering of operational taxonomic units indicate scope for quantitative genetic analysis and the possibility of selective breeding of chickens for defined enteric microbiota.

Molecular Characterization of Mx1 Gene in Native Indian Breeds of Chicken

ABSTRACTThe genetic polymorphism of Mx1 gene was explored in Indian chicken breeds. PCR-RFLP analysis in 102 bp fragment of partial intron 13 and partial exon 14 of Mx1 gene revealed two genotypes viz. RS and SS with two alleles viz. R and S both in Naked Neck and Tellicherry breeds of chicken. The homozygous genotype RR was not identified. When deduced amino acid sequences were compared, the asparagine amino acid was found to be substituted in “R” allele for serine in “S” allele. PCR-SSCP analysis of 284 bp fragment in 5′-UTR and partial promoter region revealed three genotypes viz. CC, CG, and CH with three different alleles viz. C, G, and H in Naked Neck breed of chicken and five genotypes viz. DI, JK, KK, KL, and KM with six different alleles viz. D, I, J, K, L, and M in Tellicherry breed of chicken. The homozygous genotypes viz. GG and HH in Naked Neck and DD, II, JJ, LL, and MM in Tellicherry chicken was not identified. The nucleotide substitution rate estimated to be in the range of 0.004–0.011. The identified genetic variation can be helpful for better insight to disease resistance property of the Mx1 gene.

Tackling antimicrobial resistance in food-producing animals

Tackling antimicrobial resistance in food-producing animals

Genetic diversity of Hajar1 and Hajar2 local Saudi chicken lines using mitochondrial DNA D-loop markers

This study was conducted to assess genetic diversity of Hajar1 and Hajar2 local Saudi chicken lines using mitochondrial DNA (mtDNA) D-loop partial sequences. One hundred blood samples were obtained equally from Hajar1 and Hajar2 Saudi chicken lines as 50 samples from each line. The D-loop region was partially amplified from genomic DNA with a conserved primer set, and the fragments were sequenced. Eight published reference mtDNA sequence data from the GenBank were used for comparisons, and multiple alignments were performed. The most common haplotype was assigned as a basic sequence for comparing within each line. Entropy plot and conserved region analysis were performed. Genetic distances and neighbour-joining (NJ) phylogenetic trees were estimated. The results indicated haplotype variations within and between local Saudi chicken lines, which could explain the phenotypic variation reported earlier. A close genetic relationship was shown between the Saudi local chicken lines. Unique conserved regions and nucleotide substitutions were observed between the two lines. Both lines have a close relationship with the reference Asian local chicken population, especially local Chinese and Indian chicken breeds. The current results are considered the first report of mtDNA sequence diversity for Hajar1 and Hajar2 lines. Further detailed molecular genetic studies of both lines are indispensable to genetic conservation and development. Keywords: chicken population, diversity, D-loop, Hajar1, Hajar2, mtDNA

Deeper insight into maternal genetic assessments and demographic history for Egyptian indigenous chicken populations using mtDNA analysis

This study principally sought to reveal the demographic expansion of Egyptian indigenous chickens (EIC) using representative breeds: Sinai (North), Fayoumi (Middle) and Dandarawi (South) of Egypt as well as to deeply clarify their genetic diversity, possible matrilineal origin and dispersal routes. A total of 33 partial mitochondrial DNA sequences were generated from EIC and compared with a worldwide reference dataset of 1290 wild and domestic chicken sequences. Study populations had 12 polymorphic variable sites and 7 haplotypes. A lack of maternal substructure between EIC was detected (FST=0.003). The unimodal mismatch distribution and negative values of Tajima’s D (−0.659) and Fu’s Fs (−0.157) indicated demographic expansion among EIC and pointed to Fayoumi as the oldest EIC population. Egyptian haplotypes were clustered phylogenetically into two divergent clades. Their phylogeography revealed an ancient single maternal lineage of Egyptian chickens likely derived from Indian-Subcontinent. Moreover, a recent maternal commercial heritage possibly originated in Yunnan-Province and/or surrounding areas was admixed restrictedly into Sinai. It is implied that Egypt was an entry point for Indian chicken into Africa and its further dispersal route to Europe. This study provides a clue supporting the previous assumption that urged utilizing consistent founder populations having closely related progenitors for synthetizing a stabilized homogenous crossbreed as a sustainable discipline in breeding program.

Experimental pathological studies of an Indian chicken anaemia virus isolate and its detection by PCR and FAT.

Chicken Infectious Anaemia Virus (CIAV) is one of the potent immunosuppressive and economically important agents affecting poultry industry worldwide. Recent reports indicate the emergence of this virus in the poultry flocks of the country. The present study aimed to investigate the pathogenic potential of a recent isolate of CIAV obtained from poultry flock of Uttaranchal State, India. Twenty first day-old age Specific Pathogen Free (SPF) chicks were inoculated intramuscularly with 10(4.5) median tissue culture infective dose (TCID50) of CIAV passaged in the Marek's disease virus transformed chicken splenic T lymphocyte (MDCC-MSB 1) cell line while 15 chicks were kept as control. The CIAV isolate produced consistent clinical signs, loss in body weight gain, anaemia, low haematocrit values, bone marrow aplasia and generalized lymphoid atrophy. Mean Packed Cell Volume (PCV) value of the infected chicks was significantly low (18.22±2.22) compared to control group (34.12±4.72) at 14 day post infection (dpi). The establishment of virus infection in chicks was confirmed both at molecular and antigenic levels by Polymerase Chain Reaction (PCR) and Indirect Immunofluorescent Test (IIFT), respectively. Characteristic apoptotic pattern was also detected in the affected organs and the virus was re-isolated successfully in MDCC-MSB1 cell cultures. The present results revealed that the virus circulating in poultry flocks of Uttaranchal state is both pathogenic and immunosuppressive in nature. Extensive epidemiological studies are suggested in the poultry flocks of the country along with adaptation of appropriate diagnostic, prevention and control strategies so as to prevent economic losses caused by this important poultry pathogen.

Cloning and sequence analysis of VP1, VP2 and VP3 genes of Indian chicken anemia virus

Summary Chicken anemia virus was detected by PCR in tissue samples collected from poultry flocks in Gujarat, India. The VP1, VP2 and VP3 gene sequences of CAV from Anand, Gujarat were obtained after cloning the PCR products in pDrive cloning vector. Nucleotide sequence alignment with other CAV sequences demonstrated overall identity of 95-98.8%, 98.8-99.8% and 98.8-100% for VP1, VP2 and VP3 regions, respectively. Deduced amino acid sequences revealed 91.7-99.7%, 99-100% and 97.3-100% homologies for VP1, VP2 and VP3 proteins, respectively, indicating high level of genome conservation. Further, placement of critical nucleotides and amino acids at particular positions indicated that Anand CAV is possibly of more pathogenic potential. The CAV isolates were phylogenetically grouped together independent of their geographic origin.

Multiple Maternal Lineages of Vietnamese Local Chickens Inferred by Mitochondrial DNA D-loop Sequences

Mitochondrial DNA (mtDNA) is considered a powerful source of molecular information to track the ancestry of breeds back hundreds of generations (Harpending et al., 1998). Different hypotheses about chicken domestication based on mtDNA analyses are found in the literature. Fumihito et al. (1996) suggested a monophyletic origin of domestic chickens from Gallus gallus gallus and that a single domestication event occurred in Thailand and adjacent regions, while Kanginakudru et al. (2008) found evidence for domestication of Indian chickens from Gallus gallus spadiceus and Gallus gallus gallus as well as from Gallus gallus murghi. A study that analyzed BCDO2, a gene encoding an enzyme which converts carotene into its colourless variant, suggested the introgression of the yellow skin gene from Gallus sonneratii into modern chicken breeds (Eriksson et al., 2008). Other reports assumed multiple and independent domestication events in South China, Southeast Asia and the Indian subcontinent (Liu et al., 2006 a; Oka et al., 2007). Liu et al. (2006) revealed nine divergent clades (named clades A-I) related to geographical distribution in a wide range of domestic chickens in Eurasian regions. Oka et al. (2007) identified seven clades (named clades A-G) in Japanese chickens of which the four clades A, B, C and E are identical to clades E, A, D and B, respectively, described by Liu et al. (2006).

Microsatellite Analysis of Genetic Diversity in Indian Chicken Populations

Characterization of genetic diversity by employing molecular tools is a prerequisite in developing strategies for conservation and utilization of poultry genetic resources. We assessed genetic variation within and between six Indian chicken populations (Naked Neck, White Silkies, Commercial Layer and Broiler, Giriraja and Desi) using nine microsatellite markers. Seven loci were polymorphic in all populations, with the number of alleles varying from 3 to 27 per locus and 4.1 to 8.6 per population. Average heterozygosity and gene diversity in the populations were 0.68 and 0.66, respectively. Some populations and loci deviated from Hardy-Weinberg equilibrium. Except Naked Neck, none of other populations was in genotypic disequilibrium for a single pairwise locus combination. F-statistics indicated that populations are genetically structured, ∼85% of the total genetic variation being due to genetic differentiation within the populations. Estimates of Latter’s FST and Nei’s DS genetic distances revealed relatively close genetic similarity between Naked Neck and Giriraja, while White Silkies was the most distant. An estimated divergence time between Naked Neck and Giriraja was over 100 years, with a comparatively longer (over 450 years) period of separation between Giriraja and White Silkies. We suggest that there is an essential room left for genetic improvement of Indian native breeds and commercial stocks.

Serological Screening for MHC (B)-Polymorphism in Indigenous Chickens

As part of a series of studies to characterize innate and specific immune responses of indigenous chicken lines, birds from Bolivia and India were screened serologically for MHC class IV (BG) polymorphism by direct haemagglutination using haplotype-specific antisera (B2, B4, B12, B13, B14, B15, B19, B21). The sample consisted of 95 Bolivian indigenous chickens and 119 hens from the four most common North Indian 'back-yard' chicken lines: Yellow Aseel (AP), Kadaknath (KN), frizzled typed (Ff-) and naked neck (NN). Of all chickens tested, the majority were haplotyped as B2, B15, B19 and B21. Of the Bolivian chickens, 89.5% could be haplotyped: 54.9% were homozygous (including 43.3% B15), and 34.6% were heterozygous (including 15.7% B15). B2-like haplotypes were not found among the Bolivian hens, and only 3.2% of these birds showed homozygous B21-like proteins. Of the Indian hens, MHC (BG)-like proteins could be detected in 60.0% of the AP birds, 6.7% of the KN birds; 40.0% of the Ff- birds; and 10.3% of the NN birds. In these lines, a total of 40.1% (AP), 6.7% (KN), 30.1% (Ff-) and 10.3% (NN) were homozygous for the B-haplotype. Only in the AP line (19.9%), and the Ff- line (9.9%) were heterozygous B-haplotypes types found. The B2 haplotype was found in all Indian chicken lines. Most Indian birds have completely unknown haplotypes, indicating a potentially interesting genetic pool. Subgrouping the Bolivian and Indian indigenous hens into monomorphic BG populations revealed individual differences based on the B-types.

Molecular genetics of avian proteins—X. Egg white protein polymorphism of indigenous Indian chickens

1.1. Three variants of G8 ovoglobulin (J, A and B) and all three known variants of transferrin (A, B and C) were found in small samples of Indian village fowl.2.2. This confirms an Asiatic origin for the G3B and TfC genes. The absence of the ovalbumin B variant in these fowl agrees with previous suggestions that this variant is of European origin.3.3. Gallus sonnerati egg white proteins were not found in any of the samples, supporting the view that Gallus gallus is the sole or main ancestor of the domestic fowl.4.4. The presence of frequent polymorphism in the egg white proteins of Indian fowl, the same polymorphism retained in many occidental commercial breeds, is indicative that these protein polymorphisms must often be of selective advantage.