Gallus Gallus Research Articles

Play ontogeny in young chickens is affected by domestication and early stress

Play is common in young homeotherm animals and has an important role as a tentative indicator of positive states of welfare. Furthermore, during domestication play is believed to have increased in frequency in several species as part of the domestication syndrome. Here, we studied the ontogeny of play in chickens in two experiments. The first compared the behavioural development between domesticated White Leghorn (WL) laying hen chicks and ancestral Red Junglefowl (RJF) and the second compared the same between WL chicks that had experienced the stress of commercial hatchery routines and a control group, hatched under calm conditions. In both experiments, 10 groups of four chicks each from each of the groups were moved twice per week to an enriched and fully enclosed play arena, starting at day 8 and finishing day 39 or 53 after hatch. In the arena, the frequency of play behaviours was recorded during 30 min and divided into object, locomotory and social play. In experiment one, total play as well as object play was significantly more common in WL whereas locomotor and social play was more common in RJF. In experiment two, total play was significantly more frequent in commercially hatched chicks, despite that none of the sub-categories differed significantly between the groups. In conclusion, domestication as well as early stress does affect the occurrence of play in chickens, but the effects are complex and require further research.

DNA Barcode of Red Junglefowl Gallus gallus L, 1958 (Aves: Phasianidae) of Sumatra Based on Mitochondrial COI DNA Gene

Genetic data of red junglefowl (Gallus gallus) from southern Sumatra is valuable for conservation efforts in Indonesia. A mitochondrial COI DNA gene sequencing was performed to elucidate its genetic character, single nucleotide polymorphism, genetic distance, and phylogeny. Blood samples (±0.5 ml) from 20 individuals of Gallus gallus were taken from the living collections of the people of Bengkulu Province (Central Bengkulu Regency and Seluma Regency) and South Sumatra Province (North Musi Rawas Regency) from May to November 2021. Total DNA isolation followed the procedure of The Spin-Column Protocol Kit uses the Dneasy® Blood and Tissue Kit, Qiagen. DNA replication using the Polymerase Chain Reaction technique with primers (COIGG_F and COIGG_R) using MEGA 10.0 software and Bioedit for data analysis. The results revealed716 conserved sites, 16 variable sites, 9 parsimony sites, and 6 singleton sites from the 732 bp nucleotide sequence. Six specific sites (SNPs) as barcodes for Sumatran Junglefowl were found at sequences 51, 273, 327, 721, 729, and 732. The mean genetic distance between individuals was 0.1%, between populations was 0.8%, between species was 7.4%, and between genera was 15.5%. The red junglefowlof South Sumatra Province and Bengkulu Province are closely related with 98% bootstrapping and separated from other Gallus in the same group (ingroup) with 100% bootstrap. The Gallus-gallus group is quite far apart from the outgroup species in the Phasianidae family with 47-100% bootstrap. Red junglefowl from southern Sumatra has genetic differences from other chickens in the world and these differences can be used as a species barcode and as origin identification the widely traded red jungle fowl.

First report of haemosporidia and associated risk factors in red junglefowl (Gallus gallus) in China

BackgroundAvian haemosporidia infect both domestic and wild birds, causing anemia, acute tissue degeneration, and depopulation in wild birds. Poultry and wild birds have been reported as common reservoirs of haemosporidia, but limited information is available for red junglefowl (Gallus gallus) in China. The present study investigated the prevalence and molecular characterization of haemosporidia in red junglefowl.MethodsBlood samples were collected from 234 red junglefowl from Jinghong City of Yunnan Province, and genomic DNA was extracted from these samples. The prevalence of haemosporidia was determined by nested PCR targeting the mitochondrial cytochrome b (cytb) gene. Molecular characterization was investigated based on phylogenetic analysis of cytb sequences, and associated risk factors were analyzed using the Chi-square (χ2) test.ResultsThe overall prevalence of haemosporidia was 74.8% (175/234), and three species were identified, namely Haemoproteus enucleator, Leucocytozoon californicus, and Plasmodium juxtanucleare. The prevalence of haemosporidia in adult fowl (81.1%, 107/132) was significantly higher (χ2 = 6.32, df = 1, P = 0.012) than that in juveniles (66.7%, 68/102). Three novel haemosporidian lineages were revealed.ConclusionsThis study examined the prevalence and identified species of avian haemosporidians in red junglefowl, providing new information on the molecular epidemiology and geographical distribution of haemosporidian parasites. Our results indicated high prevalence and diverse species distribution of these haemosporidians in red junglefowl. To the best of our knowledge, this is the first record of haemosporidian infection in red junglefowl in China.Graphical

The vocalization of the red junglefowl is a signal of body size and individual health.

Bird songs are considered a sexually selected trait that can reflect the individual health of males as well as the vitality of potential mates and their competitors. Vocalization features should, therefore, be related to parasite load and body condition. Here, we performed a thorough acoustic analysis of the display calls of 9-month-old sub-adults and 18-month-old adults of pasture-raised red junglefowls Gallus gallus. We investigated whether the calls of pasture-raised red junglefowls can indicate body size and body condition, in addition to the influence of parasitic infection intensity on the expression of sexual traits. We found that frequency-related syllable parameters were significantly positively correlated with wing length in adults, whereas body weight was independent of both the frequency and temporal parameters of calls. In addition, we correlated parasitic load with the expression of sexually selected traits and discovered a positive association between the intensity of parasite infection and wing length in sub-adults, independent of vocal parameters. Overall, the results suggest that the vocalization of red junglefowls may convey reliable body size information, which will facilitate further studies of different vocal parameters in the transmission of bird vocalizations.

Genomic and gene expression associations to morphology of a sexual ornament in the chicken.

How sexual selection affects the genome ultimately relies on the strength and type of selection, and the genetic architecture of the involved traits. While associating genotype with phenotype often utilizes standard trait morphology, trait representations in morphospace using geometric morphometric approaches receive less focus in this regard. Here, we identify genetic associations to a sexual ornament, the comb, in the chicken system (Gallus gallus). Our approach combined genome-wide genotype and gene expression data (>30k genes) with different aspects of comb morphology in an advanced intercross line (F8) generated by crossing a wild-type Red Junglefowl with a domestic breed of chicken (White Leghorn). In total, 10 quantitative trait loci were found associated to various aspects of comb shape and size, while 1,184 expression QTL were found associated to gene expression patterns, among which 98 had overlapping confidence intervals with those of quantitative trait loci. Our results highlight both known genomic regions confirming previous records of a large effect quantitative trait loci associated to comb size, and novel quantitative trait loci associated to comb shape. Genes were considered candidates affecting comb morphology if they were found within both confidence intervals of the underlying quantitative trait loci and eQTL. Overlaps between quantitative trait loci and genome-wide selective sweeps identified in a previous study revealed that only loci associated to comb size may be experiencing on-going selection under domestication.

Genetic structure, population diversity and ancestry of Nicobari fowl based on mtDNA complete D-loop sequences

Nicobari fowl constitute an endemic poultry germplasm of Andaman and Nicobar Islands, India. Genetic diversity, population structure and ancestry of Nicobari fowl were analysed with mitochondrial D-loop sequences. Analysis of complete D-loop sequences (1231-1232 bp) showed 46 polymorphic sites resulting in 26 haplotypes with overall haplotype diversity of 0.895 and nucleotide diversity of 0.0064. Analysis of molecular variance of spatial populations (sampling sites) of Nicobari fowl revealed that the estimated FST value as 0.229 among the populations. Tajima's D and Fu's FS tests indicated nonsignificant deviation from neutrality and the multimodal pattern of mismatch distribution in demographic expansion suggested that Nicobari fowl populations are in equilibrium. The median-joining (MJ) network of D-loop sequences with reference haplogroup sequences identifies the presence of haplogroups A, B, E1, E2, F and I in Nicobari fowl. The major haplogroup in Nicobari fowl was E (60%), which is otherwise found mainly in the Indian subcontinent. Phylogenetic analysis of Nicobari fowl with junglefowl by maximum likelihood method showed Gallus gallus murghi and G. g. spadiceus as maternal progenitors. Grouping of Nicobari fowl with their primary ancestor, Indian red Junglefowl (G. g. murghi) and the presence of Indian subcontinent-specific haplogroups (E2 and I) support the independent domestication of chickens in India. This study will help to design breeding strategy for conservation of Nicobari fowl in its island habitat.

Red Junglefowl Resource Management Guide: Bioresource Reintroduction for Sustainable Food Security in Thailand

The domestication of wild animals represents a major milestone for human civilization. Chicken is the largest domesticated livestock species and used for both eggs and meat. Chicken originate from the red junglefowl (Gallus gallus). Its adaptability to diverse environments and ease of selective breeding provides a unique genetic resource to address the challenges of food security in a world impacted by climatic change and human population growth. Habitat loss has caused population declines of red junglefowl in Thailand. However, genetic diversity is likely to remain in captive stocks. We determine the genetic diversity using microsatellite genotyping and the mitochondrial D-loop sequencing of wild red junglefowl. We identified potential distribution areas in Thailand using maximum entropy models. Protected areas in the central and upper southern regions of Thailand are highly suitable habitats. The Bayesian clustering analysis of the microsatellite markers revealed high genetic diversity in red junglefowl populations in Thailand. Our model predicted that forest ranges are a highly suitable habitat that has enabled the persistence of a large gene pool with a nationwide natural distribution. Understanding the red junglefowl allows us to implement improved resource management, species reintroduction, and sustainable development to support food security objectives for local people.

The biocultural origins and dispersal of domestic chickens

Though chickens are the most numerous and ubiquitous domestic bird, their origins, the circumstances of their initial association with people, and the routes along which they dispersed across the world remain controversial. In order to establish a robust spatial and temporal framework for their origins and dispersal, we assessed archaeological occurrences and the domestic status of chickens from ∼600 sites in 89 countries by combining zoogeographic, morphological, osteometric, stratigraphic, contextual, iconographic, and textual data. Our results suggest that the first unambiguous domestic chicken bones are found at Neolithic Ban Non Wat in central Thailand dated to ∼1650 to 1250 BCE, and that chickens were not domesticated in the Indian Subcontinent. Chickens did not arrive in Central China, South Asia, or Mesopotamia until the late second millennium BCE, and in Ethiopia and Mediterranean Europe by ∼800 BCE. To investigate the circumstances of their initial domestication, we correlated the temporal spread of rice and millet cultivation with the first appearance of chickens within the range of red junglefowl species. Our results suggest that agricultural practices focused on the production and storage of cereal staples served to draw arboreal red junglefowl into the human niche. Thus, the arrival of rice agriculture may have first facilitated the initiation of the chicken domestication process, and then, following their integration within human communities, allowed for their dispersal across the globe.

White Leghorn and Red Junglefowl female chicks use distal and local cues similarly, but differ in persistency behaviors, during a spatial orientation task

Although there is evidence to suggest that animal domestication acts as a modulator of spatial orientation, little is known on how domesticated animals, compared to their wild counterparts, orientate themselves when confronted to different environmental cues. Here, using domesticated White Leghorn chicks, and their ancestor, the Red Junglefowl (Gallus gallus), our main objective was to investigate how bird domestication influences the use of distal and local cues, during an orientation task. We also investigated the memory retention of these cues over time, and how persistent/flexible individuals from both breeds were at pecking at unreachable mealworms. Our results showed that the breeds did not differ in their use of distal or local cues, with both showing a marked preference for the use of local cues over distal ones. Over time, individual performance declined, but this was not influenced by the type of cue present during the tests, nor by the breed. Domesticated chicks showed greater signs of persistency compared to their wild conspecifics. In conclusion, domestication did not seem to alter how birds orientate spatially, but may have caused more subtle changes, such as an increase in behavioral persistency, a feature that may be adaptative in human-controlled and homogenous environments.

Domestication effects on social information transfer in chickens

Red junglefowl (RJF), ancestor of all domesticated chickens, is a highly social, omnivorous bird species, presumably with a capacity for social information sharing. During domestication, birds have been selected to live in large, dynamic groups, and this may have affected their social cognition. Here, we studied social information transfer in female RJF and domesticated White Leghorn (WL) chickens. Individuals were trained to open a puzzle-box feeder by pecking a lid and we then recorded the behaviour towards the same puzzle-box feeder for birds that had either observed the trained individual (“guided”) or saw the puzzle-box feeder for the first time (“naïve”). WL were considerably faster in approaching the feeder regardless of prior demonstration and pecked more at it. Both breeds were significantly faster to approach the puzzle-box feeder and pecked more after prior demonstration, but the effects were significantly stronger in WL. We conclude that both RJF and WL can utilize social information to address a novel problem, but during domestication this ability appears to have increased. The effects can be an effect of either social learning or stimulus enhancement. Some caution in this conclusion is necessary since we tested relatively few WL. Furthermore, possible confounding explanations include higher fearfulness in RJF and different effects of dominance interactions between demonstrators and observers.

Effects of extenders and cryoprotectants on cryopreservation of Thai red junglefowl (Gallus gallus gallus) spermatozoa

Semen cryopreservation is crucial maintain genetic diversity of avian species. Little is known about suitable extenders for post-thaw survival of spermatozoa from Thai red junglefowl (Gallus gallus gallus). Therefore, the present study aimed to compare the suitability of the modified Thai red junglefowl extender (TRJFE) for cryopreservation of Thai red junglefowl spermatozoa with other extenders, including the Schramm extender, the red junglefowl extender (RFE), and the HS1 extender, in terms of sperm viability, motility, and fertility. First, the effects of adding 6% and 9% (v/v) N,N-dimethylacetamide, N,N-dimethylformamide (DMF), or N-methyl acetamide to these extenders on the post-thaw sperm quality of pooled ejaculates from 25 male fowls. The viability of thawed sperm was assessed by using nigrosin–eosin staining and sperm motility was determined by using computer-assisted sperm analysis. Fertility was assessed by inseminating 144 laying hens. The TRJFE +6% DMF combination significantly improved post-thaw viability (64.88 ± 0.51%) and motility (68.58 ± 1.13%) of Thai red junglefowl sperm, and the semen had the highest fertility (60.97 ± 0.72%). The findings suggest that TRJFE +6% DMF is a suitable freezing medium to conserve Thai red jungle fowl genetic resources.

Intermittent fasting induces chronic changes in the hepatic gene expression of Red Jungle Fowl (Gallus gallus)

BackgroundIntermittent fasting (IF), the implementation of fasting periods of at least 12 consecutive hours on a daily to weekly basis, has received a lot of attention in recent years for imparting the life-prolonging and health-promoting effects of caloric restriction with no or only moderate actual restriction of caloric intake. IF is also widely practiced in the rearing of broiler breeders, the parent stock of meat-type chickens, who require strict feed restriction regimens to prevent the serious health problems associated with their intense appetites. Although intermittent fasting has been extensively used in this context to reduce feed competition and its resulting stress, the potential of IF in chickens as an alternative and complementary model to rodents has received less investigation. In both mammals and birds, the liver is a key component of the metabolic response to IF, responding to variations in energy balance. Here we use a microarray analysis to examine the liver transcriptomics of wild-type Red Jungle Fowl chickens fed either ad libitum, chronically restricted to around 70% of ad libitum daily or intermittently fasted (IF) on a 2:1 (2 days fed, 1 day fasted) schedule without actual caloric restriction. As red junglefowl are ancestral to domestic chicken breeds, these data serve as a baseline to which existing and future transcriptomic results from farmed birds such as broiler breeders can be compared.ResultsWe find large effects of feeding regimen on liver transcriptomics, with most of the affected genes relating to energy metabolism. A cluster analysis shows that IF is associated with large and reciprocal changes in genes related to lipid and carbohydrate metabolism, but also chronic changes in genes related to amino acid metabolism (generally down-regulated) and cell cycle progression (generally up-regulated). The overall transcription pattern appears to be one of promoting high proliferative plasticity in response to fluctuations in available energy substrates. A small number of inflammation-related genes also show chronically changed expression profiles, as does one circadian rhythm gene.ConclusionsThe increase in proliferative potential suggested by the gene expression changes reported here indicates that birds and mammals respond similarly to intermittent fasting practices. Our findings therefore suggest that the health benefits of periodic caloric restriction are ubiquitous and not restricted to mammals alone. Whether a common fundamental mechanism, for example involving leptin, underpins these benefits remains to be elucidated.

How Inhibitory Control Relates to Positive and Negative Affective States in Red Junglefowl.

Individual differences in inhibitory control, an aspect of cognition, are found in many species. How this variation links to affective states is not much explored, and could be relevant for welfare. As less fearful, more optimistic, individuals may act more impulsively, inhibitory control could link to less negative, more positive, affective states. Alternatively, poorer inhibitory control could associate with more negative, less positive, affective states, as poorer inhibitory control can result in individuals being less able to adapt to changing environments and more likely to show stereotypies. We here explored in three cohorts (N = 209) of captive red junglefowl, the ancestor of domestic chickens, how inhibitory control associated with affective states. Specifically, we measured inhibitory control with a detour task, and negative and positive affective states with a tonic immobility test and a cognitive judgement bias test, respectively. Cognition and behaviour can differ between ages and sexes. Therefore, we investigated how inhibitory control related to affective states in younger chicks (≈2.5 weeks old), older chicks (≈5 weeks old) and sexually mature adults (≈28 weeks old) of both sexes. In younger chicks, poorer inhibitory control associated with less negative, more positive, affective states. We found no relationship between inhibitory control and affective states in older chicks or adults, nor sex differences regarding how inhibitory control related to affective states. Overall, our results suggest that inhibitory control can link to affective states and that the nature of these links can change over ontogeny.

Revisit the Development of Native Indonesian Chickens from Red Jungle Fowls (Gallus gallus bankiva) to Commercial Chickens

Kampung chicken which is one of native Indonesian chickens has been domesticated from the ancestor of Red Fowl Jungle, and developed by the village community from generation to generation through an extensive rearing method. Before the intensive management of kampung chicken was introduced, the chickens were allowed to scavange around the household yard during the day, they slept in the trees, on the roofs or underneath of the household at night. It has been for many years that kampung chickens were crossed with imported exotic breeds, and unplanned selection. As a result, kampung chickens have developed to a considerable high phenotype and genetic varieties with several different names and purposes. There have been selection programs, which have resulted a considerable strain of improved egg type of Kampung chicken (KUB-1 chicken), and a strain of broiler type of local chicken (Sensi-1 Agrinak chicken and Gaoksi chicken). KUB-1 chickens can be used as female lines, and Sensi-Agrinak and Gaoksi chickens can be used as male lines to produce local commercial broilers. The article is to provide information on the domestication process of Red Jungle Fowl chickens into Kampung chickens and their development to become layer and broiler line chickens.

Population Genomic Sequencing Delineates Global Landscape of Copy Number Variations that Drive Domestication and Breed Formation of in Chicken.

Copy number variation (CNV) is an important genetic mechanism that drives evolution and generates new phenotypic variations. To explore the impact of CNV on chicken domestication and breed shaping, the whole-genome CNVs were detected via multiple methods. Using the whole-genome sequencing data from 51 individuals, corresponding to six domestic breeds and wild red jungle fowl (RJF), we determined 19,329 duplications and 98,736 deletions, which covered 11,123 copy number variation regions (CNVRs) and 2,636 protein-coding genes. The principal component analysis (PCA) showed that these individuals could be divided into four populations according to their domestication and selection purpose. Seventy-two highly duplicated CNVRs were detected across all individuals, revealing pivotal roles of nervous system (NRG3, NCAM2), sensory (OR), and follicle development (VTG2) in chicken genome. When contrasting the CNVs of domestic breeds to those of RJFs, 235 CNVRs harboring 255 protein-coding genes, which were predominantly involved in pathways of nervous, immunity, and reproductive system development, were discovered. In breed-specific CNVRs, some valuable genes were identified, including HOXB7 for beard trait in Beijing You chicken; EDN3, SLMO2, TUBB1, and GFPT1 for melanin deposition in Silkie chicken; and SORCS2 for aggressiveness in Luxi Game fowl. Moreover, CSMD1 and NTRK3 with high duplications found exclusively in White Leghorn chicken, and POLR3H, MCM9, DOCK3, and AKR1B1L found in Recessive White Rock chicken may contribute to high egg production and fast-growing traits, respectively. The candidate genes of breed characteristics are valuable resources for further studies on phenotypic variation and the artificial breeding of chickens.

Effects of heat stress on cyto(chemo)kine and inflammasome gene expression and mechanical properties in isolated red and white blood cells from 4 commercial broiler lines and their ancestor jungle fowl

Commercial broilers have been selected for high growth rate and productivity; however, this has negatively impacted their susceptibility to heat stress (HS). Insight into the molecular mechanisms underlying this vulnerability can help design targeted strategies for improvement of HS tolerance. Red blood cells (RBC) and white blood cells (WBC) were isolated from red jungle fowl and 4 lines of commercial modern broilers. Lines A and B are considered standard-yielding lines, whereas Lines C and D are high-yielding. Cells were cultured at either 37°C or 45°C for 2 h to induce heat stress (HS). Gene expression of cytokines, chemokines, and inflammasome components were measured. Heat shock proteins 27 and 70 (HSPs) in RBC were significantly affected by line (P < 0.05), whereas HSP27 and 60 were affected by temperature (P < 0.05). In WBC, there was a significant line effect on HSP gene expression (P < 0.05), and a significant increase (P < 0.05) in HSP90 in Line D in HS compared to TN conditions. In RBC, there was a main effect of HS on TNFα, CCL4, and CCLL4 (P < 0.05). HS significantly increased IL-8L1 (>30-fold, P < 0.0001) in Line C. Inflammasome genes (NLRP3, NLRC5 and NLRC3) were significantly affected by the line studied (P < 0.05). In WBC, the effect of line was significant for all cytokines, chemokines, and inflammasome components studied (P < 0.05). To examine the mechanical properties of isolated RBC from the 4 commercial lines and jungle fowl, RBC were placed into nematic liquid crystals, where Lines B and D were the most strained, and Line A and the jungle fowl were the least strained. Together, these findings indicate not only the dynamic nature of circulating cells, but the differences in the stress and inflammatory response among commercially available lines and their common ancestor. These profiles have the potential to serve as a future marker for stress responses in broilers, though further study is warranted.

Variation in inhibitory control does not influence social rank, foraging efficiency, or risk taking, in red junglefowl females

Individual variation in cognition, seen in many taxa, is not well understood, despite its potential evolutionary consequences. Inhibitory control is an aspect of cognition which differs between individuals. However, how selection could act on this variation remains unclear. First, individual consistency over time of behaviours affected by inhibitory control, and how these behaviours relate to each other, is not well understood. Second, consequences in ecologically relevant contexts of variation in behaviours affected by inhibitory control, are scarcely investigated. Therefore, we explored the temporal consistency and inter-relatedness of two behaviours influenced by inhibitory control (impulsive action and persistence) and how these link to social rank, foraging efficiency, and risk taking in adult female red junglefowl (Gallus gallus). We measured impulsive action in a detour test, and persistence in both a detour test and a foraging test. Impulsive action and persistence, measured in a detour test, were moderately consistent over time, and positively correlated. This implies that selection could act on inhibitory control via these behaviours, and selection on one behaviour could affect the other. However, we found no evidence of links between inhibitory control and social rank, foraging efficiency, or risk taking. This implies that selection may not act on inhibitory control via these measures, and that, in general, there may be a lack of strong selection on inhibitory control. This, in turn, could help explain individual variation in this aspect of cognition. Future research should explore the specificity of when inhibitory control has implications for individuals, and continue to investigate how variation in cognitive traits influences how individuals behave in contexts with potential evolutionary implications.

Sistem Pakar Mendiagnosa Penyakit Ayam Kampung Menggunakan Metode Certainty Factor

Animal husbandry is the activity of breeding and raising livestock to obtain the benefits and results of these activities. Activities in the field of animal husbandry can be divided into two groups, namely livestock farming of large animals such as cows, buffaloes and horses, while the second group is farming of small animals such as chickens, ducks, birds and others. Village chicken farming activities have existed since ancient times. Village chickens start from the first generation, namely from the descendants of the red jungle fowl (Gallus gallus). Raising free-range chickens is not easy because there are many things that must be considered and must have problems, therefore an expert system is needed to assist farmers in diagnosing and knowing the type of disease and symptoms experienced by the free-range chicken using a computer system automatically. This expert system uses the Certainty Factor method which aims to measure the level of certainty of facts or rules to describe an expert's belief in the problem at hand. This study shows how the process of calculating the Certainty Factor method in diagnosing free-range chicken disease with the initial combination rule to the last combination rule based on the selected symptoms, it can be concluded that the highest weight value is D01 Avian Influenza with a weight value of 0.99 x 100% = 99%

Genetic diversity and population genetic structure of Cambodian indigenous chickens.

ObjectiveCambodia is located within the distribution range of the red junglefowl, the common ancestor of domestic chickens. Although a variety of indigenous chickens have been reared in Cambodia since ancient times, their genetic characteristics have yet to be sufficiently defined. Here, we conducted a large-scale population genetic study to investigate the genetic diversity and population genetic structure of Cambodian indigenous chickens and their phylogenetic relationships with other chicken breeds and native chickens worldwide.MethodsA Bayesian phylogenetic tree was constructed based on 625 mitochondrial DNA D-loop sequences, and Bayesian clustering analysis was performed for 666 individuals with 23 microsatellite markers, using samples collected from 28 indigenous chicken populations in 24 provinces and three commercial chicken breeds.ResultsA total of 92 haplotypes of mitochondrial D-loop sequences belonging to haplogroups A to F and J were detected in Cambodian chickens; in the indigenous chickens, haplogroup D (44.4%) was the most common, and haplogroups A (21.0%) and B (13.2%) were also dominant. However, haplogroup J, which is rare in domestic chickens but abundant in Thai red junglefowl, was found at a high frequency (14.5%), whereas the frequency of haplogroup E was considerably lower (4.6%). Population genetic structure analysis based on microsatellite markers revealed the presence of three major genetic clusters in Cambodian indigenous chickens. Their genetic diversity was relatively high, which was similar to findings reported for indigenous chickens from other Southeast Asian countries.ConclusionCambodian indigenous chickens are characterized by mitochondrial D-loop haplotypes that are common to indigenous chickens throughout Southeast Asia, and may retain many of the haplotypes that originated from wild ancestral populations. These chickens exhibit high population genetic diversity, and the geographical distribution of three major clusters may be attributed to inter-regional trade and poultry transportation routes within Cambodia or international movement between Cambodia and other countries.

Analysis of the mtDNA D-loop Region Casts New Light on Philippine Red Junglefowl Phylogeny and Relationships to Other Junglefowl Species in Asia.

Red junglefowl (RJF) is considered the ancestor of domestic chickens. However, the possible maternal origin, genetic diversity, and subspecies classification of the Philippine (PH) RJF remains uncertain. In this study, the complete mitochondrial DNA (mtDNA) D-loop sequence of 55 PH RJFs collected from the mountainous areas of Occidental Mindoro, Palawan, Agusan del Norte, Capiz, Leyte, Iloilo, and Guimaras were analyzed and compared with chicken reference sequences. Phylogenetic analysis revealed multiple maternal origins of the PH RJFs based on haplogroups D, E, and Y classification. This was supported by PH RJFs and RJFs from other Asian countries sharing a clade. A median-joining network also revealed the haplotype sharing of the PH RJFs and Indonesian RJF, demonstrating common maternal ancestry. High haplotype and nucleotide diversity were also observed at all sampling sites. Analysis of molecular variance indicated that the principal molecular variance existed within populations (81.23%) rather than among populations (18.77%). A population neutrality test and Bayesian skyline plot (BSP) analysis elucidated the RJF maternal effective population size expansion in the Philippines that possibly started approximately 2,800-3,000 years ago. The co-existence of Gallus gallus bankiva and Gallus gallus gallus in the Philippines was also verified. The haplotype sharing of the current RJF samples with commercial chickens suggested the need to formulate conservation programs that would protect the RJFs in the Philippines.