Search

The feralization of domestic chicken makes the conservation and management of red jungle fowl (Gallus gallus) more complicated and challenging. We collected two Sulawesi feral chickens, located east of the Wallace Line, for whole-genome sequencing and de novo genome assembly. Phylogenetic and f4-statistics analyses indicated that the Sulawesi feralized domestic chickens (G. g. domesticus) received gene flow from G. g. gallus. We integrated ~45× ultra-long Oxford Nanopore Technology reads and ~28× PacBio HiFi reads to generate a de novo genome assembly of a female Sulawesi feral chicken (GGsula) with a contig N50 of 19.88 Mbp. We characterized structural variations in GGsula, and found some were related to nervous system. Our study provides the first genome assembly of feral chickens, which is a unique genomic resource to explore the process of chicken domestication and feralization., (© 2024 Stichting International Foundation for Animal Genetics.)

The aim of the study was to assess the effect of feeding the same diet to different breeds of chickens and at different ages on fatty acid (FA) composition of the breast and thigh muscles. A total of 150 chickens comprising 50 each of red jungle fowl (RJ) and village chicken (VC), the slow-growing birds, and the commercial broiler (CB), fast-growing birds, were used for this study. Ten chickens from each breed were serially euthanized at days 1, 10, 20, 56, and 120 post hatch, and pectoralis major and bicep femoris were harvested to represent the breast and thigh muscles respectively. It was revealed that the breast muscle concentrations of saturated fatty acids (SFA), monounsaturated fatty acids (MUFA), and total polyunsaturated fatty acids (PUFA) are significantly different (p<0.05) among the breeds. Also, the FA composition of breast and thigh muscles among RJ, VC, and CB at various ages studied varied significantly (p<0.05) but without a definite pattern. The composition of MUFA was lower, but that of PUFA was higher in the RJ and VC than in the CB breast muscles. Within the breeds, the composition of total MUFA decreased, while that of PUFA increased with age. The total MUFA and PUFA showed no significant difference (p>0.05) between the breast and thigh muscles at different ages evaluated. This study suggests that slow-growing birds (RJ and VC) might be better sources of desirable FA than the fast-growing birds, CB., (© 2021. The Author(s), under exclusive licence to Springer Nature B.V.)

Keel bone damage (KBD) is a highly prevalent problem in commercial egg production. KBD consists of two different conditions affecting the keel: Keel bone deviation and keel bone fractures (KBF). Deviations are linked to pressure on the keel, e.g., from perching. The causative factors for KBF are not clear; however, selection for efficient egg production has been suggested as a major contributing factor. An important step to shed light on the role of selective breeding as an underlying cause of KBF in modern laying hens is to evaluate the keel bones of the ancestor, the red jungle fowl. To the authors' knowledge, this has never previously been published. The aim of this study was therefore to describe the prevalence of KBD in a study group of red jungle hens and roosters housed in an aviary system. The present study examined 29 red jungle fowls 112 weeks of age post-mortem; 12 hens and 17 roosters. Keel bones were evaluated by external palpation for deviations and fractures. Palpation was followed by autopsy. No fractures were detected in the 17 roosters; one had a very slight deviation. Of the 12 red jungle hens in this pilot study, one had a single fracture and 10 hens had a very slight deviation.

1. The skulls and postcranial skeletons of the red jungle fowl (Gallus gallus) were compared osteometrically between the populations from North and South Vietnam, North and Central Laos and Southeast Bangladesh. The populations include the three subspecies of G. g. spadiceus, G. g. gallus and G. g. murghi and were sampled to reveal the geographical morphological variations among populations in G. gallus. 2. The morphometric characteristics of subspecies murghi could be clearly distinguished from those of the other subspecies using a canonical discriminant analysis. However, the size and shape of the skull of the gallus population from South Vietnam were not statistically different from that of the subspecies spadiceus from North Laos. The canonical discriminant scores also clearly indicated that there were morphological similarities in the skulls of the populations from North Laos and South Vietnam. 3. From the results, therefore, it is concluded that red jungle fowls do not exhibit high levels of osteometric variation between geographical localities at least within the Indochinese Peninsula. 4. This contrasts with previous studies which have described these subspecies as having various external morphological differences and have argued that zoogeographical barriers exist between the north and south areas of the Indochinese Peninsula.

Great variations in the size, shape, color, feather structure and behavior are observed among fowl breeds. Because many types of domestic fowls have been bred for various purposes, they are ideal to assess the relationship between brain morphology and avian biology. However, little is known about changes in brain shape that may have occurred during fowl domestication. We analyzed the brains of red jungle fowl and domestic fowl to clarify differences in the brain shape between these breeds, as well as the shape changes associated with size enlargement using three-dimensional geometric morphometrics. Principal component and multivariate regression analyses showed that ventrodorsal bending, anteroposterior elongation and width reduction were significantly correlated with brain size. According to the size-dependent analysis, the red jungle fowl brain has an intermediate shape between the brain of young broilers and that of large domestic fowl and adult broilers. After the size effect is removed, geometric morphometric analyses show that the brain of red jungle fowl is different from that of domestic fowl, with large round cerebral hemispheres. Significant correlations exist between the skull length and brain volume among fowl, while the brain volume relative to the skull length is distinctly larger in red jungle fowl compared with domestic fowl. The distinct brain shape and increased relative brain size of red jungle fowl may be driven by the presence of large, rounded cerebral hemispheres., (© 2017 Anatomical Society.)

PIWI-interacting RNAs (piRNAs) protect the germ line by targeting transposable elements (TEs) through the base-pair complementarity. We do not know how piRNAs co-evolve with TEs in chickens. Here we reported that all active TEs in the chicken germ line are targeted by piRNAs, and as TEs lose their activity, the corresponding piRNAs erode away. We observed de novo piRNA birth as host responds to a recent retroviral invasion. Avian leukosis virus (ALV) has endogenized prior to chicken domestication, remains infectious, and threatens poultry industry. Domestic fowl produce piRNAs targeting ALV from one ALV provirus that was known to render its host ALV resistant. This proviral locus does not produce piRNAs in undomesticated wild chickens. Our findings uncover rapid piRNA evolution reflecting contemporary TE activity, identify a new piRNA acquisition modality by activating a pre-existing genomic locus, and extend piRNA defense roles to include the period when endogenous retroviruses are still infectious.

The rhythmic locomotor behavior of flies and mice provides a phenotype for the identification of clock genes, and the underlying molecular mechanism is well studied. However, interestingly, when examining locomotor rhythm in the wild, several key laboratory-based assumptions on circadian behavior are not supported in natural conditions. The rooster crowing 'cock-a-doodle-doo' is a symbol of the break of dawn in many countries. Previously, we used domestic inbred roosters and showed that the timing of roosters' crowing is regulated by the circadian clock under laboratory conditions. However, it is still unknown whether the regulation of crowing by circadian clock is observed under natural conditions. Therefore, here we used red jungle fowls and first confirmed that similar crowing rhythms with domesticated chickens are observed in red jungle fowls under the laboratory conditions. Red jungle fowls show predawn crowing before light onset under 12:12 light : dim light conditions and the free-running rhythm of crowing under total dim light conditions. We next examined the crowing rhythms under semi-wild conditions. Although the crowing of red jungle fowls changed seasonally under semi-wild conditions, predawn crowing was observed before sunrise in all seasons. This evidence suggests that seasonally changed crowing of red jungle fowls is under the control of a circadian clock., (© 2016 Japanese Society of Animal Science.)

Transposable elements (TEs) are nearly ubiquitous among eukaryotic genomes, but TE contents vary dramatically among phylogenetic lineages. Several mechanisms have been proposed as drivers of TE dynamics in genomes, including the fixation/loss of a particular TE insertion by selection or drift as well as structural changes in the genome due to mutation (e.g., recombination). In particular, recombination can have a significant and directional effect on the genomic TE landscape. For example, ectopic recombination removes internal regions of long terminal repeat retrotransposons (LTR-RTs) as well as one long terminal repeat (LTR), resulting in a solo LTR. In this study, we focus on the intra-species dynamics of LTR-RTs and solo LTRs in bird genomes. The distribution of LTR-RTs and solo LTRs in birds is intriguing because avian recombination rates vary widely within a given genome. We used published linkage maps and whole genome assemblies to study the relationship between recombination rates and LTR-removal events in the chicken and zebra finch. We hypothesized that regions with low recombination rates would harbor more full-length LTR-RTs (and fewer solo LTRs) than regions with high recombination rates. We tested this hypothesis by comparing the ratio of full-length LTR-RTs and solo LTRs across chromosomes, across non-overlapping megabase windows, and across physical features (i.e., centromeres and telomeres). The chicken data statistically supported the hypothesis that recombination rates are inversely correlated with the ratio of full-length to solo LTRs at both the chromosome level and in 1-Mb non-overlapping windows. We also found that the ratio of full-length to solo LTRs near chicken telomeres was significantly lower than those ratios near centromeres. Our results suggest a potential role of ectopic recombination in shaping the chicken LTR-RT genomic landscape.

Aim: The red jungle fowl is generally considered as one of the endangered Asian wild Galleopheasants due to man-made encroachment of their habitats, coupled with the effect of disease and disease causing organisms like ticks and tick-borne infections. This study aimed to determine the tick fauna of the red jungle fowl and their predilection sites based on developmental stages., Materials and Methods: A total of 33 jungle fowls were sampled for this study from Bangi area of Selangor State, Peninsular Malaysian. The birds were captured using a locally made trap made-up of loops and bites. Ticks present on their bodies were detached using fine forceps and identified morphologically under a dissecting microscope., Results: 91% of the jungle fowls were infested with ticks, all of which belongs to the species Haemaphysalis wellingtoni. The ear region appeared to be the most common predilection site (63%) for all the developmental stages in which the larval stages are solely restricted to that region. Nymphal and adult stages were distributed on the comb, wattle, and facial region in addition to the ear region., Conclusion: This study was the first in its kind and showed a high prevalence of tick infestation among jungle fowls. H. wellingtoni was known to be a vector in transmission of many tick-borne pathogens. Therefore, there is the need for further investigation to identify the various pathogens associated with this tick.

The present study was conducted to assess the genetic diversity, population structure, and relatedness in Indian red jungle fowl (RJF, Gallus gallus murgi) from northern India and three domestic chicken populations (gallus gallus domesticus), maintained at the institute farms, namely White Leghorn (WL), Aseel (AS) and Red Cornish (RC) using 25 microsatellite markers. All the markers were polymorphic, the number of alleles at each locus ranged from five (MCW0111) to forty-three (LEI0212) with an average number of 19 alleles per locus. Across all loci, the mean expected heterozygosity and polymorphic information content were 0.883 and 0.872, respectively. Population-specific alleles were found in each population. A UPGMA dendrogram based on shared allele distances clearly revealed two major clusters among the four populations; cluster I had genotypes from RJF and WL whereas cluster II had AS and RC genotypes. Furthermore, the estimation of population structure was performed to understand how genetic variation is partitioned within and among populations. The maximum ▵K value was observed for K = 4 with four identified clusters. Furthermore, factorial analysis clearly showed four clustering; each cluster represented the four types of population used in the study. These results clearly, demonstrate the potential of microsatellite markers in elucidating the genetic diversity, relationships, and population structure analysis in RJF and domestic chicken populations.

The current build (galGal4) of the genome of the ancestor of the modern chicken, the Red Jungle Fowl, contains a single endogenous avian leukosis viral element (ALVE) on chromosome 1 (designated RSV-LTR; family ERVK). The assembly shows the ALVE provirus juxtaposed with a member of a second family of avian endogenous retroviruses (designated GGERV20; family ERVL); however, the status of the 3' end of the ALVE element as well as its flanking region remain unclear due to a gap in the reference genome sequence. In this study, we filled the gap in the assembly using a combination of long-range PCR (LR-PCR) and a short contig present in the unassembled portion of the reference genome database. Our results demonstrate that the ALVE element (ALVE-JFevB) is inserted into the putative envelope region of a GGERV20 element, roughly 1 kbp from its 3' end, and that ALVE-JFevB is complete, and depending on its expression status, potentially capable of directing the production of virus. Moreover, the unassembled portion of the genome database contains junction fragments for a second, previously characterized endogenous proviral element, ALVE-6., (©2014 Poultry Science Association Inc.)