Complete mitochondrial genome of the Thai Red Junglefowl(Gallus gallus) and phylogenetic analysis

正DEAR EDITOR,In this study,we sequenced the complete mitochondrial genome(mitogenome)of the Thai Red Junglefowl(RJF;Gallus gallus)using the next-generation sequencing(NGS)platform of the Ion Torrent PGM.Samples were taken from Mae Wang District,Chiang Mai Province,northern Thailand.Our data showed the complete mitogenome to be 16 785bp in length,composed by 13 protein-coding genes,22tRNA genes,two rRNA genes,and one control region.The genome nucleotide composition was 30.3%A,23.7%T,32.5%C,and 13.5%G,resulting in a high percentage of A+T     

Genetic characterization of Bhutanese native chickens based on an analysis of Red Junglefowl (Gallus gallus gallus and Gallus gallus spadecieus), domestic Southeast Asian and commercial chicken lines (Gallus gallus domesticus)

The genetic diversity of Bhutanese chickens needs to be understood in order to develop a suitable conservation strategy for these birds in Bhutan. In this, work, we used microsatellite markers to examine the genetic diversity of Bhutanese chickens. Four Bhutanese chicken varieties (Black plumage, Frizzle, Naked neck and Red Junglefowl-like, corresponding to Yuebjha Narp, Phulom, Khuilay and Seim, respectively), two subspecies of Red Junglefowl (Gallus gallus gallus and Gallus gallus spadecieus), two varieties of Thai native chickens (Pradhu Hang Dam and Chee; Gallus gallus domesticus) representing the Southeast Asian domestic chicken, and two commercial lines (Broiler and Single Comb White Leghorn) were genotyped with 18 microsatellites that included 16 loci recommended by the FAO/ISAG for investigations of genetic variability in chickens. All loci were polymorphic, with the number of alleles ranging from six (MCW0111) to 23 (MCW0183). Substantial genetic variation was observed in all populations, with the Bhutanese native chicken Yuebjha Narp (Black plumage chicken) showing the lowest genetic variability. Despite extensive intrapopulation variation, the genetic differentiation among 10 populations was moderate. A neighbor-joining tree revealed the genetic relationships involved while principal component analysis showed that Bhutanese native chickens should be given priority in conservation efforts because of their genetic distinctiveness. Chee chickens are especially valuable as a reservoir of predomestic diversity, as indicated by their greater genetic variation and their position in the phylogenetic tree.     

Red Junglefowl (Gallus gallus) selected for low fear of humans are larger,more dominant and produce larger offspring

Many traits associated with domestication are suggested to have developed as correlated responses to reduced fear of humans. Tameness may have reduced the stress of living in human proximity and improved welfare in captivity. We selected Red Junglefowl (ancestors of all domestic chickens) for four generations on high or low fear towards humans, mimicking an important aspect of the earliest period of domestication, and tested birds from the third and fourth generation in three different social tests. Growth and plumage condition, as well as size of eggs and offspring were also recorded, as indicators of some aspects of welfare. Birds selected for low fear had higher weight, laid larger eggs and generated larger offspring, and had a better plumage condition. In a social dominance test they also performed more aggressive behaviour and received less of the same, regardless of whether the restricted resource was feed or not. Hence, dominance appeared to increase as a consequence of reduced fear of humans. Furthermore, egg size and the weight of the offspring were larger in the less fearful birds, and plumage condition better, which could be interpreted as the less fearful animals being better adapted to the environment in which they were selected.     

红原鸡与家鸡的亲缘关系研究

对中国红原鸡滇地亚种和海南亚种与我国茶花鸡,泰和鸡和寿光鸡等地方鸡种以及芦花鸡,洛岛红等外国鸡种进行了血型（３个位点,１３个等位基因）,蛋白质（酶）多态（５个位点,１１个等位基因）和ＤＮＡ指纹分析,结果表明,红原鸡与茶花鸡（原始型品种）的亲缘关系较近;与泰和鸡,寿光鸡,芦花鸡,洛岛红（进化型品种）的亲缘关系较远,呈红原鸡－茶花鸡－泰和鸡,寿光鸡或芦花鸡,洛岛红这样一个进化阶梯,以上结果与国外资料（     

Genetic characterization of Red Junglefowl (Gallus gallus), Thai indigenous chicken (Gallus domesticus), and two commercial lines using selective functional genes compared to microsatellite markers

Genetic characterization among Red Junglefowl (GS, Gallus gallus spadiceus), Thai indigenous chicken (TIC, Gallus domesticus) and commercial lines has been widely used for studies of genealogical origin, genetic diversity, and effects of selection. We compared the efficiency of genetic characterization of chicken populations that had been under different intensities of selection using selective functional gene versus microsatellite marker analyses. We genotyped 151 chickens from five populations: Red Junglefowl, TIC and commercial lines (BR, broiler and WL, White Leghorn). Genetic structure analyses using six loci of five functional genes - corresponding to heat tolerance (heat shock protein 70, HSP70/C, HSP70/M), broodiness (vasoactive intestinal peptide receptor-1, VIPR-1), egg production-[24-bp indel (insertion or deletion) prolactin, 24bpPRL], ovulation rate (growth hormone receptor, GHR), and growth (insulin-like growth factor-1, IGF-1) - were compared with 18 microsatellite markers. PCR-RFLP and allele specific PCR were used for functional gene typing. A neighbor-joining tree from Nei's genetic distance was constructed to show genetic relationships. A similar pattern was found with both functional genes and microsatellites. Three groups consisting of BR, WL and TIC-GS-GG were formed. A principal component plot based on individual similarity using Dice's coefficient was also constructed to confirm the relationship. Different patterns were found when using functional genes versus microsatellites. A principal component plot with functional genes also gave three clusters consisting of BR, WL and TIC-GS-GG. A principal component plot using microsatellites gave four clusters, consisting of WL, GG, TIC, and BR-GS. Characterization of BR and GS differs from previous studies. We concluded that genetic characterization with appropriate functional genes is more accurate when differences in genetic make-up among populations are known. Genetic characterization using functional gene data was consistent in neighbor joining and principal component plot analyses, while genetic characterization using microsatellite data gave varied results depending on the analysis methodology.     

Genetic structure in Red Junglefowl (Gallus gallus) populations: Strong spatial patterns in the wild ancestors of domestic chickens in a core distribution range

Red Junglefowl (Gallus gallus) are among the few remaining ancestors of an extant domesticated livestock species, the domestic chicken, that still occur in the wild. Little is known about genetic diversity, population structure, and demography of wild Red Junglefowl in their natural habitats. Extinction threats from habitat loss or genetic alteration from domestic introgression exacerbate further the conservation status of this progenitor species. In a previous study, we reported extraordinary adaptive genetic variation in the MHC B‐locus in wild Red Junglefowl and no evidence of allelic introgression between wild and domestic chickens was observed. In this study, we characterized spatial genetic variation and population structure in naturally occurring populations of Red Junglefowl in their core distribution range in South Central Vietnam. A sample of 212 Red Junglefowl was obtained from geographically and ecologically diverse habitats across an area of 250 × 350 km. We used amplified fragment‐length polymorphism markers obtained from 431 loci to determine whether genetic diversity and population structure varies. We found that Red Junglefowl are widely distributed but form small and isolated populations. Strong spatial genetic patterns occur at both local and regional scales. At local scale, population stratification can be identified to approximately 5 km. At regional scale, we identified distinct populations of Red Junglefowl in the southern lowlands, northern highlands, and eastern coastal portions of the study area. Both local and long‐distance genetic patterns observed in wild Red Junglefowl may reflect the species’ ground‐dwelling and territorial characteristics, including dispersal barriers imposed by the Annamite Mountain Range. Spatially explicit analyses with neutral genetic markers can be highly informative and here elevates the conservation profile of the wild ancestors of domesticated chickens.     

中国红原鸡和泰国红原鸡遗传多样性分析

利用29个微卫星DNA标记对来自中国的红原鸡Gallus gallus spadiceus亚种和来自泰国的红原鸡Gallus gallus gallus亚种进行遗传多样性分析, 评估亚种内的遗传变异和亚种间的遗传分化, 结果表明: 共检测到168个等位基因, 每个位点的等位基因数从2到13不等, 所有位点平均的期望杂合度和PIC值分别为0.5780和0.53。中国和泰国红原鸡29个微卫星位点平均有效等位基因数分别为3.79和4.79, 平均基因杂合度为0.5379和0.6385, 两个红原鸡亚种均表现出较高的群体杂合度和丰富的遗传多样性。群体分化系数为19.4%(P<0.01), 两个红原鸡亚种间的Reynolds’遗传距离和Nm值分别为0.157和1.040。由此可见, Gallus gallus spadiceus亚种和Gallus gallus gallus亚种群体具有不同的群体遗传结构, 群体之间存在明显的遗传分化, 并不能将其认定为是同一亚种, 这也为中国家鸡具有独立的起源提供了一定的佐证。     

广东省原鸡种群数量、分布及栖息地现状的初步调查

广东原鸡栖息地分布在徐闻,雷州,信宜,高州,阳春5个县（市）,为孤立的三块,呈岛屿状分布,总面积2501.62km^2,总体数量680-750只,原鸡数量最多,面积最大的一块栖息地是由信宜,高州,阳春3块小栖息地组合而成,成为广东原鸡的主要栖息和分布地。     

Systematic identification and characterization of chicken (Gallus gallus) ncRNAs

Recent studies have demonstrated that non-coding RNAs (ncRNAs) play important roles during development and evolution. Chicken, the first genome-sequenced non-mammalian amniote, possesses unique features for developmental and evolutionary studies. However, apart from microRNAs, information on chicken ncRNAs has mainly been obtained from computational predictions without experimental validation. In the present study, we performed a systematic identification of intermediate size ncRNAs (50–500 nt) by ncRNA library construction and identified 125 chicken ncRNAs. Importantly, through the bioinformatics and expression analysis, we found the chicken ncRNAs has several novel features: (i) comparative genomic analysis against 18 sequenced vertebrate genomes revealed that the majority of the newly identified ncRNA candidates is not conserved and most are potentially bird/chicken specific, suggesting that ncRNAs play roles in lineage/species specification during evolution. (ii) The expression pattern analysis of intronic snoRNAs and their host genes suggested the coordinated expression between snoRNAs and their host genes. (iii) Several spatio-temporal specific expression patterns suggest involvement of ncRNAs in tissue development. Together, these findings provide new clues for future functional study of ncRNAs during development and evolution.     

Effects of Isolation on Stress Responses to Novel Stimuli in Subadult Chickens (Gallus gallus)

Extensive research has examined the effects of social isolation in neonatal and adult animal populations, but few studies have examined the effect of social isolation in early adulthood. Animals reaching reproductive age often experience extensive social changes as they leave their natal site, and a social stressor like isolation may uniquely affect this age group. Furthermore, adolescence is a time when sex differences in behavior become more pronounced. As such, the effects of social stressors are likely to vary by sex. In this study, we used noninvasive methods to evaluate stress responses to social change in male and female subadult chickens (Gallus gallus). Half of the birds experienced regular sessions of social isolation over the course of 2 wk, while the other half were never isolated. Subsequently, all of the animals were exposed to a suite of three novel probes, including an open‐field test. We monitored the birds’ behavioral (head movements) and physiological (fecal glucocorticoid metabolites, FGM) response to the tests. Our results indicate that, for subadult chickens, the effect of social isolation is sex dependent: Male FGM and behavioral responses did not change with subsequent experiences, in contrast to females. Females also exhibited more social reinstatement behavior compared to males. Our results are consistent with the expectations of differences between the sexes based on changes in the social environment due to sex‐biased dispersal patterns. For both sexes, the FGM and behavioral responses varied independently, which highlights the necessity for multiple measures of stress in animal populations.     

A histochemical study of keratinization in the domestic fowl (Gallus gallus)

The microanatomy of the epidermis of the domestic fowl is described and related to the distribution of various histochemical constituents involved in keratinization.
The avian horny layer over the back is composed of a loose network of structurally solid horny cells. This is in contrast to most mammalian epidermal horny cells in which structural keratin is found only in the peripheral cytoplasm, and the interior of the keratinocyte contains soluble products of cytolysis with possibly some free keratin filaments dispersed in the fluid material.
The avian tarsal epidermal horny scales show similarities to both the scales of lizards and snakes and to mammalian tail scales which appear to be homologous structures.
It is suggested that a thin layer of cells containing no detectable disulphide bonds, found in the tarsal scale region of the young chick, is probably mechanically weak and may function as a fission plane for sloughing of the horny layer. A specialized epidermis and thickened horny layer is developed in the fowl on the plantar underside of the toes, but this is quite different in structure from the mammalian plantar epidermis.
The overlapping of zones rich in ribonucleic acid (RNA) and bound cysteine (SH) in the growing feather suggests that protein synthesis and the preparatory stages to keratin disulphide bonding normally occur concurrently in feather formation. This is in contrast to the growing hair which has a region rich in RNA followed immediately before it becomes keratinized by a discrete keratogenous zone weak in RNA but rich in bound cysteine.     

Long-Term and Transgenerational Effects of Stress Experienced during Different Life Phases in Chickens (Gallus gallus)

Stress in animals causes not only immediate reactions, but may affect their biology for long periods, even across generations. Particular interest has been paid to perinatal stress, but also adolescence has been shown to be a sensitive period in mammals. So far, no systematic study has been performed of the relative importance of stress encountered during different life phases. In this study, groups of chickens were exposed to a six-day period of repeated stress during three different life phases: early (two weeks), early puberty (eight weeks) and late puberty (17 weeks), and the effects were compared to an unstressed control group. The short-term effects were assessed by behaviour, and the long-term and transgenerational effects were determined by effects on behavior and corticosterone secretion, as well as on hypothalamic gene expression. Short-term effects were strongest in the two week group and the eight week group, whereas long-term and transgenerational effects were detected in all three stress groups. However, stress at different ages affected different aspects of the biology of the chickens, and it was not possible to determine a particularly sensitive life phase. The results show that stress during puberty appears to be at least equally critical as the previously studied early life phase. These findings may have important implications for animal welfare in egg production, since laying hens are often exposed to stress during the three periods pinpointed here.     

Myocardial contractility in chickens (Gallus gallus): analysis of systolic time intervals

The avian cardiovascular system is of special interest because avian hearts are relatively larger than mammalian hearts, and activation of ventricular myocardium in birds has a "flash" pattern. Systolic time intervals and indices of myocardial contractility were examined in anaesthetized open-chest chickens by polycardiography, including synchronous recordings of electrocardiogram, phonocardiogram, and apex cardiogram. The asynchronous contraction time, isometric contraction time, pre-ejection period and ejection time were 26 +/- 3 (Mean +/- SD), 21 +/- 9, 47 +/- 12, and 83 +/- 23 ms, respectively, for heart rates of 260 +/- 57 bpm. The myocardial tension index, isometric contraction index and the pre-ejection period/ejection time ratio were 0.39 +/- 0.11, 0.42 +/- 0.10, and 0.54 +/- 0.14, respectively. A "flash" pattern of ventricular myocardial depolarization causes more rapid excitation and as a consequence shorter asynchronous contraction time of relatively larger chicken hearts compared with rabbit hearts. Inverse relation (P < 0.05) of the asynchronous contraction time to the heart rate in chickens is probably associated with the specific activation pattern of avian ventricles. Establishment of the values of systolic time intervals will facilitate a better understanding of cardiac function in birds. The obtained results are discussed in comparison with the rabbit. The indices calculated from the systolic time intervals show disadvantageous contractile function of chicken heart compared to rabbit heart.     

Domestication effects on behavioural synchronization and individual distances in chickens (Gallus gallus)

Behavioural synchrony (allelomimetic behaviour), and inter-individual distances are aspects of social and anti-predator strategies which may have been affected by domestication. Chickens are known to adjust synchronization and inter-individual distances depending on behaviour. We hypothesized that White Leghorn (WL) chickens would show less synchronized behaviour than the ancestor, the red jungle fowl (RJF). Sixty birds, 15 female and 15 male WL and the same number of RJF (28 weeks old) were studied in groups of three in furnished pens (1 m × 2 m) for 24 consecutive hours per group, following 24 h of habituation. Video tapes covering 4 h per group (dawn, 9-10 am, 1-2 pm and dusk) were analysed. Red junglefowl perched significantly more, but there were no breed effects on the frequency or daily rhythm of any other activities, or on average inter-individual distances. Red junglefowl were more synchronized during perching and a tendency for the same was found for social behaviour. After performance of the two most synchronized behaviours, perching and comfort behaviour, individual distance increased more for RJF than WL. According to this study domestication of chickens appears not to have significantly altered the relative frequencies of different activities or average inter-individual distances, but have caused some changes in behavioural synchronization and maintenance of activity-specific inter-individual distances in chickens. The changes may indicate an adaptive response to captivity and domestication.     

Effects of early prenatal exposure to 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) on postnatal reproduction in the laying hen (Gallus gallus)

This study demonstrates the long-term effects of very early embryonic exposure to a single dose of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) (0, 10 and 20 ng/egg), administered before the beginning of embryonic development, on growth and reproductive performance in laying hens. Hatchability and body weight gain from 11 weeks onwards were significantly depressed in 20 ng treated hens. All hens started laying egg at around the same age and the laying performance of TCDD-treated hens was normal. No disturbances in the age-related pattern and concentrations of oestradiol, LH or FSH in plasma could be found but mean progesterone concentrations were significantly lower in 20 ng treated hens. Moreover, follicular distribution was changed with less small white follicles and smaller yellow follicles, which probably resulted in the lower egg weight of the 20 ng treated hens. At 43 weeks of age, hens treated in ovo with TCDD showed a retained right oviduct, mostly filled with clear fluid. From these results, it seems that in ovo exposure to TCDD interferes in the right oviduct regression during embryonic development and induces some changes in follicular distribution but without impairment of reproductive performance in the adult laying hen.     

Behavioural differences between two captive populations of red jungle fowl (Gallus gallus) with different genetic background,raised under identical conditions

Ex situ conservation of threatened species may lead to behavioural adaptation, which can affect success of reintroduction attempts. In previous studies, we investigated the effects of captivity on the behaviour of red jungle fowl (Gallus gallus) and found that captive populations differed behaviourally as well as genetically. The aim of the present study was to compare the behaviour of two of the previously studied populations, raised under identical conditions. Eggs were collected from birds at Copenhagen zoo (Cop) and Götala research station (Got) and were incubated and hatched together. Twenty-eight birds (16 Got and 12 Cop) were reared together and tested in eight different behavioural tests, measuring different aspects of fear-related behaviours as well as exploratory and social behaviours. The study revealed several differences in fear-related behaviours between the populations but none in exploratory or social behaviours. In general, one of the populations (Cop) showed more intense fear behaviours than the other (Got), which instead were less fearful in their behaviours. This indicates that breeding animals in captivity may lead to behavioural modifications, which can affect the outcome of reintroductions. The results further suggest that fear-related behaviours are dependent on the genetic background of the animals while social behaviours may be more influenced by the social environment. Since fear-related behaviours, such as predator avoidance and fear of humans, are essential for a life in the wild, these aspects are crucial for the breeding of animals in captivity for conservation purposes.