Distribution of Melanin Pigmentation in 33 Organs of Thai Black-Bone Chickens (Gallus gallus domesticus)

Dynamic Transcriptome Profile Analysis of Mechanisms Related to Melanin Deposition in Chicken Muscle Development

The pectoral muscle is an important component of skeletal muscle. The blackness of pectoral muscles can directly affect the economic value of black-boned chickens. Although the genes associated with melanogenesis in mammals and birds have been thoroughly investigated, only little is known about the key genes involved in muscle hyperpigmentation during embryonic development. Here, we analyzed melanin deposition patterns in the pectoral muscle of Yugan black-boned chickens and compared differentially expressed genes (DEGs) between the muscles of Wenchang (non-black-boned chickens) and Yugan black-boned chickens on embryonic days 9, 13, 17, and 21. Melanin pigments were found to gradually accumulate in the muscle fibers over time. Using RNA-seq, there were 40, 97, 169, and 94 genes were identified as DEGs, respectively, between Yugan black-boned chicken muscles and Wenchang chickens at embryonic day 9, 13, 17, and 21 stages (fold change ≥2.0, false discovery rate (FDR) < 0.05). Thirteen DEGs, such as MSTRG.720, EDNRB2, TYRP1, and DCT, were commonly identified among the time points observed. These DEGs were mainly involved in pigmentation, melanin biosynthetic and metabolic processes, and secondary metabolite biosynthetic processes. Pathway analysis of the DEGs revealed that they were mainly associated with melanogenesis and tyrosine metabolism. Moreover, weighted gene co-expression network analysis (WGCNA) was used to detect core modules and central genes related to melanogenesis in the muscles of black-boned chickens. A total of 24 modules were identified. Correlation analysis indicated that one of them (the orange module) was positively correlated with muscle pigmentation traits (r > 0.8 and p < 0.001). Correlations between gene expression and L* values of the breast muscle were investigated in Yugan and Taihe black-boned chickens after hatching. The results confirmed that EDNRB2, GPNMB, TRPM1, TYR, and DCT expression levels were significantly associated with L* values (p < 0.01) in black-boned chickens (p < 0.05). Our results suggest that EDNRB2, GPNMB, TRPM1, TYR, and DCT are the essential genes regulating melanin deposition in the breast muscle of black-boned chickens. MSTRG.720 is a potential candidate gene involved in melanin deposition in the breast muscles of Yugan black-boned chickens.

Single-nucleus RNA sequencing reveals cell types, genes, and regulatory factors influencing melanogenesis in the breast muscle of Xuefeng black-bone chicken

The black-bone chicken, known for its high melanin content, holds significant economic value due to this unique trait. Particularly notable is the prominent melanin deposition observed in its breast muscle. However, the molecular mechanisms governing melanin synthesis and deposition in the breast muscle of black-bone chickens remain largely unknown. This study employed a single-nucleus transcriptome assay to identify genes associated with melanin deposition in the breast muscle of black-bone chickens, which are presumed to influence pigmentation levels. A comprehensive analysis of the nuclear transcriptome was conducted on the breast muscle of Xuefeng black-bone chickens, encompassing 18 distinct cell types, including melanocytes. Our findings revealed that STIMATE, LRRC7, ENSGALG00000049990, and GLDC play pivotal regulatory roles in melanin deposition within the breast muscle. Further exploration into the molecular mechanisms unveiled transcription factors and protein interactions suggesting that RARB, KLF15, and PRDM4 may be crucial regulators of melanin accumulation in the breast muscle. Additionally, HPGDS, GSTO1, and CYP1B1 may modulate melanin production and deposition in the breast muscle by influencing melanocyte metabolism. Our findings also suggest that melanocyte function in the breast muscle may be intertwined with intercellular signaling pathways such as PTPRK-WNT5A, NOTCH1-JAG1, IGF1R-IGF1, IDE-GCG, and ROR2-WNT5A. Leveraging advanced snRNA-seq technology, we generated a comprehensive single-cell nuclear transcriptome atlas of the breast muscle of Xuefeng black-bone chickens. This facilitated the identification of candidate genes, regulatory factors, and cellular signals potentially influencing melanin deposition and melanocyte function. Overall, our study provides crucial insights into the molecular basis of melanin deposition in chicken breast muscle, laying the groundwork for future breeding programs aimed at enhancing black-bone chicken cultivation.

Identification of Metabolites in Muscles of Lueyang Black-Bone Chickens: A Comparative Analysis of Caged and Cage-Free Rearing Modes Using Untargeted Metabolomic Techniques

The Lueyang black-bone chicken is a specific native chicken strain in China. This study aimed to investigate the effects of different rearing systems on the meat quality of Lueyang black-bone chickens. Six hundred Lueyang black-bone hens were randomly divided into two groups at 7 weeks of age and raised in cage and cage-free systems for 20 weeks. The carcass yield, meat quality, and total metabolites were measured in both the leg and breast muscles. By comparison, the carcass yield of hens in the cage-free (CF) group (1.26 ± 0.09 kg) was significantly lower than that in the caged rearing (CR) group (1.52 ± 0.15 kg). However, the shear force of leg muscles in the CF group (27.98 ± 2.43 N) was significantly greater than that in the CR group (24.15 ± 1.93 N). In addition, six samples from each group were randomly selected and their metabolites were detected by the non-targeted metabolomics technique. Among these metabolites, 408 and 354 significantly differentially abundant metabolites were identified in breast and leg muscles, which were mainly involved in glycerophospholipid metabolism, unsaturated fatty acid biosynthesis, arginine and proline metabolism, and nucleotide metabolism. We found that the levels of 19 phospholipids, mainly phosphatidylcholines and lysophosphatidylcholines, were significantly greater in the CF group than in the CR group. Additionally, the contents of eight unsaturated fatty acids, linoleic acid, and linolenic acid were dramatically greater in the CF group than in the caged group. The accumulation of 4-hydroxy-proline, glutamate, and adenosine 3'-monophosphate (AMP) was enhanced in the CF group. Moreover, many more volatile organic compounds were identified in the muscles of the cage-free group, enhancing the flavor of the chicken meat. In conclusion, the cage-free rearing mode facilitates the accumulation of nutrients and flavor substances in the chicken meat and is a better rearing system for Lueyang black-bone chickens.

Investigating the impact of pigmentation variation of breast muscle on growth traits, melanin deposition, and gene expression in Xuefeng black-bone chickens

The blackness traits, considered an important economic factor in the black-bone chicken industry, still exhibits a common phenomenon of significant difference in blackness of breast muscle. To improve this phenomenon, this study compared growth traits, blackness traits, and transcriptome of breast muscles between the High Blackness Group (H group) and Low Blackness Group (L group) in the Xuefeng black-bone chickens. The results are as follows: 1) There was no significant difference in growth traits between the H group and the L group (P > 0.05). 2) The skin/breast muscle L values in the H group were significantly lower than those in the L group, while the breast muscle melanin content exhibited the opposite trend (P < 0.05). 3) A significant negative correlation was observed between breast muscle melanin content and skin/breast muscle L value (P < 0.05), and skin L value exhibiting a significant positive correlation with breast muscle L value (P < 0.05). 4) The breast muscle transcriptome comparison between the H group and L group revealed 831 and 405 DEGs in female and male chickens, respectively. This included 37 shared DEGs significantly enriched in melanosome, pigment granule, and the melanogenesis pathway. Seven candidate genes (DCT, PMEL, MLANA, TYRP1, OCA2, EDNRB2, and CALML4) may play a crucial role in the melanin production of breast muscle in Xuefeng black-bone chicken. The findings could accelerate the breeding process for achieving desired levels of breast muscle blackness and contribute to the exploration of the mechanisms underlying melanin production in black-bone chickens.

A comparative review on Ayam Cemani chicken - A comparison with the most common chicken species in terms of nutritional values, LCA, price and consumer acceptance

Chickens are definitely among the most prevalent and broadly distributed domestic species. Among these, Ayam Cemani, also known as black chicken, is a rare Indonesian chicken breed originating from the island of Java. The main characteristic of this breed is that the body, both internally and externally, is entirely black. This is due to a condition named fibro melanosis, in which there is an over accumulation of melanin pigment in body tissues. In addition to this, Ayam Cemani meat results to be also higher in protein content and lower in fat. Moreover, Ayam Cemani meat is also known to have antioxidant and glucose-binding capacities. These properties make it very desirable within the market and consequently very expensive. Their meat is also used traditionally by tribal healers in the treatment of some chronic illnesses. In general, compared to other chicken species, the Ayam Cemani showed an higher genetic resistance to some infectious diseases commonly affecting poultry species. As regard the breeding, Ayam Cemani is a unique breed which may only be raised in specific locations, characterized to be a slowly growing breed with a lower body weight in comparison to the other poultry breeds. Nowadays, due to an improvement in the management, the nutrition and diseases control, it is possible to enhance their productivity. To date, there are not many studies in the literature on the specific breed of Ayam Cemani. For this reason, this review aims to provide a comprehensive overview of all the knowledge of the Ayam Cemani breed, the nutritional composition of the meat and consumer acceptance.

Transcriptome Profile Analysis Identifies Candidate Genes for the Melanin Pigmentation of Skin in Tengchong Snow Chickens

Tengchong Snow chickens are one of the most precious, black-boned chickens in Yunnan province and usually produce black meat. However, we found a small number of white meat traits in the chicken population during feeding. In order to determine the pattern of melanin deposition and the molecular mechanism of formation in the Tengchong Snow chicken, we measured the luminance value (L value) and melanin content in the skin of black meat chickens (Bc) and white meat chickens (Wc) using a color colorimeter, ELISA kit, and enzyme marker. The results showed that the L value of skin tissues in black meat chickens was significantly lower than that of white meat chickens, and the L value of skin tissues gradually increased with an increase in age. The melanin content of skin tissues in black meat chickens was higher than that of white meat chickens, and melanin content in the skin tissues gradually decreased with an increase in age, but this difference was not significant (p > 0.05); the L value of skin tissues in black meat chickens was negatively correlated with melanin content, and the correlation coefficient was mostly above -0.6. In addition, based on the phenotypic results, we chose to perform the comparative transcriptome profiling of skin tissues at 90 days of age. We screened a total of 44 differential genes, of which 32 were upregulated and 12 were downregulated. These DEGs were mainly involved in melanogenesis, tyrosine metabolism and RNA transport. We identified TYR, DCT, and EDNRB2 as possible master effector genes for skin pigmentation in Tengchong Snow black meat chickens through DEGs analysis. Finally, we measured the mRNA of TYR, DCT, MC1R, EDNRB2, GPR143, MITF, and TYRP1 genes through a quantitative real-time polymerase chain reaction (qPCR) and found that the mRNA of all the above seven genes decreased with increasing age. In conclusion, our study initially constructed an evaluation system for the black-boned traits of Tengchong Snow chickens and found key candidate genes regulating melanin deposition, which could provide an important theoretical basis for the selection and breeding of black-boned chickens.

Hyperpigmentation Inhibits Early Skeletal Muscle Development in Tengchong Snow Chicken Breed

Tengchong snow, which has white feathers and black meat, is one of the most important black-bone chicken breeds and a genetic treasure of black food in China. Although the black meat traits are dominant, there are some chickens with white meat traits born in the process of folk selection and breeding. The purpose of this study was to compare the differences in skeletal muscle development between Tengchong snow black meat chickens (BS) and white meat chickens (WS), as well as whether excessive melanin deposition has an effect on skeletal muscle development. The BS and WS groups were selected to determine their muscle development difference at stages of 1, 7, 14, 21, and 42 days, using histological stain methods to analyze the development and composing type of breast and leg muscle fibers, as well as the count of melanin in BS muscle fibers. Finally, we were validated key candidate genes associated with muscle development and melanin synthesis. The results showed that BS breast muscle development was inhibited at 7, 14, and 21 days, while the leg muscle was inhibited at 7, 14, 21, and 42 days, compared to WS. Melanin deposition was present in a temporal migration pattern and was greater in the leg muscles than in the breast muscles, and it focused around blood vessels, as well as the epithelium, perimysium, endomysium, and connective tissue. Additionally, melanin produced an inhibitory effect similar to MSTN during skeletal muscle fiber development, and the inhibition was strongest at the stage of melanin entry between muscle fibers, but the precise mechanisms need to be confirmed. This study revealed that melanin has an inhibitory effect on the early development of skeletal muscle, which will provide new insights into the role of melanin in the black-boned chicken and theoretical references for the future conservation and utilization of black-boned chicken.

Combining Abilities, Heterosis, Growth Performance, and Carcass Characteristics in a Diallel Cross from Black-Bone Chickens and Thai Native Chickens

The purpose of this study was to determine the combining abilities and heterosis for the growth performance and carcass characteristics in crosses between Hmong black-bone (HB), Chinese black-bone (CB), and Thai native (TN) chickens using a mating system diallel crossing. Nine crossbred chickens including HB × HB, CB × CB, TN × TN, HB × TN, TN × HB, CB × HB, HB × CB, TN × CB, and CB × TN, were tested. The total data were 699 recorded at the beginning of the experiment to 595 recorded in weeks 14 of age. Body weight (BW), average daily gain (ADG), feed conversion ratio (FCR), and survival rate (SUR) were recorded. Heterosis and combining ability regarding general combining ability (GCA), specific combining ability (SCA), and reciprocal combining ability (RCA) were estimated. The study found that CB had the greatest BW and ADG at all weeks (p < 0.05) except for hatch, while those of HB were the lowest. The highest GCA was found in CB; meanwhile, GCA was significantly negative in HB of all ages. Crossing between TN × CB had the greatest BW from 8 weeks of age, which was related to positive SCA and RCA values. However, the RCA value of TN × CB was lower than the SCA value of CB × TN. The yield percentages of the carcass in CB (87.00%) were higher than those in TN (85.05%) and HB (82.91%) (p < 0.05). The highest breast and thigh meat lightness (L*) values were obtained in TN (p < 0.05), while those of CB and HB were not different (p > 0.05). In the crossbreed, the yield percentage of the carcass was highest in TN × CB (89.65%) and CB × TN (88.55%) (p > 0.05) and was lowest in TN × HB (71.91%) (p < 0.05). The meat and skin color of the breast and thigh parts in the crossbreed had the lowest lightness in HB × CB (27.91 to 38.23) (p < 0.05), while those of TN × CB and CB × TN were insignificant (p > 0.05). In conclusion, crossing between the TN sires and CB dams has the preferable potential to develop crossbred Thai native chickens for commercial use based on their high growth performance.

Genetic parameters for production traits in F1 reciprocal crossbred Chee Fah and Fah Luang chickens

ContextRecently, Chee Fah and Fah Luang chickens have been registered as a black-bone native chicken in Thailand. Only a few studies revealed genetic information about them. No publication has reported any data related to their cross-mating, particularly, genetic parameters.AimsThis study aimed to estimate genetic parameters for production traits of F1 generation of reciprocal crossbred Chee Fah and Fah Luang chickens.MethodsA dataset of production traits of two crossbred groups was used in the present study. Effects of breed, month-day of incubation and sex were tested at P&lt;0.05. Genetic parameters were estimated using the restricted maximum likelihood method with multi-trait animal model.Key resultsThe crossbred Chee Fah×Fah Luang was significantly heavier and consumed more feed than Fah Luang×Chee Fah (P&lt;0.05). Male chickens had significantly better 20-week-old bodyweight, feed conversion ratio and average daily gain compared with females for both crossbred groups (P&lt;0.05). The effect of month-day of incubation had a significant influence on production traits (P&lt;0.05), except for day-old bodyweight. Heritabilities for production traits of crossbred chickens were low to high. The highest estimate was observed for day-old bodyweight (0.97), followed by feed intake (0.40), 20-week-old bodyweight (0.06), average daily gain (0.05) and feed conversion ratio (0.03), respectively. Both positive and negative genetic correlations were found among their production traits. Favourable relationships were found between average daily gain versus bodyweight and versus feed conversion ratio (rgg=0.99 and −0.90, respectively). Similarly, production traits showed phenotypic correlations in both directions, which ranged from −0.95 to 0.99.ConclusionsHeritability estimations for production traits were found in low to high magnitude. The desirable genetic relationships were found between feed conversion ratio and day-old bodyweight, 20-week-old bodyweight and average daily gain, and between 20-week-old bodyweight and average daily gain.ImplicationsThese findings could be considered as a source of genetic data for enhancing production traits of crossbred black-bone native chickens.

Evolution and development of parrot pseudoteeth

Parrot embryos carry peculiar appendages at their developing beak that have been described as pseudoteeth. To better characterize the pattern of development responsible for the emergence of these dental appendages, we examined parrot embryos combining conventional histology and microtomography approaches. Using immunohistochemistry, we observed the epithelial and mesenchymal expression of several proteins involved in tooth development in mammals. Parrot pseudoteeth arose by epithelial and mesenchymal evagination, and their early development was similar to the ontogeny of scales and feathers. There was no enamel tissue, and the evaginations were surrounded by the rhamphotheca. In adults, the rhamphotheca covers entirely the appendages, now represented by bone evaginations, which were more numerous in the lower than in the upper beak, being similar to the osseous teeth of the fossil Pelagornithidae. These embryonic pseudoteeth resembled reptile's first-generation teeth and dental appendages of chicken talpid² mutants. Proteins involved in mammalian odontogenesis, such as SHH, BMP4, PITX2, and PAX9, were found to be generally expressed in beak epithelium and mesenchyme during parrot pseudoteeth development, with clusters of high-level expression in the pseudoteeth rudiments. This suggests that a similar, highly conserved gene expression program gives rise to the appearance of odontode derivatives in numerous species, despite their divergent developmental paths. These results provide new insights into the development and evolution of odontode-derived structures in vertebrates.

Mitochondrial DNA diversity and demographic history of Black-boned chickens in China

Black-boned chickens (Gallus domesticus, herein abbreviated BBCs) are well known for their unique appearance and medicinal properties and have a long breeding history in China. However, the genetic diversity and demographic history of BBCs remain unclear. In this study, we analyzed 844 mitochondrial DNA D-loop sequences, including 346 de novo sequences and 498 previously published sequences from 20 BBC breeds. We detected a generally high level of genetic diversity among the BBCs, with average haplotype and nucleotide diversities of 0.917 ± 0.0049 and 0.01422, respectively. Nucleotide diversity was highest in populations from Southwest China (0.01549 ± 0.00026), particularly in Yunnan Province (0.01624 ± 0.00025). Significant genetic divergence was detected between most breeds, particularly between Yunnan chickens and those from all other provinces. Haplogroups F and G had the highest levels of genetic diversity and were restricted to Southwest China, particularly Yunnan Province. Based on neutrality tests and mismatch distribution analyses, we did not obtain evidence for rapid population expansions and observed similar demographic histories in BBCs and local non-BBCs. Our results suggest that Chinese BBCs have complex breeding histories and may be selected in situ from local domestic chickens. These results improve our understanding of the genetic heritage and breeding histories of these desirable chickens.

Genetics and breeding of a black-bone and blue eggshell chicken line. 1. Body weight, skin color, and their combined selection

An experimental population of chickens was developed from the cross between 2 indigenous Chinese breeds, Dongxiang blue eggshell and Jiangshan black-bone. This breeding was aimed at eventually combining dark heavy black-bone body and blue eggshell, into a single dual-purpose breed. BW was recorded and skin L∗, a∗, and b∗ color parameters were measured by a Chroma Meter at several ages (56, 105, 150, 200, 250, and 300 d). At 250 d, 3 independent observers classified skin darkness using a 3-level visual scale (1 = light, 2 = intermediate, 3 = dark). The 7-level average visual skin darkness, calculated for each chicken, was highly correlated (−0.658 and −0.612 in females and males, respectively) with skin L∗ (lightness), indicating that the accurately measured L∗ is reliable and useful reverse expression of visual skin darkness of black-bone chickens. Mean BW and skin L∗ of both sexes increased with age, to 2,063 and 1,522 g in males and females, respectively, at 300 d, and to 63 and 55 L∗ units in males and females, respectively, at 250 d. The population's full-pedigree allowed estimating heritability and genetic correlations between traits. The heritability estimates of BW were similar in both sexes, increasing from around 0.25 at 56 d, to 0.53 to 0.60 at 150 d, and 0.57 to 0.62 at 300 d. Over the 5 ages, heritability estimates of skin L∗ were moderate to high, ranging from 0.45 to 0.58 in females, and from 0.31 to 0.65 in males, and the genetic correlations between BW and L∗ ranged mostly from 0.20 to 0.45. These low-to-moderate correlations between high BW and high L∗ (low darkness) are unfavorable; hence they were combined into an index, standardized BW minus standardized L∗, allowing future selection for high BW with low L∗. With high heritability of this index, 0.487 (females at 300 d) and 0.410 to 0.555 (males at 150 d or older), simultaneous improvements in BW and skin darkness appear to be feasible. The methodology used in this study can be useful in chicken populations experimentally bred for combination of high BW and other body characteristics.

Consistency of dark skeletal muscles in Thai native black-bone chickens (Gallus gallus domesticus)

Black-bone chickens (Gallus gallus domesticus) have become economically valuable, particularly in Southeast Asia as a consequence of popular traditional Chinese medical practices. Chickens with whole body organ darkness are considered to have higher value and are, therefore, more often requested. This research study aimed to investigate the darkness in 34 skeletal muscles of 10 Thai black-bone chickens (five males and five females). The evaluation of muscle darkness was done on two levels: (i) a color chart was employed at the macroanatomical level and (ii) by using melanin pigment to evaluate the structure at the microanatomy level. The results revealed that the accumulation of melanin pigment in the muscle tissue was observed in the endomysium, perimysium and epimysium. With respect to the results of the color chart test, iliotibialis lateralis pars preacetabularis, gastrocnemius, fibularis longus and puboischiofemoralis pars medialis showed the highest degree of darkness, while serratus profundus, pectoralis, iliotibialis cranialis, flexor cruris lateralis, and flexor cruris medialis appeared to be the least dark. In addition, we found that the highest and lowest amounts of melanin pigment was noted in the flexor carpi ulnaris and pectoralis (p < 0.05), respectively; however, there was no significant difference (p > 0.05) observed between the sexes. These results reveal that the 34 specified muscles of black-bone chickens showed uneven distribution of darkness due to the differing accumulations of melanin pigments of each muscle.This information may provide background knowledge for a better understanding of melanin accumulation and lead to breeding improvements in Thai black-bone chickens.