Common Ancestry of the Id Locus: Chromosomal Rearrangement and Polygenic Possibilities

The diversity in dermal pigmentation and plumage color among domestic chickens is striking, with Black Bone Chickens (BBC) particularly notable for their intense melanin hyperpigmentation. This unique trait is driven by a complex chromosomal rearrangement on chromosome 20 at the Fm locus, resulting in the overexpression of the EDN3 (a gene central to melanocyte regulation). In contrast, the inhibition of dermal pigmentation is regulated by the Id locus. Although prior studies using genetic crosses, GWAS, and gene expression analysis have investigated the genetic underpinnings of the Id locus, its precise location and functional details remain elusive. Our study aims to precisely locate the Id locus, identify associated chromosomal rearrangements and candidate genes influencing dermal pigmentation, and examine the ancestral status of the Id locus in BBC breeds. Using public genomic data from BBC and non-BBC breeds, we refined the Id locus to a ~1.6 Mb region that co-localizes with Z amplicon repeat units at the distal end of the q-arm of chromosome Z within a 10.36 Mb inversion in Silkie BBC. Phylogenetic and population structure analyses reveal that the Id locus shares a common ancestry across all BBC breeds, much like the Fm locus. Selection signatures and highly differentiated BBC-specific SNPs within the MTAP gene position it as the prime candidate for the Id locus with CCDC112 and additional genes, suggesting a possible polygenic nature. Our results suggest that the Id locus is shared among BBC breeds and may function as a supergene cluster in shank and dermal pigmentation variation.

PPP3R1 Promoter Polymorphism (Allelic Variation) Affects Tacrolimus Treatment Efficacy by Modulating E2F6 Binding Affinity

BACKGROUND

Tacrolimus is widely used as a first-line immunosuppressant in transplant immunology; however, its clinical application is constrained by the narrow therapeutic index and considerable interindividual variability. In this study, we identified the potential regulatory role of a novel PPP3R1 promoter polymorphism, rs4519508 C > T, in the tacrolimus pharmacodynamic pathway.

METHODS

Dual-luciferase reporter assays and bioinformatic analysis were applied to assess the impact of allelic variation. Electrophoretic mobility shift assays (EMSA) validated the altered binding of transcription factors. Quantitative real-time PCR (qRT-PCR), enzyme-linked immunosorbent assay (ELISA) and Western blots were used to determine the immunosuppressive effect of tacrolimus.

RESULTS

Assays revealed that rs4519508 C > T markedly enhanced PPP3R1 promoter activity. EMSA assays validated the binding of E2F6 to rs4519508 C (wild-type) and the binding was significantly weaker to the rs4519508 T (mutant-type). The overexpression of E2F6 significantly reduced the transcriptional activity and expression of PPP3R1 when the rs4519508 site presented as major C allele, an effect that was not observed with the rs4519508 T allele. Furthermore, the downregulation of E2F6 raises the level of downstream immune cytokines inhibited by TAC.

CONCLUSIONS

This study proposed that E2F6 suppresses the expression of PPP3R1, while rs4519508 C > T impairs the binding of E2F6, and thus elevates the level of PPP3R1, so that the inhibition of the downstream immune cytokines by TAC is attenuated. Our findings reported the potential regulatory role of a novel polymorphism, PPP3R1 rs4519508 C > T, which may serve as pharmacodynamic-associated pharmacogenetic biomarker indicating individual response variability of tacrolimus, and thus aid the clinical management of transplant immunology.

A genome-wide association study for eumelanin pigmentation in chicken plumage using a computer vision approach

Chicken plumage colouration is an important trait related to productivity in poultry industry. Therefore, the genetic basis for pigmentation in chicken plumage is an area of great interest. However, the colour trait is generally regarded as a qualitative trait and representing colour variations is difficult. In this study, we developed a method to quantify and classify colour using an F₂ population crossed from two pure lines: White Leghorn and the Korean indigenous breed Yeonsan Ogye. Using red, green, and blue values in the cropped body region, we identified significant genomic regions on chromosomes 33:3 160 480-7 447 197 and Z:78 748 287-79 173 793. Furthermore, we identified two potential candidate genes (PMEL and MTAP) that might have significant effects on melanin-based plumage pigmentation. Our study presents a new phenotyping method using a computer vision approach and provides new insights into the genetic basis of melanin-based feather colouration in chickens.

Revealing the Regulatory Mechanism of lncRNA-LMEP on Melanin Deposition Based on High-Throughput Sequencing in Xichuan Chicken Skin

The therapeutic, medicinal, and nourishing properties of black-bone chickens are highly regarded by consumers in China. However, some birds may have yellow skin (YS) or light skin rather than black skin (BS), which causes economic losses every year. Long noncoding RNAs (lncRNAs) are widely present in living organisms, and they perform various biological functions. Many genes associated with BS pigmentation have been discovered, but the lncRNAs involved and their detailed mechanisms have remained untested. We detected 56 differentially expressed lncRNAs from the RNA-seq of dorsal skin (BS versus YS) and found that TCONS_00054154 plays a vital role in melanogenesis by the combined analysis of lncRNAs and mRNAs. We found that the full length of the TCONS_00054154 sequence was 3093 bp by RACE PCR, and we named it LMEP. Moreover, a subcellular localization analysis identified that LMEP is mainly present in the cytoplasm. After the overexpression and the interference with LMEP, the tyrosinase content significantly increased and decreased, respectively (p < 0.05). In summary, we identified the important lncRNAs of chicken skin pigmentation and initially determined the effect of LMEP on melanin deposition.

Avian Coloration Genetics: Recent Advances and Emerging Questions

The colorful phenotypes of birds have long provided rich source material for evolutionary biologists. Avian plumage, beaks, skin, and eggs-which exhibit a stunning range of cryptic and conspicuous forms-inspired early work on adaptive coloration. More recently, avian color has fueled discoveries on the physiological, developmental, and-increasingly-genetic mechanisms responsible for phenotypic variation. The relative ease with which avian color traits can be quantified has made birds an attractive system for uncovering links between phenotype and genotype. Accordingly, the field of avian coloration genetics is burgeoning. In this review, we highlight recent advances and emerging questions associated with the genetic underpinnings of bird color. We start by describing breakthroughs related to 2 pigment classes: carotenoids that produce red, yellow, and orange in most birds and psittacofulvins that produce similar colors in parrots. We then discuss structural colors, which are produced by the interaction of light with nanoscale materials and greatly extend the plumage palette. Structural color genetics remain understudied-but this paradigm is changing. We next explore how colors that arise from interactions among pigmentary and structural mechanisms may be controlled by genes that are co-expressed or co-regulated. We also identify opportunities to investigate genes mediating within-feather micropatterning and the coloration of bare parts and eggs. We conclude by spotlighting 2 research areas-mechanistic links between color vision and color production, and speciation-that have been invigorated by genetic insights, a trend likely to continue as new genomic approaches are applied to non-model species.

Comparative transcriptome and histological analyses provide insights into the skin pigmentation in Minxian black fur sheep (Ovis aries)

Background

Minxian black fur (MBF) sheep are found in the northwestern parts of China. These sheep have developed several special traits. Skin color is a phenotype subject to strong natural selection and diverse skin colors are likely a consequence of differences in gene regulation.

Methods

Skin structure, color differences, and gene expression (determined by RNA sequencing) were evaluated the Minxian black fur and Small-tail Han sheep (n = 3 each group), which are both native Chinese sheep breeds.

Results

Small-tail Han sheep have a thicker skin and dermis than the Minxian black fur sheep (P < 0.01); however, the quantity of melanin granules is greater (P < 0.01) in Minxian black fur sheep with a more extensive distribution in skin tissue and hair follicles. One hundred thirty-three differentially expressed genes were significantly associated with 37 ontological terms and two critical KEGG pathways for pigmentation (“tyrosine metabolism” and “melanogenesis” pathways). Important genes from those pathways with known involvement in pigmentation included OCA2 melanosomal transmembrane protein (OCA2), dopachrome tautomerase (DCT), tyrosinase (TYR) and tyrosinase related protein (TYRP1), melanocortin 1 receptor (MC1R), and premelanosome protein (PMEL). The results from our histological and transcriptome analyses will form a foundation for additional investigation into the genetic basis and regulation of pigmentation in these sheep breeds.

A functional mutation in the AMPD1 promoter region affects promoter activity and breast meat freshness in chicken

Freshness is an important index to determine the quality deterioration (protein degradation and changes in appearance) of chilled chicken meat and is a primary consideration of consumers. Adenosine monophosphate deaminase 1 (AMPD1) catalyzes the deamination of adenosine monophosphate to inosine monophosphate in skeletal muscle and is the rate-limiting step in the purine nucleotide cycle. Inosine monophosphate is regarded as an important indicator of meat freshness in chicken. This study investigated the association of polymorphisms in the chicken AMPD1 promoter region with meat freshness during freezing storage. An SNP (c. -905G>A) was found to be associated with the freshness (K-value) of chicken breast meat. Chickens with the AA genotype had significantly lower K-values than those with GG and AG genotypes (P < 0.01). Individuals with the AA genotype also had higher breast meat AMPD1 mRNA levels than did those with the GG and AG genotypes (P < 0.01, P < 0.05). A luciferase assay revealed that genotype AA had greater transcriptional activity than genotype GG. Transcription factor binding site analysis identified distinct putative transcription factor binding sites in the two alleles of mutation site c. -905. In summary, we identified an SNP (c. -905G>A) in the promoter region of the AMPD1 gene that may modulate the binding affinity of different transcription factors to control AMPD1 expression and affect the freshness K-value of chicken meat.

Identification of differentially expressed genes associated with egg production in black-boned chicken

1. Muchuan black-bone chicken is well known in China for its meat quality and medicinal properties; however, its egg-laying performance is not ideal. To better understand the molecular mechanisms of black-boned chicken egg-laying, high-throughput RNA sequencing was performed to compare differences in the pituitary transcriptome between three high-rate (group H) and three low-rate (group L) egg production chickens. 2. In total, 171 differentially expressed genes (DEGs) were identified between the two groups, of which 113 were upregulated and 58 were downregulated in group L. Some of these genes are known to be related to hormone secretion or the regulation of reproductive processes; these include prolactin-releasing hormone (PRLH), distal-less homeobox 6 (DLX6), interferon regulatory factor 4 (IRF4), and cilia and flagella associated protein 69 (CFAP69). Notably, expression pattern analysis indicated that both PRLH and DLX6 may influence egg-laying performance. 3. The dataset provided a foundation for discovering important genes and pathways involved in the chicken egg-laying process, and may help to improve understanding of the molecular mechanisms of chicken reproduction.

Identification of key microRNAs affecting melanogenesis of breast muscle in Muchuan black-boned chickens by RNA sequencing

1. Melanin content is considered an important indicator of meat quality in black-boned chickens, which have a high market value. To understand the complex physiological processes underlying muscle melanogenesis in this chicken, differentially expressed miRNAs (DEMs) were detected between black muscle (BM) and white muscle (WM) of chickens using high-throughput sequencing technology. Six small RNA libraries were constructed, and more than 16.75 million clean reads were obtained for each library. 2. A total of 582 known miRNAs and 65 novel miRNAs were identified from the six chicken sequence libraries. A total of 19 DEMs were identified between the two groups, of which nine were upregulated and 10 were downregulated. Furthermore, the DEMs were predicted to target 572 genes. 3. Certain DEMs (such as miR-204, miR-133b, and miR-12 229-3p) and their target genes may play an important role in muscle melanogenesis of chickens. These findings provide a foundation for clarifying the miRNA regulatory mechanisms involved in muscle pigmentation in avian species.

Analysis of Expression and Single Nucleotide Polymorphisms of INHA Gene Associated with Reproductive Traits in Chickens

Inhibin α (INHA) is a candidate gene controlling ovulation in poultry. As the functional center of inhibin, INHA is a molecular marker associated with egg-laying performance. The objective of the current study was to analyze the expression differences of INHA in reproductive system and single nucleotide polymorphisms (SNPs) associations with reproductive traits in chickens. A total of 260 LuHua chickens (barred-feather chicken) were adopted. Twelve SNPs were detected in INHA gene. Among the exonic SNPs, three (g. 22177991A>G, g. 22178249G>C, and g. 22178414G>A) were missense mutations, resulting in the amino acid substitutions Val→Ala, Ala→Gly, and Ala→Gly, respectively. Four SNPs in the 3＇ untranslated region of INHA were predicted to either disturb or create microRNA-target interactions. Five SNPs (g. 22176870T>C, g. 22177100T>C, g. 22177149T>C, g. 22177991A>G, and g. 22178975G>A) were significantly associated with the number of eggs at 300 d of age (EN) (P < 0.05). Birds carrying GA genotype exhibited more EN than those with AA genotype (P < 0.01). In addition, quantitative real-time PCR revealed that INHA is mainly expressed in follicles on d 300 in chickens. Firstly, INHA expression increased and then decreased. The highest INHA mRNA abundance was found in the fifth largest preovulatory follicle (F5) (P < 0.01). In the prehierarchical follicles, INHA mRNA expression increased dramatically in small yellow follicles (SYF) (P < 0.01). Western blotting analysis showed that the INHA protein expression profile in the follicle was similar to its mRNA counterpart with greater expression in F5 and SYF follicles and lowest expression in F1 follicles (P < 0.05). These results suggest that INHA is a potential candidate gene improving reproductive traits in chickens.

Molecular-genetic bases of plumage coloring in chicken

The color of plumage in birds is an important feature, often determining descent to a particular species or breed. It serves as a key factor in the interaction of birds with each other due to their well-developed visual perception of the surrounding world. In poultry including chickens, the color of the plumage can be treated as a genetic marker, useful for identifying breeds, populations and breeding groups with their specific traits. The origin of diverse color plumage is the result of two interrelated physical processes, chemical and optical, due to which pigment and structural colors in the color are formed. The pigment melanin, which is presented in two forms, eumelanin and pheomelanin, is widely spread in birds. The basis for the formation of melanin is the aromatic amino acid tyrosine. The process of melano-genesis involves many loci, part of the complex expression of plumage color genes. In birds, the solid black color locus encodes the melanocortin 1 receptor (MC1R), mutations in which lead to a change in receptor activation and form different variants of the E locus. Using the GWAS analysis, possible genes affecting the formation of color in chickens were detected. The biosynthesis and types of melanin are affected by the activity of the enzyme tyrosine, and mutations in the tyrosinase gene (TYR) cause albinism in different species. The formation mechanism of brown, silver, gold, lavender and a number of other shades is determined by the influence on the work of the MC1R genes and TYR specific modifier genes. Thus, locus I currently associated with the PMEL17 gene inhibits the expression of eumelanin, and the MLPH gene affects tyrosinase function. Research on the mechanisms of formation of the secondary coloring of plumage in chickens is being actively conducted nowadays. The formation of a marble feather pattern is associated with the mutation of the endothelin B2 receptor (EDNRB2), in the coding part of the gene of which a polymorphism is found associated with the mo locus. The molecular base that causes the feather banding (locus B and autosomal recessive banding) is identified. Today, only some genes that determine the color of the plumage of chickens are studied and described. Different genes can produce similar plumage patterns, and different phenotypes can be determined by the polymorphism of a single gene. Using molecular methods, you can more accurately identify these differences. This overview shows the nature of melanin coloration in birds using the example of chickens of various breeds and also attempts to systematize knowledge about the molecular-genetic mechanisms of the appearance of various types of coloration.

Five alternative splicing variants of the TYR gene and their different roles in melanogenesis in the Muchuan black-boned chicken

1. The TYR gene encodes tyrosinase, a multifunctional enzyme that is essential for melanin biosynthesis in melanocytes. This experiment involved the cloning and characterisation of the TYR gene in chicken. Five alternative splice variants were identified in the black feather bulb and designated as TYR-AS1, TYR-AS2, TYR-AS3, TYR-AS4 and TYR-AS5. 2. Among the 11 chicken tissues examined, the feather bulb, comb and skin showed higher levels of all TYR variants. All TYR variants were expressed at significantly different levels in black and white feather bulbs (P < 0.05) and may be involved in melanin formation in plumage. Only TYR-AS1, which plays an important role in muscle melanogenesis, was significantly differentially expressed between black and white muscle (P < 0.01). All TYR variants were expressed at significantly different levels in black and white skin (P < 0.01). 3. The mRNA expression levels of the 5 variants were closely associated with skin melanogenesis in the chicken. These findings provide new clues to the molecular mechanism of melanin formation in the Muchuan black-boned chicken.