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The economic losses incurred due to reduced muscle pigmentation highlight the crucial role of melanin-based coloration in the meat of black-bone chickens. Melanogenesis in the breast muscle of black-bone chickens is currently poorly understood in terms of molecular mechanisms. This study employed whole-transcriptome sequencing to analyze black and white breast muscle samples from black-bone chickens, leading to the identification of 367 differentially expressed (DE) mRNAs, 48 DElncRNAs, 104 DEcircRNAs, and 112 DEmiRNAs involved in melanin deposition. Based on these findings, a competitive endogenous RNA (ceRNA) network was developed to better understand the complex mechanisms of melanin deposition. Furthermore, our analysis revealed key DEmRNAs (TYR, DCT, EDNRB, MLPH and OCA2) regulated by DEmiRNAs (gga-miR-140-5p, gga-miR-1682, gga-miR-3529, gga-miR-499-3p, novel-m0012-3p, gga-miR-200b-5p, gga-miR-203a, gga-miR-6651-5p, gga-miR-7455-3p, gga-miR-31-5p, miR-140-x, miR-455-x, novel-m0065-3p, gga-miR-29b-1-5p, miR-455-y, novel-m0085-3p, and gga-miR-196-1-3p). These DEmiRNAs competitively interacted with DElncRNAs including MSTRG.2609.2, MSTRG.4185.1, LOC112530666, LOC112533366, LOC771030, LOC107054724, LOC121107411, LOC100859072, LOC101750037, LOC121108550, LOC121109224, LOC121110876, and LOC101749016, as well as DEcircRNAs, such as novel_circ_000158, novel_circ_000623, novel_001518, and novel_circ_003596. The findings from this study provide insight into the mechanisms that regulate lncRNA, circRNA, miRNA, and mRNA expression in chicken melanin deposition., (Copyright © 2024 The Authors. Published by Elsevier Inc. All rights reserved.)

The "Yufen 1" H line chicken (YF) has excellent characteristics including early sexual maturity and high egg production, and the conservation of its genetic diversity is the core of the breeding activity. To overcome misrepresented breeds and protect the integrity of the germplasm genetic resources, it is important to develop accurate and convenient methods to identify YF. In this study, whole genome resequencing was performed on the YF population, and bioinformatics analysis was conducted by combining the data from different breeds. Linkage disequilibrium (LD) analysis revealed that YF had the slowest LD-decay rate, suggesting strong natural and artificial selection in its history. Through selective sweep analysis, 1,126 selected regions in YF were identified, which contained 163,661 single nucleotide polymorphisms (SNPs). In particular, 5 specific SNPs (SNP1: Chr2:45509616, SNP2: Chr2:45510792, SNP3: Chr9:13788193, SNP4: Chr9:13795646, SNP5: Chr9:13798154) were found exclusively in the YF population. Subsequently, PCR amplification and Sanger sequencing confirmed the presence of these 5 SNPs in YF. Finally, 4 SNPs (SNP1, SNP2, SNP4, SNP5) were screened and verified using the Kompetitive Allele Specific PCR (KASP) typing technique. These SNPs can be used as specific molecular identity cards (IDs) for YF authentication. The present study is of great significance to ensure sustainable conservation and promotion of YF germplasm resources., (Copyright © 2023 The Authors. Published by Elsevier Inc. All rights reserved.)

The reproductive performance of breeder roosters has significant economic importance in the poultry industry. Breeder roosters have severely reduced semen quality with age and will be at risk of culling in the following years. In order to extend the use of breeder roosters, we drew on the induced molting model of hens and selected 35 Houdan roosters aged 50 wk for induced molting. By comparing the body weight, testicular weight, semen quality, and reproductive performance before and after induced molting, we found that induced molting could restore the body weight and testicular weight to the levels before molting (P > 0.05). At the same time, it significantly improved sperm motility (P < 0.05) and also improved reproductive performance such as fertilization rate and hatching rate. To further reveal the mechanism underlying the effects of induced molting on semen quality and reproductive performance in aged Houdan roosters, we collected testes from 3 periods: 1 d before fasting (F0), 15 d after fasting (F15), and 32 d after recovery feeding (R32) for transcriptome sequencing analysis. A total of 5,671 genes were detected in F0, F15, and R32, and trend analysis of the 5,671 differential genes showed 2 significant trends (profile 5 and profile 2). KEGG enrichment analysis of the genes in the 2 profiles, revealed significantly enriched pathway regulation of actin cytoskeleton. In the regulation of actin cytoskeleton pathway, we found a protein kinase gene (SRC) and a senescence gene (ROCK2). SRC was highly expressed at F15, leading to the phosphorylation of key substrates, which in turn disrupted the Sertoli cell spermatid connection and the spermiogenesis process, resulting in no mature spermatozoa produced from F15, SRC expression was inhibited at R32, the expression level was reduced, and mature spermatozoa reappeared. The senescence gene ROCK2 was highly expressed at F15 compared to F0 and R32, which may have been responsible for inducing senescence atrophy in the testes., (Copyright © 2023 The Authors. Published by Elsevier Inc. All rights reserved.)

Induced molting (IM) can restore the laying rate of aged laying hens to the peak level of laying and rejuvenate ovarian function for the second laying cycle. To explore the mechanism of ovarian function remodeling during IM in laying hens, in this study, ninety 71-wk-old laying lady hens with 60% laying rate and uniform weight were selected for molting induction by fasting. Samples (serum and fresh ovarian tissue) were collected on the day before fasting (F0), the 3rd and 16th days of fasting (F3, F16), and the 6th, 15th, 32nd days of refeeding (R6, R15, and R32), and the number of follicles in each period was counted. Then, the reproductive hormone levels in serum and antioxidant levels in ovarian tissues were detected at different stages, and the gene expression of the KIT-PI3K-PTEN-AKT pathway and GDF-9 in ovaries was measured by qRT-PCR. The results showed that the laying rate increased rapidly after refeeding and returned to the prefasting level by R32. At F16 and R6, the number of mature follicles significantly decreased; the number of primary and secondary follicles significantly increased; the contents of follicle stimulating hormone (FSH), luteinizing hormone (LH), estradiol (E2), and progesterone (P4) in serum decreased; the relative expression of KIT, PI3K, AKT, and GDF-9 significantly increased; and that of PTEN significantly decreased. At R15 and R32, except for GDF-9, which maintained a high expression state, other indicators showed opposing trends to those observed at F16 and R6. In conclusion, IM activated the KIT-PI3K-PTEN-AKT signaling pathway and promoted the activation of primordial follicles during the fasting period and early resumption of feeding; gonadotropin secretion increased gradually, which promoted the rapid development of primary and secondary follicles to mature follicles and ovulation. This study explained the mechanism of ovarian function remodeling in the process of IM and provided a theoretical basis for improving the ovarian function of laying hens and optimizing the IM program., (Copyright © 2023 The Authors. Published by Elsevier Inc. All rights reserved.)

Several recent studies investigated the role of the miR-29 family in muscle development. However, only a few studies focused on chicken skeletal muscle. In the present study, cell cycle, 5-ethynyl-2'-deoxyuridine (EdU), cell counting kit-8 (CCK-8), and other assays indicated that miR-29b-1-5p can inhibit the proliferation of chicken primary myoblasts (CPMs); the western blot assay and immunofluorescence detection of MYHC demonstrated that miR-29b-1-5p can promote the differentiation of myoblasts. The functional enrichment analysis revealed that the target genes of miR-29b-1-5p may be involved in muscle tissue development, muscle organ development, and striated muscle tissue development, which are biological processes related to muscle development. The correlation analysis showed that these 6 genes, that is, ankyrin repeat domain 9 (ANKRD9), lactate dehydrogenase A (LDHA), transcription factor 12 (TCF12), FAT atypical cadherin 1 (FAT1), lin-9 homolog (LIN9), and integrin beta 3 binding protein (ITGB3BP), can be used as effective candidate target genes of miR-29b-1-5p. Moreover, miR-29b-1-5p inhibits the expression of ANKRD9 by directly binding the 3'UTR of ANKRD9. Overall, these data indicate that miR-29b-1-5p inhibits the proliferation of primary chicken myoblasts, stimulates their differentiation, and is involved in the process of muscle development and that its effective target gene is ANKRD9. This study identified the molecular mechanism of miR-29b-1-5p in chicken muscle development., Competing Interests: DISCLOSURES The author declares that there is no conflict of interest that could be perceived as prejudicing the impartiality of the research reported., (Copyright © 2021 The Authors. Published by Elsevier Inc. All rights reserved.)

The large economic losses caused by leg disorders have raised concerns in the broiler industry. Several types of leg disorders in broilers have been identified, such as tibial dyschondroplasia (TD), femoral head necrosis (FHN), and valgus-varus deformity (VVD). In this study, phenotypic changes associated with VVD were examined using clinical diagnosis, anatomical examination, measured growth performance, bone traits, and serum indicators. The incidence of VVD among the chicken population at a commercial facility in Tangshan China was 1.75% (n = 52,000), distributed about 1:1 (n = 122), between females and males. A majority of chickens were characterized by a unilaterally abnormality, while appropriately 17.6% by bilateral abnormality. Approximately 97.9% of affected broilers were classified as the "valgus" type. Growth traits, including body weight, shank length, and shank girth, were significantly lower in chickens with VVD, while tibia and metatarsal bone indexes were about 1.3-fold higher in the affected birds than in the normal birds. Bone mineral density, bone breaking strength, and several serum indicators were significantly different between affected and normal broilers. Sparse and disarranged bony trabecular was observed in abnormal broilers by histological analysis. Generally, leg disorders are associated with compromised growth, bone quality, bone structure, and lipid metabolism. This study provides a reference for clinical diagnosis of VVD and lays a foundation for exploring its underlying mechanisms., (© 2019 Poultry Science Association Inc.)

Many studies have reported that cyclin-dependent kinase inhibitor 3 (CDKN3) is involved in the cell cycle. However, the function of CDKN3 has not been well elucidated in organisms. In this study, a multiallelic indel caused by a 19-bp fragment and a 2 × 19 bp fragment was shown for the first time to be inserted into the promoter of the CDKN3 gene in 1994 chickens from 9 different breeds. In addition, 6 genotypes (C5C5, C4C4, C3C3, C4C5, C3C4, and C3C5) were observed (C3C3, C4C4, C5C5 have 3 × 19 bp, 4 × 19 bp, and 5 × 19 bp, respectively). Among these genotypes, the C4C4 genotype was the most dominant genotype in 9 breeds. The results of χ2 analysis of CDKN3 gene in different breeds showed that there were significant differences in the distribution of genotypes among different cultivars (P < 0.01). In addition, association study with F2 chicken resource population which produced by Anka and Gushi chickens showed that the C3C4 genotypes had the greatest semi-evisceration weight (SEW, 1163.94 ± 46.84), evisceration weight (EW, 964.15 ± 41.16), head weight (HW, 45.55 ± 1.43), claw weight (CW, 63.42±2.86), wing weight (WW, 129.15±5.48), liver weight (LW, 29.96±1.27), carcass weight (cW, 1286.96±49.53), weight at 10 (1190.68±45.68) and 12 (1430.65±54.45) wk, followed by C3C3, C4C4, C5C5, C4C5, whereas C3C5 genotypes having the lowest SEW (989.21±47.71), EW (841.38±40.55), HW (41.03±1.46), CW (54.36±2.81), WW (116.31±5.39), LW (27.31±1.25), cW (1093.29±49.99), weight at 10 (1036.10±44.99) and 12 (1246.28±53.59) wk. Expression levels of CDKN3 in breast muscle of chickens with C4C4 (0.72±0.02), C3C3 (0.95±0.41), and C4C5 (0.74±0.13) genotypes were significantly lower than those with C5C5 (1.80±0.01) and C3C5 (2.14±0.17) genotypes (P < 0.05). In conclusion, we investigated the effect of a multiallelic indel in the CDKN3 gene on the economic traits of chickens, and this indel was significantly associated with growth and carcass traits in chickens. Collectively, our findings provide useful information about the repeat sequence indel in the promoter region of the CDKN3 gene as a potential molecular marker for chicken breeding., (© 2018 Poultry Science Association Inc.)

Chinese domestic chickens have been routinely subjected to artificial selection for the production of meats and eggs. Selection results in distinctive signatures in the genome that can reveal the genes underlying phenotypes of interest to breeders. In this study, we used the Chicken60K SNP chip to analyze DNA from Dwarf Brown-egg Layers (DB, n = 203) and Silky Fowls (SF, n = 181) and then examined the relative extended haplotype homozygosity (REHH) and fixation index (FST) to detect selection signatures. Since population structure analysis showed that SF was stratified into 2 subpopulations (SF1 and SF2), we removed the 20 SF1 chickens, and the remaining individuals (DB and SF2) were scanned for genome-wide selection signatures. A total of 939 selection signatures, including 446 candidate genes, were found to be potential selection targets using the FST test. REHH analysis identified 93 and 128 core regions, including 112 and 181 genes, in DB and SF2, respectively. Among the candidate genes, domestication-related genes such as NELL1 were found. After comparing the candidate genes with the Animal QTL database, we identified additional genes possibly associated with growth, reproduction, egg laying, and immune response, including GRHL3, CDK1, AKT1, and KMD3A. Functional enrichment analysis suggests that genes associated with muscle development have undergone positive selection. Our findings provide a genome-wide selection signature draft for DB and SF, and establish a resource that can be exploited in chicken breeding programs to manipulate the genes that underlie desired phenotypes., (© 2017 Poultry Science Association Inc.)

The reproductive performance of chicken breeders has significant economic importance in the poultry industry, and sperm motility is an indicator of reproductive performance. This study performed RNA-seq of the testes of Gushi chicken roosters with high and low sperm motility and identified differentially expressed RNAs involved in sperm motility. RNA-seq analysis showed that 73 and 67 differentially expressed mRNAs were up- and downregulated, and 47 and 56 differentially expressed long non-coding RNAs were up- and downregulated, respectively. The genes related to sperm motility and spermatogenesis included KIFC1, KCNK2, and REC8. Functional enrichment analysis revealed that the pathways related to sperm motility included oxidative phosphorylation and glycine, serine, and threonine metabolism. In addition, the MSTRG.15920.1- REC8 -MSTRG.11860.2- VWC2 pathway may regulate sperm motility. This study helped elucidate the molecular genetic mechanism of sperm motility in chicken. [ABSTRACT FROM AUTHOR]

The conservation of genetic resources is becoming increasingly important for the sustainable development of the poultry industry. In the present study, we systematically analyzed the population structure, conservation priority, runs of homozygosity (ROH) of chicken breeds globally, and proposed rational conservation strategies. We used a 600K Affymetrix Axiom HD genotyping SNP array dataset of 2,429 chickens from 134 populations. The chickens were divided into 5 groups based on their country of origin and sampling location: Asian chickens (AS-LOC), African chickens (AF), European local chickens (EU-LOC), Asian breeds sampled in Germany (AS-DE), and European breeds sampled in Germany (EU-DE). The results indicated that the population structure was consistent with the actual geographical distribution of the populations. AS-LOC had the highest positive contribution to the total gene (HT , 1.00%,) and allelic diversity (AT , 0.0014%), the lowest inbreeding degree and the fastest linkage disequilibrium (LD) decay rate; the lowest contribution are derived by European ex situ chicken breeds (EU-DE:HT = −0.072%, AT = −0.0014%), which showed the highest inbreeding and slowest LD decay. Breeds farmed in ex situ (AS-DE, EU-DE) conditions exhibited reduced genetic diversity and increased inbreeding due to small population size. Given limited funds, it is a better choice for government to conserve the breeds with the highest contribution to genetic diversity in each group. Therefore, we evaluated the contribution of each breed to genetic and allelic diversity in 5 groups. Among each group, KUR(AF), BANG(AS-LOC), ALxx(EU-LOC), BHwsch(AS-DE), and ARw(EU-DE) had the highest contribution to gene diversity in the order of the above grouping. Similarly, according to the allelic diversity standard (in the same order), ZIMxx, PIxx, ALxx, SHsch, and ARsch had the highest contribution. After analyzing ROH, we found a total of 144,708 fragments and 27 islands. The gene and genome regions identified by the ROH islands and QTLs indicate that chicken breeds have potential for adaptation to different production systems. Based on these findings, it is recommended to prioritize the conservation of breeds with the highest genetic diversity in each group, while paying more attention to the conservation of Asian and African breeds. Furthermore, providing a valuable reference for the conservation and utilization of chicken. [ABSTRACT FROM AUTHOR]