Background China has the richest local chicken breeding resources in the world and is the world’s second largest producer of meat-type chickens. Development of a moderate-density SNP array for genetic analysis of chickens and breeding of meat-type chickens taking utility of those resources is urgently needed for conventional farms, breeding industry, and research areas. Results Eight representative local breeds or commercial broiler lines with 3 pools of 48 individuals within each breed/line were sequenced and supplied the major SNPs resource. There were 7.09 million - 9.41 million SNPs detected in each breed/line. After filtering using multiple criteria such as preferred incorporation of trait-related SNPs and uniformity of distribution across the genome, 52.18 K SNPs were selected in the final array. It consists of: (i) 19.22 K SNPs from the genomes of yellow-feathered, cyan-shank partridge and white-feathered chickens; (ii) 5.98 K SNPs related to economic traits from the Illumina 60 K SNP Bead Chip, which were found as significant associated SNPs with 15 traits in a Beijing-You crossed Cobb F2 resource population by genome-wide association study analysis; (iii) 7.63 K SNPs from 861 candidate genes of economic traits; (iv) the 0.94 K SNPs related to residual feed intake; and (v) 18.41 K from chicken SNPdb. The polymorphisms of 9 extra local breeds and 3 commercial lines were examined with this array, and 40 K - 47 K SNPs were polymorphic (with minor allele frequency > 0.05) in those breeds. The MDS result showed that those breeds can be clearly distinguished by this newly developed genotyping array. Conclusions We successfully developed a 55K genotyping array by using SNPs segregated from typical local breeds and commercial lines. Compared to the existing Affy 600 K and Illumina 60 K arrays, there were 21,41 K new SNPs included on our Affy 55K array. The results of the 55K genotyping data can therefore be imputed to high-density SNPs genotyping data. The array offers a wide range of potential applications such as genomic selection breeding, GWAS of interested traits, and investigation of diversity of different chicken breeds. Electronic supplementary material The online version of this article (10.1186/s12864-019-5736-8) contains supplementary material, which is available to authorized users.

The eukaryotic cytoplasm contains a variety of ribonucleoprotein (RNP) granules in addition to the better-understood membrane-bound organelles. These granules form in response to specific stress conditions and contain a number of signaling molecules important for the control of cell growth and survival. However, relatively little is known about the mechanisms responsible for, and the ultimate consequences of, this protein localization. Here, we show that the Hrr25/CK1d protein kinase is recruited to cytoplasmic processing bodies (P-bodies) in an evolutionarily conserved manner. This recruitment requires Hrr25 kinase activity and the Dcp2 decapping enzyme, a core constituent of these RNP granules. Interestingly, the data indicate that this localization sequesters active Hrr25 away from the remainder of the cytoplasm and thereby shields this enzyme from the degradation machinery during these periods of stress. Altogether, this work illustrates how the presence within an RNP granule can alter the ultimate fate of the localized protein.KEYWORDS ribonucleoprotein granules; processing bodies; protein kinase; protein stability; Dcp2 decapping enzyme; casein kinase 1 T HE eukaryotic cell is subdivided into distinct functional areas by the presence of a variety of organelles. The best understood of these are the membrane-bound structures, like the nucleus, endoplasmic reticulum, and mitochondria. These traditional compartments are relatively stable and essential for the proper compartmentalization of the different reactions occurring in the cytoplasm. However, the cell also contains a collection of nonmembraneous organelles that are more dynamic in nature and form in response to particular cellular and environmental stimuli. Perhaps the two best characterized of these are the centrosome and nucleolus, which act as a microtubule-organizing center and a subnuclear site of ribosome assembly, respectively (Greenan et al. 2010;Brangwynne 2011;Brangwynne et al. 2011). This latter class also includes a number of recently identified cytoplasmic ribonucleoprotein (RNP) granules like the processing body (P-body) and stress granule (Anderson and Kedersha 2009;Balagopal and Parker 2009;Thomas et al. 2011). These cytoplasmic structures have been conserved through evolution and have been linked to a variety of human diseases, including certain neurodegenerative disorders, cancers, and autoimmune conditions (Li et al. 2013;Anderson et al. 2015). Despite this importance to human health, relatively little is known about the manner in which these RNP granules influence biological processes in the cell.These cytoplasmic RNP granules typically assemble in response to environmental stress or particular developmental cues (Thomas et al. 2011). Granule formation occurs as a consequence of the regulated coalescence of specific sets of proteins and translationally repressed mRNAs at discrete sites in the cytoplasm (Anderson and Kedersha 2009;Balagopal and Parker 2009). The presence of these core proteins often depends upon specific RNA-...

Simple Summary: Intramuscular fat is an important factor affecting meat quality and consumer acceptance. Appropriate increases in the intramuscular fat content contribute to the improvement of meat quality, and genetic selection is an effective method to increase the intramuscular fat content in chickens. In this study, chicken lines divergently selected for their intramuscular fat content were used to investigate the mechanisms behind differential intramuscular fat deposition. These results found in this study may contribute to the improvement of meat quality in chickens.Abstract: Intramuscular fat (IMF)-an important factor affecting meat quality-can be appropriately increased by genetic selection. Chicken lines divergently selected for IMF content were used in this study to investigate the mechanisms behind differential IMF deposition. Sixty 15th generation chickens were genotyped using the IASCHICK 55K single nucleotide polymorphism (SNP) chip. After quality control, 59 chickens and 36,893 SNPs were available for subsequent analysis. Population structure assessment indicated that the lines were genetically differentiated. Based on the top 1% paired fixation index values, three pathways were significantly (p < 0.05) enriched, and nine genes were considered candidate genes for differential IMF deposition. Differences between the lines in the expressions of representative genes involved in the above pathways were detected in 16th generation chickens. This study suggests that genetic selection for increased IMF in the pectoralis major muscle may enhance fatty acid synthesis, transport, and esterification, and reduce triglyceride hydrolysis. The peroxisome proliferator-activated receptor (PPAR) signaling pathway, glycerolipid metabolism, and fatty acid degradation pathway may have contributed to the differences in IMF deposition between the lines. These results contribute to the understanding of the genetic mechanisms behind IMF deposition, and the improvement of chicken meat quality.

Fat traits are important in the chicken industry where there is a desire for high intramuscular fat (IMF) and low abdominal fat. However, there is limited knowledge on the relationship between the dynamic status of gene expression and the body fat deposition in chicken. Transcriptome data were obtained from breast muscle and abdominal fat of female chickens from nine developmental stages (from embryonic day 12 to hatched day 180). In total, 8,545 genes in breast muscle and 6,824 genes in abdominal fat were identified as developmentally dynamic genes. Weighted correlation network analysis was used to identify gene modules and the hub genes. Twenty-one hub genes were identified, e.g., ENSGALG00000041996, which represents a candidate for high IMF, and CREB3L1, which relates to low abdominal fat weight. The transcript factor L3MBTL1 and the transcript factor cofactors TNIP1, HAT1, and BEND6 related to both high breast muscle IMF and low abdominal fat weight. Our results provide a resource of developmental transcriptome profiles in chicken breast muscle and abdominal fat. The candidate genes can be used in the selection for increased IMF content and/or a decrease in abdominal fat weight which would contribute to the improvement of these traits.

Intramuscular fat (IMF) content contributes to meat flavor and improves meat quality. Excessive abdominal fat, however, leads to a waste of feed resources. Here, an independent up-selection for IMF was used as a control (Line C), and a balanced selection program, with up-selection for IMF and down-selection AFP (Line B), was studied in JingXing yellow chickens. The mean of IMF and AFP within a family was the phenotypic value upon which selection was based. The selective pressures of IMF in line B and line C were the same in each generation. At G5, the IMF was significantly higher (P < 0.05) than that at G0 in both lines. For AFP, Line C was significantly higher at G5 (P < 0.05) than at G0, but the difference in Line B was not significant (P > 0.05). IMF increased by 11.4% and AFP decreased by 1.5% in Line B compared with the G0 generation. In contrast, the IMF increased by 17.6%, but was accompanied by an 18.7% increase in AFP, in control Line C. Of 10 other traits measured, body weight at 56 d age (BW56) and the percentages of eviscerated weight (EWP) showed a significant difference between the 2 lines (P < 0.05). The heritabilities for IMF and AFP, estimated by the DMU package, were 0.16 and 0.32, respectively. A moderate positive correlation existed between IMF and AFP (0.35). A balanced selection program for increasing IMF while controlling AFP (Line B) is shown here to be effective in practical chicken breeding.

BackgroundSkeletal muscle development is closely linked to meat production and its quality. This study is the first to quantify the proteomes and metabolomes of breast muscle in two distinct chicken breeds at embryonic day 12 (ED 12), ED 17, post-hatch D 1 and D 14 using mass spectrometry-based approaches.ResultsResults found that intramuscular fat (IMF) accumulation increased from ED 17 to D 1 and that was exactly the opposite of when most obvious growth of muscle occurred (ED 12 - ED 17 and D 1 - D 14). For slow-growing Beijing-You chickens, Ingenuity Pathway Analysis of 77–99 differential abundance (DA) proteins and 63–72 metabolites, indicated significant enrichment of molecules and pathways related to protein processing and PPAR signaling. For fast-growing Cobb chickens, analysis of 68–95 DA proteins and 56–59 metabolites demonstrated that molecules and pathways related to ATP production were significantly enriched after ED12. For IMF, several rate-limiting enzymes for beta-oxidation of fatty acid (ACADL, ACAD9, HADHA and HADHB) were identified as candidate biomarkers for IMF deposition in both breeds.ConclusionsThis study found that ED 17 - D 1 was the earliest period for IMF accumulation. Pathways related to protein processing and PPAR signaling were enriched to support high capacity of embryonic IMF accumulation in Beijing-You. Pathways related to ATP production were enriched to support the fast muscle growth in Cobb. The beta-oxidation of fatty acid is identified as the key pathway regulating chicken IMF deposition at early stages.Electronic supplementary materialThe online version of this article (10.1186/s12864-017-4150-3) contains supplementary material, which is available to authorized users.

P-bodies are liquid droplet-like compartments that lack a limiting membrane and are present in many eukaryotic cells. These structures contain specific sets of proteins and mRNAs at concentrations higher than that in the surrounding environment. Although highly conserved, the normal physiological roles of these ribonucleoprotein (RNP) granules remain poorly defined. Here, we report that P-bodies are required for the efficient completion of meiosis in the budding yeast P-bodies were found to be present during all phases of the meiotic program and to provide protection for the Hrr25/CK1 protein kinase, a key regulator of this developmental process. A failure to associate with these RNP granules resulted in diminished levels of Hrr25 and an ensuing inability to complete meiosis. This work therefore identifies a novel function for these RNP granules and indicates how protein recruitment to these structures can have a significant impact on eukaryotic cell biology.

Background The development of skeletal muscle is closely related to the efficiency of meat production and meat quality. Chicken skeletal muscle development depends on myogenesis and adipogenesis and occurs in two phases—hyperplasia and hypertrophy. However, cell profiles corresponding to the two-phase muscle development have yet to be determined. Single-cell RNA-sequencing (scRNA-seq) can elucidate the cell subpopulations in tissue and capture the gene expression of individual cells, which can provide new insights into the myogenesis and intramuscular adipogenesis. Results Ten cell clusters at the post-hatching developmental stage at Day 5 and seven cell clusters at the late developmental stage at Day 100 were identified in chicken breast muscles by scRNA-seq. Five myocyte-related clusters and two adipocyte clusters were identified at Day 5, and one myocyte cluster and one adipocyte cluster were identified at Day 100. The pattern of cell clustering varied between the two stages. The cell clusters showed clear boundaries at the terminal differentiation stage at Day 100; by contrast, cell differentiation was not complete at Day 5. APOA1 and COL1A1 were selected from up-regulated genes in the adipocyte cluster and found to be co-expressed with the ADIPOQ adipocyte marker gene in breast muscles by RNA in situ hybridization. Conclusions This study is the first to describe the heterogeneity of chicken skeletal muscle at two developmental stages. The genes APOA1 and COL1A1 were identified as biomarkers for chicken intramuscular fat cells.