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Intramuscular fat (IMF) plays an important role in the tenderness, water-holding capacity, and flavor of chicken meat, which directly affect meat quality. In recent years, regulatory mechanisms underlying IMF deposition and the development of effective molecular markers have been hot topics in poultry genetic breeding. Therefore, this review focuses on the current understanding of regulatory mechanisms underlying IMF deposition in chickens, which were identified by multiple genomic approaches, including genome-wide association studies, whole transcriptome sequencing, proteome sequencing, single-cell RNA sequencing (scRNA-seq), high-throughput chromosome conformation capture (HiC), DNA methylation sequencing, and m6A methylation sequencing. This review comprehensively and systematically describes genetic and epigenetic factors associated with IMF deposition, which provides a fundamental resource for biomarkers of IMF deposition and provides promising applications for genetic improvement of meat quality in chicken. [ABSTRACT FROM AUTHOR]

Background: Serum biochemical indicators are often regarded as direct reflections of animal metabolism and health. The molecular mechanisms underlying serum biochemical indicators metabolism of chicken (Gallus Gallus) have not been elucidated. Herein, we performed a genome-wide association study (GWAS) to identify the variation associated with serum biochemical indicators. The aim of this research was to broaden the understanding of the serum biochemical indicators in chickens. Results: A GWAS of serum biochemical indicators was carried out on 734 samples from an F2 Gushi× Anka chicken population. All chickens were genotyped by sequencing, 734 chickens and 321,314 variants were obtained after quality control. Based on these variants, a total of 236 single-nucleotide polymorphisms (SNPs) on 9 chicken chromosomes (GGAs) were identified to be significantly (-log10(P) > 5.72) associated with eight of seventeen serum biochemical indicators. Ten novel quantitative trait locis (QTLs) were identified for the 8 serum biochemical indicator traits of the F2 population. Literature mining revealed that the ALPL, BCHE, GGT2/GGT5 genes at loci GGA24, GGA9 and GGA15 might affect the alkaline phosphatase (AKP), cholinesterase (CHE) and γ-glutamyl transpeptidase (GGT) traits, respectively. Conclusion: The findings of the present study may contribute to a better understanding of the molecular mechanisms of chicken serum biochemical indicator regulation and provide a theoretical basis for chicken breeding programs. [ABSTRACT FROM AUTHOR]

Domestication and breeding have reshaped the genomic architecture of chicken, but the retention and loss of genomic elements during these evolutionary processes remain unclear. We present the first chicken pan-genome constructed using 664 individuals, which identified an additional approximately 66.5-Mb sequences that are absent from the reference genome (GRCg6a). The constructed pan-genome encoded 20,491 predicated protein-coding genes, of which higher expression levels are observed in conserved genes relative to dispensable genes. Presence/absence variation (PAV) analyses demonstrated that gene PAV in chicken was shaped by selection, genetic drift, and hybridization. PAV-based genome-wide association studies identified numerous candidate mutations related to growth, carcass composition, meat quality, or physiological traits. Among them, a deletion in the promoter region of IGF2BP1 affecting chicken body size is reported, which is supported by functional studies and extra samples. This is the first time to report the causal variant of chicken body size quantitative trait locus located at chromosome 27 which was repeatedly reported. Therefore, the chicken pan-genome is a useful resource for biological discovery and breeding. It improves our understanding of chicken genome diversity and provides materials to unveil the evolution history of chicken domestication. [ABSTRACT FROM AUTHOR]

Liver is the main organ of lipid metabolism in chicken, especially for laying hens. To explore the molecular mechanism of lipid metabolism in chicken, five novel genes discovered in chicken liver tissue were systematically studied. Bioinformatic analysis was used to analyze the gene characteristics. The expression patterns and regulatory molecular mechanism of the five genes were examined. Our results showed that all five novel genes contain a common NADP-binding site that belongs to the NADB-Rossmann superfamily, and the genes were designated NADB-LER 1-5. Phylogenetic tree of the NADB-LERs gene family in different species suggested these five genes originated from the same ancestor. Tissue distributions showed that NADB-LER1-4 genes were highly expressed in lipid metabolism organs, including liver, kidney and duodenum, and that the NADB-LER5 gene was highly expressed in liver and kidney. The spatiotemporal expression indicated that the expression levels of NADB-LER1-5 genes in liver tissue were significantly greater in sexually mature hens than that of immature pullets (P -value ≤ 0.05). The expression levels of NADB-LER1-5 were significantly induced by 17β-estradiol in primary cultured chicken embryo hepatocytes (P -value ≤ 0.05), and 17β-estradiol regulated the expression of NADB-LER1-5 mediated by ERα. Individual assays verified that under induction of 17β-estradiol, the five novel genes were significantly upregulated, with subsequent alteration in serum TG, TC, and VLDLs in 10-week-old pullets. This study proved NADB-LERs family mainly expressed in liver, kidney, and duodenum tissues. 17β-estradiol induces the expression of NADB-LER1-5 genes predominantly mediated via ERα. They likely involved in lipid metabolism in the liver of chicken. [ABSTRACT FROM AUTHOR]

The Xichuan black-bone chicken, which is a rare local chicken species in China, is an important genetic resource of black-bone chickens. Tyrosine can affect melanin production, but the molecular mechanism underlying tyrosine-induced melanin deposition in Xichuan black-bone chickens is poorly understood. Here, the blackness degree and melanin content of the breast muscle of Xichuan black-bone chickens fed a basic diet with five levels of added tyrosine (i.e., 0.2, 0.4, 0.6, 0.8, and 1.0%; these groups were denoted test groups I-V, respectively) were assessed, and the results showed that 0.8% tyrosine was the optimal level of added tyrosine. Moreover, the effects of tyrosine supplementation on the proliferation and tyrosinase content of melanocytes in Xichuan black-bone chickens were evaluated. The results revealed a dose-dependent relationship between tyrosine supplementation and melanocyte proliferation. In addition, 417 differentially expressed genes (DEGs), including 160 upregulated genes and 257 downregulated genes, were identified in a comparative analysis of the transcriptome profiles constructed using the pooled total RNA from breast muscle tissues of the control group and test group IV, respectively (fold change ≥2.0, P < 0.05). These DEGs were mainly involved in melanogenesis, the calcium signaling pathway, the Wnt signaling pathway, the mTOR signaling pathway, and vascular smooth muscle contraction. The pathway analysis of the DEGs identified some key genes associated with pigmentation, such as DCT and EDNRB2. In summary, the melanin content of breast muscle could be markedly enhanced by adding an appropriate amount of tyrosine to the diet of Xichuan black-bone chickens, and the EDNRB2 -mediated molecular regulatory network could play a key role in the biological process of tyrosine-induced melanin deposition. These results have deepened the understanding of the molecular regulatory mechanism of melanin deposition in black-bone chickens and provide a basis for the regulation of nutrition and genetic breeding associated with melanin deposition in Xichuan black-bone chickens. [ABSTRACT FROM AUTHOR]

There is a lack of understanding surrounding the molecular mechanisms involved in the development of chicken skeletal muscle in the late postnatal stage, especially in the regulation of breast muscle development related genes, pathways, miRNAs and other factors. In this study, 12 cDNA libraries and 4 small RNA libraries were constructed from Gushi chicken breast muscle samples from 6, 14, 22, and 30 weeks. A total of 15,508 known transcripts, 25,718 novel transcripts, 388 known miRNAs and 31 novel miRNAs were identified by RNA-seq in breast muscle at the four developmental stages. Through correlation analysis of miRNA and mRNA expression profiles, it was found that 417, 370, 240, 1,418, 496, and 363 negatively correlated miRNA–mRNA pairs of W14 vs. W6 , W22 vs. W6 , W22 vs. W14 , W30 vs. W6 , W30 vs. W14 , and W30 vs. W22 comparisons, respectively. Based on the annotation analysis of these miRNA–mRNA pairs, we constructed the miRNA–mRNA interaction network related to biological processes, such as muscle cell differentiation, striated muscle tissue development and skeletal muscle cell differentiation. The interaction networks for signaling pathways related to five KEGG pathways (the focal adhesion, ECM-receptor interaction, FoxO signaling, cell cycle, and p53 signaling pathways) and PPI networks were also constructed. We found that ANKRD1 , EYA2 , JSC , AGT , MYBPC3 , MYH11 , ACTC1 , FHL2 , RCAN1 , FOS , EGR1 , and FOXO3 , PTEN , AKT1 , GADD45 , PLK1 , CCNB2 , CCNB3 and other genes were the key core nodes of these networks, most of which are targets of miRNAs. The FoxO signaling pathway was in the center of the five pathway-related networks. In the PPI network, there was a clear interaction among PLK1 and CDK1 , CCNB2 , CDK1 , and GADD45B , and CDC45 , ORC1 and MCM3 genes. These results increase the understanding for the molecular mechanisms of chicken breast muscle development, and also provide a basis for studying the interactions between genes and miRNAs, as well as the functions of the pathways involved in postnatal developmental regulation of chicken breast muscle. [ABSTRACT FROM AUTHOR]

The adiponectin receptor 2 (ADIPOR2) is a receptor for both globular and full-length adiponectin. In the current study, two genetic variations in ADIPOR2 gene were identified in an F2resource population of Gushi chicken and Anka broiler. Association analysis between the two SNPs and chicken performance traits were determined using the linear mixed model. The data revealed that the g.34490C > T mutation in intron 3 was significantly associated with liver weight and globulin, the g.35363T > C polymorphism in exon 5 was significantly associated with body weights at 6, 10, and 12 weeks of age. Both polymorphisms have no significant effects on serum glucose and fat-related traits. The g.34490C > T mutation might play an important role in regulating liver weight. The g.35363T > C polymorphism does contribute in a significant manner to growth traits at the medium and later development stage but it is uncertain whether it could be a molecular marker for liver disease. [ABSTRACT FROM AUTHOR]

An increasing number of studies have shown that quantitative trait loci (QTLs) at the end of chromosome 1 identified in different chicken breeds and populations exert significant effects on growth traits in chickens. Nevertheless, the causal genes underlying the QTL effect remain poorly understood. Using an updated gene database, a novel lncRNA (named LncFAM) was found at the end of chromosome 1 and located in a growth and digestion QTL. This study showed that the expression level of LncFAM in pancreas tissues with a high weight was significantly higher than that in pancreas tissues with a low weight, which indicates that the expression level of LncFAM was positively correlated with various growth phenotype indexes, such as growth speed and body weight. A polymorphism screening identified four polymorphisms with strong linkage disequilibrium in LncFAM : a 5-bp indel in the second exon, an A/G base mutation, and 7-bp and 97-bp indels in the second intron. A study of a 97-bp insertion in the second intron using an F2 chicken resource population produced by Anka and Gushi chickens showed that the mutant individuals with genotype II had the highest values for body weight (BW) at 0 days and 2, 4, 6, 8, 10 and 12 weeks, shank girth (SG) at 4, 8 and 12 weeks, chest width (CW) at 4, 8 and 12 weeks, body slant length (BSL) at 8 and 12 weeks, and pelvic width (PW) at 4, 8 and 12 weeks, followed by ID and DD genotypes. The amplification and typing of 2,716 chickens from ten different breeds, namely, the F2 chicken resource population, dual-type chickens, including Xichuan black-bone chickens, Lushi green-shell layers, Dongxiang green-shell layers, Changshun green-shell layers, and Gushi chickens, and commercial broilers, including Ross 308, AA, Cobb and Hubbard broilers, revealed that II was the dominant genotype. Interestingly, only genotype II existed among the tested populations of commercial broilers. Moreover, the expression level in the pancreas tissue of Ross 308 chickens was significantly higher than that in the pancreas tissue of Gushi chickens (P < 0.001), which might be related to the conversion rates among different chickens. The prediction and verification of the target gene of LncFAM showed that LncFAM might regulate the expression of its target gene FAM48A through cis-expression. Our results provide useful information on the mutation of LncFAM , which can be used as a potential molecular breeding marker. [ABSTRACT FROM AUTHOR]

The "KNDy neurons" located in the hypothalamic arcuate nucleus (ARC) of mammals are known to co-express kisspeptin, neurokinin B (NKB), and dynorphin (DYN), and have been identified as key mediators of the feedback regulation of steroid hormones on gonadotropin-releasing hormone (GnRH). However, in birds, the genes encoding kisspeptin and its receptor GPR54 are genomic lost, leaving unclear mechanisms for feedback regulation of GnRH by steroid hormones. Here, the genes tachykinin 3 ( TAC3 ) and prodynorphin ( PDYN ) encoding chicken NKB and DYN neuropeptides were successfully cloned. Temporal expression profiling indicated that TAC3, PDYN and their receptor genes (TACR3, OPRK1) were mainly expressed in the hypothalamus, with significantly higher expression at 30W than at 15W. Furthermore, overexpression or interference of TAC3 and PDYN can regulate the GnRH mRNA expression. In addition, in vivo and in vitro assays showed that estrogen (E2) could promote the mRNA expression of TAC3, PDYN , and GnRH , as well as the secretion of GnRH/LH. Mechanistically, E2 could dimerize the nuclear estrogen receptor 1 (ESR1) to regulate the expression of TAC3 and PDYN , which promoted the mRNA and protein expression of GnRH gene as well as the secretion of GnRH. In conclusion, these results revealed that E2 could regulate the GnRH expression through TAC3 and PDYN systems, providing novel insights for reproductive regulation in chickens. [ABSTRACT FROM AUTHOR]

Long noncoding RNAs (lncRNAs) have emergingly been implicated in mammalian lipid metabolism. However, their biological functions and regulatory mechanisms underlying adipogenesis remain largely elusive in chicken. Here, we systematically characterized the genome-wide full-length lncRNAs in the livers of pre- and peak-laying hens, and identified a novel intergenic lncRNA, lncHLEF , an RNA macromolecule with a calculated molecular weight of 433 kDa. lncHLEF was primarily distributed in cytoplasm of chicken hepatocyte and significantly up-regulated in livers of peak-laying hens. Functionally, lncHLEF could promote hepatocyte lipid droplet formation, triglycerides and total cholesterol contents. Mechanistically, lncHLEF could not only serve as a competitive endogenous RNA to modulate miR-2188-3p/GATA6 axis, but also encode three small functional polypeptides that directly interact with ACLY protein to enable its stabilization. Importantly, adeno-associated virus-mediated liver-specific lncHLEF overexpression resulted in increased hepatic lipid synthesis and intramuscular fat (IMF) deposition, but did not alter abdominal fat (AbF) deposition. Furthermore, hepatocyte lncHLEF could be delivered into intramuscular and abdominal preadipocytes via hepatocyte-secreted exosome to enhance intramuscular preadipocytes differentiation without altering abdominal preadipocytes differentiation. In conclusion, this study revealed that the lncHLEF could promote hepatic lipid synthesis through two independent regulatory mechanisms, and could enhance IMF deposition via hepatocyte-adipocyte communications mediated by exosome. • Nanopore sequencing identifies full-length lncRNAs involving hepatic adipogenesis. • LncRNA lncHLEF promotes hepatic adipogenesis in vitro and in vivo. • lncHLEF serves as a ceRNA and can be translated into three functional peptides. • Hepatocyte-derived exosome-laden lncHLEF enhances intramuscular fat deposition. [ABSTRACT FROM AUTHOR]

It has been reported that adiponectin (AdipoQ), an adipokine secreted by white adipose tissue, plays an important role in the control of animal reproduction in addition to its function in energy homeostasis by binding to its receptors AdipoR1/2. However, the molecular mechanisms of AdipoQ in the regulation of animal reproduction remain elusive. In this study, we investigated the effects of AdipoQ on hypothalamic reproductive hormone (GnRH) secretion and reproduction-related receptor gene (estrogen receptor [ ER ] and progesterone receptor [ PR ]) expression in hypothalamic neuronal cells (HNCs) of chickens by using real-time fluorescent quantitative PCR (RT-qPCR), enzyme-linked immunosorbent assay (ELISA), Western blot (WB) and cell counting kit-8 (CCK-8) assays and found that overexpression of AdipoQ could increase the expression levels of AdipoR1/2 and reproduction-related receptor genes (P < 0.05) while decreasing the expression level of GnRH. In contrast, interference with AdipoQ mRNA showed the opposite results in HNCs. Furthermore, we demonstrated that AdipoQ exerts its functions through the AMPK and PI3K signaling pathways. Finally, our in vitro experiments found that AdipoRon (a synthetic substitute for AdipoQ) treatment and AdipoR1/2 RNAi interference co-treatment resulted in no effect on GnRH secretion, suggesting that the inhibition of GnRH secretion by AdipoQ is mediated by the AdipoR1/2 signaling axis. In summary, we uncovered, for the first time, the molecular mechanism of AdipoQ in the regulation of reproductive hormone secretion in hypothalamic neurons in chickens. [ABSTRACT FROM AUTHOR]

Abstract Zinc finger proteins are a class of transcription factors with finger-like domains and have diverse uses in biological processes, including development, differentiation, and metabolism. In this study, we identified the absence of the 24 bp sequence in the third exon of the zinc finger protein 764-like (ZNF764L) gene that lead to the production of two new transcripts, ZNF764L-SV1 and ZNF764L-SV2 , and the sum of the expression levels of the two transcripts is approximately equal the total RNA expression level. Temporal and spatial expression showed that ZNF764L had higher expression during the embryonic stage. Moreover, the research study revealed a 22-bp indel mutation in the first exon region of ZNF764L gene. Statistically significant results (P < 0.05) were encountered for this indel for chicken growth and carcass traits, which include birth weight, chest breadth and body slanting length at 4 weeks of age and subcutaneous fat weight and others. Genetic parameter analysis showed that D is the predominant allele in the commercial chicken population. Gene expression for each genotype showed that birds carrying the II allele had a higher expression level than the other genotypes. These findings enrich the understanding of ZNF764L gene function and enhance reproduction in the chicken industry. Highlights • The absence of the third exon of the ZNF764L gene led to two new transcripts. • The ZNF764L have higher expression during embryonic stage. • A new 22-bp insertion variant sequence on the first exon of the ZNF764L gene contains a stop codon (TAG). [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Adiponectin is a key hormone secreted by fat tissues that has multiple biological functions, including regulating the energy balance and reproductive system by binding to its receptors AdipoR1 and AdipoR2. This study investigated the correlation between the levels of adiponectin and reproductive hormones in the hypothalamic-pituitary-ovarian (HPO) axis of laying hens at 4 different developmental stages (15, 20, 30, and 68 wk) and explored the effects of AdipoRon (an activator of adiponectin receptors) on the hypothalamic-pituitary-gonadal (HPG) axis and follicle and testicular Leydig cells in vitro and in vivo. The results demonstrated that the adiponectin level was significantly correlated with that of reproductive hormones in the HPO axis (e.g., GnRH, FSH, LH, and E2) in laying hens at 4 different ages. Moreover, AdipoRon could promote the expression of AdipoR1 and AdipoR2 and the secretion of reproductive hormones in the HPG axis, including GnRH, FSH, LH, P4, and T. AdipoRon could also upregulate the expression of genes related to follicular steroidogenesis (STAR, CYP19A1, CYP17A1, and CYP11A1), hepatic lipid synthesis (OVR, MTP), follicular lipid uptake (PPAR-g), and follicular angiogenesis (VEGFA1, VEGFA2, VEGFR1, ANGPT1, ANGPT2, TEK) in the oviposition period, and all of these findings were consistent with the results obtained from in vitro experiments after the transfection of small white follicles (SWFs) with AdipoRon. Furthermore, the results suggest that AdipoRon increases the diameter of testicular seminiferous tubules, the number of spermatogenic cells and sperm production in vivo and enhances the expression of AdipoR1, AdipoR2 and steroid hormones in vitro. Collectively, the findings suggest that AdipoRon could facilitate the expression and secretion of reproductive hormones in the HPG axis by activating its receptors and then improve the growth and development of follicles and testes in chickens. [ABSTRACT FROM AUTHOR]

Glycoprotein nonmetastatic melanoma protein B (GPNMB) is a vital secreted factor that promotes the occurrence of obesity in mammals. However, the effects of GPNMB on abdominal fat deposition is still unknown in chickens. In this study, we looked into the genetic and expression association of GPNMB gene with abdominal fat traits in chicken, and found that a genetic variation rs31126482 in GPNMB promoter was significantly associated with abdominal fat weight (AFW , P < 0.05) and abdominal fat percentage (AFP , P < 0.01). Express profile analysis of the GPNMB indicated that the gene was mainly expressed in abdominal fat tissue, and its expression level was strongly positively correlated with AFW (R2 = 0.6356, P = 4.10E−05) and AFP (R2 = 0.6450, P = 2.90E−05). We then investigated biological function of GPNMB on adipogenesis in chicken, and found that GPNMB could inhibit abdominal preadipocyte proliferation, but promote abdominal preadipocyte differentiation and lipid deposition. Furthermore, we explored regulatory mechanism of GPNMB gene in chicken, and detected one nonclassical estrogen regulatory element (AP1) and one peroxisome proliferator-activated receptor α (PPARα) responsive element in the 2 kb promoter region of GPNMB gene, and demonstrated that estrogen could up-regulate GPNMB mRNA expression in adipose tissue and primary abdominal preadipocytes, while PPARα could down-regulate GPNMB expression in primary preadipocytes. Taken together, this study brings new insights into understanding the function and transcriptional control of GPNMB gene, and provides genetic markers for breeding selection to improve abdominal fat traits in chicken. [ABSTRACT FROM AUTHOR]

Genetic variations in microRNAs (miRNAs) including primary miRNAs, precursor miRNAs and mature miRNAs can lead to phenotypic variation by altering the biogenesis of miRNAs and/or their binding to target mRNAs. Increasing functional studies suggest that polymorphisms occurring in miRNAs can lead to phenotypic variation in farm animal. Here, we identified a single nucleotide polymorphism (SNP) located in the precursor of chicken miRNA-1606 gene. The association study on body indexes, body weight at different growth stages, and carcass traits was performed in a Gushi–Anka F 2 population resource. The SNP was not only significantly associated with body weight at 10 and 12 weeks, respectively, but also with chicken shank length, chest depth and body slanting length at 8 weeks; shank length, pectoral angle, body slanting length and pelvis breadth at 12 weeks, respectively. And the polymorphism was also significantly associated with carcass traits including semi-evisceration weight, evisceration weight, breast muscle weight, leg weight and carcass weight as well. The observed values of individuals with CA genotype were significantly higher than CC genotype both in body weight at different stages and carcass traits. This SNP altered the predicted second structure of pre-mir-1606, with the altering of the free energy values. And the relative expression level of mature miRNA between CA and AA was significantly changed in leg muscle. Our data suggested that miRNA-1606 may be a candidate gene associated with chicken growth traits. [ABSTRACT FROM AUTHOR]

• A 31-bp indel located in LDB2 gene was detected in chicken for the first time. • The indel cause significant differences in growth and carcass traits of F2. • The expression of LDB2 gene in breast muscle was higher than that in other tissues. • In the breast muscle, it reached the highest at the age of 6 weeks. • The 31-bp indel can be used as a genetic marker in chicken molecular breeding. Many studies have shown that the LDB2 gene plays a regulatory role in retinal development and the cell cycle, but its biological role remains unclear. In this study, a 31-bp indel in the LDB2 gene was found for the first time on the basis of 2797 individuals from 10 different breeds, which led to different genotypes among individuals (II, ID and DD). Among these genotypes, DD was the most dominant. Association analysis of an F 2 resource population crossed with the Gushi (GS) chicken and Anka chicken showed that the DD genotype conferred a significantly greater semi-evisceration weight (SEW, 1108.665 g ± 6.263), evisceration weight (EW, 927.455 g ± 5.424), carcass weight (CW, 1197.306 g ± 6.443), breast muscle weight (BMW, 71.05 g ± 0.574), and leg muscle weight (LMW, 100.303 g ± 0.677) than the ID genotype (SEW, 1059.079 g ± 16.86; EW, 879.459 g ± 14.446; CW, 1141.821 g ± 17.176; BMW, 67.164 g ± 1.523; and LMW, 96.163 g ± 1.823). In addition, LDB2 gene expression in different breeds was significantly higher in the breast muscles and leg muscles than in other tissues. The expression level in the breast muscle differed significantly among stages of GS chicken development, with the highest expression observed at 6 weeks. The expression levels in the pectoral muscles differed significantly among Ross 308 genotypes. In summary, we studied the relationships between a 31-bp indel in the LDB2 gene and economic traits in chickens. The indel was significantly correlated with multiple growth and carcass traits in the F 2 resource population and affected the expression of the LDB2 gene in muscle tissue. In short, our study revealed that the LDB2 gene 31-bp indel can be used as a potential genetic marker for molecular breeding. [ABSTRACT FROM AUTHOR]