The association of very low-density lipoprotein receptor (VLDLR) haplotypes with egg production indicates VLDLR is a candidate gene for modulating egg production

Transcriptomic data reveals MYC as an upstream regulator in laying hen follicular recruitment

Understanding the mechanisms of follicular recruitment is essential for improving laying hen and broiler breeder productivity, as it directly influences egg production. Despite advancements in poultry breeding for enhanced egg production, the factors driving successful ovarian follicle maturation remain inadequately understood. This study investigates the genetic drivers mediating the transition of pre-recruitment follicles to the pre-ovulatory phase, a crucial stage before ovulation. Using RNA sequencing and bioinformatics approaches such as a differential gene expression analysis, we compared pre-recruitment follicles with the recently recruited F5 pre-ovulatory follicle to identify key genes and upstream regulators involved in this transition. Further validation through qRT-PCR confirmed these findings. Using Qiagen's Ingenuity Pathway Analysis we identified MYC proto-oncogene (C-Myc) as a pivotal upstream regulator, controlling genes essential for cell proliferation and differentiation. Additionally, TGFβ1 emerged as a key regulator, influencing pathways involving SMAD3, TNF, and TP53. The study highlights the intricate regulatory network involving MYC and other transcription factors such as CTNNB1, crucial for follicular development. These findings provide valuable insights into the molecular mechanisms governing follicular selection and maturation, which are essential for enhancing egg production efficiency. Future research should explore the roles of MYC, CTNNB1, and other driver genes in follicular development to further understand and improve reproductive efficiency in poultry.

Integrating genomics and transcriptomics to identify candidate genes for high-altitude adaptation and egg production in Nixi chicken

1. This study combined genome-wide selection signal analysis with RNA-sequencing to identify candidate genes associated with high altitude adaptation and egg production performance in Nixi chickens (NXC).2. Based on the whole-genome data from 20 NXC (♂:10; ♀:10), the population selection signal was analysed by sliding window analysis. The selected genes were screened by combination with the population differentiation statistic (FST). The sequence diversity statistic (θπ). RNA-seq was performed on the ovarian tissues of NXC (n = 6) and Lohmann laying hens (n = 6) to analyse the differentially expressed genes (DEGs) between the two groups. The functional enrichment analysis of the selected genes and differentially expressed genes was performed.3. There were 742 genes under strong positive selection and 509 differentially expressed genes screened in NXC. Integrated analysis of the genome and transcriptome revealing 26 overlapping genes. The candidate genes for adaptation to a high-altitude environment, as well as for egg production, disease resistance, vision and pigmentation in NXC were preliminarily screened.4. The results provided theoretical guidance for further research on the genetic resource protection and utilisation of NXC.

Yolk precursor synthesis and deposition in hierarchical follicles and effect on egg production performance of hens

Egg production of hens is related to ovarian follicles development. The hierarchical follicle development accompanies the deposition of a large amount of yolk precursor. The aim of this study was to illustrate the effects of strain and age on yolk deposition and egg production. The experiment compared yolk synthesis, transport, and deposition in 3 groups of hens: one of a high-yield commercial hybrid laying breed (Jinghong No.1) in 2 stages (35 wk and 75 wk; JH35, JH75) and one of Chinese native breed (Lueyang Black-Boned chicken) at 35 wk (LY35). The results showed that the number of hierarchical follicles in JH35 and JH75 was significantly more than in LY35. At the same time, the yolk weight of the LY35 and JH75 was significantly higher than that of JH35. The expression of apolipoprotein A1 and apolipoprotein B genes in the liver of JH35 was higher than that of JH75. The expression of the very low-density lipoprotein receptor gene in the JH75 ovary was higher than that of the other 2 groups. The plasma concentrations of very low-density lipoprotein and vitellogenin were no significant difference among groups. The yolk deposition in hierarchical follicles based on the fat-soluble dyes measurement meant that the rate of yolk deposition of LY35 was lower than the other 2 groups. In most cases, the yolk deposition of JH75 was higher than that of the other groups, but the process showed greater fluctuation over time. These results meant that the rate and stability of yolk deposition played an essential role in affecting egg performance. In summary, both strain and age were related to egg production, but the 2 factors might impact yolk deposition and egg-laying performance differently. The egg performance may be affected by both yolk precursor synthesis and deposition for different strains, but it may be affected by yolk precursor deposition for the old laying hens.

A new molecular mechanism supports that blue-greenish egg color evolved independently across chicken breeds

Chicken blue-greenish coloration (BGC) was known as a classic Mendel trait caused by a retrovirus (EAV-HP) insertion in the SLCO1B3 gene. Lueyang black-boned chicken (LBC) BGC is light and varies continuously, implying that LBC BGC may be controlled by a new molecular mechanism. The aim of this study was to provide an insight into the molecular basis of LBC BGC. The EAV-HP was detected in the BGC (n = 105) and non-BGC LBC (n = 474) using a PCR-based method. The association of SLCO1B3 expression in shell glands and sequence variants in a 1.6-kb region upstream from the transcription start site of SLCO1B3 with eggshell color and biliverdin (pigment for BGC) concentration was studied. Promoter activities of haplotypes in the 1.6-kb region were analyzed by luciferase reporter assay. This study did not found the EAV-HP in BGC and Non-BGC LBC, but detected a strong positive correlation between levels of SLCO1B3 expression in shell glands and biliverdin concentrations. A total of 31 SNP were found in the 1.6-kb region. Twenty-two of 31 SNP formed 42 types of haplotypes in the re-sequenced samples (n = 94). Haplotype 4 was present in higher frequency in the BGC (52%) than Non-BGC (3%). Haplotype 13 was significantly associated with Non-BGC (Non-BGC vs. BGC = 26% vs. 6%). In line with the above associations, Haplotype 4 showed higher (P < 0.05) levels of SLCO1B3 expression in shell glands, biliverdin concentration, and promoter activity than Haplotype 13. This study confirms that LBC BGC is not caused by the EAV-HP, but remains to be associated with the change of SLCO1B3 expression. Haplotype 4 accounts to some extents for the molecular basis of LBC BGC. The new molecular mechanism supports LBC BGC independently evolved.

The study of candidate genes in the improvement of egg production in ducks – a review

Duck is the second-largest poultry species aside from chicken. The rate of egg production is a major determinant of the economic income of poultry farmers. Among the reproductive organs, the ovary is a major part of the female reproductive system which is highly important for egg production. Based on the importance of this organ, several studies have been carried out to identify candidate genes at the transcriptome level, and also the expression level of these genes at different tissues or egg-laying conditions, and single nucleotide polymorphism (SNPs) of genes associated with egg production in duck. In this review, expression profile and association study analyses at SNPs level of different candidate genes with egg production traits of duck were highlighted. Furthermore, different studies on transcriptome analysis, Quantitative Trait Loci (QTL) mapping, and Genome Wide Association Study (GWAS) approach used to identify potential candidate genes for egg production in ducks were reported. This review would widen our knowledge on molecular markers that are associated or have a positive correlation to improving egg production in ducks, for the increasing world populace.

Research Note: Fine mapping of sequence variants associated with body weight of Lueyang black-boned chicken in the CCKAR gene

Cholecystokinin A receptor (CCKAR) is a key receptor mediating satiety. Previous studies found that decreased expression of CCKAR attenuated satiety, and thus contributed to the high-growth of broiler chickens. The objective of this study is to map sequence variants associated with the growth of chickens in the CCKAR. The CCKAR and upstream 1.4 kb genomic sequences were resequenced to find out all sequence variants using 35 Lueyang black-boned chickens (LBC). Haplotypes were reconstructed using the PHASE program. Linkage disequilibrium between variants was analyzed using the Haploview software. Associations of 33 tag SNPs that captured 89% of all variants with body weight of LBC (n = 675) at 16 (BW16), 20 (BW20) weeks of age and the onset (BWOEP) of egg production were tested using linear mixed models. A total of 126 SNPs were found and formed 41 haplotypes in 35 resequenced samples. Average length of haplotype blocks is 129 bp, indicating that LBC maintains low linkage disequilibrium at the CCKAR locus. Eleven of 33 tag SNPs were significantly associated with BW16, but not with BW20 and BWOEP. These significantly associated variants were most (8/11) distributed in a 2 kb region (chr4:73206169-73208244) around the Exon3. They together with 33 captured variants potentially disrupted binding sites of 471 transcription factors. Twelve variants can disrupt appetite (FOXO1) or lipid metabolism-related TF (AR and C/EBP) motifs. This study recognized chr4:73206169-73208244 as a key region harboring functional variants affecting the growth of chickens.

Expression and analysis of ESR1, IGF-1, FSH, VLDLR, LRP, LH, PRLR genes in Pekin duck and Black Muscovy duck

In order to explore the influence of egg-laying regulatory genes on egg production in ducks at different laying stages, Pekin duck and Black Muscovy duck were used in this study, including early laying stage (20-30 weeks old), peak laying period (31-48 weeks old) and late laying stage (49-66 weeks old). Relative quantitative RT-PCR was used to detect the mRNA transcription level of selected egg-laying regulatory genes in the ovary tissues of ducks at different laying stages. Study shows: during the laying period of Pekin duck, ESR1, LRP1, IGF-1 and LHR were involved in the regulation of egg-laying, and the high expression of LRP1 in the late stage could inhibit egg production. Still, the expression products of the other three genes showed promoting effect. During the laying period of Black Muscovy duck, FSH, VLDLR, IGF-1, PRLR, LHR and LRP1 participated in the regulation of egg-laying, in which the expression products of the first five genes could promote egg production, while LRP1 showed inhibitory effect. Through our experiments, these data will provide strong theoretical support for the breeding of Pekin duck and Black Muscovy duck.

Novel Polymorphisms in RAPGEF6 Gene Associated with Egg-Laying Rate in Chinese Jing Hong Chicken using Genome-Wide SNP Scan

The improvement of egg production is of vital importance in the chicken industry to maintain optimum output throughout the laying period. Because of the elongation of the egg-laying cycle, a drop in egg-laying rates in the late laying period has provoked great concern in the poultry industry. In this study, we calculated the egg-laying rate at weeks 61–69 (60 days) of Jing Hong chickens parent generation as the phenotype, and the genotype were detected by the chicken 600K Affymetrix Axiom High Density (HD) Single Nucleotide Polymorphisms (SNP)-array. The Genome-Wide Association Study (GWAS) result showed that the egg production trait is significantly associated with five SNPs (AX-75745366, AX-75745380, AX-75745340, AX-75745388, and AX-75745341), which are in the rap guanine nucleotide exchange factor 6 (RAPGEF6) gene on chicken chromosome 13. A total of 1676 Chinese commercial Jing Hong laying hens—including two populations, P1 population (858 hens) and P2 population (818 hens)—were genotyped using the Polymerase Chain Reaction-Restriction Fragments Length Polymorphisms (PCR-RFLP) method for the association analysis of egg-laying rates for the verification of the GWAS results. Genotypic and allelic frequencies of five SNPs were inconsistent with Hardy–Weinberg equilibrium, and the average population genetics parameters considering all the SNP values; i.e., gene homozygosity (Ho), gene heterozygosity (He), the effective number of alleles (Ne), and the polymorphism information content (PIC) were 0.75, 0.25, 1.40, and 0.20 in P1; 0.71, 0.29, 1.46, and 0.24 in P2; and 0.73, 0.27, 1.43, and 0.22 in P1 + P2 populations, respectively. The association analysis results revealed that out of the five polymorphisms, three of them (AX-75745366, AX-75745340, and AX-75745341; Patent applying No: 201810428916.5) had highly significant effects on egg-laying rates according to the GWAS results. Population-specific association analyses also showed similar significant association effects with this trait. Four haplotypes (AAGG, AAAG, AGGG, and AGAG) were inferred based on significant loci (AX-75745340 and AX-75745341) and also showed significant associations with the egg-laying rate, where haplotype AAGG had the highest egg-laying rate, with the exception of the egg-laying rate in P1 population, followed by other haplotypes. Furthermore, genotypes TT, AA, and GG showed the highest egg-laying rate compared to the corresponding genotypes at AX-75745366, AX-75745340, and AX-75745341 SNP loci in P1+P2, respectively. A similar result was found in the population-specific analysis except for the P1 population, in which TC genotype showed the highest egg-laying rate. No significant association was found in the egg-laying rate during the 60 days laying period for the SNPs (AX-75745380 and AX-75745388) in any group of population (p ≥ 0.05). Collectively, we report for the first time that 3 SNPs in the RAPGEF6 gene were significantly associated with the egg-laying rate during the later stage of egg production, which could be used as the potential candidate molecular genetic markers that would be able to facilitate in the selection and improvement of egg production traits through chicken breeding.