Microarray analysis of genes involved with shell strength in layer shell gland at the early stage of active calcification

Transcriptomic and Metabolomic Analysis of the Uterine Tissue of Yaoshan Chicken and Its Crossbreeds to Reveal the Molecular Mechanism Influencing Eggshell Quality

Background/Objectives: Eggshell quality is a critical factor influencing consumer preference and the economic benefits of poultry enterprises, and the uterus is the key site for eggshell synthesis. Yaoshan chicken (YS), an indigenous chicken breed in China, is renowned for its flavorful meat and high-quality eggs. However, its egg production is lower compared to specialized strains. Therefore, the GYR crossbreed was developed by three-line hybridization for YS chicken, which can produce green-shelled eggs with better eggshell thickness and strength than YS chicken (p < 0.01). To explore the molecular mechanisms underlying the differences in eggshell quality between GYR and YS chickens, we conducted an integrated transcriptomic and metabolomic analysis. Methods: Twelve uterus samples (six from GYR and six from YS chickens) were collected during the period of eggshell calcification at 260 days of age. RNA sequencing (RNA-seq) and liquid chromatography-mass spectrometry (LC-MS/MS) were performed to identify differentially expressed genes (DEGs) and differential metabolites (DMs), respectively. Results: A total of 877 DEGs were identified in the GYR group, including 196 upregulated and 681 downregulated genes (|log2 (fold change)| > 1, p-value < 0.05). Additionally, 79 DMs were detected, comprising 50 upregulated and 29 downregulated metabolites (|log₂ (fold change)| > 1, VIP > 1). Notably, the key DEGs (SLCO1B3, SLCO1B1, PTGR1, LGR6, MELTF, CRISP2, GVINP1, and OVSTL), important DMs (prostaglandin-related DMs and biliverdin) and signaling pathways (calcium signaling, neuroactive ligand-receptor interaction, arachidonic acid metabolism, bile secretion, and primary bile acid biosynthesis) were major regulators of the eggshell quality. Furthermore, an integrated transcriptomic and metabolomic analysis revealed two significant gene-metabolite pairs associated with eggshell quality: PTGDS-prostaglandin E2 and PTGS1-prostaglandin E2. Conclusions: This study provides a theoretical foundation for the improved eggshell quality of Yaoshan chicken.

Genomic scans for selection and runs of homozygosity in southern Italian turkey populations

Basilicata and Apulian (BAS-APU) turkeys, a native population in the Basilicata and Puglia regions of southern Italy, are known for their high meat quality and tolerance to local conditions. Understanding the genomic patterns of BAS-APU turkeys is critical for effective breeding and preservation strategies. In this study, we characterized runs of homozygosity (ROH), and selection signatures using the integrated haplotype score (iHS) and ROH approaches. A total of 73 BAS-APU turkeys from five populations were sequenced (12X). The inbreeding coefficients based on ROH ranged from 0.177 to 0.405. A total of 120,956 ROH were detected in BAS-APU populations. We identified 27 genomic regions that harbor 61 candidate genes in ROH islands in which single nucleotide polymorphisms (SNPs) occur in more than 90 % of individuals. In addition, we detected 608 genomic regions under positive selection using the iHS method being 104, 98, 130, 102, and 174 for BAS, APU_C, APU_M, APU_PN, and APU_PS, respectively. For both methods, most of the genes within these regions are related to production performance, reproduction, immune responses, and adaptation. This study contributes significantly to our understanding of the genetic makeup of native turkey populations in southern Italy. The identified genes under selection can aid future breeding and conservations programs for southern Italian native turkeys. The results of inbreeding levels, especially in the absence of complete pedigrees or when only a few samples are available, which is often the case for local breeds, will help to avoid genetic relatedness in the mating plan in breeding and conservation plans for BAS-APU populations. Also, the detected genes in the selective sweep regions could be used as a marker-assisted selection to improve productive traits and adaptation of BAS-APU local populations.

Chinese herb ultrafine powder supplementation improves egg nutritional value and quality in laying hens

This study evaluates the effects of dietary Chinese herb ultrafine powder (CHUP) supplementation in late-phase laying hens on the quality and nutritional values of eggs. A total of 576 Xinyang black-feather laying hens (300-day-old) were randomly allocated into eight groups for a 120-day feeding trial. Each group contained eight replicates with nine hens per replicate. The experimental groups included the control (basal diet) and different levels of CHUP groups (details in 'Materials and methods'). The results showed that the eggshell strength was increased (p < 0.05) in the L, LF, L-LF, L-T, and LF-T groups on day 60 of the trial. In addition, the plasma estradiol level in the L-LF, LF-T, and L-LF-T groups and unsaturated fatty acids concentrations in egg yolk of the CHUP groups (except LF-T group) were increased, whereas total cholesterol (T, L-LF, L-T, and L-LF-T groups) in egg yolk and the atherogenicity (T, L-T, and L-LF-T groups) and thrombogenicity (T, L-LF, L-T, and L-LF-T groups) indexes were decreased (p < 0.05) on day 60 of the trial compared with the control group. Moreover, bitter amino acids in egg albumen were decreased (p < 0.05) in the L-LF group on day 60 and the L-LF-T group on day 120 of the trial. Collectively, these findings indicate that dietary CHUP supplementation could improve eggshell quality and increase plasma reproductive hormone, fatty acid and amino acid composition, and nutritional values of eggs, especially L-LF and L-LF-T.

Identification of SNPs and INDELS associated with duck egg quality traits through a genome-wide association analysis

Egg quality traits are economically important in the poultry industry. To explore the genetic architecture and identify potential candidate genes, a genome-wide association study (GWAS) was performed for 13 egg quality traits using data from whole-genome sequencing of 299 Longyan Shan-ma female ducks, including 12 quantitative traits and one qualitative trait, eggshell color (ESC; white, light green, green). From estimation of pedigree genetic parameters, heritability (h2) ranged from 0.022 to 0.996 for the 12 quantitative traits, with the highest h2 (0.996) for eggshell color a* value (ESCA) and the lowest h2 (0.022) for egg yolk percentage relative to EW. A total of 8,874 single nucleotide polymorphism (SNP)-based significant associations (1.0 × 10-6) and 247 insertion-deletion (indel)-based significant associations (1.00 × 10-5) were identified, including 5,980 SNPs and 159 indel markers. From 5,924 SNPs and 143 indels associated with ESC traits, 181 potential candidate genes were identified, and most significant SNPs and indels (P < 1.0 × 10-20) were located at 1.86 Mb (44.29-46.15 Mb) on chromosome 4. The top SNP (chr4:45325309:C>A; P = 7.97 × 10-43) and the top indel (chr4:45299595:delTTCCACTCCAC; P = 4.20 × 10-36) for the ESC a* value were within two known ESC candidate genes; ATP-binding cassette subfamily G member 2 (ABCG2) and protein kinase cGMP-dependent 2 (PRKG2). Of 56 SNPs and 16 indels associated with other egg quality traits, 46 potential candidate genes were identified including synapse differentiation-inducing 1-like (SYNDIG1L) for EW, and core histone macro-H2A.1 (LOC101795967) and neurogenin 1 (NEUROG1) for egg shape index; and four genes including collagen type VI alpha 3 chain (COL6A3), lysine demethylase 7A (KDM7A), LOC101802169, and sperm-associated antigen 16 (SPAG16) for egg yolk weight and the percentage of yolk to total egg weight. Of the 46 genes, the molecular functions of 22 are related to protein binding, indicating important roles in the formation of egg quality traits. Our findings provide new insight into the genetic basis of egg quality traits in ducks.

DMT1 differentially regulates mitochondrial complex activities to reduce glutathione loss and mitigate ferroptosis

Mitochondria are vital for energy production and redox homeostasis, yet knowledge of relevant mechanisms remains limited. Here, through a genome-wide CRISPR-Cas9 knockout screening, we have identified DMT1 as a major regulator of mitochondria membrane potential. Our findings demonstrate that DMT1 deficiency increases the activity of mitochondrial complex I and reduces that of complex III. Enhanced complex I activity leads to increased NAD+ production, which activates IDH2 by promoting its deacetylation via SIRT3. This results in higher levels of NADPH and GSH, which improve antioxidant capacity during Erastin-induced ferroptosis. Meanwhile, loss of complex III activity impairs mitochondrial biogenesis and promotes mitophagy, contributing to suppression of ferroptosis. Thus, DMT1 differentially regulates activities of mitochondrial complex I and III to cooperatly suppress Erastin-induced ferroptosis. Furthermore, NMN, an alternative method of increasing mitochondrial NAD+, exhibits similar protective effects against ferroptosis by boosting GSH in a manner similar to DMT1 deficiency, shedding a light on potential therapeutic strategy for ferroptosis-related pathologies.

Probiotic Bacillus subtilis C-3102 Improves Eggshell Quality after Forced Molting in Aged Laying Hens

This study was carried out to evaluate the effects of probiotic Bacillus subtilis C-3102 feed additive on quality characteristics including strength, thickness, and weight of eggshells of Boris Brown laying hens. The control group (n=64) was fed a basal diet comprised of maize and feed rice, whereas the experimental group (n=64) was fed a basal diet supplemented with B. subtilis C-3102 (3×105 CFU/g) starting at 49 weeks of age. From 67 to 69 weeks, all hens were induced to molt using an anorexic program; then, the birds in both groups returned to their respective diets (from 69 to 82 weeks). Eggshell strength, measured six times with 60 eggs selected before the molting treatment, was significantly greater in the C-3102 group than in the control group at 51, 59, 63, and 66 weeks (3.45, 3.44, 3.28, and 3.13 kg/cm2; P<0.05, 0.05, 0.01, and 0.01, respectively). Moreover, eggshell strength-measured three times after the molting treatment-was significantly greater in the C-3102 group than in the control group at 73 and 77 weeks (3.79 and 3.65 kg/cm2; P<0.01 and 0.01, respectively). Eggshell thickness was also significantly greater in the C-3102 group than in the control group at 73 and 77 weeks (0.400 and 0.390 mm; P<0.01 and 0.01, respectively). Fecal samples collected from eight hens of each group at 70 weeks of age after forced molting, showed a significantly higher proportion of Lactobacillus spp. in the C-3102 group (8.94 log CFU/g) (P<0.05) than in the control group (8.63 log CFU/g). Clostridium spp. abundance was significantly lower in the C-3102 group (2.92 log CFU/g) than in the control group (4.3 log CFU/g). These results suggest that C-3102 supplementation improves eggshell quality in aged laying hens, particularly after forced molting.

Expression of follistatin is associated with egg formation in the oviduct of laying hens

The objective of this study was to examine the expression profiles of follistatin (FST) and its associated molecules (MSTN, INHA, INHBB, INHBA, ACVR2A, and ACVR2B) in the oviduct of laying hens at 3 hr and 20 hr post-ovulation (p.o., n = 5; 35 weeks old), molting (n = 5; 60 weeks old), and non-laying (n = 4; 35-60 weeks old) hens and also to localize the FST by using immunohistochemistry assay. Expression of FST was significantly higher (p < .05), and MSTN was lower in the uterus of laying hens around 15-20 hr p.o. (during eggshell formation), however, their expressions in the magnum remain unchanged across different physiological stages of hens. FST was mainly expressed in the luminal and glandular epithelium of the uterine tissues, and their expression intensity was highest in laying hens during the eggshell mineralization. There was a relatively increased expression of INHA in the magnum of laying hens around 3 hr p.o. as compared to non-laying and molting hens. At the same time (3 hr p.o.), there was a significant (p < .05) decrease in the expression of the INHBB, ACVR2A, and ACV2B. These results indicate that follistatin may regulate the differentiation of uterine luminal and glandular epithelium during eggshell biomineralization.

Reference gene selection for gene expression study in shell gland and spleen of laying hens challenged with infectious bronchitis virus

Ten reference genes were investigated for normalisation of candidate target gene expression data in the shell gland and spleen of laying hens challenged with two strains of infectious bronchitis virus (IBV). Data were analysed with geNorm, NormFinder and BestKeeper, and a comprehensive ranking (geomean) was calculated. In the combined data set of IBV challenged shell gland samples, the comprehensive ranking showed TATA-box binding protein (TBP) and tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein zeta (YWHAZ) as the two most stable, and succinate dehydrogenase complex flavoprotein subunit A (SDHA) and albumin (ALB) as the two least stable reference genes. In the spleen, and in the combined data set of the shell gland and spleen, the two most stable and the two least stable reference genes were TBP and YWHAZ, and ribosomal protein L4 (RPL4) and ALB, respectively. Different ranking has been due to different algorithms. Validation studies showed that the use of the two most stable reference genes produced accurate and more robust gene expression data. The two most and least stable reference genes obtained in the study, were further used for candidate target gene expression data normalisation of the shell gland and spleen under an IBV infection model.

Reference gene selection for the shell gland of laying hens in response to time-points of eggshell formation and nicarbazin

Ten reference genes were investigated for normalization of gene expression data in the shell gland of laying hens. Analyses performed with geNorm revealed that hypoxanthine phosphoribosyltransferase 1 (HPRT1) and hydroxymethylbilane synthase (HMBS) were the two most stable reference genes in response to post-oviposition time alone (POT) or with nicarbazin treatment (POT+N) of laying hens. NormFinder analyses showed that the two most stable reference genes in response to POT and POT+N were 18S ribosomal RNA (18S rRNA), ribosomal protein L4 (RPL4) and HMBS, RPL4, respectively. BestKeeper analyses showed that 18S rRNA, RPL4 and HPRT1, HMBS were the two most stable reference genes for POT, and POT+N, respectively. Of the ten reference genes, all except B2M showed geNorm M <0.5, suggesting that they were stably expressed in the shell gland tissue. Consensus from these three programs suggested HPRT1 and HMBS could be used as the two most stable reference genes in the present study. Expression analyses of four candidate target genes with the two most and the two least stable genes showed that a combination of stable reference genes leads to more discriminable quantification of expression levels of target genes, while the least stable genes failed to do so. Therefore, HMBS and HPRT1 are recommended as the two most stable reference genes for the normalization of gene expression data at different stages of eggshell formation in brown-egg laying hens. Available statistical programs for reference gene ranking should include more robust analysis capability to analyse the gene expression data generated from factorial design experiments.

Genome-wide association study revealed a promising region and candidate genes for eggshell quality in an F2 resource population

Background

Eggshell is subject to quality loss with aging process of laying hens, and damaged eggshells result in economic losses of eggs. However, the genetic architecture underlying the dynamic eggshell quality remains elusive. Here, we measured eggshell quality traits, including eggshell weight (ESW), eggshell thickness (EST) and eggshell strength (ESS) at 11 time points from onset of laying to 72 weeks of age and conducted comprehensive genome-wide association studies (GWAS) in 1534 F₂ hens derived from reciprocal crosses between White Leghorn (WL) and Dongxiang chickens (DX).

Results

ESWs at all ages exhibited moderate SNP-based heritability estimates (0.30 ~ 0.46), while the estimates for EST (0.21 ~ 0.31) and ESS (0.20 ~ 0.27) were relatively low. Eleven independent univariate genome-wide screens for each trait totally identified 1059, 1026 and 1356 significant associations with ESW, EST and ESS, respectively. Most significant loci were in a region spanning from 57.3 to 71.4 Mb of chromosome 1 (GGA1), which together account for 8.4 ~ 16.5 % of the phenotypic variance for ESW from 32 to 72 weeks of age, 4.1 ~ 6.9 % and 2.95 ~ 16.1 % for EST and ESS from 40 to 72 weeks of age. According to linkage disequilibrium (LD) and conditional analysis, the significant SNPs in this region were in extremely strong linkage disequilibrium status. Ultimately, two missense SNPs in GGA1 and one in GGA4 were considered as promising loci on three independent genes including ITPR2, PIK3C2G, and NCAPG. The homozygotes of advantageously effective alleles on PIK3C2G and ITPR2 possessed the best eggshell quality and could partly counteract the negative effect of aging process. NCAPG had certain effect on eggshell quality for young hens.

Conclusions

Identification of the promising region as well as potential candidate genes will greatly advance our understanding of the genetic basis underlying dynamic eggshell quality and has the practical significance in breeding program for the improvement of eggshell quality, especially at the later part of laying cycle.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1795-7) contains supplementary material, which is available to authorized users.

Spatiotemporal expression profile of a putative β propeller WDR72 in laying hens

The purpose of this study is to characterize the expression profile of a novel gene WDR72 in laying hens. Sixty-week old Hy-line Brown layers with similar laying sequence, egg weight, and shell strength, were selected and divided into 5 groups. The oviduct segments, such as magnum, white isthmus, and uterus, were sampled from each group of hens which were killed at 3 h post-oviposition (3 h P.O.), 4.15-4.5 h P.O., 8.5-9 h P.O., 12 h P.O. and 18 h P.O., respectively. To the 8.5-9 h P.O. hens, additional organs were also sampled besides oviduct tissues. Moreover, another group of hens with weak shell strength were selected and their oviduct segments were sampled at 12 h P.O. Then the expression profile of WDR72 was analyzed using real-time quantitative RT-PCR. The results showed as follows. (1) WDR72 transcripts specifically distributed in parts of organs investigated. At 8.5-9 h P.O., WDR72 appeared to be much more abundantly expressed in hens' oviduct sections, then followed in turn by brain, kidney, lung, glandular stomach and spleen. However, there were almost no WDR72 transcripts expressed in pectoral muscle, liver, heart and jejunum. (2) During the process of an "egg" passing through an oviduct, the expression of WDR72 in the magnum was greatly superior to that in the other two oviduct segments at 3 h P.O., 8.5-9 h P.O., and 12 h P.O.; while it was white isthmus in which WDR72 transcript levels were the highest at 4.15-4.5 h P.O. and 18 h P.O. (3) To any oviduct segment, not only uterus but also magnum and white isthmus, the expression of WDR72 in which was significantly up-regulated at the stages of active calcification. (4) WDR72 transcript levels in any oviduct segments of strong-shell hens were significantly higher than that of weak-shell layers (P < 0.01), which arose the possibility that WDR72 was positively associated with chicken eggshell strength. In conclusion, the expression profile of WDR72 gene in laying hens has been characterized, which would facilitate to further probe into its functions.