Insights into the Mitochondrial and Nuclear Genome Diversity of Two High Yielding Strains of Laying Hens.
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ABSTRACT:
SUBMITTER: Heumann-Kiesler C
PROVIDER: S-EPMC8001891 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:The reproductive physiology and laying performance of laying hens are regulated by the hypothalamus and pituitary. To understand the mechanism of egg laying regulation, we sequenced and analysed the hypothalamus and pituitary expression profiles in high- and low-yielding laying Chinese Dagu Chickens (CDC) using RNA-seq. More than 46 million clean reads and 24,873 tentative genes were obtained using the Gallus gallus genome as a reference. Transcriptome analysis in hypothalamus and pituitary revealed seven and 39 differentially expressed genes (DEGs) between high- and low-yielding CDC hens, respectively. A total of 24 and 22 DEGs were up-regulated and down-regulated, respectively, and 13 novel genes were identified. Functional annotation and pathway enrichment analysis showed that DEGs in the hypothalamus were mainly enriched in glycosaminoglycan biosynthesis. DEGs significantly enriched in the pituitary primarily affected the extracellular matrix, the protein extracellular matrix, and the extracellular space. Pathways involving phenylalanine metabolism, 2-oxocarboxylic acid metabolism, the glycosphingolipid biosynthesis-ganglion series, and local adhesion were significantly enriched in the pituitary. Eight DEGs, PRDX6, TRIB2, OVCH2, CFD, Peptidase M20, SLC7A10, and two other amino acid transporters, are involved in the metabolism and transport of amino acids. To our knowledge, this is the first study comparing the hypothalamus and pituitary transcriptomes of high- and low-yielding laying hens. Our findings suggest that putative differences in gene expression can provide a base for further research in this field. Moreover, we identified increased expression of genes involved in amino acid metabolism, glycosaminoglycan biosynthesis, and oestrogen negative feedback systems in low-yielding laying hens, highlighting their potential as biomarkers of egg production.
| S-EPMC6635495 | biostudies-literature
Project description:The cellular energy metabolism is one of the most conserved processes, as it is present in all living organisms. Mitochondria are providing the eukaryotic cell with energy and thus their genome and gene expression has been of broad interest for a long time. Mitochondrial gene expression changes under different conditions and is regulated by genes encoded in the nucleus of the cell. In this context, little is known about non-model organisms and we provide the first large-scaled gene expression analysis of mitochondrial-linked genes in laying hens. We analysed 28 mitochondrial and nuclear genes in 100 individuals in the context of five life-stages and strain differences among five tissues. Our study showed that mitochondrial gene expression increases during the productive life span, and reacts tissue and strain specific. In addition, the strains react different to potential increased oxidative stress, resulting from the increase in mitochondrial gene expression. The results suggest that the cellular energy metabolism as part of a complex regulatory system is strongly affected by the productive life span in laying hens and thus partly comparable to model organisms. This study provides a starting point for further analyses in this field on non-model organisms, especially in laying-hens.
| S-EPMC8757906 | biostudies-literature
Project description:Comparative analysis of gene expression profiles in newly developed housing systems is important to understand gene functions in chicken for adaptation and possible gene-environment interactions among layer lines. Therefore, the objective of this study was to characterize the molecular processes that are different among the two layer lines Lohmann Selected Leghorn (LSL) and Lohmann Brown (LB) using whole genome RNA expression profiles. Despite their approximately identical egg production performance these layer lines differ markedly in other phenotypic traits. The two layer lines were kept under the production environment of the newly developed small group housing system Eurovent German with two different group sizes and three tiers.
2012-09-12 | GSE40802 | GEO
Project description:We used a chicken RNA microarray to identify differentially expressed genes in order to compare two layer lines kept in a small group housing system Eurovent Deutsch.
2016-04-30 | GSE55570 | GEO
Project description:BackgroundChangshun green-shell laying hens are unique to Guizhou Province, China, and have high egg quality. Improving egg production performance has become an important breeding task, and in recent years, the development of high-throughput sequencing technology provides a fast and exact method for genetic selection. Therefore, we aimed to use this technology to analyze the differences between the ovarian mRNA transcriptome of low and high-yield Changshun green-shell layer hens, identify critical pathways and candidate genes involved in controlling the egg production rate, and provide basic data for layer breeding.ResultsThe egg production rates of the low egg production group (LP) and the high egg production group (HP) were 68.00 ± 5.56 % and 93.67 ± 7.09 %, with significant differences between the groups (p < 0.01). Moreover, the egg weight, shell thickness, strength and layer weight of the LP were significantly greater than those of the HP (p < 0.05). More than 41 million clean reads per sample were obtained, and more than 90 % of the clean reads were mapped to the Gallus gallus genome. Further analysis identified 142 differentially expressed genes (DEGs), and among them, 55 were upregulated and 87 were downregulated in the ovaries. KEGG pathway enrichment analysis identified 9 significantly enriched pathways, with the neuroactive ligand-receptor interaction pathway being the most enriched. GO enrichment analysis indicated that the GO term transmembrane receptor protein tyrosine kinase activity, and the DEGs identified in this GO term, including PRLR, NRP1, IL15, BANK1, NTRK1, CCK, and HGF may be associated with crucial roles in the regulation of egg production.ConclusionsThe above-mentioned DEGs may be relevant for the molecular breeding of Changshun green-shell laying hens. Moreover, enrichment analysis indicated that the neuroactive ligand-receptor interaction pathway and receptor protein tyrosine kinases may play crucial roles in the regulation of ovarian function and egg production.
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Project description:Climate change is increasingly manifesting in temperate regions. Laying hens are highly sensitive to heat stress and mitigation strategies should be implemented to reduce the negative effects. The goal of this experiment was to evaluate the effects of betaine in drinking water (0.55 g/L) and 4 h feed restriction during peak heat stress on laying performance, egg quality, blood gas parameters, body temperature (Tb), and oxidative stress in 2 different breeds of laying hens. Therefore, 448 ISA Brown hens (25 wk) and 448 Lohmann LSL classic laying hens (26 wk) were housed in 128 cages (7 hens/cage). Thermoneutral (TN) data was collected for 21 d before cyclic heat stress (HS) (21d; 32 ± 2°C; 6 h daily). During HS, hens were divided into 4 treatments: 1) feed restriction (FR), 2) betaine supplementation in drinking water (BET), 3) feed restriction and betaine supplementation in drinking water (FR-BET), or 4) control (CON). The effects were evaluated after 1 wk of HS (acute heat stress; AHS) and 3 wk of HS (chronic heat stress; CHS). Laying rate and egg mass (EM) diminished during CHS but decreased more in white than brown hens (2.78% and 1.94%; -1.57% and -0.81%, respectively; P = 0.004) and remained unaltered by BET or FR. During AHS, average daily feed intake (ADFI) increased compared to TN, but the increase was higher in white than brown hens (6.36% and 2.62%, respectively; P = 0.001). Egg shell quality deteriorated during AHS and CHS, but was most affected in white hens, FR or BET did not impact this. Blood pCO2, HCO3- and base excess significantly decreased during AHS and CHS, but pH and iCa were unaltered. Blood glucose increased in white hens during AHS compared to TN (P < 0.001), while plasma malondialdehyde increased in brown hens (P < 0.001). Results indicated that laying hens experienced HS, but breed differences were observed and white hens were generally most affected. FR affected feed conversion ratio negatively during CHS. However, FR and BET could not improve laying performance, egg quality, Tb, or blood parameters during HS.
| S-EPMC11347855 | biostudies-literature
Project description:A high prevalence of deviations and fractures of the keel bone is a widespread welfare problem in laying hens. The aim of this study was to experimentally investigate this multifactorial problem throughout the laying period and to compare the prevalence and severity in different layer lines and different housing systems. High performing white (WLA) and brown (BLA) pure bred layer lines and low performing white (R11, G11) and brown layer lines (L68) were kept in both single cages and a floor housing system. A total of 97 hens (19 or 20 from each line, respectively) were repeatedly radiographed in the 35th, 51st and 72nd week of age. Fracture prevalence increased with age (p<0.001). The proportion of deviated keel bone area increased only for caged BLA, WLA and R11 hens (p<0.05) and was significantly higher for caged WLA and R11 hens compared to floor-housed WLA and R11 hens in the 72nd week of age (p<0.05). In the 72nd week of age hens in the floor housing system showed significantly more fractures than hens kept in cages (p<0.05). Prevalence of keel bone deviations was significantly higher in the white layer line R11 but significantly lower in the white layer line G11 compared to both brown layer lines and WLA (p<0.05). Brown layers showed significantly more fractures than white layers (p<0.05) in the 51st and 72nd week of age. Within the brown layers there was a significantly lower prevalence of deviations (p<0.05) and fractures (p<0.05) in the low performing (L68) compared to the high performing line (BLA). Our results show a different development of keel bone damage in caged compared to floor-housed hens under experimental conditions. Additionally, they indicate genetic effects on keel bone damage.
| S-EPMC5942800 | biostudies-literature
Project description:Comparative analysis of gene expression profiles in newly developed housing systems is important to understand gene functions in chicken for adaptation and possible gene-environment interactions among layer lines. Therefore, the objective of this study was to characterize the molecular processes that are different among the two layer lines Lohmann Selected Leghorn (LSL) and Lohmann Brown (LB) using whole genome RNA expression profiles. Despite their approximately identical egg production performance these layer lines differ markedly in other phenotypic traits. The two layer lines were kept under the production environment of the newly developed small group housing system Eurovent German with two different group sizes and three tiers. We used a chicken RNA microarray to identify differentially expressed genes among the two layer lines LSL and LB.
2012-09-12 | E-GEOD-40802 | biostudies-arrayexpress
Project description:Due to animal welfare issues, European Union has banned the use of conventional cages (CC) and non-EU countries including the US are also under constant public pressure to restrict their use in egg production. Very limited information is available on the composition of the microbial community of hens raised in different housing environments. This study was conducted to determine the effects of CC and enriched colony cages (EC) on cecal microbiota of two commercial laying hen strains, Hy-Line W36 (W36) and Hy-Line Brown (HB) during the late production stage (53, 58, 67, and 72 weeks of age). Cecal microbiota was studied by analyzing 16S rRNA gene sequences with Quantitative Insights Into Microbial Ecology (QIIME) 2 ver. 2018.8. Differentially abundant taxa were identified by Linear discriminant analysis Effect Size (LEfSe) analysis (P < 0.05, LDA score > 2.0). At phylum level, Actinobacteria was significantly enriched in W36 at all time points while Synergistetes (53 weeks), Spirochaetes (58 weeks), and Synergistetes and Spirochaetes (67 weeks) were significantly higher in HB. At genus level, Bifidobacterium (at all time points) and butyric acid producing genera such as Butyricicoccus and Subdoligranulum (58 and 72 weeks) were significantly higher in W36 as compared to HB. Moreover, Proteobacteria (72 weeks) and its associated genus Campylobacter (67 and 72 weeks) were significantly enriched in EC as compared to CC. Alpha diversity was significantly higher in HB (at all time points) and in EC (67 weeks) as compared to W36 and CC, respectively. Similarly, there was a significant difference in community structure (beta diversity) between W36 and HB (all time points) as well as between EC and CC (67 weeks). The effect of housing and strains was not only seen at the bacterial composition and structure but also reflected at their functional level. Notably, KEGG metabolic pathways predicted to be involved in carbohydrates degradation and amino acids biosynthesis by PICRUSt analysis were significantly different between W36 and HB housed at CC and EC. In sum, cecal microbiota composition, diversities, and their functional pathways were affected by housing type which further varied between two commercial laying hen strains, HB and W36. This suggests that both housing and genetic strains of laying hens should be considered for selection of the alternative housing systems such as enriched colony cage.
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Project description:Bone fracture in egg laying hens is a growing welfare and economic concern in the industry. Although environmental conditions and management (especially nutrition) can exacerbate it, the primary cause of bone weakness and the resulting fractures is believed to have a genetic basis. To test this hypothesis, we performed a genome-wide association study to identify the loci associated with bone strength in laying hens. Genotype and phenotype data were obtained from 752 laying hens belonging to the same pure line population. These hens were genotyped for 580,961 SNPs, with 232,021 SNPs remaining after quality control. Each of the SNPs were tested for association with tibial breaking strength using the family-based score test for association. A total of 52 SNPs across chromosomes 1, 3, 8, and 16 were significantly associated with tibial breaking strength with the genome-wide significance threshold set as a corrected P value of 10e-5. Based on the local linkage disequilibrium around the significant SNPs, 5 distinct and novel QTLs were identified on chromosomes 1 (2 QTLs), 3 (1 QTL), 8 (1 QTL) and 16 (1 QTL). The strongest association was detected within the QTL region on chromosome 8, with the most significant SNP having a corrected P value of 4e-7. A number of candidate genes were identified within the QTL regions, including the BRD2 gene that is required for normal bone physiology. Bone-related pathways involving some of the genes were also identified including chloride channel activity, which regulates bone reabsorption, and intermediate filament organization, which plays a role in the regulation of bone mass. Our result supports previous studies that suggest that bone strength is highly regulated by genetics. It is therefore possible to reduce bone fractures in laying hens through genetic selection and ultimately improve hen welfare.
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