ArticlePloS one2015
Integrating transcriptome and genome re-sequencing data to identify key genes and mutations affecting chicken eggshell qualities.
Article in PloS one, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
20 citing papers in PubMed, 70 citations in OpenAlex.
- Age-associated changes in the shell gland transcriptomics and eggshell quality of broiler breeder hens.BMC genomics · 2026Article
- Genome-Wide Egg Hunt: Unhiding Candidate Genes for Egg Component Traits in Layers of an FAnimals : an open access journal from MDPI · 2025Article
- Multi-omics reveals key cell types and gene families regulating eggshell strength in chicken uteri.Zoological research · 2025Article
- Article
- Advances in Genomics and Postgenomics in Poultry Science: Current Achievements and Future Directions.International journal of molecular sciences · 2025Review
- Article
- Genome-wide association study exploring the genetic architecture of eggshell speckles in laying hens.BMC genomics · 2023Article
- Review
- Genome-Wide Analysis of lncRNA and mRNA Expression in the Uterus of Laying Hens during Aging.Genes · 2023Article
- Hypothalamic and ovarian transcriptome profiling reveals potential candidate genes in low and high egg production of white Muscovy ducks (Cairina moschata).Poultry science · 2021Article
- Effect of organic and inorganic dietary selenium supplementation on gene expression in oviduct tissues and Selenoproteins gene expression in Lohman Brown-classic laying hens.BMC veterinary research · 2021Article
- Detection of loci exhibiting pleiotropic effects on body weight and egg number in female broilers.Scientific reports · 2021Article
- Whole-Genome Re-sequencing and Transcriptome Reveal Oogenesis-Related Genes in Autotetraploid Carassius auratus.Marine biotechnology (New York, N.Y.) · 2021Article
- Study on the transcriptome for breast muscle of chickens and the function of key gene RAC2 on fibroblasts proliferation.BMC genomics · 2021Article
- Hybrids generated by crossing elite laying chickens exhibited heterosis for clutch and egg quality traits.Poultry science · 2020Article
- Uterine transcriptome analysis reveals mRNA expression changes associated with the ultrastructure differences of eggshell in young and aged laying hens.BMC genomics · 2020Article
- RNA sequencing-based analysis of the laying hen uterus revealed the novel genes and biological pathways involved in the eggshell biomineralization.Scientific reports · 2018Article
- Integrating genome and transcriptome profiling for elucidating the mechanism of muscle growth and lipid deposition in Pekin ducks.Scientific reports · 2017Article
- A genome-wide study to identify genes responsible for oviduct development in chickens.PloS one · 2017Article
- The calcified eggshell matrix proteome of a songbird, the zebra finch (Taeniopygia guttata).Proteome science · 2015Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Eggshell damages lead to economic losses in the egg production industry and are a threat to human health. We examined 49-wk-old Rhode Island White hens (Gallus gallus) that laid eggs having shells with significantly different strengths and thicknesses. We used HiSeq 2000 (Illumina) sequencing to characterize the chicken transcriptome and whole genome to identify the key genes and genetic mutations associated with eggshell calcification. We identified a total of 14,234 genes expressed in the chicken uterus, representing 89% of all annotated chicken genes. A total of 889 differentially expressed genes were identified by comparing low eggshell strength (LES) and normal eggshell strength (NES) genomes. The DEGs are enriched in calcification-related processes, including calcium ion transport and calcium signaling pathways as revealed by gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) pathway analysis. Some important matrix proteins, such as OC-116, LTF and SPP1, were also expressed differentially between two groups. A total of 3,671,919 single-nucleotide polymorphisms (SNPs) and 508,035 Indels were detected in protein coding genes by whole-genome re-sequencing, including 1775 non-synonymous variations and 19 frame-shift Indels in DEGs. SNPs and Indels found in this study could be further investigated for eggshell traits. This is the first report to integrate the transcriptome and genome re-sequencing to target the genetic variations which decreased the eggshell qualities. These findings further advance our understanding of eggshell calcification in the chicken uterus.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.