title: Integrating transcriptome and genome re-sequencing data to identify key genes and mutations affecting chicken eggshell qualities.
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.
authors.affiliation: National Engineering Laboratory for Animal Breeding and Ministry of Agriculture Key Laboratory of Animal Genetics and Breeding, Department of Animal Genetics and Breeding, China Agricultural University, Beijing, 100193, China.
authors.forename: Quan
authors.initials: Q
authors.lastname: Zhang
authors.affiliation: National Engineering Laboratory for Animal Breeding and Ministry of Agriculture Key Laboratory of Animal Genetics and Breeding, Department of Animal Genetics and Breeding, China Agricultural University, Beijing, 100193, China.
authors.forename: Feng
authors.initials: F
authors.lastname: Zhu
authors.affiliation: National Engineering Laboratory for Animal Breeding and Ministry of Agriculture Key Laboratory of Animal Genetics and Breeding, Department of Animal Genetics and Breeding, China Agricultural University, Beijing, 100193, China.
authors.forename: Long
authors.initials: L
authors.lastname: Liu
authors.affiliation: National Engineering Laboratory for Animal Breeding and Ministry of Agriculture Key Laboratory of Animal Genetics and Breeding, Department of Animal Genetics and Breeding, China Agricultural University, Beijing, 100193, China.
authors.forename: Chuan Wei
authors.initials: CW
authors.lastname: Zheng
authors.affiliation: National Engineering Laboratory for Animal Breeding and Ministry of Agriculture Key Laboratory of Animal Genetics and Breeding, Department of Animal Genetics and Breeding, China Agricultural University, Beijing, 100193, China.
authors.forename: De He
authors.initials: de H
authors.lastname: Wang
authors.affiliation: National Engineering Laboratory for Animal Breeding and Ministry of Agriculture Key Laboratory of Animal Genetics and Breeding, Department of Animal Genetics and Breeding, China Agricultural University, Beijing, 100193, China.
authors.forename: Zhuo Cheng
authors.initials: ZC
authors.lastname: Hou
authors.affiliation: National Engineering Laboratory for Animal Breeding and Ministry of Agriculture Key Laboratory of Animal Genetics and Breeding, Department of Animal Genetics and Breeding, China Agricultural University, Beijing, 100193, China.
authors.forename: Zhong Hua
authors.initials: ZH
authors.lastname: Ning
mesh_terms: D000818:Animals; D030161:Avian Proteins / Q000235:genetics; D002113:Calcification, Physiologic; D002118:Calcium / Q000378:metabolism*; D002645:Chickens / Q000033:anatomy & histology / Q000235:genetics* / Q000502:physiology; D004527:Egg Proteins / Q000235:genetics; D004528:Egg Shell / Q000033:anatomy & histology / Q000502:physiology*; D005260:Female; D063990:Gene Ontology; D009154:Mutation; D020641:Polymorphism, Single Nucleotide; D015398:Signal Transduction; D059467:Transcriptome
chemical_list: D030161:Avian Proteins; D004527:Egg Proteins; C402224:ovocleidin-116; D002118:Calcium