Zhang Quan, Zhu Feng, Liu Long, Zheng Chuan Wei, Wang De He, Hou Zhuo Cheng, Ning Zhong Hua
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.
PLoS One. 2015 May 14;10(5):e0125890. doi: 10.1371/journal.pone.0125890. eCollection 2015.
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.
蛋壳损伤会导致蛋鸡生产行业的经济损失，并对人类健康构成威胁。我们研究了49周龄的罗德岛白鸡（原鸡），这些鸡所产鸡蛋的蛋壳强度和厚度存在显著差异。我们使用HiSeq 2000（Illumina）测序技术对鸡的转录组和全基因组进行表征，以确定与蛋壳钙化相关的关键基因和基因突变。我们共鉴定出在鸡子宫中表达的14234个基因，占所有注释鸡基因的89%。通过比较低蛋壳强度（LES）和正常蛋壳强度（NES）基因组，共鉴定出889个差异表达基因。基因本体论（GO）和京都基因与基因组百科全书（KEGG）通路分析显示，这些差异表达基因在钙化相关过程中富集，包括钙离子运输和钙信号通路。两组之间一些重要的基质蛋白，如OC-116、乳铁传递蛋白（LTF）和分泌性磷蛋白1（SPP1）也存在差异表达。通过全基因组重测序，在蛋白质编码基因中检测到总共3671919个单核苷酸多态性（SNP）和508035个插入缺失（Indel），其中包括差异表达基因中的1775个非同义变异和19个移码插入缺失。本研究中发现的SNP和Indel可进一步用于蛋壳性状的研究。这是第一份整合转录组和基因组重测序以靶向降低蛋壳质量的遗传变异的报告。这些发现进一步加深了我们对鸡子宫中蛋壳钙化的理解。
