Transcriptome Profiling of the Goose (Anser cygnoides) Ovaries Identify Laying and Broodiness Phenotypes

Abstract

BackgroundThe geese have strong broodiness and poor egg performance. These characteristics are the key issues that hinder the goose industry development. Yet little is known about the mechanisms responsible for follicle development due to lack of genomic resources. Hence, studies based on high-throughput sequencing technologies are needed to produce a comprehensive and integrated genomic resource and to better understand the biological mechanisms of goose follicle development.Methodology/Principal FindingsIn this study, we performed de novo transcriptome assembly and gene expression analysis using short-read sequencing technology (Illumina). We obtained 67,315,996 short reads of 100 bp, which were assembled into 130,514 unique sequences by Trinity strategy (mean size = 753bp). Based on BLAST results with known proteins, these analyses identified 52,642 sequences with a cut-off E-value above 10−5. Assembled sequences were annotated with gene descriptions, gene ontology and clusters of orthologous group terms. In addition, we investigated the transcription changes during the goose laying/broodiness period using a tag-based digital gene expression (DGE) system. We obtained a sequencing depth of over 4.2 million tags per sample and identified a large number of genes associated with follicle development and reproductive biology including cholesterol side-chain cleavage enzyme gene and dopamine beta-hydroxylas gene. We confirm the altered expression levels of the two genes using quantitative real-time PCR (qRT-PCR).Conclusions/SignificanceThe obtained goose transcriptome and DGE profiling data provide comprehensive gene expression information at the transcriptional level that could promote better understanding of the molecular mechanisms underlying follicle development and productivity.

Effect of photoperiod on serum hormone concentrations during the annual reproductive cycle in geese

“…Photoperiod and season regulate the gene expression and secretion of reproductive hormones in geese. For example, many goose genes are significantly up-regulated in the pituitary, ovaries, and hypothalamus between the pre-laying and laying periods (Xu et al, 2013;Luan et al, 2014;Ding et al, 2014;Gao et al, 2014Gao et al, , 2015. Furthermore, the concentrations of plasma prolactin (PRL), luteinizing hormone (LH), progesterone (P4), and estradiol (E2) differ significantly in geese between the pre-laying, laying, and ceased-laying periods (Shi et al, 2004Fang et al, 2009;Gumułka and Rozenboim, 2015b).…”

Differential gene expression in pre-laying and laying period ovaries of Sichuan White geese (Anser cygnoides)

“…Although some differentially expressed genes were found, involving multiple functional classifications, we cannot establish the direct relationship of these genes with egg-laying performance on the basis of the current data. Moreover, genes known to be important in egg formation and ovarian development appear not to have direct roles in high reproductive performance (Xu et al, 2013). Nevertheless, our study provides some novel insights into the molecular mechanisms of high egg-laying performance determination in geese, as well as a valuable functional genomics resource and a list of candidate genes for functional analysis in the future.…”

“…This study is one of several extensive efforts to detect genes related to high reproductive performance that are expressed in developing ovarian tissue or reproductive organs (El-Hanoun et al, 2012;Xu et al, 2013;Zhang et al, 2013;Zhao et al, 2013), yet the critical genes have not yet been discovered. It is noteworthy that low egg-laying performance is common in most species of geese, so the differentially expressed genes are associated with physiological and biochemical characteristics that distinguish geese from other poultry.…”

De novo transcriptome assembly of Ipomoea nil using Illumina sequencing for gene discovery and SSR marker identification

“…Due to the lack of genomic resources for I. nil, its mRNAs with full-length CDS from GenBank were considered as "gold standard" (Tao et al 2012;Xu et al 2013). We searched these reference sequences in the transcript database using BLASTN with a cutoff E value of 10 −3 , identity of 90 % and alignment length of 200 bp (Hsu et al 2012).…”