RNA-Seq reveals seven promising candidate genes affecting the proportion of thick egg albumen in layer-type chickens

Abstract

Eggs with a much higher proportion of thick albumen are preferred in the layer industry, as they are favoured by consumers. However, the genetic factors affecting the thick egg albumen trait have not been elucidated. Using RNA sequencing, we explored the magnum transcriptome in 9 Rhode Island white layers: four layers with phenotypes of extremely high ratios of thick to thin albumen (high thick albumen, HTA) and five with extremely low ratios (low thick albumen, LTA). A total of 220 genes were differentially expressed, among which 150 genes were up-regulated and 70 were down-regulated in the HTA group compared with the LTA group. Gene Ontology (GO) analysis revealed that the up-regulated genes in HTA were mainly involved in a wide range of regulatory functions. In addition, a large number of these genes were related to glycosphingolipid biosynthesis, focal adhesion, ECM-receptor interactions and cytokine-cytokine receptor interactions. Based on functional analysis, ST3GAL4, FUT4, ITGA2, SDC3, PRLR, CDH4 and GALNT9 were identified as promising candidate genes for thick albumen synthesis and metabolism during egg formation. These results provide new insights into the molecular mechanisms of egg albumen traits and may contribute to future breeding strategies that optimise the proportion of thick egg albumen.

Transcriptomic analysis of the liver in aged laying hens with different intensity of brown eggshell color

“…A r t i c l e physiological or production stages [8]. Regarding eggshell quality, previous studies have focused primarily on transcriptomic analysis in the uterus, which can reveal the molecular mechanisms that may cause laying hens with different eggshell quality [9,10]. For the eggshell color, Wang et al [11] conducted transcriptomic analysis to identify molecular factors affecting blue coloration in the uterus of duck with blue-green eggshells and reported a large difference in cholesterol biosynthesis and ion levels involved in the modulation of the transporting activity of bile pigment transporters.…”

Decitabine Augments Chemotherapy-Induced PD-L1 Upregulation for PD-L1 Blockade in Colorectal Cancer

“…Message RNA was extracted from the total RNA and cut into short fragments with~200 bases as templates for cDNA synthesis. The cDNAs subsequently used to establish a cDNA library by PCR amplification and sequenced by using an Illumina HiSeqTM 2500 platform [31]. Clean reads were obtained by trimming the adaptor sequences from raw reads, and these reads were then were used for further transcript annotation and calculation bases on the fragments per kilobase per million reads (FPKM) method.…”

“…Differential gene expressions (DEGs) were identified with the DESeq software package. The Benjamini-Hochberg false discovery rate was employed to correct the p values with a significant level set at 0.05 [31].…”

Distinct cell proliferation, myogenic differentiation, and gene expression in skeletal muscle myoblasts of layer and broiler chickens

“…More recently, RNA sequencing (RNA-seq) has become a powerful method for precise quantification of not only coding but also non-coding RNAs. With recent improvements of chicken genome information, RNA-seq successfully revealed the intriguing genes affecting egg albumen in layers 9 and comb size of cocks 10 . The latest studies using RNA-seq have also reported differential gene expression profiles in breast muscles of modern and foundation broiler lines 11,12 or those in broiler lines with high- and low-ultimate pH 13 .…”