Since the feed cost is a major determinant of profitability in poultry industry, how to improve feed efficiency through genetic selection is an intriguing subject for breeders and producers. As a more suitable indicator assessing feed efficiency, residual feed intake (RFI) is defined as the difference between observed and expected feed intake based on maintenance and growth. However, the genetic mechanisms responsible for RFI in chickens are still less well appreciated. In this study, we investigated the duodenal transcriptome architecture of extreme RFI phenotypes in the six brown-egg dwarf hens (three per group) using RNA sequencing technology. Among all mapped reads, an average of 75.62% fell into annotated exons, 5.50% were located in introns, and the remaining 18.88% were assigned to intergenic regions. In total, we identified 41 promising candidate genes by differential expression analysis between the low and high RFI groups. Furthermore, qRT-PCR assays were designed for 10 randomly chosen genes, and nine (90.00%) were successfully validated. Functional annotation analyses revealed that these significant genes belong to several specific biological functions related to digestibility, metabolism and biosynthesis processes as well as energy homeostasis. We also predicted 253 intergenic coding transcripts, and these transcripts were mainly involved in fundamental biological regulation and metabolism processes. Our findings provided a pioneering exploration of biological basis underlying divergent RFI using RNA-Seq, which pinpoints promising candidate genes of functional relevance, is helpful to guide future breeding strategies to optimize feed efficiency and assists in improving the current gene annotation in chickens.
The dynamic change in brown eggshell color as hens age has been observed, but much uncertainty still exists. We aimed to analyze the depth of eggshell color and quantity of protoporphyrin ΙΧ throughout the laying period to explore the reasons for color variation. In this study, 120 Rhode Island Red hens were used, and two eggs were collected from each individual at 26, 34, 42, 50, 60, and 70 wk of age. The eggshell color (L*, a*, b*), egg weight, eggshell dry weight, and protoporphyrin ΙΧ quantity in eggshell were measured for individual eggs. Our results showed that the intensity of brown eggshell color weaken as hens aged from 26 to 60 wk of age (L* gradually increased from 61.43 to 68.07), while eggshell lightness recovered slightly at 70 wk (L* = 64.77). The correlation analysis indicated that the content of protoporphyrin ΙΧ deposited in the eggshell was an important factor for lightness fading with the ageing process (the average r was 0.66, P < 0.01), while the egg weight had little impact on the eggshell color (the average r was 0.07, P > 0.05). The shade of the eggshell color (L* and a*) at the early laying period (26 or 34 wk) had a low correlation with the other age points (42, 50, 60, and 70 wk). However, high correlations between the shell color at 42 wk of age and subsequent ages (50, 60, and 70 wk) were found, suggesting that the intensity of eggshell color is more stable after egg-laying peaks (such as 42 wk of age). In conclusion, the intensity of brown eggshell color varies greatly among the whole laying cycle and breeders can choose the proper age for eggshell color measurements to ensure the degree of shell color in the late laying period.
Glucose metabolism plays an important role in many normal and pathological physiological processes in the body. The breakdown and synthesis of muscle glycogen provides ATP for muscle activities. A genome-wide association study for muscle glycogen was performed in 474 Jingxing yellow chickens to identify significant single nucleotide polymorphisms (SNPs) and insertions and deletions (INDELs) involved in muscle glycogen metabolism. A total of nine SNPs (p < 1/699341) and three INDELs (p < 1/755733) reached a significant level of potential association. The following results were obtained through a series of analyses, including additive effects and gene function annotation. Two significant SNPs were found in introns 12 and 13 of copine 4 (CPNE4) on chromosome 2. The wild-type and mutant individuals had significant differences in glycogen metabolism at two loci (p < 0.01 for both). Individuals carrying two mutations had increased muscle glycogen content. According to the gene annotation of chromosome 11, there is a significant INDEL in intron 6 of naked cuticle homolog 1 (NKD1). After the INDEL mutation, the glycogen content increased significantly. There was a significant difference between wild-type and mutant individuals (p < 0.01). These mutations likely affecting two genes (CPNE4 and NKD1) may affect glycogen storage in a pleiotropic manner. Gene annotation indicates that CPNE4 and NKD1 may affect the process of glucose metabolism. Our findings contribute to understanding the genetic regulation of muscle glycogen metabolism and provide theoretical support.
The underlying molecular mechanisms that determine long day versus short day breeders remain unknown in any organism. Atlantic herring provides a unique opportunity to examine the molecular mechanisms involved in reproduction timing, because both spring and autumn spawners exist within the same species. Although our previous whole genome comparisons revealed a strong association of TSHR alleles with spawning seasons, the functional consequences of these variants remain unknown. Here we examined the functional significance of six candidate TSHR mutations strongly associated with herring reproductive seasonality. We show that the L471M missense mutation in the spring-allele causes enhanced cAMP signaling. The best candidate non-coding mutation is a 5.2 kb retrotransposon insertion upstream of the TSHR transcription start site, near an open chromatin region, which is likely to affect TSHR expression. The insertion occurred prior to the split between Pacific and Atlantic herring and was lost in the autumn-allele. Our study shows that strongly associated coding and non-coding variants at the TSHR locus may both contribute to the regulation of seasonal reproduction in herring.
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