A novel minisequencing single-nucleotide polymorphism marker of the lysozyme gene detects high hatchability of Tsaiya ducks (Anas platyrhynchos)

The relationship between lysozyme gene polymorphism and quality changes during the storage of eggs derived from 2 commercial strains of Japanese quail

During the storage irreversible changes occur in eggs that result in a deterioration of their quality. The most significant changes affect the albumen. One of the major proteins of albumen present in egg white is lysozyme, which protects the embryo from microorganisms. This enzyme also contributes to the qualitative characteristics of albumen. It is possible that its polymorphism also affects the quality and stability of the obtained raw material that is, table eggs. Therefore, the aim of this study was to assess the potential effect of polymorphism in the lysozyme gene and protein on the quality changes during the storage of eggs derived from 2 genetic strains of Japanese quail belonging to various utility types. Eggs from selected females of laying and meat-type breeds were stored for 14 wk. During this period the egg quality traits were evaluated 10 times. DNA was isolated from each female and all exons of the lysozyme gene had been sequenced. In total, fourteen SNPs' and one 4-bp indel mutation were identified in exons and adjacent intronic sequences, among which SNP1 (1:32140723) resulted in a substitution of lysine with glutamine (Q21K). The results showed that SNP1 (strain S22), as well as the SNP2, SNP5, SNP7, SNP8, SNP10, SNP11, SNP12 and SNP13 were significantly associated with breaking strength during egg storage in both investigated Japanese quail strains. Furthermore, a 3 haplotype blocks containing nine SNPs (2, 5, 6, 7, 8, 10, 11, 12 and 13) were identified. These blocks displayed 8 distinct haplotypes that had significant association with breaking strength at all storage time points where egg quality analyses were performed. The study also revealed significant effects of breed and storage time on the egg quality traits. These results provide new insights into the genetic basis of egg quality during storage and could be incorporated into the breeding programs involving these strains.

Managing Gut Microbiota through In Ovo Nutrition Influences Early-Life Programming in Broiler Chickens

The chicken gut is the habitat to trillions of microorganisms that affect physiological functions and immune status through metabolic activities and host interaction. Gut microbiota research previously focused on inflammation; however, it is now clear that these microbial communities play an essential role in maintaining normal homeostatic conditions by regulating the immune system. In addition, the microbiota helps reduce and prevent pathogen colonization of the gut via the mechanism of competitive exclusion and the synthesis of bactericidal molecules. Under commercial conditions, newly hatched chicks have access to feed after 36-72 h of hatching due to the hatch window and routine hatchery practices. This delay adversely affects the potential inoculation of the healthy microbiota and impairs the development and maturation of muscle, the immune system, and the gastrointestinal tract (GIT). Modulating the gut microbiota has been proposed as a potential strategy for improving host health and productivity and avoiding undesirable effects on gut health and the immune system. Using early-life programming via in ovo stimulation with probiotics and prebiotics, it may be possible to avoid selected metabolic disorders, poor immunity, and pathogen resistance, which the broiler industry now faces due to commercial hatching and selection pressures imposed by an increasingly demanding market.

A new DNA marker of the TMIGD1 gene used to identify high fertilization rates in Tsaiya ducks (Anas platyrhynchos)

In a prior study, comparisons of individuals of Anas platyrhynchos with higher/lower reproductive performances showed that the expression of the transmembrane and immunoglobulin domain containing 1 (TMIGD1) gene significantly differed between the two groups. Here, we demonstrate that ducks with the TMIGD1 GG genotype have a significantly higher fertilization rate than other TMIGD1 genotypes. Primers designed based on the TMIGD1 sequence of Pekin duck were able to successfully amplify a TMIGD1 fragment from Tsaiya ducks, and sequencing results indicated that a single nucleotide polymorphism (SNP) of the TMIGD1 gene existed. We also developed a cost-effective method of restriction fragment length polymorphism. Using the above methods, ducks were classified into three genotypes. To identify the relationships between genotypes and traits, we recorded the ducks’ performance; to ensure the coverage of the entire duration of the fertile period, the egg collection period was extended to 18 days, and therefore, lower than usual fertilization rates were observed. Further assessment using a high-throughput system showed that the ducks with the GG genotype exhibited the highest fertilization rates among genotypes (P < 0.05). We suggest that TMIGD1 may affect the release of sperm protection factors from the female genital tract, and thus alter fertilization rate. In conclusion, the results of this study demonstrate that the TMIGD1 GG genotype can be used as a new DNA marker to identify animals with high fertilization rates at a young age, a process which could improve farming efficiency.

Global transcriptional expression in ovarian follicles from Tsaiya ducks (Anas platyrhynchos) with a high-fertilization rate

Novel candidates for biomarkers of a high-fertilization rate were identified here through global transcriptional profiling of ovarian follicles. Some other differentially expressed candidate genes were first noted to influence animal reproduction in our previous cDNA microarray analysis and are now recognized as markers for marker-assisted selection. In the present study, we compared gene expression in ovarian follicles from animals with high- and low-fertilization rates using an oligonucleotide array. On the basis of a fold change of greater than 1.2 and less than -1.2, a difference of >100 Affymetrix arbitrary units between the two groups, and a P value of less than 0.05, 47 genes were found to be associated with fertilization rate. GOEAST and MetaCore software were further used to identify the functional categories of genes that were differentially expressed. Then, we focused on three interesting genes associated with a high-fertilization rate: one of these genes was discovered to participate in signaling pathways of fertilization, and two genes take roles in lipid metabolism. An oligonucleotide array showed that the levels of orthodenticle homeobox 2 (OTX2) and lecithin:cholesterol acyltransferase (LCAT) gene expression were 1.62-fold and 1.95-fold higher in the high-fertilization rate group than in the low-fertilization rate group, respectively (P < 0.05). The level of apolipoprotein A-I (APOA1) gene expression was also higher in the high-fertilization rate group, with a difference of 2.31-fold (P < 0.05). The data were validated through quantitative polymerase chain reaction analysis. These results confirm the usefulness of the array technique and data mining methods in the discovery of new biomarkers and add knowledge to our understanding of the factors affecting fertilization rates in ovarian follicles.

Discovering All Transcriptome Single-Nucleotide Polymorphisms and Scanning for Selection Signatures in Ducks (Anas platyrhynchos)

The duck is one of the most economically important waterfowl as a source of meat, eggs, and feathers. Characterizing the genetic variation in duck species is an important step toward linking genes or genomic regions with phenotypes. Human-driven selection during duck domestication and subsequent breed formation has likely left detectable signatures in duck genome. In this study, we employed a panel of >1.4 million single-nucleotide polymorphisms (SNPs) identified from the RNA sequencing (RNA-seq) data of 15 duck individuals. The density of the resulting SNPs is significantly positively correlated with the density of genes across the duck genome, which demonstrates that the usage of the RNA-seq data allowed us to enrich variant functional categories, such as coding exons, untranslated regions (UTRs), introns, and downstream/upstream. We performed a complete scan of selection signatures in the ducks using the composite likelihood ratio (CLR) and found 76 candidate regions of selection, many of which harbor genes related to phenotypes relevant to the function of the digestive system and fat metabolism, including TCF7L2, EIF2AK3, ELOVL2, and fatty acid-binding protein family. This study illustrates the potential of population genetic approaches for identifying genomic regions affecting domestication-related phenotypes and further helps to increase the known genetic information about this economically important animal.