No abstract

The sperm storage tubules located in the mucosal folds of the uterovaginal junction ( UVJ ) are the primary site of sperm storage in chicken hens after natural mating or artificial insemination ( AI ). The short-term sperm storage (24 h after mating or AI) in hens was highly associated with immunity and pH-related pathway genes. However, the underlying mechanism of longer duration of sperm storage in female birds remains largely unclear. In the present study, transcriptome analysis was applied to uncover the dynamic gene expression changes in chicken UVJ tissues at two time points (day 3 and day 9) after AI. A total of 574 differentially expressed genes ( DEG ) were enriched, including 266 upregulated and 308 downregulated DEG. The validation of 5 DEG using quantitative PCR showed a similar expression tendency with RNA sequencing results. The gene ontology terms of DEG were highly enriched in heparin binding (9 genes including COMP , CTGF , and IMPG2 ), glycosaminoglycan binding (10 genes including PCOLCE , POSTN , and RSPO3 ), and response to estradiol and ion transport ( AREG , RAMP3 , SFRP1 , and SSTR1 ). Kyoto encyclopedia of genes and genomes pathway-enrichment analyses of DEG revealed 10 significant pathways ( P < 0.05) represented by calcium signaling pathway (7 genes including CACNA1G , PDE1C , PDGFRB , and SLC8A1 ) and glycosaminoglycan biosynthesis ( B3GNT7 , CSGALNACT1 , GLCE , and ST3GAL1 ). Protein-protein interaction network of DEG established the connection-regulating epithelial cell or cell-matrix adhesion and migration. The enriched pathways and genes were highly correlated with temporary sperm storage in and possibly sequential sperm release from chicken UVJ overtime after AI. Of these, HIP1 , PDE1C , and calcium-related genes were the most interesting candidates associated with sperm storage duration. This report provided a global gene expression profile of the chicken UVJ regarding the capacity of sperm storage overtime after AI. The outcome of this study will contribute to further understanding of the long-term sperm maintenance in avian females and eventually improving the duration of fertile egg performance by selected chicken breeding.

Identifying the signals of artificial selection can contribute to further shaping economically important traits. Here, a chicken 600k SNP-array was employed to detect the signals of artificial selection using 331 individuals from 9 breeds, including Jingfen (JF), Jinghong (JH), Araucanas (AR), White Leghorn (WL), Pekin-Bantam (PB), Shamo (SH), Gallus-Gallus-Spadiceus (GA), Rheinlander (RH) and Vorwerkhuhn (VO). Per the population genetic structure, 9 breeds were combined into 5 breed-pools, and a ‘two-step’ strategy was used to reveal the signals of artificial selection. GA, which has little artificial selection, was defined as the reference population, and a total of 204, 155, 305 and 323 potential artificial selection signals were identified in AR_VO, PB, RH_WL and JH_JF, respectively. We also found signals derived from standing and de-novo genetic variations have contributed to adaptive evolution during artificial selection. Further enrichment analysis suggests that the genomic regions of artificial selection signals harbour genes, including THSR, PTHLH and PMCH, responsible for economic traits, such as fertility, growth and immunization. Overall, this study found a series of genes that contribute to the improvement of chicken breeds and revealed the genetic mechanisms of adaptive evolution, which can be used as fundamental information in future chicken functional genomics study.

Avian sperm storage tubules ( SSTs ), which are located in the uterovaginal junction ( UVJ ) of the oviduct, are primary sperm storage sites after mating or artificial insemination. The mechanism underlying reduced sperm storage efficiency of SSTs which is highly correlated with decreased fertility rates in aged laying breeders remains largely unclear. Here, comparative transcriptomic analysis between the aged and young White Leghorn hens (120 vs. 30 wk) was applied to identify gene expression changes of UVJs containing SSTs. Bioinformatics analysis revealed 567 upregulated and 1998 downregulated differentially expressed genes. Gene ontology analysis was highly enriched in terms of immune system, cell adhesion, and cytoskeleton proteins. Kyoto Encyclopedia of Genes and Genomes analysis revealed 5 significant ( P < 0.05) pathways including inositol phosphate and glycerophospholipid metabolism. β-Galactosidase staining of chicken UVJ sections suggested increased cell senescence via aging. Oil Red O staining and immunohistochemistry detection of ADFP both confirmed distribution of lipid droplets in SST cells with increased intensity in aged breeders. The lipid synthesis and metabolism-related genes represented by TFAP2 and PLD1 were differentially expressed in aged laying breeders. The upregulation of IL15 and downregulation of a large number of immune-related genes in aged breeders indicate altered immune homeostasis in UVJs and SSTs. The increased accumulation of lipids, and altered immunity homeostasis, combined with other factors ( TJP1 , MYL9 , AFDN , and RPL13 , etc.) are potentially dominant effectors to decrease the sperm storage efficiency and egg fertility in aged laying breeders.

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.