The uterus is a critical pregnancy organ for mammals. The normal growth and development of ruminant uterus caruncles are crucial to maintain gestation and fetal health in goats. Quantitative real-time polymerase chain reaction (qRT-PCR) is a reliable tool to study gene expression profiling for exploring the intrinsic mechanism underlying the conversion process of uterus caruncle tissue. However, the candidate housekeeping genes (HKGs) are required for normalizing the expression of function genes. In our study, 22 HKGs were selected from analyzing transcriptome data at non-pregnancy and pregnancy processes and previous reports about HKGs in goat tissues. We assessed them for expression suitability in 24 samples from uterus tissues at 15 non-pregnant days (Stage 1), early (Stage 2), and medium-later pregnant days (Stage 3). The expression stability of these genes was evaluated by using geNorm, Normfinder, Bestkeeper, and Delta Ct algorithms and, comprehensively, by ReFinder. In addition, the most and least stable HKGs were used to normalize the target genes expression of SPP1, VEGFA, and PAG8. It was found that traditional reference genes, such as ACTB and GAPDH, were not suitable for target gene normalization. In contrast, PPIB selected from RNA sequencing data and EIF3K selected from previous references showed the least variation and were recommended as the best HKGs during the nonpregnant stage and the whole stages of goat uterus caruncle tissue, respectively. It is the first time the HKGs genes in uterus during the non-pregnant day and throughout the total pregnancy have been explored. These findings found suitable HKGs in uterus caruncle tissues at various stages of non-pregnancy and pregnancy; these can be useful for gene expression studies to reveal the molecular mechanisms of uterus development in goats.

The genetic diversity and population structures of five Chongqing local chicken populations were investigated using by 24 microsatellite markers. Results revealed that the mean number of alleles (N_A) ranged from 7.08 (Daninghe chicken, DN) to 8.46 (Nanchuan chicken, NC). The highest observed heterozygosity (H_O) and expected heterozygosity (H_E) were observed in DN (H_O = 0.7252; H_E = 0.7409) and the lowest H_O and H_E were observed in XS (Xiushan native chicken [XS], H_O = 0.5910 and H_E = 0.6697). The inbreeding coefficient (F_IS) within population ranged from 0.022 (DN) to 0.119 (XS). Among the 24 microsatellite markers, four loci (MCW0111, MCW0016, ADL0278, and MCW0104) deviated from the Hardy–Weinberg equilibrium in all the studied populations. The results of population polygenetic analysis based on Nei’s genetic distance and STRUCTURE software showed that the clustering of the five populations was incomplete consistent with geographical distribution. Moreover, a large number of gene flows were widespread among different populations, suggesting that genetic material exchanges occurred due to human activities and migration which was also verified by PCoA. In summary, this study preliminarily showed that Chongqing local chicken populations had rich genetic diversity and remarkable genetic divergence, but still high risk in conversion. These findings would be useful to the management of conservation strategies and the utilization of local chicken populations in further.

Background: As a crucial economic characteristic and a major indicator of reproductive performance in layers, egg production is controlled by a series of complex regulatory heredity basis. In particular, the interacting regulatory function between noncoding RNAs (ncRNAs) and coding RNA plays important roles in regulating laying performance. Methods: In this study, the RNA sequencing (RNA-seq) of ovarian tissues from Lohmann hens (n = 3) and Chengkou Mountain chicken (n = 3) under the laying peak period was performed to identify RNA transcriptional differences among different laying-performance populations. Results: Results showed that the expression level of 303 mRNAs, 68 long ncRNAs (lncRNAs), 533 circular RNAs (circRNAs), and 79 microRNAs (miRNAs) was significantly different among the groups. Functional enrichment analysis of these differentially expressed (DE) mRNAs revealed that the laying process was implicated in numerous significantly enriched pathways (p < 0.05), such as the neuroactive ligand-receptor interaction, steroid hormone biosynthesis, and calcium-signaling pathway. Furthermore, the lncRNA/circRNA–miRNA–mRNA regulatory networks related to the regulation of laying performance were constructed. Some randomly selective DE RNAs were verified by Real Time Quantitative (RT-qRCR), indicating that the bioinformatics analysis results of RNA-seq data were credible. Conclusions: This study could increase our understanding of the heredity basis of transcriptome in the laying performance of chicken.

In this study, we investigated the genetic diversity and phylogeny pattern in five chicken populations from Chongqing, China, using a part of mitochondrial DNA (mtDNA) D-loop sequences. The results revealed that the overall haplotype diversity (Hd) and nucleotide diversity (Pi) among the five chicken populations were 0.91646 and 0.01273, respectively. Forty-one polymorphic sites were identified within the 506-bp length of the mtDNA D-loop sequence in 239 animals. The Neighbor-Joining phylogenetic tree based on F_ST values demonstrated that the five Chongqing local chicken populations are divided into three clusters. We discovered 35 haplotypes clustered into six mtDNA haplogroups (A, B, C, E, G, and Y). Among the haplogroups, haplogroup A had the highest frequency of approximately 54.3%, whereas haplogroups G and Y had the lowest frequencies of approximately 2.9% each. Furthermore, all the five populations carried multiple haplogroups. Haplogroups A, B and E were shared by all the populations. Mismatch distribution analysis showed that no population expanded, and pairwise comparison of the populations revealed that a significant divergence (p < 0.05) existed among all the populations. The results of this study suggested that all the five chicken populations in Chongqing possessed a rich genetic diversity. The phylogenetic network demonstrated the existence of gene flows from commercial populations. This study provides theoretical basis for the conservation and further utilization of these populations.