Genome-wide SNP discovery and genetic diversity evaluation of Liangshan cattle in China.

Liangshan cattle are a very small indigenous breed with adult weight of less than 300 Kg and have been mainly distributed in the Liangshan Yi Autonomous Prefecture of Southwestern Sichuan, China. Due to its long-term adaptation to local environments, Liangshan cattle is a valuable genetic resource and should be paid with more attentions. However, the genetic diversity of Liangshan cattle have not been specifically investigated yet, which would be required when designing the appropriate conservation and utilization programs. In this study, we successfully employed the restriction-site-associated DNA sequencing (RAD-seq) approach to explore a total of 84,854 genome-wide and high-confidence SNPs of Liangshan cattle. All these SNPs were evenly distributed through all chromosomes with an average of 98 SNPs per 1-Mb region. The nucleotide diversity, expected heterozygosity, polymorphism information content of Liangshan cattle were 0.227, 0.223 and 0.183, respectively. Furthermore, there was no obvious difference on the genetic diversity among the three studied geographical populations. In conclusion, we provided a list of SNPs that could be used in the follow-up studies for Liangshan cattle and revealed a relatively high genetic variation in this gene pool.

Genome-wide identification and characterization of long non-coding RNAs during differentiation of visceral preadipocytes in rabbit.

Emerging evidence suggests that long non-coding RNAs (lncRNAs) are critical regulators of diverse biological processes, including adipogenesis. Despite being considered an ideal animal model for studying adipogenesis, little is known about the roles of lncRNAs in the regulation of rabbit preadipocyte differentiation. In the present study, visceral preadipocytes isolated from newborn rabbits were cultured in vitro and induced for differentiation, and global lncRNA expression profiles of adipocytes collected at days 0, 3, and 9 of differentiation were analyzed by RNA-seq. A total of 2066 lncRNAs were identified from nine RNA-seq libraries. Compared to protein-coding transcripts, lncRNA transcripts exhibited characteristics of a longer length and lower expression level. Furthermore, 486 and 357 differentially expressed (DE) lncRNAs were identified when comparing day 3 vs. day 0 and day 9 vs. day 3, respectively. Target genes of DE lncRNAs were predicted by the cis-regulating approach. Prediction of functions revealed that DE lncRNAs when comparing day 3 vs. day 0 were involved in gene ontology (GO) terms of developmental growth, growth, developmental cell growth, and stem cell proliferation, and involved in Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways of PI3K-Akt signaling pathway, fatty acid biosynthesis, and the insulin signaling pathway. The DE lncRNAs when comparing day 9 vs. day 3 were involved in GO terms that associated with epigenetic modification and were involved in the KEGG pathway of cAMP signaling pathway. This study provides further insight into the regulatory function of lncRNAs in rabbit visceral adipose and facilitates a better understanding of different stages of preadipocyte differentiation.

Mammary epithelial cell derived exosomal MiR-221 mediates M1 macrophage polarization via SOCS1/STATs to promote inflammatory response.

Lactational mastitis seriously alters the normal physiological function of mammary gland and activates the innate immune. Mammary epithelial cells (MECs) secret cytokines and regulate the function of immune system. However, the mechanism MECs mediated crosstalk with immune cells, such as macrophages, during mastitis is unclear. In this study, mouse mammary epithelial cells (HC11), treated with Lipoteichoic acid (LTA), and macrophages (RAW264.7) were used to mimic intercellular communication. Our results showed that exosomal miR-221 level was up-regulated and reached the peak at 12 h after infected by LTA. The expression of miR-211, CD11b protein and TNF-α mRNA were upregulated and the expression of CD206 protein and Arg-1 mRNA were inhibited in RAW264.7 treated with exosomes. In addition, miR-221 mimics and inhibitors enhanced and depressed HC11-derived exosomal miR-221 level, respectively. After treatment of Exo(mimic) in RAW264.7, the expression of CD11b protein and TNF-α mRNA were up-regulated, the expression of CD206 and Arg-1 mRNA were down-regulated. Additionally, Exo(inhibitor) enhanced CD206 protein and Arg-1 mRNA levels and inhibited CD11b protein and TNF-α mRNA levels. Furthermore, SOCS1 was identified to be a target gene of miR-221 by using Luciferase assays. And western blot assays showed that the expression of p-STAT1 and p-STAT3 were elevated and repressed, respectively. Taken together, we suggest that exosomal miR-221 promotes polarization of M1 macrophages via SOCS1, STAT1 and STAT3. And we reveal a novel crosstalk signaling pathway between mammary epithelial cells and macrophages in the process of inflammation.

Genetic diversity and population structure of four Chinese rabbit breeds.

There are a few well-known indigenous breeds of Chinese rabbits in Sichuan and Fujian provinces, for which the genetic diversity and population structure have been poorly investigated. In the present study, we successfully employed the restriction-site-associated DNA sequencing (RAD-seq) approach to comprehensively discover genome-wide SNPs of 104 rabbits from four Chinese indigenous breeds: 30 Sichuan White, 34 Tianfu Black, 32 Fujian Yellow and eight Fujian Black. A total of 7,055,440 SNPs were initially obtained, from which 113,973 high-confidence SNPs (read depth ≥ 3, calling rate = 100% and biallelic SNPs) were selected to study the genetic diversity and population structure. The mean polymorphism information content (PIC) and nucleotide diversity (π) of each breed slightly varied with ranging from 0.2000 to 0.2281 and from 0.2678 to 0.2902, respectively. On the whole, Fujian Yellow rabbits showed the highest genetic diversity, which was followed by Tianfu Black and Sichuan White rabbits. The principal component analysis (PCA) revealed that the four breeds were clearly distinguishable. Our results first reveal the genetic differences among these four rabbit breeds in the Sichuan and Fujian provinces and also provide a high-confidence set of genome-wide SNPs for Chinese indigenous rabbits that could be employed for gene linkage and association analyses in the future.