Cloning, chromosomal localization, SNP detection and association analysis of the porcine IRS-1 gene

Candidate genes associated with reproductive traits in rabbits

In the era of scientific advances and genetic progress, opportunities in the livestock sector are constantly growing. The application of molecular-based methods and approaches in farm animal breeding would accelerate and improve the expected results. The current work aims to comprehensively review the most important causative mutations in candidate genes that affect prolificacy traits in rabbits. Rabbits are a source of excellent-tasting meat that is high in protein and low in fat. Their early maturity and intensive growth are highly valued all over the world. However, improving reproductive traits and prolificacy in rabbits could be very tricky with traditional selection. Therefore, traditional breeding programs need new methods based on contemporary discoveries in molecular biology and genetics because of the complexity of the selection process. The study and implementation of genetic markers related to production in rabbits will help to create populations with specific productive traits that will produce the desired results in an extremely short time. Many studies worldwide showed an association between different genes and productive traits in rabbits. The study of these polymorphisms and their effects could be useful for molecular-oriented breeding, particularly marker-assisted selection programs in rabbit breeding.

Transcriptomic Profile of New Gene Markers Encoding Proteins Responsible for Structure of Porcine Ovarian Granulosa Cells

Simple Summary

The extracellular matrix (ECM) is involved in many physiological processes that occur in the ovary and affect reproduction in animals and humans. The ECM has been shown to significantly affect folliculogenesis, ovulation, and corpus luteum formation. This is mainly due to the involvement of ECM in intercellular signaling. In the present study, we report the gene expression profile of porcine granulosa cells during their primary in vitro culture. The genes presented are related to ECM formation but also to cadherins and integrins that influence intercellular dialogue. During the study, it was shown that most of the genes were upregulated. A detailed understanding of the expression of genes such as POSTN, CHI3L1, CAV-1, IRS1, DCN in in vitro culture of granulosa cells may provide a basis for further studies on the molecular mechanisms occurring within the ovary. Knowledge of ECM-related gene expression within granulosa cells can also be used to study the recently discovered stemness of these cells. Moreover, the presented data may serve for the development of assisted reproduction techniques, which, especially in vitro, are becoming increasingly common.

Abstract

The extracellular matrix (ECM) in granulosa cells is functionally very important, and it is involved in many processes related to ovarian follicle growth and ovulation. The aim of this study was to describe the expression profile of genes within granulosa cells that are associated with extracellular matrix formation, intercellular signaling, and cell–cell fusion. The material for this study was ovaries of sexually mature pigs obtained from a commercial slaughterhouse. Laboratory-derived granulosa cells (GCs) from ovarian follicles were cultured in a primary in vitro culture model. The extracted genetic material (0, 48, 96, and 144 h) were subjected to microarray expression analysis. Among 81 genes, 66 showed increased expression and only 15 showed decreased expression were assigned to 7 gene ontology groups “extracellular matrix binding”, “extracellular matrix structural constituent”, “binding, bridging”, “cadherin binding”, “cell adhesion molecule binding”, “collagen binding” and “cadherin binding involved in cell-cell adhesion”. The 10 genes with the highest expression (POSTN, ITGA2, FN1, LAMB1, ITGB3, CHI3L1, PCOLCE2, CAV1, DCN, COL14A1) and 10 of the most down-regulated (SPP1, IRS1, CNTLN, TMPO, PAICS, ANK2, ADAM23, ABI3BP, DNAJB1, IGF1) were selected for further analysis. The results were validated by RT-qPCR. The current results may serve as preliminary data for further analyses using in vitro granulosa cell cultures in assisted reproduction technologies, studies of pathological processes in the ovary as well as in the use of the stemness potential of GCs.

CRIP1, a novel immune-related protein, activated by Enterococcus faecalis in porcine gastrointestinal epithelial cells

Cysteine-rich intestinal protein 1 (CRIP1) is an important transcriptional regulation factor during the tumor development. Although it was largely studied in the human or mouse, no report has provided functional evidence for it in the swine. To date, the real sequence of porcine CRIP1 (poCRIP1) was also still unknown. In this study, clear characteristics for the poCRIP1 were represented. A 552bp poCRIP1 cDNA was obtained from porcine brain tissue using real time reverse transcriptase PCR. The poCRIP1 showed 89% and 93% homologous with human and cattle, respectively. And it also contained one conserved domain, LIM-CRIP domain. Meanwhile, the genomic structure and promoter map was done and several conserved transcriptional regulatory sites were also predicted in this study. The expression pattern of poCRIP1 indicated that poCRIP1 is expressed in mucosal tissue. An infection experiment about the gut was designed to analyze whether or not poCRIP1 was functional in gut immunity, and an interesting result was that poCRIP1 was only activated by an opportunistic pathogen, Enterococcus faecalis FA2-2. It was the first report to identify the full-length sequence of poCRIP1 gene, represent a clear characteristic and immunologic role of CRIP1 in domestic animal until now.

Identification and characterization of nucleotide variations in the genome of Ziziphus jujuba (Rhamnaceae) by next generation sequencing

In this study, single-nucleotide polymorphisms (SNPs) and insertions/deletions (InDels) in the genome of Ziziphus jujuba were identified using sequences generated by the Roche 454 GS-FLX sequencer. A total of, 573,141 reads were produced with an average read length of 360 bp. After quality control, 258,754 of the filtered reads were assembled into 23,864 contigs, and 293,458 remained as singletons. Using the contig assemblies as a reference, 17,160 SNPs and 478 InDels were identified. Among the SNPs, transitions occurred three times more frequently than transversions. In transitions, the number of C/T and G/A transitions was similar. Among the transversions, A/T was the most abundant, and C/G was much rarer than any of the other types of transversions, accounting for only about half the numbers of A/C, A/T and G/T transversions. For the InDels, mononucleotide changes amounted to 64.4% of the total number of InDels. In general, the frequency of detected InDels decreased as the length of the InDels increased. This study provides valuable marker resources for future genetic studies of Ziziphus spp.

SNPs discovery and CAPS marker conversion in soybean

To discover new SNPs and develop an easy assay method in soybean, we compared the high-throughput pyrosequencing ESTs with whole genome sequences in different soybean varieties and identified 3899 SNPs. Transitions were found to be much more frequent than transversions in these SNPs. We found that SNPs were widely distributed in the soybean genome, targeting numerous genes involved in various physiological and biochemical processes influencing important agronomic traits. A set of 16 SNPs were validated in nine soybean varieties, and seven SNPs were converted into CAPS. From functional gene association analysis, the marker CAPS282 on the 3'-UTR of gene Glyma07g03490 was identified as associated with 100-seed weight in soybean. The SNP discovery and CAPS markers conversion system developed in this study is fast and cost effective, and holds great promise for molecular-assisted breeding of soybean.

MyoD control of SKIP expression during pig skeletal muscle development

Skeletal muscle and kidney enriched inositol phosphatase (SKIP) was identified as a 5'-inositol phosphatase that hydrolyzes PI(3,4,5)P3 to PI(3,4)P2 that negatively regulates insulin-induced phosphatidylinositol 3-kinase signaling in skeletal muscle. In this study, we obtained a 1575-bp mRNA sequence of porcine SKIP that included the full coding region encoding a protein of 450 amino acids. With the use of comparative mapping, we mapped this gene to SSC12 q1.3, where many QTLs affect Backfat thickness at 10th rib, carcass yield, the number of muscle fibers, and ham weight traits. As a candidate gene for growth and carcass traits, a novel single nucleotide polymorphism in exon 12 (G>A) was detected by PCR-RFLP. The results showed that the GG genotype had higher skin percentage (SP), carcass length to first spondyle (CL1), carcass length to first rib (CL2), but lower intramuscular fat (IMF) as compared with genotype AG (P<0.05), and allele G seemed to be associated with an increase in the growth trait. Porcine SKIP was expressed abundantly in skeletal muscle tissue and was transcriptionally upregulated during skeletal muscle differentiation. Analysis of the porcine SKIP promoter sequence demonstrated that MyoD was involved in regulating SKIP mRNA expression in myotubes, partly via the cis-acting elements in SKIP promoter. In summary, we suggested that SKIP might play a role in the regulation of skeletal muscle development in pigs.