A novel candidate gene CLN8 regulates fat deposition in avian

Background The fat deposition has a crucial role in animal meat flavor,and fat deposition-related traits are vital for breeding in the commercial duck industry.Avian fat-related traits are typical complex phenotypes,which need a large amount of data to analyze the genetic loci.Results In this study,we performed a new phenotypic analysis of fat traits and genotyped whole-genome varia-tions for 1,246 ducks,and combed with previous GWAS data to reach 1,880 ducks for following analysis.The carcass composition traits,subcutaneous fat weight(SFW),subcutaneous fat percentage(SFP),abdominal fat weight(AFW),abdominal fat percentage(AFP)and the body weight of day 42(BW42)for each duck were collected.We identified a set of new loci that affect the traits related to fat deposition in avian.Among these loci,ceroid-lipofuscinosis,neuronal 8(CLN8)is a novel candidate gene controlling fat deposition.We investigated its novel function and regulation in avian adipogenesis.Five significant SNPs(the most significant SNP,P-value=21.37E-12)and a single haplotype were detected in the upstream of CLN8 for subcutaneous fat percentage.Subsequently,luciferase assay demonstrated that 5 linked SNPs in the upstream of the CLN8 gene significantly decreased the transcriptional activity of CLN8.Further,ATAC-seq analysis showed that transcription factor binding sites were identified in a region close to the haplotype.A set of luciferase reporter gene vectors that contained different deletion fragments of the CLN8 promoter were con-structed,and the core promoter area of CLN8 was finally identified in the-1,884/-1,207 bp region of the 5′flanking sequences,which contains adipogenesis-related transcription factors binding sites.Moreover,the over-expression of CLN8 can remarkably facilitate adipocyte differentiation in ICPs.Consistent with these,the global transcriptome profiling and functional analysis of the over-expressed CLN8 in the cell line further revealed that the lipid biosynthetic process during the adipogenesis was significantly enriched.Conclusions Our results demonstrated that CLN8 is a positive regulator of avian adipocyte differentiation.These findings identify a novel function of CLN8 in adipocyte differentiation,which provides important clues for the further study of the mechanism of avian fat deposition.

Comparative analysis between endometrial proteomes of pregnant and non-pregnant ewes during the peri-implantation period

Background： Early pregnancy failure has a profound impact on both human reproductive health and animal production. 2/3 pregnancy failures occur during the peri-implantation period; however, the underlying mechanism（s） remains unclear. Well-organized modification of the endometrium to a receptive state is critical to establish pregnancy Aberrant endometrial modification during implantation is thought to be largely responsible for early pregnancy loss. Result： In this study, using well-managed recipient ewes that received embryo transfer as model, we compared the endometrial proteome between pregnant and non-pregnant ewes during implantation period. After embryo transfer, recipients were assigned as pregnant or non-pregnant ewes according to the presence or absence of an elongated conceptus at Day 17 of pregnancy. By comparing the endometrial proteomic profiles between pregnant and non-pregnant ewes, we identified 94 and 257 differentially expressed proteins （DEPs） in the endometrial caruncular and intercaruncular areas, respectively. Functional analysis showed that the DEPs were mainly associated with immune response, nutrient transport and utilization, as well as proteasome-mediated proteolysis. Conclusion： These analysis imply that dysfunction of these biological processes or pathways of DEP in the endometrium is highly associated with early pregnancy loss. In addition, many proteins that are essential for the establishment of pregnancy showed dysregulation in the endometrium of non-pregnant ewes. These proteins, as potential candidates, may contribute to early pregnancy loss.

The liver transcriptome of two full-sibling Songliao black pigs with extreme differences in backfat thickness

Background： Fatness traits in animals are important for their growth, meat quality, reproductive performance, and immunity. The liver is the principal organ of the regulation of lipid metabolism, and this study used massive parallelized high-throughput sequencing technologies to determine the porcine liver tissue transcriptome architecture of two full-sibling Songliao black pigs harboring extremely different phenotypes of backfat thickness. Results： The total number of reads produced for each sample was in the region of 53 million, and 8,226 novel transcripts were detected. Approximately 92 genes were differentially regulated in the liver tissue, while 31 spliced transcripts and 33 primary transcripts showed significantly differential expression between pigs with higher and lower backfat thickness. Genes that were differentially expressed were involved in the metabolism of various substances, smal molecule biochemistry, and molecular transport. Conclusions： Genes involved in the regulation of iipids could play an important role in lipid and fatty acid metabolism in the liver. These results could help us understand how liver metabolism affects the backfat thickness of pigs.

MYOD1 inhibits avian adipocyte differentiation via miRNA-206/KLF4 axis

Background:A considerable number of muscle development-related genes were differentially expressed in the early stage of avian adipocyte differentiation.However,the functions of them in adipocyte differentiation remain largely known.In this study,the myoblast determination protein 1(MYOD1)was selected as a representative of muscle development.We investigated its expression,function,and regulation in avian adipocyte differentiation.Results:The expression of MYOD1 decreased significantly in the early stage of avian adipocyte differentiation.CRIS PR/Cas9-mediated deletion of MYOD1 induced adipocyte differentiation,whereas over-expression of MYOD1 inhibited adipogenesis.The mRNA-seq data showed that MYOD1 could perturb the lipid biosynthetic process during differentiation.Our results showed that MYOD1 directly up-regulates the miR-206 expression by binding the upstream 1200 bp region of miR-206.Then,over-expression of miR-206 can inhibit the adipogenesis.Furthermore,MYOD1 affected the expression of endogenous miR-206 and its target gene Kruppel-like factor 4(KLF4),which is an important activator of adipogenesis.Accordingly,the inhibition of miR-206 or over-expression of KLF4 could counteract the inhibitory effect of MYOD1 on adipocyte differentiation.Conclusions:Our results establish that MYOD1 inhibits adipocyte differentiation by up-regulating miR-206 to suppress the KLF4 expression.These findings identify a novel function of MYOD1 in adipocyte differentiation,suggesting a potential role in body-fat distribution regulation.

Revolutionize livestock breeding in the future: an animal embryo-stem cell breeding system in a dish

Meat and milk production needs to increase ～ 70–80% relative to its current levels for satisfying the human needs in 2050.However,it is impossible to achieve such genetic gain by conventional animal breeding systems.Based on recent advances with regard to in vitro induction of germ cell from pluripotent stem cells,herein we propose a novel embryo-stem cell breeding system.Distinct from the conventional breeding system in farm animals that involves selecting and mating individuals,the novel breeding system completes breeding cycles from parental to offspring embryos directly by selecting and mating embryos in a dish.In comparison to the conventional dairy breeding scheme,this system can rapidly achieve 30–40 times more genetic gain by significantly shortening generation interval and enhancing selection intensity.However,several major obstacles must be overcome before we can fully use this system in livestock breeding,which include derivation and mantaince of pluripotent stem cells in domestic animals,as well as in vitro induction of primordial germ cells,and subsequent haploid gametes.Thus,we also discuss the potential efforts needed in solving the obstacles for application this novel system,and elaborate on their groundbreaking potential in livestock breeding.This novel system would provide a revolutionary animal breeding system by offering an unprecedented opportunity for meeting the fast-growing meat and milk demand of humans.

Systematic analysis of feeding behaviors and their effects on feed efficiency in Pekin ducks

Background： Feeding behavior study is important for animal husbandry and production. However, few studies were conducted on the feeding behavior and their relationship with feeding efficiency in Pekin ducks. In order to investigate the feeding behavior and their relationship with feed efficiency and other economic traits in Pekin ducks, we selected 358 male Pekin ducks and recorded feeding information between 3 to 6 wk of age using automatic electronic feeders, and compared the feeding behavior under different residual feed intake（RFI） levels.Results： We observed that total feed time, daily feed intake and feed intake per meal had strong positive correlations with feed efficiency traits; moreover, strong correlation between feed intake per meal and body weight was found（R=0.32, 0.36）. Daily feeding rate meal and meal duration had weak correlations with feed efficiency（R=0.14~0.15）. The phenotypic correlation of between-meal pauses, with feed efficiency was not observed. When daily changes were analyzed, high RFI ducks had the highest feed consumption over all times, and obvious differences in daily visits were found among different RFI level animals during the middle period; these differences were magnified with age, but there was no difference in daily meal number. Moreover, our data indicate that high RFI birds mainly take their meals at the edge of the population enclosure, where they are more susceptible to environmental interference.Conclusions： Overal, this study suggests that the general feeding behaviors can be accurately measured using automatic electronic feeders and certain feeding behaviors in Pekin ducks are associated with improved feed efficiency.

Comparative analysis of proteomic profiles between endometrial caruncular and intercaruncular areas in ewes during the peri-implantation period

The endometrium of sheep consists of plenty of raised intercaruncular areas （IC）. In order to better understand aglandular areas called caruncular （C）, and intensely glandular the endometrium involved mechanisms of implantation, we used LC-MS/MS technique to profile the proteome of ovine endometrial C areas and IC areas separately during the peri-implantation period, and then compared the proteomic profiles between these two areas. We successfully detected 1740 and 1813 proteins in C areas and IC areas respectively. By comparing the proteome of these two areas, we found 170 differentially expressed proteins （DEPs） （P 〈 0.05）, functional bioinformatics analysis showed these DEPs were mainly involved in growth and remodeling of endometrial tissue, cell adhesion and protein transport, and so on Our study, for the first time, provided a proteomic reference for elucidating the differences between C and IC areas, as an integrated function unit respectively, during the peri-implantation period. The results could help us to better understand the implantation in the ewes. In addition, we established a relatively detailed protein database of ovine endometrium, which provide a unique reference for further studies.

Mining Unknown Porcine Protein Isoforms by Tissue-based Map of Proteome Enhances Pig Genome Annotation

A lack of the complete pig proteome has left a gap in our knowledge of the pig genome and has restricted the feasibility of using pigs as a biomedical model.In this study,we developed a tissue-based proteome map using 34 major normal pig tissues.A total of 5841 unknown protein isoforms were identified and systematically characterized,including 2225 novel protein isoforms,669 protein isoforms from 460 genes symbolized beginning with LOC,and 2947 protein isoforms without clear NCBI annotation in the current pig reference genome.These newly identified protein isoforms were functionally annotated through profiling the pig transcriptome with high-throughput RNA sequencing of the same pig tissues,further improving the genome annotation of the corresponding protein-coding genes.Combining the well-annotated genes that have parallel expression pattern and subcellular witness,we predicted the tissue-related subcellular locations and potential functions for these unknown proteins.Finally,we mined 3081 orthologous genes for 52.7% of unknown protein isoforms across multiple species,referring to 68 KEGG pathways as well as 23 disease signaling pathways.These findings provide valuable insights and a rich resource for enhancing studies of pig genomics and biology,as well as biomedical model application to human medicine.