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Assisted reproductive technologies in all mammals are critically dependent on the quality of the oocytes used to produce embryos. For reasons not fully clear, oocytes matured in vitro tend to be much less competent to become fertilized, advance to the blastocyst stage, and give rise to live young than their in vivo-produced counterparts, particularly if they are derived from immature females. Here we show that a chemically defined maturation medium supplemented with three cytokines (FGF2, LIF, and IGF1) in combination, so-called “FLI medium,” improves nuclear maturation of oocytes in cumulus–oocyte complexes derived from immature pig ovaries and provides a twofold increase in the efficiency of blastocyst production after in vitro fertilization. Transfer of such blastocysts to recipient females doubles mean litter size to about nine piglets per litter. Maturation of oocytes in FLI medium, therefore, effectively provides a fourfold increase in piglets born per oocyte collected. As they progress in culture, the FLI-matured cumulus–oocyte complexes display distinctly different kinetics of MAPK activation in the cumulus cells, much increased cumulus cell expansion, and an accelerated severance of cytoplasmic projections between the cumulus cells outside the zona pellucida and the oocyte within. These events likely underpin the improvement in oocyte quality achieved by using the FLI medium.

Hu sheep (HS), a breed of sheep carrying the FecB mutation gene, is known for its “year-round estrus and multiple births” and is an ideal model for studying the high fecundity mechanisms of livestock. Through analyzing and comparing the genomic selection features of Hu sheep and other sheep breeds, we identified a series of candidate genes that may play a role in Hu sheep’s high fecundity mechanisms. In this study, we conducted whole-genome resequencing on six breeds and screened key mutations significantly correlated with high reproductive traits in sheep. Notably, the CC2D1B gene was selected by the fixation index ( F ST ) and the cross-population composite likelihood ratio (XP-CLR) methods in HS and other five breeds. It was worth noting that the CC2D1B gene in HS was different from that in other sheep breeds, and seven missense mutations have been identified. Furthermore, the linkage disequilibrium (LD) analysis revealed a strong linkage disequilibrium in this specific gene region. Subsequently, by performing different grouping based on FecB genotypes in Hu sheep, genome-wide selective signal analysis screened several genes related to reproduction, such as BMPR1B and PPM1K . Besides, F ST analysis identified functional genes related to reproductive traits, including RHEB , HSPA2 , PPP1CC , HVCN1 , and CCDC63 . Additionally, a missense mutation was found in the CCDC63 gene and the haplotype was different between the high reproduction (HR) group and low reproduction (LR) group in HS. In summary, we discovered genetic differentiation among six distinct breeding sheep breeds at the whole genome level. Additionally, we identified a set of genes which were associated with reproductive performance in Hu sheep and visualized how these genes differed in different breeds. These findings laid a theoretical foundation for understanding genetic mechanisms behind high prolific traits in sheep.

This study aimed to investigate the effects of single nucleotide polymorphisms (SNPs) in progestogen-associated endometrial protein ( PAEP ), keratin 10 ( KRT 10), and bone morphogenetic protein 7 ( BMP 7) genes on reproductive traits (total number of piglets born, number of piglets born alive, litter birth weight, number of piglets weaned and litter weight weaned) in Kele pigs. We used 255 multiparous Kele sow (2–4 parities) as research materials. SNPs were identified by using a PCR amplification instrument and sequence alignment software DANMAN. The population genetic characteristics of SNPs were analyzed using the SHEsis online software. Bioinformatics analyses of SNPs were conducted using RNAfold, SOPMA, SWISS-MODEL, and Swiss-PdbViewer programs. The associations between the SNPs and reproductive traits in Kele pigs were analyzed through SPSS 22.0 software. In this study, nine SNPs were identified in the three genes: g.1884992 T > C (exon 4), g.1885125 G > C (intron 4), and g.1885158 G > A (intron 4) in PAEP , g.21643703 C > T (intron 4), g.21643714 G > A (intron 4) and g.21643741 G > A (exon 5) in KRT 10, and g.57647887 G > A (intron 3), g.57647990 C > T (intron 3) and g.57648145 C > G (intron 3) in BMP 7. In SNPs g.1884992 T > C of PAEP, missense mutation eventuated structural changes in mRNA and proteins’ secondary structure. In SNPs g.21643741 G > A of KRT 10 , the synonymous mutation led to an alteration in mRNA secondary structure. For PAEP, the CC genotype in SNPs g.1885125 G > C and the AA genotype in SNPs g.1885158 G > A showed significantly higher values than other genotypes in all reproduction traits except for litter birth weight, preliminarily identified as the favorable genotypes. For KRT 10, the GG genotype in SNPs g.21648641 G > A showed significant superiority to the AA genotype ( P <  0.05) in all aspects except for litter birth weight and notably surpassed the GA genotype in the total number of piglets born ( P <  0.05), preliminarily recognized as a favorable genotype. Regarding BMP 7, the GA genotype in SNPs g.57647887 G > A and the CT genotype in SNPs g.57647990 C > T exhibited significantly higher number of piglets born alive and number of piglets born alive compared to other genotypes ( P <  0.05). The GG genotype in SNPs g.57648145 C > G was significantly associated with higher litter birth weight ( P <  0.05). The result of diplotype analyses indicated that the H3H3 (CCGGGG) of PAEP and H3H3 (CCGGAA) of KRT 10 had a significant effect on the five traits. For BMP 7, the H4H4 (AATTGG) diplotype showed a significant influence on all genotypes except litter birth weight.

Litter size is one of the most important economic traits in sheep. Identification of gene variants that are associated with the prolificacy rate is an important step in breeding program success and profitability of the farm. So, to identify genetic mechanisms underlying the variation in litter size in Iranian Baluchi sheep, a two-step genome-wide association study (GWAS) was performed. GWAS was conducted using genotype data from 91 Baluchi sheep. Estimated breeding values (EBVs) for litter size calculated for 3848 ewes and then used as the response variable. Besides, a pathway analysis using GO and KEGG databases were applied as a complementary approach. A total of three single nucleotide polymorphisms (SNPs) associated with litter size were identified, one each on OAR2, OAR10, and OAR25. The SNP on OAR2 is located within a novel putative candidate gene, Neurotrophic receptor tyrosine kinase 2. This gene product works as a receptor which is essential for follicular assembly, early follicular growth, and oocyte survival. The SNP on OAR25 is located within RAB4A which is involved in blood vessel formation and proliferation through angiogenesis. The SNP on OAR10 was not associated with any gene in the 1Mb span. Moreover, gene-set analysis using the KEGG database identified several pathways, such as Ovarian steroidogenesis, Steroid hormone biosynthesis, Calcium signaling pathway, and Chemokine signaling. Also, pathway analysis using the GO database revealed several functional terms, such as cellular carbohydrate metabolic, biological adhesion, cell adhesion, cell junction, and cell-cell adherens junction, among others. This is the first study that reports the NTRK2 gene affecting litter size in sheep and our study of this gene functions showed that this gene could be a good candidate for further analysis.

If humans ever start to live permanently in space, assisted reproductive technology using preserved spermatozoa will be important for producing offspring; however, radiation on the International Space Station (ISS) is more than 100 times stronger than that on Earth, and irradiation causes DNA damage in cells and gametes. Here we examined the effect of space radiation on freeze-dried mouse spermatozoa held on the ISS for 9 mo at −95 °C, with launch and recovery at room temperature. DNA damage to the spermatozoa and male pronuclei was slightly increased, but the fertilization and birth rates were similar to those of controls. Next-generation sequencing showed only minor genomic differences between offspring derived from space-preserved spermatozoa and controls, and all offspring grew to adulthood and had normal fertility. Thus, we demonstrate that although space radiation can damage sperm DNA, it does not affect the production of viable offspring after at least 9 mo of storage on the ISS.

Abstract Background Selection for increased homogeneity of litter size has been proposed to improve resistance to stress and diseases in animals. Previous studies have shown that lines selected for decreased litter size variability (L lines) have higher litter sizes at parity than lines selected for increased litter size variability (H lines), possibly due to higher embryo survival in the oviduct. Thus, the study aimed at examining the effect of the line selection on the oviduct environment and its contribution to embryo development, particularly via extracellular vesicles (EVs). Oviductal EVs (oEVs) and their molecular cargo play essential roles in supporting early embryo development in different species, but little is so far known in rabbits. Results Oviductal fluid was collected by flushing oviducts from pregnant (with embryos at 72 h p.c., P) and control does (non-ovulated/non-pregnant, NO) from the two lines, resulting in 4 experimental groups: pregnant H line (H_P); pregnant L line (L_P); non-pregnant H line (H_NO); non-pregnant L line (L_NO). Oviductal EVs were isolated and characterized. RNA cargo of oEVs was analyzed by RNA-sequencing, revealing a high number of differential abundant (DA) genes between P vs. NO does in both lines (1223 DA genes in H line and 1519 in L line, FDR<0.1%). Additionally, 27 and 25 miRNAs were found as DA between P vs. NO in H and L lines, respectively. Interestingly, functional enrichment analysis of DA genes and predicted target genes of identified miRNAs revealed biological terms such as embryo development, epithelium morphogenesis and differentiation, and cilium movement, which were only associated to L line for P and NO groups. Furthermore, the comparison between H and L lines identified 169 DA RNAs in NO does, but without significant differences in P does. For miRNAs, no differences were detected in H vs. L lines in P or NP does. Conclusions This is the first study unveiling the differential oEV RNA cargo between lines selected for low versus high variation in litter size, and in each line, between P and NO does. The changes in protein-coding RNA and miRNA cargo might reflect the different maternal support to the early embryo development in the different lines

Hu sheep is a renowned prolific local sheep breed in China, widely distributed across the country due to its excellent reproductive performance. Deciphering the molecular mechanisms underlying the high fecundity of Hu sheep is crucial for improving the litter size of ewes. In this study, we genotyped 830 female Hu sheep using the Illumina OvineSNP50 BeadChip and performed genetic diversity analysis, selection signature detection, and a genome-wide association study (GWAS) for litter size. Our results revealed that the Hu sheep population exhibits relatively high genetic diversity. A total of 4927 runs of homozygosity (ROH) segments were detected, with the majority (74.73%) being short in length. Different genomic inbreeding coefficients (FROH, FHOM, FGRM, and FUNI) ranged from −0.0060 to 0.0126, showing low levels of inbreeding in this population. Additionally, we identified 91 candidate genomic regions through three complementary selection signature methods, including ROH, composite likelihood ratio (CLR), and integrated haplotype score (iHS), and annotated 189 protein-coding genes. Moreover, we observed two significant SNPs related to the litter size of Hu sheep using GWAS analysis based on a repeatability model. Integrating the selection signatures and the GWAS results, we identified 15 candidate genes associated with litter size, among which BMPR1B and UNC5C were particularly noteworthy. These findings provide valuable insights for improving the reproductive performance and breeding of high-fecundity lines of Hu sheep.

The community-based breeding program was introduced to enhance the productivity of Bonga sheep. Data evaluating animals’ potential regarding key traits was gathered from 2009–2021. This study estimated covariance components and genetic parameters for growth (birth, weaning, and six-months weight), reproductive (lambing interval, annual reproductive rate, litter size at birth and weaning, litter weight at birth and weaning), and survival (0–3, 3–6, and 0–6 months) traits using a multivariate animal model. The Average Information Restricted Maximum Likelihood method in WOMBAT was used for growth and reproductive traits, while Derivative-free MUltivariate analysis was employed for survival traits. The results revealed that the additive heritability for growth, reproductive, and survival traits ranged from 0.15–0.26, 0.06–0.08, and 0.10–0.17, respectively. The variance ratio of maternal permanent environment for growth traits ranged from 0.07–0.25, while that of animal environment for reproductive traits ranged from 0.33–0.45. Maternal genetic heritability for birth, weaning, and six-months weights were 0.14, 0.19, and 0.19, respectively, while it ranged from 0.01–0.14 for reproductive traits. Additive genetic correlations among growth traits ranged from 0.04–0.79, and from 0.36–0.62 between growth and reproductive traits. Low to high additive genetic correlations (0.002–0.537) were recorded between growth and survival traits. Significant (P<0.001) and positive genetic trends were observed for most reproductive traits, though annual genetic trends were low. Moderate additive heritability for growth traits indicates potential for genetic improvement via selection, while the pronounced environmental impact on reproductive and survival traits suggests the need for improved management practices in addition to selection. The presence of positive genetic correlations of growth traits with reproductive and with survival traits suggests that selecting for improved weaning/six-month weight has the potential to enhance ewe productivity and lamb survival. This highlights the importance of considering both growth and reproductive/survival traits in breeding programs to achieve optimal outcomes in sheep production.

Litter size is a critical economic trait in the sheep industry. Like many other breeds, Duolang sheep typically produce one lamb per ewe per lambing. To date, genetic studies of this trait in that breed have largely relied on candidate gene approaches. To expand the genomic resources for this breed, we sequenced 297 genomes, generating approximately 10.52 trillion bases with an average coverage of 13.35X. High-quality alignments with a mapping rate exceeding 99% enabled the identification of 43,968,128 SNPs and 6,504,047 InDels. This dataset provides a valuable resource for identifying genetic variants associated with litter size through genome-wide association studies (GWAS) and lays the foundation for future genetic improvement efforts through genomic selection in Duolang sheep. Beyond trait mapping, the dataset also supports broader applications, including analyses of genetic diversity, phylogenetic relationships, population history, adaptive introgression, and breed-specific characteristics. Additionally, the moderate-coverage WGS data are suitable for structural variant (SV) detection and downstream analyses such as association mapping and the identification of SVs underlying phenotypic traits.

Background After long-term artificial selection and lineage mixing, the Danish Landrace pig (DLR), has developed characteristics such as a long body length, high lean meat rate, rapid growth rate, high litter size, and a longer gestation period, with an average gestation length of 117 days. However, the genes responsible for these desirable traits remain partly unknown. According to the breeding history of DLR pigs, it has undergone introgression from British Large White pigs (BLW), selection for high lean meat rate and long body length within the population, and a rapid improvement in reproductive performance since 1992. Research on Danish Duroc and Large White pigs has detected that the lineage of pigs in Taihu Lake region (TL) has introgressed into these two breeds. Therefore, we performed resequencing and chip scanning on 106 TL pigs and 557 DLR pigs, and downloaded 163 resequencing data from Eurasian pigs for shared haplotype analysis, selective sweep analysis, and GWAS. Results The results indicate that 12 important genes, including CREB3L2 , PRKAB2 , HIF1A , IGF1 , have introgressed from BLW into DLR pigs. These genes enhance lean meat percentage by participating in thermogenesis, oxidative phosphorylation and HIF-1 signaling pathways. In the DLR pig population, 13 shared selected genes were identified across three selective sweep methods. These genes including HBM , RHBDF1 , POLR3K , ZNF484 , were found to be associated with growth rate, body length, lean meat percentage, and reproductive performance by pheWAS analysis. Interestingly, reproductive performance is primarily related to gestational trait. GWAS for gestational trait in DLR pig population revealed 13 significant genes which also under selection in selective sweeps. These genes include INSYN1 , NPTN , NEO1 , ZDHHC21 . Our study clarifies that the lineage of TL pigs has also introgressed into DLR pigs, with NDUFS4 being an important introgressed gene influencing reproductive performance. Moreover, compared to the low-fertility American Landrace pigs, HTR7 , RPP30 , ANKRD1 , ARHGAP42 , and CNTN5 may be important genes selected for enhancing litter size within the DLR pigs. Conclusions Our research deepens the understanding of the breeding history of DLR pigs, preliminarily identifies genes associated with the characteristics of high lean meat percentage, long body length, and high fertility in DLR pigs, and also finds that the high litter size of DLR pigs may be related to gestation length.