Genomic analyses of wild argali, domestic sheep, and their hybrids provide insights into chromosome evolution, phenotypic variation, and germplasm innovation.

Understanding the genetic mechanisms of phenotypic variation in hybrids between domestic animals and their wild relatives may aid germplasm innovation. Here, we report the high-quality genome assemblies of a male Pamir argali (O ammon polii, 2n = 56), a female Tibetan sheep (O aries, 2n = 54), and a male hybrid of Pamir argali and domestic sheep, and the high-throughput sequencing of 425 ovine animals, including the hybrids of argali and domestic sheep. We detected genomic synteny between Chromosome 2 of sheep and two acrocentric chromosomes of argali. We revealed consistent satellite repeats around the chromosome breakpoints, which could have resulted in chromosome fusion. We observed many more hybrids with karyotype 2n = 54 than with 2n = 55, which could be explained by the selfish centromeres, the possible decreased rate of normal/balanced sperm, and the increased incidence of early pregnancy loss in the aneuploid ewes or rams. We identified genes and variants associated with important morphological and production traits (e.g., body weight, cannon circumference, hip height, and tail length) that show significant variations. We revealed a strong selective signature at the mutation (c.334C > A, p.G112W) in TBXT and confirmed its association with tail length among sheep populations of wide geographic and genetic origins. We produced an intercross population of 110 F2 offspring with varied number of vertebrae and validated the causal mutation by whole-genome association analysis. We verified its function using CRISPR-Cas9 genome editing. Our results provide insights into chromosomal speciation and phenotypic evolution and a foundation of genetic variants for the breeding of sheep and other animals.

Comparison of the efficiency and precision of Base editor and CRISPR/Cas9 for inducing defined point mutation (S395F) in ovine embryos.

Cytosine base editors (CBEs) and CRISPR/Cas9-mediated HDR method both have the ability to introduce nucleotide substitution into genomes, which exhibit great potential for improving economically important traits in livestock species. The FecGH mutation (g. C1184T, p. S395F) of growth differentiation factor 9 (GDF9) gene increases prolificacy in Cambridge sheep and Belclare sheep. In the present study, we aimed to compare the efficiency and precision of BE4-Gam and CRISPR/Cas9 systems on generating FecGH mutation in ovine genome. First, the microinjection of BE4-Gam mRNA had no adverse effects on development rate after cleavage, and the efficiencies of total mutants and targeted mutants were 8.9% and 7.1%, respectively. Then, the total mutation and targeted mutation rates were improved from 8.5% to 22.5% (p < .01), and 6.4% to 16.3%, respectively, by adjusting the injection time of BE4-Gam mRNA from 14 to 12 hr post-insemination (hpi). Furthermore, CRISPR/Cas9-mediated HDR method introduced the FecGH mutation at the efficiency of 16.1%, which was comparable to BE4-Gam system (16.3%). There was no bystander editing event happened in edited embryos caused by CRISPR/Cas9, but the bystander editing efficiency was as high as 15.0% in BE4-Gam-edited embryos. In summary, our findings demonstrated that CRISPR/Cas9-mediated HDR method was more accurate than BE4-Gam system in introducing FecGH into ovine genome, and highlight the potential of the former strategy to modify economically important trait-associated SNPs.

Conversion of rat embryonic stem cells into neural precursors in chemical-defined medium.

Rat embryonic stem (ES) cells hold great interest for the research of neurodevelopment and neurodegenerative diseases. However, neural conversion of rat ES cells in vitro has proven to be a challenge owing to the proliferation arrest and apoptosis. Here we report that rat ES cells can commit efficiently to a neural fate in the presence of CHIR99021 and Y-27632 (CY medium). In addition, CHIR99021 is crucial for maintaining the metabolic activity of differentiated rat ES cells, while Y-27632 facilitates the neural differentiation of rat ES cells by inhibiting bone morphogenetic protein expression. The chemical-defined CY medium also provides a platform for exploring the mechanism of neural commitment and optimizing the production efficiency of neural precursor from rat ES cells.

Introduction of the FecGF mutation in GDF9 gene via CRISPR/Cas9 system with single-stranded oligodeoxynucleotide.

The clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated (Cas) 9 system has been a recent focus of breeders owing to its potential to improve economically significant traits of livestock. The introduction of defined point mutations into the ovine genome via CRISPR/Cas9-mediated homology-directed repair has been reported; however, indel and mosaic events observed in genetically modified animals limit the practical application of this system in sheep breeding. The FecGF mutation (g. G1111A, p. V371 M) in the growth differentiation factor 9 (GDF9) gene is strongly associated with litter size in Belclare and Norwegian White Sheep. In the present study, we introduced the FecGF mutation in GDF9 by co-injecting the CRISPR/Cas9 system, single-stranded oligodeoxynucleotide (ssODN), and Scr7 into ovine zygotes. Scr7 at various concentrations (0 µM, 1 µM, and 2 µM) had no adverse effects on embryonic development in vitro. No significant differences in total mutation, point mutation, and indel rates in embryos were observed among groups treated with different concentrations of Scr7. However, the mosaicism rates of embryos from zygotes microinjected with 1 and 2 µM Scr7 were significantly lower than that for 0 µM Scr7 (7.7% and 7.5% vs. 19.7%). We successfully obtained lambs with defined nucleotide substitutions by the coinjection of Cas9 mRNA, sgRNA, ssODN, and 1 µM Scr7 into Altay sheep zygotes. The single nucleotide mutation efficiency was 7.69% (3/39) in newborn lambs, with one mosaic. Our findings provide evidence that Scr7 could improve the specificity of the CRISPR/Cas9 system for the introduction of a defined point mutation in livestock to some extent.

Wnt/beta-catenin signaling in embryonic stem cell converted tumor cells.

BACKGROUND: Embryonic stem cells (ESCs) are pluripotent stem cells and can form tumors containing cells from all three germ layers. Similarities between pluripotent stem cells and malignant tumor cells have been identified. The purpose of this study was to obtain ESCs-converted tumor cell lines and to investigate the mechanism of malignancy in pluripotent stem cells. METHODS: Mouse ESCs were subcutaneously injected into nude mice to obtain tumors from which a tumor-like cell line (ECCs1) was established by culturing the cells in chemical-defined N2B27 medium supplied with two small molecular inhibitors CHIR99021 and PD0325901 (2i). The ECCs1 were then subcutaneously injected into nude mice again to obtain tumors from which another tumor-like cells line (ECCs2) was established in the same 2i medium. The malignant degree of ESCs, ECCs1 and ECCs2 was compared and the underlying mechanism involved in the malignancy development of ESCs was examined. RESULTS: The three ESCs, ECCs1 and ECCs2 cell lines were cultured in the same 2i condition and showed some likeness such as Oct4-expression and long-term expansion ability. However, the morphology and the tumor-formation ability of the cell lines were different. We identified that ECCs1 and ECCs2 gradually acquired malignancy. Moreover, Wnt signaling-related genes such as CD133 and ß-catenin expression were up-regulated and Frizzled related protein (FRP) was down-regulated during the tumor development of ESCs. CONCLUSIONS: The two tumor-like cell lines ECCs1 and ECCs2 stand for early malignant development stage of ESCs and the ECCs2 was more malignant than the ECCs1. Moreover, we identified that Wnt/ß-catenin signaling played an important role in the malignancy process of ESCs.

[Density fluctuation of microfilariae and the role of residual infection source in filariasis transmission after its interruption].

OBJECTIVE: To investigate the density fluctuation of microfilariae, persistence of microfilaremia and possible new infection due to residual microfilaremia in areas with filariasis transmission interrupted. METHODS: The observation site was made in a village of Jishou City, Hunan Province. Inhabitants were regularly examined by thick blood smear and the density fluctuation of residual microfilaremia in known and newly-found cases were followed up. With a consent from the cases with residual microfilaremia, no treatment was given until they naturally turned negative. Antifilarial antibody level was detected by IFAT and a test kit for filariasis-special IgG4. Culex quinquefociatus was dissected to determine the natural infection rate and density of III stage filarial larvae in transmission season. The identified cases were followed-up by interviews and physical examinations to see if clinical manifestations appeared. RESULTS: Blood examination was carried out for all inhabitants for 10 times, 4 cases with microfilaremia, including 3 cases found at the beginning of the project and one newly infected case, were discovered after the interruption of filariasis transmission in the 19-year period. Among the 4 cases followed up, one case naturally turned negative within 7 years, one case became negative in the 9th year but returned positive in the 12th year, and then naturally turned negative in the 13th year. The 3rd case turned negative in the 14th year and was again positive in the 19th and the 20th years, and became negative through diethylcarbamazine (DEC) treatment in the 21st year. The new case was found to have microfilaremia in the 16th year and kept positive for 5 years until DEC treatment. Serological tests (IFAT and special IgG4) revealed no new positive cases. The natural infection rate and larvae density in Culex quinquefasciatus decreased annually. Conclusion The persistence period of residual microfilaremia in individual cases might last for more than 20 years after filariasis transmission has been interrupted.

Disruption of the sheep BMPR-IB gene by CRISPR/Cas9 in in vitro-produced embryos.

BMPR-IB (also known as FecB) is a key candidate gene for the genetic control of sheep reproductive performance. Loss-of-function mutations in the sheep BMPR-IB gene lead to an increase in ovulation rate and consequently larger litter size. However, the BMPR-IB gene has been identified in only a few sheep breeds. To improve sheep reproduction through modification of the BMPR-IB gene, we designed an sgRNA to target the sheep BMPR-IB gene by using the CRISPR/Cas9 system. First, we performed gene editing by injecting Cas9/sgRNA into the cytoplasm of one-cell fertilized eggs. A total of 88 embryos were assayed by T7EI digestion and Sanger sequencing. The results reported that the efficiency of gene modification was 37.5% (33/88) and increased with the developmental stage of embryo from the 2-cell stage to the blastocyst stage. Of the 33 gene editing embryos, 12 (36%, 12/33) were homozygous and 21 (64%, 21/33) were heterozygous. Moreover, sequence analysis of the PCR products from the positive embryos revealed that there were more than 10 modification forms that resulted in frame shift and truncated proteins. Further analysis by cloning and sequencing of each individual embryo showed a high level of mosaicism. In addition, off-target event analysis revealed that none of the off-target mutations was introduced into the embryos. Our results indicated that the Cas9/sgRNA system is a simple and efficient tool that may potentially be used in the genetic modification of the sheep BMPR-IB gene in vivo.

Alteration of sheep coat color pattern by disruption of ASIP gene via CRISPR Cas9.

Coat color is an important characteristic and economic trait in domestic sheep. Aiming at alteration of Chinese merino sheep coat color by genome manipulation, we disrupted sheep agouti signaling protein gene by CRISPR/Cas9. A total of seven indels were identified in 5 of 6 born lambs. Each targeted lamb happened at least two kinds of modifications, and targeted lambs with multiple modifications displayed variety of coat color patterns. Three lambs with 4 bp deletion showed badgerface with black body coat color in two lambs, and brown coat color with light ventral pigmentation in another one. The black-white spotted color was observed in two lambs with 2 bp deletion. Further analysis unraveled that modifications happened in one or more than two copies of ASIP gene, and moreover, the additional spontaneous mutations of D9 and/or D5 preceding the targeting modification could also involve the formation of coat color patterns. Taken together, the entanglement of ASIP modifications by CRISPR/Cas9, spontaneous D9/D5 mutations, and ASIP gene duplications contributed to the variety of coat color patterns in targeted lambs.

CRISPR/Cas9-mediated loss of FGF5 function increases wool staple length in sheep.

Fibroblast growth factor 5 (FGF5) regulates hair length in humans and a variety of other animals. To investigate whether FGF5 has similar effects in sheep, we used clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated 9 (Cas9) to generate loss-of-function mutations with the FGF5 gene in Chinese Merino sheep. A total of 16 lambs were identified with genetic mutations within the targeting locus: 13 lambs had biallelic modifications and three lambs had monoallelic modifications. Characterization of the modifications revealed that 13 were frameshift mutations that led to premature termination, whereas the other three were in-frame deletions. Thus, CRISPR/Cas9 efficiently generated loss-of-function mutations in the sheep FGF5 gene. We then investigated the effect of loss of FGF5 function on wool traits in 12 lambs and found that wool staple length and stretched length of genetically modified (GM) yearling sheep were significantly longer compared with that of wild-type (WT) control animals. The greasy fleece weight of GM yearling sheep was also significantly greater compared with that of WT sheep. Moreover, the mean fiber diameter in GM sheep showed no significant difference compared with WT sheep, suggesting that the increase in greasy fleece weight was likely attributed to the increase in wool length. The results of this study suggest that CRISPR/Cas9-mediated loss of FGF5 activity could promote wool growth and, consequently, increase wool length and yield.

Germline transmission of an embryonic stem cell line derived from BALB/c cataract mice.

Mice embryonic stem (ES) cells have enabled the generation of mouse strains with defined mutation(s) in their genome for putative disease loci analysis. In the study of cataract, the complex genetic background of this disease and lack of long-term self-renewal ES cells have hampered the functional researches of cataract-related genes. In this study, we aimed to establish ES cells from inherited cataract mice (BALB/CCat/Cat). Embryos of cataract mice were cultured in chemical-defined N2B27 medium with the presence of two small molecules PD0325901 and CHIR99021 (2i) and an ES cell line (named EH-BES) was successfully established. EH-BES showed long-term self-renewal in 2i medium and maintained capacity of germline transmission. Most importantly, the produced chimera and offspring developed congenital cataract as well. Flow cytometry assay revealed that EH-BES are homogeneous in expression of Oct4 and Rex1in 2i medium, which may account for their self-renewal ability. With long-term self-renewal ability and germline-competent, EH-BES cell line can facilitate genetic and functional researches of cataract-related genes and better address mechanisms of cataract.

Germ-line-competent embryonic stem cells of the Chinese Kunming mouse strain with long-term self-renewal ability.

Kunming (KM) mice are the most widely used strain in China. However, authentic embryonic stem cells (ESCs) from KM mice have never been available, and this hampers the genetic manipulation of this valuable mice strain. In this study, we show that KM ESCs can be efficiently derived and maintained in chemically defined N2B27 medium with the presence of two small molecules PD0325901 and CHIR99021 (2i medium). These KM ESCs exhibit all features of ESCs, including long-term self-renewal ability, expression of key molecular markers (Oct4, Nanog, and Sox2), the ability to form teratomas, and the capacity to incorporate into the developing embryo and then transmit through the germ line.

Establishment of mouse teratocarcinomas stem cells line and screening genes responsible for malignancy.

The sequential transplantation of embryonal carcinoma cells in vivo can accelerate the growth and malignancy of teratocarcinomas. However, the possible molecular mechanisms in this process that reflect cancer formation in the early stage are largely unknown and. To identify which genes are associated with the changes of malignancy of teratocarcinomas, we established a tumorigenesis model in which teratocarcinoma were induced via injecting embryonic stem cells into immuno-deficiency mice, isolating teratocarcinoma stem cell from a teratocarcinoma in serum-free culture medium and injecting teratocarcinoma stem cells into immune-deficient mice continuously. By using high-throughput deep sequence technology, we identified 26 differentially expressed genes related to the changes of characteristics of teratocarcinoma stem cell in which 18 out of 26 genes were down-regulated and 8 genes were up-regulated. Among these genes, several tumor-related genes such as Gata3, Arnt and Tdgf1, epigenetic associated genes such as PHC1 and Uty were identified. Pathway enrichment analysis result revealed that Wnt signaling pathway, primary immunodeficiency pathway, antigen processing and presentation pathway and allograft rejection pathway were involved in the teratocarcinoma tumorigenesis (corrected p value<0.05). In summary, our study established a tumorigenesis model and proposed some candidate genes and signaling pathways that may play a key role in the early stage of cancer occurrence.

Addition of alpha-tocopherol to culture medium improves the quality and cryosurvival of nuclear-transferred ovine embryos.

The aim of this study was to reconstruct and cryopreserve somatic cell nuclear transferred (SCNT) ovine embryos and evaluate the effect of alpha-tocopherol on blastocyst development and subsequent cryosurvival of the SCNT embryos. The alpha-tocopherol (100 microg/ml) was added into culture medium for the SCNT embryos, the yield and total cell numbers of blastocysts were determined and the apoptosis incidences of the blastocysts were evaluated using the TUNEL assay. The blastocysts from the alpha-tocopherol and untreated groups were then frozen-thawed, and their cryosurvival was assessed by in vitro culture for 48 h. The results showed that there were no significant differences in blastocyst yield (26.3 vs. 22.3%) and total cell number (68.2 vs. 64.3) between the alpha-tocopherol and untreated groups. However, addition of alpha-tocopherol to the culture medium significantly decreased the apoptotic cell number (3.4 vs. 5.5) and significantly increased the cryosurvival of SCNT blastocysts (66.8 vs. 50.7%). In conclusion, addition of alpha-tocopherol to SCNT embryo culture medium was beneficial for improving embryo quality by decreasing the apoptotic blastocyst cell number and improving the tolerance of the embryos to cryopreservation.