Novel Variants in GDF9 Gene Affect Promoter Activity and Litter Size in Mongolia Sheep

The relationship between G1 (c.260 G>A) and G4 (c.721 G>A) polymorphisms in the GDF9 gene and the litter size of sheep: A meta-analysis study

Objective

The results of G1 and G4 polymorphisms as litter-size (LS) markers of ewes remain contradictory. The aim was to evaluate the impact of G1 (c.260 G>A) and G4 (c.721 G>A) polymorphisms on the LS of sheep by synthesizing data from multiple previous studies.

Methods

Data were extracted from 14 eligible articles. The genotypes of G1 and G4 polymorphisms were homozygous wild-type (WW), heterozygous (WM), and homozygous mutant-type (MM). The standardized mean difference (SMD) method using random effect models was employed to determine the effect size of G1 and G4 polymorphisms on LS under dominant, recessive, additive, and co-dominant genetic models. Heterogeneity was analyzed with the I2 statistic index. Publication bias was depicted with funnel plots and tested by Egger's and Begg's tests.

Results

The study showed that the correlation between G1 polymorphism and LS in sheep was not significant (p > 0.05) under all genetic models. The influence of G4 polymorphism on the LS of sheep was found significantly (p < 0.05) under dominant [SMD = 0.28, I2 = 0% (no heterogeneity)] and co-dominant [SMD = -0.14, I2 = 36% (moderate heterogeneity)] genetic models. The WM genotype of G4 polymorphism increased LS, while the MM genotype reduced LS in sheep. Publication bias among G1 and G4 polymorphism studies was absent in all genetic models.

Conclusion

Thus, the study revealed that G4 polymorphism could be a potential genetic marker for LS in ewes. On the contrary, G1 polymorphism has no association with the LS of ewes.

Assessment of FecGE genotypes on reproductive traits in Brazilian Morada Nova and Santa Inês sheep

The aim of this study was to evaluate the effect of the polymorphic FecGE allele on reproductive traits in Santa Inês and Morada Nova ewes. The traits evaluated were as follows: total progeny weights at birth (PWB) and weaning (PWW) and progeny survival rates at birth (PSRB) and weaning (PSRW). A total of 389 animals, belonging to two Santa Inês herds and one Morada Nova herd, were genotyped. There was a difference between the averages for all the traits studied regarding type of parturition, herd/breed, genotype/herd, and genotype/type of parturition. For each additional progeny, if the female was FecGE/E, the PWB decreased by 1.02 kg and the PWW by 3.16 kg, also with a 0.04% reduction in PSRB and no change in PSRW. If the female was FecGE/+, the reduction in PWB was 0.24 kg, with an increase in PSRW by 0.11%, but no change in PWW and PSRB. In general, these results demonstrate that FecG+/+ females have a better ability to increase their number of progenies without reducing PWB and PWW (also similar to FecGE/+). Thus, it is suggested that further studies on the association between the traits of interest and candidate genes in sheep should be carried out so that the regions which have the greatest effect on the expression of these traits are actually identified. It was not possible to verify the effect of the FecGE allele on the PWB, PWW, PSRB, and PSRW in these Morada Nova and Santa Inês herds.

FecB mutation and litter size are associated with a 90-base pair deletion in BMPR1B in East Friesian and Hu crossbred sheep

Litter size is a critical economic trait in livestock, but only a few studies have focused on associated indel mutations in BMPR1B, a key regulator of ovulation and litter size in sheep. We evaluated the effects of BMPR1B mutations on the reproductive performance of sheep. We used Hu, East Friesian, and East Friesian/Hu crossbred sheep as experimental subjects and identified a novel 90 bp deletion in BMPR1B, which coincides with the c.746A > G (FecB mutation) genotype. The correlation between the two loci and litter size was then evaluated. We identified three genotypes for the Del-90bp locus, namely, II, ID, and DD, and three genotypes for the c.746A > G locus, namely ++, B+, and BB. Both Del-90bp and c.746A > G significantly affected the litter size of Hu and East Friesian/Hu crossbred sheep. Linkage disequilibrium analysis revealed a strong linkage disequilibrium between these loci in Hu sheep and the F1 population (r2 > 0.33), which suggests that detecting this 90 bp deletion might be a simple method to identify the likely carriers of c.746A > G. However, the function of this 90-bp deletion still needs further exploration. We provide genetic data that can be used as a reference for the breeding of improved prolific traits in sheep.

CREB1 Is Involved in miR-134-5p-Mediated Endometrial Stromal Cell Proliferation, Apoptosis, and Autophagy

The successful establishment of endometrial receptivity is a key factor in ensuring the fertility of ewes and their economic benefits. Hu sheep have attracted attention due to their high fecundity and year-round estrus. In this study, we found that in the luteal phase, the uterine gland density, uterine coefficient, and number of uterine caruncles of high-fertility Hu sheep were higher than those of low-fertility Hu sheep. Thousands of differentially expressed genes were identified in the endometrium of Hu sheep with different fertility potential using RNA sequencing (RNA-Seq). Several genes involved in endometrial receptivity were screened using bioinformatics analysis. The qRT-PCR analysis further revealed the differential expression of cAMP reactive element binding protein-1 (CREB1) in the Hu sheep endometrium during the estrous cycle. Functionally, our results suggested that CREB1 significantly affected the expression level of endometrial receptivity marker genes, promoted cell proliferation by facilitating the transition from the G1 phase to the S phase, and inhibited cell apoptosis and autophagy. Moreover, we observed a negative linear correlation between miR-134-5p and CREB1 in the endometrium. In addition, CREB1 overexpression prevented the negative effect of miR-134-5p on endometrial stromal cell (ESC) growth. Taken together, these data indicated that CREB1 was regulated by miR-134-5p and may promote the establishment of uterine receptivity by regulating the function of ESCs. Moreover, this study provides new theoretical references for identifying candidate genes associated with fertility.

Association of Novel C319T Variant of PITX2 Gene 3'UTR Region With Reproductive Performance in Awassi Sheep

Several genes influence sheep's reproductive performance, among them the paired-like homeodomain transcription factor 2 (PITX2) gene. Thus, this study aimed to examine whether the variability within the PITX2 gene is associated with the reproductive performance of Awassi ewes. A total of 123 single-progeny ewes and 109 twin ewes were used to extract genomic DNA. An amplicon of 4 sequence fragments from exons 2, 4, 5 (upstream portion), and 5 (downstream portion) of the PITX2 gene was generated by polymerase chain reaction (PCR), 228, 304, 381, and 382 bp, respectively. Three genotypes of 382 bp amplicons were identified: CC, CT, and TT. Sequence analysis revealed a novel mutation in the CT genotype 319C > T. Statistical analysis revealed that single-nucleotide polymorphism (SNP) 319C > T was associated with reproductive performance. Single-nucleotide polymorphism 319C > T-carrying ewes had significantly (P ⩽ .01) lower litter sizes, twinning rates, lambing rates, and more days to lambing than those carrying CT and CC genotypes. Based on a logistic regression analysis, it was confirmed that the 319C > T SNP decreased litter size. Ewes with TT genotype produced fewer lambs than ewes with CT and CC genotypes. According to these results, the variant 319C> T SNP negatively affects the reproductive performance of Awassi sheep. Ewes carrying the 319C > T SNP have a lower litter size and are less prolific than those without the SNP.

Effects of New Mutations in BMPRIB, GDF9, BMP15, LEPR, and B4GALNT2 Genes on Litter Size in Sheep

Prolificacy is a crucial characteristic of livestock, particularly for species such as sheep that have many births. The objectives of this study were as follows: (1) to investigate the genetic diversity of the 13 new and 7 known variants in the BMPRIB, GDF9, BMP15, LEPR, and B4GALNT2 genes in Ujimqin (UM), the F1 population of Dorper × Ujimqin crossbred (DPU), the F1 population of Suffolk × Ujimqin crossbred (SFKU), Sonid sheep (SN), Tan sheep (Tan), Hu sheep (Hu), and Small-tailed Han sheep (STH) sheep breeds/populations; (2) to perform an association analysis of the above 20 variants with litter size in 325 UM, 304 DPU, and 66 SFKU sheep populations; (3) to compare the frequencies of the litter-size-related alleles of these 20 variants among 8 sheep breeds/populations (the above seven sheep breeds + Mongolia sheep breed). With the use of the Sequenom MassARRAY®SNP assay technology, these 20 mutations were genotyped. The association analysis results showed that the c.746A>G (FecB) mutation in BMPR1B was significantly associated with the litter size of UM and DPU, the c.994A>G (FecGA) in GDF9 was significantly associated with the litter size of SFKU, and the c.31_33CTTinsdel (B1) in BMP15 was significantly associated with the litter size of UM. Our findings might provide valuable genetic markers for expanding sheep litter sizes.

Effects of novel variants in BMP15 gene on litter size in Mongolia and Ujimqin sheep breeds

Reproductive traits, such as ovulation rate and litter size, are important factors influencing the sheep industry. The bone morphogenetic protein 15 (BMP15) is a major gene affecting the reproductive traits in sheep, and multiple mutations in BMP15 gene could affect the ovulation rate and litter size in many sheep breeds, showing high breed specificity. However, identification of novel variations and seeking breed-specific markers associated with litter size in other sheep breeds are still important. In this study, we sequenced the BMP15 gene of Mongolia sheep, and 12 novel variants were detected by direct sequencing and whole-genome resequencing. Among them, the g.50985975 G > A polymorphism in intron and synonymous c.755 T > C (Leu252Pro) in exon 2 of BMP15 were significantly associated with the litter sizes of Mongolia ewes (P < 0.01 and P < 0.01, respectively), as well as the g.50988478C > A and g.50987863G > A in the promoter region of BMP15 were significantly associated with the litter sizes of Ujimqin ewes (P < 0.05 and P < 0.01, respectively). The c.755 T > C mutation is predicted to change the tertiary structure of BMP15. Our findings may provide potentially useful genetic markers for increasing litter size in sheep.

Single-nucleotide polymorphisms in <i>FLT3</i>, <i>NLRP5</i>, and <i>TGIF1</i> are associated with litter size in Small-tailed Han sheep

Previous studies have indicated that FLT3, NLRP5, and TGIF1 play a pivotal role in sheep fecundity. Nevertheless, little is known about the association of the polymorphisms of these genes with litter size (LS). In this study, the selected single-nucleotide polymorphisms (SNPs) were genotyped using a Sequenom MassARRAY® platform, and the distribution of different genotypes of the SNPs in the seven sheep breeds (Small-tailed Han, Hu, Cele Black, Suffolk, Tan, Prairie Tibetan, and Sunite sheep) were analyzed. The reliability of the estimated allele frequency for all seven SNPs was at least 0.9545. Given the association of the TGIF1 g.37866222C > T polymorphism with LS in Small-tailed Han sheep (p<0.05), fecundity differences might be caused by the change in amino acid from proline (Pro) to serine (Ser), which has an impact on secondary, tertiary protein structures with concomitant TGIF1 functionality changes. The FLT3 rs421947730 locus has a great effect on the LS (p<0.05), indicating that the locus of FLT3 in synergy with KILTG is likely to facilitate ovarian follicle maturation and ovulation. Moreover, NLRP5 rs426897754 is associated with the LS of the second and third parities (p<0.05). We speculate that a synonymous variant of NLRP5 may be involved in folliculogenesis accompanied by BMP15, FSHR, BMPR1B, AMH, and GDF9, resulting in the different fecundity of Small-tailed Han sheep. Our studies provide valuable genetic markers for sheep breeding.

Single-Cell RNA-Seq Revealed the Gene Expression Pattern during the In Vitro Maturation of Donkey Oocytes

Donkeys are an important domesticated animal, providing labor, meat, milk, and medicinal materials for humans. However, the donkey population is continuously declining and even at risk of extinction. The application of modern animal production technology, such as oocyte in vitro maturation, is a promising method to improve the donkey population. In this study, we explore the gene expression patterns of donkey germinal vesicle (GV) and in vitro matured metaphase II (MII) oocytes using single cell RNA-seq of the candidate genes along with the regulatory mechanisms that affect donkey oocyte maturation. We identified a total of 24,164 oocyte genes of which 9073 were significant differentially expressed in the GV and MII oocytes. Further Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis indicated that these genes were associated with the meiotic cell cycle, mitochondrion activity, and N-glycan biosynthesis, which might be the key genes and regulatory mechanisms affecting the maturation of donkey oocytes. Our study provides considerable understanding regarding the maturation of donkey oocytes and serves as a theoretical basis for improving the development of donkey oocytes, which could ultimately benefit the expansion of the donkey population and conservation of biodiversity and genetic resources.

Polymorphisms in BMPRIB gene affect litter size in Chinese indigenous sheep breed

The BMPRIB gene belongs to the TGF-β superfamily and is considered to be a regulator of sheep reproductive performance. Single nucleotide polymorphisms (SNPs) of BMPRIB gene in the Small Tail Han, Hu, Mongolian, Oula, Gansu Alpine Fine-wool, Dorper and Australian White sheep were detected by Sanger sequencing. Five SNPs (rs427897187 G > A, rs418841713 A > G, rs159952533 T > C, rs429416173 C > A and rs403555643 A > G) of BMPRIB gene were identified. For rs427897187 G > A, further analysis revealed that genotype GG and GA had 0.26 (p < 0.05) and 0.33 (p < 0.05) litter size less than those with genotype AA in Oula sheep. For rs403555643 A > G, further analysis revealed that genotype GG and AG had 0.65 (p < 0.05) and 0.38 (p < 0.05) litter size more than those with genotype AA in Oula sheep, and genotype GG had 0.56 (p < 0.05) litter size more than those with genotype AA in Mongolian sheep. The results showed that rs427897187 G > A and rs403555643 A > G are potential molecular markers wich could improve litter size of Chinese indigenous sheep and be used in Chinese indigenous sheep breeding.

Association between novel variants in BMPR1B gene and litter size in Mongolia and Ujimqin sheep breeds

Prolificacy is an important trait of animals, specifically for sheep. The Bone morphogenetic protein receptor 1B (BMPR1B) is a major gene affecting the litter size of many sheep breeds. The well-known FecB mutation (Q249R) was associated fully with the hyper prolific phenotype of Booroola Merino. However, the identification of variation in all exonic regions of BMPR1B was rare. In this study, we sequenced all exonic regions of BMPR1B gene of Mongolia sheep breed, and ten novel variants were detected by direct sequencing. Among them, the litter size of the Mongolia ewes with the CC genotype was significantly higher (0.34 additional lambs, p < .05) than those with the TT genotype of the g.29346567C>T single nucleotide polymorphism (SNP). The litter size of the Mongolia ewes with the TT genotype was significantly higher (0.19 additional lambs, p < .05 and .31 additional lambs, p < .01, respectively) than those with the GT and GG genotypes of the c.1470G>T SNP. The silent c.1470G>T mutation is predicted to increase the stability of the mRNA secondary structure through reducing minimum free energy and is predicted to change the mRNA secondary structure of BMPR1B. Our findings may give potentially useful genetic markers for increasing litter size in sheep.

Polymorphism Detection of GDF9 Gene and Its Association with Litter Size in Luzhong Mutton Sheep (Ovis aries)

Simple Summary

GDF9 and BMPR1B are two important reproduction genes. In this study, the whole coding region of GDF9 was sequenced, of which the mutations were detected in Luzhong mutton sheep. The results suggested that two single nucleotide polymorphisms (SNPs), g.41768501A > G and g.41768485 G > A in GDF9 gene were associated with litter size. The g.41768485 G > A is a missense mutation which is predicted to affect the tertiary structure of the protein. Thus, these two mutations may be potential effective genetic markers to improve the litter size in sheep.

Abstract

Litter size is one of the most important economic traits in sheep. GDF9 and BMPR1B are major genes affecting the litter size of sheep. In this study, the whole coding region of GDF9 was sequenced and all the SNPs (single nucleotide polymorphisms) were determined in Luzhong mutton ewes. The FecB mutation was genotyped using the Sequenom MassARRAY^®SNP assay technology. Then, the association analyses between polymorphic loci of GDF9 gene, FecB, and litter size were performed using a general linear model procedure. The results showed that eight SNPs were detected in GDF9 of Luzhong mutton sheep, including one novel mutation (g.41769606 T > G). The g.41768501A > G, g.41768485 G > A in GDF9 and FecB were significantly associated with litter size in Luzhong mutton ewes. The g.41768485 G > A is a missense mutation in the mature GDF9 protein region and is predicted to affect the tertiary structure of the protein. The results preliminarily demonstrated that GDF9 was a major gene affecting the fecundity of Luzhong mutton sheep and the two loci g.41768501A > G and g.41768485 G > A may be potential genetic markers for improving litter size.

Deletion mutation within the goat PPP3CA gene identified by GWAS significantly affects litter size

The protein phosphatase 3 catalytic subunit α (PPP3CA) gene is a high reproduction traits candidate gene for goats as revealed by a genome-wide association study. The aim of this work was to explore the genetic variations of the goat PPP3CA as well as to evaluate the genetic effects on litter size. Three novel insertions/deletions (indels) within the goat PPP3CA were found and their minor allelic frequencies (MAF) were 0.105, 0.066, and 0.042, respectively. The results showed that only the 20bp indel polymorphism was significantly associated with litter size in Shaanbei white cashmere goats (P<0.05) and individuals with deletion/deletion (DD) genotypes demonstrated the junior phenotypes when compared with those with other genotypes. These findings suggested that the 20bp indel is a potential DNA marker for selecting superior individuals in marker-assisted selection for breeding concerning fecundity in goats.

G1 point mutation in growth differentiation factor 9 gene affects litter size in Sudanese desert sheep

BACKGROUND AND AIM

Sudanese desert sheep encompass different sheep breeds named according to the different Sudanese tribes that rear them such as the Dubasi, Shugor, and Watish sheep. The objectives of this study were to screen for G1 point mutation in the polymorphic growth differentiation factor 9 (GDF9) gene, investigate its association with litter size, and construct the phylogeny of the different tribal breeds that belong to the Sudanese Desert sheep tribal types.

MATERIALS AND METHODS

Genomic DNA was extracted from whole blood of three tribal Desert sheep breeds (Dubasi, Watish, and Shugor) using the guanidine chloride method. Polymerase chain reaction-restriction fragment length polymorphism with HhaI restriction enzyme and sequencing techniques was used for genotyping the GDF9 locus for possible mutations associated with litter size in the three desert sheep tribal types.

RESULTS

G1 mutation in GDF9 caused the replacement of Arginine by Histidine at residue 87. The wild type allele (A) had the highest frequency, whereas the mutant type allele (a) had the lowest in all the sequenced subtypes. The genotype frequencies of the wild type ewes (AA) were higher than the heterozygous (Aa) and the mutant type (aa) frequencies in the three studied desert sheep types. No significant differences were found in the allele frequency between the three tribal types. Litter size was significantly influenced by the genotypes of GDF9 gene, parities, and subtypes (p≤0.01, 0.01, and 0.05, respectively). In the Watish sheep type, heterozygous sheep in their second parity recorded the highest litter size. Sequence alignment of GDF9 gene samples with the database entry indicated that all three tribal types were similar and identical to the reference sequence. The phylogenetic tree revealed that Shugor is the common ancestor of the studied types and Watish is more closely related to Shugor than Dubasi. This result mi ght partly explain the lower reproductive performance of Dubasi compared to Watish and Shugor.

CONCLUSION

The presence of one copy of GDF9 gene increased litter size in the studied Sudanese Desert sheep. This locus may be used as a biomarker for litter size improvement through genotypic selection and allele or gene introgression.

Novel indel variations of the sheep FecB gene and their effects on litter size

Various studies had shown that the FecB gene (also known as BMPRIB, BMPR1B or ALK-6) was the major gene influencing sheep litter size, for which its SNPs' variations were reportedly linked. Yet, surprisingly, there was no published information on the insertion/deletion (indel) variation of this gene. Herein, using a population of Chinese Australian White sheep (n = 932), we identified five novel indels in the different introns of the FecB gene. Among them, the 12-bp indel was distinguished as a splicing region variation that was completely linked to the 17-bp indel. Analysis of variance revealed that only the 10-bp indel was significantly associated with sheep litter size (P = 0.010), for which the deletion/deletion (DD) genotype was the harmful one for fecundity. Nevertheless, the combined genotypes of these five indels were significantly (P = 0.033) correlated with the litter size. These findings would provide fresh insight into developing a sounder basis to accelerate molecular breeding in sheep via DNA markers in a marker-assisted selection strategy.