A missense mutation in growth differentiation factor 9 (GDF9) is strongly associated with litter size in sheep

Genetic variant of the sheep E2F8 gene and its associations with litter size

The economic efficiency of sheep breeding, aiming to enhance productivity, is a focal point for improvement of sheep breeding. Recent studies highlight the involvement of the Early Region 2 Binding Factor transcription factor 8 (E2F8) gene in female reproduction. Our group's recent genome-wide association study (GWAS) emphasizes the potential impact of the E2F8 gene on prolificacy traits in Australian White sheep (AUW). Herein, the purpose of this study was to assess the correlation of the E2F8 gene with litter size in AUW sheep breed. This work encompassed 659 AUW sheep, subject to genotyping through PCR-based genotyping technology. Furthermore, the results of PCR-based genotyping showed significant associations between the P1-del-32bp bp InDel and the fourth and fifth parities litter size in AUW sheep; the litter size of those with genotype ID were superior compared to those with DD and II genotypes. Thus, these results indicate that the P1-del-32bp InDel within the E2F8 gene can be useful in marker-assisted selection (MAS) in sheep.

Detection of Booroola Polymorphism of Bone Morphogenetic Protein Receptor 1b and Embrapa Polymorphism of Growth Differentiation Factor 9 in Sheep in Thailand

This study aimed to investigate the appearance and frequencies of the Booroola polymorphism of the bone morphogenetic protein receptor 1b (BMPR1B) gene (FecB) and the Embrapa polymorphism of the growth differentiation factor 9 (GDF9) gene (FecGE) in sheep in Thailand. A total of 454 crossbred sheep blood samples were collected from four provinces in Thailand during August 2022 to July 2023. The polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method was used to identify the FecB and FecGE genotypes. The history of ewe birth types was collected from the owners to analyze the association between fecundity (Fec) genotypes and the history of birth types. The genotypic frequencies of FecB for homozygous genotype (B/B), heterozygous genotype (+/B), and wildtype (+/+) were 0.22%, 1.54%, and 98.24%, respectively. Meanwhile, the genotypic frequencies of FecGE for homozygous genotype (E/E), heterozygous genotype (+/E), and wildtype (+/+) were 0.00%, 2.42%, and 97.58%, respectively. Furthermore, three ewes exhibited both FecB and FecGE genotypes. Fisher's exact test revealed that possession of the FecB genotype was associated with multiple births (p < 0.01). Both FecB and FecGE mutations were identified in crossbred sheep in Thailand. Sheep containing FecB allele could be alternative candidates to be selected to improve the prolificacy of crossbred sheep in Thailand.

Investigating the expression of fertility-regulating LncRNAs in multiparous and uniparous Shal ewe's ovaries

Sheep is the primary source of animal protein in Iran. Birth type is one of the significant features that determine total meat output. Little is known about how long non-coding RNAs (LncRNAs) affect litter size. The purpose of this research is to investigate the DE-LncRNAs in ovarian tissue between multiparous and uniparous Shal ewes. Through bioinformatics analyses, LncRNAs with variable expression levels between ewes were discovered. Target genes were annotated using the DAVID database, and STRING and Cytoscape software were used to evaluate their interactions. The expression levels of 148 LncRNAs were different in the multiparous and uniparous ewe groups (false discovery rate (FDR) < 0.05). Eight biological process terms, nine cellular component terms, 10 molecular function terms, and 38 KEGG pathways were significant (FDR < 0.05) in the GO analysis. One of the most significant processes impacting fertility is mitogen-activated protein kinase (MAPK) signaling pathway, followed by oocyte meiosis, gonadotropin-releasing hormone signaling pathway, progesterone-mediated oocyte maturation, oxytocin signaling pathway, and cAMP signaling pathway. ENSOARG00000025710, ENSOARG00000025667, ENSOARG00000026034, and ENSOARG00000026632 are LncRNAs that may affect litter size and fertility. The most crucial hub genes include MAPK1, BRD2, GAK, RAP1B, FGF2, RAP1B, and RAP1B. We hope that this study will encourage researchers to further investigate the effect of LncRNAs on fertility.

Detection of genetic variations in the GDF9 and BMP15 genes in Kazakh meat-wool sheep

Kazakh meat-wool sheep are of great interest because of the intrabreed multifetal type's high productivity of 140 %-160 %. Genes encoding growth differentiation factor-9 (GDF9) and bone morphogenetic protein 15 (BMP15) are promising candidates for studying sheep productivity, as they affect fertility in mammals, including sheep. Thus, the purpose of this study was to assess the fertility of the Kazakh meat-wool sheep breed based on GDF9 and BMP15 candidate genes of fecundity for the selection of animals with valuable genotypes. We selected 300 heads of the Kazakh meat-wool sheep breed from two populations for PCR-RFLP (polymerase chain reaction-restriction fragment length polymorphism) analysis, 15 of which were subsequently used for sequencing of exon regions of the GDF9 and BMP15 genes. The sheep populations were tested for G1 and G8 mutations of the GDF9 gene and B2 and B4 mutations of the BMP15 gene. The PCR-RFLP analysis revealed that 59 (19.7 %) of the 300 Kazakh meat-wool breed sheep were heterozygous carriers of the G1 mutation (genotype AG) of the GDF9 gene, and sequencing analysis supported these results. The comparative phylogenetic analysis showed a clear separation of Kazakh meat-wool sheep wild types and carriers of the G1 mutation. This mutation was reported to have a relationship with the animals' litter size in other sheep breeds. For this reason, similar relationships should be investigated in Kazakh meat-wool sheep. However, G8, B2, and B4 mutations were not detected among the studied animal populations, showing that these mutations are not characteristic of the Kazakh meat-wool sheep breed.

Candidate genes for litter size in Xinjiang sheep identified by Specific Locus Amplified Fragment (SLAF) sequencing

The aim of this study was to investigate the selection signatures at a genome-wide level in 'Pishan' sheep using Specific Locus Amplified Fragment (SLAF)-seq. Blood samples from 126 ewes were sequenced using SLAF tags, and the ovarian tissues from 8 ewes (Bashbay sheep, a single litter size group (SG group); 'Pishan' sheep, double litter size group (DG group)) were collected to detect expression levels by quantitative real-time reverse transcription polymerase chain reaction (qRT-PCR). Selection signature analysis was performed using global fixation index (Fst) and nucleotide diversity (π) ratio. A total of 1,192,168 high-quality SLAFs were identified. Notably, 2380 candidate regions under selection using two approaches were identified. A total of 2069 genes were identified, which were involved in dopaminergic synapses, thyroid hormone synthesis, ovarian steroidogenesis and thyroid hormone signalling pathways. Furthermore, Growth Differentiation Factor 9 (GDF9), Period Circadian Regulator 2 (PER2), Thyroid Stimulating Hormone Receptor (TSHR), and Nuclear Receptor Coactivator 1 (NCOA1) reside within these regions and pathways. The expression levels of GDF9 and PER2 genes in sheep tissue of the DG group were significantly higher than those in the SG group. These genes are interesting candidates for litter size and provide a starting point for further identification of conservation strategies for 'Pishan' 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.

Single-cell sequencing reveals the reproductive variations between primiparous and multiparous Hu ewes

BACKGROUND

In the modern sheep production systems, the reproductive performance of ewes determines the economic profitability of farming. Revealing the genetic mechanisms underlying differences in the litter size is important for the selection and breeding of highly prolific ewes. Hu sheep, a high-quality Chinese sheep breed, is known for its high fecundity and is often used as a model to study prolificacy traits. In the current study, animals were divided into two groups according to their delivery rates in three consecutive lambing seasons (namely, the high and low reproductive groups with ≥ 3 lambs and one lamb per season, n = 3, respectively). The ewes were slaughtered within 12 h of estrus, and unilateral ovarian tissues were collected and analyzed by 10× Genomics single-cell RNA sequencing.

RESULTS

A total of 5 types of somatic cells were identified and corresponding expression profiles were mapped in the ovaries of each group. Noticeably, the differences in the ovary somatic cell expression profiles between the high and low reproductive groups were mainly clustered in the granulosa cells. Furthermore, four granulosa cell subtypes were identified. GeneSwitches analysis revealed that the abundance of JPH1 expression and the reduction of LOC101112291 expression could lead to different evolutionary directions of the granulosa cells. Additionally, the expression levels of FTH1 and FTL in mural granulosa cells of the highly reproductive group were significantly higher. These genes inhibit necroptosis and ferroptosis of mural granulosa cells, which helps prevent follicular atresia.

CONCLUSIONS

This study provides insights into the molecular mechanisms underlying the high fecundity of Hu sheep. The differences in gene expression profiles, particularly in the granulosa cells, suggest that these cells play a critical role in female prolificacy. The findings also highlight the importance of genes such as JPH1, LOC101112291, FTH1, and FTL in regulating granulosa cell function and follicular development.

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.

Comparative proteomics of ovaries elucidated the potential targets related to ovine prolificacy

Small Tail Han (STH) sheep, a unique Chinese breed, is recognized for its early maturity, year-round estrus, and prolificacy. However, the molecular mechanism of its high prolificacy has not been fully elucidated. The Proteomics approach is feasible and effective to reveal the proteins involved in the complex physiological processes of any organism. Given this, we performed the protein expression profiling of ovarian tissues during the luteal phase using polytocous STH sheep (litter size ≥2, three consecutive lambings) and monotocous STH sheep (litter size =1, three consecutive lambings) (PL vs. ML), and the follicular phase using polytocous STH sheep (litter size ≥2, three consecutive lambings) and monotocous STH sheep (litter size =1, three consecutive lambings) (PF vs. MF), respectively. Parallel Reaction Monitoring (PRM) was conducted to validate the differentially abundant proteins (DAPs). The tandem mass tag (TMT) quantitative proteomic results showed that a total of 5,237 proteins were identified, of which 49 and 44 showed differential abundance in the PL vs. ML and PF vs. MF groups, respectively. Enrichments analyses indicated that the DAPs including TIA1 cytotoxic granule-associated RNA-binding protein-like 1 (TIAL1), nicotinamide phosphoribosyltransferase (NAMPT), and cellular retinoic acid-binding protein 1 (CRABP1) were enriched at the luteal phase, while TIAL1, inhibin beta-a-subunit (A2ICA4), and W5PG55 were enriched at the follicular phase, potentially mediating reproductive processes in polytocous ewes. Furthermore, six DAPs were verified using PRM, confirming the accuracy of the TMT data acquired in this study. Together, our work expanded the database of indigenous sheep breeds and provided new ovarian candidate molecular targets, which will help in the study of the genetic mechanisms of ovine prolificacy.

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 FecG^F 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 FecG^F 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.

Detection of polymorphism in growth differentiation factor 9 gene (GDF9) Exon1 and its association with litter size in local Iraqi goats

Litter size is one of the most important economic traits in goats. Growth Differential Factor 9 (GDF9) Gene is suggested as a functional candidate for fertility, fecundity and twining rate. This study was performed to identify SNPs in exon1 of the GDF9 gene and their association with fertility traits in local Iraqi goats. The exon 1 of GDF9 was sequenced, and the SNP (Single nucleotide polymorphism ) was determined in 36 local Iraqi goats. Then the association analyses between polymorphic locals of GDF9 and litter size were performed using the chi-square analysis procedure. The result shows that mutation (C 1902 G) was significantly associated with litter size in local Iraqi goats and the location of C1902 G mutation with three genotypes CC, CG and GG. A significant effect was found for birth weight, weaning weight and twin ratio, where the homozygous dominant genotype outperformed CC. A significant impact was seen for fertility and mortality, where CC topped CG and GG in fertility percentage and superiority of CG over CC and GG in mortality rate. The results preliminarily demonstrated that GDF9 was a critical gene affecting the fecundity of local Iraqi goats and that (C 1902 G) could be a potential genetic marker. Keywords: GDF9 gene, litter size, polymorphism, Iraqi goats

Loss of growth differentiation factor 9 causes an arrest of early folliculogenesis in zebrafish-A novel insight into its action mechanism

Growth differentiation factor 9 (GDF9) was the first oocyte-specific growth factor identified; however, most information about GDF9 functions comes from studies in the mouse model. In this study, we created a mutant for Gdf9 gene (gdf9-/-) in zebrafish using TALEN approach. The loss of Gdf9 caused a complete arrest of follicle development at primary growth (PG) stage. These follicles eventually degenerated, and all mutant females gradually changed to males through sex reversal, which could be prevented by mutation of the male-promoting gene dmrt1. Interestingly, the phenotypes of gdf9-/- could be rescued by simultaneous mutation of inhibin α (inha-/-) but not estradiol treatment, suggesting a potential role for the activin-inhibin system or its signaling pathway in Gdf9 actions. In gdf9-null follicles, the expression of activin βAa (inhbaa), but not βAb (inhbab) and βB (inhbb), decreased dramatically; however, its expression rebounded in the double mutant (gdf9-/-;inha-/-). These results indicate clearly that the activation of PG follicles to enter the secondary growth (SG) requires intrinsic factors from the oocyte, such as Gdf9, which in turn works on the neighboring follicle cells to trigger follicle activation, probably involving activins. In addition, our data also support the view that estrogens are not involved in follicle activation as recently reported.

Polymorphisms and association of GRM1, GNAQ, and HCRTR1 genes with seasonal reproduction and litter size in three sheep breeds

Litter size is one of the important economic traits of livestock. Seasonal estrus, ovulation, and lambing of sheep have severely restricted the development of sheep farming in Xinjiang China. The purpose of this study was to investigate the polymorphisms and genetic correlation between GRM1, GNAQ, and HCRTR1 genes and the seasonal reproduction and litter size in three sheep breeds. The DNA mixed pool sequencing and PCR-SSCP methods were used to detect single nucleotide polymorphisms (SNPs) of GRM1, GNAQ, and HCRTR1 genes in seasonal estrus (Kazakh and Chinese Merino [Xinjiang Junken type]) and perennial estrus (Hu) sheep breeds. The association between genetic polymorphism and litter size was also analyzed. The results showed that T945C in exon 2 of GRM1 gene, C589T in exon 2 of HCRTR1 gene and A191G in exon 2 of GNAQ gene were identified by Sanger sequencing, and three genotypes were existed in each SNP sites, which all belonged to the synonymous mutation. GRM1 (CC), GNAQ (GA) and HCRTR1 (TC) were the dominant genotypes of seasonal reproduction and litter size in Kazakh sheep and Chinese Merino sheep, respectively. While, in perennial estrus Hu sheep populations, the dominant genotypes were GRM1 (TC), GNAQ (GA) and HCRTR1 (TC) respectively, and association analysis was also confirmed the results. Above results implied that GRM1, GNAQ and HCRTR1 genes are significantly associated with lambing traits in Kazakh, Chinese Merino and Hu sheep. Among them, locus of GRM1 (T945C), GNAQ (A191G) and HCRTR1 (C589T) might be considered as a potential molecular marker which controls seasonal reproduction and litter size in sheep.

The performance of phenomic selection depends on the genetic architecture of the target trait

The phenomic predictive ability depends on the genetic architecture of the target trait, being high for complex traits and low for traits with major QTL. Genomic selection is a powerful tool to assist breeding of complex traits, but a limitation is the costs required for genotyping. Recently, phenomic selection has been suggested, which uses spectral data instead of molecular markers as predictors. It was shown to be competitive with genomic prediction, as it achieved predictive abilities as high or even higher than its genomic counterpart. The objective of this study was to evaluate the performance of phenomic prediction for triticale and the dependency of the predictive ability on the genetic architecture of the target trait. We found that for traits with a complex genetic architecture, like grain yield, phenomic prediction with NIRS data as predictors achieved high predictive abilities and performed better than genomic prediction. By contrast, for mono- or oligogenic traits, for example, yellow rust, marker-based approaches achieved high predictive abilities, while those of phenomic prediction were very low. Compared with molecular markers, the predictive ability obtained using NIRS data was more robust to varying degrees of genetic relatedness between the training and prediction set. Moreover, for grain yield, smaller training sets were required to achieve a similar predictive ability for phenomic prediction than for genomic prediction. In addition, our results illustrate the potential of using field-based spectral data for phenomic prediction. Overall, our result confirmed phenomic prediction as an efficient approach to improve the selection gain for complex traits in plant breeding.

Physiological and molecular implications of multiple abiotic stresses on yield and quality of rice

Abiotic stresses adversely affect rice yield and productivity, especially under the changing climatic scenario. Exposure to multiple abiotic stresses acting together aggravates these effects. The projected increase in global temperatures, rainfall variability, and salinity will increase the frequency and intensity of multiple abiotic stresses. These abiotic stresses affect paddy physiology and deteriorate grain quality, especially milling quality and cooking characteristics. Understanding the molecular and physiological mechanisms behind grain quality reduction under multiple abiotic stresses is needed to breed cultivars that can tolerate multiple abiotic stresses. This review summarizes the combined effect of various stresses on rice physiology, focusing on grain quality parameters and yield traits, and discusses strategies for improving grain quality parameters using high-throughput phenotyping with omics approaches.

Novel InDel variations of the Cry2 gene are associated with litter size in Australian White sheep

Cryptochrome 2 (Cry2) gene regulates circadian rhythm and affects reproduction and pregnancy. Therefore, this study aimed to explore polymorphisms of the Cry2 gene and their associations with litter size at different parity in Australian White (AuW) ewes. Five putative insertion or deletion mutations within the Cry2 gene were selected to study their association with litter size. Two novel deletion mutations were identified in intronic region of Cry2 gene and were genotyped by agarose gel electrophoresis and DNA sequencing. The polymorphism information content (PIC) indicated that both mutations were low polymorphism in tested groups. Statistical analysis revealed that the P1-Del-6-bp was significantly correlated with litter size at third parity (P = 0.010), in which individuals with insertion/deletion (ID) genotype had larger litter size than insertion/insertion (II) genotype (P < 0.05). Whereas, the P2-Del-6-bp was significantly correlated with litter size at first parity (P = 0.036), in which individuals with insertion/insertion (II) genotype had larger litter size than insertion/deletion (ID) genotype (P < 0.05). Collectively, these findings may provide new insights to expedite molecular breeding in sheep through marker-assisted selection strategies (MAS).

Trends towards revealing the genetic architecture of sheep tail patterning: Promising genes and investigatory pathways

Different sheep breeds have evolved after initial domestication, generating various tail phenotypic patterns. The phenotypic diversity of sheep tail patterns offers ideal materials for comparative analysis of its genetic basis. Evolutionary biologists, animal geneticists, breeders, and producers have been curious to clearly understand the underlying genetics behind phenotypic differences in sheep tails. Understanding the causal gene(s) and mutation(s) underlying these differences will help probe an evolutionary riddle, improve animal production performance, promote animal welfare, and provide lessons that help comprehend human diseases related to fat deposition (i.e., obesity). Historically, fat tails have served as an adaptive response to aridification and climate change. However, the fat tail is currently associated with compromised mating and animal locomotion, fat distribution in the animal body, increased raising costs, reduced consumer preference, and other animal welfare issues such as tail docking. The developing genomic approaches provide unprecedented opportunities to determine causal variants underlying phenotypic differences among populations. In the last decade, researchers have performed several genomic investigations to assess the genomic causality underlying phenotypic variations in sheep tails. Various genes have been suggested with the prominence of several potentially significant causatives, including the BMP2 and PDGFD genes associated with the fat tail phenotype and the TBXT gene linked with the caudal vertebrae number and tail length. Although the potential genes related to sheep tail characteristics have been revealed, the causal variant(s) and mutation(s) of these high-ranking candidate genes are still elusive and need further investigation. The review discusses the potential genes, sheds light on a knowledge gap, and provides possible investigative approaches that could help determine the specific genomic causatives of sheep tail patterns. Besides, characterizing and revealing the genetic determinism of sheep tails will help solve issues compromising sheep breeding and welfare in the future.

An investigation of the effects of BMPR1B, BMP15, and GDF9 genes on litter size in Ramlıç and Dağlıç sheep

This study was carried out to determine the presence of polymorphisms in genes affecting litter size. The SNPs in bone morphogenetic protein receptor type 1B (BMPR1B), bone morphogenetic protein 15 (BMP15), and growth differentiation factor 9 (GDF9) genes were detected in 60 uniparous and 60 multiparous ewes from Ramlıç and Dağlıç breeds. The ewes are maintained in nine public herds at the breeding station of the Afyonkarahisar Sheep and Goats Breeders' Association and lambed in two consecutive breeding seasons. PCR and DNA sequencing analyses were conducted, and 36, 4, and 11 SNPs in Ramlıç and 40, 3, and 11 SNPs in Dağlıç were detected in BMPR1B, BMP15, and GDF9 genes, respectively. A total of 16 SNPs in Ramlıç and 10 SNPs in Dağlıç breeds for three genes were found to be significant (P<0.05). The resulting analyses showed that four SNPs (g.49496G>A, c.1658A>C, c.2037C>T, c.2053C>T) of the BMPR1B gene and one deletion mutation (c.28_30delCTT) in the BMP15 gene of the Ramlıç breed as well as five SNPs (c.1487C>A, c.2492C>T, c.2523G>A, c.2880A>G, and c.2763G>A) of the BMPR1B gene of the Dağlıç breed have significant positive regression coefficients in the desired direction of the rare allele. The observed mutations have potential to be used as genetic markers in the selection of prolific animals for both breeds.

Influence of FecGE mutation on the reproductive variables of Pelibuey ewes in the anestrus period

The growth and differentiation factor 9 (GDF9) intervenes in the fecundity and prolificacy of the ewe, which are important variables that participate in the reproductive efficiency of a flock. The objective of this study was to evaluate the influence of FecG^E mutation of the gene GDF9 in the natural response of the manifestation to estrus, return to estrus, ovulation rate, pregnancy, lambing, prolificacy, and fecundity rate in Pelibuey ewes, during the anestrus period. The sequences of the exon 2 of the gene GDF9 were obtained from blood samples collected in Whatman™ FTA™ cards from 42 multiparous Pelibuey ewes with reproductive records. For this purpose, the quality of the sequences was analyzed and the polymorphisms and genotypes were searched for. The ewes were grouped according to their group: (a) homozygous or Embrapa (GG), (b) wild (AA), and (c) group without gene (sG). All the ewes studied manifested estrus behavior, but none showed signs of return to estrus after natural mating (p > 0.05); likewise, the pregnancy and lambing rates (p > 0.05) did not show differences between groups. However, the group GG presented higher ovulation rate, prolificacy, and fecundity rate (p < 0.05), compared to groups AA and sG. Although no differences were found in the manifestation of estrus, return to estrus, and percentage of pregnancy and lambing in females from the genotypes studied, the homozygous ewes GG presented 1.22 and 1.72 more corpus luteum (CL, p < 0.05), prolificacy of 0.7 and 0.7, and fecundity rate of 0.8 and 1.0 more lambs per ewe (p < 0.05) than the ones produced by the wild-type AA and sG groups, respectively.

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.

Frequency of BMP15 and GDF9 mutations increasing litter size and their phenotypic effects in Olkuska sheep population

Two mutations affecting the ovulation rate and litter size are segregating in Olkuska sheep population, FecXO in the BMP15 gene, and the G7 site mutation in GDF9 gene. Homozygous carriers of both mutations are hyperprolific, contrary to the sterility observed in homozygous carriers of most other BMP15 and GDF9 mutations. The objective of this study was to assess frequency and phenotypic effects of both mutations. Blood samples were obtained from 740 individuals, 111 rams and 629 ewes, out of which 91 rams and 561 ewes were successfully genotyped for the BMP15 and GDF9 loci. The reproductive performance included a number of lambs born/born alive and a number of lambs reared until 60 days of age, and for a subset of ewe ovulation rates. The study proved a high frequency of the FecXO mutation in two flocks that have been selected for many years for increased litter size (0.7–1.0 in breeding ewes and rams respectively), and a moderate frequency in another 19 private flocks (0.4–0.5). The frequency of the GDF9 mutation was low, with only 50 sheep out of 312 genotyped being carriers of the GDF9/G7 mutation, including three homozygous carriers. The FecXO mutation in the BMP15 had a significant effect on both litter size and the ovulation rate. The single copy in heterozygous carriers increased litter size by 0.255 (0.063), while the effect of two copies in homozygous genotypes was +0.874 (0.081) lambs born. Due to the low frequency of the GDF9 mutation, it can only be preliminarily concluded that litter size has been increased in double carriers of both the BM15 and GDF9 mutation, which may suggest their additive interaction. The positive effect of both mutations supports their direct use in selection programmes.

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.

Identification and Characterization of Hypothalamic Alternative Splicing Events and Variants in Ovine Fecundity-Related Genes

Simple Summary

Previous studies revealed that alternative splicing (AS) events and gene variants played key roles in reproduction. However, their location and distribution in hypothalamic fecundity-related genes in sheep without the FecB mutation remain largely unknown. In this study, we performed a correlation analysis of transcriptomics and proteomics, and the results suggested several differentially expressed genes (DEGs)/differentially expressed proteins (DEPs), including galectin 3 (LGALS3), aspartoacylase (ASPA) and transthyretin (TTR), could be candidate genes influencing ovine litter size. Further analysis suggested that AS events, single nucleotide polymorphisms (SNPs) and microRNA (miRNA)-binding sites existed in key DEGs/DEPs, such as ASPA and TTR. This study provides a new insight into ovine and even other mammalian reproduction.

Abstract

Previous studies revealed that alternative splicing (AS) events and gene variants played key roles in reproduction; however, their location and distribution in hypothalamic fecundity-related genes in sheep without the FecB mutation remain largely unknown. Therefore, in this study, we described the hypothalamic AS events and variants in differentially expressed genes (DEGs) in Small Tail Han sheep without the FecB mutation at polytocous sheep in the follicular phase vs. monotocous sheep in the follicular phase (PF vs. MF) and polytocous sheep in the luteal phase vs. monotocous sheep in the luteal phase (PL vs. ML) via an RNA-seq study for the first time. We found 39 DEGs with AS events (AS DEGs) in PF vs. MF, while 42 AS DEGs were identified in PL vs. ML. No DEGs with single nucleotide polymorphisms (SNPs) were observed in PF vs. MF, but five were identified in PL vs. ML. We also performed a correlation analysis of transcriptomics and proteomics, and the results suggested several key DEGs/differentially expressed proteins (DEPs), such as galectin 3 (LGALS3) in PF vs. MF and aspartoacylase (ASPA) and transthyretin (TTR) in PL vs. ML, could be candidate genes influencing ovine litter size. In addition, further analyses suggested that AS events, SNPs and miRNA-binding sites existed in key DEGs/DEPs, such as ASPA and TTR. All in all, this study provides a new insight into ovine and even other mammalian reproduction.

Identification of polymorphisms in the oocyte-derived growth differentiation growth factor 9 (GDF9) gene associated with litter size in New Zealand sheep (Ovis aries) breeds

Having the ability to control litter size is important for sheep farmers and breeders worldwide. However, making genetic gain in key livestock traits like reproductive performance needs typically a lot of time, and both the fecundity and fertility traits have a great economic importance. Attention has therefore turned to better understanding the genes that control reproductive performance. Of these genes, research has focussed on the growth differentiation growth factor 9 (GDF9) gene (GDF9). In this study, a PCR-single strand conformation polymorphism (PCR-SSCP) approach was used to investigate variation in this gene in separate groups of purebred Finnish Landrace sheep, Finnish Landrace × Texel-cross sheep and composite sheep of undefined breed background, but based on New Zealand Romney-type genetics. Three GDF9 variants (named A, B and C) were found, and upon DNA sequencing, the nucleotide substitutions c.978A>G, c.994G>A and c.1111G>A were revealed. The frequency of variant A (containing nucleotides c.978A, c.994G and c.1111G) in the Finnish Landrace, Finnish Landrace × Texel-cross and composite sheep was 0.86, 0.78 and 0.76, respectively. In these three sheep groups, the frequency of B (defined by the presence of nucleotides c.978G and c.994A) was 0.01, 0.03 and 0.23 and for C (containing c.1111A) was 0.13, 0.18 and 0.01, respectively. An animal model was used to estimate the additive effect of fertility data for Finnish Landrace × Texel-cross sheep and revealed an association between litter size and the c.1111G>A variation (p = .036), but this was not observed for the Finnish Landrace sheep (p = .27) or the composite sheep (p = .17). When all the sheep were analysed together, the presence of c.1111A was associated (p < .05) with increased litter size, when compared to ewes that had c.1111G. Litter size did not differ between sheep with and without c.994A in all three groups of sheep investigated. This study suggests that c.1111A could be a useful genetic marker for improving fecundity in New Zealand sheep breeds and that it could be introgressed into other breeds, but analysis of more sheep will be required to confirm the associations that have been observed here.

Genome-wide association study of four composite reproductive traits in Iranian fat-tailed sheep

Composite reproductive traits are a combination of growth and reproductive traits. They have the advantage of being better attuned to the market drivers since producers are paid on a per kilogram basis and not on a per head basis. In this study, 124 Lori---Bakhtiari ewes were genotyped using the medium-density Illumina Ovine SNP50 array. A genome-wide association study was performed on estimated breeding values of four composite reproductive traits and genetic parameters were also estimated. The traits were litter mean weight at birth, litter mean weight at weaning, total litter weight at birth and total litter weight at weaning. Several suggestive and associated single nucleotide polymorphisms (SNPs) were identified. Neighbouring the top SNPs there were five genes, inhibin β E subunit (INHBE), inhibin β C subunit (INHBC), testis expressed 12 (TEX12), β-carotene oxygenase 2 (BCO2) and WD Repeat Domain 70 (WDR70) identified as possible candidate genes for composite reproductive traits of the Lori-Bakhtiari sheep. These genes are in pathways known to be relevant to fertility and growth characteristics. The results provide new information for the functional annotation of genes associated with fertility traits and add new evidence towards a consensus of quantitative trait loci associated with reproductive traits in sheep.

Using High-Density SNP Array to Reveal Selection Signatures Related to Prolificacy in Chinese and Kazakhstan Sheep Breeds

Selection signature provides an efficient tool to explore genes related to traits of interest. In this study, 176 ewes from one Chinese uniparous breed and three Kazakhstan multiparous breeds are genotyped using Affymetrix 600K HD single nucleotide polymorphism (SNP) arrays, F-statistics (Fst), and a Cross Population Extend Haplotype Homozygosity Test (XPEHH). These are conducted to identify genomic regions that might be under selection in three population pairs comprised the one multiparous breed and the uniparous breed. A total of 177 and 3072 common selective signatures were identified by Fst and XPEHH test, respectively. Nearly half of the common signatures detected by Fst were also captured by XPEHH test. In addition, 1337 positive and 1735 common negative signatures were observed by XPEHH in three Kazakhstan multiparous breeds. In total, 242 and 798 genes were identified in selective regions and positive selective regions identified by Fst and XPEHH, respectively. These genes were further clustered in 50 gene ontology (GO) functional terms and 66 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways in enrichment analysis. The GO terms and pathways were relevant with reproductive processes, e.g., oxytocin signaling pathway, thyroid hormone synthesis and GnRH signaling pathway, vascular smooth muscle contraction and lipid metabolism (alpha-Linolenic acid metabolism and Linoleic acid metabolism), etc. Based on the findings, six potential candidate genes ESR1, OXTR, MAPK1, RYR1, PDIA4, and CYP19A1, under positive selection related to characteristics of multiparous sheep breeds were revealed. Our results improve our understanding of the mechanisms of selection that underlies the prolificacy trait in sheep, and provide essential references for future sheep breeding.

TGIF1 and SF1 polymorphisms are associated with litter size in Small Tail Han sheep

TGF‐β induced factor homeobox 1 (TGIF1) and splicing factor 1 (SF1) are important for mammalian reproduction; however, the effects of these genes on litter size in sheep remain unexplored. In this study, we genotyped 768 ewes from seven sheep breeds at two loci: g.37871539C>T, a synonymous mutation of TGIF1; and g.42314637T>C, a 3′UTR variant of SF1. Our analysis of polymorphism revealed only two genotypes at locus g.37871539C>T in TGIF1, with most sheep populations being moderately polymorphic (0.25 < PIC < 0.5) at this site. In contrast, most breeds exhibited low polymorphism (PIC ≤0.25) at the SF1 locus g.42314637T>C. The association analysis revealed that a synonymous mutation at g.37871539C>T in TGIF1 was highly associated with litter size in Small Tail Han sheep, in which it causes a significant decrease in litter size. Conversely, while the SF1 3′UTR variant g.42314637T>C was also highly associated with litter size in sheep, it causes a significant increase in the number of litter size. Combined, these data provide valuable information regarding candidate genetic markers for sheep breeding programs.

On the origin of European sheep as revealed by the diversity of the Balkan breeds and by optimizing population-genetic analysis tools

Background

In the Neolithic, domestic sheep migrated into Europe and subsequently spread in westerly and northwesterly directions. Reconstruction of these migrations and subsequent genetic events requires a more detailed characterization of the current phylogeographic differentiation.

Results

We collected 50 K single nucleotide polymorphism (SNP) profiles of Balkan sheep that are currently found near the major Neolithic point of entry into Europe, and combined these data with published genotypes from southwest-Asian, Mediterranean, central-European and north-European sheep and from Asian and European mouflons. We detected clines, ancestral components and admixture by using variants of common analysis tools: geography-informative supervised principal component analysis (PCA), breed-specific admixture analysis, across-breed \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$f_{4}$$\end{document}f4 profiles and phylogenetic analysis of regional pools of breeds. The regional Balkan sheep populations exhibit considerable genetic overlap, but are clearly distinct from the breeds in surrounding regions. The Asian mouflon did not influence the differentiation of the European domestic sheep and is only distantly related to present-day sheep, including those from Iran where the mouflons were sampled. We demonstrate the occurrence, from southeast to northwest Europe, of a continuously increasing ancestral component of up to 20% contributed by the European mouflon, which is assumed to descend from the original Neolithic domesticates. The overall patterns indicate that the Balkan region and Italy served as post-domestication migration hubs, from which wool sheep reached Spain and north Italy with subsequent migrations northwards. The documented dispersal of Tarentine wool sheep during the Roman period may have been part of this process. Our results also reproduce the documented 18th century admixture of Spanish Merino sheep into several central-European breeds.

Conclusions

Our results contribute to a better understanding of the events that have created the present diversity pattern, which is relevant for the management of the genetic resources represented by the European sheep population.

Gene Expression Profiling of Corpus luteum Reveals Important Insights about Early Pregnancy in Domestic Sheep

The majority of pregnancy loss in ruminants occurs during the preimplantation stage, which is thus the most critical period determining reproductive success. Here, we performed a comparative transcriptome study by sequencing total mRNA from corpus luteum (CL) collected during the preimplantation stage of pregnancy in Finnsheep, Texel and F1 crosses. A total of 21,287 genes were expressed in our data. Highly expressed autosomal genes in the CL were associated with biological processes such as progesterone formation (STAR, CYP11A1, and HSD3B1) and embryo implantation (e.g., TIMP1, TIMP2 and TCTP). Among the list of differentially expressed genes, sialic acid-binding immunoglobulin (Ig)-like lectins (SIGLEC3, SIGLEC14, SIGLEC8), ribosomal proteins (RPL17, RPL34, RPS3A, MRPS33) and chemokines (CCL5, CCL24, CXCL13, CXCL9) were upregulated in Finnsheep, while four multidrug resistance-associated proteins (MRPs) were upregulated in Texel ewes. A total of 17 known genes and two uncharacterized non-coding RNAs (ncRNAs) were differentially expressed in breed-wise comparisons owing to the flushing diet effect. The significantly upregulated TXNL1 gene indicated potential for embryonic diapause in Finnsheep and F1. Moreover, we report, for the first time in any species, several genes that are active in the CL during early pregnancy (including TXNL1, SIGLEC14, SIGLEC8, MRP4, and CA5A).

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

Litter size is an economically important trait in sheep breeding. The objectives of this study were as follows: (1) to ascertain if any of the 19 known variants in the BMPRIB, BMP15, and GDF9 genes are present and associated with the litter size of Mongolia sheep; (2) to identify novel variants in GDF9 and perform association analysis; and (3) to validate the effects of these GDF9 promoter variants on the activity of the gene. The results of the 19 known variants showed that the FecB^B affected the litter size of Mongolia sheep (p < 0.001). The association analysis results of novel variants showed that the g.46544883A>G (GenBank accession: NC_040256, the same below) in the 3' untranslated region (3' UTR), the c.1040T>C (Phe347Ser) in the exon 2, and the g.46547859C>T SNP in the promotor of GDF9 were significantly associated with litter size of Mongolia ewes (p < 0.01, p < 0.05, and p < 0.001, respectively). In addition, the GDF9 promoter activity analysis showed that the C allele at the -332 position (g.46547859C>T) could decrease luciferase activity compared with the T allele (p < 0.01). Our findings may facilitate effective marker-assisted selection to increase litter size in Mongolia sheep populations, as well as bring new insights into GDF9 expression.

Genomic Signatures of Selection Associated With Litter Size Trait in Jining Gray Goat

Litter size (LS), an important economic trait in livestock, is so complicate that involves many aspects of reproduction, the underlying mechanism of which particularly in goat has always been scanty. To uncover the genetic basis of LS, the genomic sequence of Jining Gray goat groups (one famous breed for high prolificacy in China) with LS 1, 2, and 3 for firstborn was analyzed, obtaining 563.67 Gb sequence data and a total of 31,864,651 high-quality single nucleotide polymorphisms loci were identified. Particularly, the increased heterozygosity in higher LS groups, and large continuous homozygous segments associated with lower LS group had been uncovered. Through an integrated analysis of three popular methods for detecting selective sweeps (Fst, nucleotide diversity, and Tajima’s D statistic), 111 selected regions and 42 genes associated with LS were scanned genome wide. The candidate genes with highest selective signatures included KIT, KCNH7, and KMT2E in LS2 and PAK1, PRKAA1, and SMAD9 in LS3 group, respectively. Meanwhile, functional terms of programmed cell death involved in cell development and regulation of insulin receptor signaling pathway were mostly enriched with 42 candidate genes, which also included reproduction related terms of steroid metabolic process and cellular response to hormone stimulus. In conclusion, our study identified novel candidate genes involving in regulation of LS in goat, which expand our understanding of genetic fundament of reproductive ability, and the novel insights regarding to LS would be potentially applied to improve reproductive performance.

Genome-Wide Association Study Reveals Candidate Genes for Litter Size Traits in Pelibuey Sheep

The Pelibuey sheep has adaptability to climatic variations, resistance to parasites, and good maternal ability, whereas some ewes present multiple births, which increases the litter size in farm sheep. The litter size in some wool sheep breeds is associated with the presence of mutations, mainly in the family of the transforming growth factor β (TGF-β) genes. To explore genetic mechanisms underlying the variation in litter size, we conducted a genome-wide association study in two groups of Pelibuey sheep (multiparous sheep with two lambs per birth vs. uniparous sheep with a single lamb at birth) using the OvineSNP50 BeadChip. We identified a total of 57 putative SNPs markers (p < 3.0 × 10^-3, Bonferroni correction). The candidate genes that may be associated with litter size in Pelibuey sheep are CLSTN2, MTMR2, DLG1, CGA, ABCG5, TRPM6, and HTR1E. Genomic regions were also identified that contain three quantitative trait loci (QTLs) for aseasonal reproduction (ASREP), milk yield (MY), and body weight (BW). These results allowed us to identify SNPs associated with genes that could be involved in the reproductive process related to prolificacy.

Association of missense variants in GDF9 with litter size in Entlebucher Mountain dogs

In the past two decades, average litter size (ALS) in Entlebucher Mountain dogs decreased by approximately 0.8 puppies. We conducted a GWAS for ALS using the single-step methodology to take advantage of 1632 pedigree records, 892 phenotypes and 372 genotypes (173 662 markers) for which only 12% of the dogs had both phenotypes and genotypes available. Our analysis revealed associations towards the growth differentiation factor 9 gene (GDF9), which is known to regulate oocyte maturation. The trait heritability was estimated at 43.1%, from which approximately 15% was accountable by the GDF9 locus alone. Therefore, markers flanking GDF9 explained approximately 6.5% of the variance in ALS. Analysis of WGSs revealed two missense substitutions in GDF9, one of which (g.11:21147009G>A) affected a highly conserved nucleotide in vertebrates. The derived allele A was validated in 111 dogs and shown to be associated with decreased ALS (-0.75 ± 0.22 puppies per litter). The variant was further predicted to cause a proline to serine substitution. The affected residue was immediately followed by a six-residue deletion that is fixed in the canine species but absent in non-canids. We further confirmed that the deletion is prevalent in the Canidae family by sequencing three species of wild canids. Since canids uniquely ovulate oocytes at the prophase stage of the first meiotic division, requiring maturation in the oviduct, we conjecture that the amino acid substitution and the six-residue deletion of GDF9 may serve as a model for insights into the dynamics of oocyte maturation in canids.

Association between single-nucleotide polymorphisms within candidate genes and fertility in Landrace and Duroc pigs

Finding effective predictors of traits related to boar fertility is essential for increasing the efficiency of artificial insemination systems in pig breeding. The objective of this study was to find associations between single-nucleotide polymorphisms (SNPs) within candidate genes and fertility in the breeds Landrace and Duroc. Animals with breeding values for total number of piglets born, were re-sequenced for exonic regions of 14 candidate genes related to male and female fertility using samples from 16 Landrace boars and 16 Duroc boars (four with high and four with low breeding value of total number of piglets born for each breed for male fertility, and the same for female fertility) to detect genetic variants. Genotyping for the detected SNPs was done in 619 Landrace boars and 513 Duroc boars. Two SNPs in BMPR1 and one SNP in COX-2 were found significantly associated with the total number of piglets born in Landrace. In Duroc, two SNPs in PLC_z, one SNP in VWF and one SNP in ZP3 were found significantly associated with total number of piglets born. These SNPs explained between 0.27% and 1.18% of the genetic variance. These effects are too low for being used directly for selection purposes but can be of interest in SNP-panels used for genomic selection.

Genetic Effects of Single Nucleotide Polymorphisms in the Goat GDF9 Gene on Prolificacy: True or False Positive?

Simple Summary

As an important regulator factor, which was secreted by female oocytes, the growth differentiation factor 9 (GDF9) plays an essential role during the growth and differentiation of ovarian follicles. Single nucleotide polymorphisms (SNPs) within the GDF9 gene have been found to be involved in reproductive traits in livestock, and some of these mutations have been used as the effective makers in animal molecular breeding. However, it is remarkable that the SNPs of the goat GDF9 gene have not been systematically sorted and analyzed from the reported studies, which leads to an inability to find effective loci that could be applied in improving the prolificacy of goats via the molecular breeding method. In this study, we gathered and sorted 45 SNPs of the goat GDF9 gene from all relevant studies and the National Center for Biotechnology Information Search database (NCBI), and especially analyzed and discussed the relationship between part controversial and potentially effective SNPs and the reproductive traits. The results indicated that non-synonymous SNPs A240V, Q320P, and V397I and synonymous SNPs L61L, N121N, and L141L were six “true” positive SNPs in improving goat fertility. Nevertheless, the regulation pathways and the specific mechanism of these six SNPs on goat fecundity are not clear, which still need further study in more goat breeds and a large sample size. These results provided an effective tool for follow-up research studies on the molecular genetic breeding of goats’ reproductive traits.

Abstract

Goat reproductive traits are complex quantitative traits controlled by polygenes and multipoint. To date, some high-fertility candidate genes in livestock have been unearthed and the growth differentiation factor 9 (GDF9) gene is one of them, which plays a crucial role in early folliculogenesis. According to the relevant previous studies and the National Center for Biotechnology Information Search database (NCBI), a total of 45 single nucleotide polymorphisms (SNPs) have been detected in the goat GDF9 gene, but which one or which ones have important effects on goat fecundity is still uncertain. Hence, in order to find effective molecular markers for goat genetic breeding and accelerate the goat improvement, this study summarized and classified the above 45 SNPs into four kinds, as well as compared and analyzed the same SNP effects and the different SNPs linkage effects on the reproductive traits in different goat breeds. Since there were many SNPs in the goat GDF9 gene, only 15 SNPs have been identified in more than 30 goat breeds worldwide and they showed different effects on the litter size. Therefore, this study mainly chose these 15 SNPs and discussed their relationship with goat productivity. Results showed that three non-synonymous SNPs A240V, Q320P, and V397I and three synonymous ones L61L, N121N, and L141L played a “true” role in the litter size trait in many goat breeds around the world. However, the regulatory mechanisms still need further research. These results provide an effective tool for follow-up research developing the goat molecular breeding strategies and improving the goat reproductive traits.

Evaluation of morphology, morphometry and follicular dynamics in FecGE genotyped ewes

This study aimed to evaluate the effect of FecG^E mutation on the development of ovarian follicles. To this end, 42 Santa Inês ewes were genotyped for FecG^E mutation and classified as wild-type (FecG^+/+), heterozygous (FecG^+/E) or mutant homozygous (FecG^E/E). Ovarian fragments were processed, and the follicles were analyzed with regard to the morphology and morphometry using classical histology. For the evaluation of follicular dynamics, ewes underwent oestrous synchronization and were monitored throughout an interovulatory period. A higher (P < 0.05) percentage of morphologically normal follicles in the primordial stage was identified in FecG^E/E (90.0%) and FecG^+/E (88.1%) ewes than in the FecG^+/+ (73.0%) ewes. There was also a significantly greater (P < 0.05) number of morphologically normal follicles in the FecG^E/E (87.3%) and FecG^+/E (83.3%) ewes than in FecG^+/+ (76.8%) ewes in the transitional stage. A smaller (P < 0.05) diameter was observed in the secondary follicles in FecG^E/E (93.8 μm) ewes than in FecG^+/E (171.8 μm) ewes. Regarding follicular dynamics, FecG^E/E ewes showed a greater (P < 0.05) number of ovulations (2.5 ± 0.2) than FecG^+/+ ewes (1.5 ± 0.3) ewes. Ovulatory follicles were smaller (P < 0.05) in the FecG^E/E (5.1 mm) and FecG^+/E (5.2 mm) ewes than in FecG^+/+ (5.8 mm) ewes. Santa Inês nulliparous ewes carrying the FecG^E mutation showed a greater proportion of morphologically normal follicles in the primordial and transitional stages than those not carrying the mutation. FecG^E/E ewes demonstrated a higher number of ovulated follicles and that FecG^E/E and FecG^+/E ewes presented ovulatory follicles with a smaller diameter.

Trio a novel bovine high-fecundity allele: II. Hormonal profile and follicular dynamics underlying the high ovulation rate

The newly discovered Trio high-fecundity allele produces multiple ovulations in cattle. This study evaluated (1) size and growth rates of follicles in Trio carriers during a synchronized follicular wave, induced by follicle aspiration; (2) follicle-stimulating hormone (FSH) patterns associated with the follicular wave; (3) size of corpora lutea (CL) and circulating progesterone; and (4) intrafollicular estradiol concentrations prior to normal deviation. Trio carriers had mean dominant follicles that were significantly smaller in diameter and volume than noncarriers. Onset of diameter deviation occurred at ∼3 days after the last follicle aspiration in both genotypes despite Trio carriers having much smaller individual follicles. Follicles of Trio carriers grew at a slower rate than noncarrier follicles (∼65% in mm/day or ∼30% in mm3/day) resulting in much smaller individual dominant follicles (∼25% volume). However, total dominant follicle volume, calculated as the sum of all dominant follicles in each animal, was similar in carriers and noncarriers of Trio throughout the entire follicular wave. Circulating FSH was greater in Trio carriers during the 24 h encompassing deviation. Trio carriers had significantly more ovulations than noncarriers, and individual CL volume was smaller, although total luteal tissue volume and circulating P4 were not different. Thus, increased ovulation rate in Trio carriers relates to smaller individual follicles (one-third the volume) near the time of deviation due to slower follicle growth rate, although time of deviation is similar, with increased circulating FSH near deviation leading to selection of multiple dominant follicles in Trio carriers with similar total follicle volume.

Single nucleotide polymorphisms in BMP2 and BMP7 and the association with litter size in Small Tail Han sheep

Although it has been investigated for many years, the physiological processes regulating prolificacy in sheep remains unclear because of regulation by many genes. To better understand the effects of three single nucleotide polymorphisms (SNPs) comprising g.48462350C>T in BMP2, g.58171856C>G and g.58171886A>C in BMP7, a population genetic analysis was conducted using data obtained from genotyping in 768 sheep from six breeds (three polytocous and three monotocous). The results indicate that all the sheep breeds were considered to conform to the Hardy-Weinberg equilibrium (P > 0.05). The associations of these three SNPs with litter size in 384 Small Tail Han sheep were analyzed, therefore, and found to be correlated with fecundity as assessed by mean litter size (P < 0.05). Bioinformatic analysis indicated there was a transmembrane domain change that occurred after a mutation in BMP2 at g.48462350C>T, and changes involving transcription factors such as USF1, USF2 and INMS1 in the BMP7 promoter region might be involved in greater sheep prolificacy.

A 5-Methylcytosine Site of Growth Differentiation Factor 9 (GDF9) Gene Affects Its Tissue-Specific Expression in Sheep

Simple Summary

Growth differentiation factor 9 (GDF9) is an important gene for ovine fertility. GDF9 is highly expressed in the ovary as opposed to other tissues, but the reason for this is unknown. Our study found this can be caused by the methylation level of the promoter CpG island mC-4 site. This finding contributes to the understanding of the regulatory mechanism of GDF9 gene in reproduction.

Abstract

Growth differentiation factor 9 (GDF9) plays an important role in the early folliculogenesis of sheep. This study investigated the mRNA expression of ovine GDF9 in different tissues by real-time PCR. GDF9 exhibits significantly higher levels of expression (p < 0.01) in the ovary, relative to other tissues, indicating that its expression is tissue specific. To explore the regulatory mechanism of this tissue-specific expression, the methylation level of one CpG island (−1453 to −1854) of GDF9 promoter in ovary and heart was determined. In this region (−1987 to −1750), only the mC-4 site was present in the Sp4 binding site showed differential methylation between the heart and ovary; with increased (p < 0.01) methylation being observed in the heart. Additionally, the methylation level was negatively correlated with GDF9 mRNA expression (R = −0.75, p = 0.012), indicating that the methylation of this site plays an important role in transcriptional regulation of GDF9. The methylation effect of the mC-4 site was confirmed by using dual-luciferase. Site-directed mutation (methylation) of mC-4 site significantly reduced (p < 0.05) basal transcriptional activity of GDF9 promoter in oocytes. These results imply that methylation of GDF9 promoter CpG island mC-4 site may affect the binding of the Sp4 transcription factor to the GDF9 promoter region in sheep, thereby regulating GDF9 expression and resulting in a tissue-specific expression.

Polymorphism identification in GDF9 gene and its association analysis with reproduction traits in Jinghai Yellow chicken

GDF9 (growth differentiation factor 9) belongs to the transforming growth factor-β (TGF-β) superfamily and plays an irreplaceable role in female fertility. To reveal its genetic effects on productivity performance in chickens, 373 Jinghai Yellow chickens were chosen randomly to detect SNPs in GDF9 by PCR-SSCP and DNA sequencing methods. Eventually, four SNPs (g.2053G > A, g.2275T > C, g.2338C > T, g.2420T > C) in total had been detected. Amongst them, g.2420T > C was first found significantly associated with reproduction trait in chickens and heterozygous type C₂T₂ had higher average egg weight at 300 days of age (AEWD300) than T₂T₂ (p < 0.01). Least squares analysis showed that age at first laying (AFE) of H1 and H1H1 chickens were significantly earlier than that of H7 and H7H7 ones, respectively (p < 0.05). H1H5 hens showed higher AEWD300 than H4H7 ones (p < 0.05). For total egg number at 300 days of age (END300), mean of H5H5 was significantly higher than that of H4H4 (p < 0.05). Hence, the study suggested that hybrid vigor at g.2420T > C could be utilized in practice. H1H1, H1H5 and H5H5 could be the dominant diplotypes for chicken breeding. The study may contribute to the breeding progress of productive chickens and supply reference for oviparous animal production practice.

Two strongly linked single nucleotide polymorphisms (Q320P and V397I) in GDF9 gene are associated with litter size in cashmere goats

Growth differentiation factor 9 (GDF9) gene is an effective intra-ovarian regulator; it plays a crucial role in early folliculogenesis in female mammals. The non synonymous mutations: g.3905A > C (also known as p.Gln320Pro/Q320P) and g.4135G > A (also know as p.Val397Ile/V397I), are two well-known and controversial single nucleotide polymorphisms (SNPs) within GDF9 gene in goats with different prolificacy, and so far, there were no studies on linkage between Q320P and V397I. Therefore, the aim of this work was to study whether Q320P and V397I mutations have a significant effect on litter size, in Shaanbei white cashmere goats (SBWC, n = 1511), and to explore the specific relationship between these two SNPs. The results showed that both of Q320P and V397I mutations exhibited three genotypes; the minor allele frequencies (MAF) of the SNPs were 0.286 and 0.477, respectively; and these two SNPs were in strong linkage disequilibrium (D' = 0.976, r² = 0.348) in the studied goats. Moreover, association analyses revealed that Q320P was significantly associated with the first-born litter size in goats irrespective of the sample size (n = 1511; P = 0.008), while V397I significantly affected litter size until the sample size crossed 1300 (P = 0.015). Meanwhile, the diplotypes PP-II and QP-VI were observed to have a superior effect on litter size (P = 3.78 × 10^-5) to that of the haplotypes (P = 1.12 × 10^-7). Thus, the findings led us to assume that Q320P mutation was the major SNP affecting goat litter size. These findings can provide useful DNA markers for selecting superior individuals in marker-assisted selection (MAS) for breeding in relation to fecundity in goats.

Polymorphisms in the Chicken Growth Differentiation Factor 9 Gene Associated with Reproductive Traits

The aim of the study was to investigate GDF9 gene polymorphisms and their association with reproductive traits in chicken using DNA sequencing. A total of 279 Dongxiang blue-shelled (DX) chickens and 232 Luhua (LH) chickens were used for validation. We detected 15 single nucleotide polymorphisms (SNPs): nine SNPs were previously unreported in chicken, two were missense mutations, and only three exhibited significant associations with reproductive traits. G.17156387C>T was significantly associated with age at first egg (AFE) and weight of first egg (WFE) in both breeds. Birds carrying the CC genotype exhibited higher AFE and WFE values than those with the TT genotype. The SNP g.17156427A>G exhibited an association with egg weight at 300 days of age (EWTA) in DX but not in LH chickens. The SNP g.17156703A>C affected the AFE and EN (total number of eggs at 300 days of age) in DX chickens. In addition, certain diplotypes significantly affected AFE, BWTA (body weight at 300 days of age), and EN in both breeds. RT-PCR results showed that the GDF9 gene was highly expressed in stroma with cortical follicles (STR) and prehierarchal follicles. These results provided further evidence that the GDF9 gene is involved in determining reproductive traits in chicken.

Integrating RNA-seq and GWAS reveals novel genetic mutations for buffalo reproductive traits

Genome-wide association study (GWAS) has been applied in buffalo breeding programs and been used to identify a number of candidate genes associated with buffalo reproductive traits. The genetic code of specific genes underlying buffalo reproductive traits remains unclear. Association study that measures both genetic and transcriptional variation has been applied for the investigation of complex traits. To investigate genes involved in buffalo reproductive traits, integrated RNA-seq results were investigated of buffalo granulosa cells and candidate genes which were reported to be associated with buffalo reproductive traits in a previous GWAS. A large number of variants were detected by RNA-seq, and 214 variants were located within the buffalo reproductive candidate genes identified by GWAS. A further association study in 462 Italian Mediterranean buffalo indicated that 25 SNPs distributed in 13 genes were associated with reproductive traits. Of the 13 genes, 11 were expressed in granulosa cells of all antral follicle development stages, and significant difference was found in the expression of NDUFS2 between follicles of diameter <8 mm and > 8 mm. These findings extend the results of GWAS by expanding the knowledge about new and potentially functional single-nucleotide polymorphisms and provide useful information about regulatory genes affecting buffalo reproductive traits.

Genome-wide association study to identify genomic regions affecting prolificacy in Lori-Bakhtiari sheep

Several causative mutations in candidate genes affecting prolificacy have been detected in various sheep breeds. A genome-wide association study was performed on estimated breeding values for litter size in Lori-Bakhtiari sheep. Prolific ewes with twinning records and others with only singleton records were genotyped using the medium-density Illumina Ovine SNP50 array. Four single nucleotide polymorphisms (SNPs) associated with litter size were identified on chromosomes 3, 6 and 22. The region on sheep chromosome 3 between 75 739 167 and 75 745 152 bp included two significant SNPs (s52383.1 and OAR3_80038014_X.1) in high linkage disequilibrium with each other. The region that surrounds these SNPs contains a novel putative candidate gene: luteinizing hormone/choriogonadotropin receptor (LHCGR), known to be involved in ovarian steroidogenesis and organism-specific biosystem pathways in sheep. Known prolificacy genes BMPR1B, BMP15 and GDF9 were not associated with litter size in Lori-Bakhtiari sheep, suggesting that other biological mechanisms could be responsible for the trait's variation in this breed.