A new polymorphism in the Growth and Differentiation Factor 9 (GDF9) gene is associated with increased ovulation rate and prolificacy in homozygous 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.

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.

Reproductive seasonality of hair rams under tropical conditions: an alternative for non-seasonal lamb production?

Reproductive seasonality limits the periods of breeding on the year and, therefore, productive output. However, some breeds appear as probably non-seasonal. The aim of the study was to characterize the seasonal pattern of Santa Inês rams, including an ultrasound characterization of the reproductive tract, testosterone concentrations, and semen characteristics. Fifteen Santa Inês rams remained in a grazing system with concentrate supplementation, and measurements of the reproductive tract and ultrasound evaluation (biometrics and pixel intensity) of the testicles and accessory sex glands were monthly recorded. Computerized seminal evaluations were also performed monthly, and serum testosterone concentration was measured every 15 days. Body weight and condition remained stable throughout the year. In general, reproductive traits varied along the year and reached maximum values during autumn and minimum in spring. Despite that, as fresh semen remained with enough quality to breed all along the year, seasonality does not appear as a limiting factor to breed along the year. Therefore, Santa Inês rams can be used for all-year-round breeding or for crossbreeding when rams from other breeds decrease their fertilizing ability.

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.

Polymorphisms Analysis of BMP15, GDF9 and BMPR1B in Tibetan Cashmere Goat (Capra hircus)

The Tibetan cashmere goat is a prolific goat breed in China. In sheep breeds, natural mutations have demonstrated that the transforming growth factor beta (TGF-β) super family ligands, such as growth differentiation factor 9 (GDF9), bone morphogenetic protein 15 (BMP15) and their type I receptor (bone morphogenetic protein receptor (BMPR1B), are essential for ovulation and increasing litter size. In this study, 216 female Tibetan cashmere goats were sampled, and candidate genes with fecundity traits were detected via restriction fragment length polymorphism (RFLP) and sequenced. Four polymorphic loci were found in specific amplification fragments of BMP15 and GDF9. Two SNP sites of the BMP15 gene were discovered, namely G732A and C805G. The G732A mutation did not cause the change in amino acids, and the frequencies of each genotype were 0.695 for the GG type, 0.282 for the GA type and 0.023 for the AA type. The C805G mutation caused amino acids to change from glutamine to glutamate. The genotype frequencies were 0.620 for the CC type, 0.320 for the CG type and 0.320 for the CG type. For the GG type 0.060, the G3 and G4 mutations of the GDF9 gene were all homozygous mutations. Two known SNP sites, C719T and G1189A, were detected in the Tibetan cashmere goat GDF9 gene, of which the C719T mutation caused a change of alanine to valine, with a genotype frequency of 0.944 for the CC type and 0.056 for the CT type, whereas no TT type was found. The G1189A mutation caused valine to become isoleucine, and the frequencies of each genotype were 0.579 for the GG type, 0.305 for the GA type and 0.116 for the AA type; G1, B2, B3, B4, FecX^H, FecX^I, FecX^L, G2, G5, G6, G7, G8, FecG^E, FecTT and FecB mutations were not found in Tibetan cashmere goats. The results of this study provide a data basis for future studies of BMP15, GDF9 and BMPR1B gene mutations in goats.

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

Use of logistic models to evaluate the response of superovulation treatment and embryo production in Santa Inês ewes

The study aimed to verify the influence of the FecG^E mutation in superovulated ewes and to evaluate the probability of logistic models to determine the response capacity of these ewes to superovulatory treatment. Santa Inês ewes (n = 29) were genotyped for the FecG^E mutation and separated for their genotype group in carriers of the mutant E allele (FecG^E/E, FecG^+/E) and non-carrier (FecG^+/+) alleles. The ewes underwent hormonal treatment for superovulation. Aside from the genotypes, variables included in the statistical model were reproductive status (empty, early lactation, or late lactation), age (> or < 6 years), and number of births (nulliparous, primiparous, multiparous). The carriers of the mutation could be discriminated from the non-carriers based on the number of corpora lutea, rate of frozen embryos, and fecundity. Recovery rate was significantly higher (P < 0.05) in FecG^E/E (94.31%) compared to FecG^+/E (63.15%) and FecG^+/+ (61.90%) (P < 0.05), whereas fecundity rate of FecG^+/+ ewes (50.76%) was significantly higher than FecG^+/E (18.96%) and FecG^E/E (32.53%) (P < 0.05). We determined in this study that the response to superovulation and embryo production can be discriminated between FecG^E/E and FecG^+/E ewes in relation to the FecG^+/+ genotype. Logistic models that included reproductive status and mutation, or reproductive status and age, or reproductive status and number of births were effective in predicting the response to superovulatory treatment.

Small RNA sequencing reveals sex-related miRNAs in Collichthys lucidus

Collichthys lucidus (C. lucidus) is an economically important fish species, exhibiting sexual dimorphism in its growth rate. However, there is a lack of research on its underlying sex-related mechanisms. Therefore, small RNA sequencing was performed to better comprehend these sex-related molecular mechanisms. In total, 171 differentially expressed miRNAs (DE-miRNAs) were identified between the ovaries and testes. Functional enrichment analysis revealed that the target genes of DE-miRNAs were considerably enriched in the p53 signaling, PI3K–Akt signaling, and TGF-beta signaling pathways. In addition, sex-related miRNAs were identified, and the expression of miR-430c-3p and miR-430f-3p was specifically observed in the gonads compared with other organs and their expression was markedly upregulated in the testes relative to the ovaries. Bmp15 was a target of miR-430c-3p and was greatly expressed in the ovaries compared with the testes. Importantly, miR-430c-3p and bmp15 co-expressed in the ovaries and testes. This research provides the first detailed miRNA profiles for C. lucidus concerning sex, likely laying the basis for further studies on sex differentiation in C. lucidus.

De novo gonad transcriptome analysis of elongate loach (Leptobotia elongata) provides novel insights into sex-related genes

Elongate loach (Leptobotia elongata) is endemic in middle and upper reaches of the Yangtze River in China. Because of many anthropogenic factors such as overfishing and dam construction, the loach has become a highly endangered species. So far, the genomic resources which benefit for species conservation and utilization are still lacking in elongate loach. Therefore, the first gonad transcriptome analysis of the loach was conducted in this study, providing novel insights into sex-related genes. A total of 286,800,660 clean reads with a total length of 42.02 Gb were obtained. 18,975 differentially expressed genes (DEGs) were identified, where 12,976 DEGs, especially Sox9a, Sox9b, Igf2 and Fgfr2, were upregulated in the testis, and 5999 DEGs, especially Zp3, Eg2, Plk1, Ccnb1, Cdc20 and Mos, were upregulated in the ovary. Meanwhile, some testis-specific genes (i.e. Cald1, Atp1a, Muc2 and Ca2) and ovary-specific genes (i.e. Ca4, Tuba, Acp5, Ccna, Larp6 and Nop4) were identified and verified. According to Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses of DEGs, we found a series of enrichment pathways related to reproduction in elongate loach, such as the MAPK signaling pathway, oxytocin signaling pathway and oocyte meiosis pathway. Twelve DEGs were randomly selected to verify RNA-seq results by qPCR. In conclusion, this study provides a data source to study the molecular characteristics and regulatory mechanisms of sex-related genes in elongate loach, which has a potential to improve the resource protection and aquaculture production of the loach.

Technologies Used in Production Systems for Santa Inês Sheep: A Systematic Review

This study identifies the number of publications that presented technologies used in the production systems of Santa Inês sheep in the last 5 years (2017–2021) carried out in Brazil. Therefore, the objective was to identify where we are in terms of knowledge about technologies in different fields (health, reproduction, animal breeding, behavior and welfare, nutrition and feeding, forage and pasture, carcass and meat quality, and economics and management of livestock systems). After rigorous selection, 114 studies were appointed and classified by knowledge field, and the main approaches within each theme were evaluated, pointing out research gaps. Most technologies have been in northeastern states. However, government agencies should develop public policies to disseminate techniques in rural areas because the production system in this region is still subsistence. This study highlighted the need for works that present management practices and tools that impact the improvement of animal welfare. Agro-industrial by-products have been widely used as an alternative for sheep feeding. However, economic feasibility analyses are recommended with these foodstuffs to substantiate their use as an option to reduce production costs. There is a lack of research allusive to the management of production systems, especially those related to estimates of economic feasibility indicators.

Genome-wide detection of selective signals for fecundity traits in goats (Capra hircus)

Fecundity in livestock is an economically important complex quantitative trait that is influenced by both genetics and the environment. However, the underlying genetic mechanism of reproductive performance in goats has not been well investigated. To investigate the genomic basis of fecundity in goats, genomic sequencing data of the Jining grey goat (a high prolificacy breed in China) were collected, as well as data for other commonly available goat breeds, and a mass of genomic variants were generated after variation calling. We screened the Jining grey goat (20 individuals) using a selective sweep with the Asian wild goat population (5 individuals), and potential candidate genes were proposed, such as STIM1, ESR1, LRRC14B and SLC9A3. Among, STIM1 is a most promising one associated with high reproductive capacity. When compared to Chinese domestic goats with low fecundity (17 individuals), the genes including MLLT10, SPIRE2, TCF25, ZNF276 and FANCA were screened, and the SPIRE2 gene was thought to be associated with fecundity traits. Meanwhile, the functional enrichment of these candidate genes revealed that they were involved in biological processes of mammary gland morphogenesis, uterus development, gastrulation, mesoderm morphogenesis and formation, and blood vessel development, which might undergo natural or artificial selection during reproductive trait formation in goats. Thus, our findings could enrich the genetic basis of reproductive trait selection during goat domestication, which may serve to improve goat breeding practices.

A frameshift deletion in the GDF9 gene in Icelandic Loa prolific sheep

Several genetic variants have been shown to affect the mean number of offspring in different sheep breeds. Here, we analyzed samples from Icelandic sheep with the aim of identifying the genetic cause of the Icelandic Loa phenotype using three previously identified prolificacy genes as candidates. We demonstrate that a 4-bp frameshift deletion positioned in the mature region of the GDF9 protein in the Loa animals is a likely causal mutation for the observed increase in prolificacy; however, sequencing showed that not all ewes with a high number of offspring carried the deletion, suggesting the presence of a second mutation segregating within this group of animals.

Population validation of reproductive gene mutation loci and association with the litter size in Nubian goat

Litter size is an important component trait of doe reproduction. By improving it, production efficiency and economic benefits can be significantly provided. Genetic marker-assisted selection (MAS) based on proven molecular indicators could enhance the efficacy of goat selection, as well as litter size trait. Many molecular markers have been identified that they can be used to improve litter size in different goat breeds. However, the presence and value of these markers vary among goat breeds. In the present study, we used the reported loci on other breeds of goat as candidate loci to detect whether these loci appear in this Nubian goat population; then we proceed to genotype and detect surrounding loci (50 bp) by multiplex PCR and sequencing technology. As a result, 69 mutations (59 SNPs and 10 indels) were screened out from 23 candidate genes in Nubian goat population, 12 loci were significantly associated with the litter size of first-parity individuals; 5 loci were significantly associated with the litter size of second-parity individuals; 3 loci were significantly associated with the litter size of third-parity individuals. In addition, five loci were significantly associated with the average litter size. The additive effect value of KITLG: g.18047318 G>A in first parity, KITLG: g.18152042G>A in third parity, KISS-1: g.1341674 C>G in first parity, and GHR: g.32134187G>A in second parity exceed more than 0.40, and the preponderant alleles are G, C, A and G, respectively. Further, linkage disequilibrium analysis of 21 mutation loci shows that 3 haplotype blocks are formed, and the litter size of combination type AACC in KISS-1 gene and AAGG in KITLG gene are significantly lower than that of other combinations genotype in first parity (P<0.05). These findings can provide effective candidate DNA markers for selecting superior individuals in Nubian goat breeding.

A study on mutation points of GDF9 gene and their association with prolificacy in Egyptian small ruminants

Background

Genetic variants of the GDF9 gene were considered to be the potent gene markers for improving fecundity traits in Egyptian sheep and goats. Also, these favorable gene variants could be applied in the breeding program by gene-assisted selection (GAS), aiming towards the potential amelioration of reproduction and production in such small ruminants. The present investigation was designed to evaluate the genetic variants of the GDF9 gene on fecundity traits including the mean number of lambing “MNL” and mean number of twin production “MNTP” of Egyptian sheep and goats.

Results

This experiment involved 113 mothers, 83 of sheep and 30 of goats, at first, second, third, and fourth parity, and also 26 young females, 12 of sheep and 14 of goats at age of sexual maturation. T-ARMS-PCR analysis was performed on five mutation points (G1, G4, G6, G7, and G8). In sheep, the heterozygous mothers of G4 had significant elevation (P ≤ 0.05) of MNL and MNTP than wild-type homozygous ewes. However, the heterozygous mothers of G1 and G6 gave a reduction of MNL and MNTP as compared to mothers with wild-type genotypes. The ewes of G7 had heterozygous genotype (AG), and the ewes of G8 had wild type (CC). In goat, G4 and G7 were polymorphic, and G1, G6, and G8 were monomorphic type. Based on these findings, it must be selected the young sheep females of heterozygous in G4, and the young goat females of heterozygous in G4 and G7 for participating in a successful breeding program, because they will have potential high fecundity traits.

Conclusion

The present results confirmed that the genetic variants of the GDF9 gene were considered to be the major gene markers for enhancement of the prolificacy in Egyptian sheep and goats and could be applied in a successful breeding program by gene-assisted selection (GAS) in small ruminants.

Origin and population structure of Brazilian hair sheep breeds

Brazilian hair sheep constitute a genetic diversity hotspot. These animals are found in the harsh environments of the Brazilian Northwest (semi-arid) region. Genotypes (50K SNP chip) from seven Brazilian sheep breeds (five hair and two coarse wool types) and 87 worldwide breeds were used to test for population structure, admixture and genetic diversity. Moreover, phylogenetic trees evaluating migration events between genetic groups were built. Brazilian Somali, a fat-tailed breed, had a close relationship with East African breeds and clustered distinctly from other Brazilian breeds. Brazilian Blackbelly and Barbados Blackbelly had a close relationship. The Morada Nova breed did not show close relationships with European or African breeds, revealing a single migration event from an Algerian hair breed. Brazilian Fat-tail and Morada Nova share a common ancestor, but the former showed introgressions from Brazilian Somali and Afrikaner breeds, explaining the fat-tail phenotype. The Santa Inês breed received a substantial contribution from Brazilian Bergamasca and showed an admixed origin with recent introgressions from other breeds, mainly from Suffolk. Furthermore, Brazilian Somali and Brazilian Fat-tail are the most endangered sheep genetic resources in Brazil and should be the focus for ex situ conservation programs. In conclusion, Brazilian hair sheep show an African origin and are characterized by diverse genetic composition, reinforcing the need for conservation of these genetic resources, and at the same time, this highly diverse group has variability that can be used in breeding programs.

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.

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.

Occurrence, morphology, and morphometry of follicles containing multiple oocytes in FecGE mutant Santa Inês ewes

This study was conducted to characterize the morphology and morphometry of follicles containing multiple oocytes (MOFs) and determine the association with the FecG^E mutation in Santa Inês ewes. Based on the genotypes, 65 ewes were characterized as being homozygous wild-type (n = 25; FecG^+/+), heterozygous mutant (n = 27, FecG^+/E), and homozygous mutant (n = 13, FecG^E/E). The variables evaluated were follicle developmental stage, number of oocytes per follicle, morphology, and morphometry of MOFs. The FecG^E mutation did not affect the frequency of MOFs (P > 0.05) (3.0 % in FecG^+/+; 3.3 % in FecG^+/E; and 3.5 % in FecG^E/E). The greater viability (P < 0.05) of MOFs was identified in transitory stage of the FecG^E/E (95.0 %) and FecG^+/E (90.9 %) when compared to the FecG^+/+ genotype (73.3 %). Furthermore, the morphology of transitory follicles with two oocytes was the variable and when evaluated was the most reliable determinant for predicting which ewes had an FecG^E mutation. In conclusion, the FecG^E mutation did not affect the frequency of MOFs. The ewes with FecG^E mutation had a greater frequency of morphologically normal MOFs in the transitory stage. Furthermore, the ewes with the FecG^E mutation had a greater likelihood of having MOFs containing two morphologically normal oocytes.

A nonsense mutation of bone morphogenetic protein-15 (BMP15) causes both infertility and increased litter size in pigs

Background

Atypical external genitalia are often a sign of reproductive organ pathologies and infertility with both environmental or genetic causes, including karyotypic abnormalities. Genome-wide association studies (GWAS) provide a means for identifying chromosomal regions harboring deleterious DNA-variants causing such phenotypes. We performed a GWAS to unravel the causes of incidental cases of atypically small vulvae in German Landrace gilts.

Results

A case-control GWAS involving Illumina porcine SNP60 BeadChip-called genotypes of 17 gilts with atypically small vulvae and 1818 control animals (fertile German Landrace sows) identified a significantly associated region on the X-chromosome (P = 8.81 × 10^− 43). Inspection of whole-genome sequencing data in the critical area allowed us to pinpoint a likely causal variant in the form of a nonsense mutation of bone morphogenetic protein-15 (BMP15; Sscrofa11.1_X:g.44618787C>T, BMP15:p.R212X). The mutant allele occurs at a frequency of 6.2% in the German Landrace breeding population. Homozygous gilts exhibit underdeveloped, most likely not functional ovaries and are not fertile. Male carriers do not seem to manifest defects. Heterozygous sows produce 0.41±0.02 (P=4.5 × 10^-83) piglets more than wildtype animals. However, the mutant allele’s positive effect on litter size accompanies a negative impact on lean meat growth.

Conclusion

Our results provide an example for the power of GWAS in identifying the genetic causes of a fuzzy phenotype and add to the list of natural deleterious BMP15 mutations that affect fertility in a dosage-dependent manner, the first time in a poly-ovulatory species. We advise eradicating the mutant allele from the German Landrace breeding population since the adverse effects on the lean meat growth outweigh the larger litter size in heterozygous sows.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-020-07343-x.

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 Identification of a Regulatory Mutation in BMP15 Controlling Prolificacy in Sheep

The search for the genetic determinism of prolificacy variability in sheep has evidenced several major mutations in genes playing a crucial role in the control of ovulation rate. In the Noire du Velay (NV) sheep population, a recent genetic study has evidenced the segregation of such a mutation named FecL L . However, based on litter size (LS) records of FecL L non-carrier ewes, the segregation of a second prolificacy major mutation was suspected in this population. In order to identify this mutation, we have combined a case/control genome-wide association study with ovine 50k SNP chip genotyping, whole genome sequencing, and functional analyses. A new single nucleotide polymorphism (OARX:50977717T > A, NC_019484) located on the X chromosome upstream of the BMP15 gene was evidenced to be highly associated with the prolificacy variability (P = 1.93E-11). The variant allele was called FecX N and shown to segregate also in the Blanche du Massif Central (BMC) sheep population. In both NV and BMC, the FecX N allele frequency was estimated close to 0.10, and its effect on LS was estimated at +0.20 lamb per lambing at the heterozygous state. Homozygous FecX N carrier ewes were fertile with increased prolificacy in contrast to numerous mutations affecting BMP15. At the molecular level, FecX N was shown to decrease BMP15 promoter activity and supposed to impact BMP15 expression in the oocyte. This regulatory action was proposed as the causal mechanism for the FecX N mutation to control ovulation rate and prolificacy in sheep.

A Comparative Analysis of Oocyte Development in Mammals

Sexual reproduction requires the fertilization of a female gamete after it has undergone optimal development. Various aspects of oocyte development and many molecular actors in this process are shared among mammals, but phylogeny and experimental data reveal species specificities. In this chapter, we will present these common and distinctive features with a focus on three points: the shaping of the oocyte transcriptome from evolutionarily conserved and rapidly evolving genes, the control of folliculogenesis and ovulation rate by oocyte-secreted Growth and Differentiation Factor 9 and Bone Morphogenetic Protein 15, and the importance of lipid metabolism.

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.

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.

Comparative transcriptome analysis of male and female gonads reveals sex-biased genes in spotted scat (Scatophagus argus)

Scatophagus argus is a new emerging aquaculture fish in East and Southeast Asia. To date, research on reproductive development and regulation in S. argus is lacking. Additionally, genetic and genomic information about reproduction, such as gonadal transcriptome data, is also lacking. Herein, we report the first gonadal transcriptomes of S. argus and identify genes potentially involved in reproduction and gonadal development. A total of 136,561 unigenes were obtained by sequencing of testes (n = 3) and ovaries (n = 3) at stage III. Genes upregulated in males and females known to be involved in gonadal development and gametogenesis were identified, including male-biased dmrt1, amh, gsdf, wt1a, sox9b, and nanos2, and female-biased foxl2, gdf9, bmp15, sox3, zar1, and figla. Serum estradiol-17β and 11-ketotestosterone levels were biased in female and male fish, respectively. Sexual dimorphism of serum steroid hormone levels were interpreted after expression analysis of 20 steroidogenesis-related genes, including cyp19a1a and cyp11b2. This gonadal transcript dataset will help investigate functional genes related to reproduction in S. argus.

Single Nucleotide Polymorphisms in SLC5A1, CCNA1, and ABCC1 and the Association with Litter Size in Small-Tail Han Sheep

Simple Summary

Litter size is one of the most important reproductive traits in sheep. Four single nucleotide polymorphisms (SNPs), g.70067210 T > C in SLC5A1, g.25350431 C > T and g.25360220 T > C in CCNA1, and g.14413132 C > T in ABCC1, were identified by mass spectrometry and may be associated with litter size in sheep. Four SNPs were genotyped in Small-Tail Han, Hu, Cele Black, Suffolk, Sunite, Prairie Tibetan, and Tan sheep, and the expression patterns of SLC5A1, CCNA1, and ABCC1 were determined in Small-Tail Han sheep with different fecundities. Furthermore, we also studied the FecB mutation’s association with litter size in Small-Tail Han sheep. The results indicated that all genes included in this study were differentially expressed in the ovary and uterus of polytocous and monotocous Small-Tail Han sheep. Furthermore, association analysis indicated that both g.70067210 T > C in SLC5A1 and the FecB mutation in BMPR-IB were significantly associated with litter size in Small-Tail Han sheep. Linear regression analysis of the association of multiple markers (FecB and g.70067210 T > C in SCL5A1) with litter size indicated that homozygous ewes carrying the BB/TT genotype had a larger litter size than any other genotype.

Abstract

SLC5A1, CCNA1, and ABCC1 have been extensively studied as candidate genes because of their great influence on the reproductive traits of animals. However, little is known about the association between polymorphisms of the SLC5A1, CCNA1, and ABCC1 genes and litter size in Small-Tail Han sheep. In this study, the expression levels of SLC5A1, CCNA1, and ABCC1 in HPG (hypothalamic–pituitary–gonadal) axis tissues of polytocous and monotocous Small-Tail Han sheep were analyzed by qPCR. To better understand the effects of four single nucleotide polymorphisms (SNPs) comprising of g.70067210 T > C in SLC5A1, g.25350431 C > T and g.25360220 T > C in CCNA1, and g.14413132 C > T in ABCC1, a population genetic analysis was conducted using data obtained from genotyping in 728 sheep from seven breeds. The results indicated that all genes included in this study were differentially expressed in the pituitary and uterus of polytocous and monotocous Small-Tail Han sheep (p < 0.05). The associations of these four SNPs and the FecB mutation with litter size in 384 Small-Tail Han sheep were analyzed, therefore, and it was found that both g.70067210T > C and the FecB mutation were significantly associated with litter size (p < 0.05). The linear regression analysis of the association of multiple markers (FecB and g.70067210 T > C in SCL5A1) with litter size indicated that homozygous ewes carrying the BB/TT genotype had larger litter size than any ewes with any other genotype. In conclusion, the SLC5A1 SNPs significantly affect litter size in sheep and are useful as genetic marker for litter size.

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.

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.

Molecular Cloning of the B4GALNT2 Gene and Its Single Nucleotide Polymorphisms Association with Litter Size in Small Tail Han Sheep

Simple Summary

In French Lacaune sheep, the B4GALNT2 (beta-1, 4-N-acetyl-galactosaminyl transferase 2) gene was considered as the potential gene for a FecL (mutation), which regulates the ovine ovulation rate. Three specific mutation sites linked with the FecL mutation have not been previously found in 11 sheep breeds. However, two mutations of g.36946470C > T and g.36933082C > T in the exon of B4GALNT2 were found to have had a significant effect on the litter size in the first parity for Small Tail Han (STH) Sheep (p < 0.05). B4GALNT2, which is mainly expressed in ovine ovary, also plays an important role in sheep reproduction. Furthermore, we discovered two transcription start sites (TSS) of B4GALNT2 in its 5′-flanking region in ovine granule cells in vitro.

Abstract

A new fecundity gene named the FecL (mutation), which regulates the ovulation rate, was discovered in French Lacaune sheep. The B4GALNT2 (beta-1, 4-N-acetyl-galactosaminyl transferase 2) gene was considered as the potential FecL mutation gene. This study explores whether the effect of the FecL mutation exists in other sheep breeds, and the features of the B4GALNT2 gene in terms of the molecular structure and its expression profile. Using Sanger sequencing, we found that high and low fecundity breeds from among 11 measured sheep breeds all had no variation in the three specific mutation sites, which were linked with the FecL mutation. However, two mutations of g.36946470C > T and g.36933082C > T in the exon of B4GALNT2 had a significant effect on litter size in the first parity for Small Tail Han (STH) Sheep (p < 0.05). Two transcription start sites (TSS) of B4GALNT2 in its 5′-flanking region were discovered in ovine granule cells in vitro, through the RACE (Rapid amplification of cDNA ends) method. Except for in the kidney and oviduct, no significant difference in expression levels had been found between STH sheep and Tan sheep breeds. The B4GALNT2 gene, as a candidate for FecL, may have a relationship with the differences in litter size in STH sheep. B4GALNT2 is mainly expressed in the ovine ovary, which also suggests that B4GALNT2 plays an important role in sheep reproduction.

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.

Detection of single nucleotide polymorphisms at major prolificacy genes in the Mehraban sheep and association with litter size

The present study aimed to investigate the presence of polymorphisms at four known genes controlling ovine prolificacy i.e. BMP15, GDF9, BMPR1B and B4GALNT2 in a sample of 115 Iranian Mehraban ewes and their association with litter size (LS) and lambs’ birth weight (BW) traits. Using Sanger sequencing of exons and polymorphism specific genotyping, ten SNPs (Single Nucleotide Polymorphisms) were observed in only two genes, GDF9 and BMPR1B. Seven SNPs were found in the GDF9 gene on the chromosome 5. Among them, six were already described in the coding sequence, and a new one (g.41840985C>T) was found in the 3’UTR. In the BMPR1B gene on the chromosome 6, three novel SNPs were detected in the exon 7 (g.29382184G>A; g.29382337G>A and g.29382340G>A). Allelic frequencies were established for six SNPs among the ten identified and they were in Hardy-Weinberg equilibrium. A significant association was found between the novel SNPs found in the exon 7 of BMPR1B and LS. Present results indicate the potential role of the BMPR1B locus in controlling prolificacy of Mehraban sheep and provide genetic markers for further exploitation in selection to improve reproductive efficiency.

Genome-Wide Association Analyses Highlight the Potential for Different Genetic Mechanisms for Litter Size Among Sheep Breeds

Reproduction is an important trait in sheep breeding as well as in other livestock. However, despite its importance the genetic mechanisms of litter size in domestic sheep (Ovis aries) are still poorly understood. To explore genetic mechanisms underlying the variation in litter size, we conducted multiple independent genome-wide association studies in five sheep breeds of high prolificacy (Wadi, Hu, Icelandic, Finnsheep, and Romanov) and one low prolificacy (Texel) using the Ovine Infinium HD BeadChip, respectively. We identified different sets of candidate genes associated with litter size in different breeds: BMPR1B, FBN1, and MMP2 in Wadi; GRIA2, SMAD1, and CTNNB1 in Hu; NCOA1 in Icelandic; INHBB, NF1, FLT1, PTGS2, and PLCB3 in Finnsheep; ESR2 in Romanov and ESR1, GHR, ETS1, MMP15, FLI1, and SPP1 in Texel. Further annotation of genes and bioinformatics analyses revealed that different biological pathways could be involved in the variation in litter size of females: hormone secretion (FSH and LH) in Wadi and Hu, placenta and embryonic lethality in Icelandic, folliculogenesis and LH signaling in Finnsheep, ovulation and preovulatory follicle maturation in Romanov, and estrogen and follicular growth in Texel. Taken together, our results provide new insights into the genetic mechanisms underlying the prolificacy trait in sheep and other mammals, suggesting targets for selection where the aim is to increase prolificacy in breeding projects.

Anti-Müllerian hormone and antral follicle count are more effective for selecting ewes with good potential for in vivo embryo production than the presence of FecGE mutation or eCG pre-selection tests

This study aims to compare four different methods for selecting high responding sheep donors for in vivo embryo production. These methods include a pre-selection eCG test (eCG), antral follicle count (AFC), plasma anti-Müllerian hormone measurement (AMH) and genotyping for the presence of the FecG^E mutation (a polymorphism in the GDF9 gene associated with increased ovulation rate). Santa Ines ewe lambs (n = 25) underwent superovulation (SOV) with 800 IU equine chorionic gonadotropin (eCG) and the corpus luteum (CL) count was recorded by laparoscopy after eight days. At the D0_eCG, blood samples for AMH and genotyping analysis were collected. Twenty-one days after the end of the eCG test, the same animals underwent SOV with 200 mg of FSH, administered in six decreasing doses, and then naturally mated. Immediately before the beginning of the FSH protocol (D0_FSH), and at the moment of the first FSH dose (D9_FSH), the AFC was assessed. Plasma AMH was again determined at the D9_FSH. After each screening process, animals were classified as having a high (HR), or low (LR), potential of response (using specific thresholds for each method). Then, the ewes' response to SOV and embryo yield for each screening method, classified as HR or LR, were compared. Animals classified as HR by AFC (HR_AFC) and by AMH concentration (HR_AMH) at the D9_FSH, produced more viable embryos than those classified as LR_AFC and LR_AMH (HR_AFC 6.2 ± 3.2 vs LR_AFC 2.8 ± 3.0 and HR_AMH 6.6 ± 3.6 vs LR_AMH 3.0 ± 2.9). Pre-selection tests with eCG and different FecG^E genotypes, either heterozygous (+/E) or wild type (+/+), were unable to discriminate HR or LR animals. A tendency (P = 0.06) to have lower plasma AMH was observed in heterozygous FecG^E (+/E) ewes. In conclusion, both AFC and plasma AMH can be used to select donor ewes with a higher potential of response for in vivo embryo production.

Immunogenomics of gastrointestinal nematode infection in ruminants - breeding for resistance to produce food sustainably and safely

Gastrointestinal nematode (GIN) infection of ruminants represents a major health and welfare challenge for livestock producers worldwide. The emergence of anthelmintic resistance in important GIN species and the associated animal welfare concerns have stimulated interest in the development of alternative and more sustainable strategies aimed at the effective management of the impact of GINs. These integrative strategies include selective breeding using genetic/genomic tools, grazing management, biological control, nutritional supplementation, vaccination and targeted selective treatment. In this review, the logic of selecting for "resistance" to GIN infection as opposed to "resilience" or "tolerance" is discussed. This is followed by a review of the potential application of immunogenomics to genetic selection for animals that have the capacity to withstand the impact of GIN infection. Advances in relevant genomic technologies are highlighted together with how these tools can be advanced to support the integration of immunogenomic information into ruminant breeding programmes.

Using sheep genomes from diverse U.S. breeds to identify missense variants in genes affecting fecundity

Background:  Access to sheep genome sequences significantly improves the chances of identifying genes that may influence the health, welfare, and productivity of these animals.  

Methods:  A public, searchable DNA sequence resource for U.S. sheep was created with whole genome sequence (WGS) of 96 rams.  The animals shared minimal pedigree relationships and represent nine popular U.S. breeds and a composite line.  The genomes are viewable online with the user-friendly Integrated Genome Viewer environment, and may be used to identify and decode gene variants present in U.S. sheep.

Results:  The genomes had a combined average read depth of 16, and an average WGS genotype scoring rate and accuracy exceeding 99%.  The utility of this resource was illustrated by characterizing three genes with 14 known coding variants affecting litter size in global sheep populations:  growth and differentiation factor 9 ( GDF9), bone morphogenetic protein 15 ( BMP15), and bone morphogenetic protein receptor 1B ( BMPR1B).  In the 96 U.S. rams, nine missense variants encoding 11 protein variants were identified.  However, only one was previously reported to affect litter size ( GDF9 V371M, Finnsheep).  Two missense variants in BMP15 were identified that had not previously been reported:  R67Q in Dorset, and L252P in Dorper and White Dorper breeds. Also, two novel missense variants were identified in BMPR1B:  M64I in Katahdin, and T345N in Romanov and Finnsheep breeds.  Based on the strict conservation of amino acid residues across placental mammals, the four variants encoded by BMP15 and BMPR1B are predicted to interfere with their function.  However, preliminary analyses of litter sizes in small samples did not reveal a correlation with variants in BMP15 and BMPR1B with daughters of these rams. 

Conclusions: Collectively, this report describes a new resource for discovering protein variants in silico and identifies alleles for further testing of their effects on litter size in U.S. breeds.

Genetic polymorphism of growth differentiation factor 9 (GDF9) gene related to fecundity in two Egyptian sheep breeds

PURPOSE

This study explores polymorphisms in the growth differentiation factor 9 (GDF9) gene (exon 1) with respect to fertility in Egyptian sheep.

METHODS

Blood samples were collected, and genomic DNA was extracted from 24 Saidi and 13 Ossimi ewes. A 710 bp portion of the GDF9 gene, was amplified using specific primers, and the sequence was analyzed to clarify the phylogenetic relationship of Egyptian breed sheep. In addition, the PCR-RFLP method using Pst1 or Msp1 restriction enzymes was used to mask polymorphisms of partial exon 1 of GDF9 gene to establish molecular markers for twinning.

RESULTS

The lambing rate percentage and litter size showed significant difference between ewes, which produce single and twin lamb for each breed individually, whereas the coefficient of variation of the Saidi breed is greater than that of the Ossimi breed. The results suggested that the GDF9 gene shared a similarity in sequence compared to six accession numbers of Ovis aries found in GenBank. Molecular phylogenetic analyses were performed based on nucleotide sequences in order to examine the position of the Egyptian breeds among many other sheep breeds. The results indicate that accession number AF078545 of O. aries is closely related with Saidi and Ossimi ewes that produce single or twin lamb using the unweighted pair group method with arithmetic mean (UPGMA) analysis. Results showed that Msp1 enzyme digestion revealed polymorphic restriction pattern consisting of one band with 710 bp for ewes producing single lamb and two bands with 710 and 600 bp for ewes producing twin lamb in Saidi sheep breed.

CONCLUSION

Sequence analysis and diversity of polymorphisms in the GDF9 gene (exon 1) have a novel base substitution (A-T) for detection of Fec^G mutations that serve as a molecular marker for twinning.