Genotyping of BMPR1B, BMP15 and GDF9 genes in Chilean sheep breeds and association with prolificacy

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.

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.

Variation in Milk Composition and Fatty Acid Profile during the Lactation of Araucana Creole Ewes in a Pasture-Based System

Araucana creole sheep are a local animal genetic resource adapted to environmental conditions in rural production systems in southern Chile. The aim of the present study was to analyze the milk yield and composition of Araucana creole ewe's milk from ewes maintained in a traditional grazing system of natural pastures. Twenty healthy single-bearing Araucana creole ewes were selected immediately after lambing (body condition score (BCS) of 2.8 ± 0.2, ewe weight (EW) of 62 ± 3.5 kg, and age of 3.8 ± 0.7 years). BCS, EW, and lamb weights were determined. Milk samples were obtained using the oxytocin technique at 10 days postpartum and then twice a month during the lactation stage (90 days). Protein, fat, lactose, total solids (TS), solid non-fat (SNF), urea contents, and fatty acid (FA) composition were analyzed. The Araucana ewe's milk yield was lower than that of other dairy sheep but was higher than that of meat breeds. The milk fat had a higher content of oleic acid in the early lactation period, which decreased slowly according to the progress of lactation. The increase in oleic acid improved the milk health indexes during this period and thus provided a healthier milk product for human consumption than later in lactation. During lactation, higher conjugated linoleic acid (CLA) levels were obtained only at day 60. Our research suggests that Araucana creole sheep can provide high-quality milk during early lactation, which is rich in oleic acid and represents an alternative for the production of dairy products, improving the profitability of the productive systems of small-holder farmers in Chile.

Expression Analysis of the Prolific Candidate Genes, BMPR1B, BMP15, and GDF9 in Small Tail Han Ewes with Three Fecundity (FecB Gene) Genotypes

Simple Summary

As important prolific candidate genes, BMPR1B, BMP15, and GDF9 may affect the lambing performance of sheep. Therefore, regarding the three FecB genotypes of Small Tail Han (STH) sheep (FecB BB, FecB B+, and FecB ++), this study explored the gene expression characteristics of different tissues using reverse transcription PCR (RT-PCR) and real-time quantitative PCR (qPCR). The results showed that BMPR1B, BMP15, and GDF9 expression differed between the selected tissues, with all being highly expressed in the ovaries. Further analysis indicated that there was no significant difference in BMPR1B expression among the three FecB genotypes, but both GDF9 and BMP15 had the highest expression in FecB B+. As for other non-ovarian tissues, expression also varied. This study is relevant to understanding the high prolificacy of the STH breed.

Abstract

The expression characteristics of the prolific candidate genes, BMPR1B, BMP15, and GDF9, in the major visceral organs and hypothalamic–pituitary–gonadal (HPG) axis tissues of three FecB genotypes (FecB BB, FecB B+, and FecB ++) were explored in STH ewes using RT-PCR and qPCR. The results were as follows, BMPR1B was expressed in all FecB BB genotype (Han BB) tissues, and GDF9 was expressed in all selected tissues, but BMP15 was specifically expressed in the ovaries. Further study of ovarian expression indicated that there was no difference in BMPR1B expression between genotypes, but the FecB B+ genotype (Han B+) had greater expression of GDF9 and BMP15 than Han BB and FecB ++ genotype (Han ++) (p < 0.05, p < 0.01). BMP15 expression was lower in the ovaries of Han BB than in Han ++ sheep, but the reverse was shown for GDF9. The gene expression in non-ovarian tissues was also different between genotypes. Therefore, we consider that the three genes have an important function in ovine follicular development and maturation. This is the first systematic analysis of the tissue expression pattern of BMPR1B, BMP15, and GDF9 genes in STH sheep of the three FecB genotypes. These results contribute to the understanding of the molecular regulatory mechanism for ovine reproduction.

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.

Single Nucleotide Polymorphisms in the HIRA Gene Affect Litter Size in Small Tail Han Sheep

Simple Summary

Litter size is one of the most important reproductive traits in sheep. Two single nucleotide polymorphisms (SNPs), g.71874104G>A and g.71833755T>C, in the Histone Cell Cycle Regulator (HIRA) gene, were identified by whole-genome sequencing (WGS) and may be correlated with litter size in sheep. The two SNPs were genotyped and expression patterns of HIRA was determined in sheep breeds with different fecundity and in groups of Small Tail Han sheep producing large or small litters. Association analysis indicated that both SNPs were significantly correlated with litter size in Small Tail Han sheep. Furthermore, high levels of HIRA expression may have a negative effect on litter size in Small Tail Han sheep.

Abstract

Maintenance of appropriate levels of fecundity is critical for efficient sheep production. Opportunities to increase sheep litter size include identifying single gene mutations with major effects on ovulation rate and litter size. Whole-genome sequencing (WGS) data of 89 Chinese domestic sheep from nine different geographical locations and ten Australian sheep were analyzed to detect new polymorphisms affecting litter size. Comparative genomic analysis of sheep with contrasting litter size detected a novel set of candidate genes. Two SNPs, g.71874104G>A and g.71833755T>C, were genotyped in 760 Small Tail Han sheep and analyzed for association with litter size. The two SNPs were significantly associated with litter size, being in strong linkage disequilibrium in the region 71.80–71.87 Mb. This haplotype block contains one gene that may affect litter size, Histone Cell Cycle Regulator (HIRA). HIRA mRNA levels in sheep with different lambing ability were significantly higher in ovaries of Small Tail Han sheep (high fecundity) than in Sunite sheep (low fecundity). Moreover, the expression levels of HIRA in eight tissues of uniparous Small Tail Han sheep were significantly higher than in multiparous Small Tail Han sheep (p < 0.05). HIRA SNPs significantly affect litter size in sheep and are useful as genetic markers for litter size.

Genome-wide differential expression profiling of mRNAs and lncRNAs associated with prolificacy in Hu sheep

Reproductive ability, especially prolificacy, impacts sheep profitability. Hu sheep, a unique Chinese breed, is recognized for its high prolificacy (HP), early sexual maturity, and year-round estrus. However, little is known about the molecular mechanisms underlying HP in Hu sheep. To explore the potential mRNAs and long non-coding RNAs (lncRNAs) involved in Hu sheep prolificacy, we performed an ovarian genome-wide analysis of mRNAs and lncRNAs during the follicular stage using Hu sheep of HP (litter size = 3; three consecutive lambings) and low prolificacy (LP, litter size = 1; three consecutive lambings). Plasma luteinizing hormone (LH) concentration was higher in the HP group than in the LP group (P<0.05) during the follicular stage. Subsequently, 76 differentially expressed mRNAs (DE-mRNAs) and five differentially expressed lncRNAs (DE-lncRNAs) were identified by pairwise comparison; quantitative real-time PCR (qRT-PCR) analysis of ten randomly selected DE genes (mRNA and lncRNA) were consistent with the sequencing results. Gene Ontology (GO) analysis of DE-mRNAs revealed significant enrichment in immune response components, actin filament severing and phagocytosis. Pathway enrichment analysis of DE-mRNAs indicated a predominance of immune function pathways, including phagosomes, lysosomes, and antigen processing. We constructed a co-expression network of DE-mRNAs and mRNA-lncRNAs, with C1qA, CD53, cathepsin B (CTSB), CTSS, TYROBP, and AIF1 as the hub genes. Finally, the expression of lysosomal protease cathepsin genes, CTSB and cathepsin D (CTSD), were significantly up-regulated in sheep ovaries in the HP group compared with the LP group (P<0.05). These differential mRNAs and lncRNAs may provide information on the molecular mechanisms underlying sheep prolificacy.

Screening for Causative Mutations of Major Prolificacy Genes in Iranian Fat-Tailed Sheep

Background

The presence of different missense mutations in sheep breeds have shown that the bone morphogenetic protein receptor 1B (BMPR1B), bone morphogenetic protein 15 (BMP15) and growth differentiation factor 9 (GDF9) genes play a vital role in ovulation rate and prolificacy in ewes. Therefore, the present study aims to investigate BMPR1B, BMP15 and GDF9 gene mutations in prolific ewes of Iranian fat-tailed Lori-Bakhtiari sheep.

MATERIALS AND METHODS

In the present experimental study, genomic DNA was extracted from whole blood of 10 prolific Lori-Bakhtiari ewes with at least two twinning records in the first four parities to identify point mutations of the BMPR1B, BMP15 and GDF9 genes, using DNA sequencing.

RESULTS

The results obtained from DNA sequencing showed a new synonymous mutation (g.66496G>A) in exon 8 of the BMPR1B gene, without any amino acid change. Sequencing of the BMP15 gene revealed a deletion of 3 bp (g.656_658delTTC) in exon 1, leading to an amino acid deletion (p.Leu19del). Four single nucleotide polymorphisms (G1:g.2118G>A, G2:g.3451T>C, G3:g.3457A>G and G4:g.3701G>A), were detected in exons 1 and 2 of the GDF9 gene, two of which caused amino acid substitutions (G1: p.87Arg>His and G4: p.241Glu>Lys). These amino acid alterations are proposed to have a benign impact on structure and function of the GDF9 polypeptide sequence.

CONCLUSION

Three major prolificacy genes (BMPR1B, BMP15 and GDF9) were polymorphic in Lori-Bakhtiari sheep, although none of the major causative mutation was detected in this sheep type. Further studies using high throughput methods such as genome-wide association study (GWAS) and evaluation of other candidate genes are necessary in the future.

qPCR and HRM-based diagnosis of SNPs on growth differentiation factor 9 (GDF9), a gene associated with sheep (Ovis aries) prolificacy

Prolificacy is a desirable trait for genetic improvement of sheep flocks, since it holds the potential to improve productivity. Animals carrying single-nucleotide polymorphisms (SNPs) in genes associated with this trait can be identified and employed to increase prolificacy in flocks. In this study, we report a diagnostic method based on quantitative PCR and high-resolution melting curves to detect different SNPs in the prolificacy-associated gene growth differentiation factor 9 (GDF9). The diagnostic method was validated using artificial sequences representing known SNPs in GDF9, then applied to a real flock comprising four breeds and admixed animals (n = 306). Five different SNPs were identified in this flock, as was a low or null frequency of occurrence of SNPs positively associated with prolificacy. This indicates a need to implement a breeding strategy for recovering or reintroducing such SNPs. Our method provides a genotyping strategy for identifying individuals with SNPs of interest for prolificacy, which will help producers plan a breeding strategy for this trait. This method can be adapted and expanded for the diagnosis of other traits of interest.