Expression Analysis of Genes Associated with Prolificacy in FecB Carrier and Noncarrier Indian Sheep

FecB Was Associated with Litter Size and Follows Mendel's Laws of Inheritance When It Transited to Next Generation in Suhu Meat Sheep Breeding Population

In order to investigate the effect of FecB on litter size and growth and development traits of Suhu meat sheep and the inheritance patterns of FecB between parents and offspring in the population. In this experiment, 2241 sheep from the Suhu meat sheep population were tested for FecB using capillary electrophoresis. We combined the lambing records of 473 ewes, the growth trait records of 881 sheep at both the birth and weaning (2-month-old) stages, and the complete genealogical records of 643 lambs to analysis the distribution of FecB in the Suhu meat sheep breeding population, its effect on litter size of ewes, growth and development of lambs, and the inheritance patterns of FecB. The results showed that there were three genotypes of FecB in the Suhu meat sheep population, namely the AA genotype, AG genotype, and GG genotype. FecB in this population has a moderate polymorphism (0.25 < PIC < 0.5), and deviates from Hardy-Weinberg disequilibrium (p < 0.05). The litter size of GG genotype ewes was significantly higher than that with the AG and AA genotypes (p < 0.01). A Chi-square test showed that the inheritance patterns of FecB follows Mendel's Laws of Inheritance (p > 0.05). An association analysis of different genotypes of FecB with body weight and body size of Suhu meat sheep at birth and weaning revealed that FecB adversely affects the early growth and development of Suhu meat sheep. In summary, FecB can improve the litter size of ewes but it has negative effects on the early growth and survival rate of lambs in sheep. Therefore, FecB test results and feeding management measures should be comprehensively applied to improve the reproductive performance of ewes, the survival rate and production performance of lambs in sheep production, and thus improve the economic benefits of sheep farms.

Transcriptomic Analysis Reveals Differentially Expressed Circular RNAs Associated with Fecundity in the Sheep Hypothalamus with Different FecB Genotypes

Circular RNAs (circRNAs) are a specific type of noncoding RNA, and some have defined roles in cellular and biological processes. However, little is known about the role of circRNAs in follicular development in sheep with FecB (fecundity Booroola) mutations. Here, the expression profiles of circRNAs were investigated using RNA sequencing (RNA-seq) in the follicular phase (F) and the luteal phase (L) of FecB mutant homozygous (BB) and wild-type (WW) Small Tail Han sheep. A total of 38,979 circRNAs were identified, and 314, 343, 336, and 296 of them were differentially expressed (DE) between BB_F and BB_L, WW_F and WW_L, BB_F and WW_F, and BB_L and WW_L, respectively. The length, type, and chromosome distribution of the circRNAs and the expression characteristic between the circRNAs and their host genes in the sheep hypothalamus were ascertained. Enrichment analysis showed that the host genes of DE circRNAs in the follicular and luteal phases were annotated to MAPK, gap junctions, progesterone-mediated oocyte maturation, oocyte meiosis, and other hormone-related signaling pathways, and the different FecB genotypes were annotated to the gap junctions, circadian entrainment, MAPK, and other hormone-related signaling pathways. The competing endogenous RNA network prediction revealed that the 129 target miRNAs might be bound to 336 DE circRNAs. oar_circ_0000523 and oar_circ_0028984, which were specifically expressed during the follicular phase in the BB genotype sheep, probably acted as miRNA sponges involved in the regulation of LH synthesis and secretion. This study reveals the expression profiles and characterization of circRNAs at two phases of follicular development considering different FecB genotypes, thereby providing an improved understanding of the roles of circRNAs in the sheep hypothalamus and their involvement in follicular development and ovulation.

Comparative Transcriptomic Analysis of Hu Sheep Pituitary Gland Prolificacy at the Follicular and Luteal Phases

The pituitary gland directly regulates the reproduction of domestic animals. Research has increasingly focused on the potential regulatory mechanism of non-coding RNA in pituitary development. Little is known about the differential expression pattern of lncRNAs in Hu sheep, a famous sheep breed with high fecundity, and its role in the pituitary gland between the follicular phase and luteal phase. Herein, to identify the transcriptomic differences of the sheep pituitary gland during the estrus cycle, RNA sequencing (RNA-Seq) was performed. The results showed that 3529 lncRNAs and 16,651 mRNAs were identified in the pituitary gland. Among of them, 144 differentially expressed (DE) lncRNA transcripts and 557 DE mRNA transcripts were screened in the follicular and luteal phases. Moreover, GO and KEGG analyses demonstrated that 39 downregulated and 22 upregulated genes interacted with pituitary functions and reproduction. Lastly, the interaction of the candidate lncRNA XR_001039544.4 and its targeted gene LHB were validated in sheep pituitary cells in vitro. LncRNA XR_001039544.4 and LHB showed high expression levels in the luteal phase in Hu sheep. LncRNA XR_001039544.4 is mainly located in the cytoplasm, as determined by FISH analysis, indicating that XR_001039544.4 might act as competing endogenous RNAs for miRNAs to regulate LHB. LncRNA XR_001039544.4 knockdown significantly inhibited LH secretion and cell proliferation. LncRNA XR_001039544.4 may regulate the secretion of LH in the luteal-phase pituitary gland via affecting cell proliferation. Taken together, these findings provided genome-wide lncRNA- and mRNA-expression profiles for the sheep pituitary gland between the follicular and luteal phases, thereby contributing to the elucidation of the molecular mechanisms of pituitary function.

Identification of polymorphism of FecX gene in indigenous sheep of Meghalaya

Fecundity gene such as FecX, govern fertility and litter size in sheep. Selection of animals with the help of molecular markers through identification of polymorphism of fecundity genes is an impactful method of genetic improvement. The present study was carried out to identify the polymorphism of FecX gene in indigenous sheep of Meghalaya. Blood samples were collected from 50 randomly selected ewes from 2 districts of Meghalaya namely, East Khasi Hills and West Khasi Hills. Genomic DNA was extracted from the samples and PCR amplification of FecX gene with specific primer set was done. PCR product size of 141 bp was obtained. Further, digestion of the PCR product with restriction enzyme HinfI through PCR-RFLP technique was conducted to identify the variants in FecX gene. Upon digestion, 2 types of fragment pattern identified, arbitrarily designated as AA and AB genotype, where AA genotype yielded one fragment (141 bp) and AB genotype yielded 2 fragments (100 and 41 bp). Presence of polymorphism can be an important indicator for selection with the help of molecular markers.

The expression and mutation of BMPR1B and its association with litter size in small-tail Han sheep (Ovis aries)

Previous studies have shown that BMPR1B promotes follicular development and ovarian granulosa cell proliferation, thereby affecting ovulation in mammals. In this study, the expression and polymorphism of the BMPR1B gene associated with litter size in small-tail Han (STH) sheep were determined. The expression of BMPR1B was detected in 14 tissues of STH sheep during the follicular phase as well as in the hypothalamic–pituitary–gonadal (HPG) axis of monotocous and polytocous STH sheep during the follicular and luteal phases using quantitative polymerase chain reaction (qPCR). Sequenom MassARRAY^® single nucleotide polymorphism (SNP) technology was also used to detect the polymorphism of SNPs in seven sheep breeds. Here, BMPR1B was highly expressed in hypothalamus, ovary, uterus, and oviduct tissue during the follicular phase, and BMPR1B was expressed significantly more in the hypothalamus of polytocous ewes than in monotocous ewes during both the follicular and luteal phases (P<0.05). For genotyping, we found that genotype and allele frequencies of three loci of the BMPR1B gene were extremely significantly different (P<0.01) between the monotocous and polytocous groups. Association analysis results showed that the g.29380965A>G locus had significant negative effects on the litter size of STH sheep, and the combination of g.29380965A>G and FecB (Fec – fecundity and B – Booroola; A746G) at the BMPR1B gene showed that the litter size of AG–GG, AA–GG, and GG–GG genotypes was significantly higher compared with other genotypes (P<0.05). This is the first study to find a new molecular marker affecting litter size and to systematically analyze the expression of BMPR1B in different fecundity and physiological periods of STH sheep.

Genome-wide transcriptome profiling uncovers differential miRNAs and lncRNAs in ovaries of Hu sheep at different developmental stages

Ovary development is an important determinant of the procreative capacity of female animals. Here, we performed genome-wide sequencing of long non-coding RNAs (lncRNAs) and mRNAs on ovaries of 1, 3 and 8 months old Hu sheep to assess their expression profiles and roles in ovarian development. We identified 37,309 lncRNAs, 45,404 messenger RNAs (mRNAs) and 330 novel micro RNAs (miRNAs) from the transcriptomic analysis. Six thousand, seven hundred and sixteen (6716) mRNAs and 1972 lncRNAs were significantly and differentially expressed in ovaries of 1 month and 3 months old Hu sheep (H1 vs H3). These mRNAs and target genes of lncRNAs were primarily enriched in the TGF-β and PI3K-Akt signalling pathways which are closely associated with ovarian follicular development and steroid hormone biosynthesis regulation. We identified MSTRG.162061.1, MSTRG.222844.7, MSTRG.335777.1, MSTRG.334059.16, MSTRG.188947.6 and MSTRG.24344.3 as vital genes in ovary development by regulating CTNNB1, CCNA2, CDK2, CDC20, CDK1 and EGFR expressions. A total of 2903 mRNAs and 636 lncRNAs were differentially expressed in 3 and 8 months old ovaries of Hu sheep (H3 vs H8); and were predominantly enriched in PI3K-Akt, progesterone-mediated oocyte maturation, estrogen metabolism, ovulation from the ovarian follicle and oogenesis pathways. These lncRNAs were also found to regulate FGF7, PRLR, PTK2, AMH and INHBA expressions during follicular development. Our result indicates the identified genes participate in the development of the final stages of follicles and ovary development in Hu sheep.

Effect of the Booroola fecundity (FecB) gene on the reproductive performance of ewes under assisted reproduction

Reproductive traits are important factors in sheep production. The Booroola fecundity (FecB) gene-the first major gene for prolificacy identified in sheep-has a positive effect on ovulation rates and litter size under natural reproductive conditions. However, the effect of the FecB gene on reproductive performance under assisted reproduction, which uses many artificial hormones, remains unclear. In the present study, we evaluated the effect of FecB (BMPR-1B mutation) on reproductive performance under assisted reproduction, and examined offspring body weight at birth and weaning and survival rate at weaning. There were no differences among three genotype groups (homozygous carrier, BB; heterozygous carrier, B+; non-carrier, ++) in terms of estrus detection rate, time to estrus onset, or estrus duration following estrus synchronization (P > 0.05). The pregnancy rates at 60 d were similar among three genotype groups after artificial insemination (P > 0.05). However, the B allele had an additive effect on litter size (one copy resulted in an increase of 0.88 lambs and two copies produced an additional 0.41 lambs; P < 0.01), and increased lambing and fecundity rates (P < 0.01). After multiple ovulation, the average numbers of recovered embryos per ewe were 9.16 ± 0.79, 8.20 ± 0.77, and 8.44 ± 0.61 in the BB, B+, and ++ ewes, respectively (P > 0.05). There were no differences in the fertilization rate or numbers of grade 1-2 embryos among different groups (P > 0.05). The birth and weaning weights of lambs from BB and B+ ewes were lower than those of lambs born from ++ ewes (P < 0.01) owing to the high fecundity. The survival rate of lambs at weaning did not differ among groups (P > 0.05). Our results indicated that the presence of the B allele had an additive effect on litter size after artificial insemination, but it did not influence the parameters of estrus synchronization and multiple ovulation. Furthermore, the higher prolificacy in ewes carrying the B allele was associated with a reduction in offspring body weight at birth and weaning.

Quantitative expression of mRNA encoding BMP/SMAD signalling genes in the ovaries of Booroola carrier and non-carrier GMM sheep

The GMM sheep is a carrier of Booroola fecundity (FecB) gene, which produces the twins and triplets in one lambing. The homozygous carrier GMM (FecB^BB ), non-carrier GMM and Malpura (FecB⁺⁺ ) ewes were synchronized by progesterone sponges, and the plasma progesterone concentration was measured by RIA. The results showed that the progesterone concentration did not differ significantly (p > .05) in homozygous carrier GMM (5.74 ± 1.2 ng/ml), non-carrier GMM (5.42 ± 1.4 ng/ml) and non-carrier Malpura ewes (5.67 ± 1.5 ng/ml). Further, quantitative expression of BMP factors/receptors and SMAD signalling genes were analysed in the ovaries of sheep by qRT-PCR. The study showed that the expression of BMP2 was slightly higher (p > .05) in carrier GMM than that of non-carrier GMM, but it was almost similar to Malpura ewes. Expression of BMP4 and BMP7 was significantly higher (p < .001; p < .05) in carrier GMM than that of non-carrier GMM and Malpura ewes. Although BMP6 expression was higher (p > .05) in carrier GMM than that of non-carrier GMM, but lower (p > .05) than the Malpura ewes. Expression of BMP15 (p < .05), GDF5 (p < .01) and GDF9 (p < .05) was significantly higher in carrier GMM than non-carrier GMM ewes. Surprisingly, BMPR1B expression was significantly higher (p < .001) in non-carrier GMM and Malpura than the carrier GMM ewes, while TGFβRI did not differ significantly (p > .05) among both GMM genotypes. On the other hand, expression of BMPR1A (p > .05) and BMPRII (p < .05) was higher in carrier GMM than the non-carrier GMM, but significantly lower (p < .001) than the Malpura ewes. It was interesting to note that the expression of SMAD1 (p > .05), SMAD2 (p < .001), SMAD3 (p < .05), SMAD4 (p < .001), SMAD5 (p < .001) and SMAD8 (p < .001) was lower in the carrier GMM than that of non-carrier GMM ewes. It is concluded that the FecB mutation alters the expression of BMPR1B and SMAD signalling genes in the ovaries of homozygous carrier GMM ewes.

Genetic polymorphisms of fecundity genes in Watish Sudanese desert sheep

BACKGROUND AND AIM

The Watish sheep is a strain of desert sheep of smaller size compared to other desert sheep ecotypes, and there is anecdotal evidence that it is endowed with high litter size. The present study was designed for screening for polymorphisms in the known fecundity genes (bone morphogenetic protein receptor type 1B A

MATERIALS AND METHODS

The study involved 156 Watish ewes of 2-6 years of age, along with data on litter size in the first, second, and third parity from Sinnar state and contiguous Blue Nile State. Genomic DNA was isolated and genotyped using polymerase chain reaction-restriction fragment length polymorphism. Allele and genotype frequencies were calculated by direct counting. Chi-square test for goodness of fit was performed for agreement with Hardy-Weinberg expectations and association testing.

RESULTS

The results demonstrated that all individuals were non-carriers for the target mutations of FecB, BMP15 (FecXB, FecXH , and FecXI ), and GDF9-G8. With regard to the GDF9-G1 gene, the genotypic frequencies were 0.07% (G+) and 0.93% (++), in FecXG gene they were 0.993% (++) and 0.006% (B+), in PRL gene 0.516(++), 0.347(B+), and 0.137(BB). The Chi-square test showed a non-significant association between ewe's type of birth and the detected mutations genotypes.

CONCLUSION

These results preliminarily indicated that GDF9-G1, BMP15 (FecXG ), and PRL genes might have had some contribution for improving litter size in Watish Sudanese sheep. However, further studies using larger samples are needed to detect the effects of those mutations on Watish sheep litter size.

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Key Words

• Watish
• fecundity
• genes
• litter size
• sheep

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MESH Headings Collapse

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Affiliation(s)

Sara E. Ibrahim Mohamed Animal Production Research Centre, Animal Resources Research Corporation, Ministry of Animal Resources, Khartoum, Sudan
Romaz M. Ahmed Institute for Studies and Promotion of Animal Exports, University of Khartoum, Khartoum, Sudan
Khaleel I. Z. Jawasreh Department of Animal Production, Faculty of Agriculture, Jordan University of Science and Technology, Irbid, Jordan
M. A. M. Salih Institute of Endemic Disease, University of Khartoum, Khartoum, Sudan Department of Genetics and Bioinformatics, Central Laboratory, Ministry of Higher education and Scientific Research, Khartoum, Sudan
Dalia Mursi Abdelhalim Department of Genetics and Bioinformatics, Central Laboratory, Ministry of Higher education and Scientific Research, Khartoum, Sudan
A. W. Abdelgadir Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, Al-Neelain University, Khartoum, Sudan
Md. T. Obeidat Department of Animal Production, Faculty of Agriculture, Jordan University of Science and Technology, Irbid, Jordan
L. M. A. Musa Department of Genetics and Animal Breeding, Faculty of Animal Production, University of Khartoum, Sudan
Mohammed-Khair A. Ahmed Department of Genetics and Animal Breeding, Faculty of Animal Production, University of Khartoum, Sudan

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A polymorphism in the transcriptional regulatory region strongly influences ovine FSHR mRNA decay

Follicle-stimulating hormone receptor (FSHR) is an important G protein-coupled receptor, which is required for steroidogenesis, follicular development and female infertility. Here, we report a novel polymorphism in the 3'-UTR that strongly influences ovine FSHR mRNA decay. The partial 3'-UTR sequence of Hu sheep FSHR gene was isolated and characterized, and a polymorphism (c.2327A>G) was identified. Luciferase assay and qRT-PCR showed that c.2327A>G polymorphism in the 3'-UTR exerts a strong regulatory role in FSHR transcription. This regulatory role is achieved by affecting FSHR mRNA decay. Furthermore, the c.2327A>G mutation in the 3'-UTR influences ARE (AU-rich element, a cis-acting element promoting mRNA decay)-mediated mRNA decay of Hu sheep FSHR gene. Together, our study identified a novel polymorphism and elucidated a new mechanism underlying transcriptional regulation of FSHR in mammals.

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.

Genome-wide analysis of DNA Methylation profiles on sheep ovaries associated with prolificacy using whole-genome Bisulfite sequencing

Background

Ovulation rate and litter size are important reproductive traits in sheep with high economic value. Recent work has revealed a potential link between DNA methylation and prolificacy. However, a genome-wide study that sought to identify potential DNA methylation sites involved in sheep prolificacy indicated that it is still unknown. Here, we aimed to investigate the genome-wide DNA methylation profiles of Hu sheep ovaries by comparing a high-prolificacy group (HP, litter size of three for at least 2 consecutive lambings) and low prolificacy group (LP, litter size of one for at least 2 consecutive lambings) using deep whole-genome bisulfite sequencing (WGBS).

Results

First, our results demonstrated lower expression levels of DNA methyltransferase (DNMT) genes in the ovaries of the HP group than that in the ovaries of the LP group. Both groups showed similar proportions of methylation at CpG sites but different proportions at non-CpG sites. Subsequently, we identified 70,899 differential methylated regions (DMRs) of CG, 16 DMRs of CHG, 356 DMRs of CHH and 12,832 DMR-related genes(DMGs). Gene Ontology (GO) analyses revealed that some DMGs were involved in regulating female gonad development and ovarian follicle development. Finally, we found that 10 DMGs, including BMP7, BMPR1B, CTNNB1, FST, FSHR, LHCGR, TGFB2 and TGFB3, are more likely to be involved in prolificacy of Hu sheep, as assessed by correlation analysis and listed in detail.

Conclusions

This study revealed the global DNA methylation pattern of sheep ovaries associated with high and low prolificacy groups, which may contribute to a better understanding of the epigenetic regulation of sheep reproductive capacity.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-017-4068-9) contains supplementary material, which is available to authorized users.