Polymorphism of fecundity genes (BMPR1B, BMP15 and GDF9) in the Indian prolific Black Bengal goat

Structural variant landscapes reveal convergent signatures of evolution in sheep and goats

BACKGROUND

Sheep and goats have undergone domestication and improvement to produce similar phenotypes, which have been greatly impacted by structural variants (SVs). Here, we report a high-quality chromosome-level reference genome of Asiatic mouflon, and implement a comprehensive analysis of SVs in 897 genomes of worldwide wild and domestic populations of sheep and goats to reveal genetic signatures underlying convergent evolution.

RESULTS

We characterize the SV landscapes in terms of genetic diversity, chromosomal distribution and their links with genes, QTLs and transposable elements, and examine their impacts on regulatory elements. We identify several novel SVs and annotate corresponding genes (e.g., BMPR1B, BMPR2, RALYL, COL21A1, and LRP1B) associated with important production traits such as fertility, meat and milk production, and wool/hair fineness. We detect signatures of selection involving the parallel evolution of orthologous SV-associated genes during domestication, local environmental adaptation, and improvement. In particular, we find that fecundity traits experienced convergent selection targeting the gene BMPR1B, with the DEL00067921 deletion explaining ~10.4% of the phenotypic variation observed in goats.

CONCLUSIONS

Our results provide new insights into the convergent evolution of SVs and serve as a rich resource for the future improvement of sheep, goats, and related livestock.

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.

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 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.

Polymorphism of fecundity genes (BMP15 and GDF9) and their association with litter size in Bangladeshi prolific Black Bengal goat

Goat farming in Bangladesh is primarily centred on indigenous Black Bengal goat, a highly prolific breed. Searching for genetic markers associated with prolificacy in this breed is vital for the country's goat breeding industry. However, there are no reports on polymorphisms associated with the fertility of Bangladeshi Black Bengal goats. This study investigated two major fecundity genes-bone morphogenetic protein 15 (BMP15) and growth differentiation factor 9 (GDF9) to detect any possible mutations in these two genes associated with litter size in Black Bengal goats. Blood samples were collected from 40 raised goats in Hathazari Government Goat Farm, Bangladesh. Genomic DNA was extracted; PCR amplification was performed; and sequencing of PCR products was performed to detect polymorphism loci in the target genes. Five SNPs viz. C735A, C743A, G754T, C781A and C808G were detected in exon 2 of BMP15 gene. A SNP (T1173A) was detected in GDF9 exon 2. Association results show that SNPs at the 735, 754 and 781 nucleotide positions of BMP15 exon 2 had a significant association with litter size in Black Bengal goat. The effect of parity was also highly significant (P < 0.001) on litter size. For the first time, this study explored SNP loci in fecundity genes in Bangladeshi prolific Black Bengal goats. Further studies with many genetically unrelated animals for assessing the association of these loci and others in the fecundity genes with litter size may be useful.

Discovery of single nucleotide polymorphisms in bone morphogenetic protein (BMP) genes of goats by double digest restriction-site associated DNA sequencing

Context Two native goat breeds from Kerala, Malabari and Attappady Black, differ significantly in prolificacy (i.e. no. of kids born/kidding). Prolificacy is an important economic trait and the subject of genetic research showing that bone morphogenetic protein (BMP) genes have a significant effect. Double digest restriction-site associated DNA sequencing (ddRADseq) is a highly efficient and low cost technology for high density discovery of single nucleotide polymorphisms (SNPs), which could serve as predictive markers for animal breeding programs. Aims The study was aimed at discovering SNPs in BMP genes that affect prolificacy, using ddRADseq followed by validation of selected SNP. Methods Blood DNA samples of 10 highly prolific Malabari and 10 less prolific Attappady Black goats were pooled by group and subjected to ddRADseq. SNPs observed in BMP genes were investigated and compared between groups. A validation study was done for the c.614–32789C&gt;T variant in 100 Malabari and 50 Attappady Black goats by using PCR-RFLP. Key results In total, 6333 variants were identified by ddRADseq. Three variants were identified in BMP genes, which included two intronic variants c.614–32789C&gt;T and c.490+6793T&gt;C, in genes BMP6 and BMP5 and a downstream gene variant near the BMPR1B gene. According to ddRADseq data, variants in BMP5 and BMP6 differed in allelic distribution between Malabari and Attappady Black goats. For c.490+6793T&gt;C in BMP5, the CC genotype was predominant in the highly prolific Malabari whereas TC was present in the Attappady Black group. The variant c.614–32789C&gt;T in BMP6 was genotyped as TC in Malabari and CC in Attappady Black goats by ddRADseq. This variant was predicted to have an effect on splicing, according to the tool SplicePort. On the basis of bioinformatics analysis and the role of BMP6 gene in follicular dynamics, the variant in BMP6 was selected for further validation studies. All three genotypes were identified by PCR-RFLP; the C allele was the rare allele in the population with an allele frequency of 0.36. Presence of both alleles C and T and the three genotypes CC, TC and TT in this larger population substantiated the robustness of ddRADseq technique. Conclusions The technique discovered high confidence SNPs, which could be used for further validation and association studies to develop markers for selection of animals and for genetic improvement of this complex trait. Implications Techniques such as ddRADseq provide a large number of SNPs, and investigation of those polymorphisms found across the genome will help to identify new loci affecting traits of interest. This, in turn, will aid in exploring genetically complex traits in a faster and cheaper manner.

Investigating the Polymorphism of Bone Morphogenetic Protein Receptor-1B (BMPR1B) Gene in Markhoz Goat Breed

Reproductive traits in livestock species are genetically controlled by the action of single genes with a major effect, commonly known as fecundity genes. One of the genes involved in controlling prolificacy is BMPR1B (FecB), a dominant autosomal gene located in chromosome 6 responsible for the fecundity and twinning rate in sheep and goat species. Markhoz goat is a valuable Iranian genetic resource endangered by extinction. Increasing the genetic variability and reproductive performances of Markhoz goat could preserve and enhance its economic value. This study was carried out to detect possible polymorphisms in BMPR1B gene in a sample of 100 Markhoz goats from Iran. DNA samples were screened by PCR-RFLP to assess the presence of the previously reported FecB mutation. Finally, the amplicons from seven goats out of the 100 samples were sequenced. The results showed that all the analyzed individuals did not carry the previously reported FecB mutant allele. However, our findings revealed two novel possible mutations in exon 8 of BMPR1B gene (775A > G and 777G > A) that need further investigations.

Goat Genomic Resources: The Search for Genes Associated with Its Economic Traits

Goat plays a crucial role in human livelihoods, being a major source of meat, milk, fiber, and hides, particularly under adverse climatic conditions. The goat genomics related to the candidate gene approach is now being used to recognize molecular mechanisms that have different expressions of growth, reproductive, milk, wool, and disease resistance. The appropriate literature on this topic has been reviewed in this article. Several genetic characterization attempts of different goats have reported the existence of genotypic and morphological variations between different goat populations. As a result, different whole-genome sequences along with annotated gene sequences, gene function, and other genomic information of different goats are available in different databases. The main objective of this review is to search the genes associated with economic traits in goats. More than 271 candidate genes have been discovered in goats. Candidate genes influence the physiological pathway, metabolism, and expression of phenotypes. These genes have different functions on economically important traits. Some genes have pleiotropic effect for expression of phenotypic traits. Hence, recognizing candidate genes and their mutations that cause variations in gene expression and phenotype of an economic trait can help breeders look for genetic markers for specific economic traits. The availability of reference whole-genome assembly of goats, annotated genes, and transcriptomics makes comparative genomics a useful tool for systemic genetic upgradation. Identification and characterization of trait-associated sequence variations and gene will provide powerful means to give positive influences for future goat breeding program.

Two Novel Rare Strongly Linked Missense SNPs (P27R and A85G) Within the GDF9 Gene Were Significantly Associated With Litter Size in Shaanbei White Cashmere (SBWC) Goats

Growth differentiation factor 9 (GDF9) is a high-fertility candidate gene that plays a crucial role in early folliculogenesis in female mammals. In this study, direct sequencing was used to screen possible SNP loci in the goat GDF9 gene. Three SNP loci, p.proline27alanine (P27R), p.leucine61leucine (L61L), and p.alanine85glycine (A85G), were identified in Shaanbei white cashmere (SBWC) goats. Among the three SNPs, two rare missense SNP loci (P27R and A85G) were discovered to be strongly linked with each other (D′ value = 0.926, r² value = 0.703). Both P27R and A85G loci had two genotypes: wild type and heterozygous type. A85G exerted a significant effect on litter size (P = 0.029) in SBWC goats, and the heterozygous genotype was superior in comparison with the wild type. The heterozygous genotype was also superior in P27R but no significant association was found. However, the combination genotypes of P27R and A85G were identified to have superior effects on litter size (P = 3.8E−15). This information suggested that these two SNPs influenced litter size in goats synergistically. Combining this information with our previous studies, we propose that the GDF9 gene is the principal high-fertility candidate gene and that the A85G locus is a promising SNP that affects litter size in goats. These results may fill a research gap regarding rare mutations as well as provide crucial molecular markers that could be useful in marker-assisted selection (MAS) goat rearing when selecting superior individuals.

Analysis of genome-wide DNA arrays reveals the genomic population structure and diversity in autochthonous Greek goat breeds

Goats play an important role in the livestock sector in Greece. The national herd consists mainly of two indigenous breeds, the Eghoria and Skopelos. Here, we report the population structure and genomic profiles of these two native goat breeds using Illumina’s Goat SNP50 BeadChip. Moreover, we present a panel of candidate markers acquired using different genetic models for breed discrimination. Quality control on the initial dataset resulted in 48,841 SNPs kept for downstream analysis. Principal component and admixture analyses were applied to assess population structure. The rate of inbreeding within breed was evaluated based on the distribution of runs of homozygosity in the genome and respective coefficients, the genomic relationship matrix, the patterns of linkage disequilibrium, and the historic effective population size. Results showed that both breeds exhibit high levels of genetic diversity. Level of inbreeding between the two breeds estimated by the Wright’s fixation index F_ST was low (Fst = 0.04362), indicating the existence of a weak genetic differentiation between them. In addition, grouping of farms according to their geographical locations was observed. This study presents for the first time a genome-based analysis on the genetic structure of the two indigenous Greek goat breeds and identifies markers that can be potentially exploited in future selective breeding programs for traceability purposes, targeted genetic improvement schemes and conservation strategies.

Comparison of the sequences and expression levels of genes related to follicular development and atresia between prolific and nonprolific goat breeds

This study investigated the variations of the nucleotide sequences and ovarian expression levels of genes related to follicular development and atresia in prolific Jintang black goats and nonprolific Tibetan goats. Eight genes, FSHB, LHB, FSHR, LHCGR, ESR2, B4GANT2, BCL2 and BAX, were examined using reverse transcription‐polymerase chain reaction and quantitative real‐time PCR. The results showed that the nucleotide and deduced amino acid sequences of the LHB and BAX genes were not different, but there was one base change in the FSHR genes between the two breeds. There was one base change in the FSHB gene, which resulted in one amino acid substitution; there were nine base changes in the LHCGR gene, which resulted in five amino acid substitutions; and there were six base changes in the B4GANT2 gene, which resulted in four amino acid substitutions. The expression levels of the FSHR, LHCGR, ESR2, B4GANT2, BCL2 and BAX genes in the ovaries were not different between the two breeds. The plasma concentrations of FSH were not different, but the plasma concentrations of LH, P₄ and E₂ were lower in prolific Jintang black goats than in nonprolific Tibetan goats (P ˂ 0.05) at 40 hr after removal of the Controlled Internal Drug Release Devices. These results provide some foundations elucidating the endocrine and molecular mechanisms controlling ovulation rate in goats, but these need to be further verified.

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

Simple Summary

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

Abstract

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

Association of polymorphisms in bone morphogenetic protein receptor-1B gene exon-9 with litter size in Dorset, Mongolian, and Small Tail Han ewes

OBJECTIVE

The present study was to investigate the association of polymorphisms in exon-9 of the bone morphogenetic protein receptor-1B (BMPR-1B) gene (C864T) with litter size in 240 Dorset, 232 Mongolian, and 124 Small Tail Han ewes.

METHODS

Blood samples were collected from 596 ewes and genomic DNA was extracted using the phenol: chloroform extraction method. The 304-bp amplified polymerase chain reaction product was analyzed for polymorphism by single-strand conformation polymorphism method. The genotypic frequency and allele frequency of BMPR-1B gene exon-9 were computed after sequence alignment. The χ2 independence test was used to analyze the association of genotypic frequency and litter size traits with in each ewe breed, where the phenotype was directly treated as category.

RESULTS

The results indicated two different banding patterns AA and AB for this fragment, with the most frequent genotype and allele of AA and A. Calculated Chi-square test for BMPR-1B gene exon-9 was found to be more than that of p value at the 5% level of significance, indicating that the population under study was in Hardy-Weinberg equilibrium for all ewes. The χ2 independence test analyses indicated litter size differences between genotypes was not the same for each breed. The 304-bp nucleotide sequence was subjected to BLAST analysis, and the C864T mutation significantly affected litter size in singletons, twins and multiples. The heterozygosity in exon-9 of BMPR-1B gene could increase litter size for all the studied ewes.

CONCLUSION

Consequently, it appears that the polymorphism BMPR-1B gene exon-9 detected in this study may have potential use in marker assisted selection for litter size in Dorset, Mongolian, and Small Tail Han ewes.

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

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

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.

A novel indel within goat casein alpha S1 gene is significantly associated with litter size

The ruminant casein gene family (CSNs, link as CSN1S1-CSN2-CSN1S2-CSN3) is characterized by diverse variations and has been extensively studied for ruminant milk traits, however, studies on insertion/deletion (indel) mutations within this gene family and their effects on prolificacy are extremely limited. This study aimed to detect possible novel indels within CSNs in an indigenous Chinese goat breed-Shaanbei White Cashmere goat (SBWC, n = 3047) and four other Chinese goat breeds (n = 1136) with varied litter size rates (105%-283%) and different estrus types (seasonal vs. perennial), as well as exploring the association between these potential indels and litter size. Only one novel 11-bp indel within the CSN1S1 gene was found. The association analyses uncovered that this novel indel was related to the first-birth litter size of SBWC population (n = 2690) (P < 1.0 E-8). Individuals with the II genotype (n = 676) had the best litter size when compared with those ID genotype (n = 1098) and DD genotype (n = 916) individuals. Animals with the II genotype were found to have higher relative expression level of CSN1S1 gene in the ovary (P < 0.01). Besides, Chi-square tests for different litter size and estrous cycle breeds showed that perennial-estrus breeds and multi-kids breeds had higher "I" allelic frequencies and "II" genotypic frequencies. These findings suggest the 11-bp indel within the CSN1S1 gene is significantly associated with reproduction traits and can be an effective molecular marker for litter size of goat breeding.

Variant <i>GDF9</i> mRNA is likely not the main cause of larger litter size in Iranian Lori-Bakhtyari, Shal, Ghezel, and Afshari sheep breeds

Abstract. This study was carried out to screen the GDF9 gene and evaluate the polymorphism effect on litter size of four Iranian sheep breeds using the PCR-RFLP and PCR-SSCP methods. First, sequencing of the GDF9 gene in 16 twin-birth, 4 triplet-birth, and 2 infertile ewes showed that, in addition to G2, G3, G4, G5, and G6 mutations that have been previously reported in other breeds, a new G0 mutation, called C25T, exists in the GDF9 sequence of 1 out of 22 ewes and causes L9F substitution in the signal peptide region. None of the triplet-birth or infertile ewes carried G1, G4, G7, FecGE, G8, or FecGT mutations. In the second experiment, a large dataset was used: 605 individuals including 496 ewes (145 Afshari, 54 Shal, 126 Ghezel, and 171 Lori-Bakhtyari sheep), and 109 rams (26 Afshari, 23 Shal, 10 Ghezel, and 50 Lori-Bakhtyari sheep. There were no sheep carrying the G7, G8, or Thoka mutations. Among all 109 rams that were used in this study, none of them were homozygous for the G1 mutation. Moreover, abundance of heterozygote rams (G1/G+) varied from 0.0 (Afshari) to 28.6 % (Lori-Bakhtyari and Ghezel). The highest and the lowest frequencies of the G4 mutation were 30.6 and 3.0 % in Shal and Afshari breeds, respectively. Moreover, G4 abundance varied from 0.0 to 42.3 %, from 3.0 to 26.9, and from 3.0 to 30.6 % in rams, ewes, and overall, respectively. There was a significant difference in the abundance of G1 and G4 mutations between breeds. However, neither the G1 nor the G4 mutation was associated with litter size in Afshari, Ghezel, Lori-Bakhtyari, or Shal sheep breeds. In conclusion, the results of this study showed that GDF9 G1 and G4 mutations are not the reason for higher litter size in Iranian sheep. Moreover, the GDF9 G0 and G6 mutations do not cause triplet births or infertility in Iranian ewes. Therefore, it is unlikely that variant GDF9 mRNA induces larger litter size or infertility in Iranian ewes.

Genetic polymorphism of bone morphogenetic protein receptor type-1 (BMPR1B) gene in crossbred does of Bihar

Screening of bone morphogenetic protein receptor type- 1 gene (BMPR1B gene) also known as Fec B gene polymorphism was done for detecting the genetic basis of prolificacy in crossbred does of Bihar. The study revealed two allelic variants (A=0.48 and G=0.52) and three genotypes (AA=0.16, AG=0.62 and GG=0.22).The findings of thestudy indicate sign of introgression of mutant allele (G) into Jamunapari, Barbari, and Sirohi goats at village level from Black Bengal breed. The variation in litter size among the genotypes revealed the benefits of introgression of Fec B mutation in the crosses. The litter size showed variation among the three genotypes. Percentage singles, twins and triplets were 69, 29 and 2 in AA genotype; 42, 52 and 6 in AG genotype and 14, 66 and 20 in GG genotype, respectively.

Genome-wide transcriptome analysis in the ovaries of two goats identifies differentially expressed genes related to fecundity

The goats are widely kept as livestock throughout the world. Two excellent domestic breeds in China, the Laiwu Black and Jining Grey goats, have different fecundities and prolificacies. Although the goat genome sequences have been resolved recently, little is known about the gene regulations at the transcriptional level in goat. To understand the molecular and genetic mechanisms related to the fecundities and prolificacies, we performed genome-wide sequencing of the mRNAs from two breeds of goat using the next-generation RNA-Seq technology and used functional annotation to identify pathways of interest. Digital gene expression analysis showed 338 genes were up-regulated in the Jining Grey goats and 404 were up-regulated in the Laiwu Black goats. Quantitative real-time PCR verified the reliability of the RNA-Seq data. This study suggests that multiple genes responsible for various biological functions and signaling pathways are differentially expressed in the two different goat breeds, and these genes might be involved in the regulation of goat fecundity and prolificacy. Taken together, our study provides insight into the transcriptional regulation in the ovaries of 2 species of goats that might serve as a key resource for understanding goat fecundity, prolificacy and genetic diversity between species.

A Study on BMPR-IB Genes of Bayanbulak Sheep

The average twin lambing rate of Bayanbulak sheep is 2% to 3%. However, a flock of sheep with a close genetic relationship and an average of 2 to 3 lambs per birth has been found recently. To determine the major genes controlling the prolificacy of the flock in the present study, the flock was designated A while 100 normal Bayanbulak sheep were randomly selected to comprise the control flock B. Ligase detection reaction method was applied to detect and analyze the 10 mutational loci of the 3 candidate prolificacy genes including bone morphogenetic protein type I receptors, bone morphogenetic protein 15, and growth differentiation factor 9. The 10 mutational loci are as follows: FecB locus of the BMPR-IB gene; FecX^I, FecX^B, FecX^L, FecX^H, FecX^G, and FecX^R of the BMP15 gene; and G1, G8, and FecTT of the GDF9 gene. Two mutations including BMPR-IB/FecB and GDF9/G1 were found in Bayanbulak sheep. Independence test results of the two flocks demonstrate that the FecB locus has a significant effect on the lambing number of Bayanbulak sheep. However, the mutation frequency of the G1 locus in GDF9 is very low. Independence test results demonstrate that the GDF9 locus does not have a significant impact on the lambing performance of Bayanbulak sheep. Among the 10 detected loci, BMPR-IB/FecB is the major gene that influences the high lambing rate of Bayanbulak sheep.

Association of BMPR-1B and GDF9 genes polymorphisms and secondary protein structure changes with reproduction traits in Mehraban ewes

BMPR-1B and GDF9 genes are well known due to their important effects on litter size and mechanisms controlling ovulation rate in sheep. In the present study, polymorphisms of BMPR-1B gene exon 8 and GDF9 gene exon 1 were detected by single strand conformational polymorphism (SSCP) analysis and DNA sequencing methods in 100 Mehraban ewes. The PCR reaction forced to amplify 140 and 380-bp fragments of BMPR-1B and GDF9 genes, respectively. Two single nucleotide polymorphisms (SNPS) were identified in two different SSCP patterns of BMPR-1B gene (CC and CA genotypes) that deduced one amino acid exchange. Also, two SNPS were identified in three different SSCP patterns of GDF9 gene (AA, AG and GG genotypes) that deduced one amino acid exchanges. Two different secondary structures of protein were predicted for BMPR-1B exon 8, but the secondary protein structures predicted for GDF9 exon 1 were similar together. The evaluation of the associations between the SSCP patterns and the protein structure changes with reproduction traits showed that BMPR-1B exon 8 genotypes have significant effects on some of reproduction traits but the GDF9 genotypes did not have any significant effect. The CA genotype of BMPR-1B exon 8 had a significant positive effect on reproduction performance and could be considered as an important and new mutation, affecting the ewes reproduction performance. Marker assisted selection using BMPR-IB gene could be noticed to improve the reproduction traits in Mehraban sheep.

Screening of indigenous goats for prolificacy associated DNA markers of sheep

The present study was undertaken to explore the genetic basis of caprine prolificacy and to screen indigenous goats for prolificacy associated markers of sheep in BMPR1B, GDF9 and BMP15 genes. To detect the associated mutations and identify novel allelic variants in the candidate genes, representative samples were collected from the breeding tract of indigenous goat breeds varying in prolificacy and geographic distribution. DNA was extracted and PCR amplification was done using primers designed or available in literature for the coding DNA sequence of candidate genes. Direct sequencing was done to identify the genetic variations. Mutations in the candidate genes associated with fecundity in sheep were not detected in Indian goats. Three non-synonymous SNPs (C818T, A959C and G1189A) were identified in exon 2 of GDF9 gene out of which mutation A959C has been associated with prolificacy in exotic goats. Two novel SNPs (G735A and C808G) were observed in exon 2 of BMP15 gene.

Polymorphism of fecundity genes (FecB, FecX, and FecG) in the Indian Bonpala sheep

The present study was designed for screening polymorphism of known fecundity genes in prolific Indian Bonpala sheep. Employing tetra-primer amplification refractory mutation system PCR, 11-point mutations of BMP1B, BMP15, and GDF9 genes of 97 Bonpala ewes were genotyped. The FecB locus of the BMPR1B gene and two loci (G1 and G4) of GDF9 gene were found to be polymorphic. In FecB locus, three genotypes, namely, wild type (Fec++, 0.02), heterozygous (FecB+, 0.23), and mutant (FecBB, 0.75) were detected. At G1 locus of GDF9 gene, three genotypes, namely, wild type (GG, 0.89), heterozygous (GA, 0.10), and mutant (AA, 0.01) were detected. At G4 locus of GDF9 gene, three genotypes, namely, wild type (AA, 0.01), heterozygous (AG, 0.14), and mutant (GG, 0.85) were detected. Statistically no significant correlation of polymorphism of FecB, G1, and G4 loci and litter size was found in this breed. All five loci of BMP15 and three loci of GDF 9 genes were monomorphic. This study reports Bonpala sheep as the first sheep breed where concurrent polymorphism at three important loci (FecB, G1, and G4) of two different fecundity genes (BMPR1B and GDF9) has been found.

The association of two single nucleotide polymorphisms (SNPs) in growth hormone (GH) gene with litter size and superovulation response in goat-breeds

Two active mutations (A 781 G and A 1575 G) in growth hormone (GH) gene, and their associations with litter size (LS), were investigated in both a high prolificacy (Matou, n = 182) and a low prolificacy breed (Boer, n = 352) by using the PCR-RFLP method. Superovulation experiments were designed in 57 dams, in order to evaluate the effect of different genotypes of the GH gene on superovulation response. Two genotypes (AA and AB, CC and CD) in each mutation were detected in these two goat breeds. Neither BB nor DD homozygous genotypes were observed. The genotypic frequencies of AB and CC were significantly higher than those of AA and CD. In the third parity, Matou dams with AB or CC genotypes had significantly larger litter sizes than those with AA and CD (p < 0.05). On combining the two loci, both Matou and Boer dams with ABCD genotype had the largest litter sizes when compared to the other genotypes (p < 0.05). When undergoing like superovulation treatments, a significantly higher number of corpora lutea and ova, with a lower incidence of ovarian cysts, were harvested in the AB and CC genotypes than in AA and CD. These results show that the two loci of GH gene are highly associated with abundant prolificacy and superovulation response in goat breeds.

Polymorphism of BMPR1B, BMP15 and GDF9 fecundity genes in prolific Garole sheep

Mutation studies in different prolific sheep breeds have shown that the transforming growth factor beta super family ligands viz. the growth differentiation factor 9 (GDF9/FecG), bone morphogenetic protein 15 (BMP15/FecX) and associated type I receptors, bone morphogenetic protein receptor (BMPR1B/FecB), are major determinant of ovulation rate and consequent increase in litter size. The Garole sheep is a highly prolific sheep breed of India. Characterization of fecundity genes in these animals could substantially improvise the breeding programme in these animals as well as other sheep breeds of the region. The present study was therefore designed with the objective of polymorphism study of fecundity genes in these prolific microsheep. A total of 11 point mutations were detected by polymerase chain reaction (PCR)-based method. A competitive technique called tetra-primer amplification refractory mutation system-PCR was adapted to type a total of ten points of two ovine fecundity genes (GDF9 and BMP15). The FecB locus of the BMPR1B gene and G1 locus of GDF9 gene were found to be polymorphic. In FecB locus, two genotypes, wild type (FecB(+)) and mutant (FecBB), were detected with allele frequencies of 0.39 and 0.61, respectively. At G1 locus, two genotypes, mutant (A) and wild types (G) were detected with allele frequencies of 0.18 and 0.82, respectively. This study reports Garole sheep as the fourth sheep breed after Belclare/Cambridge, Lacaune and Small-tailed Han sheep, where coexisting polymorphism has been found in two different fecundity genes (BMPRIB and GDF9 genes).