Polymorphism of GDF9 and BMPR1B genes and their association with litter size in Markhoz goats

Identification of polymorphisms in GDF9 and BMP15 genes in Jamunapari and crossbred goats in Bangladesh

Polymorphisms in growth differentiation factor 9 (GDF9) and bone morphogenetic protein 15 (BMP15) genes have been found to be associated with litter size in goats across the globe. Our previous study detected single-nucleotide polymorphisms (SNPs) in GDF9 and BMP15 genes associated with litter size in Black Bengal, Bangladesh's primary native goat breed. However, Jamunapari and crossbred goats in Bangladesh are yet to be investigated for litter size-associated polymorphisms. In this study, we screened Jamunapari and crossbred (50% Black Bengal × 50% Jamunapari) goats to identify polymorphisms in the GDF9 and BMP15 genes and to assess the association between identified SNPs and litter size. The genomic DNA from 100 female goats (50 Jamunapari and 50 crossbred) was used in polymerase chain reactions (PCRs) to amplify exon 2 of the GDF9 and exon 2 of the BMP15 genes. PCR products were sequenced employing the BigDye Terminator cycle sequencing protocol to identify SNPs. We used a generalized linear model to perform the association analysis for identified SNPs and litter size. Seven SNPs were identified, of which four, C818CT, G1073A, G1189A, and G1330T, were in the GDF9 gene and three, G616T, G735A, and G811A, were in the BMP15 gene. G735A was a synonymous SNP, whereas the remaining were non-synonymous SNPs. Identified SNP loci in GDF9 were low polymorphic (PIC < 0.25), while loci in BMP15 were moderately polymorphic (PIC ≥ 0.25). The genotypes at the G1330T locus had a significant (p < 0.05) difference in litter size in Jamunapari goats, but no significant difference was observed for all genotypes at other loci. Therefore, the G1330T loci could be useful as a marker in marker-assisted selection for litter size traits in goats of Bangladesh.

Genome-Wide Selective Analysis of Boer Goat to Investigate the Dynamic Heredity Evolution under Different Stages

Boer goats, as kemp in meat-type goats, are selected and bred from African indigenous goats under a long period of artificial selection. Their advantages in multiple economic traits, particularly their plump growth, have attracted worldwide attention. The current study displayed the genome-wide selection signature analyses of South African indigenous goat (AF), African Boer (BH), and Australian Boer (AS) to investigate the hereditary basis of artificial selection in different stages. Four methods (principal component analysis, nucleotide diversity, linkage disequilibrium decay, and neighbor-joining tree) implied the genomic diversity changes with different artificial selection intensities in Boer goats. In addition, the θπ, FST, and XP-CLR methods were used to search for the candidate signatures of positive selection in Boer goats. Consequently, 339 (BH vs. AF) and 295 (AS vs. BH) candidate genes were obtained from SNP data. Especially, 10 genes (e.g., BMPR1B, DNER, ITGAL, and KIT) under selection in both groups were identified. Functional annotation analysis revealed that these genes are potentially responsible for reproduction, metabolism, growth, and development. This study used genome-wide sequencing data to identify inheritance by artificial selection. The results of the current study are valuable for future molecular-assisted breeding and genetic improvement of goats.

Single nucleotide polymorphisms in the 3′ UTR of follistatin-like 4 and scavenger receptor class B member 1 are associated with Dazu black goat litter size

The untranslated regions (UTR) of genes play crucial roles in regulating gene expression at the post-transcriptional level such as affecting mRNA stabilization. In this study, 26 single nucleotide polymorphisms (SNPs) and one deletion located in UTR were genotyped from 186 Dazu black goats via SNaPshot, and the correlation between genotype and litter size was analyzed. Results indicated that two SNP loci, SNP_chr17-20182525 and SNP_chr7-65652612, which are located at the 3′UTR of scavenger receptor class B member 1 and follistatin-like 4, are significantly (p<0.05) correlated with the litter size of first parity goats. SNP_chr7-65652612 is also significantly associated with the total litter size of first and second parity offspring (p<0.05). In conclusion, SNP_chr7-65652612 and SNP_chr17-20182525 have correlation with the litter size of Dazu black goat and they are potential genetic markers for litter size breeding.

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.

Association of a genetic polymorphism in the BMPR-1B gene, and non-genetic factors with the natural prolificacy of the Colombian-haired sheep

INTRODUCTION

Colombian-haired sheep (OPC) is a creole breed with very good adaptation to the tropical conditions of our country. In sheep, it has been shown that the litter size (LS) is associated with ovulation rate, the number of fertilized eggs, and embryo survival. Also, LS is determined by genetic and environmental effects. In this sense, the receptor 1B of bone morphogenetic protein (BMPR-1B) has been described as a genetic factor. Therefore, the aim of the present work was to characterize and associate the SNP C864T in the BMPR-1B gene with LS in the specific OPC biotypes Ethiopian and Sudan.

MATERIALS AND METHODS

Reproductive history (LS, number of calving in the mother, identification of the father, conception year, and conception period) of 200 OPC sheep was assessed. Additionally, sheep were genotyped by sequencing for the SNP C864T. An association between LS, reproductive history, and C864T variation was performed using a GLM fixed-effect model.

RESULTS

The frequency of the T allele (0.75 ± 0.03) was higher than that of the C allele (P<0.05). The genotypic frequencies were 0.55 ± 0.06, 0.38 ± 0.04, and 0.07 ± 0.01, for TT, TC, and CC, respectively. An average value of He (0.37 ± 0.03) and HWE (P=0.97) was found. The LS found was 1.45 ± 0.15. This varied, between biotypes, with number of calving in the mother, with the father, and at the time of conception (P <0.05).

CONCLUSION

The LS varied between genotypes (P<0.05). The CC genotype was the most prolific (1.81 ± 0.4), followed by the heterozygous (1.45 ± 0.04) and the TT homozygous (1.09 ± 0.04). However, we did not find a variation between biotypes within the genotypes (P>0.05). In conclusion, the polymorphism target in the exon 9 of the BMPR-1B gene and non-genetic factors affected significantly the litter size in the OPC.

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.

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.

Genomic Diversity, Population Structure, and Signature of Selection in Five Chinese Native Sheep Breeds Adapted to Extreme Environments

Through long term natural and artificial selection, domestic sheep (Ovis aries) have become adapted to a diverse range of agro-ecological environments and display multiple phenotypic traits. Characterization of diversity and selection signature is essential for genetic improvement, understanding of environmental adaptation, as well as utilization and conservation of sheep genetic resources. Here, we aimed to assess genomic diversity, population structure, and genomic selection among five Chinese native sheep breeds using 600K high density SNP genotypes. A total of 96 animals of the five breeds were selected from different geographical locations with extremely dry or humid conditions. We found a high proportion of informative SNPs, ranging from 93.3% in Yabuyi to 95.5% in Wadi, Hu, and Hetian sheep. The average pairwise population differentiation (F_ST) between the breeds was 0.048%, ranging from 0.022% to 0.054%, indicating their low to moderate differentiation. PCA, ADMIXTURE, and phylogenetic tree analyses revealed a clustering pattern of the five Chinese sheep breeds according to their geographical distribution, tail type, coat color, body size, and breeding history. The genomic regions under putative selection identified by F_ST and XP-EHH approaches frequently overlapped across the breeds, and spanned genes associated with adaptation to extremely dry or humid environments, innate and adaptive immune responses, and growth, wool, milk, and reproduction traits. The present study offers novel insight into genomic adaptation to dry and humid climates in sheep among other domestic animals and provides a valuable resource for further investigation. Moreover, it contributes useful information to sustainable utilization and conservation of sheep genetic resources.

A Mini-Atlas of Gene Expression for the Domestic Goat (Capra hircus)

Goats (Capra hircus) are an economically important livestock species providing meat and milk across the globe. They are of particular importance in tropical agri-systems contributing to sustainable agriculture, alleviation of poverty, social cohesion, and utilisation of marginal grazing. There are excellent genetic and genomic resources available for goats, including a highly contiguous reference genome (ARS1). However, gene expression information is limited in comparison to other ruminants. To support functional annotation of the genome and comparative transcriptomics, we created a mini-atlas of gene expression for the domestic goat. RNA-Seq analysis of 17 transcriptionally rich tissues and 3 cell-types detected the majority (90%) of predicted protein-coding transcripts and assigned informative gene names to more than 1000 previously unannotated protein-coding genes in the current reference genome for goat (ARS1). Using network-based cluster analysis, we grouped genes according to their expression patterns and assigned those groups of coexpressed genes to specific cell populations or pathways. We describe clusters of genes expressed in the gastro-intestinal tract and provide the expression profiles across tissues of a subset of genes associated with functional traits. Comparative analysis of the goat atlas with the larger sheep gene expression atlas dataset revealed transcriptional similarities between macrophage associated signatures in the sheep and goats sampled in this study. The goat transcriptomic resource complements the large gene expression dataset we have generated for sheep and contributes to the available genomic resources for interpretation of the relationship between genotype and phenotype in small ruminants.

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.

Genome-wide selection signatures analysis of litter size in Dazu black goats using single-nucleotide polymorphism

Litter size is considered to be the most important index for estimating domestic animal productivity. The number of indigenous goats in China with higher litter sizes than those of commercial breeds in other countries may be helpful for accelerating genetic improvements in goat breeding. We performed a genome-wide selective sweep analysis of 31 Dazu black goats with extreme standard deviation in litter size within the third fetus to identify significant genomic regions and candidate genes through different analyses. The analysis identified a total of 33,917,703 variants, including 32,262,179 SNPs and 1,655,524 indels. In addition, two novel candidate genes (LRP1B and GLRB), which are related to litter size, were obtained with π, Tajima's D, πA/πB, and F _ST at the individual level with a 95% threshold for each parameter. These two genes were annotated in five GO terms (localization, binding, macromolecular complex, membrane part, and membrane) and two pathways (long-term depression and neuroactive ligand-receptor interaction pathway). Regarding the result of linkage disequilibrium (LD) analysis, in LRP1B and GRID2, the high-yield Dazu black goats exhibit significantly different LD patterns from low-yield goats. Litter size variability has low heritability and is related to multiple complex factors found in domestic animals. Obtaining a clear explanation and significant signal by genome-wide selective sweep analysis with a small sample size is difficult. However, we investigated some candidate genes, particularly LRP1B and GLRB, which may provide useful information for further research.

Correlation analysis of candidate gene SNP for high-yield in Liaoning cashmere goats with litter size and cashmere performance

This study was designed to identify the relationship of four genes (GDF9, BMPR-IB, FecB and ESR) polymorphisms in the 3'UTR region with litter size and cashmere performance of Liaoning cashmere goats (LCG, n = 1140). The ESR C463T and T575G loci of LCG were genotyped. The results of correlation analysis showed that five effective single nucleotide polymorphisms (SNPs) loci (C47T, C94T, C299T, C463T and T575G) were found in the four genes. The lambing number of CC and CT genotypic individuals at FecB C94T locus was significantly higher than that of TT genotypic individuals (45.7 and 46.8%, respectively); the lambing number of CC genotypic individuals at ESR C463T locus was significantly higher than that of CT, TT genotypic individuals (9 and 15%, respectively); There was a positive correlation between CC genotype at C463T locus and cashmere fineness. In this study, the relationship between FecB C94T and ESR C463T loci C alleles and lambing number in LCG was preliminarily revealed. These results further confirmed that FecB and ESR genes may be significantly correlated with high fecundity of LCG.

Association between c.1189G>A single nucleotide polymorphism of GDF9 gene and litter size in goats: A meta-analysis

Litter size is one of the most important traits in goat production and breeding. The most common and presumed single nucleotide polymorphism (SNP) detected in the Growth Differentiation Factor 9 gene is c.1189G>A (rs637044681, Ensembl) which results in an altered sequence of the encoded protein. In some studies, there was no effect of this SNP on litter size, while in other studies there was an effect. In the present study there was a meta-analysis conducted by pooling results from 11 eligible published studies to investigate effects of c.1189G>A polymorphism on litter size using four different genetic models including dominant (AA + AG compared with GG), recessive (AA compared with AG + GG), additive (AA compared with GG) and co-dominant (AA + GG compared with AG). Data were analyzed using fixed and random-effect models based on the I-squared value. Results indicate the c.1189G>A polymorphism is positively associated with litter size with use of the dominant model (SMD = 0.093, 95% CI = 0.028 to 0.158, P-Value = 0.005). There, however, was no effect of the c.1189G>A polymorphism using the recessive (SMD = 0.065, 95% CI = -0.164 to 0.295, P-Value = 0.577), additive (SMD = 0.172, 95% CI = -0.169 to 0.513, P-Value = 0.324) and co-dominant (SMD = -0.083, 95% CI = -0.200 to 0.034, P-Value = 0.164) genetic models. Results from use of the sensitivity analysis indicate the GG genotype affect litter size with use of the additive model (P < 0.01). The results from this meta-analysis indicate the GG genotype is associated with litter size in goats.

Polymorphism in inhibin alpha (INHA) gene is not associated with litter size in Markhoz goats

The present study was aimed to survey the polymorphisms in 2 loci (exon 2) of inhibin alpha (INHA) gene in Markhoz goats. Blood samples collected from 150 female goats were used for extraction of genomic DNA; and 2 fragments related to exon 2 with 332 bp (G567A, P1 locus) and 478 bp (T911C, P2 locus) in length were amplified using polymerase chain reaction (PCR). PCR products were subjected to digestion using Bsp143II endonuclease. The results showed that 2 alleles (G and A) with the frequency of 0.526 and 0.473, and 3 genotypes (GG, GA and AA) with the frequency of 0.138, 0.085 and 0.773 were identified for P1 locus in Markhoz goats but P2 locus was monomorphic. Investigation on effect of genotypes in P1 locus on litter size trait showed that P1 locus genotypes had no association with litter size in Markhoz goats. The results demonstrated, for the first time, that polymorphism in a locus in exon 2 of the INHA gene had no significant association with litter size in Markhoz goats.

No polymorphism of melatonin receptor 1A (MTNR1A) gene was found in Markhoz goat

Melatonin is the main hormone of seasonal breeding in sheep and goat which has an effect on reproductive organs via its receptors. Studies have shown that mutations in melatonin receptor 1A (MTNR1A) gene are related to litter size as well as the ovulation rate in sheep and goats. In this study, polymorphism of two loci in MTNR1A melatonin receptor gene was studied in order to survey their relationship with litter size in Markhoz goats. PCR primers were employed to mask polymorphisms of MTNR1A in 150 does by PCR‐RFLP method. After DNA extraction, the PCR‐RFLP was performed using Ecol31I and HpaI restriction enzymes. Results showed that these loci were not polymorphic. These results show that the fecundity of Markhoz goats is not linked to MTNR1A. No polymorphism in MTNR1A was found in Markhoz goats, therefore, it is essential to test polymorphism of other genes or loci to facilitate marker‐assisted selection techniques to improve reproduction traits in Markhoz goats.

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.