Detection of genetic variations in the GDF9 and BMP15 genes in Kazakh meat-wool sheep

Kazakh meat-wool sheep are of great interest because of the intrabreed multifetal type's high productivity of 140 %-160 %. Genes encoding growth differentiation factor-9 (GDF9) and bone morphogenetic protein 15 (BMP15) are promising candidates for studying sheep productivity, as they affect fertility in mammals, including sheep. Thus, the purpose of this study was to assess the fertility of the Kazakh meat-wool sheep breed based on GDF9 and BMP15 candidate genes of fecundity for the selection of animals with valuable genotypes. We selected 300 heads of the Kazakh meat-wool sheep breed from two populations for PCR-RFLP (polymerase chain reaction-restriction fragment length polymorphism) analysis, 15 of which were subsequently used for sequencing of exon regions of the GDF9 and BMP15 genes. The sheep populations were tested for G1 and G8 mutations of the GDF9 gene and B2 and B4 mutations of the BMP15 gene. The PCR-RFLP analysis revealed that 59 (19.7 %) of the 300 Kazakh meat-wool breed sheep were heterozygous carriers of the G1 mutation (genotype AG) of the GDF9 gene, and sequencing analysis supported these results. The comparative phylogenetic analysis showed a clear separation of Kazakh meat-wool sheep wild types and carriers of the G1 mutation. This mutation was reported to have a relationship with the animals' litter size in other sheep breeds. For this reason, similar relationships should be investigated in Kazakh meat-wool sheep. However, G8, B2, and B4 mutations were not detected among the studied animal populations, showing that these mutations are not characteristic of the Kazakh meat-wool sheep breed.

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.

G1 point mutation in growth differentiation factor 9 gene affects litter size in Sudanese desert sheep

BACKGROUND AND AIM

Sudanese desert sheep encompass different sheep breeds named according to the different Sudanese tribes that rear them such as the Dubasi, Shugor, and Watish sheep. The objectives of this study were to screen for G1 point mutation in the polymorphic growth differentiation factor 9 (GDF9) gene, investigate its association with litter size, and construct the phylogeny of the different tribal breeds that belong to the Sudanese Desert sheep tribal types.

MATERIALS AND METHODS

Genomic DNA was extracted from whole blood of three tribal Desert sheep breeds (Dubasi, Watish, and Shugor) using the guanidine chloride method. Polymerase chain reaction-restriction fragment length polymorphism with HhaI restriction enzyme and sequencing techniques was used for genotyping the GDF9 locus for possible mutations associated with litter size in the three desert sheep tribal types.

RESULTS

G1 mutation in GDF9 caused the replacement of Arginine by Histidine at residue 87. The wild type allele (A) had the highest frequency, whereas the mutant type allele (a) had the lowest in all the sequenced subtypes. The genotype frequencies of the wild type ewes (AA) were higher than the heterozygous (Aa) and the mutant type (aa) frequencies in the three studied desert sheep types. No significant differences were found in the allele frequency between the three tribal types. Litter size was significantly influenced by the genotypes of GDF9 gene, parities, and subtypes (p≤0.01, 0.01, and 0.05, respectively). In the Watish sheep type, heterozygous sheep in their second parity recorded the highest litter size. Sequence alignment of GDF9 gene samples with the database entry indicated that all three tribal types were similar and identical to the reference sequence. The phylogenetic tree revealed that Shugor is the common ancestor of the studied types and Watish is more closely related to Shugor than Dubasi. This result mi ght partly explain the lower reproductive performance of Dubasi compared to Watish and Shugor.

CONCLUSION

The presence of one copy of GDF9 gene increased litter size in the studied Sudanese Desert sheep. This locus may be used as a biomarker for litter size improvement through genotypic selection and allele or gene introgression.

Genetic diversity and genetic origin of Lanping black-boned sheep investigated by genome-wide single-nucleotide polymorphisms (SNPs)

Lanping black-boned sheep was first discovered in the 1950s in Lanping county of China and characterized by black pigmentation on skin and internal organs. Due to the novel and unique trait, the genetic background of Lanping black-boned sheep is of great interest. Here, we genotyped genome-wide SNPs (single nucleotide polymorphisms) of Lanping black-boned sheep and Lanping normal sheep using Illumina OvineSNP50 BeadChip to investigate the genetic diversity and genetic origin of Lanping black-boned sheep. We also downloaded a subset SNP dataset of two Tibet-lineage sheep breeds and four other sheep breeds from the International Sheep Genomics Consortium (ISGC) as a reference for interpreting. Lanping black-boned sheep had a lower genetic diversity level when compared to seven other sheep breeds. Principal component analysis (PCA) showed that Lanping black-boned sheep and Lanping normal sheep were clustered into the Asian group, but there was no clear separation between the two breeds. Structure analysis demonstrated a high ancestry coefficient in Lanping black-boned sheep and Lanping normal sheep. However, the two populations were separated into two distinct branches in a neighbor-joining (NJ) tree. We further evaluated the genetic divergence using population F ST , which showed that the genetic differentiation that existed between Lanping black-boned sheep and Lanping normal sheep was higher than that between Tibet sheep and Changthangi sheep, which revealed that Lanping black-boned sheep is a different breed from Lanping normal sheep on the genetic level. In addition, structure analysis and NJ tree showed that Lanping black-boned sheep had a relatively close relation with Tibet sheep. The results reported herein are a first step toward understanding the genetic background of Lanping black-boned sheep, and it will provide informative knowledge on the unique genetic resource conservation and mechanism of novel breed formation.

Expression profiles of the MXD3 gene and association of sequence variants with growth traits in Xianan and Qinchuan cattle

Max dimerization protein 3 (MXD3) belongs to the MYC superfamily of basic helix‐loop‐helix leucine zipper transcription factors, and MXD3‐MAX heterodimers can bind to promoters of target genes to modulate their expression. The aim of this study was to determine the MXD3 mRNA expression levels in various cattle tissues comprising heart, liver, spleen, lung, kidney, Longissimus dorsi muscle and subcutaneous fat in Chinese Qinchuan and Xianan cattle breeds. The RT‐qPCR data showed that the MXD3 gene was variably expressed between all tissues and at levels that were significantly different between two breeds (p < .05). We used the polymerase chain reaction‐restriction fragment length polymorphism (PCR‐RFLP) method to investigate the possible association between single‐nucleotide polymorphisms (SNP) within the MXD3 gene and five different growth traits in cattle. We found two intronic SNPs (g.2694 C>T and g.3801 T>C) and one SNP in 3′untranslated region (3′UTR) (g.6263 G>A) of MXD3 gene. Association analysis revealed strong associations between pairwise and triple SNP combinations and the growth traits. Based on these results, we suggest that MXD3 polymorphisms could be useful as molecular markers in the Chinese beef cattle breeding program.

Effect of Point Mutation in the Growth Differentiation Factor 9 Gene of Oocytes on the Sterility and Fertility of Awassi Sheep

Growth differentiation factor 9 (GDF9) plays a critical role in ovarian follicular development and ovulation rate. The present study aimed to investigate the correlation between the single-nucleotide polymorphism (SNP) of the GDF9 gene and reproductive performance variables, such as fertility and sterility in Awassi sheep. Forty pairs of ovaries from a total of 40 slaughtered Iraqi Awassi ewes were used in this study. Twenty of the ovaries were collected from sterile ewes and the other 20 ovaries were taken from fertile ewes for genomic DNA extraction, polymerase chain reaction, and sequencing to detect GDF9 gene polymorphism. Follicles and oocytes of all the 40 ovaries were evaluated and compared with the results of genotyping. Furthermore, histopathological and microscopic evaluations were performed for 40 ovarian tissues of the two groups. The sequence analysis revealed that exon I had three SNPs, including T(114)C, G(129)R, and G(199)A. The first two SNPs were silent mutations and the last mutation was missense responsible for the substitution of glutamic acid with lysine at position 67. The current study showed a significant increase (P&amp;le;0.01) in GG, AA, CC, GA, and GG genotypes at G(129)R, G(199)A, T(114)C, G(129)R, and G(199)A loci, respectively. Moreover, the TT genotype in locus T(114)C was recorded to significantly augment (P&amp;le;0.05) in the fertile ewes. Mutant GA genotype of the G(129)R locus led to a significant (P&amp;le;0.05) increase in the percentage of follicles (4-8 mm) and oocytes number, compared to wild GG. On the other hand, a significant decrease was recorded in the mutant AA genotype in G(199)A, compared to wild GG. Differences between CC and TT genotypes at T(114)C locus were not significant. Histopathological examination revealed hypoplasia in the ovarian tissue of sterile ewes accompanied by fibrous connective tissue invasion and follicles degeneration. However, in the fertile ewes, the ovarian tissues were normal with the presence of numerous corpus albicans and degenerative corpus luteum. According to the findings of this study, the homozygote mutation in fertile ewes minimized the number of follicles and oocytes leading to sterility, while the heterozygote mutation was reported in the fertile Awassi ewes.

A computational approach for explaining the effect of the prl gene polymorphism on prolactin structure and biological activity in Japanese quails

Prolactin is a versatile hormone with multiple activities, including a negative control on egg production. This study was conducted to genotype all the coding portions of the prl gene using PCR-SSCP-sequencing, and to investigate the effects of amino acid substitutions of the prl gene on the structure and function of prolactin in quails using in silico approach. Though all genotyped exons exerted homogenous PCR-SSCP patterns, a total of 12 novel SNPs were detected in the investigated exons, including three SNPs in exon-1, 8 SNPs in exon-2, and one SNP in exon-4. Three adjacent missense SNPs were detected in exon-2, namely H69P, T70P, and S71F. Computational tools indicated obvious deleterious effects of T70P, with less extent to H69P and S71F on prolactin functions and activity, which may lead to limited participation of this hormone in the negative control of egg production. In conclusion, the introduction of in silico prediction has suggested an alternative solution for the breeders to evaluate the effect of each witnessed nsSNP in protein structure and function. The current study suggests three nsSNPs, T70P, T70P, and S71F as strong candidates for the negative effect on prolactin biological activity with a consequent reversal positive effect on egg productivity traits.

Effect of LCORL gene polymorphism on body size traits in horse populations

The aim of this study was to determine polymorphism of LCORL gene in horse breeds and its association with body size. PCR-RFLP technique was performed using AluI for genotyping of 306 horses. Results showed that C is the rare allele in Iranian Breeds, because these horses have been used since ancient times as a courier and for war and archery, hence selection has done to benefit of spiky horses with medium body that need less food and are tireless. While, for foreign breeds; frequency of C allele was high that can be concluded these breeds used in fields, forests, and mines. A UPGMA dendrogram based on the Nei's standard genetic distance among studied breeds showed separate clusters for Iranian native and exotic breeds. Statistical association analysis of three observed genotypes with body size showed that there is an association between this polymorphism and body size criteria (p < 0.01). Overall, it can be concluded that studied mutation in LCORL gene can be used as candidate marker for improving body weight in horse.

Effect of BMPRIB gene on litter size of sheep in China: A meta-analysis

Genes or genetic markers related to litter size have been studied for many years in gene selection or marker-assisted selection experiments. The bone morphogenetic protein receptor IB (BMPRIB) gene is one of the candidate genes for increasing litter size of sheep. Results of studies with different sheep breeds in China have been inconsistent with some confirming significant associations between the BMPRIB gene polymorphism and litter size and with other results being inconsistent with there not being an association. In the present study, a meta-analysis was conducted evaluating 21 studies in which 5089 samples were utilized to analyze the genetic effects of BMPRIB genes on litter size in different sheep breeds in China. Results for weighted mean differences (WMD) among BMPRIB genotypes indicated there was an association between the BPRIB gene polymorphism and litter size. Effects of the BMPRIB gene on litter size are remarkably consistent in many sheep populations of China, with each gene copy being associated with an increase in litter size of 0.4 to 0.5 lambs. There are, however, some populations in which there is no effect of a second copy of the B allele. An example is the Zeller black sheep. Furthermore, in the Tan sheep and its crosses, there was no effect of the BMPRIB gene on litter size. In conclusion, with this study, there is a summarizing of magnitude of BMPRIB gene effects on litter size for sheep breeds in China, and these results provide reference information for consideration in indigenous sheep breeding programs.

Identification of genetic markers associated with milk production traits in Chinese Holstein cattle based on post genome-wide association studies

With the rapid development of dairy industry, the breeding process of dairy cows has been accelerated. In previous genome-wide association studies (GWAS), a large number of genetic markers have been reported which may contribute to the selection of Holstein populations with superior milk-producing traits, but they remain to be further verified before practical application. In this study, 90 single nucleotide polymorphisms (SNPs) were selected, which were reported to be significantly associated with five milk production traits, including 305-day milk yield (305MY), 305-day milk fat percent (305FC), 305-day milk protein percent (305PC), 305-day milk fat yield (305FY) and 305-day milk protein yield (305PY). Effective 305-day data and fresh DNA samples were obtained from 295 healthy cows with gestational age of 1-4. Matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) was used to perform precise genotyping of these loci, followed by site association and haplotype analysis. Results showed that 36 out of 90 loci were supported to be used as genetic markers. In particular, several novel and effective haplotypes were also presented. Overall, our results verified tens of useful markers and provided a basis for further development of breeding strategies.

Diversity of indigenous sheep of an isolated population

Background

Because of the influence of genetics on animal production and the risk of losing genetic diversity of naturally adapted breeds, this study evaluated the genetic diversity of sheep of the Morada Nova breed belonging to an animal science institute in Brazil. The herd in question is one of the country’s most representative of the breed. Samples of DNA extracted from the plasma of 61 animals were used for later analysis of the genotypes using microsatellite molecular markers.

Results

The polymorphic information content was 0.66, the observed heterozygosity was 0.65 and the fixation index was 0.048. According to the results, there is moderate genetic diversity in the studied population, suggesting the implantation of breeding programs aimed at conservation of the observed genetic diversity.

Conclusion

The results obtained in this study will be of great importance to decisions on herd structure, besides contributing to other work to be carried out at the research center.

Polymorphism identification in GDF9 gene and its association analysis with reproduction traits in Jinghai Yellow chicken

GDF9 (growth differentiation factor 9) belongs to the transforming growth factor-β (TGF-β) superfamily and plays an irreplaceable role in female fertility. To reveal its genetic effects on productivity performance in chickens, 373 Jinghai Yellow chickens were chosen randomly to detect SNPs in GDF9 by PCR-SSCP and DNA sequencing methods. Eventually, four SNPs (g.2053G > A, g.2275T > C, g.2338C > T, g.2420T > C) in total had been detected. Amongst them, g.2420T > C was first found significantly associated with reproduction trait in chickens and heterozygous type C₂T₂ had higher average egg weight at 300 days of age (AEWD300) than T₂T₂ (p < 0.01). Least squares analysis showed that age at first laying (AFE) of H1 and H1H1 chickens were significantly earlier than that of H7 and H7H7 ones, respectively (p < 0.05). H1H5 hens showed higher AEWD300 than H4H7 ones (p < 0.05). For total egg number at 300 days of age (END300), mean of H5H5 was significantly higher than that of H4H4 (p < 0.05). Hence, the study suggested that hybrid vigor at g.2420T > C could be utilized in practice. H1H1, H1H5 and H5H5 could be the dominant diplotypes for chicken breeding. The study may contribute to the breeding progress of productive chickens and supply reference for oviparous animal production practice.

Molecular analysis of CIB4 gene and protein in Kermani sheep

The human calcium- and integrin-binding protein (CIB) family is composed of CIB1, CIB2, CIB3, and CIB4 proteins and the CIB4 gene affects fertility. Kermani sheep is one of the most important breeds of Iranian sheep breeds. The aim of this study was to analyze for the first time molecular characteristics of the CIB4 gene and protein in Kermani sheep. Different tissues were collected from the Kermani sheep and real time PCR was performed. The PCR products were sequenced, comparative analyses of the nucleotide sequences were performed, a phylogenetic tree was constructed, and different characteristics of CIB4 proteins were predicted. Real time PCR results showed that the CIB4 gene is expressed only in testis of Kermani sheep. The cDNA nucleotide sequence was identical with small tail Han sheep, cattle, goat, camel, horse, dog, mouse and human, respectively 100, 99, 99, 98, 98, 96, 96, and 96%. Hence, it can be suggested that the CIB4 gene plays a role in male fertility. Based on the phylogenetic analysis, sheep CIB4 gene has a close relationship with goat and cattle first, and then with camel and whale. Although we demonstrated that CIB4 is a testis-specific gene, expressed only in the testis and it interacts with other proteins, the mechanisms by which CIB4 expression is regulated need to be elucidated.

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

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

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

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

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

Using microsatellite markers to analyze genetic diversity in 14 sheep types in Iran

Abstract. Investigation of genetic relationship among populations has been traditionally based on the analysis of allele frequencies at different loci. The prime objective of this research was to measure the genetic polymorphism of five microsatellite markers (McMA2, BM6444, McMA26, HSC, and OarHH35) and study genetic diversity of 14 sheep types in Iran. Genomic DNA was extracted from blood samples of 565 individuals using an optimized salting-out DNA extraction procedure. The polymerase chain reaction (PCR) was successfully performed with the specific primers. Some locus–population combinations were not at Hardy–Weinberg equilibrium (P < 0. 05). The microsatellite analysis revealed high allelic and gene diversity in all 14 breeds. Pakistani and Arabi breeds showed the highest mean number of alleles (11.8 and 11 respectively), while the highest value for polymorphic information content was observed for the Arabi breed (0.88). A UPGMA (unweighted pair group method with arithmetic mean) dendrogram based on the Nei's standard genetic distance among studied breeds showed a separate cluster for Arabi and Pakistani breeds and another cluster for other breeds. The Shannon index (H0) for McMA2, BM6444, McMA26, HSC, and OarHH35 was 2.31, 2.17, 2.27, 2.04 and 2.18, respectively, and polymorphic information content (PIC) values were 0.88, 0.92, 0.87, 0.84, and 0.86 for McMA2, BM6444, McMA26, HSC, and OarHH35, respectively. The high degree of variability demonstrated within the studied sheep types implies that these populations are rich reservoirs of genetic diversity that must be preserved.

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

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

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.