Identification of mutations in &lt;i&gt;BMP15&lt;/i&gt; and &lt;i&gt;GDF9&lt;/i&gt; genes associated with prolificacy of Markhoz goats

Abstract. The Markhoz is a local goat breed in the Kurdistan region of Iran. The mohair obtained from these animals plays an important cultural role and is used for making local clothes in the Kurdistan region. This breed is a low-fecundity local goat, and searching for genes associated with fertility of these goats is important for their breeding. Moreover, this research is complementary to prior studies of candidate genes associated with fertility. The growth differentiation factor 9 (GDF9) and bone morphogenetic protein 15 (BMP15) are attractive candidates expressed by the oocyte and are associated with increased ovulation rate in sheep. However, there are no reports on single nucleotide polymorphisms associated with fertility of Markhoz goats. Hence, we studied these candidate genes and found two novel mutations (g.233C>A and g.755T>G) in GDF9 exon I and in BMP15 exon II, respectively. Furthermore, we investigated their association with prolificacy. These nucleotide changes are detectable with the PCR-RFLP method and can be used in the screening for highly fecund goats. Both of the mutations significantly increased litter size in heterozygote form for BMP15 and homozygote form for GDF9 in this goat breed. Homozygote females for the BMP15 mutation were not identified in the Markhoz breed, which is similar to the situation found in Belclare sheep, small-tailed Han sheep, and Jining Grey goats.

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

10.1101/2020.01.08.899443 ◽

2020 ◽

Author(s):

A. Das ◽

M. Shaha ◽

M. Das Gupta ◽

Avijit Dutta ◽

O. F. Miazi

Keyword(s):

Litter Size ◽

Nucleotide Polymorphisms ◽

Goat Breed ◽

Single Nucleotide ◽

Exon 2 ◽

Morphogenetic Protein ◽

Growth Differentiation Factor 9 ◽

Bone Morphogenetic Protein 15 ◽

First Time ◽

Black Bengal Goat

AbstractIdentification of prolificacy associated genetic markers remains vital in goat breeding industry since an increase in litter size can generate significant profit. Black Bengal is a prolific goat breed in Bangladesh. There are no inland reports on polymorphisms associated with fertility of Black Bengal goats in Bangladesh. In this study, we investigated two major fecundity genes-bone morphogenetic protein 15 (BMP15) and growth differentiation factor 9 (GDF9) in order to detect any possible mutations in these two genes in Bangladeshi Black Bengal goats. We identified six single nucleotide polymorphisms (SNP), of which five (C735A, C743A, G754T, C781A, and C808G) in BMP15 exon 2 and one (T1173A) in GDF9 exon 2. We also studied their association with litter size. Association analysis results show that polymorphism at the 735, 754 and 781 nucleotide positions of BMP15 exon 2 had significant association with litter size in Black Bengal goat. The effect of parity was also highly significant (p <0.001) on litter size. This study explored, for the first time, SNP loci in fecundity genes in Bangladeshi prolific Black Bengal goats. Further studies with a high number of genetically unrelated animals for assessing the association of these loci and others in the fecundity genes with litter size may be useful.

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IDENTIFICATION OF SINGLE NUCLEOTIDE POLYMORPHISMS IN EXON 2 OF BONE MORPHOGENETIC PROTEIN 15 GENE IN EGYPTIAN BUFFALOES

Mansoura Veterinary Medical Journal ◽

10.21608/mvmj.2017.127392 ◽

2017 ◽

Vol 18 (1) ◽

pp. 235-242

Author(s):

Khairy El-Bayomi ◽

Iman El Araby ◽

Ayman Saleh ◽

Hoda Osman ◽

Mahmoud Eltarabany ◽

...

Keyword(s):

Single Nucleotide Polymorphisms ◽

Bone Morphogenetic Protein ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Exon 2 ◽

Morphogenetic Protein ◽

Bone Morphogenetic Protein 15

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Identification of Polymorphisms in GDF9 and BMP15 Genes in Jamunapari and Crossbred Goats in Bangladesh

10.21203/rs.3.rs-1102219/v1 ◽

2021 ◽

Author(s):

Mishuk shaha ◽

Gous Miah ◽

Arjuman Lima ◽

Omar Faruk Miazi ◽

Ashutosh Das

Keyword(s):

Litter Size ◽

Future Research ◽

Nucleotide Polymorphisms ◽

Cycle Sequencing ◽

Single Nucleotide ◽

Exon 2 ◽

Morphogenetic Protein ◽

Significant Difference ◽

Growth Differentiation Factor 9 ◽

Pcr Products

Abstract Growth differentiation factor 9 (GDF9) and bone morphogenetic protein 15 (BMP15) are two crucial fecundity genes 15 associated with litter size traits in the goat. Our previous study on GDF9 and BMP15 genes detected single nucleotide polymorphisms (SNPs) associated with litter size in Bangladeshi Black Bengal goats. In this study, Jamunapari and crossbred goats of Bangladesh were screened 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 goats (50 Jamunapari and 50 crossbred) was used in Polymerase Chain Reaction (PCR) to amplify the exon 2 of the GDF9 and exon 2 of the BMP15 gene. PCR products were sequenced employing the BigDye Terminator cycle sequencing protocol, to identify SNPs. A generalized linear model was utilized 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, 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 goat, but no significant difference was observed for all genotypes at other loci. This study provides additional molecular markers that would be useful for future research on the litter size trait in goats of Bangladesh.

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Expression Profiles of the Progesterone Receptor, Cyclooxygenase-2, Growth Differentiation Factor 9, and Bone Morphogenetic Protein 15 Transcripts in the Canine Oviducts during the Oestrous Cycle

Animals ◽

10.3390/ani11020454 ◽

2021 ◽

Vol 11 (2) ◽

pp. 454

Author(s):

Jaime Palomino ◽

Javiera Flores ◽

Georges Ramirez ◽

Victor H. Parraguez ◽

Monica De los Reyes

Keyword(s):

Gene Expression ◽

Bone Morphogenetic Protein ◽

Cyclooxygenase 2 ◽

Oestrous Cycle ◽

Progesterone Concentration ◽

Plasma Progesterone ◽

Morphogenetic Protein ◽

Growth Differentiation Factor 9 ◽

Bone Morphogenetic Protein 15 ◽

Cox 2

The gene expression in the canine oviduct, where oocyte maturation, fertilization, and early embryonic development occur, is still elusive. This study determined the oviductal expression of (PR), cyclooxygenase-2 (COX-2), growth differentiation factor 9 (GDF-9), and bone morphogenetic protein 15 (BMP-15) during the canine oestrous cycle. Samples were collected from bitches at anoestrus (9), proestrus (7), oestrus (8), and dioestrus (11), after routine ovariohysterectomy and the ovarian surface structures and plasma progesterone concentration evaluated the physiological status of each donor. The oviductal cells were isolated and pooled. Total RNA was isolated, and gene expression was assessed by qPCR followed by analysis using the t-test and ANOVA. The PR mRNA increased (P < 0.05) from the anoestrus to dioestrus with the plasma progesterone concentration (r = 0.8). COX-2 mRNA expression was low in the anoestrus and proestrus, and negligible in the oestrus, while it was around 10-fold higher (P < 0.05) in the dioestrus. The GDF-9 mRNA was expressed during all phases of the oestrous cycle and was most abundant (P < 0.05) during oestrus phase. The BMP-15 mRNA decreased (P < 0.05) in the anoestrus and proestrus phases. Thus, the transcripts were differentially expressed in a stage-dependent manner, suggesting the importance of oestrous cycle regulation for successful reproduction in dogs.

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The Investigation of Associations between TP53 rs1042522, BBC3 rs2032809, CCND1 rs9344, EGFR rs2227983 Polymorphisms and Breast Cancer Phenotype and Prognosis

Diagnostics ◽

10.3390/diagnostics11081419 ◽

2021 ◽

Vol 11 (8) ◽

pp. 1419

Author(s):

Justina Bekampytė ◽

Agnė Bartnykaitė ◽

Aistė Savukaitytė ◽

Rasa Ugenskienė ◽

Erika Korobeinikova ◽

...

Keyword(s):

Breast Cancer ◽

Regression Analysis ◽

Cox Regression ◽

Cancer Prognosis ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Cox Regression Analysis ◽

Pcr Rflp ◽

Oncological Diseases ◽

Cancer Phenotype

Breast cancer is one of the most common oncological diseases among women worldwide. Cell cycle and apoptosis—related genes TP53, BBC3, CCND1 and EGFR play an important role in the pathogenesis of breast cancer. However, the roles of single nucleotide polymorphisms (SNPs) in these genes have not been fully defined. Therefore, this study aimed to analyze the association between TP53 rs1042522, BBC3 rs2032809, CCND1 rs9344 and EGFR rs2227983 polymorphisms and breast cancer phenotype and prognosis. For the purpose of the analysis, 171 Lithuanian women were enrolled. Genomic DNA was extracted from peripheral blood; PCR-RFLP was used for SNPs analysis. The results showed that BBC3 rs2032809 was associated with age at the time of diagnosis, disease progression, metastasis and death. CCND1 rs9344 was associated with tumor size, however an association resulted in loss of significance after Bonferroni correction. In survival analysis, significant associations were observed between BBC3 rs2032809 and OS, PFS and MFS. EGFR rs2227983 also showed some associations with OS and PFS (univariate Cox regression analysis). However, the results were in loss of significance (multivariate Cox regression analysis). In conclusion, BBC3 rs2032809 polymorphism was associated with breast cancer phenotype and prognosis. Therefore, it could be applied as potential markers for breast cancer prognosis.

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Dementia key gene identification with multi-layered SNP-gene-disease network

Bioinformatics ◽

10.1093/bioinformatics/btaa814 ◽

2020 ◽

Vol 36 (Supplement_2) ◽

pp. i831-i839

Author(s):

Dong-gi Lee ◽

Myungjun Kim ◽

Sang Joon Son ◽

Chang Hyung Hong ◽

Hyunjung Shin

Keyword(s):

Candidate Genes ◽

Learning Algorithm ◽

Search Space ◽

Supplementary Information ◽

Gene Identification ◽

Nucleotide Polymorphisms ◽

Disease Network ◽

Single Nucleotide ◽

Key Genes ◽

Significant Attention

Abstract Motivation Recently, various approaches for diagnosing and treating dementia have received significant attention, especially in identifying key genes that are crucial for dementia. If the mutations of such key genes could be tracked, it would be possible to predict the time of onset of dementia and significantly aid in developing drugs to treat dementia. However, gene finding involves tremendous cost, time and effort. To alleviate these problems, research on utilizing computational biology to decrease the search space of candidate genes is actively conducted. In this study, we propose a framework in which diseases, genes and single-nucleotide polymorphisms are represented by a layered network, and key genes are predicted by a machine learning algorithm. The algorithm utilizes a network-based semi-supervised learning model that can be applied to layered data structures. Results The proposed method was applied to a dataset extracted from public databases related to diseases and genes with data collected from 186 patients. A portion of key genes obtained using the proposed method was verified in silico through PubMed literature, and the remaining genes were left as possible candidate genes. Availability and implementation The code for the framework will be available at http://www.alphaminers.net/. Supplementary information Supplementary data are available at Bioinformatics online.

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