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

F1000Research ◽  
2017 ◽  
Vol 6 ◽  
pp. 1303 ◽  
Author(s):  
Michael P. Heaton ◽  
Timothy P.L. Smith ◽  
Bradley A. Freking ◽  
Aspen M. Workman ◽  
Gary L. Bennett ◽  
...  
Keyword(s):  
Bone Morphogenetic Protein ◽  
Litter Size ◽  
Read Depth ◽  
Whole Genome Sequence ◽  
Small Samples ◽  
Amino Acid Residues ◽  
Missense Variants ◽  
Protein Receptor ◽  
Morphogenetic Protein ◽  
Protein Variants

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.

scholarly journals Genetic polymorphisms of fecundity genes in Watish Sudanese desert sheep

2020 ◽  
Vol 13 (4) ◽  
pp. 614-621
Author(s):  
Sara E. Ibrahim Mohamed ◽  
Romaz M. Ahmed ◽  
Khaleel I. Z. Jawasreh ◽  
M. A. M. Salih ◽  
Dalia Mursi Abdelhalim ◽  
...  
Keyword(s):  
Bone Morphogenetic Protein ◽  
Litter Size ◽  
Goodness Of Fit ◽  
Chi Square ◽  
Association Testing ◽  
Genotype Frequencies ◽  
Protein Receptor ◽  
Morphogenetic Protein ◽  
Growth Differentiation Factor 9 ◽  
Chi Square Test

Background and Aim: The Watish sheep is a strain of desert sheep of smaller size compared to other desert sheep ecotypes, and there is anecdotal evidence that it is endowed with high litter size. The present study was designed for screening for polymorphisms in the known fecundity genes (bone morphogenetic protein receptor type 1B A<G in exon 6, bone morphogenetic protein 15 (BMP15) (FecXB, FecXG, FecXH, and FecXI) in exon2, growth differentiation factor 9 (GDF9) – G1 in exon1 and G8 in exon2 and PRLG<A in intron2) and their association with litter size in Watish. Materials and Methods: The study involved 156 Watish ewes of 2-6 years of age, along with data on litter size in the first, second, and third parity from Sinnar state and contiguous Blue Nile State. Genomic DNA was isolated and genotyped using polymerase chain reaction-restriction fragment length polymorphism. Allele and genotype frequencies were calculated by direct counting. Chi-square test for goodness of fit was performed for agreement with Hardy-Weinberg expectations and association testing. Results: The results demonstrated that all individuals were non-carriers for the target mutations of FecB, BMP15 (FecXB, FecXH, and FecXI), and GDF9-G8. With regard to the GDF9-G1 gene, the genotypic frequencies were 0.07% (G+) and 0.93% (++), in FecXG gene they were 0.993% (++) and 0.006% (B+), in PRL gene 0.516(++), 0.347(B+), and 0.137(BB). The Chi-square test showed a non-significant association between ewe's type of birth and the detected mutations genotypes. Conclusion: These results preliminarily indicated that GDF9-G1, BMP15 (FecXG), and PRL genes might have had some contribution for improving litter size in Watish Sudanese sheep. However, further studies using larger samples are needed to detect the effects of those mutations on Watish sheep litter size.

scholarly journals An investigation of the effects of <i>BMPR1B</i>, <i>BMP15</i>, and <i>GDF9</i> genes on litter size in Ramlıç and Dağlıç sheep

2021 ◽  
Vol 64 (1) ◽  
pp. 223-230
Author(s):  
Koray Çelikeloğlu ◽  
Mustafa Tekerli ◽  
Metin Erdoğan ◽  
Serdar Koçak ◽  
Özlem Hacan ◽  
...  
Keyword(s):  
Bone Morphogenetic Protein ◽  
Litter Size ◽  
Rare Allele ◽  
Regression Coefficients ◽  
Breeding Station ◽  
Protein Receptor ◽  
Morphogenetic Protein ◽  
Growth Differentiation Factor 9 ◽  
Breeding Seasons ◽  
Selection Of

Abstract. This study was carried out to determine the presence of polymorphisms in genes affecting litter size. The SNPs in bone morphogenetic protein receptor type 1B (BMPR1B), bone morphogenetic protein 15 (BMP15), and growth differentiation factor 9 (GDF9) genes were detected in 60 uniparous and 60 multiparous ewes from Ramlıç and Dağlıç breeds. The ewes are maintained in nine public herds at the breeding station of the Afyonkarahisar Sheep and Goats Breeders' Association and lambed in two consecutive breeding seasons. PCR and DNA sequencing analyses were conducted, and 36, 4, and 11 SNPs in Ramlıç and 40, 3, and 11 SNPs in Dağlıç were detected in BMPR1B, BMP15, and GDF9 genes, respectively. A total of 16 SNPs in Ramlıç and 10 SNPs in Dağlıç breeds for three genes were found to be significant (P<0.05). The resulting analyses showed that four SNPs (g.49496G>A, c.1658A>C, c.2037C>T, c.2053C>T) of the BMPR1B gene and one deletion mutation (c.28_30delCTT) in the BMP15 gene of the Ramlıç breed as well as five SNPs (c.1487C>A, c.2492C>T, c.2523G>A, c.2880A>G, and c.2763G>A) of the BMPR1B gene of the Dağlıç breed have significant positive regression coefficients in the desired direction of the rare allele. The observed mutations have potential to be used as genetic markers in the selection of prolific animals for both breeds.

Association Study of Fecundity Gene BMPR1B with Prolificacy in Surti Goats under Farm and Field Condition

2019 ◽  
Vol 14 (04) ◽  
Author(s):  
N. S. Dangar ◽  
G. M. Pandya ◽  
U. V. Ramani ◽  
Y. D. Padheriya ◽  
T. Sangma ◽  
...  
Keyword(s):  
Litter Size ◽  
Transforming Growth Factor Beta ◽  
Transforming Growth Factor ◽  
Pcr Primers ◽  
Dual Purpose ◽  
Protein Receptor ◽  
Morphogenetic Protein ◽  
Pcr Rflp ◽  
Base Size ◽  
Mutation Information

The Surti is a dual purpose goat breed of Gujarat. The bone morphogenetic protein receptor type 1B (BMPR1B) gene of transforming growth factor beta (TGF-β) superfamily ligands is playing a role in ovulation as well as litter size. Mutation in Exon-6 region of BMPR1B gene with base size 190 bp reported increasing litter size. Based on the known mutation information in goat and sheep, PCR primers were designed to screen polymorphism in total 100 Surti goats, 50 Surti goats from University Farm, Navsari and 50 Surti goats from field units of Southern part of Gujarat. During PCR-RFLP study no polymorphic sites were found for Exon-6 region of BMPR1B on Surti goats. Moreover, the twinning rate was 10% in first parity and higher in subsequent second (62.5%) and third (76.8%) parties.

scholarly journals Using diverse U.S. beef cattle genomes to identify missense mutations in EPAS1, a gene associated with pulmonary hypertension

F1000Research ◽  
2016 ◽  
Vol 5 ◽  
pp. 2003 ◽  
Author(s):  
Michael P. Heaton ◽  
Timothy P.L. Smith ◽  
Jacky K. Carnahan ◽  
Veronica Basnayake ◽  
Jiansheng Qiu ◽  
...  
Keyword(s):  
Pulmonary Hypertension ◽  
Beef Cattle ◽  
In Silico ◽  
Read Depth ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Missense Mutations ◽  
Protein Variant ◽  
Flight Mass Spectrometry ◽  
Protein Variants

The availability of whole genome sequence (WGS) data has made it possible to discover protein variantsin silico. However, existing bovine WGS databases do not show data in a form conducive to protein variant analysis, and tend to under represent the breadth of genetic diversity in global beef cattle. Thus, our first aim was to use 96 beef sires, sharing minimal pedigree relationships, to create a searchable and publicly viewable set of mapped genomes relevant for 19 popular breeds of U.S. cattle. Our second aim was to identify protein variants encoded by the bovine endothelial PAS domain-containing protein 1 gene (EPAS1), a gene associated with pulmonary hypertension in Angus cattle. The identity and quality of genomic sequences were verified by comparing WGS genotypes to those derived from other methods. The average read depth, genotype scoring rate, and genotype accuracy exceeded 14, 99%, and 99%, respectively. The 96 genomes were used to discover four amino acid variants encoded byEPAS1(E270Q, P362L, A671G, and L701F) and confirm two variants previously associated with disease (A606T and G610S). The sixEPAS1missense mutations were verified with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry assays, and their frequencies were estimated in a separate collection of 1154 U.S. cattle representing 46 breeds. A rooted phylogenetic tree of eight polypeptide sequences provided a framework for evaluating the likely order of mutations and potential impact ofEPAS1alleles on the adaptive response to chronic hypoxia in U.S. cattle. This public, whole genome resource facilitatesin silicoidentification of protein variants in diverse types of U.S. beef cattle, and provides a means of translating WGS data into a practical biological and evolutionary context for generating and testing hypotheses.

scholarly journals Identification of a Lysosomal Pathway Regulating Degradation of the Bone Morphogenetic Protein Receptor Type II

2010 ◽  
Vol 285 (48) ◽  
pp. 37641-37649 ◽  
Author(s):  
Hannah J. Durrington ◽  
Paul D. Upton ◽  
Simon Hoer ◽  
Jessica Boname ◽  
Benjamin J. Dunmore ◽  
...  
Keyword(s):  
Bone Morphogenetic Protein ◽  
Receptor Type ◽  
Type Ii ◽  
Bone Morphogenetic Protein Receptor ◽  
Protein Receptor ◽  
Morphogenetic Protein
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