Direct Evidence on the Contribution of a Missense Mutation in GDF9 to Variation in Ovulation Rate of Finnsheep

peer-reviewedThe Finnish Landrace (Finnsheep) is a well known high-prolificacy sheep breed and has been used in many countries as a source of genetic material to increase fecundity of local breeds. Analyses to date have indicated that mutations with a large effect on ovulation rate are not responsible for the exceptional prolificacy of Finnsheep. The objectives of this study were to ascertain if: 1) any of 12 known mutations with large effects on ovulation rate in sheep, or 2) any other DNA sequence variants within the candidate genes GDF9 and BMP15 are implicated in the high prolificacy of the Finnish Landrace breed; using material from lines developed by divergent selection on ovulation rate. Genotyping results showed that none of 12 known mutations (FecBB, FecXB, FecXG, FecXGR, FecXH, FecXI, FecXL, FecXO, FecXR, FecGE, FecGH, or FecGT) were present in a sample of 108 Finnsheep and, thus, do not contribute to the exceptional prolificacy of the breed. However, DNA sequence analysis of GDF9 identified a previously known mutation, V371M, whose frequency differed significantly (P<0.001) between High and Low ovulation rate lines. While analysis of ovulation rate data for Finnsheep failed to establish a significant association between this trait and V371M, analysis of data on Belclare sheep revealed a significant association between V371M and ovulation rate (P<0.01). Ewes that were heterozygous for V371M exhibited increased ovulation rate (+0.17, s.e. 0.080; P<0.05) compared to wild type and the effect was non-additive (ovulation rate of heterozygotes was significantly lower (P<0.01) than the mean of the homozygotes). This finding brings to 13 the number of mutations that have large effects on ovulation rate in sheep and to 5, including FecBB, FecGE, FecXO and FecXGR, the number of mutations within the TGFβ superfamily with a positive effect on prolificacy in the homozygous state

A note on the use of FTA™ technology for storage of blood samples for DNA analysis and removal of PCR inhibitors

peer-reviewedFTA™ technology is widely used across many molecular disciplines for sample capture, storage and analysis. The use of this technology for the long-term storage of blood samples for DNA analysis was examined as well as its potential to remove inhibitors from DNA samples previously extracted from blood with PCR inhibitors remaining. It was found that blood spots stored on FTA™ cards for 8 years at room temperature gave successful PCR products and that FTA™ cards are a useful tool for removing substances in samples which interfere with or inhibit, the PCR reaction

Investigation of Prolific Sheep from UK and Ireland for Evidence on Origin of the Mutations in BMP15 (FecXG, FecXB) and GDF9 (FecGH) in Belclare and Cambridge Sheep

peer-reviewedThis paper concerns the likely origin of three mutations with large effects on ovulation rate identified in the Belclare and Cambridge sheep breeds; two in the BMP15 gene (FecXG and FecXB) and the third (FecGH) in GDF9. All three mutations segregate in Belclare sheep while one, FecXB, has not been found in the Cambridge. Both Belclare and Cambridge breeds are relatively recently developed composites that have common ancestry through the use of genetic material from the Finnish Landrace and Lleyn breeds. The development of both composites also involved major contributions from exceptionally prolific ewes screened from flocks in Ireland (Belclare) and Britain (Cambridge) during the 1960s. The objective of the current study was to establish the likely origin of the mutations (FecXG, FecXB and FecGH) through analysis of DNA from Finnish Landrace and Lleyn sheep, and Galway and Texel breeds which contributed to the development of the Belclare breed. Ewes with exceptionally high prolificacy (hyper-prolific ewes) in current flocks on Irish farms were identified to simulate the screening of ewes from Irish flocks in the 1960s. DNA was obtained from: prolific ewes in extant flocks of Lleyn sheep (n = 44) on the Lleyn peninsula in Wales; hyper-prolific ewes (n = 41); prolific Galway (n = 41) ewes; Finnish Landrace (n = 124) and Texel (n = 19) ewes. The FecXG mutation was identified in Lleyn but not in Finnish Landrace, Galway or Texel sheep; FecXB was only found among the hyper-prolific ewes. The FecGH mutation was identified in the sample of Lleyn sheep. It was concluded from these findings that the Lleyn breed was the most likely source of the FecXG and FecGH mutations in Belclare and Cambridge sheep and that the FecXB mutation came from the High Fertility line that was developed using prolific ewes selected from commercial flocks in Ireland in the 1960′s and subsequently used in the genesis of the Belclare.Financial support through the Teagasc Walsh Fellowship Scheme, Genesis Faraday SPARK award (Lleyn survey) and Science Foundation Ireland (07/SRC/B1156) is gratefully acknowledged

Global gene expression in endometrium of high and low fertility heifers during the mid-luteal phase of the estrous cycle

peer-reviewedBackground In both beef and dairy cattle, the majority of early embryo loss occurs within the first 14 days following insemination. During this time-period, embryos are completely dependent on their maternal uterine environment for development, growth and ultimately survival, therefore an optimum uterine environment is critical to their survival. The objective of this study was to investigate whether differences in endometrial gene expression during the mid-luteal phase of the estrous cycle exist between crossbred beef heifers ranked as either high (HF) or low fertility (LF) (following four rounds of artificial insemination (AI)) using the Affymetrix® 23 K Bovine Gene Chip. Results Conception rates for each of the four rounds of AI were within a normal range: 70–73.3%. Microarray analysis of endometrial tissue collected on day 7 of the estrous cycle detected 419 differentially expressed genes (DEG) between HF (n = 6) and LF (n = 6) animals. The main gene pathways affected were, cellular growth and proliferation, angiogenesis, lipid metabolism, cellular and tissue morphology and development, inflammation and metabolic exchange. DEG included, FST, SLC45A2, MMP19, FADS1 and GALNT6. Conclusions This study highlights, some of the molecular mechanisms potentially controlling uterine endometrial function during the mid-luteal phase of the estrous cycle, which may contribute to uterine endometrial mediated impaired fertility in cattle. Differentially expressed genes are potential candidate genes for the identification of genetic variation influencing cow fertility, which may be incorporated into future breeding programmes.Teagasc Walsh Fellowship Programm

Within- and across-breed imputation of high-density genotypes in dairy and beef cattle from medium- and low-density genotypes

peer-reviewedFinancial support of the Irish Department of Agriculture Research Stimulus Fund (RSF-06-0353; RSF-06-0428; 11/SF/311), Science Foundation Ireland (09/IN.1/B2642) and the Irish dairy and beef industry are gratefully acknowledged.The objective of this study was to evaluate, using three different genotype density panels, the accuracy of imputation from lower- to higher-density genotypes in dairy and beef cattle. High-density genotypes consisting of 777 962 single-nucleotide polymorphisms (SNP) were available on 3122 animals comprised of 269, 196, 710, 234, 719, 730 and 264 Angus, Belgian Blue, Charolais, Hereford, Holstein-Friesian, Limousin and Simmental bulls, respectively. Three different genotype densities were generated: low density (LD; 6501 autosomal SNPs), medium density (50K; 47 770 autosomal SNPs) and high density (HD; 735 151 autosomal SNPs). Imputation from lower- to higher-density genotype platforms was undertaken within and across breeds exploiting population-wide linkage disequilibrium. The mean allele concordance rate per breed from LD to HD when undertaken using a single breed or multiple breed reference population varied from 0.956 to 0.974 and from 0.947 to 0.967, respectively. The mean allele concordance rate per breed from 50K to HD when undertaken using a single breed or multiple breed reference population varied from 0.987 to 0.994 and from 0.987 to 0.993, respectively. The accuracy of imputation was generally greater when the reference population was solely comprised of the breed to be imputed compared to when the reference population comprised of multiple breeds, although the impactDepartment of Agriculture, Food and the MarineScience Foundation Irelan

DATA ACQUISITION, ANALYSIS, AND MODELING OF ROTORDYNAMIC SYSTEMS

Data acquisition systems for rotordynamic analysis and machine vibration were explored for the purpose of replacing the obsolete Bently Nevada ADRE 208 and ADRE for Windows system. These included the development of Matlab based custom data acquisition systems and a user interface. A model of an anisotropic rotor response undergoing transient speed was developed for the rapid prototyping and testing of data acquisition systems. Several methods for the measurement of amplitudes and phase in both the time domain and frequency domain were developed and compared. An alternate data acquisition method which is more inline with industry practices was created for the purpose of spectral analysis. Additionally, an optimized data acquisition strategy was developed for implementation within the Matlab app which included batch processing, state-based acquisition, and differentiated vector and waveform acquisition rates. A Bently Nevada 2300/20 vibration monitor was configured for use in the lab but found unsuitable for replacing the ADRE 208. Ultimately a Bently Nevada ADAPT 3701/44 Vibration Monitor was configured and found to be an adequate replacement for the ADRE 208 system for use in the Cal Poly Vibrations Lab