Short communication: The combined use of linkage disequilibrium–based haploblocks and allele frequency–based haplotype selection methods enhances genomic evaluation accuracy in dairy cattle

The construction and use of haploblocks [adjacent single nucleotide polymorphisms (SNP) in strong linkage disequilibrium] for genomic evaluation is advantageous, because the number of effects to be estimated can be reduced without discarding relevant genomic information. Furthermore, haplotypes (the combination of 2 or more SNP) can increase the probability of capturing the quantitative trait loci effect compared with individual SNP markers. With regards to haplotypes, the allele frequency parameter is also of interest, because as a selection criterion, it allows the number of rare alleles to be reduced, and the effects of those alleles are usually difficult to estimate. We have proposed a simple pipeline that simultaneously incorporates linkage disequilibrium and allele frequency information in genomic evaluation, and here we present the first results obtained with this procedure. We used a population of 2,235 progeny-tested bulls from the Montbéliarde breed for the tests. Phenotype data were available in the form of daughter yield deviations on 5 production traits, and genotype data were available from the 50K SNP chip. We conducted a classical validation study by splitting the population into training (80% oldest animals) and validation (20% youngest animals) sets to emulate a real-life scenario in which the selection candidates had no available phenotype data. We measured all reported parameters for the validation set. Our results proved that the proposed method was indeed advantageous, and that the accuracy of genomic evaluation could be improved. Compared with results from a genomic BLUP analysis, correlations between daughter yield deviations (a proxy for true) and genomic estimated breeding values increased by an average of 2.7 percentage points for the 5 traits. Inflation of the genomic evaluation of the selection candidates was also significantly reduced. The proposed method outperformed the other SNP and haplotype-based tests we had evaluated in a previous study. The combination of linkage disequilibrium–based haploblocks and allele frequency–based haplotype selection methods is a promising way to improve the efficiency of genomic evaluation. Further work is needed to optimize each step in the proposed analysis pipeline.     

Rapid detection of Salmonella in milk with a nuclear magnetic resonance biosensor based on a streptavidin–biotin system and a polyamidoamine-dendrimer-targeted gadolinium probe

Rapid and sensitive detection technology is the key to preventing food-borne disease outbreaks. In this study, a low-field nuclear magnetic resonance (NMR) biosensor based on polyamidoamine dendrimers was prepared for the rapid detection of Salmonella in milk. The polyamidoamine dendrimer was biotinylated by amide reaction and chelated to diethylene triamine pentacetate acid and gadolinium to form magnetic complexes. The antibody and magnetic complexes were combined through a streptavidin–biotin system using streptavidin as an intermediate bridge to obtain the immunoprobe. Salmonella was captured by the immunoprobe via antigen–antibody interaction and then separated from the mixture by membrane filtration. Finally, the longitudinal relaxation signal of the filtrate was obtained by NMR. The biosensor had excellent anti-interference capability and could detect Salmonella within 1.5 h at a sensitivity of 10³ cfu mL^–1. This method based on NMR can realize detection in complex samples and has the potential to be a quick and nondestructive method for detecting target bacteria.     

Biotin exposure–based immunomagnetic separation coupled with sodium dodecyl sulfate,propidium monoazide,and multiplex real-time PCR for rapid detection of viable Salmonella Typhimurium,Staphylococcus aureus,and Listeria monocytogenes in milk

In this study, we established a rapid and sensitive method for the detection of viable Salmonella Typhimurium, Staphylococcus aureus, and Listeria monocytogenes in milk using biotin-exposure-based immunomagnetic separation (IMS) combined with sodium dodecyl sulfate (SDS), propidium monoazide (PMA), and multiplex real-time PCR (mRT-PCR). We used IMS to lessen the assay time for isolation of target bacteria. We then optimized the coupling conditions and immunomagnetic capture process. The immunoreaction and incubation times for 5 μg of mAb coupled with 500 μg of streptavidin-functionalized magnetic beads using a streptavidin-biotin system were 90 and 30 min, respectively. Treatment with SDS-PMA before mRT-PCR amplification eliminated false-positive outcomes from dead bacteria and identified viable target bacteria with good sensitivity and specificity. The limit of detection of IMS combined with the SDS-PMA-mRT-PCR assay for the detection of viable Salmonella Typhimurium, Staph. aureus, and L. monocytogenes in spiked milk matrix samples was 10 cfu/mL and remained significant even in the appearance of 10⁶ cfu/mL of nontarget bacteria. The entire detection process was able to identify viable bacteria within 9 h. The combination of biotin-exposure-mediated IMS and SDS-PMA-mRT-PCR has potential value for the rapid and sensitive detection of foodborne pathogens.