Multi-trait genomic prediction improves selection accuracy for enhancing seed mineral concentrations in pea.

Multi-trait genomic selection (MT-GS) has the potential to improve predictive ability by maximizing the use of information across related genotypes and genetically correlated traits. In this study, we extended the use of sparse phenotyping method into the MT-GS framework by split testing of entries to maximize borrowing of information across genotypes and predict missing phenotypes for targeted traits without additional phenotyping expenditure. Using 300 advanced breeding lines from North Dakota State University (NDSU) pulse breeding program and ∼200 USDA accessions that were evaluated for 10 nutritional traits, our results show that the proposed sparse phenotyping aided MT-GS can further improve predictive ability by >12% across traits compared with univariate (UNI) genomic selection. The proposed strategy departed from the previous reports that weak genetic correlation is a limitation to the advantage of MT-GS over UNI genomic selection, which was evident in the partially balanced phenotyping-enabled MT-GS. Our results point to heritability and genetic correlation between traits as possible metrics to optimize and further improve the estimation of model parameters, and ultimately, prediction performance. Overall, our study offers a new approach to optimize the prediction performance using the MT-GS and further highlight strategy to maximize the efficiency of GS in a plant breeding program. The sparse-testing-aided MT-GS proposed in this study can be further extended to multi-environment, multi-trait GS to improve prediction performance and further reduce the cost of phenotyping and time-consuming data collection process.

We extended the use of sparse phenotyping into the multi-trait genomic selection (MT-GS) framework by split testing of entries. The sparse-phenotyping-aided MT-GS can increase predictive ability by >12% across traits. Heritability and genetic correlation are possible metrics to optimize and further improve prediction performance of MT-GS. The sparse-testing-aided MT-GS can be further extended to multi-environment, multi-trait GS framework.

Prevalence and antimicrobial susceptibility of virulent and avirulent multidrug-resistant Escherichia coli isolated from diarrheic neonatal calves.

OBJECTIVE: To determine the prevalence of selected virulence genes and the antimicrobial susceptibility of multidrug-resistant (MDR) Escherichia coli isolated from diarrheic neonatal calves. SAMPLE: 97 E coli isolates from diarrheic neonatal calves. PROCEDURES: E coli isolates were tested via PCR assay for 6 virulence genes and susceptibility to 17 drugs belonging to 9 classes. A 2-sample test of proportions was used to make comparisons between proportions of virulent and avirulent MDR isolates. RESULTS: 23 of 97 (23.7%) isolates were virulent, and 74 (76.3%) were avirulent. Of the 23 virulent isolates, 15 (65.2%) were positive for K99, 14 (60.9%) for F41, 12 (52.2%) for STa, 9 (39.1%) for Stx1, 6 (26.1%) for intimin, and 0 (0%) for Stx2. Twenty of 23 (87.0%) virulent isolates expressed ≥ 2 virulence genes, and 3 of 23 (13.0%) were positive for 1 virulence factor. Eight of 23 (34.8%) virulent isolates expressed STa, K99, and F41, whereas 1 of 23 (4.4%) was positive for STa, F41, intimin, and Stx1. The second most frequent gene pattern was Stx1 and intimin. Twenty of 23 (87.0%) virulent isolates were MDR; the highest prevalence of resistance was recorded for the macrolide-lincosides, followed by the tetracyclines and penicillins. Also, 17 of 23 (74.0%) virulent isolates were resistant to sulfadimethoxine, and 10 of 23 (43.5%) were resistant to trimethoprim-sulfamethoxazole. Additionally, 60 of 74 (81.0%) avirulent isolates were MDR. CONCLUSIONS AND CLINICAL RELEVANCE: The prevalence of multidrug resistance was comparable for virulent and avirulent E coli isolated from diarrheic neonatal calves. Cephalosporins and aminoglycosides had reasonable susceptibility.

A Multiplex PCR Assay to Characterize Potato virus Y Isolates and Identify Strain Mixtures.

Potato virus Y (PVY) has become a serious problem for the seed potato industry, with increased incidence and rejection of seed lots submitted for certification. New PVY strains and strain variants have emerged in recent decades in Europe and North America, including the PVYN strain that causes veinal necrosis in tobacco, and strain variants that represent one or three recombination events between the common strain (PVYO) and PVYN. Several reverse transcription-polymerase chain reaction (RT-PCR) assays have been described that characterize PVY isolates as to strain type, but they are limited in their ability to detect some combinations of mixed strain infections. We report here the development of a single multiplex RT-PCR assay that can assign PVY strain type and detect mixed infections with respect to the major strain types. Validation of this assay was achieved using 119 archived PVY isolates, which had been previously characterized by serology and bioassay and/or previously published RT-PCR assays. Results for single-strain isolates were comparable to previous results in most cases. Interestingly, 16 mixed infections were distinguished that had previously gone undetected. The new multiplex RT-PCR assay will be useful for researchers and seed production specialists interested in determining PVY infection type using a single assay.

Production of a recombinant version of a Heligmosomoides polygyrus antigen that is preferentially recognized by resistant mouse strains.

Protective immunity to the mouse nematode parasite, Heligmosomoides polygyrus, has been characterized and found to be composed of the Th2 type. However, many inbred mouse strains cannot produce this protective immune response during a primary infection. A possible reason for this lack of protection in poor responding strains could be due to lack of recognition of specific protective antigens by these strains. Recently, evidence suggests that specific antigens exist that are only recognized by fast responding strains during a primary infection. Using monoclonal antibodies to screen an H. polygyrus cDNA library enabled the production of a recombinant protein, 3A4, which is antigenically similar to those found in the excretory/secretory antigens (E/S) of both L4 and adult parasites. Protein 3A4 shares approximately 70% sequence homology with an E/S protein that induces protection to Trichostrongylus colubriformis in guinea-pigs. Antibodies that bind to 3A4 are preferentially produced in SWR compared to BALB/c mice following immunization with L4 homogenate, although both strains of mice were able to produce comparable levels of specific antibodies after immunization with 3A4 protein. It is believed that 3A4 may have considerable importance in dissecting out the nature of the immune response to H. polygyrus infection, particularly in mouse strains of differing response phenotype.