Correcting for base-population differences and unknown parent groups in single-step genomic predictions of Norwegian Red cattle.

Bias and inflation in genomic evaluation with the single-step methods have been reported in several studies. Incompatibility between the base-populations of the pedigree-based and the genomic relationship matrix (G) could be a reason for these biases. Inappropriate ways of accounting for missing parents could be another reason for biases in genetic evaluations with or without genomic information. To handle these problems, we fitted and evaluated a fixed covariate (J) that contains ones for genotyped animals and zeros for unrelated non-genotyped animals, or pedigree-based regression coefficients for related non-genotyped animals. We also evaluated alternative ways of fitting the J covariate together with genetic groups on biases and stability of breeding value estimates, and of including it into G as a random effect. In a whole vs. partial data set comparison, four scenarios were investigated for the partial data: genotypes missing, phenotypes missing, both genotypes and phenotypes missing, and pedigree missing. Fitting J either as fixed or random reduced level-bias and inflation and increased stability of genomic predictions as compared to the basic model where neither J nor genetic groups were fitted. In most models, genomic predictions were largely biased for scenarios with missing genotype and phenotype information. The biases were reduced for models which combined group and J effects. Models with these corrected group covariates performed better than the recently published model where genetic groups were encapsulated and fitted as random via the Quaas and Pollak transformation. In our Norwegian Red cattle data, a model which combined group and J regression coefficients was preferred because it showed least bias and highest stability of genomic predictions across the scenarios.

Our study dealt with strategies on how to reduce biases (inflation and level-bias) and improve a parameter related to accuracy (stability) of genomic predictions of breeding values that combine genotyped and non-genotyped animals, which are denoted as single-step genomic predictions. We tried to remedy incompatibilities between the pedigree- and the genomics-based relationships matrices by fitting a covariate (J) that corrects for base-population differences that may occur between both relationship matrices. We also evaluated alternative ways to combine the J covariate and genetic group effects to account for missing parental information, which often occurs in practical breeding schemes. We found that fitting J either as fixed or random reduced level-bias and inflation and increased stability of genomic predictions as compared to the basic model where neither J nor genetic groups were fitted. Level-biases and inflation of breeding value estimates were reduced, and stability of genomic predictions improved for models which combined group and J effects. A model which fits group regression coefficients minus the part that could be explained from pedigree was recommended because it showed least bias and highest stability across the scenarios and has theoretical justification.

Prevalence of Rhesus D negativity among reproductive age women in Southern Ethiopia: a cross-sectional study.

BACKGROUND: The Rhesus (Rh) blood group system is the next most clinically significant blood group system following the ABO blood group. Rh D-negative women are at risk of alloimmunization following exposure to Rh D-positive blood. The exposure of Rh D-negative women to Rh D-positive fetal blood may cause hemolytic disease of the fetus or new-born due to Rh incompatibility. Knowing Rh blood phenotype has paramount importance to prevent the risk of sensitization and bad obstetric outcome in Rh D-negative women. Despite the aforementioned fact, the distribution of Rh D-negative phenotype of women was not explored in Arba Minch Zuria district, southern Ethiopia. This study was aimed to assess the prevalence of Rh D-negative blood phenotype among reproductive-age women in Arba Minch Zuria district, southern Ethiopia. METHODS AND MATERIALS: A community-based cross-sectional study was conducted among reproductive-age women in Arba Minch Zuria district, Southern Ethiopia from March to April 2019. Socio-demographic data were collected using an interviewer-administered semi-structured questionnaire and blood phenotype determination was done by laboratory technicians using the slide method principle aseptically and Statistical Package for Social Science (SPSS) version 21 was used for analysis. RESULT: The data were collected from 417 study participants with a 98.8% response rate. This study revealed that 2.1%, 1.9%, 1.2%, and 1% of study participants with blood group O, A, B, and AB were Rh D negative, respectively. In this study, the overall prevalence of Rh D negative phenotype was found 6.2% among reproductive-age women in Arba Minch Zuria district, Southern Ethiopia. CONCLUSIONS: This study showed a high prevalence of Rh D negative factor among reproductive-age women in Arba Minch Zuria district. Therefore, counseling of reproductive age women on the importance of Rh D factor status determination would be worthy to avoid the potential risk of sensitization among Rh D negative women in order to prevent hemolytic disease of the fetus and new-born.

Ethiopia's transforming wheat landscape: tracking variety use through DNA fingerprinting.

Ethiopia is the largest wheat producer in sub-Saharan Africa yet remains a net importer. Increasing domestic wheat production is a national priority. Improved varieties provide an important pathway to enhancing productivity and stability of production. Reliably tracking varietal use and dynamics is a challenge, and the value of conventional recall surveys is increasingly questioned. We report the first nationally representative, large-scale wheat DNA fingerprinting study undertaken in Ethiopia. Plot level comparison of DNA fingerprinting with farmer recall from nearly 4000 plots in the 2016/17 season indicates that only 28% of farmers correctly named wheat varieties grown. The DNA study reveals that new, rust resistant bread wheat varieties are now widely adopted. Germplasm originating from CGIAR centres has made a significant contribution. Corresponding productivity gains and economic benefits have been substantial, indicating high returns to investments in wheat improvement. The study provides an accurate assessment of wheat varietal status and sets a benchmark for national policy-makers and donors. In recent decades, the Ethiopian wheat landscape has transformed from local tetraploid varieties to widespread adoption of high yielding, rust resistant bread wheat. We demonstrate that DNA fingerprinting can be applied at scale and is likely to transform future crop varietal adoption studies.

A novel USP9Y polymorphism allowing a rapid and unambiguous classification of Bos taurus Y chromosomes into haplogroups.

A new sequence-tagged site (STS) was identified within intron 26 of the bovine USP9Y gene, showing an 81-base pair insertion (g.76439_76440ins81 in sequence with GenBank accession FJ195366) able to distinguish Y2 and Y3 Bos Y haplogroups from Y1. Moreover, four Y3-specific sequence variants allow a distinction from haplogroup Y2. The typing of a Bison bison Y chromosome indicates that the ancestral allele for the USP9Y 81-bp insertion is the short Y1 version. The results from typing the new STS in 1230 cattle Y chromosomes are fully consistent with their classification through standard methods. Thanks to the newly identified STS, it is now possible to assign cattle Y chromosomes to the currently known haplogroups using a single marker.

Active-passive gradient shielding for MRI acoustic noise reduction.

An important source of MRI acoustic noise-magnet cryostat warm-bore vibrations caused by eddy-current-induced forces-can be mitigated by a passive metal shield mounted on the outside of a vibration-isolated, vacuum-enclosed shielded gradient set. Finite-element (FE) calculations for a z-gradient indicate that a 2-mm-thick Cu layer wrapped on the gradient assembly can decrease mechanical power deposition in the warm bore and reduce warm-bore acoustic noise production by about 25 dB. Eliminating the conducting warm bore and other magnet parts as significant acoustic noise sources could lead to the development of truly quiet, fully functioning MRI systems with noise levels below 70 dB.