Breed of origin of alleles and genomic predictions for crossbred dairy cows

Background In dairy cattle, genomic selection has been implemented successfully for purebred populations, but, to date, genomic estimated breeding values (GEBV) for crossbred cows are rarely available, although they are valuable for rotational crossbreeding schemes that are promoted as efficient strategies. An attractive approach to provide GEBV for crossbreds is to use estimated marker effects from the genetic evaluation of purebreds. The effects of each marker allele in crossbreds can depend on the breed of origin of the allele (BOA), thus applying marker effects based on BOA could result in more accurate GEBV than applying only proportional contribution of the purebreds. Application of BOA models in rotational crossbreeding requires methods for detecting BOA, but the existing methods have not been developed for rotational crossbreeding. Therefore, the aims of this study were to develop and test methods for detecting BOA in a rotational crossbreeding system, and to investigate methods for calculating GEBV for crossbred cows using estimated marker effects from purebreds. Results For detecting BOA in crossbred cows from rotational crossbreeding for which pedigree is recorded, we developed the AllOr method based on the comparison of haplotypes in overlapping windows. To calculate the GEBV of crossbred cows, two models were compared: a BOA model where marker effects estimated from purebreds are combined based on the detected BOA; and a breed proportion model where marker effects are combined based on estimated breed proportions. The methods were tested on simulated data that mimic the first four generations of rotational crossbreeding between Holstein, Jersey and Red Dairy Cattle. The AllOr method detected BOA correctly for 99.6% of the marker alleles across the four crossbred generations. The reliability of GEBV was higher with the BOA model than with the breed proportion model for the four generations of crossbreeding, with the largest difference observed in the first generation. Conclusions In rotational crossbreeding for which pedigree is recorded, BOA can be accurately detected using the AllOr method. Combining marker effects estimated from purebreds to predict the breeding value of crossbreds based on BOA is a promising approach to provide GEBV for crossbred dairy cows.

Topographic Evolution of Anterior Cerebral Artery Infarction and Its Impact on Motor Impairment

<b><i>Introduction:</i></b> Motor deficit is common following anterior cerebral artery (ACA) stroke. This study aimed to determine the impact on the motor outcome, given the location of descending corticofugal fiber tracts (from the primary motor cortex [M1], dorsal and ventral premotor area [PMdv], and supplementary motor area [SMA]) and the regional variations in collateral support of the ACA territory. <b><i>Methods:</i></b> Patients with ACA vessel occlusion were included. Disruption to corticofugal fibers was inferred by overlap of tracts with a lesion on computed tomography perfusion at the onset and on magnetic resonance imaging (MRI) poststroke. The motor outcome was defined by dichotomized and combined National Institute of Health Stroke Scale (NIHSS) sub-scores for the arm and leg. Multivariate hierarchical partitioning was used to analyze the proportional contribution of the corticofugal fibers to the motor outcome. <b><i>Results:</i></b> Forty-seven patients with a median age of 77.5 (interquartile range 68.0–84.5) years were studied. At the stroke onset, 96% of patients showed evidence of motor deficit on the NIHSS, and the proportional contribution of the corticofugal fibers to motor deficit was M1-33%, SMA-33%, and PMdv-33%. By day 7, motor deficit was present in &#x3c;50% of patients and contribution of M1 fiber tracts to the motor deficit was reduced (M1-10.2%, SMA-61.0%, PMdv-28.8%). We confirmed our findings using publicly available high-resolution templates created from Human Connectome Project data. This also showed a reduction in involvement of M1 fiber tracts on initial perfusion imaging (33%) compared to MRI at a median time of 7 days poststroke (11%). <b><i>Conclusion:</i></b> Improvements in the motor outcome seen in ACA stroke may be due to the relative sparing of M1 fiber tracts from infarction. This may occur as a consequence of the posterior location of M1 fiber tracts and the evolving topography of ACA stroke due to the compensatory capacity of leptomeningeal anastomoses.

Identification of the Tyrosine- and Phenylalanine-Derived Soluble Metabolomes of Sorghum

The synthesis of small organic molecules, known as specialized or secondary metabolites, is one mechanism by which plants resist and tolerate biotic and abiotic stress. Many specialized metabolites are derived from the aromatic amino acids phenylalanine (Phe) and tyrosine (Tyr). In addition, the improved characterization of compounds derived from these amino acids could inform strategies for developing crops with greater resilience and improved traits for the biorefinery. Sorghum and other grasses possess phenylalanine ammonia-lyase (PAL) enzymes that generate cinnamic acid from Phe and bifunctional phenylalanine/tyrosine ammonia-lyase (PTAL) enzymes that generate cinnamic acid and p-coumaric acid from Phe and Tyr, respectively. Cinnamic acid can, in turn, be converted into p-coumaric acid by cinnamate 4-hydroxylase. Thus, Phe and Tyr are both precursors of common downstream products. Not all derivatives of Phe and Tyr are shared, however, and each can act as a precursor for unique metabolites. In this study, 13C isotopic-labeled precursors and the recently developed Precursor of Origin Determination in Untargeted Metabolomics (PODIUM) mass spectrometry (MS) analytical pipeline were used to identify over 600 MS features derived from Phe and Tyr in sorghum. These features comprised 20% of the MS signal collected by reverse-phase chromatography and detected through negative-ionization. Ninety percent of the labeled mass features were derived from both Phe and Tyr, although the proportional contribution of each precursor varied. In addition, the relative incorporation of Phe and Tyr varied between metabolites and tissues, suggesting the existence of multiple pools of p-coumaric acid that are fed by the two amino acids. Furthermore, Phe incorporation was greater for many known hydroxycinnamate esters and flavonoid glycosides. In contrast, mass features derived exclusively from Tyr were the most abundant in every tissue. The Phe- and Tyr-derived metabolite library was also utilized to retrospectively annotate soluble MS features in two brown midrib mutants (bmr6 and bmr12) identifying several MS features that change significantly in each mutant.

Partitioning maternal and exogenous diet contributions to otolith 87Sr/86Sr in Kokanee Salmon (Oncorhynchus nerka)

Strontium isotopes (87Sr/86Sr) recorded in the otoliths of Pacific Salmon (Oncorhynchus spp.) are commonly used to identify natal origin. For species that migrate at or soon after emergence, the embryonic region of the otolith provides the only record of provenance. However, maternal contribution of Sr from the yolk can confound the isotopic signature of the natal site. We experimentally quantified maternal and exogenous diet contributions to otolith 87Sr/86Sr over embryonic development in Kokanee salmon (O. nerka). Eggs from two populations in isotopically distinct lakes were incubated and reared in a common water source. Timing of developmental events and proportional contribution from yolk to otolith 87Sr/86Sr differed significantly between the two populations. We suggest that the magnitude of difference in 87Sr/86Sr between yolk and water, the relative concentrations of Sr and Ca in these isotopic sources, and population-specific effects on otolith growth and composition contribute to this variation. Understanding how these factors affect otolith 87Sr/86Sr could extend the use of otolith geochemistry for determining provenance to species and populations in which natal site rearing is limited.

Combining Ability Analysis of Maize Inbred Lines in Ethiopia

The study was initiated to estimate combining ability of maize inbred lines and crosses using line by tester analysis. Fifty entries consists 48 F1 single crosses developed from 24 inbred lines and 2 testers using line x tester design and two commercial check hybrids used in the study. The experiment was conducted using alpha lattice design with two replications. Analysis of variance revealed existence of significant genetic variation among genotypes for all studied traits except for plant aspect (PA). Location x entry interaction for most of the traits was not significant which suggests hybrid performance was consistent across tested locations. Line x tester analysis of variance showed that mean squares due to GCA of lines were significant (p< 0.01 or p< 0.05) for all studied traits. Mean squares of tester GCA and SCA were significant for most of studied traits. This indicates that both additive and non-additive gene effects had contributed for the variation of the crosses. However, higher proportional contribution of additive gene action for all studied traits was obtained. Several lines and crosses were identified as good general and specific combiners for yield and yield related traits. Lines L23, L11, L15 and crosses L2xT1, L3xT1, L8xT1, L11xT1, L23xT1 and L13xT2 were found to be good general and specific combiners, respectively. In conclusion, the stated inbred lines with desirable gca effects and cross combinations with desirable sca effects for grain yield and yield related traits could be used as useful genetic material.

Functional Tradeoffs Carry Phenotypes Across the Valley of the Shadow of Death

Synopsis Functional tradeoffs are often viewed as constraints on phenotypic evolution, but they can also facilitate evolution across the suboptimal valleys separating performance peaks. I explore this process by reviewing a previously published model of how disruptive selection from competing functional demands defines an intermediate performance optimum for morphological systems that cannot simultaneously be optimized for all of the functional roles they must play. Because of the inherent tradeoffs in such a system, its optimal morphology in any particular environmental context will usually be intermediate between the performance peaks of the competing functions. The proportional contribution of each functional demand can be estimated by maximum likelihood from empirically observed morphologies, including complex ones measured with multivariate geometric morphometrics, using this model. The resulting tradeoff weight can be mapped onto a phylogenetic tree to study how the performance optimum has shifted across a functional landscape circumscribed by the function-specific performance peaks. This model of tradeoff evolution is sharply different from one in which a multipeak Ornstein–Uhlenbeck (OU) model is applied to a set of morphologies and a phylogenetic tree to estimate how many separate performance optima exist. The multi-peak OU approach assumes that each branch is pushed toward one of two or more performance peaks that exist simultaneously and are separated by valleys of poor performance, whereas the model discussed here assumes that each branch tracks a single optimal performance peak that wanders through morphospace as the balance of functional demands shifts. That the movements of this net performance peak emerge from changing frequencies of selection events from opposing functional demands are illustrated using a series of computational simulations. These simulations show how functional tradeoffs can carry evolution across putative performance valleys: even though intermediate morphologies may not perform optimally for any one function, they may represent the optimal solution in any environment in which an organism experiences competing functional demands.

Sources of Nitrogen Pollution in Upstream of Fenhe River Reservoir Based on the Nitrogen and Oxygen Stable Isotope

Identification of nitrate sources is important for the management of rivers. In this study, stable isotopes (δ15N and δ18O) and a Bayesian model (stable isotope analysis in R, SIAR) were applied to identify nitrate sources and estimate the proportional contributions of multiple nitrate sources in the upstream of Fenhe River Reservoir that serves as a source of drinking water in Shanxi Province of North China. The results showed that the 86.4% of total nitrogen (TN) concentrations in the water samples exceeded the guided values of the Chinese Surface Water Environmental Quality Standard (GB 3838-2002). The influent of tributary and discharges of sewage caused the severe nitrogen pollution. SIAR was used to estimate the proportional contribution of three nitrate sources (sewage, inorganic fertilizer, and soil nitrogen). It was revealed that domestic sewage was the dominant nitrate source, and the contributions were 33%–41%. The contributions of inorganic fertilizer and soil to nitrogen load were 30%–31% and 31%–37%, respectively. Therefore, the pollution sources of nitrogen can be determined more accurately if the rules of sewage discharges are considered.

Contribution of Proximal and Distal Grains Within Spikelets in Relation to Yield and Yield Components in the Winter Wheat Production Region of China From 1948 to 2012

Grain number and weight within a spikelet are major yield components which determine the grain yield in wheat. The objective of this study was to explore genetic gains in grain performance within wheat spikelets at the individual grain level and its effect on grain yield and evaluate genetic progress in stem internode length and other yield-related traits. We conducted field experiments across three growing seasons in the western Yellow and Huai Valley of China; incorporating 17 bread wheat cultivars released from 1948 to 2012. Yields were significantly correlated with year of release. Yield gains equated to 3.95 g m−2 yr−1 in response to increases in total grain weight per m2 (GW) in proximal (G1 and G2) and distal (G3 and G4) grains, despite a decline in the proportional contribution of proximal grains to yield and increase in the proportional contribution of distal grains to yield with year of release. Grain number per m2 (GN), thousand-grain weight (TGW), and harvest index (HI) increased with year of release, but plant height decreased. Both grain number per spikelet of proximal and distal grain contributed to the increase in total GN. However, the contribution ratio of GN in proximal grains to total GN declined, and the proportion in distal grains increased. Average single grain weight (SGW) increased linearly at G1, G2, G3, and G4 with year of release and contributed to the increase in TGW. The G3 and G4 grain positions had much lower individual grain weights but increased at a faster rate than G1 and G2. At G1, G2, and G3 grain positions, from bottom to top spikelets, the newly released cultivars had the heaviest grains and the old cultivars had the lightest grains. New cultivars had more spikelets than old cultivars and the number of grains (proximal and distal grains) in the apical spike increased with year of release. The length of five internodes decreased significantly with year of release, more so in the upper than lower internodes, all of which contributed to the decline in plant height. In summary, increasing the number and weight of distal grains could increase grain yield, TGW, and GN.

The Coupled Kinematics of Scapulothoracic Upward Rotation

Background Scapulothoracic upward rotation (UR) is an important shoulder complex motion allowing for a larger functional work space and improved glenohumeral muscle function. However, the kinematic mechanisms producing scapulothoracic UR remain unclear, limiting the understanding of normal and abnormal shoulder movements. Objective The objective of this study was to identify the coupling relationships through which sternoclavicular and acromioclavicular joint motions contribute to scapulothoracic UR. Design This was a cross-sectional observational study. Methods Sixty participants were enrolled in this study; 30 had current shoulder pain, and 30 had no history of shoulder symptoms. Shoulder complex kinematics were quantified using single-plane fluoroscopy and 2D/3D shape matching and were described as finite helical displacements for 30-degree phases of humerothoracic elevation (30°–60°, 60°–90°, and 90°–120°). A coupling function was derived to estimate scapulothoracic UR from its component motions of acromioclavicular UR, sternoclavicular posterior rotation, and sternoclavicular elevation as a function of acromioclavicular internal rotation. The proportional contributions of each of the component motions were also calculated and compared between phases of humerothoracic elevation and groups. Results Scapulothoracic UR displacement could be effectively predicted using the derived coupling function. During the 30- to 60-degree humerothoracic elevation phase, acromioclavicular UR accounted for 84.2% of scapulothoracic UR, whereas sternoclavicular posterior rotation and elevation each accounted for <10%. During later phases, acromioclavicular UR and sternoclavicular posterior rotation each accounted for 32%–42%, whereas sternoclavicular elevation accounted for <11%. Limitations Error due to the tracking of sternoclavicular posterior rotation may have resulted in an underprediction of its proportional contribution and an overprediction of the proportional contribution of acromioclavicular UR. Conclusions Acromioclavicular UR and sternoclavicular posterior rotation are the predominant component motions of scapulothoracic UR. More research is needed to investigate how these coupling relationships are affected by muscle function and influenced by scapular dyskinesis.