Genome-Wide Association Study and Genomic Prediction for Soybean Cyst Nematode Resistance in USDA Common Bean (Phaseolus vulgaris) Core Collection.

Soybean cyst nematode (SCN, Heterodera glycines) has become the major yield-limiting biological factor in soybean production. Common bean is also a good host of SCN, and its production is challenged by this emerging pest in many regions such as the upper Midwest USA. The use of host genetic resistance has been the most effective and environmentally friendly method to manage SCN. The objectives of this study were to evaluate the SCN resistance in the USDA common bean core collection and conduct a genome-wide association study (GWAS) of single nucleotide polymorphism (SNP) markers with SCN resistance. A total of 315 accessions of the USDA common bean core collection were evaluated for resistance to SCN HG Type 0 (race 6). The common bean core set was genotyped with the BARCBean6K_3 Infinium BeadChips, consisting of 4,654 SNPs. Results showed that 15 accessions were resistant to SCN with a Female Index (FI) at 4.8 to 9.4, and 62 accessions were moderately resistant (10 < FI < 30) to HG Type 0. The association study showed that 11 SNP markers, located on chromosomes Pv04, 07, 09, and 11, were strongly associated with resistance to HG Type 0. GWAS was also conducted for resistance to HG Type 2.5.7 and HG Type 1.2.3.5.6.7 based on the public dataset (N = 276), consisting of a diverse set of common bean accessions genotyped with the BARCBean6K_3 chip. Six SNPs associated with HG Type 2.5.7 resistance on Pv 01, 02, 03, and 07, and 12 SNPs with HG Type 1.2.3.5.6.7 resistance on Pv 01, 03, 06, 07, 09, 10, and 11 were detected. The accuracy of genomic prediction (GP) was 0.36 to 0.49 for resistance to the three SCN HG types, indicating that genomic selection (GS) of SCN resistance is feasible. This study provides basic information for developing SCN-resistant common bean cultivars, using the USDA core germ plasm accessions. The SNP markers can be used in molecular breeding in common beans through marker-assisted selection (MAS) and GS.

Incremental scattering of the A0 Lamb wave mode from a notch emanating from a through-hole.

Lamb wave scattering from a crack originating at a through-hole is of practical importance because of the abundance of fastener holes used in engineering structures. Notches are often used to simulate cracks so that Lamb wave methods can be more conveniently investigated in the laboratory. A linear, three-dimensional finite element model is employed in this paper to study incremental scattering of the fundamental anti-symmetric (A0) Lamb wave mode from notches emanating from through-holes. The term "incremental scattering" refers to the change in scattering caused by introduction of the notch and is motivated by structural health monitoring for which transducers are fixed and signal changes are interpreted to detect damage. Far-field angular scattering patterns are generated for multiple incident angles and frequencies, and such patterns are experimentally validated at one frequency by laser vibrometry measurements. Comparisons are made between a vertical notch alone (no hole) and notches located above and below the through-hole. Additionally, holes of different sizes are considered to investigate the effect of hole diameter on incremental scattering patterns. Results show that the presence, location and size of the through-hole affect both the shape and strength of notch incremental scattering patterns.

Quantification of Shear Wave Scattering From Far-Surface Defects via Ultrasonic Wavefield Measurements.

Nondestructive evaluation methods rely on prior knowledge of the expected interaction of ultrasonic waves with defects to inform detection and characterization decisions. Wavefield imaging, which refers to the measurement of signals originating from a spatially fixed source on a 2-D rectilinear grid, can be applied to visualize the effect of a subsurface scatterer on surface-measured wave motion. Here, obliquely incident shear waves are directed at the far surface of a plate containing a through-hole using the well-known angle-beam ultrasonic inspection method. A laser vibrometer and laboratory scanner are used to record the resulting out-of-plane motion on the plate surface in the vicinity of the through-hole both before and after a far-surface corner notch is introduced and subsequently enlarged. Waves scattered from the notch are isolated from the incident and hole-scattered waves via baseline subtraction of wavefields. The scattered wavefields are then filtered in the frequency-wavenumber domain to separate Rayleigh, shear, and longitudinal contributions to the scattered wavefield. The filtered wavefields are interpolated in space to obtain 2-D radial wavefield slices originating at the base of the notch. Each radial slice is analyzed to quantify scattering as a function of observation direction, resulting in Rayleigh, shear, and longitudinal scattering profiles for each notch size. The results are compared for four different notch sizes and two transducer orientations.

A methodology for estimating guided wave scattering patterns from sparse transducer array measurements.

Ultrasonic guided waves are one of the primary methods being investigated for structural health monitoring of plate-like components. A common practice is to collect measurements from a sparse transducer array using the pitch-catch method, which enables interrogation of defects from multiple directions. Thus, knowledge of how guided waves scatter from defects is very useful for detection, localization, and characterization of damage. One way to describe scattering patterns is with a matrix indexed by incident angle and scattered angle, and sparse array measurements essentially sample this matrix. A methodology is proposed in this paper to estimate the complete scattering matrix from these limited array measurements. First, recorded array signals are compensated for geometric spreading loss, wave packet spreading loss, and transducer differences. Initial scattering values are then extracted from the scattered wave packets after baseline subtraction and are augmented using transducer reciprocity and any a priori knowledge of defect geometric symmetry. Finally, radial basis function interpolation is performed on these values to obtain the complete scattering matrix. Scattering matrices are generated from experimental data by cutting notches of different lengths originating from a through-hole in an aluminum plate specimen that is instrumented with a sparse transducer array. The methodology is validated by laser vibrometry measurements performed on a nominally identical specimen for one notch length.

Frequency-wavenumber domain analysis of guided wavefields.

Full wavefield measurements obtained with either an air-coupled transducer mounted on a scanning stage or a scanning laser vibrometer can be combined with effective signal and imaging processing algorithms to support characterization of guided waves as well as detection, localization and quantification of structural damage. These wavefield images contain a wealth of information that clearly shows details of guided waves as they propagate outward from the source, reflect from specimen boundaries, and scatter from discontinuities within the structure. The analysis of weaker scattered waves is facilitated by the removal of source waves and the separation of wave modes, which is effectively achieved via frequency-wavenumber domain filtering in conjunction with the subsequent analysis of the resulting residual signals. Incident wave removal highlights the presence and the location of weak scatterers, while the separation of individual guided wave modes allows the characterization of their separate contribution to the scattered field and the evaluation of mode conversion phenomena. The effectiveness of these methods is demonstrated through their application to detection of a delamination in a composite plate and detection of a crack emanating from a hole.

A novel cylindrical biaxial computer-controlled bioreactor and biomechanical testing device for vascular tissue engineering.

It is becoming evident that tissue-engineered constructs adapt to altered mechanical loading, and that specific combinations of multidirectional loads appear to have a synergistic effect on the remodeling. However, most studies of mechanical stimulation of engineered vascular tissue engineering employ only uniaxial stimulation. Here we present a novel computer-controlled bioreactor and biomechanical testing device designed to precisely and simultaneously control mean and cyclic values of transmural pressure (at rates up to 1 Hz and ranges of 40 mmHg), luminal flow rate, and axial length (or load) applied to gel-derived, scaffold-derived, and self-assembly-derived tissue-engineered blood vessels during culture, while monitoring vessel geometry with a resolution of 6.6 mum. Intermittent monitoring of the extracellular matrix and cells is accomplished on live tissues using multi-photon confocal microscopy under unloaded and loaded conditions at multiple time-points in culture (on the same vessel) to quantify changes in cell and extracellular matrix content and organization. This same device is capable of performing intermittent cylindrical biaxial biomechanical testing at multiple time-points in culture (on the same vessel) to quantify changes in the mechanical behavior during culture. Here we demonstrate the capabilities of this new device on self-assembly-derived and collagen-gel-derived tissue-engineered blood vessels.

An ultrasonic method for dynamic monitoring of fatigue crack initiation and growth.

Attached ultrasonic sensors can detect changes caused by crack initiation and growth if the wave path is directed through the area of critical crack formation. Dynamics of cracks opening and closing under load cause nonlinear modulation of received ultrasonic signals, enabling small cracks to be detected by stationary sensors. A methodology is presented based upon the behavior of ultrasonic signals versus applied load to detect and monitor formation and growth of cracks originating from fastener holes. Shear wave angle beam transducers operating in through transmission mode are mounted on either side of the hole such that the transmitted wave travels through the area of expected cracking. Time shift is linear with respect to load, and is well explained by path changes due to strain combined with wave speed changes due to acoustoelasticity. During subsequent in situ monitoring with unknown loads, the measured time of flight is used to estimate the load, and behavior of the received energy as a function of load is the basis for crack detection. Results are presented from low cycle fatigue tests of several aluminum specimens and illustrate the efficacy of the method in both determining the applied load and monitoring crack initiation and growth.

Detection of structural damage from the local temporal coherence of diffuse ultrasonic signals.

Permanently mounted ultrasonic transducers have the potential to interrogate large areas of a structure, and thus be effective global sensors for structural health monitoring. Recorded signals, although very sensitive to damage, are long, complex, and difficult to interpret compared to pulse echo and through transmission signals customary for nondestructive testing. These diffuse signals also are quite sensitive to environmental effects such as temperature and surface condition changes. Waveform comparison methods such as time domain differencing and spectral analysis, although effective for detecting changes, are generally unsuccessful in discriminating damage from environmental effects. This paper considers the local temporal coherence as another means of comparing two waveforms in order to provide a quantitative measure of the change in shape of a signal compared to a reference as a function of time from transmit. Experimental results show that the local temporal coherence is effective in discriminating structural damage from both temperature changes and modest changes in surface conditions; results are compared to those obtained from time domain and spectrogram differencing. The advantages of this methodology are the simplicity of the transducers, the applicability to a wide range of structures, and the straightforward signal processing.