Near-infrared reflectance spectroscopy phenomic prediction can perform similarly to genomic prediction of maize agronomic traits across environments.

For nearly two decades, genomic prediction and selection have supported efforts to increase genetic gains in plant and animal improvement programs. However, novel phenomic strategies for predicting complex traits in maize have recently proven beneficial when integrated into across-environment sparse genomic prediction models. One phenomic data modality is whole grain near-infrared spectroscopy (NIRS), which records reflectance values of biological samples (e.g., maize kernels) based on chemical composition. Predictions of hybrid maize grain yield (GY) and 500-kernel weight (KW) across 2 years (2011-2012) and two management conditions (water-stressed and well-watered) were conducted using combinations of reflectance data obtained from high-throughput, F2 whole-kernel scans and genomic data obtained from genotyping-by-sequencing within four different cross-validation (CV) schemes (CV2, CV1, CV0, and CV00). When predicting the performance of untested genotypes in characterized (CV1) environments, genomic data were better than phenomic data for GY (0.689 ± 0.024-genomic vs. 0.612 ± 0.045-phenomic), but phenomic data were better than genomic data for KW (0.535 ± 0.034-genomic vs. 0.617 ± 0.145-phenomic). Multi-kernel models (combinations of phenomic and genomic relationship matrices) did not surpass single-kernel models for GY prediction in CV1 or CV00 (prediction of untested genotypes in uncharacterized environments); however, these models did outperform the single-kernel models for prediction of KW in these same CVs. Lasso regression applied to the NIRS data set selected a subset of 216 NIRS bands that achieved comparable prediction abilities to the full phenomic data set of 3112 bands predicting GY and KW under CV1 and CV00.

Evaluating and Predicting the Performance of Sorghum Lines in an Elite by Exotic Backcross-Nested Association Mapping Population.

Maintaining or introducing genetic diversity into plant breeding programs is necessary for continual genetic gain; however, diversity at the cost of reduced performance is not something sought by breeders. To this end, backcross-nested association mapping (BC-NAM) populations, in which the recurrent parent is an elite line, can be employed as a strategy to introgress diversity from unadapted accessions while maintaining agronomic performance. This study evaluates (i) the hybrid performance of sorghum lines from 18 BC1-NAM families and (ii) the potential of genomic prediction to screen lines from BC1-NAM families for hybrid performance prior to phenotypic evaluation. Despite the diverse geographical origins and agronomic performance of the unadapted parents for BC1-NAM families, many BC1-derived lines performed significantly better in the hybrid trials than the elite recurrent parent, R.Tx436. The genomic prediction accuracies for grain yield, plant height, and days to mid-anthesis were acceptable, but the prediction accuracies for plant height were lower than expected. While the prediction accuracies increased when including more individuals in the training set, improvements tended to plateau between two and five lines per family, with larger training sets being required for more complex traits such as grain yield. Therefore, genomic prediction models can be optimized in a large BC1-NAM population with a relatively low fraction of individuals needing to be evaluated. These results suggest that genomic prediction is an effective method of pre-screening lines within BC1-NAM families prior to evaluation in extensive hybrid field trials.

Non-Destructive Direct Pericarp Thickness Measurement of Sorghum Kernels Using Extended-Focus Optical Coherence Microscopy.

Non-destructive measurements of internal morphological structures in plant materials such as seeds are of high interest in agricultural research. The estimation of pericarp thickness is important to understand the grain quality and storage stability of seeds and can play a crucial role in improving crop yield. In this study, we demonstrate the applicability of fiber-based Bessel beam Fourier domain (FD) optical coherence microscopy (OCM) with a nearly constant high lateral resolution maintained at over ~400 µm for direct non-invasive measurement of the pericarp thickness of two different sorghum genotypes. Whereas measurements based on axial profiles need additional knowledge of the pericarp refractive index, en-face views allow for direct distance measurements. We directly determine pericarp thickness from lateral sections with a 3 µm resolution by taking the width of the signal corresponding to the pericarp at the 1/e threshold. These measurements enable differentiation of the two genotypes with 100% accuracy. We find that trading image resolution for acquisition speed and view size reduces the classification accuracy. Average pericarp thicknesses of 74 µm (thick phenotype) and 43 µm (thin phenotype) are obtained from high-resolution lateral sections, and are in good agreement with previously reported measurements of the same genotypes. Extracting the morphological features of plant seeds using Bessel beam FD-OCM is expected to provide valuable information to the food processing industry and plant breeding programs.

Application of X-ray computed tomography to analyze the structure of sorghum grain.

BACKGROUND: The structural characteristics of whole sorghum kernels are known to affect end-use quality, but traditional evaluation of this structure is two-dimensional (i.e., cross section of a kernel). Current technology offers the potential to consider three-dimensional structural characteristics of grain. X-ray computed tomography (CT) presents one such opportunity to nondestructively extract quantitative data from grain caryopses which can then be related to end-use quality. RESULTS: Phenotypic measurements were extracted from CT scans of grain sorghum caryopses. Extensive phenotypic variation was found for embryo volume, endosperm hardness, endosperm texture, endosperm volume, pericarp volume, and kernel volume. CT derived estimates were strongly correlated with ground truth measurements enabling the identification of genotypes with superior structural characteristics. CONCLUSIONS: Presented herein is a phenotyping pipeline developed to quantify three-dimensional structural characteristics from grain sorghum caryopses which increases the throughput efficiency of previously difficult to measure traits. Adaptation of this workflow to other small-seeded crops is possible providing new and unique opportunities for scientists to study grain in a nondestructive manner which will ultimately lead to improvements end-use quality.

Decade review of mandible fractures and arch bar impact on outcomes of nonsubcondylar fractures.

OBJECTIVES/HYPOTHESIS: Review trends in mandible fracture management and outcomes in patients treated with and without intraoperative arch bar use. STUDY DESIGN: Retrospective chart review. METHODS: All patients with mandible fractures between October 1, 2001, and October 1, 2011, were reviewed. Excluded were those with concomitant midfacial fractures or inadequate follow-up. RESULTS: Overall, 734 patients sustained 1,312 mandible fractures. Assault was the most common etiology. The parasymphyseal, subcondylar, and angle regions were most likely fractured. In total, 85% of patients underwent open-reduction internal-fixation (ORIF). This overall number had no significant annual deviation. However, use of arch bars to achieve intraoperative maxillomandibular fixation (MMF) with ORIF decreased annually, whereas the use of manual reduction with ORIF increased annually. These trends held statistical significance. Outcomes were reviewed in patients with one or two nonsubcondylar fractures by assessing complications of malocclusion, infection, and malunion. In 228 patients meeting criteria, the incidence of complications was 12.9% in those treated using intraoperative arch bars with ORIF and 12.5% in those using manual reduction with ORIF. When assessing individual complications, there was no statistically significant difference. CONCLUSION: Our data suggest a shifting trend in mandible fracture management. Our techniques for achieving fracture reduction ideal for ORIF favors manual reduction over the use of arch bars in select cases. We found no statistical increase in the incidence of complications when using manual reduction with ORIF in patients with one and two nonsubcondylar fractures. In appropriately selected cases, manual stabilization of fractured segments is an alternative to using arch bars to achieve intraoperative MMF. LEVEL OF EVIDENCE: 4. Laryngoscope, 126:596-601, 2016.

Institutional and comprehensive review of laryngeal leukoplakia.

OBJECTIVES: The nature and interpretation of vocal fold leukoplakia has been limited by small study sizes. The present study reviewed institutional data and the published literature to better characterize vocal fold leukoplakia. METHODS: At our institution, the histopathology, age, and malignant conversion rates of 136 patients (208 biopsies) with vocal fold leukoplakia from 1990 to 2005 were reviewed. RESULTS: No dysplasia (ND), mild and/or moderate dysplasia (MM), and severe dysplasia and/or squamous cell carcinoma in situ (SS) was identified in, respectively, 110 of 208 (53%), 38 of 208 (18%), and 31 of 208 (15%) biopsies. After 30 months (range, 1 to 134 months), malignant transformation was observed in 8 patients on subsequent biopsies. Additionally, a literature search was performed from 1960 to 2005 for the medical subject headings (MeSH) premalignant laryngeal lesions, laryngeal dysplasia, laryngeal leukoplakia, vocal cord dysplasia, and hyperkeratosis of the larynx. Fifteen reports were included for review. When these were combined with our institutional data, 1,173 of 2,188 biopsies (53.6%) revealed ND. Mild and/or moderate dysplasia and SS were present in 717 of 2,140 (33.5%) and 375 of 2,471 (15.2%) biopsies, respectively. Squamous cell carcinoma developed in 52 of 1,388 (3.7%), 83 of 824 (10.1%), and 56 of 310 (18.1%) patients whose initial biopsies demonstrated ND, MM, or SS. CONCLUSIONS: More than half of the reported leukoplakia lesions with biopsies showed ND. However, even lesions characterized as ND were associated with an increased risk of development of squamous cell carcinoma. Importantly, the risk of developing malignancy appears to correlate with the severity of dysplasia present on initial biopsy. Because clinical examination does not accurately predict the risk of malignancy, future studies, including genomic evaluation of this lesion, may be necessary to further characterize its biologic behavior.