Mapping quantitative trait loci for seminal root angle in a selected durum wheat population.

Seminal root angle (SRA) is an important root architectural trait associated with drought adaptation in cereal crops. To date, all attempts to dissect the genetic architecture of SRA in durum wheat (Triticum durum Desf.) have used large association panels or structured mapping populations. Identifying changes in allele frequency generated by selection provides an alternative genetic mapping approach that can increase the power and precision of QTL detection. This study aimed to map quantitative trait loci (QTL) for SRA by genotyping durum lines created through divergent selection using a combination of marker-assisted selection (MAS) for the major SRA QTL (qSRA-6A) and phenotypic selection for SRA over multiple generations. The created 11 lines (BC1F2:5) were genotyped with genome-wide single-nucleotide polymorphism (SNP) markers to map QTL by identifying markers that displayed segregation distortion significantly different from the Mendelian expectation. QTL regions were further assessed in an independent validation population to confirm their associations with SRA. The experiment revealed 14 genomic regions under selection, 12 of which have not previously been reported for SRA. Five regions, including qSRA-6A, were confirmed in the validation population. The genomic regions identified in this study indicate that the genetic control of SRA is more complex than previously anticipated. Our study demonstrates that selection mapping is a powerful approach to complement genome-wide association studies for QTL detection. Moreover, the verification of qSRA-6A in an elite genetic background highlights the potential for MAS, although it is necessary to combine additional QTL to develop new cultivars with extreme SRA phenotypes.

Genetic dissection of root architecture in Ethiopian sorghum landraces.

KEY MESSAGE: This study quantified genetic variation in root system architecture (root number, angle, length and dry mass) within a diversity panel of 1771 Ethiopian sorghum landraces and identified 22 genomic regions associated with the root variations. The root system architecture (RSA) of crop plants influences adaptation to water-limited conditions and determines the capacity of a plant to access soil water and nutrients. Four key root traits (number, angle, length and dry mass) were evaluated in a diversity panel of 1771 Ethiopian sorghum landraces using purpose-built root chambers. Significant genetic variation was observed in all studied root traits, with nodal root angle ranging from 16.4° to 26.6°, with a high repeatability of 78.9%. Genome wide association studies identified a total of 22 genomic regions associated with root traits which were distributed on all chromosomes except chromosome SBI-10. Among the 22 root genomic regions, 15 co-located with RSA trait QTL previously identified in sorghum, with the remaining seven representing novel RSA QTL. The majority (85.7%) of identified root angle QTL also co-localized with QTL previously identified for stay-green in sorghum. This suggests that the stay-green phenotype might be associated with root architecture that enhances water extraction during water stress conditions. The results open avenues for manipulating root phenotypes to improve productivity in abiotic stress environments via marker-assisted selection.

Variation in mitogenome structural conformation in wild and cultivated lineages of sorghum corresponds with domestication history and plastome evolution.

BACKGROUND: Mitochondria are organelles within eukaryotic cells that are central to the metabolic processes of cellular respiration and ATP production. However, the evolution of mitochondrial genomes (mitogenomes) in plants is virtually unknown compared to animal mitogenomes or plant plastids, due to complex structural variation and long stretches of repetitive DNA making accurate genome assembly more challenging. Comparing the structural and sequence differences of organellar genomes within and between sorghum species is an essential step in understanding evolutionary processes such as organellar sequence transfer to the nuclear genome as well as improving agronomic traits in sorghum related to cellular metabolism. RESULTS: Here, we assembled seven sorghum mitochondrial and plastid genomes and resolved reticulated mitogenome structures with multilinked relationships that could be grouped into three structural conformations that differ in the content of repeats and genes by contig. The grouping of these mitogenome structural types reflects the two domestication events for sorghum in east and west Africa. CONCLUSIONS: We report seven mitogenomes of sorghum from different cultivars and wild sources. The assembly method used here will be helpful in resolving complex genomic structures in other plant species. Our findings give new insights into the structure of sorghum mitogenomes that provides an important foundation for future research into the improvement of sorghum traits related to cellular respiration, cytonuclear incompatibly, and disease resistance.

The Scleral Cap Technique for Porous and Nonporous Orbital Implants.

PURPOSE: To describe the results and potential benefit of a banked homologous donor scleral cap over the anterior surface of polyglactin 910 mesh-wrapped porous and nonporous orbital implants during enucleation and secondary orbital implant surgery. METHODS: This is a single center, retrospective, clinical case series of 83 patients who received a polyglactin 910 mesh (Vicryl knitted mesh, undyed, Ethicon, Sommerville, New Jersey, USA) wrapped bioceramic or polymethylmethacrylate orbital implant (sphere or mounded) following enucleation and secondary orbital implant surgery by one surgeon over a 10-year period. A homologous donor scleral cap (approximately 1.5 × 1.5 cm diameter) was also placed over the anterior mesh-wrapped implant surface as an additional barrier. A minimum of 1-year follow up was required to be included in the study. The author analyzed patient demographics, type of surgery, implant type, implant size, follow-up duration, and presence or absence of implant exposure. The data from patients with greater than 1-year follow up are detailed in this report. RESULTS: The author identified 100 patients in his case files that had a scleral cap put in place over their implant. Seventeen patients were either lost to follow up or did not have at least a 1-year follow up, leaving 83 patients (44 enucleations, 39 secondary implants) that were followed for 12 to 120 months (average 60.5 months). There were no cases of implant exposure identified in either group of patients during this time period. CONCLUSIONS: Implant exposure can occur anytime post implant placement with a porous or nonporous orbital implant. This review suggests that a homologous donor scleral cap (approximately 1.5 × 1.5 cm diameter) over the polyglactin 910 mesh-wrapped implant surface may help prevent implant exposure. Patients with porous and nonporous orbital implants should be followed on a long-term basis as exposure can occur at anytime postsurgery, even several years later.

Genetic modification of PIN genes induces causal mechanisms of stay-green drought adaptation phenotype.

The stay-green trait is recognized as a key drought adaptation mechanism in cereals worldwide. Stay-green sorghum plants exhibit delayed senescence of leaves and stems, leading to prolonged growth, a reduced risk of lodging, and higher grain yield under end-of-season drought stress. More than 45 quantitative trait loci (QTL) associated with stay-green have been identified, including two major QTL (Stg1 and Stg2). However, the contributing genes that regulate functional stay-green are not known. Here we show that the PIN FORMED family of auxin efflux carrier genes induce some of the causal mechanisms driving the stay-green phenotype in sorghum, with SbPIN4 and SbPIN2 located in Stg1 and Stg2, respectively. We found that nine of 11 sorghum PIN genes aligned with known stay-green QTL. In transgenic studies, we demonstrated that PIN genes located within the Stg1 (SbPIN4), Stg2 (SbPIN2), and Stg3b (SbPIN1) QTL regions acted pleiotropically to modulate canopy development, root architecture, and panicle growth in sorghum, with SbPIN1, SbPIN2, and SbPIN4 differentially expressed in various organs relative to the non-stay-green control. The emergent consequence of such modifications in canopy and root architecture is a stay-green phenotype. Crop simulation modelling shows that the SbPIN2 phenotype can increase grain yield under drought.

Oculopharyngeal Muscular Dystrophy Ptosis, Mueller's Muscle Involvement, and a Review of Management Over 34 Years.

PURPOSE: To review the management of the ptosis associated with oculopharyngeal muscular dystrophy (OPMD) from one author's experience over 34 years, demonstrate Mueller's muscle involvement in this disease, and how this impacts the preferred choice of surgery. METHODS: Retrospective, nonrandomized comparative case series. Forty patients with OPMD who underwent primary bilateral ptosis surgery through an anterior eyelid incision and had their Mueller's muscle biopsied (one side) and sent for histopathologic analysis were selected for chart review. The main outcome measure was the presence or absence of dystrophic changes in the biopsied Mueller's muscle. RESULTS: In 29/40 biopsies (72.5%), there were dystrophic changes and fatty infiltration of Mueller's muscle identified histopathologically. CONCLUSIONS: Mueller's muscle is involved in the dystrophic process more often than expected contributing to ptosis in the OPMD syndrome. A combined Mueller's-aponeurotic advancement is more effective at elevating the eyelid than simply advancing the aponeurosis when Mueller's is fatty infiltrated at the time of external levator advancement surgery in our experience. Management strategies for ptosis surgery in OPMD are reviewed. The age of onset, levator muscle function, previous ptosis repair, how debilitated the patient is with their disease process systemically, as well as the presence of other eye problems (e.g., dry eye, prior glaucoma filtering procedures, history of corneal surgery, laser refractive procedure) are important clinical considerations in patients with OPMD.

The Ruptured Globe, Sympathetic Ophthalmia, and the 14-Day Rule.

PURPOSE: Prophylactic enucleation of a ruptured globe with no light perception within 14 days of injury to prevent sympathetic ophthalmia (SO) has been an established dictum in academic teaching for more than 100 years. This treatment strategy was originally based on observation, speculation, and careful thought, but there was never any scientific proof. This review summarizes and updates the current state of our knowledge about globe rupture and SO, examines the origin and validity of the 14-day rule, and emphasizes the importance of trying to save the traumatized eye whenever possible. METHODS: A comprehensive literature review of SO and globe rupture was performed. RESULTS: SO is a rare disorder that may potentially occur following traumatic globe rupture as well as following a variety of other intraocular surgeries. Vitreoretinal surgery may be a more common cause than trauma according to some studies. SO may still occur despite having the eye removed within 14 days of the trauma. A variety of new medications including biologic agents are now available to treat SO with improved efficacy in suppressing the associated ocular inflammation and allowing retention of some useful vision. Removing the traumatized, blind eye may have other important psychological consequences associated with it that require consideration before eye removal is carried out. Retaining the blind, phthisical, disfigured eye avoids phantom vision and phantom pain associated with enucleation as well as providing a good platform to support and move an overlying prosthetic eye. Data on the occurrence of SO following evisceration and enucleation with and without predisposing factors confirms the exceedingly low risk. CONCLUSION: Most civilian open globe injuries can be successfully repaired with modern, advanced microsurgical techniques currently available. Because of the exceedingly low risk of SO, even with the severity of open globe trauma during military conflicts being more devastating as a result of the blast and explosive injuries, today every attempt is made to primarily close the eye rather than primarily enucleate it, providing there is enough viable tissue to repair. The 14-day rule for eye removal after severe globe ruptures is not scientifically supported and does not always protect against SO, but the safe time period for prophylactic eye removal is not definitively known. In the exceptional cases where SO does occur, several new medications are now available that may help treat SO. We advocate saving the ruptured globe whenever possible and avoiding prophylactic enucleation to prevent the rare occurrence of SO. When an eye requires removal, evisceration is an acceptable alternative to enucleation in cases that do not harbor intraocular malignancy.

A rare case of intramuscular angioma involving the medial rectus muscle.

Benign benign vascular tumors (e.g., hemangiomas) and malformations are commonly encountered lesions in all ages of life, especially in infancy and childhood. Hemangiomas are considered to be proliferative vascular lesions while malformations are defects of embryonal vascular morphogenesis. Less than 1% of hemangiomas within the body occur in skeletal muscle and of these approximately 15% have been reported to occur in the head and neck musculature (e.g. masseter, trapezius, sternocleidomastoid, mylohyoid, temporalis muscles) Intramuscular angioma (the preferred term for lesions formerly known as intramuscular hemangiomas by WHO Tumors of Soft Tissue and Bone Classification, 5th edition 2020) (IA) occurring in the extraocular muscles or palpebral muscles (orbicularis oculi) are extremely rare with only a few case reports in the English literature. To date, all the extraocular muscles have reportedly been involved. With the case reported herein, the medial rectus muscle appears to be the most common extraocular muscle involved.

Acute orbital inflammation with loss of vision: a paradoxical adverse event associated with infliximab therapy for Crohn's disease.

Anti-TNF-α agents (e.g. infliximab, adalimumab, etanercept) are effective management options in various inflammatory and autoimmune diseases (e.g. inflammatory bowel disease). The occurrence during anti-TNF-α agent therapy of a new onset or exacerbation of an inflammatory condition that usually responds to this class of drug has been termed a paradoxical adverse event (PAE). A wide range of ophthalmic PAEs have been reported including uveitis, optic neuritis/neuropathy, scleritis, orbital myositis, retinal vasculitis, and others. The patient reported herein developed a dramatic orbital inflammatory PAE during his infliximab infusions, which manifested as an acute orbital apex syndrome with vision loss. Physicians using this medication should be aware of this serious vision-threatening PAE, and urgent therapy with high dose intravenous corticosteroids may be required.

Detecting Sorghum Plant and Head Features from Multispectral UAV Imagery.

In plant breeding, unmanned aerial vehicles (UAVs) carrying multispectral cameras have demonstrated increasing utility for high-throughput phenotyping (HTP) to aid the interpretation of genotype and environment effects on morphological, biochemical, and physiological traits. A key constraint remains the reduced resolution and quality extracted from "stitched" mosaics generated from UAV missions across large areas. This can be addressed by generating high-quality reflectance data from a single nadir image per plot. In this study, a pipeline was developed to derive reflectance data from raw multispectral UAV images that preserve the original high spatial and spectral resolutions and to use these for phenotyping applications. Sequential steps involved (i) imagery calibration, (ii) spectral band alignment, (iii) backward calculation, (iv) plot segmentation, and (v) application. Each step was designed and optimised to estimate the number of plants and count sorghum heads within each breeding plot. Using a derived nadir image of each plot, the coefficients of determination were 0.90 and 0.86 for estimates of the number of sorghum plants and heads, respectively. Furthermore, the reflectance information acquired from the different spectral bands showed appreciably high discriminative ability for sorghum head colours (i.e., red and white). Deployment of this pipeline allowed accurate segmentation of crop organs at the canopy level across many diverse field plots with minimal training needed from machine learning approaches.

Manipulating assimilate availability provides insight into the genes controlling grain size in sorghum.

Variation in grain size, a major determinant of grain yield and quality in cereal crops, is determined by both the plant's genetic potential and the available assimilate to fill the grain in the absence of stress. This study investigated grain size variation in response to variation in assimilate supply in sorghum using a diversity panel (n = 837) and a backcross-nested association mapping population (n = 1421) across four experiments. To explore the effects of genetic potential and assimilate availability on grain size, the top half of selected panicles was removed at anthesis. Results showed substantial variation in five grain size parameters with high heritability. Artificial reduction in grain number resulted in a general increase in grain weight, with the extent of the increase varying across genotypes. Genome-wide association studies identified 44 grain size quantitative trait locus (QTL) that were likely to act on assimilate availability and 50 QTL that were likely to act on genetic potential. This finding was further supported by functional enrichment analysis and co-location analysis with known grain number QTL and candidate genes. RNA interference and overexpression experiments were conducted to validate the function of one of the identified gene, SbDEP1, showing that SbDEP1 positively regulates grain number and negatively regulates grain size by controlling primary branching in sorghum. Haplotype analysis of SbDEP1 suggested a possible role in racial differentiation. The enhanced understanding of grain size variation in relation to assimilate availability presented in this study will benefit sorghum improvement and have implications for other cereal crops.

Perspectives on Applications of Hierarchical Gene-To-Phenotype (G2P) Maps to Capture Non-stationary Effects of Alleles in Genomic Prediction.

Genomic prediction of complex traits across environments, breeding cycles, and populations remains a challenge for plant breeding. A potential explanation for this is that underlying non-additive genetic (GxG) and genotype-by-environment (GxE) interactions generate allele substitution effects that are non-stationary across different contexts. Such non-stationary effects of alleles are either ignored or assumed to be implicitly captured by most gene-to-phenotype (G2P) maps used in genomic prediction. The implicit capture of non-stationary effects of alleles requires the G2P map to be re-estimated across different contexts. We discuss the development and application of hierarchical G2P maps that explicitly capture non-stationary effects of alleles and have successfully increased short-term prediction accuracy in plant breeding. These hierarchical G2P maps achieve increases in prediction accuracy by allowing intermediate processes such as other traits and environmental factors and their interactions to contribute to complex trait variation. However, long-term prediction remains a challenge. The plant breeding community should undertake complementary simulation and empirical experiments to interrogate various hierarchical G2P maps that connect GxG and GxE interactions simultaneously. The existing genetic correlation framework can be used to assess the magnitude of non-stationary effects of alleles and the predictive ability of these hierarchical G2P maps in long-term, multi-context genomic predictions of complex traits in plant breeding.

Tall 3-dwarfs: oxymoron or opportunity to increase grain yield in sorghum?

MAIN CONCLUSION: Plant height was positively correlated with grain yield across a large set of 3-dwarf sorghum hybrids and production environments in north-eastern Australia. In industrialised countries, plant breeders tend to select for short plant stature in cereals like wheat, barley and rice, but also grain sorghum. This is mainly to prevent stalk lodging and to allow for machine harvesting. However, this counteracts an intrinsic positive relationship between plant height and yield potential often observed in cereals. We used data from multi-environment breeding trials comprising large sets of female sorghum lines from a range of pedigrees in hybrid combination with five different male testers. The hybrids were grown in 22 different rainfed environments in north-eastern Australia, which allowed us to thoroughly examine the relationship between plant height and yield across a range of productivity levels. Covariate analysis showed that in 38 out of the 90 tested relationships, grain yield was significantly (p < 0.05) positively and in only one case significantly negatively associated with plant height. This strong positive association between the traits was supported by the observation that 87% of the effects were either positive or zero. The effects of height on yield ranged from a decrease of 0.015 t ha-1 to an increase of 0.057 t ha-1 cm-1. The majority of the negative effects were observed in low-yielding trials and the positive effect of height tended to increase with increasing mean trial yield. Opportunities to increase yield potential by selecting for slightly taller sorghum hybrids therefore need to be explored in context with the target environments and in combination with other means to control the risks of lodging.

Multi-environment analysis of sorghum breeding trials using additive and dominance genomic relationships.

KEY MESSAGE: Multi-environment models using marker-based kinship information for both additive and dominance effects can accurately predict hybrid performance in different environments. Sorghum is an important hybrid crop that is grown extensively in many subtropical and tropical regions including Northern NSW and Queensland in Australia. The highly varying weather patterns in the Australian summer months mean that sorghum hybrids exhibit a great deal of variation in yield between locations. To ultimately enable prediction of the outcome of crossing parental lines, both additive effects on yield performance and dominance interaction effects need to be characterised. This paper demonstrates that fitting a linear mixed model that includes both types of effects calculated using genetic markers in relationship matrices improves predictions. Genotype by environment interactions was investigated by comparing FA1 (single-factor analytic) and FA2 (two-factor analytic) structures. The G×E causes a change in hybrid rankings between trials with a difference of up to 25% of the hybrids in the top 10% of each trial. The prediction accuracies increased with the addition of the dominance term (over and above that achieved with an additive effect alone) by an average of 15% and a maximum of 60%. The percentage of dominance of the total genetic variance varied between trials with the trials with higher broad-sense heritability having the greater percentage of dominance. The inclusion of dominance in the factor analytic models improves the accuracy of the additive effects. Breeders selecting high yielding parents for crossing need to be aware of effects due to environment and dominance.

Perioperative Prophylactic Antibiotics in 1,250 Orbital Surgeries.

PURPOSE: Intravenous antibiotic prophylaxis is used for many clean-contaminated surgeries or clean surgeries with an implant, but its value for clean orbital surgery has not been determined. This study investigated infection risks and adverse effects related to antibiotics in patients undergoing orbital surgery. METHODS: A prospective, nonrandomized comparative case series of all patients undergoing orbital surgery with participating surgeons between October 1, 2013, and March 1, 2015. Types of surgery, antibiotic regimens, corticosteroid use, antibiotic side effects, and surgical site infections (SSIs) were entered into an electronic database and subsequently analyzed. Cases in which patients received postoperative oral antibiotics were analyzed separately. RESULTS: Of 1,250 consecutive orbital surgeries, 1,225 met inclusion criteria. A total of 1208 patients were included in the primary analysis: 603 received no antibiotic prophylaxis (group A), and 605 received a single dose of intravenous antibiotic (group B). Five patients (0.42%) developed an SSI, 3 in group A and 2 in group B. The difference in SSI rates was not statistically significant between the 2 groups (p = 0.66). Antibiotic prophylaxis, alloplastic implants, paranasal sinus entry, and corticosteroid use were not associated with differences in SSI rates. All SSIs resolved on a single course of oral antibiotics; an implant was removed in 1 case. There were no complications associated with a single dose of intravenous prophylaxis. However, 12% of 17 patients (group C) who received 1 week of oral postoperative prophylactic antibiotics developed antibiotic-related complications (diarrhea, renal injury), yielding a number needed to harm of 8.5. CONCLUSIONS: In this large series, antibiotic prophylaxis does not appear to have reduced the already low incidence of SSI following orbital surgery. Given the detriments of systemic antibiotics, the rarity of infections related to orbital surgery, and the efficacy of treating such infections should they occur, patients undergoing orbital surgery should be educated to the early symptoms of postoperative infection and followed closely, but do not routinely require perioperative antibiotics.

Primary ductal adenocarcinoma of the lacrimal gland: A review and report of five cases.

Primary ductal adenocarcinoma (PDA) is a rare epithelial tumor of the lacrimal gland. Herein we report 5 cases and review 29 published cases of PDA of the lacrimal gland. Among these 5 cases, the most common clinical presentation was painless swelling and/or proptosis of their eye. The size of the lesions ranged from 1.6 to 2.5 cm. Histopathologic examination revealed proliferations of ductal or gland-like cells with vesiculated pleomorphic nuclei and prominent nucleoli. Tumor cells stained positive for epithelial and apocrine differentiation markers. Immunohistochemistry for human epidermal growth factor 2 was positive in 2 of the 4 cases. Four of the five patients were alive at the last follow-up visit. One died with bone metastases, which were diagnosed 25 months after exenteration and then survived an additional 51 months. On reviewing of twenty-nine previously published cases of PDA, the mean age of diagnosis was 58 years, with a male predominance (75%). Fifteen patients (54%) had distant metastases, 1 (4%) had local recurrence, and 10 (37%) suffered from a PDA-related death. PDA is a high-grade aggressive epithelial tumor of the lacrimal gland. Although rare, awareness and recognition of this malignancy are important to help determine prognosis and treatment options.

Large-scale GWAS in sorghum reveals common genetic control of grain size among cereals.

Grain size is a key yield component of cereal crops and a major quality attribute. It is determined by a genotype's genetic potential and its capacity to fill the grains. This study aims to dissect the genetic architecture of grain size in sorghum. An integrated genome-wide association study (GWAS) was conducted using a diversity panel (n = 837) and a BC-NAM population (n = 1421). To isolate genetic effects associated with genetic potential of grain size, rather than the genotype's capacity to fill the grains, a treatment of removing half of the panicle was imposed during flowering. Extensive and highly heritable variation in grain size was observed in both populations in 5 field trials, and 81 grain size QTL were identified in subsequent GWAS. These QTL were enriched for orthologues of known grain size genes in rice and maize, and had significant overlap with SNPs associated with grain size in rice and maize, supporting common genetic control of this trait among cereals. Grain size genes with opposite effect on grain number were less likely to overlap with the grain size QTL from this study, indicating the treatment facilitated identification of genetic regions related to the genetic potential of grain size. These results enhance understanding of the genetic architecture of grain size in cereal, and pave the way for exploration of underlying molecular mechanisms and manipulation of this trait in breeding practices.