Hamstrings passive and active shear modulus: Implications of conventional static stretching and warmup.

PURPOSE: This study compares the acute effects of a static stretching and a warmup protocol on the active and passive shear modulus of the hamstring muscles. METHODS: Muscle shear modulus was assessed at rest and during isometric contractions at 20 % of maximal voluntary isometric contraction (MVIC). RESULTS: After stretching, the passive shear modulus pattern was not altered, while at 20 % MVIC the biceps femoris short head (BFsh) and semimembranosus showed a shear modulus increase and decrease, respectively, which resulted on BFsh-SM pair differences (pre: 3.8 ±â€¯16.8 vs. post: 39.3 ±â€¯25.1 kPa; p < 0.001; d = 1.66) which was accompanied by a decrease of 18.3 % on MVIC. Following the warmup protocol, passive shear modulus remained unchanged, while active shear modulus was decreased for the semitendinosus (pre: 65.3 ±â€¯13.5 vs. post: 60.3 ±â€¯12.3 kPa; p = 0.035; d = 0.4). However, this difference was within the standard error of measurement (10.54 kPa), and did not impact the force production, since it increased only 1.4 % after the warmup. CONCLUSIONS: The results of this study suggest that the passive and active shear modulus responses of the individual hamstring muscles to static stretching are muscle-specific and that passive and active hamstring shear modulus are not changed by a standard warmup intervention.

Changes in passive and active hamstrings shear modulus are not related after a warmup protocol.

This study aimed to determine whether changes in hamstrings passive and active shear modulus after a warmup protocol are correlated. Twenty males without a history of hamstring strain injury participated. Muscle shear modulus was assessed using ultrasound-based shear wave elastography at rest and during isometric contractions at 20% of maximal voluntary isometric effort before and immediately after a warmup protocol. Changes in passive shear modulus did not seem to be associated with changes in active shear modulus. The results of this study suggest that changes in passive and active hamstring shear modulus are not associated after a standardized warmup intervention.

Fatigue effects on the knee flexors neuromuscular parameters during repeated sprinting.

BACKGROUND: To identify at which point fatigue on neuromuscular parameters occurs in the knee flexors during a repeated sprint protocol. METHODS: Physical active males without previous hamstring strain injury were recruited. Neuromuscular parameters such as peak torque (PT) and rate of torque development (RTD) were assessed after every two sprints in a 5 × (2 x 30 m) repeated sprint protocol. RESULTS: Twenty physical active males participated in the study. A significant effect of sprint number was found (p < 0.001; η2p = 0.643) with a decreased sprint speed by 6.9% from fastest to slowest sprint. No significant differences were observed in the time between finishing the sprint and performing the first MVIC (46.3 ± 4.7s; p = 0.423), nor in the time between finishing a set and starting the next set (121.2 ± 7.6s; p = 0.503). Regarding neuromuscular parameters, the only significant difference found was in PT between before and after two sprints (117.95 ± 5.61 N⋅m vs. 110.64 ± 5.71 N⋅m; p = 0.048, d = 0.289) and on RTD 0-50ms before and after ten sprints (465.78 ± 223.76 N⋅m/s vs. 382.30 ± 189.56 N⋅m/s; p = 0.008; η2p = 0.149). CONCLUSIONS: A recovery time of 46s between sprints and testing neuromuscular parameters (due to experimental design) seems sufficient to restore the neuromuscular system. Therefore, it can be suggested that time recovery is the principal factor in detecting fatigue on neuromuscular parameters.

Genetic Variation of Turnip Yellows Virus in Arable and Vegetable Brassica Crops, Perennial Wild Brassicas, and Aphid Vectors Collected from the Plants.

Turnip yellows virus (TuYV; Polerovirus, Solemoviridae) infects and causes yield losses in a range of economically important crop species, particularly the Brassicaceae. It is persistently transmitted by several aphid species and is difficult to control. Although the incidence and genetic diversity of TuYV has been extensively investigated in recent years, little is known about how the diversity within host plants relates to that in its vectors. Arable oilseed rape (Brassica napus) and vegetable brassica plants (Brassica oleracea), wild cabbage (B. oleracea), and aphids present on these plants were sampled in the field in three regions of the United Kingdom. High levels of TuYV (82 to 97%) were detected in plants in all three regions following enzyme-linked immunosorbent assays. TuYV was detected by reverse transcription polymerase chain reaction in Brevicoryne brassicae aphids collected from plants, and TuYV sequences were obtained. Two TuYV open reading frames, ORF0 and ORF3, were partially sequenced from 15 plants, and from one aphid collected from each plant. Comparative analyses between TuYV sequences from host plants and B. brassicae collected from respective plants revealed differences between some ORF0 sequences, which possibly indicated that at least two of the aphids might not have been carrying the same TuYV isolates as those present in their host plants. Maximum likelihood phylogenetic analyses including published, the new TuYV sequences described above, 101 previously unpublished sequences of TuYV from oilseed rape in the United Kingdom, and 13 also previously unpublished sequences of TuYV from oilseed rape in Europe and China revealed three distinct major clades for ORF0 and one for ORF3, with some distinct subclades. Some clustering was related to geographic origin. Explanations for TuYV sequence differences between plants and the aphids present on respective plants and implications for the epidemiology and control of TuYV are discussed.

Effects of repeated sprinting on hamstring shear modulus pattern and knee flexor neuromuscular parameters.

The purpose of the present study was to examine the acute effects of a maximum repeated sprint protocol on (1) hamstring shear modulus and (2) knee flexor neuromuscular parameters such as peak torque (PT) and rate of torque development (RTD). Muscle shear modulus was assessed in 18 healthy males using shear wave elastography at rest and during 30° isometric knee flexion at 20% of maximal voluntary isometric contraction, before and after a 10 × 30 m repeated sprint protocol. There was a 9% decrease in average speed between the fastest and slowest sprint (p < 0.001; d = 2.27). A pre-post decrease was observed in PT (p = 0.004; η2p = 0.399) and in the 0-50 ms (p = 0.042; η2p = 0.222), and 50-100 ms (p = 0.028; η2p = 0.254) RTD periods. For the active shear modulus, the only significant change after the sprint task was in the biceps femoris long head (BFlh) with an increase of 10% (Pre: 26.29 ± 8.89 kPa; Post: 28.93 ± 8.31 kPa; p = 0.015; d = 0.31). The present study provides evidence that repeated sprinting leads to significant decreases in average speed, PT, early RTD (0-50 ms; 50-100 ms), and to an increase in BFlh active shear modulus without changing the shear modulus of the other hamstrings muscles.

Effects of fatigue on hamstrings and gluteus maximus shear modulus in hip extension and knee flexion submaximal contraction task.

This study examined the effects of fatigue on hamstring muscles and gluteus maximus passive and active shear modulus in hip extension (HE) and knee flexion (KF) at 20% of maximal voluntary isometric contraction performed until task failure. Measurements were taken before and after the fatigue tasks and the delta (post-pre) was calculated. No differences in the fatigue effects on passive shear modulus were seen between muscles nor between tasks. For the active shear modulus: a task × muscle interaction was seen (p = 0.002; η2p = 0.401). The results for the tasks separately demonstrated only a significant effect for muscle in KF (p < 0.001; η2p = 0.598), with different individual contributions identified between BFlh-SM (p = 0.006; d = 1.10), BFlh-ST (p = 0.001; d = 1.35) and SM-ST (p = 0.020; d = 0.91). The comparisons between tasks for each muscle demonstrated significant differences for SM (p = 0.025; d = 0.60) and ST (p = 0.026; d = 0.60); however, no differences were seen for BFlh (p = 0.062; d = 0.46). Therefore, fatigue effects induce different patterns on the hamstring muscles in HE and KF tasks when performed at 20% MVIC.

Effects of Resistance Training in Individuals with Lower Limb Amputation: A Systematic Review.

Individuals with lower-limb amputations may have a significant strength deficit. This deficit may be related to the stump length and can lead to changes in gait, reduced energy efficiency, walking resistance, altered joint load, and increased risk of osteoarthritis and chronic low back pain. This systematic review used the Preferred Reporting Items for Systematic Reviews and Meta-Analyzes (PRISMA) guidelines to examine the effects of resistance training in lower limb amputees. Interventions with resistance training and other training methods were sufficient to achieve muscle strength gain in muscles of the lower limbs, improved balance, and improvements in gait pattern and speed when walking. However, it was impossible to determine from the results whether resistance training was mainly responsible for these benefits or even whether the positive effects presented would be observed with only this training method. When combined with other exercises, interventions with resistance training made possible gains for this population. Accordingly, it is noteworthy that the main finding of this systematic review is that the effects may be different according to the level of amputation, with mainly transtibial and transfemoral amputations studied.

Do Repeated Sprints Affect the Biceps Femoris Long Head Architecture in Football Players with and without an Injury History?-A Retrospective Study.

The aim of this study was to compare the biceps femoris long head (BFlh) architecture between football players with (twelve) and without (twenty) history of BFlh injury before and after a repeated sprint task. Fascicle length (FL), pennation angle (PA) and muscle thickness (MT) were assessed at rest and in the active condition before and after the repeated sprint protocol. Athletes with previous BFlh injury showed shorter FL at rest (p = 0.014; η2p = 0.196) and active state (p < 0.001; η2p = 0.413), and greater PA at rest (p = 0.002; η2p = 0.307) and active state (p < 0.001; η2p = 0.368) before and after the task. Intra-individual comparisons showed that injured limbs have shorter FL at rest (p = 0.012; η2p = 0.519) and in the active state (p = 0.039; η2p = 0.332), and greater PA in passive (p < 0.001; η2p = 0.732) and active conditions (p = 0.018; η2p = 0.412), when compared with contralateral limbs. Injured players, at rest and in the active condition, display shorter BFlh FL and greater PA than contralateral and healthy controls after repeated sprints. Moreover, the BFlh of injured players presented a different architectural response to the protocol compared with the healthy controls.

Distinct mental health profiles in children with Developmental Coordination Disorder: A latent class analysis and associations.

BACKGROUND: Children with Developmental Coordination Disorder (DCD) show indications for mental health problems. However, these problems are poorly understood. AIMS: To identify patterns (profiles) of mental health in this population and to analyze the associations between profiles and child characteristics. METHODS AND PROCEDURES: Parents of 119 children with DCD completed the Strengths and Difficulties Questionnaire. OUTCOMES AND RESULTS: Results indicated that a four latent class was the best model. Profile 1 was defined as "no" mental health problems (n = 28; 24 %), Profile 2 was defined as "hyperactivity" problems (n = 53; 43.3 %), for clinical indications for hyperactivity, Profile 3 was defined as "internalizing" problems (n = 8; 7.3 %), for clinical indications for emotional symptoms and peer problems, and Profile 4 was defined as "internalizing and externalizing problems" (n = 30; 25.4 %), for clinical indications for problems in both areas. In addition, having a co-occurring disorder, accommodation plans, and using medications were associated with the profiles. CONCLUSIONS AND IMPLICATIONS: There are distinct and unique profiles that children with DCD exhibit. Clinicians can use these profiles to better understand the presentation of mental health symptoms in this population and provide adequate services or support if mental health difficulties are present.

Genome-wide characterization of the common bean kinome: Catalog and insights into expression patterns and genetic organization.

The protein kinase (PK) superfamily is one of the largest superfamilies in plants and is the core regulator of cellular signaling. Even considering this substantial importance, the kinome of common bean (Phaseolus vulgaris) has not been profiled yet. Here, we identified and characterised the complete set of kinases of common bean, performing an in-depth investigation with phylogenetic analyses and measurements of gene distribution, structural organization, protein properties, and expression patterns over a large set of RNA-Sequencing data. Being composed of 1,203 PKs distributed across all P. vulgaris chromosomes, this set represents 3.25% of all predicted proteins for the species. These PKs could be classified into 20 groups and 119 subfamilies, with a more pronounced abundance of subfamilies belonging to the receptor-like kinase (RLK)-Pelle group. In addition to provide a vast and rich reservoir of data, our study supplied insights into the compositional similarities between PK subfamilies, their evolutionary divergences, highly variable functional profile, structural diversity, and expression patterns, modeled with coexpression networks for investigating putative interactions associated with stress response.

A review of sources of resistance to turnip yellows virus (TuYV) in Brassica species.

Turnip yellows virus (TuYV; previously known as beet western yellows virus) causes major diseases of Brassica species worldwide resulting in severe yield-losses in arable and vegetable crops. It has also been shown to reduce the quality of vegetables, particularly cabbage where it causes tip burn. Incidences of 100% have been recorded in commercial crops of winter oilseed rape (Brassica napus) and vegetable crops (particularly Brassica oleracea) in Europe. This review summarises the known sources of resistance to TuYV in B. napus (AACC genome), Brassica rapa (AA genome) and B. oleracea (CC genome). It also proposes names for the quantitative trait loci (QTLs) responsible for the resistances, Turnip Yellows virus Resistance (TuYR), that have been mapped to at least the chromosome level in the different Brassica species. There is currently only one known source of resistance deployed commercially (TuYR1). This resistance is said to have originated in B. rapa and was introgressed into the A genome of oilseed rape via hybridisation with B. oleracea to produce allotetraploid (AACC) plants that were then backcrossed into oilseed rape. It has been utilised in the majority of known TuYV-resistant oilseed rape varieties. This has placed significant selection pressure for resistance-breaking mutations arising in TuYV. Further QTLs for resistance to TuYV (TuYR2-TuYR9) have been mapped in the genomes of B. napus, B. rapa and B. oleracea and are described here. QTLs from the latter two species have been introgressed into allotetraploid plants, providing for the first time, combined resistance from both the A and the C genomes for deployment in oilseed rape. Introgression of these new resistances into commercial oilseed rape and vegetable brassicas can be accelerated using the molecular markers that have been developed. The deployment of these resistances should lessen selection pressure for resistance-breaking isolates of TuYV and thereby prolong the effectiveness of each other and extant resistance.

Análise da percepção de estagiários de educação física sobre a inclusão na escola: uma revisão integrativa / Análise da percepção de estagiários de educação física sobre a inclusão na escola: uma revisão integrativa / Análisis de la percepción de los pasantes de educación física sobre la inclusión en la escuela: una revisión integrativa

Resumo Este estudo objetivou analisar os estudos científicos acerca da percepção de estagiários de Educação Física sobre a inclusão de alunos com deficiência nas aulas de Educação Física Escolar. Foi realizada uma revisão integrativa com busca nas bases de dados Scopus, Web of Science, SciELO, BVS/Lilacs, PubMed, e ERIC via Portal de Periódicos CAPES. Os descritores utilizados foram: "Estagiário", "Educação Física Adaptada", "Educação Física Inclusiva", "Inclusão Escolar", "Estudante com Deficiência" e "Percepção", em português e inglês. Ao final, foram analisados 11 artigos científicos. Para a análise dos dados foram criadas 3 categorias. A primeira diz respeito à dificuldade encontrada pelos estagiários em conceituar inclusão; a segunda trata do papel do estágio na formação inicial e inclusiva, na qual os estagiários destacam o papel de auxiliares nos processos da educação física escolar e relatam que o estágio agregou valores e saberes sobre a inclusão. Por fim, a terceira categoria relata as dificuldades dos estagiários referentes à inclusão, sendo essas de cunho pedagógico, ligadas diretamente a lacunas na Formação Inicial.

Abstract This study aimed to analyze the scientific literature regarding the perception of Physical Education trainees about the inclusion of students with disabilities in School Physical Education classes. An integrative review was carried out with searches in the following databases: Scopus, Web of Science, SciELO, BVS/Lilacs, PubMed, and ERIC via CAPES Portal. We used the descriptors: "Trainee", "Adapted Physical Education", "Inclusive Physical Education", "School Inclusion", "Student with Disabilities" and "Perception", in Portuguese and English. 11 scientific articles were analyzed. For data analysis, 3 categories were created. The first category concerns the difficulty encountered by trainees in conceptualizing inclusion; the second category deals with the role of the internship in the inclusive initial teacher training, in which the interns highlight the function as assistants in the school physical education processes and report that the internship added values and knowledge about inclusion; finally, the third category reports the interns' difficulties regarding inclusion, these being of a pedagogical nature, directly linked to gaps in initial training.

Resumen Este estudio tuvo como objetivo analizar la literatura científica sobre la percepción de los alumnos de Educación Física sobre la inclusión de estudiantes con discapacidad en las clases de Educación Física Escolar. Se realizó una revisión integradora con búsquedas en las siguientes bases de datos: Scopus, Web of Science, SciELO, BVS/Lilacs, PubMed y ERIC a través del Portal CAPES. Utilizamos los descriptores: "Aprendiz", "Educación Física Adaptada", "Educación Física Inclusiva", "Inclusión Escolar", "Estudiante con Discapacidad" y "Percepción", en portugués e inglés. Se analizaron 11 artículos científicos. Para el análisis de datos se crearon 3 categorías. La primera categoría se refiere a la dificultad que encuentran los alumnos para conceptualizar la inclusión; la segunda categoría trata sobre el papel de la pasantía en la formación inicial docente inclusiva, en la que los pasantes destacan la función como asistentes en los procesos de educación física escolar y relatan que la pasantía agregó valores y conocimientos sobre inclusión; finalmente, la tercera categoría relata las dificultades de los pasantes en cuanto a la inclusión, siendo estas de carácter pedagógico, directamente vinculadas a los vacíos en la formación inicial.

Hamstrings mechanical properties profiling in football players of different competitive levels and positions after a repeated sprint protocol.

Purpose: This study compares the average speed, knee flexor peak torque and shear modulus of the hamstrings after a repeated sprint task, in football players of different competitive levels and playing positions. Methods: Fifty-four football field players without hamstring strain injury history participated, 15 being categorized as professional (2nd league) and 39 as semi-professional (17 in 3rd and 22 in 4th league). Muscle shear modulus was assessed using ultrasound-based shear wave elastography at rest and at 20% of maximal voluntary isometric effort before and immediately after the repeated sprint protocol. Results: No significant differences were seen in average sprint speed between competitive levels (p = 0.07; η2p = 0.28) and positions (p = 0.052; η2p = 0.29). Moreover, the sprint fatigue index showed no significant differences between competitive levels (p = 0.14; η2p = 0.08) and playing positions (p = 0.89; η2p = 0.05). No significant differences were observed in hamstring shear modulus changes between competitive levels (p = 0.94; η2p = 0.03) and positions (p = 0.92; η2p = 0.03). Peak torque changes also showed non-significant association with competitive levels (p = 0.46; η2p = 0.03) and positions (p = 0.60; η2p = 0.02). Conclusion: The results of this study suggest that the average sprint speed performance parameter and mechanical parameters are not able to distinguish football players of different competitive levels and positions.

Simultaneous extraction/derivatization for the analysis of sulfite by capillary electrophoresis: A high-throughput reference method to meet the demand of seafood inspection.

Sulfite is widely used to prevent enzymatic browning in shrimp and lobster processing. However, sulfite may cause allergy in sensitive consumers. Thus, regulatory agencies set limits for its use. Sulfite is usually controlled by the normalized Monier-Williams (MW) titrimetric method that allows a limited number of samples to be analyzed. This manuscript consolidates an innovative method for sulfite inspection in seafood by capillary zone electrophoresis with diode array detector (CZE-DAD). A simple, fast, and simultaneous extraction and derivatization method was developed to provide high throughput for analytical routine. The high instability of the sulfite was suppressed by its derivatization with formaldehyde producing hydroxymethylsulfonate. The evaluation of its analytical performance yielded excellent results in compliance with the strict parameters required for metrological accreditation. The CZE-DAD method was selective and specific when submitted to confirmatory evaluations by liquid chromatography coupled to mass spectrometry. The limit of detection (3.50 mg kg-1), limit of quantitation (11.7 mg kg-1) and recoveries (99-103%) were adequate for sample analysis. The measurement uncertainty was estimated by the propagation of errors and experimental standard uncertainties (precision, accuracy, and analytical curves) and type B uncertainties from traceable measurement instruments. The low relative uncertainty (10%) and the adequate reproducibility demonstrated method suitability. The CZE-DAD results were compared to the MW method through the respective expanded standard uncertainties and normalized error. This new method is promising to be used in seafood inspection and continuous laboratory evaluations using instrumentation not very expensive to acquire and maintain.

A joint learning approach for genomic prediction in polyploid grasses.

Poaceae, among the most abundant plant families, includes many economically important polyploid species, such as forage grasses and sugarcane (Saccharum spp.). These species have elevated genomic complexities and limited genetic resources, hindering the application of marker-assisted selection strategies. Currently, the most promising approach for increasing genetic gains in plant breeding is genomic selection. However, due to the polyploidy nature of these polyploid species, more accurate models for incorporating genomic selection into breeding schemes are needed. This study aims to develop a machine learning method by using a joint learning approach to predict complex traits from genotypic data. Biparental populations of sugarcane and two species of forage grasses (Urochloa decumbens, Megathyrsus maximus) were genotyped, and several quantitative traits were measured. High-quality markers were used to predict several traits in different cross-validation scenarios. By combining classification and regression strategies, we developed a predictive system with promising results. Compared with traditional genomic prediction methods, the proposed strategy achieved accuracy improvements exceeding 50%. Our results suggest that the developed methodology could be implemented in breeding programs, helping reduce breeding cycles and increase genetic gains.

Cassava-based materials for matrix solid phase dispersion: An alternative for sample preparation in food analysis.

Cassava-based food ingredients were evaluated as candidate materials to be used as matrix solid phase dispersion (MSPD) for sample preparation. Cassava starch, tapioca, and tapioca pearls (TP) were applied in MSPD sample preparation of several food matrices such as mussels, fish, cooked ham, sausages, and animal feed (laying mash) for the determination of pharmaceuticals, preservatives, and polycyclic aromatic hydrocarbons by liquid chromatography coupled to tandem mass spectrometry or capillary electrophoresis. The performance of the new cassava-based solid phases was compared to other materials, such as diatomaceous earth, cellulose, cork powder, and a commercial polymer (Q-matrix® Hydra). The following parameters were used to select the most appropriate solid phases for each assay: fat removal, accuracy for certified reference material analysis, interferents presence in blank samples extract, signal to noise ratio, signal enhancement, and signal suppression. Best results were observed for cassava starch, except for nitrite and nitrate analysis, where the use of cellulose have led to the best sample preparation performance. Electronic microscopy of the materials and the mixture matrix and solid phase confirmed the adequate dispersion of the matrix on cassava starch. In conclusion, cassava-based solid phases were suitable for MSPD, allowing cheaper, greener, and abundant alternatives to sample preparation.

Hybrid zone of a tree in a Cerrado/Atlantic Forest ecotone as a hotspot of genetic diversity and conservation.

The Cerrado, the largest Neotropical savanna, and the Brazilian Atlantic Forest form large ecotonal areas where savanna and forest habitats occupy adjacent patches with closely related species occurring side by side, providing opportunities for hybridization. Here, we investigated the evolutionary divergence between the savanna and forest ecotypes of the widely distributed tree Plathymenia reticulata (n = 233 individuals). Genetic structure analysis of P. reticulata was congruent with the recognition of two ecotypes, whose divergence captured the largest proportion of genetic variance in the data (F CT = 0.222 and F ST = 0.307). The ecotonal areas between the Cerrado and the Atlantic Forest constitute a hybrid zone in which a diversity of hybrid classes was observed, most of them corresponding to second-generation hybrids (F2) or backcrosses. Gene flow occurred mainly toward the forest ecotype. The genetic structure was congruent with isolation by environment, and environmental correlates of divergence were identified. The observed pattern of high genetic divergence between ecotypes may reflect an incipient speciation process in P. reticulata. The low genetic diversity of the P. reticulata forest ecotype indicate that it is threatened in areas with high habitat loss on Atlantic Forest. In addition, the high divergence from the savanna ecotype suggests it should be treated as a different unit of management. The high genetic diversity found in the ecotonal hybrid zone supports the view of ecotones as important areas for the origin and conservation of biodiversity in the Neotropics.

Genome-wide approaches for the identification of markers and genes associated with sugarcane yellow leaf virus resistance.

Sugarcane yellow leaf (SCYL), caused by the sugarcane yellow leaf virus (SCYLV) is a major disease affecting sugarcane, a leading sugar and energy crop. Despite damages caused by SCYLV, the genetic base of resistance to this virus remains largely unknown. Several methodologies have arisen to identify molecular markers associated with SCYLV resistance, which are crucial for marker-assisted selection and understanding response mechanisms to this virus. We investigated the genetic base of SCYLV resistance using dominant and codominant markers and genotypes of interest for sugarcane breeding. A sugarcane panel inoculated with SCYLV was analyzed for SCYL symptoms, and viral titer was estimated by RT-qPCR. This panel was genotyped with 662 dominant markers and 70,888 SNPs and indels with allele proportion information. We used polyploid-adapted genome-wide association analyses and machine-learning algorithms coupled with feature selection methods to establish marker-trait associations. While each approach identified unique marker sets associated with phenotypes, convergences were observed between them and demonstrated their complementarity. Lastly, we annotated these markers, identifying genes encoding emblematic participants in virus resistance mechanisms and previously unreported candidates involved in viral responses. Our approach could accelerate sugarcane breeding targeting SCYLV resistance and facilitate studies on biological processes leading to this trait.

The Wild Sugarcane and Sorghum Kinomes: Insights Into Expansion, Diversification, and Expression Patterns.

The protein kinase (PK) superfamily is one of the largest superfamilies in plants and the core regulator of cellular signaling. Despite this substantial importance, the kinomes of sugarcane and sorghum have not been profiled. Here, we identified and profiled the complete kinomes of the polyploid Saccharum spontaneum (Ssp) and Sorghum bicolor (Sbi), a close diploid relative. The Sbi kinome was composed of 1,210 PKs; for Ssp, we identified 2,919 PKs when disregarding duplications and allelic copies, and these were related to 1,345 representative gene models. The Ssp and Sbi PKs were grouped into 20 groups and 120 subfamilies and exhibited high compositional similarities and evolutionary divergences. By utilizing the collinearity between the species, this study offers insights into Sbi and Ssp speciation, PK differentiation and selection. We assessed the PK subfamily expression profiles via RNA-Seq and identified significant similarities between Sbi and Ssp. Moreover, coexpression networks allowed inference of a core structure of kinase interactions with specific key elements. This study provides the first categorization of the allelic specificity of a kinome and offers a wide reservoir of molecular and genetic information, thereby enhancing the understanding of Sbi and Ssp PK evolutionary history.

Machine learning approaches reveal genomic regions associated with sugarcane brown rust resistance.

Sugarcane is an economically important crop, but its genomic complexity has hindered advances in molecular approaches for genetic breeding. New cultivars are released based on the identification of interesting traits, and for sugarcane, brown rust resistance is a desirable characteristic due to the large economic impact of the disease. Although marker-assisted selection for rust resistance has been successful, the genes involved are still unknown, and the associated regions vary among cultivars, thus restricting methodological generalization. We used genotyping by sequencing of full-sib progeny to relate genomic regions with brown rust phenotypes. We established a pipeline to identify reliable SNPs in complex polyploid data, which were used for phenotypic prediction via machine learning. We identified 14,540 SNPs, which led to a mean prediction accuracy of 50% when using different models. We also tested feature selection algorithms to increase predictive accuracy, resulting in a reduced dataset with more explanatory power for rust phenotypes. As a result of this approach, we achieved an accuracy of up to 95% with a dataset of 131 SNPs related to brown rust QTL regions and auxiliary genes. Therefore, our novel strategy has the potential to assist studies of the genomic organization of brown rust resistance in sugarcane.