(Press-News.org)
Advancements in whole-genome sequencing have revolutionized plant species characterization, providing a wealth of genotypic data for analysis. The combination of genomic selection and neural networks, especially deep learning and autoencoders, has emerged as a promising method for predicting complex traits from this data. Despite the success in applications like plant phenotyping, challenges remain in accurately translating visual information from images into measurable data for genomic studies.
In November 2023, Plant Phenomics published a research article entitled by “GenoDrawing: An Autoencoder Framework for Image Prediction from SNP Markers”.
The study introduces an innovative approach using an autoencoder network and embedding predictor to simplify apple images into 64 dimensions and predict fruit shapes from molecular data (SNPs). This method, known as GenoDrawing, involves training the autoencoder with a large dataset of apple images. The generated embeddings, along with SNP data, are then used to predict and reconstruct apple shapes. The method showed that targeted SNPs (tSNPs) consistently outperformed randomly selected SNPs (rSNPs) in predicting image embeddings, resulting in more accurate fruit shape predictions. The best models using tSNPs achieved lower mean absolute errors (MAEs) and produced distributions closer to the original data compared to rSNPs. Additionally, the tSNP-based version predicted a wider range of fruit shapes, demonstrating its effectiveness in capturing the diversity of apple phenotypes. However, the study revealed limitations, including the model's inability to accurately capture certain fruit features and the influence of environmental factors on apple phenotypes. Despite these challenges, the approach represents a significant advancement in genomic prediction, demonstrating the potential of merging image analysis with molecular data to comprehend complex traits in crops.
In summary, the findings suggest that selecting relevant SNPs is crucial for accurate predictions and that GenoDrawing can effectively learn to predict fruit shapes when given the appropriate markers. This research lays the groundwork for future studies aiming to enhance the accuracy and applicability of genomic prediction models by incorporating image data and improving SNP selection strategies.
###
References
Authors
Federico Jurado-Ruiz1, David Rousseau2, Juan A. Botía3, and Maria José Aranzana1,4*
Affiliations
1Center for Research in Agricultural Genomics (CRAG), 08193 Barcelona, Cerdanyola, Spain.
2Université d’Angers, LARIS, INRAe UMR IRHS, 49000 Angers, France
3Department of Information and Communi-cation Engineering, University of Murcia, 30071 Murcia, Spain
4IRTA (Institut de Recerca i Tecnologia Agroalimentàries), Barcelona, Spain
About Maria José Aranzana
She is a researcher at the Institute of Agrifood Research and Technology (IRTA), Barcelona, Spain. She is working on the research program of Plant and Animal Genomics.
END
Erin Overstreet has been selected as the new executive director of the USC Stevens Center for Innovation where she will oversee the university’s commercialization of USC-driven intellectual property.
Overstreet’s expertise and experience embody technology transfer and innovation across the academic, educational, and venture capital sectors; such experience is critical for bridging USC research to a broadened, national technology transfer ecosystem, said Ishwar Puri, senior vice president of the Office of Research and Innovation.
“The university has the utmost confidence in Dr. Overstreet’s ability to ...
In the field of Landscape Architecture, Topography aims to study the complex and ongoing changing relationship between humans and the land through continuously updated and iterative tools and media. It maintains a balance between abstract concepts and concrete perceptions, which can both drive the development of science and technology in this field and hold on to openness to artistic expression. Thus, topographical design may be an effective way to help facilitate refining landscape design methods.
The work entitled “Can Topography ...
Associate Professor Andrew Baker from QUT School of Biology and Environmental Science said antechinuses are carnivorous marsupials well-known for suicidal sex sessions where all males die after the 1 to 3 week breeding period.
“During the breeding season, male and females mate promiscuously in frenzied bouts lasting as long as 14 hours. Certain stress-induced death follows for all males as surging testosterone causes cortisol to flood uncontrolled through the body, reaching pathological levels,” Professor Baker said.
“The males drop dead, which provides an opportunity ...
Protecting the world’s oceans against accelerating damage from human activities could be cheaper and take up less space than previously thought, new research has found.
The University of Queensland’s Professor Anthony Richardson collaborated on the study, which looks to halt the rapid decline of marine biodiversity from expanding industrial activities in marine areas beyond national jurisdictions (ABNJ).
“This ‘blue acceleration’ as we call it, has seen a greater diversity of stakeholders interested in ABNJs, such as the high seas and the international seabed beyond exclusive economic zones,” ...
Frequently using more than three strategies to stay alert while driving could be a sign of excessive sleepiness due to obstructive sleep apnoea (OSA), according to a study published today (Thursday) in ERJ Open Research [1].
People with OSA often snore loudly, their breathing starts and stops during the night, and they may wake up several times. Around one in five people are estimated to have OSA but the majority of sufferers do not realise they have a problem. OSA causes excessive sleepiness and people with untreated OSA are at higher risk of collisions on the road.
Researchers say that asking people ...
Globally, non-point source pollution is an important source of water quality deterioration in rivers and lakes. A ditch-pond system, consisting of ditches and ponds, is considered to be similar to free-surface wetlands, linking pollution sources to the receiving water bodies. The ditch-pond system includes vegetation, microorganisms and sediment, which can slow down the flow velocity and promote the precipitation of particulate matter carried by running water. At the same time, ditch and pond systems reduces nitrogen and phosphorus concentrations, and those of other nutrients entering the downstream water by means of plant absorption, sediment adsorption and microbial degradation, ...
The Lancet Child & Adolescent Health: Paediatric care for non-White children is universally worse across the USA; policy reform urgently needed to address disparities
Two-paper Series identifies pervasive racial inequities in paediatric care in the USA, and outlines policies to address structural racism embedded in wider sectors of society that shape children’s health.
A review of recent evidence reveals widespread patterns of inequitable care across paediatric specialties, including neonatal care, emergency medicine, surgery, developmental disabilities, mental ...
Peer reviewed – observational study - humans
Genotyping technology detects Covid variants more quickly and cheaply than ever before – according to research from the University of East Anglia and the UK Health Security Agency.
A new study published today reveals that the technique detects new variants almost a week more quickly than traditional whole genome sequencing methods.
The research team say that genotyping allowed Covid variant information to be more rapidly detected and communicated to frontline health protection professionals at the height of the pandemic.
Importantly, it helped to implement ...
People with obsessive-compulsive disorder (OCD) may have an increased risk of death from both natural and unnatural causes than those without the disorder, finds a study from Sweden published by The BMJ today.
The researchers point out that many of the natural causes of death are preventable, suggesting that better surveillance, prevention, and early intervention strategies should be implemented to reduce the risk of fatal outcomes in people with OCD.
OCD is typically a long term psychiatric disorder affecting about 2% of the population. It is characterised ...
Routinely referring patients to a tailored programme of physiotherapy after a dislocated shoulder is no better than a single session of advice, supporting materials and the option to self-refer to physiotherapy, finds a clinical trial published by The BMJ today.
The findings should help clinicians and patients have informed discussions about the best approach to non-operative rehabilitation, say the researchers.
The shoulder is the most frequently dislocated joint, with rates highest in men aged 16-20 years ...
