Dataset Information

Phenomic Selection Is a Low-Cost and High-Throughput Method Based on Indirect Predictions: Proof of Concept on Wheat and Poplar.

ABSTRACT: Genomic selection - the prediction of breeding values using DNA polymorphisms - is a disruptive method that has widely been adopted by animal and plant breeders to increase productivity. It was recently shown that other sources of molecular variations such as those resulting from transcripts or metabolites could be used to accurately predict complex traits. These endophenotypes have the advantage of capturing the expressed genotypes and consequently the complex regulatory networks that occur in the different layers between the genome and the phenotype. However, obtaining such omics data at very large scales, such as those typically experienced in breeding, remains challenging. As an alternative, we proposed using near-infrared spectroscopy (NIRS) as a high-throughput, low cost and non-destructive tool to indirectly capture endophenotypic variants and compute relationship matrices for predicting complex traits, and coined this new approach "phenomic selection" (PS). We tested PS on two species of economic interest (Triticum aestivum L. and Populus nigra L.) using NIRS on various tissues (grains, leaves, wood). We showed that one could reach predictions as accurate as with molecular markers, for developmental, tolerance and productivity traits, even in environments radically different from the one in which NIRS were collected. Our work constitutes a proof of concept and provides new perspectives for the breeding community, as PS is theoretically applicable to any organism at low cost and does not require any molecular information.

SUBMITTER: Rincent R

PROVIDER: S-EPMC6288839 | biostudies-literature | 2018 Dec

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Phenomic Selection Is a Low-Cost and High-Throughput Method Based on Indirect Predictions: Proof of Concept on Wheat and Poplar.

Rincent Renaud R Charpentier Jean-Paul JP Faivre-Rampant Patricia P Paux Etienne E Le Gouis Jacques J Bastien Catherine C Segura Vincent V

G3 (Bethesda, Md.) 20181210 12

Genomic selection - the prediction of breeding values using DNA polymorphisms - is a disruptive method that has widely been adopted by animal and plant breeders to increase productivity. It was recently shown that other sources of molecular variations such as those resulting from transcripts or metabolites could be used to accurately predict complex traits. These endophenotypes have the advantage of capturing the expressed genotypes and consequently the complex regulatory networks that occur in ...[more]

PMID: 30373914

Similar Datasets

Project description:BackgroundRemote photoplethysmography (rPPG) can record vital signs (VSs) by detecting subtle changes in the light reflected from the skin. Lifelight (Xim Ltd) is a novel software being developed as a medical device for the contactless measurement of VSs using rPPG via integral cameras on smart devices. Research to date has focused on extracting the pulsatile VS from the raw signal, which can be influenced by factors such as ambient light, skin thickness, facial movements, and skin tone.ObjectiveThis preliminary proof-of-concept study outlines a dynamic approach to rPPG signal processing wherein green channel signals from the most relevant areas of the face (the midface, comprising the cheeks, nose, and top of the lip) are optimized for each subject using tiling and aggregation (T&A) algorithms.MethodsHigh-resolution 60-second videos were recorded during the VISION-MD study. The midface was divided into 62 tiles of 20×20 pixels, and the signals from multiple tiles were evaluated using bespoke algorithms through weighting according to signal-to-noise ratio in the frequency domain (SNR-F) score or segmentation. Midface signals before and after T&A were categorized by a trained observer blinded to the data processing as 0 (high quality, suitable for algorithm training), 1 (suitable for algorithm testing), or 2 (inadequate quality). On secondary analysis, observer categories were compared for signals predicted to improve categories following T&A based on the SNR-F score. Observer ratings and SNR-F scores were also compared before and after T&A for Fitzpatrick skin tones 5 and 6, wherein rPPG is hampered by light absorption by melanin.ResultsThe analysis used 4310 videos recorded from 1315 participants. Category 2 and 1 signals had lower mean SNR-F scores than category 0 signals. T&A improved the mean SNR-F score using all algorithms. Depending on the algorithm, 18% (763/4212) to 31% (1306/4212) of signals improved by at least one category, with up to 10% (438/4212) improving into category 0, and 67% (2834/4212) to 79% (3337/4212) remaining in the same category. Importantly, 9% (396/4212) to 21% (875/4212) improved from category 2 (not usable) into category 1. All algorithms showed improvements. No more than 3% (137/4212) of signals were assigned to a lower-quality category following T&A. On secondary analysis, 62% of signals (32/52) were recategorized, as predicted from the SNR-F score. T&A improved SNR-F scores in darker skin tones; 41% of signals (151/369) improved from category 2 to 1 and 12% (44/369) from category 1 to 0.ConclusionsThe T&A approach to dynamic region of interest selection improved signal quality, including in dark skin tones. The method was verified by comparison with a trained observer's rating. T&A could overcome factors that compromise whole-face rPPG. This method's performance in estimating VS is currently being assessed.Trial registrationClinicalTrials.gov NCT04763746; https://clinicaltrials.gov/ct2/show/NCT04763746.

Project description:Forest trees like poplar are particular in many ways compared to other domesticated species. They have long juvenile phases, ongoing crop-wild gene flow, extensive outcrossing, and slow growth. All these particularities tend to make the conduction of breeding programs and evaluation stages costly both in time and resources. Perennials like trees are therefore good candidates for the implementation of genomic selection (GS) which is a good way to accelerate the breeding process, by unchaining selection from phenotypic evaluation without affecting precision. In this study, we tried to compare GS to pedigree-based traditional evaluation, and evaluated under which conditions genomic evaluation outperforms classical pedigree evaluation. Several conditions were evaluated as the constitution of the training population by cross-validation, the implementation of multi-trait, single trait, additive and non-additive models with different estimation methods (G-BLUP or weighted G-BLUP). Finally, the impact of the marker densification was tested through four marker density sets. The population under study corresponds to a pedigree of 24 parents and 1,011 offspring, structured into 35 full-sib families. Four evaluation batches were planted in the same location and seven traits were evaluated on 1 and 2 years old trees. The quality of prediction was reported by the accuracy, the Spearman rank correlation and prediction bias and tested with a cross-validation and an independent individual test set. Our results show that genomic evaluation performance could be comparable to the already well-optimized pedigree-based evaluation under certain conditions. Genomic evaluation appeared to be advantageous when using an independent test set and a set of less precise phenotypes. Genome-based methods showed advantages over pedigree counterparts when ranking candidates at the within-family levels, for most of the families. Our study also showed that looking at ranking criteria as Spearman rank correlation can reveal benefits to genomic selection hidden by biased predictions.

Dataset Information

Phenomic Selection Is a Low-Cost and High-Throughput Method Based on Indirect Predictions: Proof of Concept on Wheat and Poplar.

Publications

Phenomic Selection Is a Low-Cost and High-Throughput Method Based on Indirect Predictions: Proof of Concept on Wheat and Poplar.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets