21 papers · ranked by Valyu relevance
Donghyun Jeon, Yuna Kang, Solji Lee, Sehyun Choi + 3 more
'Tae-Ho Lee' 'Changsoo Kim'] As the world’s population grows and food needs diversification, the demand for cereals and horticultural crops with beneficial traits increases. In order to meet a variety of demands, suitable cultivars and innovative breeding methods need to be developed. Breeding methods have changed over…
Vanda M Lourenço, Joseph O Ogutu, Hans-Peter Piepho
Genomic prediction (GP) is used in animal and plant breeding to help identify the best genotypes for selection. One of the most important measures of the effectiveness and reliability of GP in plant breeding is predictive accuracy. An accurate estimate of this measure is thus central to GP. Moreover, regression models…
Ce Liu, Shengli Du, Aimin Wei, Zhihui Cheng + 3 more
In the context of rapidly increasing population and diversified market demands, the steady improvement of yield and quality in horticultural crops has become an urgent challenge that modern breeding efforts must tackle. Heterosis, a pivotal theoretical foundation for plant breeding, facilitates the creation of superior…
Emily R. Bartusiak, Míriam Barrabés, Aigerim Rymbekova, Julia Gimbernat-Mayol + 5 more
We analyze dog genotypes (i.e., positions of dog DNA sequences that often vary between different dogs) in order to predict the corresponding phenotypes (i.e., unique observed characteristics). More specifically, given chromosome data from a dog, we aim to predict the breed, height, and weight. We explore a variety of…
Sarah A Kostick, Rex Bernardo, James J Luby
Many fruit quality traits in apple (Malus domestica Borkh.) are controlled by multiple small-effect quantitative trait loci (QTLs). Genomewide selection (genomic selection) might be an effective breeding approach for highly quantitative traits in woody perennial crops with long generation times like apple. The goal of…
Jérôme Bartholomé, Parthiban Thathapalli Prakash, Joshua N. Cobb
Genomic prediction can be a powerful tool to achieve greater rates of genetic gain for quantitative traits if thoroughly integrated into a breeding strategy. In rice as in other crops, the interest in genomic prediction is very strong with a number of studies addressing multiple aspects of its use, ranging from the…
Fabio Morgante, Wen Huang, Peter Sørensen, Christian Maltecca + 1 more
An important challenge in genetics is to be able to predict complex traits accurately. Despite recent advances, prediction accuracy for most complex traits remains low. Here, we used the Drosophila Genetic Reference Panel (DGRP), a collection of 200 lines with whole-genome sequences and deep RNA sequencing data, to…
Bjarke Grove Poulsen, Tage Ostersen, Bjarne Nielsen, Ole Fredslund Christensen
Background In livestock breeding, selection for some traits can be improved with direct selection for crossbred performance. However, genetic analyses with phenotypes from crossbred animals require methods for multibreed relationship matrices; especially when some animals are rotationally crossbred. Multiple methods…
Sidi Boubacar Ould Estaghvirou, Joseph O Ogutu, Torben Schulz-Streeck, Carsten Knaak + 3 more
'Carsten Knaak' 'Milena Ouzunova' 'Andres Gordillo' 'Hans-Peter Piepho'] Background In genomic prediction, an important measure of accuracy is the correlation between the predicted and the true breeding values. Direct computation of this quantity for real datasets is not possible, because the true breeding value is…
André M. Hidalgo, John W. M. Bastiaansen, Marcos S. Lopes, Barbara Harlizius + 2 more
'Barbara Harlizius' 'Martien A. M. Groenen' 'Dirk-Jan de Koning'] Genomic selection has been widely implemented in dairy cattle breeding when the aim is to improve performance of purebred animals. In pigs, however, the final product is a crossbred animal. This may affect the efficiency of methods that are currently…
Michaela Jung, Marius Hodel, Andrea Knauf, Daniela Kupper + 5 more
Apple breeding schemes can be improved by using genomic prediction models to forecast the performance of breeding material. These models’ predictive ability depends on factors like trait genetic architecture, training set size, relatedness of the selected material to the training set, and the validation method used.…
Yunxuan Dong, Siyuan Chen, Jisen Zhang
Genotype-to-Phenotype (G2P) prediction plays a pivotal role in crop breeding, enabling the identification of superior genotypes based on genomic data. Rice (Oryza sativa), one of the most important staple crops, faces challenges in improving yield and resilience due to the complex genetic architecture of agronomic…
Daniel Gianola
Genome-assisted prediction of complex (e.g., quantitative) traits is an ingredient of “Genomic Selection,” a paradigm adopted successfully in animals and plants of agricultural importance. The approach has impacted the timing of selection decisions, and it has delivered improvements in the quality of predictions…
Elaheh Vojgani, Torsten Pook, Johannes W.R. Martini, Armin C. Hölker + 3 more
We compared the predictive ability of various prediction models for a maize dataset derived from 910 doubled haploid lines from European landraces (Kemater Landmais Gelb and Petkuser Ferdinand Rot), which were tested in six locations in Germany and Spain. The compared models were Genomic Best Linear Unbiased Prediction…
Marco Scutari, Ian Mackay, David J. Balding
The prediction of phenotypic traits using high-density genomic data has many applications such as the selection of plants and animals of commercial interest; and it is expected to play an increasing role in medical diagnostics. Statistical models used for this task are usually tested using cross-validation, which…
Daniel E Runcie
Genomic Selection (GS) is widely considered to be a transformative approach for plant breeding, and has been a subject of well over a thousand papers since its proposal 25 years ago. The reduced costs of marker genotyping and genome sequencing, the proliferation of powerful statistical methods, and innovative breeding…
Deniz Akdemir, Julio Isidro y Sánchez
In this article, we propose an approach to breeding which focuses on mating instead of truncation selection, our method uses genome-wide marker information in a similar fashion to genomic selection so we refer it to as genomic mating. Using concepts of estimated breeding values, risk (usefulness) and inbreeding, an…
Richard B. Bernstein, Manuel Du, Zhipei G. Du, Anja Strauß + 2 more
'Andreas Hoppe' 'Kaspar Bienefeld'] Genomic selection has increased genetic gain in several livestock species, but due to the complicated genetics and reproduction biology not yet in honey bees. Recently, 2 970 queens were genotyped to gather a reference population. For the application of genomic selection in honey…
Katie Fan
This review explores the substantial progress in metabolomics and its essential role in deciphering plant-microbe interactions. It details how metabolomics has revealed the metabolic changes during pathogen attacks, pinpointed crucial metabolites associated with plant resistance, and supported the breeding of crops…
Authors not listed
The use of hybrid models, combing mechanistic and machine learning (ML), has emerged as a promising approach, contributing to the development of Industry 4.0. This work presents a hybrid model that forecasts minibioreactor (MBR) production runs of mammalian cell culture recombinant for monoclonal antibodies (mAbs)…
Authors not listed
We present a multi-stage framework for predictive modeling that integrates automated feature engineering, selective dimensionality reduction, and targeted ensembling. Our pipeline begins with feature generation using a GPU-accelerated adaptation of AutoFeat, followed by variance-based pruning and LightGBM gain-based…