[HTML][HTML] Machine learning approaches for crop improvement: Leveraging phenotypic and genotypic big data

H Tong, Z Nikoloski - Journal of plant physiology, 2021 - Elsevier
Highly efficient and accurate selection of elite genotypes can lead to dramatic shortening of
the breeding cycle in major crops relevant for sustaining present demands for food, feed …

Review of applications of artificial intelligence (AI) methods in crop research

S Bose, S Banerjee, S Kumar, A Saha, D Nandy… - Journal of Applied …, 2024 - Springer
Sophisticated and modern crop improvement techniques can bridge the gap for feeding the
ever-increasing population. Artificial intelligence (AI) refers to the simulation of human …

Improvement of genomic prediction in advanced wheat breeding lines by including additive-by-additive epistasis

MA Raffo, P Sarup, X Guo, H Liu, JR Andersen… - Theoretical and Applied …, 2022 - Springer
Key message Including additive and additive-by-additive epistasis in a NOIA
parametrization did not yield orthogonal partitioning of genetic variances, nevertheless, it …

MoBPS-modular breeding program simulator

T Pook, M Schlather, H Simianer - G3: Genes, Genomes …, 2020 - academic.oup.com
The R-package MoBPS provides a computationally efficient and flexible framework to
simulate complex breeding programs and compare their economic and genetic impact …

Bayesian analysis and prediction of hybrid performance

FC Alves, ÍSC Granato, G Galli, DH Lyra… - Plant Methods, 2019 - Springer
Background The selection of hybrids is an essential step in maize breeding. However,
evaluating a large number of hybrids in field trials can be extremely costly. However …

Incorporating gene annotation into genomic prediction of complex phenotypes

N Gao, JWR Martini, Z Zhang, X Yuan, H Zhang… - Genetics, 2017 - academic.oup.com
Gao et al. propose several approaches to incorporate gene annotation into genomic
prediction and evaluate these new methods on populations..... Today, genomic prediction …

Using local convolutional neural networks for genomic prediction

T Pook, J Freudenthal, A Korte, H Simianer - Frontiers in genetics, 2020 - frontiersin.org
The prediction of breeding values and phenotypes is of central importance for both livestock
and crop breeding. In this study, we analyze the use of artificial neural networks (ANN) and …

Dominance effects and functional enrichments improve prediction of agronomic traits in hybrid maize

GP Ramstein, SJ Larsson, JP Cook, JW Edwards… - Genetics, 2020 - academic.oup.com
Single-cross hybrids have been critical to the improvement of maize (Zea mays L.), but the
characterization of their genetic architectures remains challenging. Previous studies of …

Genomic prediction using information across years with epistatic models and dimension reduction via haplotype blocks

E Vojgani, AC Hölker, M Mayer, CC Schön… - PLoS one, 2023 - journals.plos.org
The importance of accurate genomic prediction of phenotypes in plant breeding is
undeniable, as higher prediction accuracy can increase selection responses. In this regard …

HaploBlocker: creation of subgroup-specific haplotype blocks and libraries

T Pook, M Schlather, G de Los Campos, M Mayer… - Genetics, 2019 - academic.oup.com
The concept of haplotype blocks has been shown to be useful in genetics. Fields of
application range from the detection of regions under positive selection to statistical methods …