Features and applications of haplotypes in crop breeding

JA Bhat, D Yu, A Bohra, SA Ganie… - Communications …, 2021 - nature.com
Climate change with altered pest-disease dynamics and rising abiotic stresses threatens
resource-constrained agricultural production systems worldwide. Genomics-assisted …

From markers to genome-based breeding in wheat

A Rasheed, X Xia - Theoretical and Applied Genetics, 2019 - Springer
Key message Recent technological advances in wheat genomics provide new opportunities
to uncover genetic variation in traits of breeding interest and enable genome-based …

Non-linear machine learning models incorporating SNPs and PRS improve polygenic prediction in diverse human populations

M Elgart, G Lyons, S Romero-Brufau… - Communications …, 2022 - nature.com
Polygenic risk scores (PRS) are commonly used to quantify the inherited susceptibility for a
trait, yet they fail to account for non-linear and interaction effects between single nucleotide …

Achievements and challenges of genomics-assisted breeding in forest trees: From marker-assisted selection to genome editing

S Ahmar, P Ballesta, M Ali, F Mora-Poblete - International Journal of …, 2021 - mdpi.com
Forest tree breeding efforts have focused mainly on improving traits of economic importance,
selecting trees suited to new environments or generating trees that are more resilient to …

Deep kernel for genomic and near infrared predictions in multi-environment breeding trials

J Cuevas, O Montesinos-López… - G3: Genes …, 2019 - academic.oup.com
Kernel methods are flexible and easy to interpret and have been successfully used in
genomic-enabled prediction of various plant species. Kernel methods used in genomic …

An integrated molecular and conventional breeding scheme for enhancing genetic gain in maize in Africa

M Gedil, A Menkir - Frontiers in Plant Science, 2019 - frontiersin.org
Maize production in West and Central Africa (WCA) is constrained by a wide range of
interacting stresses that keep productivity below potential yields. Among the many problems …

Haplotype blocks for genomic prediction: a comparative evaluation in multiple crop datasets

SE Weber, M Frisch, RJ Snowdon… - Frontiers in Plant …, 2023 - frontiersin.org
In modern plant breeding, genomic selection is becoming the gold standard for selection of
superior genotypes. The basis for genomic prediction models is a set of phenotyped lines …

Simultaneous selection for grain yield and protein content in genomics-assisted wheat breeding

S Michel, F Löschenberger, C Ametz, B Pachler… - Theoretical and Applied …, 2019 - Springer
Key message Large genetic improvement can be achieved by simultaneous genomic
selection for grain yield and protein content when combining different breeding strategies in …

A sorghum practical haplotype graph facilitates genome‐wide imputation and cost‐effective genomic prediction

SE Jensen, JR Charles, K Muleta… - The Plant …, 2020 - Wiley Online Library
Successful management and utilization of increasingly large genomic datasets is essential
for breeding programs to accelerate cultivar development. To help with this, we developed a …

Gene-set association and epistatic analyses reveal complex gene interaction networks affecting flowering time in a worldwide barley collection

T He, CB Hill, TT Angessa, XQ Zhang… - Journal of …, 2019 - academic.oup.com
Single-marker genome-wide association studies (GWAS) have successfully detected
associations between single nucleotide polymorphisms (SNPs) and agronomic traits such …