Applications of deep learning in understanding gene regulation

Z Li, E Gao, J Zhou, W Han, X Xu, X Gao - Cell Reports Methods, 2023 - cell.com
Gene regulation is a central topic in cell biology. Advances in omics technologies and the
accumulation of omics data have provided better opportunities for gene regulation studies …

There and back again; historical perspective and future directions for Vaccinium breeding and research studies

PP Edger, M Iorizzo, NV Bassil… - Horticulture …, 2022 - academic.oup.com
Abstract The genus Vaccinium L.(Ericaceae) contains a wide diversity of culturally and
economically important berry crop species. Consumer demand and scientific research in …

Exploring deep learning for complex trait genomic prediction in polyploid outcrossing species

LM Zingaretti, SA Gezan, LFV Ferrão… - Frontiers in plant …, 2020 - frontiersin.org
Genomic prediction (GP) is the procedure whereby the genetic merits of untested candidates
are predicted using genome wide marker information. Although numerous examples of GP …

Genome synteny has been conserved among the octoploid progenitors of cultivated strawberry over millions of years of evolution

MA Hardigan, MJ Feldmann, A Lorant, KA Bird… - Frontiers in plant …, 2020 - frontiersin.org
Allo-octoploid cultivated strawberry (Fragaria× ananassa) originated through a combination
of polyploid and homoploid hybridization, domestication of an interspecific hybrid lineage …

AGHmatrix: genetic relationship matrices in R

RR Amadeu, AAF Garcia, PR Munoz… - Bioinformatics, 2023 - academic.oup.com
Motivation The resemble between relatives computed from pedigree and genomic data is an
important resource for geneticists and ecologists, who are interested in understanding how …

Genome‐wide association of volatiles reveals candidate loci for blueberry flavor

LFV Ferrão, TS Johnson, J Benevenuto… - New …, 2020 - Wiley Online Library
Plants produce a range of volatile organic compounds (VOCs), some of which are perceived
by the human olfactory system, contributing to a myriad flavors. Despite the importance of …

Improved genomic prediction of clonal performance in sugarcane by exploiting non-additive genetic effects

S Yadav, X Wei, P Joyce, F Atkin, E Deomano… - Theoretical and Applied …, 2021 - Springer
Key message Non-additive genetic effects seem to play a substantial role in the expression
of complex traits in sugarcane. Including non-additive effects in genomic prediction models …

polyRAD: Genotype calling with uncertainty from sequencing data in polyploids and diploids

LV Clark, AE Lipka, EJ Sacks - G3: Genes, Genomes, Genetics, 2019 - academic.oup.com
Low or uneven read depth is a common limitation of genotyping-by-sequencing (GBS) and
restriction site-associated DNA sequencing (RAD-seq), resulting in high missing data rates …

Genomic selection in an outcrossing autotetraploid fruit crop: lessons from blueberry breeding

LFV Ferrão, RR Amadeu, J Benevenuto… - Frontiers in plant …, 2021 - frontiersin.org
Blueberry (Vaccinium corymbosum and hybrids) is a specialty crop with expanding
production and consumption worldwide. The blueberry breeding program at the University of …

Genomic selection in tropical forage grasses: current status and future applications

RM Simeão, MDV Resende, RS Alves… - Frontiers in Plant …, 2021 - frontiersin.org
The world population is expected to be larger and wealthier over the next few decades and
will require more animal products, such as milk and beef. Tropical regions have great …