Plant pan-genomics and its applications

J Shi, Z Tian, J Lai, X Huang - Molecular Plant, 2023 - cell.com
Plant genomes are so highly diverse that a substantial proportion of genomic sequences are
not shared among individuals. The variable DNA sequences, along with the conserved core …

From single-to multi-omics: future research trends in medicinal plants

L Yang, Y Yang, L Huang, X Cui… - Briefings in bioinformatics, 2023 - academic.oup.com
Medicinal plants are the main source of natural metabolites with specialised
pharmacological activities and have been widely examined by plant researchers. Numerous …

Biotechnological advances to improve abiotic stress tolerance in crops

MA Villalobos-López, A Arroyo-Becerra… - International Journal of …, 2022 - mdpi.com
The major challenges that agriculture is facing in the twenty-first century are increasing
droughts, water scarcity, flooding, poorer soils, and extreme temperatures due to climate …

Exploring pan-genomes: an overview of resources and tools for unraveling structure, function, and evolution of crop genes and genomes

S Naithani, CH Deng, SK Sahu, P Jaiswal - Biomolecules, 2023 - mdpi.com
The availability of multiple sequenced genomes from a single species made it possible to
explore intra-and inter-specific genomic comparisons at higher resolution and build clade …

The genomic route to tomato breeding: past, present, and future

Y Wang, C Sun, Z Ye, C Li, S Huang, T Lin - Plant Physiology, 2024 - academic.oup.com
Abstract Over the past 10,000 years, tomato species have undergone both unintentional and
intentional selection to enhance their favorable traits for human consumption and …

GWAS supported by computer vision identifies large numbers of candidate regulators of in planta regeneration in Populus trichocarpa

MF Nagle, J Yuan, D Kaur, C Ma… - G3: Genes …, 2024 - academic.oup.com
Plant regeneration is an important dimension of plant propagation and a key step in the
production of transgenic plants. However, regeneration capacity varies widely among …

Legume pangenome: status and scope for crop improvement

UC Jha, H Nayyar, EJB von Wettberg, YD Naik… - Plants, 2022 - mdpi.com
In the last decade, legume genomics research has seen a paradigm shift due to advances in
genome sequencing technologies, assembly algorithms, and computational genomics that …

Genomic decoding of Theobroma grandiflorum (cupuassu) at chromosomal scale: evolutionary insights for horticultural innovation

RM Alves, VAC de Abreu, RP Oliveira… - …, 2024 - academic.oup.com
Abstract Background Theobroma grandiflorum (Malvaceae), known as cupuassu, is a tree
indigenous to the Amazon basin, valued for its large fruits and seed pulp, contributing …

k-mer-Based Genome-Wide Association Studies in Plants: Advances, Challenges, and Perspectives

B Karikari, MA Lemay, F Belzile - Genes, 2023 - mdpi.com
Genome-wide association studies (GWAS) have allowed the discovery of marker–trait
associations in crops over recent decades. However, their power is hampered by a number …

Differences in activity and stability drive transposable element variation in tropical and temperate maize

S Ou, T Collins, Y Qiu, AS Seetharam, CC Menard… - bioRxiv, 2022 - biorxiv.org
Much of the profound interspecific variation in genome content has been attributed to
transposable elements (TEs). To explore the extent of TE variation within species, we …