Technological development and advances for constructing and analyzing plant pangenomes

H Hu, R Li, J Zhao, J Batley… - Genome biology and …, 2024 - academic.oup.com
A pangenome captures the genomic diversity for a species, derived from a collection of
genetic sequences of diverse populations. Advances in sequencing technologies have …

Machine learning for plant stress modeling: A perspective towards hormesis management

AK Rico-Chávez, JA Franco, AA Fernandez-Jaramillo… - Plants, 2022 - mdpi.com
Plant stress is one of the most significant factors affecting plant fitness and, consequently,
food production. However, plant stress may also be profitable since it behaves hormetically; …

A pangenome analysis pipeline provides insights into functional gene identification in rice

J Wang, W Yang, S Zhang, H Hu, Y Yuan, J Dong… - Genome Biology, 2023 - Springer
Background A pangenome aims to capture the complete genetic diversity within a species
and reduce bias in genetic analysis inherent in using a single reference genome. However …

[HTML][HTML] Pear genomes display significant genetic diversity and provide novel insights into the fruit quality traits differentiation

B Ding, H Hu, Y Cao, R Xu, Y Lin, Y Song, G He… - Horticultural plant …, 2024 - Elsevier
The pear (Pyrus spp.) is well known for diverse flavors, textures, and global horticultural
importance. However, the genetic diversity responsible for its extensive phenotypic …

Impact of whole-genome duplications on structural variant evolution in Cochlearia

T Hämälä, C Moore, L Cowan, M Carlile… - Nature …, 2024 - nature.com
Polyploidy, the result of whole-genome duplication (WGD), is a major driver of eukaryote
evolution. Yet WGDs are hugely disruptive mutations, and we still lack a clear understanding …

ZW sex chromosome structure in Amborella trichopoda

SB Carey, L Aközbek, JT Lovell, J Jenkins, AL Healey… - Nature Plants, 2024 - nature.com
Sex chromosomes have evolved hundreds of times across the flowering plant tree of life;
their recent origins in some members of this clade can shed light on the early consequences …

[HTML][HTML] Advances in genomics and genome editing for breeding next generation of fruit and nut crops

S Savadi, S Mangalassery, MS Sandesh - Genomics, 2021 - Elsevier
Fruit tree crops are an essential part of the food production systems and are key to achieve
food and nutrition security. Genetic improvement of fruit trees by conventional breeding has …

[HTML][HTML] Adapting crops for climate change: regaining lost abiotic stress tolerance in crops

M Palmgren, S Shabala - Frontiers in Science, 2024 - frontiersin.org
It is often stated that agricultural outputs need to increase substantially to meet the demands
for more food posed by a growing population. However, when accounting for climate …

Comparative pangenome analyses provide insights into the evolution of Brassica rapa resistance gene analogues (RGAs)

JC Amas, PE Bayer, W Hong Tan… - Plant Biotechnology …, 2023 - Wiley Online Library
Brassica rapa is grown worldwide as economically important vegetable and oilseed crop.
However, its production is challenged by yield‐limiting pathogens. The sustainable control …

[HTML][HTML] Plant pangenomics, current practice and future direction

H Hu, J Wang, S Nie, J Zhao, J Batley… - Agriculture …, 2024 - Elsevier
A pangenome encompasses the complete genetic diversity of a species, by assembling a
range of representative individuals from various populations. This review describes the …