Plant pan-genomes are the new reference

PE Bayer, AA Golicz, A Scheben, J Batley, D Edwards - Nature plants, 2020 - nature.com
genomic basis of traits; for example, the wheat rust resistance gene Lr49 shows significant
structural variation … such that we can start to connect pan-genomes on the genus or even the …

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 …

Multi-parent populations in crops: a toolbox integrating genomics and genetic mapping with breeding

MF Scott, O Ladejobi, S Amer, AR Bentley, J Biernaskie… - Heredity, 2020 - nature.com
… dissection of complex traits and support modern plant breeding. … ) may have a physiological
connection causing them to be … genetic variation (including structural variation) and gene

Genomic architectural variation of plant mitochondria—A review of multichromosomal structuring

ZQ Wu, XZ Liao, XN Zhang… - … of Systematics and …, 2022 - Wiley Online Library
… transfer to the nuclear genome, and genome structural variation and … complex features of
plant mt genomes, the number of finished mt genomes from plants is far fewer than that of plant

Combined GWAS and eQTL analysis uncovers a genetic regulatory network orchestrating the initiation of secondary cell wall development in cotton

Z Li, P Wang, C You, J Yu, X Zhang, F Yan… - New …, 2020 - Wiley Online Library
… for cell wall biosynthesis, which controls the trait of fibre length. This study opens the way
for linking regulatory variants to gene transcription in cotton fibre development and provides a …

Discovery of beneficial haplotypes for complex traits in maize landraces

M Mayer, AC Hölker, E González-Segovia… - Nature …, 2020 - nature.com
… landraces is successful in linking molecular variation to meaningful phenotypes, and in
identifying alleles for quantitative traits that will enrich the genetic diversity of our crops. …

Intraspecific trait variation in plants: a renewed focus on its role in ecological processes

AC Westerband, JL Funk, KE Barton - Annals of botany, 2021 - academic.oup.com
… Despite this recent interest, still lacking are thorough descriptions of ITV’s extent, the spatial
and temporal structure of ITV, and stronger connections between ITV and community and …

The landscape of gene–CDS–haplotype diversity in rice: Properties, population organization, footprints of domestication and breeding, and implications for genetic …

F Zhang, C Wang, M Li, Y Cui, Y Shi, Z Wu, Z Hu… - Molecular plant, 2021 - cell.com
… for the detection of causal genes that affect complex traits. The rice gcHap diversity dataset
… -joining phylogenetic tree showing the relationships between the 18 AA-genome wild rice …

A high-quality chromosome-level genome assembly reveals genetics for important traits in eggplant

Q Wei, J Wang, W Wang, T Hu, H Hu… - Horticulture …, 2020 - academic.oup.com
genomes identified three types of variations, including single-nucleotide polymorphisms (SNPs),
insertions/deletions (indels) and structural variants (… points were connected to construct …

A large‐scale genomic association analysis identifies the candidate causal genes conferring stripe rust resistance under multiple field environments

J Wu, R Yu, H Wang, C Zhou, S Huang… - Plant biotechnology …, 2021 - Wiley Online Library
… that underlie agronomic traits directly from GWAS results remains difficult. First, population
genetic structure can limit the detection of rare allele variants and occasionally generate false …