Pan-genomics in the human genome era

RM Sherman, SL Salzberg - Nature Reviews Genetics, 2020 - nature.com
Since the early days of the genome era, the scientific community has relied on a single
'reference'genome for each species, which is used as the basis for a wide range of genetic …

Evolution of plant genome architecture

JF Wendel, SA Jackson, BC Meyers, RA Wing - Genome biology, 2016 - Springer
We have witnessed an explosion in our understanding of the evolution and structure of plant
genomes in recent years. Here, we highlight three important emergent realizations:(1) that …

A complete telomere-to-telomere assembly of the maize genome

J Chen, Z Wang, K Tan, W Huang, J Shi, T Li, J Hu… - Nature …, 2023 - nature.com
A complete telomere-to-telomere (T2T) finished genome has been the long pursuit of
genomic research. Through generating deep coverage ultralong Oxford Nanopore …

Insights into the maize pan-genome and pan-transcriptome

CN Hirsch, JM Foerster, JM Johnson, RS Sekhon… - The Plant …, 2014 - academic.oup.com
Genomes at the species level are dynamic, with genes present in every individual (core) and
genes in a subset of individuals (dispensable) that collectively constitute the pan-genome …

Switchgrass genomic diversity, ploidy, and evolution: novel insights from a network-based SNP discovery protocol

F Lu, AE Lipka, J Glaubitz, R Elshire, JH Cherney… - PLoS …, 2013 - journals.plos.org
Switchgrass (Panicum virgatum L.) is a perennial grass that has been designated as an
herbaceous model biofuel crop for the United States of America. To facilitate accelerated …

Genotyping‐by‐sequencing approaches to characterize crop genomes: choosing the right tool for the right application

A Scheben, J Batley, D Edwards - Plant biotechnology journal, 2017 - Wiley Online Library
In the last decade, the revolution in sequencing technologies has deeply impacted crop
genotyping practice. New methods allowing rapid, high‐throughput genotyping of entire …

Enhancing genetic gain in the era of molecular breeding

Y Xu, P Li, C Zou, Y Lu, C Xie, X Zhang… - Journal of …, 2017 - academic.oup.com
As one of the important concepts in conventional quantitative genetics and breeding, genetic
gain can be defined as the amount of increase in performance that is achieved annually …

Doubling down on genomes: polyploidy and crop plants

S Renny‐Byfield, JF Wendel - American journal of botany, 2014 - Wiley Online Library
Polyploidy, or whole genome multiplication, is ubiquitous among angiosperms. Many crop
species are relatively recent allopolyploids, resulting from interspecific hybridization and …

Progress toward understanding heterosis in crop plants

PS Schnable, NM Springer - Annual review of plant biology, 2013 - annualreviews.org
Although heterosis, or hybrid vigor, is widely exploited in agriculture, a complete description
of its molecular underpinnings has remained elusive despite extensive investigation. It …

RNA sequencing of laser-capture microdissected compartments of the maize kernel identifies regulatory modules associated with endosperm cell differentiation

J Zhan, D Thakare, C Ma, A Lloyd, NM Nixon… - The Plant …, 2015 - academic.oup.com
Endosperm is an absorptive structure that supports embryo development or seedling
germination in angiosperms. The endosperm of cereals is a main source of food, feed, and …