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 …

Natural variation in crops: realized understanding, continuing promise

Y Liang, HJ Liu, J Yan, F Tian - Annual review of plant biology, 2021 - annualreviews.org
Crops feed the world's population and shape human civilization. The improvement of crop
productivity has been ongoing for almost 10,000 years and has evolved from an experience …

Convergent selection of a WD40 protein that enhances grain yield in maize and rice

W Chen, L Chen, X Zhang, N Yang, J Guo, M Wang… - Science, 2022 - science.org
A better understanding of the extent of convergent selection among crops could greatly
improve breeding programs. We found that the quantitative trait locus KRN2 in maize and its …

De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes

MB Hufford, AS Seetharam, MR Woodhouse… - Science, 2021 - science.org
We report de novo genome assemblies, transcriptomes, annotations, and methylomes for
the 26 inbreds that serve as the founders for the maize nested association mapping …

De novo genome assembly and analyses of 12 founder inbred lines provide insights into maize heterosis

B Wang, M Hou, J Shi, L Ku, W Song, C Li, Q Ning… - Nature Genetics, 2023 - nature.com
Hybrid maize displays superior heterosis and contributes over 30% of total worldwide cereal
production. However, the molecular mechanisms of heterosis remain obscure. Here we …

Benchmarking transposable element annotation methods for creation of a streamlined, comprehensive pipeline

S Ou, W Su, Y Liao, K Chougule, JRA Agda… - Genome biology, 2019 - Springer
Background Sequencing technology and assembly algorithms have matured to the point
that high-quality de novo assembly is possible for large, repetitive genomes. Current …

De novo domestication of wild tomato using genome editing

A Zsögön, T Čermák, ER Naves, MM Notini… - Nature …, 2018 - nature.com
Breeding of crops over millennia for yield and productivity has led to reduced genetic
diversity. As a result, beneficial traits of wild species, such as disease resistance and stress …

Stepwise selection on homeologous PRR genes controlling flowering and maturity during soybean domestication

S Lu, L Dong, C Fang, S Liu, L Kong, Q Cheng… - Nature Genetics, 2020 - nature.com
Adaptive changes in plant phenology are often considered to be a feature of the so-called
'domestication syndrome'that distinguishes modern crops from their wild progenitors, but …

Widespread long-range cis-regulatory elements in the maize genome

WA Ricci, Z Lu, L Ji, AP Marand, CL Ethridge… - Nature plants, 2019 - nature.com
Genetic mapping studies on crops suggest that agronomic traits can be controlled by gene–
distal intergenic loci. Despite the biological importance and the potential agronomic utility of …

Teosinte ligule allele narrows plant architecture and enhances high-density maize yields

J Tian, C Wang, J Xia, L Wu, G Xu, W Wu, D Li, W Qin… - Science, 2019 - science.org
Increased planting densities have boosted maize yields. Upright plant architecture facilitates
dense planting. Here, we cloned UPA1 (Upright Plant Architecture1) and UPA2, two …