Multiple maize reference genomes impact the identification of variants by genome‐wide association study in a diverse inbred panel

JL Gage, B Vaillancourt, JP Hamilton… - The plant …, 2019 - Wiley Online Library
Use of a single reference genome for genome‐wide association studies (GWAS) limits the
gene space represented to that of a single accession. This limitation can complicate …

Extreme‐phenotype genome‐wide association study (XP‐GWAS): a method for identifying trait‐associated variants by sequencing pools of individuals selected from a …

J Yang, H Jiang, CT Yeh, J Yu, JA Jeddeloh… - The Plant …, 2015 - Wiley Online Library
Although approaches for performing genome‐wide association studies (GWAS) are well
developed, conventional GWAS requires high‐density genotyping of large numbers of …

Complementation contributes to transcriptome complexity in maize (Zea mays L.) hybrids relative to their inbred parents

A Paschold, Y Jia, C Marcon, S Lund… - Genome …, 2012 - genome.cshlp.org
Typically, F1-hybrids are more vigorous than their homozygous, genetically distinct parents,
a phenomenon known as heterosis. In the present study, the transcriptomes of the reciprocal …

Genome-wide association studies in maize: praise and stargaze

Y Xiao, H Liu, L Wu, M Warburton, J Yan - Molecular plant, 2017 - cell.com
Genome-wide association study (GWAS) has become a widely accepted strategy for
decoding genotype-phenotype associations in many species thanks to advances in next …

Development of highly polymorphic SNP markers from the complexity reduced portion of maize [Zea mays L.] genome for use in marker-assisted breeding

JA Mammadov, W Chen, R Ren, R Pai… - Theoretical and applied …, 2010 - Springer
The duplicated and the highly repetitive nature of the maize genome has historically
impeded the development of true single nucleotide polymorphism (SNP) markers in this …

RNA-seq based analysis of population structure within the maize inbred B73

Z Liang, JC Schnable - PloS one, 2016 - journals.plos.org
Recent reports have shown than many identically named genetic lines used in research
around the world actually contain large amounts of uncharacterized genetic variation as a …

Association mapping across a multitude of traits collected in diverse environments in maize

RV Mural, G Sun, M Grzybowski, MC Tross, H Jin… - …, 2022 - academic.oup.com
Classical genetic studies have identified many cases of pleiotropy where mutations in
individual genes alter many different phenotypes. Quantitative genetic studies of natural …

A common resequencing‐based genetic marker data set for global maize diversity

MW Grzybowski, RV Mural, G Xu, J Turkus… - The Plant …, 2023 - Wiley Online Library
Maize (Zea mays ssp. mays) populations exhibit vast ranges of genetic and phenotypic
diversity. As sequencing costs have declined, an increasing number of projects have sought …

Genes identified by visible mutant phenotypes show increased bias toward one of two subgenomes of maize

JC Schnable, M Freeling - PloS one, 2011 - journals.plos.org
Not all genes are created equal. Despite being supported by sequence conservation and
expression data, knockout homozygotes of many genes show no visible effects, at least …

[HTML][HTML] Genome–phenome wide association in maize and arabidopsis identifies a common molecular and evolutionary signature

Z Liang, Y Qiu, JC Schnable - Molecular plant, 2020 - cell.com
Linking natural genetic variation to trait variation can help determine the functional roles
ofdifferent genes. Variations of one or several traits are often assessed separately. High …