Deciphering Pleiotropic Signatures of Regulatory SNPs in Zea mays L. Using Multi-Omics Data and Machine Learning Algorithms

A Haleem, S Klees, AO Schmitt, M Gültas - International Journal of …, 2022 - mdpi.com
Maize is one of the most widely grown cereals in the world. However, to address the
challenges in maize breeding arising from climatic anomalies, there is a need for developing …

In Silico Identification of the Complex Interplay between Regulatory SNPs, Transcription Factors, and Their Related Genes in Brassica napus L. Using Multi-Omics …

S Klees, TM Lange, H Bertram, A Rajavel… - International journal of …, 2021 - mdpi.com
Regulatory SNPs (rSNPs) are a special class of SNPs which have a high potential to affect
the phenotype due to their impact on DNA-binding of transcription factors (TFs). Thus, the …

Transcriptome-Wide Association Supplements Genome-Wide Association in Zea mays

KAG Kremling, CH Diepenbrock… - G3: Genes …, 2019 - academic.oup.com
Modern improvement of complex traits in agricultural species relies on successful
associations of heritable molecular variation with observable phenotypes. Historically, this …

Elucidating the patterns of pleiotropy and its biological relevance in maize

M Khaipho-Burch, T Ferebee, A Giri, G Ramstein… - PLoS …, 2023 - journals.plos.org
Pleiotropy—when a single gene controls two or more seemingly unrelated traits—has been
shown to impact genes with effects on flowering time, leaf architecture, and inflorescence …

Transcriptome reveals allele contribution to heterosis in maize

J Wu, D Sun, Q Zhao, H Yong, D Zhang… - Frontiers in Plant …, 2021 - frontiersin.org
Heterosis, which has greatly increased maize yields, is associated with gene expression
patterns during key developmental stages that enhance hybrid phenotypes relative to …

Advancements and prospects of genome-wide association studies (GWAS) in maize

JH Sahito, H Zhang, ZGN Gishkori, C Ma… - International Journal of …, 2024 - mdpi.com
Genome-wide association studies (GWAS) have emerged as a powerful tool for unraveling
intricate genotype–phenotype association across various species. Maize (Zea mays L.) …

MaizeNet: a co‐functional network for network‐assisted systems genetics in Zea mays

T Lee, S Lee, S Yang, I Lee - The Plant Journal, 2019 - Wiley Online Library
Maize (Zea mays) has multiple uses in human food, animal fodder, starch and sweetener
production and as a biofuel, and is accordingly the most extensively cultivated cereal …

Multi-trait genome-wide association studies reveal loci associated with maize inflorescence and leaf architecture

BR Rice, SB Fernandes, AE Lipka - Plant and Cell Physiology, 2020 - academic.oup.com
Maize inflorescence is a complex phenotype that involves the physical and developmental
interplay of multiple traits. Given the evidence that genes could pleiotropically contribute to …

Phenomic data-driven biological prediction of maize through field-based high-throughput phenotyping integration with genomic data

A Adak, M Kang, SL Anderson… - Journal of …, 2023 - academic.oup.com
High-throughput phenotyping (HTP) has expanded the dimensionality of data in plant
research; however, HTP has resulted in few novel biological discoveries to date. Field …

Structural variants contribute to phenotypic variation in maize

NS Catlin, HI Agha, AE Platts, M Munasinghe… - bioRxiv, 2024 - biorxiv.org
Comprehensively identifying the loci shaping trait variation has been challenging, in part
because standard approaches often miss many types of genetic variants. Structural variants …