Article
Trait association and prediction through integrative k-mer analysis.
The Plant journal : for cell and molecular biology - 1 Oct 2024
He Cheng, Washburn Jacob D, Schleif Nathaniel, Hao Yangfan, Kaeppler Heidi, Kaeppler Shawn M, Zhang Zhiwu, Yang Jinliang, Liu Sanzhen
Abstract excerpt
Genome-wide association study (GWAS) with single nucleotide polymorphisms (SNPs) has been widely used to explore genetic controls of phenotypic traits. Alternatively, GWAS can use counts of substrings of length k from longer sequencing reads, k-mers, as genotyping data. Using maize cob and kernel color traits, we demonstrated that k-mer GWAS can effectively identify associated k-mers. Co-expression analysis of...
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