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Eberly College of Arts and Sciences




Forward genetics remains a powerful method for revealing the genes underpinning organismal form and function, and for revealing how these genes are tied together in gene networks. In maize, forward genetics has been tremendously successful, but the size and complexity of the maize genome made identifying mutant genes an often arduous process with traditional methods. The next generation sequencing revolution has allowed for the gene cloning process to be significantly accelerated in many organisms, even when genomes are large and complex. Here, we describe a bulked-segregant analysis sequencing (BSA-Seq) protocol for cloning mutant genes in maize. Our simple strategy can be used to quickly identify a mapping interval and candidate single nucleotide polymorphisms (SNPs) from whole genome sequencing of pooled F2 individuals. We employed this strategy to identify narrow odd dwarf as an enhancer of teosinte branched1, and to identify a new allele of defective kernel1. Our method provides a quick, simple way to clone genes in maize.

Source Citation

Klein, H., Xiao, Y., Conklin, P. A., Govindarajulu, R., Kelly, J. A., Scanlon, M. J., Whipple, C. J., & Bartlett, M. (2018). Bulked-Segregant Analysis Coupled to Whole Genome Sequencing (BSA-Seq) for Rapid Gene Cloning in Maize. G3: Genes|Genomes|Genetics, 8(11), 3583–3592.


Copyright © 2018 Klein et al. doi: Manuscript received June 13, 2018; accepted for publication September 5, 2018; published Early Online September 7, 2018. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International License ( licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Supplemental material available at Figshare:


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