BSA101: Unlocking Historical Mutant Collections with BSA-Seq
- 1Oregon State University
Abstract
Forward genetics is a powerful approach for gene discovery, but identifying causal mutations becomes difficult when mutants are maintained in heterogeneous populations with uncertain pedigrees. This is exemplified by classical tasselseed (ts) mutants, which have long served as a genetic model for studying sex determination and carpel suppression. Decades of repeated outcrossing to diverse inbred lines have created substantial genetic heterogeneity, limiting the effectiveness of conventional bulked-segregant analysis sequencing (BSA-Seq). To address this, we developed a BSA-Seq framework that integrates flexible experimental designs, multiple reference genomes, and complementary statistical methods tailored for genetically heterogeneous populations. Applying this framework revealed that reference genome selection is critical for mapping success and that Euclidean distance raised to the fourth power (ED4) outperformed homozygosity mapping (HM). Furthermore, the framework enables simultaneous mapping of multiple mutations within a single population, eliminating the need for additional mapping populations. Applying this framework to 26 ts mutant stocks from the Maize Genetics Cooperation Stock Center, we successfully mapped 24 mutants to genomic intervals containing known ts genes, while the remaining mutants mapped to distinct genomic intervals, defining novel candidate regions underlying carpel suppression. Together, these results demonstrate that historical mutant collections represent an underutilized resource for gene discovery and establish a generalizable mapping strategy for unlocking their genetic potential across diverse species.
Related
- Harnessing historical collections to reconstruct the invasion history of Microstegium vimineum (Poaceae)
- Development and Validation of PCR-Based Ancient DNA Analysis for Italian and Western Balkan Archaeological Collections
- Organizing activities with plant genetic resource collections in Russia: stages, challenges, and solutions
- Hidden but Expanding Sampling Bias Distorts Prokaryotic Genome Collections
- Development of Core KASP Marker Panel for DNA Fingerprinting of Pear (Pyrus spp.) Germplasm Collections.
BibTeX
@misc{zebosi2026bsa101,
title = {{BSA101: Unlocking Historical Mutant Collections with BSA-Seq}},
author = {B. Zebosi and C. Bonney Arku and M. Bartlett and S. Leiboff},
howpublished = {bioRxiv},
year = {2026},
month = sep,
doi = {10.64898/2026.09.24.754120},
url = {https://www.biorxiv.org/content/10.64898/2026.09.24.754120v1},
note = {CC BY},
}
RIS
TY - UNPB
TI - BSA101: Unlocking Historical Mutant Collections with BSA-Seq
AU - B. Zebosi
AU - C. Bonney Arku
AU - M. Bartlett
AU - S. Leiboff
PY - 2026
DA - 2026/09/24
PB - bioRxiv
DO - 10.64898/2026.09.24.754120
UR - https://www.biorxiv.org/content/10.64898/2026.09.24.754120v1
AB - Forward genetics is a powerful approach for gene discovery, but identifying causal mutations becomes difficult when mutants are maintained in heterogeneous populations with uncertain pedigrees. This is exemplified by classical tasselseed (ts) mutants, which have long served as a genetic model for studying sex determination and carpel suppression. Decades of repeated outcrossing to diverse inbred lines have created substantial genetic heterogeneity, limiting the effectiveness of conventional bulked-segregant analysis sequencing (BSA-Seq). To address this, we developed a BSA-Seq framework that integrates flexible experimental designs, multiple reference genomes, and complementary statistical methods tailored for genetically heterogeneous populations. Applying this framework revealed that reference genome selection is critical for mapping success and that Euclidean distance raised to the fourth power (ED4) outperformed homozygosity mapping (HM). Furthermore, the framework enables simultaneous mapping of multiple mutations within a single population, eliminating the need for additional mapping populations. Applying this framework to 26 ts mutant stocks from the Maize Genetics Cooperation Stock Center, we successfully mapped 24 mutants to genomic intervals containing known ts genes, while the remaining mutants mapped to distinct genomic intervals, defining novel candidate regions underlying carpel suppression. Together, these results demonstrate that historical mutant collections represent an underutilized resource for gene discovery and establish a generalizable mapping strategy for unlocking their genetic potential across diverse species.
ER -