---
title: "Microscale 96-Well Bulk Segregant Analysis Increases X-QTL Throughput"
id: "biorxiv-2-microscale-bulk-segregant-analysis"
canonical_url: "https://medichelpline.com/clinical-feed/biorxiv-2-microscale-bulk-segregant-analysis"
content_type: "clinical_feed_article"
specialty: "General"
source_name: "bioRxiv (Biomedical Preprints)"
source_url: "https://www.biorxiv.org/content/10.64898/2026.10.09.757075v1?rss=1"
published_at: "2026-10-15T12:00:00.000Z"
evidence_level: "Verified Feed"
license: "CC-BY-NC-4.0 / Informational Use"
---
# Microscale 96-Well Bulk Segregant Analysis Increases X-QTL Throughput
## Provenance & Clinical Metadata
- **Canonical URL:** https://medichelpline.com/clinical-feed/biorxiv-2-microscale-bulk-segregant-analysis
- **Specialty:** [General](https://medichelpline.com/clinical-feed/general.md)
- **Primary Source:** bioRxiv (Biomedical Preprints)
- **Source URL:** [Original Journal Publication](https://www.biorxiv.org/content/10.64898/2026.10.09.757075v1?rss=1)
- **Published At:** 2026-10-15T12:00:00.000Z
- **Evidence Rating:** Verified Feed
## Executive GIST (TL;DR)
- The authors implemented a 96-well liquid format for extreme **bulk segregant analysis** (X-QTL) in yeast, enabling parallel processing of many crosses and conditions. - They crossed 40 natural isolates to a common parent engineered with mating-type–specific drug-resistance markers at HO to permit selection of diploids and haploids in 1 mL cultures. - Each well contained a single segregant pool; pools were grown in four conditions: standard glucose medium, glucose plus sodium chloride, glucose plus caffeine, and acetate as the carbon source. - DNA from 384 wells was barcoded and sequenced on a single Illumina NovaSeq X run; 181 segregant pools passed quality-control filters and were analyzed further. - From 35 successful crosses, investigators mapped 1,472 quantitative trait loci (QTL) associated with growth differences across the tested conditions. - The study replicated a subset of QTL previously identified by conventional X-QTL in the same conditions, according to the authors. - The 96-well approach accelerated sample handling and multiplexed sequencing, increasing throughput at every step of X-QTL workflows. - The source linked code, data, and a project page; it reported funding sources but declared no competing interests. - The preprint did not provide additional experimental parameter details beyond those summarized (for example, the source did not report exact quality-control thresholds or the precise sequencing depths per well in the abstract).
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Giancarlo Noe Bruni 1 1 Department of Human Genetics, University of California Los Angeles, Los Angeles, CA,; * [Find this author on Google Scholar](https://www.biorxiv.org/lookup/google-scholar?link_type=googlescholar&gs_type=author&author%5B0%5D=Giancarlo%2BNoe%2BBruni%2B "Open in new tab") * [Find this author on PubMed](https://www.biorxiv.org/lookup/external-ref?access_num=Bruni%20GN&link_type=AUTHORSEARCH "Open in new tab") * [Search for this author on this site](https://www.biorxiv.org/search/author1%3AGiancarlo%2BNoe%2BBruni%2B) * [ORCID record for Giancarlo Noe Bruni](http://orcid.org/0000-0003-2850-4633 "Open in new tab") * For correspondence: gnb.phd@gmail.com Lauren C Crisman 2 1 Department of Human Genetics, University of California Los Angeles, Los Angeles, CA, 2 Howard Hughes Medical Institute, Chevy Chase, MD; * [Find this author on Google Scholar](https://www.biorxiv.org/lookup/google-scholar?link_type=googlescholar&gs_type=author&author%5B0%5D=Lauren%2BC%2BCrisman%2B "Open in new tab") * [Find this author on PubMed](https://www.biorxiv.org/lookup/external-ref?access_num=Crisman%20LC&link_type=AUTHORSEARCH "Open in new tab") * [Search for this author on this site](https://www.biorxiv.org/search/author1%3ALauren%2BC%2BCrisman%2B) * [ORCID record for Lauren C Crisman](http://orcid.org/0000-0001-7851-9652 "Open in new tab") Leslie A Alamo 3 Department of Human Genetics, University of California Los Angeles, Los Angeles, CA * [Find this author on Google Scholar](https://www.biorxiv.org/lookup/google-scholar?link_type=googlescholar&gs_type=author&author%5B0%5D=Leslie%2BA%2BAlamo%2B "Open in new tab") * [Find this author on PubMed](https://www.biorxiv.org/lookup/external-ref?access_num=Alamo%20LA&link_type=AUTHORSEARCH "Open in new tab") * [Search for this author on this site](https://www.biorxiv.org/search/author1%3ALeslie%2BA%2BAlamo%2B) * [ORCID record for Leslie A Alamo](http://orcid.org/0009-0000-0007-1675 "Open in new tab") Heriberto Marquez 2 1 Department of Human Genetics, University of California Los Angeles, Los Angeles, CA, 2 Howard Hughes Medical Institute, Chevy Chase, MD; * [Find this author on Google Scholar](https://www.biorxiv.org/lookup/google-scholar?link_type=googlescholar&gs_type=author&author%5B0%5D=Heriberto%2BMarquez%2B "Open in new tab") * [Find this author on PubMed](https://www.biorxiv.org/lookup/external-ref?access_num=Marquez%20H&link_type=AUTHORSEARCH "Open in new tab") * [Search for this author on this site](https://www.biorxiv.org/search/author1%3AHeriberto%2BMarquez%2B) * [ORCID record for Heriberto Marquez](http://orcid.org/0009-0003-7096-4606 "Open in new tab") James Boocock 3 Department of Human Genetics, University of California Los Angeles, Los Angeles, CA * [Find this author on Google Scholar](https://www.biorxiv.org/lookup/google-scholar?link_type=googlescholar&gs_type=author&author%5B0%5D=James%2BBoocock%2B "Open in new tab") * [Find this author on PubMed](https://www.biorxiv.org/lookup/external-ref?access_num=Boocock%20J&link_type=AUTHORSEARCH "Open in new tab") * [Search for this author on this site](https://www.biorxiv.org/search/author1%3AJames%2BBoocock%2B) * [ORCID record for James Boocock](http://orcid.org/0000-0003-0323-8818 "Open in new tab") Joshua S Bloom 2 1 Department of Human Genetics, University of California Los Angeles, Los Angeles, CA, 2 Howard Hughes Medical Institute, Chevy Chase, MD; * [Find this author on Google Scholar](https://www.biorxiv.org/lookup/google-scholar?link_type=googlescholar&gs_type=author&author%5B0%5D=Joshua%2BS%2BBloom%2B "Open in new tab") * [Find this author on PubMed](https://www.biorxiv.org/lookup/external-ref?access_num=Bloom%20JS&link_type=AUTHORSEARCH "Open in new tab") * [Search for this author on this site](https://www.biorxiv.org/search/author1%3AJoshua%2BS%2BBloom%2B) * [ORCID record for Joshua S Bloom](http://orcid.org/0000-0002-7241-1648 "Open in new tab") Leonid Kruglyak 2 1 Department of Human Genetics, University of California Los Angeles, Los Angeles, CA, 2 Howard Hughes Medical Institute, Chevy Chase, MD; * [Find this author on Google Scholar](https://www.biorxiv.org/lookup/google-scholar?link_type=googlescholar&gs_type=author&author%5B0%5D=Leonid%2BKruglyak%2B "Open in new tab") * [Find this author on PubMed](https://www.biorxiv.org/lookup/external-ref?access_num=Kruglyak%20L&link_type=AUTHORSEARCH "Open in new tab") * [Search for this author on this site](https://www.biorxiv.org/search/author1%3ALeonid%2BKruglyak%2B) * [ORCID record for Leonid Kruglyak](http://orcid.org/0000-0002-8065-3057 "Open in new tab") * [Abstract](https://www.biorxiv.org/content/10.64898/2026.10.09.757075v1)[](https://www.biorxiv.org/panels_ajax_tab/biorxiv_tab_art/node:5872251/1) * [Info/History](https://www.biorxiv.org/content/10.64898/2026.10.09.757075v1.article-info)[](https://www.biorxiv.org/panels_ajax_tab/biorxiv_tab_info/node:5872251/1) * [Metrics](https://www.biorxiv.org/content/10.64898/2026.10.09.757075v1.article-metrics)[](https://www.biorxiv.org/panels_ajax_tab/article_tab_metrics/node:5872251/1) * [Supplementary material](https://www.biorxiv.org/content/10.64898/2026.10.09.757075v1.supplementary-material)[](https://www.biorxiv.org/panels_ajax_tab/biorxiv_tab_data/node:5872251/1) * [Data/Code](https://www.biorxiv.org/content/10.64898/2026.10.09.757075v1.external-links)[](https://www.biorxiv.org/panels_ajax_tab/article_tab_data_code/node:5872251/1) * [ Preview PDF](https://www.biorxiv.org/content/10.64898/2026.10.09.757075v1.full.pdf+html)[](https://www.biorxiv.org/panels_ajax_tab/biorxiv_tab_pdf/node:5872251/1) ![Loading](https://www.biorxiv.org/sites/all/modules/contrib/panels_ajax_tab/images/loading.gif) ## Abstract The traits of an organism depend on its genetic background and environment. Bulk segregant analysis (BSA) maps quantitative trait loci (QTL) by measuring parental allele frequencies in pools of genetically recombined progeny (segregants). Conventional BSA requires laborious separate sample handling for each cross and environmental condition. Here, we describe a 96-well liquid format for extreme QTL mapping (X-QTL) in Saccharomyces cerevisiae. We crossed 40 isolates to a common parent carrying mating-type-specific drug-resistance markers at HO, which enabled us to select diploids and haploid segregants in 1 mL cultures. Each well held one segregant pool, which we then grew in deep wells in four conditions: the standard glucose medium, sodium chloride or caffeine added to the standard medium, or acetate replacing glucose as a carbon source. We barcoded DNA samples from each of 384 wells and sequenced them in one Illumina Nova-seq X run. Sequencing data for 181 segregant pools passed quality control steps and was used to map 1,472 QTL in 35 crosses. We replicated a subset of QTL previously mapped in these growth conditions by conventional X-QTL. The 96-well approach increases the throughput of every step of X-QTL, enabling genetic analysis of many more cross and conditions. ### Competing Interest Statement The authors have declared no competing interest. ## Footnotes * * * ## Funder Information Declared Howard Hughes Medical Institute, https://ror.org/006w34k90 NIH Common Fund, https://ror.org/001d55x84, 2RO1GM102308 Copyright The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a [CC-BY-NC 4.0 International license](http://creativecommons.org/licenses/by-nc/4.0/). bioRxiv and medRxiv thank the following for their generous financial support: > The Chan Zuckerberg Initiative, Cold Spring Harbor Laboratory, the Sergey Brin Family Foundation, California Institute of Technology, Centre National de la Recherche Scientifique, Fred Hutchinson Cancer Center, Imperial College London, Massachusetts Institute of Technology, Stanford University, The University of Edinburgh, University of Washington, and Vrije Universiteit Amsterdam. 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[ Download PDF](https://www.biorxiv.org/content/10.64898/2026.10.09.757075v1.full.pdf) Print/Save Options [Download PDF](https://www.biorxiv.org/content/biorxiv/early/2026/10/15/2026.10.09.757075.full.pdf)Full Text & In-line FiguresXML [More Info](https://www.biorxiv.org/about/FAQ#PrintOptions "More Information on Print/Save Options") [Supplementary Material ](https://www.biorxiv.org/content/10.64898/2026.10.09.757075v1.supplementary-material) [ Data/Code](https://www.biorxiv.org/content/early/2026/10/15/2026.10.09.757075.external-links) [ Email](https://www.biorxiv.org/ "Email this Article") [ Share](https://www.biorxiv.org/) Microscale bulk segregant analysis Giancarlo Noe Bruni, Lauren C Crisman, Leslie A Alamo, Heriberto Marquez, James Boocock, Joshua S Bloom, Leonid Kruglyak bioRxiv 2026.10.09.757075; doi: https://doi.org/10.64898/2026.10.09.757075 This article is a preprint and has not been certified by peer review [[what does this mean?](https://www.biorxiv.org/about/FAQ#unrefereed)]. 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