# Empowering functional genomics of An. gambiae through inversion genotyping

> **NIH NIH R01** · UNIVERSITY OF NOTRE DAME · 2020 · $486,262

## Abstract

In Africa, where Anopheles gambiae is the primary vector, the intensity of transmission and the spread of
resistance in parasite and vector populations pose major challenges to malaria control. New insecticides and
novel vector control strategies complementary to existing ones are badly needed. Foundational genomic
resources for novel vector-based strategies are newly available for An. gambiae. Together, they enable
detailed population genomics and genome-wide association studies (GWAS) aimed at understanding the
genetic basis of epidemiologically important traits. However, An. gambiae is highly polymorphic for
chromosomal inversions. Failing to account for inversions can mislead population genetic and genome-wide
association studies and obscure relationships between inversions and epidemiologically relevant traits. Yet
despite rapid advances in genome technology, cytogenetic determination of inversion status is the only method
currently available. Inversion status is not obvious from genome re-sequencing data, as alleles are mapped to
their position on a reference genome and not to their actual physical locations. Unfortunately, cytogenetic
analysis is impractical or even prohibitive. Addressing this gap, the central goal of this R01 is to develop and
validate computational and molecular inversion genotyping approaches, enabling a modern assessment of the
association between inversions and epidemiologically relevant traits. Toward this end, we propose three
specific Aims: (1) Develop a computational karyotyping approach applicable to SNP genotype data. Our
preliminary data for two inversions, based on existing Ag1000G sequences, indicates that there are SNPs that
can serve as surrogate markers for alternative orientations. Using field-collected mosquitoes of known
karyotype and with sequencing support from Ag1000G, we will validate these results on wider geographic
samples and extend them to additional inversions. (2) Develop a molecular karyotyping approach applicable
without sequencing. Using an existing battery of karyotyped samples, we will develop simple and rapid
molecular assays that eliminate the need to PCR amplify across variable breakpoint regions, and are
accessible to any lab. (3) Assess the association between karyotype and malariologically important parameters.
Leveraging existing An. gambiae samples, we will apply our computational and molecular karyotyping methods
to test for a relationship between karyotype, indoor resting behavior, and parasite rate. Together, these tools
will empower efforts to map and monitor epidemiologically important traits in vector populations.

## Key facts

- **NIH application ID:** 9852972
- **Project number:** 5R01AI125360-04
- **Recipient organization:** UNIVERSITY OF NOTRE DAME
- **Principal Investigator:** Nora Jessie Besansky
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $486,262
- **Award type:** 5
- **Project period:** 2017-02-14 → 2022-01-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/9852972

## Citation

> US National Institutes of Health, RePORTER application 9852972, Empowering functional genomics of An. gambiae through inversion genotyping (5R01AI125360-04). Retrieved via AI Analytics 2026-05-23 from https://api.ai-analytics.org/grant/nih/9852972. Licensed CC0.

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