# Application of Exon Primed Intron Crossing Markers to Cross‐Amplify Oreochromis Species in Eastern Africa

## TL;DR

Researchers developed genetic markers to study and conserve fish species in Eastern Africa, finding they can track genetic diversity and help with conservation efforts.

## Contribution

The study introduces 50 EPIC markers for Oreochromis species, demonstrating their effectiveness in cross-amplification and biodiversity monitoring.

## Key findings

- 45 out of 50 EPIC markers successfully cross-amplified across four Oreochromis species.
- Oreochromis niloticus showed the highest genetic diversity compared to other species.
- AMOVA results confirmed significant genetic differentiation among species.

## Abstract

Oreochromis species are of economic importance in fisheries and aquaculture but threatened by human‐mediated activities. Effective conservation and their sustainable management require genetic monitoring tools that can assess genetic variation across species. Various neutral markers have been used to monitor biodiversity in organisms, but they are limited in cross‐amplification among various taxa. Non‐neutral markers such as Exon‐Primed Intron Crossing (EPIC) not only cross amplify various taxa but also target gene regions that are likely to be involved in adaptive responses to selective pressure. This study therefore developed 50 EPIC markers from
Oreochromis niloticus
reference genome targeting immune related genes to assess their potential to cross‐amplify Oreochromis species. Genetic diversity, population structure, and differentiation was measured among
Oreochromis niloticus, O. jipe, O. esculentus and O. leucostictius species and their respective populations from eleven African water bodies and two aquaculture farms. 45 EPIC markers successfully amplified target regions across the four Oreochromis species.
O. niloticus
exhibited the highest diversity (He = 0.50), followed by
O. jipe
(He = 0.29),
O. leucostictus
(He =0.28) and
O. esculentus
with the lowest (He = 0.25). The highest differentiation values were observed among populations of different species while the lowest was among farmed
O. niloticus
. This was supported by AMOVA results that showed highest genetic differentiation among species. Population structure analyses were concordant with species boundaries while showing detailed intraspecific clustering patterns among the
O. niloticus
populations that reflected geographical origin. The observed genetic diversity, gene flow, and population differentiation confirms the applicability of EPIC markers as molecular tools for monitoring biodiversity and guiding the conservation of Oreochromis species under increasing anthropogenic and environmental pressures.

This study developed 50 exon‐primed intron‐crossing (EPIC) markers in Oreochromis niloticus to assess their cross‐amplification potential in four Oreochromis species. Forty‐five markers successfully amplified across species, revealing significant genetic differentiation among species and populations. These findings demonstrate the utility of EPIC markers for monitoring genetic diversity and informing conservation of Oreochromis species under anthropogenic and environmental pressures.