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Enhancing tiny millets through genome editing: current status and future prospects

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Micheale Yifter Yifter Weldemichael at Mekelle University
Micheale Yifter Yifter Weldemichael
Hailay Mehari at Mekelle University
Hailay Mehari
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Abstract

This study aims to address the critical need for genetic improvement of small millets, which are vital yet underutilized cereal crops cultivated in semi-arid regions of Africa and Asia. Given their high nutritional value and climate resilience, small millets hold significant potential for food security and sustainable agriculture in arid regions. However, traditional breeding methods have proven to be time-consuming and inefficient in enhancing desirable traits. This study highlights the transformative potential of genome editing technologies, particularly the CRISPR/Cas9 system, in accelerating the development of improved small millet varieties. The findings presented in this paper detail recent advancements in using CRISPR/Cas for enhancing resistance to biotic stresses, including bacterial, viral, and fungal pathogens. Additionally, we explore how genome editing can be applied to improve abiotic stress tolerance, addressing challenges such as drought, cold, heat, and herbicides in small millets. We discuss the existing challenges faced by breeders, including issues related to ploidy levels, off-target effects, and limitations in organelle genome modification. The review also suggests potential strategies for overcoming these bottlenecks, aiming to develop stress-resistant super cultivars. Overall, this paper provides an overview of the current state of genome editing research in small millets while identifying future opportunities to enhance key traits for nutrient enrichment and climate resilience, ultimately paving the way for advancements in these crucial crops.
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Vol.:(0123456789)
Molecular Genetics and Genomics (2025) 300:22
https://doi.org/10.1007/s00438-025-02231-z
REVIEW
Enhancing tiny millets throughgenome editing: current status
andfuture prospects
MichealeYifterWeldemichael1 · HailayMehariGebremedhn1
Received: 2 September 2024 / Accepted: 5 February 2025
© The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature 2025
Abstract
This study aims to address the critical need for genetic improvement of small millets, which are vital yet underutilized cereal
crops cultivated in semi-arid regions of Africa and Asia. Given their high nutritional value and climate resilience, small
millets hold significant potential for food security and sustainable agriculture in arid regions. However, traditional breeding
methods have proven to be time-consuming and inefficient in enhancing desirable traits. This study highlights the transforma-
tive potential of genome editing technologies, particularly the CRISPR/Cas9 system, in accelerating the development of
improved small millet varieties. The findings presented in this paper detail recent advancements in using CRISPR/Cas for
enhancing resistance to biotic stresses, including bacterial, viral, and fungal pathogens. Additionally, we explore how genome
editing can be applied to improve abiotic stress tolerance, addressing challenges such as drought, cold, heat, and herbicides
in small millets. We discuss the existing challenges faced by breeders, including issues related to ploidy levels, off-target
effects, and limitations in organelle genome modification. The review also suggests potential strategies for overcoming these
bottlenecks, aiming to develop stress-resistant super cultivars. Overall, this paper provides an overview of the current state of
genome editing research in small millets while identifying future opportunities to enhance key traits for nutrient enrichment
and climate resilience, ultimately paving the way for advancements in these crucial crops.
Keywords Biotic and abiotic stresses· CRISPR/Cas9· Functional genomics· Gene editing· Small millet
Introduction
Millets, belonging to the "Poaceae" family, are crucial
food crops primarily cultivated in the semi-arid tropics of
Africa and Asia. Their remarkable ability to thrive under
challenging environmental conditions with limited rain-
fall, poor soil quality, and frequent droughts makes them
vital source of food and feed, particularly in drought-prone
areas (Sapara etal. 2024). Millets significantly contribute
to nutrient security and serve as a staple food source for
populations in desert and arid areas (Ceasar 2022). Foxtail
millet (Setaria italica), pearl millet (Pennisetum glaucum),
kodo millet (Paspalum scrobiculatum), finger millet (Eleu-
sine coracana), proso millet (Panicum miliaceum), barnyard
millet (Echinochloa frumentacea), and little millet (Panicum
sumatrense) are among the most commonly grown millet
species. Despite their importance, the genetic and genomic
research on millets has lagged behind that of major cere-
als like rice (Antony Ceasar etal. 2018). However, the
recent publication of millet genome sequences has sparked
renewed interest, driven by their high nutrient content and
resilience to climate change, which have garnered attention
from researchers globally (Vetriventhan etal. 2020). Their
adaptability to a range of habitats, reduced water demands,
andreduced vulnerability to diseases and pests underscore
their value as climate-resilient crops(Saxena etal. 2018).
In the current era of advanced plant genetic research,
genome editing has emerged as transformative tool to
enhance the valuable traits of millets. The CRISPR (clus-
tered regularly interspaced palindromic repeats) and
CRISPR-associated protein 9 (Cas9), a recent Nobel Prize-
winning technology, has revolutionized genome editing by
Communicated by Bing Yang.
* Micheale Yifter Weldemichael
y.mickye@gmail.com
Hailay Mehari Gebremedhn
micheale.yifter1@mu.edu.et
1 Department ofBiotechnology, College ofDryland
Agriculture andNatural Resources, Mekelle University, P.O.
Box231, Mekelle, Tigrai, Ethiopia
Content courtesy of Springer Nature, terms of use apply. Rights reserved.
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