TRPLSC 1600 No.
of Pages 3
Spotlight
Pearl Millet Genome:
Lessons from a
Tough Crop
Marilyne Debieu,1,2
Ghislain Kanfany,2,3 and
Laurent Laplaze1,2,4,*
Pearl millet is an important cereal
for food security in the arid regions
of Africa and India. The recently
published genome of this tough
cereal crop has shed new light
on its history and adaptation to
dry, hot climates and paves the
way for much-needed genomic-
based breeding efforts.
The world’s human population is
expected to reach 9.1 billion by 2050.
Given that most models predict that cli-
mate change will have a negative impact
on agricultural yields, particularly in Africa
[1], new breeding strategies and adaptive
agronomical practices are needed to face
the future increase in food demand result-
ing from this expanding population.
Pearl millet (Pennisetum glaucum L.) is the
sixth cereal in terms of world production
and has a central role in food security in
arid areas of sub-Saharan Africa and India
with limited agronomic potential where
other crops would fail. In these areas, it
is the staple crop for an estimated 90
million small farmers because it repre-
sents a cheap source of essential micro-
nutrients (such as iron and zinc) and
proteins, as well as an important source
of fodder for cattle and other animals.
Nevertheless, pearl millet yields are low
and it is considered to be an orphan crop
because it lags well behind other cereals
in terms of associated research and
genetic improvement.
Pearl millet is a C4 crop that was domes-
ticated approximately 4500 years ago in
West Africa and it is well adapted to biotic are autogamous crops. In such crops,
and abiotic stresses. Moreover, some
wild pearl millet strains can survive in
purifying selection may contribute to the
elimination of TE (Figure 1B). Experimen-
extreme environments (up to the limit of tal validations are needed to confirm
the Sahara desert) and, therefore, repre-
sent an interesting resource for allele min-
those hypotheses among diploid plant
species.
ing. Thus, pearl millet is an interesting
biological model to understand the adap- By combining transcriptome data and
tation of cereals to dry, hot climates. bioinformatics analyses, Varshney et al.
[2] predicted that the pearl millet genome
As part of an international effort tocontains 38 579 genes. Interestingly,
comparison of gene families with other
increase genetic gain in pearl millet,
cereal genomes revealed a strong enrich-
Varshney et al. [2] sequenced and ana-
lyzed the genome of a reference geno-ment in gene families involved in cutin,
suberin, and wax biosynthesis. The cuti-
type. The good-quality genome sequence
cle is known to be important in protecting
of the reference line revealed interesting
plants from excessive water loss [5] and
features. First, the 1.79-GB pearl millet
genome is characterized by a high GC constitutes a barrier to pathogen infec-
content (47.9%). Increased GC contenttion. Below ground, drought can enhance
root suberization, especially in the endo-
has been associated with desiccation tol-
dermis [6]. In this layer, the Casparian
erance in monocots [3], suggesting that
strip and suberin lamellae may prevent
this genome characteristic contributes to
water loss and desiccation of inner tis-
the adaption of pearl millet to dry environ-
ments. Moreover, 80% of the genome sues. The ABC transporter gene families
were also significantly expanded in pearl
comprises repetitive elements, a propor-
millet (Figure 1A). ABC transporters are
tion similar to that in the maize (Zea mays)
involved in the transport of a range of
genome (>85%) but higher than in other
secondary metabolites, including some
cereals, such as sorghum (61%), foxtail
cuticle components. ABC transporters
millet (46%), or rice (42%). Transpos-
able [29_TD$IF]elements (TEs) can induce are also involved in pathogen response,
mutations and have been proposed to phytate accumulation in seeds, root exu-
confer a higher adaptive potential to their dation, and transport of the phytohor-
host. In maize, TEs contribute to the acti- mones auxin and abscisic acid (ABA)
vation of genes in response to abiotic [7]. The latter might be relevant for the
[30_TD$IF]stresses [4]. TE insertions can generate
adaptation of pearl millet to arid climates
because it has been shown that ABA
genetic and epigenetic variation favored
exudation from roots contributes to
by natural and artificial selection and,
thus, contribute to adaptation and enhanced drought tolerance in rice [8].
Thus, expansion of the cutin, suberin,
domestication. From an evolutionary per-
and wax biosynthesis and ABC transport-
spective, the mating system may have an
ers families could reflect an increase in,
important role in governing TE evolution,
and refinement of (via sub- [31_TD$IF]28or neofunc-
as predicted by theoretical models. The
genomes of the highly allogamous crops
tionalization of duplicated genes), physio-
pearl millet and maize are TE rich. In such
logical roles associated with them and
species, outcrossing and recombination
might have contributed to pearl millet
may compensate for deleterious muta- adaptation to drought and heat stress.
tions resulting from TE insertions and
Clearly, more work is needed to test these
allow the spread of repetitive elements
exciting hypotheses.
throughout the species, increasing the
genomic TE content. By contrast, species Varshney et al. [2] also resequenced 994
such as foxtail millet and rice, whose pearl millet lines, including 31 wild acces-
genomes comprise less than 50% TE, sions. This provides new information on
Trends in Plant Science, Month Year, Vol. xx, No. yy 1
 TRPLSC 1600 No. of Pages 3

pearl millet diversity and domestication.

Comparison of the cultivated and wild
accessions established that pearl millet
domestication occurred in central West
Africa (East Mali and Niger), as suggested
by previous studies [9]. Comparison of
diversity loss between cultivated and wild
plants also revealed genomic regions that
might have been instrumental in the
developmental changes associated with
domestication. For instance, the genomic
region containing the PINOID gene in
pearl millet showed a tenfold reduction
in diversity, suggesting that it has been
actively selected. Interestingly, a maize
ortholog of PINOID (bif2) involved in
changes in inflorescence development
was probably the target of selection dur-
ing maize domestication [10]. This analy-
sis also provided essential resources for
genetic investigations (simple sequence
repeats, single nucleotide polymor-
phisms, indels, etc.) such as genome-
wide association studies, which identified
1054 significant associations for 15 agro-
morphological traits [2]. These data were
also used for accurate prediction of grain
yield in crosses (genomic selection) and to
identify potential parents to create high-
yield hybrids.

This new wealth of genomic resources in

pearl millet opens many avenues for
future research. First, it will facilitate gene
discovery in one of the toughest cereal
crops. This will require the development
of functional genomic tools, such as gene
editing or tilling populations. Most impor-
tantly, these results pave the way for a
new era of genomic-based breeding in
pearl millet. Its genetic diversity is large
and could be used to create varieties
combining high yield, improved nutritional
qualities, and resilience to abiotic and
Figure 1. Pearl Millet Features Likely Associated with Drought and Heat Adaptation Revealed by
biotic stresses, which will require a large
the Analysis of the Reference Genome Sequence of this Tough Crop. (A) (i) Transverse section of
pearl millet leave. Wax and cutin of cuticle are shown in brown and the ABC transporters in blue; m, mesophyll; phenotyping effort to fully characterize
ue, upper epidermis; le, lower epidermis; st, stoma; v, vessels (including phloem and xylem); cw, cell wall; pm, and exploit the available diversity (includ-
plasma membrane. (ii) Transverse section of a mature pearl millet crown root. Suberized endodermis and ing wild pearl millets). Together, these
sclerenchyma are shown in red. Cellular location of Casparian strip and suberin lamellae as well as ABC
approaches could be used to adapt agri-
transporters (in blue) are shown; rh, root hair; e, epidermis; c, cortex; s, stele; mx, metaxylem vessel; px,
peripheric xylem vessel. (B) Illustration of genomic features of five diploid cereals differing in matting system and cultural crops and practices to future
transposable element (TE) content. According to theoretical models, outcrossing and recombination may allow climates in arid and semiarid regions of
TEs to spread throughout the species and increase the genomic TE content. Africa, and to increase food security as

2 Trends in Plant Science, Month Year, Vol. xx, No. yy

 TRPLSC 1600 No. of Pages 3
well as economic development in some of
the poorest areas of the world.
Acknowledgments
We thank Daniel Moukouanga for providing us with
the image of a transversal section of a pearl millet root
used to draw Figure 1. We also thank Alexandre
Grondin, Yves Vigouroux, Soazig Guyomarc’h, Ndjido
Kane, and Vincent Vadez for their critical comments
on our manuscript. M.D. is supported by the New-
Pearl grant funded in the frame of the CERES initiative

by Agropolis Fondation (N AF 1301-015 to LL, as
part of the ‘Investissement d’Avenir’ ANR-l0-LABX-
0001-0l) and by Fondazione Cariplo (N FC 2013-
0891).
1
Institut de Recherche pour le Développement, UMR
Diversité Adaptation et Développement des Plantes
(DIADE), 911 Avenue Agropolis, 34394 Montpellier cedex
5, France
2
Laboratoire Mixte International Adaptation des Plantes et
Microorganismes Associés aux Stress Environnementaux
(LAPSE), Centre de Recherche de Bel Air, BP 1386,
Dakar, Senegal
3 tribute to activation of maize genes in response to abiotic
Centre d’Etudes Régional pour l’Amélioration de
l’Adaptation à la Sècheresse (CERAAS), Institut
Sénégalais de Recherches Agricoles, BP 3320, Route de
Khombole, Thiès, Senegal
4
Laboratoire Commun de Microbiologie IRD/ISRA/UCAD,
Centre de Recherche de Bel Air, BP 1386, Dakar, Senegal
*Correspondence: Laurent.laplaze@ird.fr (L. Laplaze).
http://dx.doi.org/10.1016/j.tplants.2017.09.006
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