ll Molecular Plant
Review articleRedesigning crop varieties to win the race
between climate change and food security
Kevin V. Pixley1,*, Jill E. Cairns2, Santiago Lopez-Ridaura1, Chris O. Ojiewo3,
Maryam Abba Dawud4, Inoussa Drabo5, Taye Mindaye6, Baloua Nebie5, Godfrey Asea7,
Biswanath Das3, Happy Daudi8, Haile Desmae5, Benoit Joseph Batieno9, Ousmane Boukar10,
Clare T.M. Mukankusi11, Stanley T. Nkalubo7, Sarah J. Hearne1, Kanwarpal S. Dhugga1,
Harish Gandhi3, Sieglinde Snapp1 and Ernesto Adair Zepeda-Villarreal1
1International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
2International Maize and Wheat Improvement Center (CIMMYT), Harare, Zimbabwe
3International Maize and Wheat Improvement Center (CIMMYT), Nairobi, Kenya
4Lake Chad Research Institute (LCRI), Maidiguri, Nigeria
5International Maize and Wheat Improvement Center (CIMMYT), Dakar, Senegal
6Ethiopian Institute of Agricultural Research (EIAR), Addis Ababa, Ethiopia
7National Agricultural Research Organization (NARO), Kampala, Uganda
8Tanzania Agricultural Research Institute (TARI), Naliendele, Tanzania
9Institut de l’Environnement et de Recherches Agricoles (INERA), Ouagadougou, Burkina Faso
10International Institute of Tropicl Agriculture (IITA), Kano, Nigeria
11Alliance of Bioversity International and CIAT, Kampala, Uganda
*Correspondence: Kevin V. Pixley (k.pixley@cgiar.org)
https://doi.org/10.1016/j.molp.2023.09.003
ABSTRACT
Climate changeposesdauntingchallenges toagricultural productionand foodsecurity.Rising temperatures,
shiftingweatherpatterns,andmore frequentextremeeventshavealreadydemonstrated their effectson local,
regional, and global agricultural systems. Crop varieties thatwithstand climate-related stresses and are suit-
able for cultivation in innovativecroppingsystemswill becrucial tomaximize riskavoidance,productivity, and
profitability under climate-changed environments. We surveyed 588 expert stakeholders to predict current
and novel traits that may be essential for future pearl millet, sorghum, maize, groundnut, cowpea, and com-
monbean varieties, particularly in sub-SaharanAfrica.We then review the current progress andprospects for
breeding three prioritized future-essential traits for each of these crops. Experts predict that most current
breeding priorities will remain important, but that rates of genetic gain must increase to keep pace with
climate challenges and consumer demands. Importantly, the predicted future-essential traits include innova-
tive breeding targets that must also be prioritized; for example, (1) optimized rhizosphere microbiome, with
benefits for P, N, andwater use efficiency, (2) optimized performance across or in specific cropping systems,
(3) lower nighttime respiration, (4) improved stover quality, and (5) increased early vigor. We further discuss
cutting-edge tools and approaches to discover, validate, and incorporate novel genetic diversity from exotic
germplasm into breeding populationswith unprecedented precision, accuracy, and speed.We conclude that
the greatest challenge to developing crop varieties towin the race between climate change and food security
might be our innovativeness in defining and boldness to breed for the traits of tomorrow.
Key words: climate change, food security, crop breeding, cropping systems, expert survey, sub-Saharan Africa
Pixley K.V., Cairns J.E., Lopez-Ridaura S., Ojiewo C.O., DawudM.A., Drabo I., Mindaye T., Nebie B., Asea G.,
Das B., Daudi H., DesmaeH., Batieno B.J., Boukar O., Mukankusi C.T.M., Nkalubo S.T., Hearne S.J., Dhugga
K.S., Gandhi H., Snapp S., and Zepeda-Villarreal E.A. (2023). Redesigning crop varieties to win the race between
climate change and food security. Mol. Plant. 16, 1590–1611.Published by the Molecular Plant Shanghai Editorial Office in association with
Cell Press, an imprint of Elsevier Inc., on behalf of CSPB and CEMPS, CAS.
1590 Molecular Plant 16, 1590–1611, October 2 2023 ª 2023 The Author.
This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
Redesigning crop varieties for changed climate Molecular PlantINTRODUCTION
The world’s climate is changing, and while some expected ef-
fects can be predicted (USGCRP, 2018; IPCC, 2022), future
crops will grow in unprecedented environments, facing new
challenges and offering new opportunities. Most recent
estimates of the effects of climate change on crop yields are
negative, e.g., –17% overall by 2050 (Nelson et al., 2014),
median of –6% for major staple crops in West Africa (Carr
et al., 2022), and median of –10% to –15% for maize in Africa
(Zhai et al., 2021). Entomologists and pathologists warn that,
although the effects of rising temperatures will vary, pest and
pathogen generation times (life cycles) will likely shorten, their
ranges will expand, and species with suitable hosts will prevail
in less-favorable environments, all of which would have negative
or unpredictable effects on crops (Bebber, 2015; Fones et al.,
2020; Chaloner et al., 2021; Skend
zic et al., 2021; Harvey et al.,
2023). Molds and mycotoxins may also expand their ranges
and become more problematic; for example, Aspergillus flavus
thrives in high temperatures and aflatoxin (AFB1) production is
stimulated by increased temperatures, drought stress, and CO2
levels (Zingales et al., 2022). Finally, nutritional quality,
particularly micronutrient and protein contents are expected to
decline under increased CO2 conditions (Soares et al., 2019),
especially for C3 crops (Myers et al., 2014).
Sustainably achieving food and nutrition security for the growing
global population under likely climate change scenarios is one
of humanity’s greatest challenges. There will be no single solu-
tion to this problem. A strategic approach begins with an
assessment of the current scenario: our strengths, weaknesses,
opportunities, and threats to achieve sustainable nutrition secu-
rity for all.Strengths
Vast collections of largely unexploited crop genetic diversity are
easily accessible through national and international germplasm
banks (Ramirez-Villegas et al., 2022), often with precise
information about their site of origin, which allows accessing
environmental and climate data defining their range of
adaptation. Genetic resources are the fundamental building
blocks or raw materials for all the food we eat, and dozens of
examples have demonstrated the value of exotic genetic
resources (crop wild relatives or landraces) in conferring pest
or disease resistance, abiotic stress tolerance, quality, and
other traits in crop improvement (Pimentel et al., 1997;
Dempewolf et al., 2014; Kilian et al., 2021; Bohra et al., 2022).
Genomic and pangenome data are available for major and
minor crops (Sansaloni et al., 2020; Chapman et al., 2022),
and molecular and biotechnology tools are widely available for
discovery and breeding applications National Academies of
Sciences, Engineering, and Medicine, 2016; Pixley et al. (2019).Weaknesses
We cannot predict the effects of climate-changed environments
on crop physiology or the complex genotypic and epigenomic
characteristics (Kakoulidou et al., 2021) that will succeed in
them. The complexity that characterizes crop and disciplinary
science encourages specialization at the expense of
transdisciplinary approaches that could elucidate innovativeMolecsolutions to cope with changing climate. While germplasm
banks contain large, untapped sources of alleles that can help
in mitigating the effects of future climate, many wild crop
species, especially in conflict areas, remain under-conserved
and unavailable Vincent et al. (2019); Ramirez-Villegas et al.
(2022). Finally, declining trends in public sector agricultural
research investment (Beintema and Stads, 2017; Heisey and
Fuglie, 2018) adversely affect the scientific community and its
rate of progress on crop improvement.Opportunities
Data science has and continues to advance, enabling the use and
integration, including via machine learning and artificial intelli-
gence, of big data from genomics, transcriptomics, phenomics,
climate, soils, and other fields (Parmley et al., 2019; Siddiqui
et al., 2021). Modern breeding methods, including genomic
selection, speed breeding, doubled haploids, and genome
editing promise faster development of new varieties that can
quickly respond to emerging challenges (Atlin et al., 2017).
Perhaps the most promising opportunity, however, is to design
crop varieties for innovative cropping systems that maximize
climate resilience, minimize climate risk, and benefit from
climate-changed environments, e.g., by shifting cropping calen-
dars, rotations, and relays (Swastika et al., 2004; Thanh Ha et al.,
2004; Gathala et al., 2020), or exploiting genotype by
environment and crop management interactions (Haug et al.,
2020; Cooper and Messina, 2021; Zhai et al., 2021; Farooq
et al., 2023). There may also be important opportunities to reap
large returns on investments in research in low-income countries,
where current yield gaps and predicted negative impacts of
climate change are largest (especially in the tropics), and invest-
ment in agricultural research are currently smallest (Pixley et al.,
2019; Yoshida and Iizumi, 2023).Threats
The biggest threat is complacency and ‘‘business as usual.’’ We
are not on-track toward healthy nutrition security for all (World
Resources Institute, 2019), nor for producing our food within
safe planetary boundaries (Steffen et al., 2015). Recent crises
have highlighted the vulnerability of food systems to external
factors and have the potential to re-direct funding away from
food and nutritional food security objectives (Mottaleb et al.,
2022; Jr. Tabe-Ojong et al., 2023). Given the limited resources
for agricultural research, the risk of unwisely prioritizing
investments is huge, as is the risk of failing to seize the
available opportunities.
The objectives of this paper are to: (1) survey experts from diverse
disciplines for six major staple crops of Africa to elucidate (1a)
likely agronomic changes in future cropping systems seeking
sustainability, intensification, resilience and productivity under
climate change, and (1b) associated desirable or essential crop
traits, particularly those that are not currently prioritized in crop
improvement programs, (2) review the current status and oppor-
tunities for improving (2a) future, prioritized traits and (2b) future
traits that the authors consider potential ‘‘blind spots’’ among
the surveyed experts, and (3) discuss novel approaches to
harness genetic diversity to develop climate-resilient crops for
combating climate change.ular Plant 16, 1590–1611, October 2 2023 ª 2023 The Author. 1591
Molecular Plant Redesigning crop varieties for changed climate
Table 1. Factors likely to drive changes in crop agronomy or cropping systems for future climates across six crops, expressed as
percentage of 588 survey respondents.
Numbers may not equal 100 due to the exclusion of "I don’t know" responses.DRIVERS OF CHANGE FOR CROP
AGRONOMY AND CROPPING SYSTEMS
MANAGEMENT AND LIKELIHOOD OF
ADOPTION OF CROP MANAGEMENT
INNOVATIONS UNDER FUTURE
CLIMATES
The majority of survey respondents across all crops considered
13 drivers of crop and cropping systems change to be of high
or very high importance. Climate change-related factors, such
as increased likelihood of lesser rainfall, higher temperatures,
and increased frequency of erratic or extreme climatic events,
were perceived as the strongest drivers for changes in agronomy
or cropping systems, followed by increased demand from a
growing population, and the (re)emergence of pests and diseases
(Table 1, supplemental Tables 2–7, and supplemental Figures 1–1592 Molecular Plant 16, 1590–1611, October 2 2023 ª 2023 The Auth4). For the three cereal crops (pearl millet, sorghum, and maize),
soil degradation through erosion or loss of fertility was
considered an important driver by more than half of the
respondents. In addition, for sorghum and maize, increased
demand for stover for animal feed and grain for feed and
industrial uses were identified as important drivers. For cowpea
and beans, the increased demand for nutrient-dense crops
was considered of high importance (supplemental Tables 8–43
and supplemental Figures 5–28 include crop specific survey
results).
Regarding the likelihood of adoption of crop management innova-
tions, the majority of respondents across crops considered likely
or very likely that farmerswill need to innovate aroundcropping sys-
tems diversification and intensification through, for example, opti-
mized crop rotations, intercropping, relay, or double cropping,
increased use of mechanization, and early sowing to extend theor.
Redesigning crop varieties for changed climate Molecular Plant
Table 2. Likelihoodof adoption of cropmanagement innovations in sub-SaharanAfrica under future climates, expressed as percentage
of 588 survey respondents.
Numbers may not equal 100 due to the exclusion of "I don’t know" responses.cropping season and optimize crop rotations (Table 2). For the
legume crops (groundnut, cowpea, and bean), increasing planting
density was considered highly likely, while the use of hybrids was
considered unlikely. An inverse pattern was found for cereals,
whereby increased planting density was considered less likely
than the increased use of hybrids. Notably for maize, greater use
of hybrids was considered the most likely technological change.
The adoption of sustainable agriculture techniques that maintain
soil cover with crop residues and reduce tillage, adoption of
precision agriculture machinery, and increased prioritization of
fodder versus grain production were perceived to have a low
likelihood of adoption by farmers across crops.BREEDING FOR FUTURE CLIMATES
Current product profiles in pearl millet, sorghum, maize,
groundnut, cowpea, and bean breeding programs in sub-
Saharan Africa (SSA) primarily focus on increasing grain yield un-
der abiotic and biotic stresses (see Table 3 and Concluding
remarks). To sustainably reach food and nutritional security
under changing climate may require realignments in breeding
targets. We surveyed nearly 100 crop scientists for each of
these six crops (see supplemental material: methods, figures,
and tables) to elicit expert opinions about essential and
desirable traits to enhance resilience and productivity of future
crop varieties. About 90% of the survey respondents are based
and work in Africa, half are plant breeders, 20% are women, andMolec16% work in CGIAR institutions. The small percent of female re-
spondents, which was less marked for bean than all other crops,
is slightly lower than previous estimates of women enrolled in
higher education in science and technology fields in SSA
(Tiedeu et al., 2019; Fisher et al., 2020). While this study focused
on researchers working within a specific area of science and
technology, it suggests a gender disparity in crop improvement
teams in SSA.
Figure 1 summarizes the results of the survey, while extensive
details across and per individual crop are available in
supplemental materials. Highly impactful traits for future
varieties can be grouped as very or not innovative, and as
readily (feasible) or difficult to breed for. Below, we discuss
two characteristics or traits for each crop, chosen to
maximize both impact potential and innovativeness, because
non-innovative traits are by our definition adequately ad-
dressed by current breeding programs. We also discuss for
each crop one trait whose impact potential and innovativeness
we believe may have been overlooked by the survey respon-
dents (Table 4).
Pearl millet (Pennisetum glaucum)
Pearl millet is the sixth most extensively grown cereal crop in the
world and has large area-expansion potential because of its
excellent adaptation to drought and heat and exceptionally
good nutritional value (Ghatak et al., 2021). Its production andular Plant 16, 1590–1611, October 2 2023 ª 2023 The Author. 1593
Molecular Plant Redesigning crop varieties for changed climate
Figure 1. Perceived degree of innovation (X axis) and potential impact (Y axis) of characteristics or traits for breeding for future
climates.
(A–F) (A) Millet, (B) sorghum, (C) maize, (D) groundnut, (E) cowpea, and (F) bean. The size and color of bubbles represents the likely feasibility of
incorporating individual traits into breeding pipelines. BioFort, biofortification/nutritional enhancement; BirdResist, bird resistance; CarbhSTRG, car-
bohydrate storage and remobilization; CookTime, reduced cooking time; CropSyst, changed cropping systems; DT, drought tolerance; EarlyMat, early
maturity; EarlyVig, early vigor; FunctSG, functional stay-green; GrainYLD, grain yield; HT, heat tolerance; LateMat, later maturity (longer season);
LightIntercep, light interception; LowNgtResp, lower respiration under high nighttime temperatures; Mech, mechanization; Microbiome, root micro-
biome; NUE, nitrogen use efficiency; NUpE, nitrogen uptake efficiency; P&D, emerging or re-emerging pests and diseases; PhotoSens, reduced
photoperiod sensitivity; PoorSoils, poor soil quality including acidity; PUE, phosphorus use efficiency; Roots, root architecture; SoilD, resistance to soil-
borne diseases; StoverQLTY, stover quality for feed; StoverYLD, stover yield; Till, tillering ability; WUE, water use efficiency.use are largely limited to arid and semi-arid regions in SSA and
India.With increasing temperatures and expected consequences
of climate change, continued or increased breeding for climate-
adaptive traits will be necessary (Serba et al., 2020). Pearl millet
is known for its exceptional heat tolerance, and further
improvement for this character is possible (Satyavathi et al.,
2021), aided by recent elucidation of underlying regulatory and
genomic factors (Yan et al., 2023). Our expert survey identified
stay-green and nutrient biofortification as innovative and poten-
tially impactful traits for future varieties, and we also discuss1594 Molecular Plant 16, 1590–1611, October 2 2023 ª 2023 The Authbreeding for bird resistance because it is currently not within
product profiles and was highlighted as a potentially highly im-
pactful trait to breed for (Figure 1A and Table 4). Detailed
survey results for pearl millet are summarized in supplemental
Figures 5–8 and supplemental Tables 8–13.
Stay-green enables pearl millet genotypes to sustain photosyn-
thetic activity during terminal drought, contributing to grain filling
and yield (Ghatak et al., 2021). The effect of stay-green on water
extraction by pearl millet after anthesis under drought stress isor.
Redesigning crop varieties for changed climate Molecular Plant
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
     
Table 3. Current target traits of CGIAR-NARS breeding pipelines in pearl millet, sorghum, maize, groundnut, cowpea, and common
bean in sub-Saharan Africa.
Each crop has several breeding pipelines targeting different market segments. Blue cells with ‘‘+’’ indicate a trait is included in all breeding pipelines,
green cells with ‘‘+/
’’ indicate the trait is included in certain breeding pipelines, and yellow cells with ‘‘
’’ indicate the trait is not used in selection within
any breeding pipelines in sub-Saharan Africa, as known or assumed by the authors.crucial for grain filling (Vadez et al., 2013). Molecular markers
have been identified for stay-green in pearl millet (Debieu et al.,
2018); for example, an InDel in a putative chlorophyll a/b
binding protein gene was associated with stay-green and grain
yield under drought conditions (Sehgal et al., 2015). Molecular
markers associated with stay-green were mapped on chromo-
some 6, two of whichwere also associated with biomass yield un-
der early drought (Debieu et al., 2018). Stay-green also contrib-
utes to fodder quality for animal feed (Kamal et al., 2019),
making it a valuable trait for dual-purpose (food and feed)Molecbreeding, which was assessed as moderately impactful and
innovative by survey respondents.
Compared with other cereals, pearl millet has high concentrations
ofantioxidants,aminoacids, leucine, isoleucine,and lysine,andmi-
cronutrients, Fe and Zn, and provitamins A (Dube et al., 2021). Diet
diversification, food fortification, and nutrition supplementation are
used to address micronutrient deficiencies; however, these
solutions are not affordable and accessible to all who need
them. Biofortification of pearl millet can be a sustainable andular Plant 16, 1590–1611, October 2 2023 ª 2023 The Author. 1595
Molecular Plant Redesigning crop varieties for changed climate
Characteristics prioritized by Characteristics prioritized by Blind spot prioritized by authors and
Crop surveys and discussed surveys but not discussed discussed
Pearl millet stay green water use efficiency bird resistance
nutritional enhancement emerging pests and diseases
cropping systems
Sorghum early maturity drought tolerance low soil phosphorus
stay green stover quality
emerging pests and diseases
Maize cropping systems drought tolerance microbiome
heat tolerance early maturity
emerging pests and diseases
Groundnut nutritional enhancement early maturity dual purpose
mechanization emerging pests and diseases
water use efficiency
Cowpea early maturity drought tolerance root architecture
emerging pests and diseases cropping systems
water use efficiency
Bean short cooking time emerging pests and diseases low soil fertility tolerance
nutritional enhancement drought tolerance
early maturity
Table 4. Characteristics or traits prioritized as impactful and innovative to breed for future climate-resilient varieties of six crops:
prioritized by survey respondents and selected by authors for discussion; prioritized by survey respondents but not discussed due to
space constraint; and characteristic or trait chosen and discussed by the authors but not prioritized by survey respondents, i.e.,
potential ‘‘blind spots’’ among respondents.
Note: grain yield was always prioritized by survey respondents as impactful, albeit not innovative for future varieties; it was not included for discussion to
avoid repetitiveness and to focus on more innovative breeding opportunities.cost-effective approach to alleviating micronutrient deficiencies
and may have income-generating value for farmers. Genetic vari-
ability and molecular breeding strategies are available to enable
breeding of Fe- and Zn-rich varieties (Govindaraj et al., 2016,
2022; Kumar et al., 2016; Singhal et al., 2021).
Although few studies have examined bird resistance in pearl millet,
several for sorghum have reported high tannin grain, drooping and
open panicles to have least bird damage (Mofokeng and Shargie,
2016). Sorghum cultivars expressing tannin binding proteins at
immature grain stage, but not in ripened grain, would not
significantly impact nutritional quality while reducing bird
damage. A recent study revealed that Tannin1, which encodes a
D40Wprotein that functions in theWD40/MYB/bHLHprotein com-
plex, controls bird feeding behavior in sorghum by affecting the
accumulation of anthocyanins and tannin compounds in grain
(Xie et al., 2019). Identifying and breeding for favorable alleles of
an analog in pearl millet could make significant progress for bird
tolerance. The extent to which bird damage can be controlled in
pearl millet through genetic traits of the host plant is unclear;
however, dense panicles with long bristles have been reported to
suffer least bird damage (Akromah et al., 2008; Drabo et al.,
2019). Unfortunately, varieties with these traits may be rejected
by farmers who harvest and thresh the crop manually (Drabo
et al., 2019), although the recent release of a bristled panicle
millet in Nigeria suggests that some farmers are interested in
growing them. Currently, non-genetic approaches, e.g., bird
scaring or bird destruction, are the most effective, but with
increased use of mechanization, as predicted by survey respon-
dents (Table 2), and availability of novel breeding technologies
such as genome editing, new opportunities to breed for traits that
deter bird feeding may become feasible. The very likely increased1596 Molecular Plant 16, 1590–1611, October 2 2023 ª 2023 The Authuse of hybrids will also facilitate mechanization of harvest. Finally,
research on biochemical compounds and pathways may
elucidate opportunities to breed or apply genome editing (e.g., to
edit tannin genes) to confer resistance or non-preference by birds.Sorghum (Sorghum bicolor)
Sorghum is the second most widely grown crop in Africa with
28.1 M ha (69% of the global area) grown mainly across arid
and semi-arid zones by smallholder farmers in a diversity of crop-
ping systems. Most of the grain production is consumed at the
household level, and the stover is increasingly used as livestock
feed, especially during dry seasons where natural pasture is
limited. Sorghum is a ‘‘climate smart’’ crop due to its water use
efficiency and tolerance to high temperatures and rainfall vari-
ability. However, changing climate is predicted to increase tem-
peratures, the numbers of dry days and heavy rainfall events,
and cause yields to change by +10% to –40% by the end of the
century (Akinseye et al., 2020; Mohammed and Misganaw,
2022; Alvar-Beltrán et al., 2023). The survey identified early
maturity and stay-green among the most impactful traits for
future sorghum production, and we selected low soil phosphorus
as a potentially overlooked, high-value future trait (Figure 1B and
Table 4). Detailed survey results for sorghum are summarized in
supplemental Figures 9–12 and supplemental Tables 14–19
Previous reports indicating farmers’ preference for early maturity
and stay-green varieties in Ethiopia, Zimbabwe, Mali, and Nigeria
(Belay andWale, 2021;Melesse et al., 2021; AhmadYahaya et al.,
2022; Traore et al., 2022) support the importance of these traits for
adaptation to the changing environments. Early maturity may
allow escape from terminal drought, reducing production risks.or.
Redesigning crop varieties for changed climate Molecular PlantFlowering time genes activate the transition from vegetative to
reproductive growth (Faye et al., 2022); while stay-green genes
delay leaf senescence and increase water and nitrogen use effi-
ciency under post-flowering water stress (Abebe et al., 2021;
Hou et al., 2021). Stay-green QTLs are co-located with genes
associated with narrow root angle, which contributes to deep
rooting and greater water extraction (Tebeje et al., 2020). In
addition to its importance to drought stress adaptation, stay-
green contributes to maintaining stover quality of dual-purpose
(grain for food and stover for feed) varieties. Stover digestibility,
which is severely reduced under drought (Somegowda et al.,
2021) may be less affected for lines expressing stay-green. Mo-
lecular marker-assisted selection (MAS) has been reported for
stay-green in elite lines (Nofou et al., 2017; Kamal et al., 2021).
Sorghum’s yield gap in Africa can be reduced using improved va-
rieties and appropriate fertilization, especially phosphorus and ni-
trogen. The survey did not identify P uptake and use as future im-
pactful traits for sorghum improvement; however, low soil P
availability is a major constraint for crop production in tropical re-
gions (Hufnagel et al., 2014). P uptake in low-P soils is correlated
with root architecture (length and surface area) and with grain
yield. Breeding for increased P uptake will enhance crop resil-
ience to climate change and increase yield in low-P soils. Signif-
icant genetic diversity and high heritabilities have been reported
for P uptake and use efficiency among west and central African
sorghums under low- and high-P conditions (Leiser et al.,
2014). These traits are positively correlated and are controlled
by few genes, including Al tolerance gene sbMATE (Bernardino
et al., 2019) for which markers are available for MAS.
Maize (Zea mays)
Survey respondents, especially non-breeders, identified breeding
for increased cropping systemdiversity as innovative with high po-
tential for impact (Figure 1C). Breeders, however, identified heat
tolerance as the most innovative trait, which all respondents
believe has moderate impact potential although we believe it
may be highly impactful in key maize-producing regions of SSA
under climate change. Increasing cropping system diversity can
increase productivity per unit area, reduce risk, suppress pests
and diseases, and optimize resource capture while reducing
erosion, soil carbon loss, and nutrient runoff from increased crop
cover (Li et al., 2020; Burgess et al., 2022). We now discuss
breeding for: (1) increased cropping system diversity, (2) co-
occurrence of heat and drought, and as a potentially overlooked
trait, (3) breeding to optimize the rhizospheremicrobiome. Detailed
survey results for maize are summarized in supplemental
Figures 13–16 and supplemental Tables 20–25.
Despite the advantages of intercropping, maize breeding in SSA
is primarily conducted under a mono-cropping system (Prasanna
et al., 2022). While many farmers use intercropping when testing
elite candidate hybrids from breeding programs (on-farm testing),
this typically happens late in the product development process,
when genetic variation and opportunity to select hybrids that
perform optimally under intercrop systems is limited (Voss
et al., 2021). Breeding varieties specifically for an intercrop-
based system is complex because it requires the optimization
of two or more crops simultaneously for complementarity in the
same ecosystem (Moore et al., 2023). Genomic selection was
recently shown to significantly increase the rate of genetic gain
relative to phenotypic selection for grain yield alone whenMolecbreeding for intercrop systems, regardless of the genetic
correlation of intercrop with monocrop yield (Banc
ic
 et al., 2021).
Over the past 30 years, there has been a two-fold increase in the
probability of the co-occurrence of heat and drought stress during
maize-growing seasons (Heino et al., 2023). The co-occurrence of
heat and drought stress reduces maize yields by 1.7% for every
accumulated degree day above 30C (Lobell et al., 2011).
Research in southern Africa showed that screening for drought
tolerance under moderate temperatures indirectly selected
against heat tolerance, resulting in elite drought tolerant lines,
widely used in commercial hybrids that are highly susceptible to
combined drought and heat stress (Cairns et al., 2013).
Therefore, the study highlighted the importance of selection for
both heat and drought tolerance. Increased temperatures under
climate change will result in many African countries experiencing
temperatures unrepresented under current climates and
increased germplasm exchange from countries identified as
analogs of future climates will be essential (Burke et al., 2009).
Low and variable profitability of fertilizers in maize production is a
key driver of sub-optimal fertilizer use and subsequently the maize
yield gap in SSA (Bonilla-Cedrez et al., 2021). Although exploiting
the root microbiome was identified as low in terms of feasibility
and potential impact, and moderately high for innovativeness as
a breeding target, it could play an important role in increasing
fertilizer use efficiency (York et al., 2022; Michl et al., 2023). Maize
genotypes vary in their ability to mediate soil organic matter
mineralization, which can result in the mobilization of ammonium
and subsequent nitrification providing nitrogen for plant uptake
(Mwafulirwa et al., 2021). Biological nitrification inhibition (BNI)
could play a significant role in nitrogen use efficiency in maize
production (Petroli et al., 2023). Soil P content is a major driver of
bacterial and fungal communities, with low soil P, which is
pervasive in SSA, favoring microbial communities that suppress
maize growth (Gomes et al., 2018). Measuring the rhizosphere
microbial diversity is possible under field conditions (Peiffer et al.,
2013), but quantifying rates of soil organic matter mineralization
and nitrification is complex and generally conducted under
controlled conditions (Mwafulirwa et al., 2021). Decades of
selection in breeding programs for yield primarily under high-
input conditions may have indirectly modified interactions
between maize and its microbiome and altered the recruitment of
specific N-cycling or low-P-tolerance functional groups within the
rhizosphere. Landraces, including those held in germplasm banks,
may provide an important source of novel alleles for improving the
microbiome in the maize rhizosphere (Favela et al., 2021), while
genomic selection may offer the needed tactic to incorporate
such complex traits into breeding pipelines (Baggs et al., 2023).Groundnut (peanut, Arachis hypogaea)
The future traits survey revealed grain yield, early maturity,
emerging pest and disease resistance, drought tolerance, water
use efficiency, and nutritional fortification, followed bymechaniza-
tion, early vigor, stay-green, N use efficiency, soil borne diseases,
and cropping systems as impactful traits for future groundnut vari-
eties (Figure 1D). Several previous studies have also ranked grain
yield, drought tolerance, early maturity, and disease resistance as
essential for future groundnut varieties (Banla et al., 2018; Daudi
et al., 2018; Sinare et al., 2021). While breeders and non-breedersular Plant 16, 1590–1611, October 2 2023 ª 2023 The Author. 1597
Molecular Plant Redesigning crop varieties for changed climategenerally agreed on the most impactful future traits, they often dis-
agreed on which traits are innovative breeding targets. All agreed
that mechanization, nutritional enhancement, and cropping sys-
temsare innovative targets,while only breeders felt that early vigor,
microbiome, and N use efficiency are innovative, and only non-
breeders believe that water use efficiency, early maturity, and
stay-green are innovative targets. We focus on three traits judged
to have high potential impact and to be innovative targets for
breeding: (1) nutritional enhancement, (2) mechanization, and (3)
dual-purpose (grain and haulm production). Detailed survey results
for groundnut are summarized in supplemental Figures 17–20 and
supplemental Tables 26–31.
Groundnut is known for its high nutritional value and is a preferred
ingredient for nutrient-dense foods to prevent malnutrition in chil-
dren and pregnant and nursing women (Parmar et al., 2022).
Nonetheless, substantial genetic variability exists to further
improve the nutrient composition of groundnut, particularly oil
content (Janila et al., 2016) and oleic-linoleic oil ratio
(Deshmukh et al., 2020; Kamdar et al., 2021). Recent advances
in analytical tools have enabled cost-effective and non-
destructive phenotyping for oil and high oleic (HO) content using
near-infrared reflectance spectroscopy (Misra et al., 2000;
Pasupuleti and Nigam, 2013). In SSA, breeding HO groundnut
is in its infancy despite documented health benefits (Bimro
et al., 2020) and longer shelf-life through reduced oxidative
rancidity (Deshmukh et al., 2020). Several QTL and marker-trait
associations have been reported for oil and HO content
(Sarvamangala et al., 2011; Pandey et al., 2014; Shasidhar
et al., 2017; Liu et al., 2020; Guo et al., 2021), and MAS and
marker-assisted backcrossing have been used to enhance oil
quality for groundnut (Janila et al., 2016; Bera et al., 2018;
Huang et al., 2019). Mutant ahFAD2 alleles, conferring HO,
have been successfully used for trait introgession (Huang et al.,
2019). Nonetheless, HO groundnut varieties remain rare in SSA
in contrast to other groundnut producing regions. Efforts to
develop high Fe, Zn, pro-vitamin A, or protein groundnut varieties
in SSA have been limited, but genetic variability exists for these
traits within the primary gene pool (Janila et al., 2015;
Chandrashekar et al., 2016; Kadirimangalam et al., 2022).
Groundnut harvesting and pod stripping are labor intensive and
expensive and are often complicated by dry soil at harvest. For
smallholder farmers, especially the women who are themain pro-
ducers, labor is becoming more expensive and scarcer. Mecha-
nization of the groundnut production process is one of the key
factors that can improve efficiency and profit margins. Stay-
green is a trait that would facilitate mechanized harvesting
through the maintenance of peg and stem strength, thus mini-
mizing pod losses during harvest. Stay-green may also protect
the crop from yield loss (e.g., peg detachment, and termite and
insect damage) when the harvest is delayed due to labor short-
ages or competing priorities. Stay-green also contributes to
drought tolerance (Williams et al., 2022) and improved fodder
quality. The underlying physiological mechanisms leading to
stay-green expression, QTL identification, and gene discovery
have been important research areas for various crops including
sorghum (Borrell et al., 2014), wheat and barley (Williams
et al., 2022), and groundnut (Vadez and Ratnakumar, 2016).
Introgression of QTL for stay-green has resulted in sorghum vari-
eties with improved drought tolerance and yield (Vadez et al.,1598 Molecular Plant 16, 1590–1611, October 2 2023 ª 2023 The Auth2011; Sintayehu et al., 2018). Simultaneous selection for stay-
green and grain yield has been recommended to ensure that de-
layed senescence is not caused by low sink demand (Borrell
et al., 2014). In addition to contributing tolerance to terminal
drought stress, stay-green contributes to groundnut haulm quan-
tity and quality, disease tolerance (Danful et al., 2019), and grain
quality. Drone-based sensors canmeasure physiologic and agro-
nomic characteristics useful for breeding stay-green varieties
with high yield (Sarkar et al., 2022).
Because the price of groundnut’s haulm can equal or exceed that
of its grain, breeding for dual-purpose (grain and fodder) varieties
with stay-green, nutritious haulm would be valuable. Dual use
groundnut was not highlighted as a critical future trait, particularly
by non-breeders, but evidence suggests that fodder quality
should be included in selection criteria for future groundnut vari-
eties (Samireddypalle et al., 2017). Already groundnut haulms are
exported as livestock feed from Sudan to the Middle East, and
changing climate is likely to increase pressure on cropping
systems to produce feed for livestock as rangeland areas are
reduced (Godde et al., 2021). Substantial genetic variation
exists, and fodder quality is already being mainstreamed as a
release criterion for groundnut varieties for some market
segments. With the existing genetic diversity for nutritional
quality traits, stay-green traits, and haulm quality traits, and the
advances in phenotyping and genomic tools, it is feasible for
breeding programs to develop nutrient-rich, stay-green, and
dual-purpose groundnut varieties that are climate resilient and
meet farmer and market demands.Cowpea (Vigna unguiculata)
The survey of experts identified early maturity and resistance to
emerging pests and diseases as the most impactful traits for
adaptation and to diminish the risks of cowpea crop failure under
changing climate (Figure 1E). Breeding for optimal root
architecture would address two of the characteristics prioritized
as future-impactful, drought tolerance and water use efficiency.
Breeding for root architecture would also be highly innovative,
likely because of the challenges for phenotyping and hence
currently low feasibility for breeding. For these reasons, we
discuss root architecture as a potentially overlooked trait, after
discussing breeding for early maturity and resistance to emerging
or re-emerging pests and diseases. Detailed survey results for
cowpea are summarized in supplemental Figures 21–24 and
supplemental Tables 32–37.
In the Sahel and Sudan Savanna, early maturing cowpea varieties
provide food during critical hunger periods when food supplies
from the previous cropping season run out. Early maturity allows
cowpea to escape terminal drought and thrive in arid and semi-
arid environments. Adaptation to short growing seasons sacri-
fices yield potential in favor of stable and reliable yield during
most cropping seasons (Thierfelder et al., 2016; Acevedo et al.,
2020). Genetic variation for earliness exists (Ribeiro et al., 2014;
Owusu et al., 2018b) and earliness is an important objective
in most cowpea breeding programs in SSA (Padi, 2007;
Santos et al., 2020). In addition to escaping unfavorably high
temperatures during flowering and podding stages, early
maturity is valuable for avoidance of pests and diseases (Halder
and Srinivasan, 2011; Owusu et al., 2018a; Mulwa et al., 2023).or.
Redesigning crop varieties for changed climate Molecular PlantEmerging pests and diseases pose threats to crop production,
and currently minor pests may become major pests under
changed climate (Sadda et al., 2021). As examples, evolving
aphid biotypes have overcome resistance in improved cowpea
varieties (Abdou et al., 2013) and leaf thrips (Hydatothrips
adolfifriderici Karny), formerly occurring sporadically, now pose
a serious threat and cause devastating effects through regular
outbreaks in some areas in Nigeria (Moritz et al., 2013). Multiple
races of Striga gesnerioides have recently been reported in
West African countries where previously only one race was
present (Ohlson and Timko, 2020; Sawadogo et al., 2021). After
resurgence of scab disease in Uganda in 2010, widespread
presence with moderate to severe disease symptom levels was
found in all the 17 cowpea growing districts surveyed in 2015
(Afutu et al., 2017).
Few respondents to the survey opined that root architecture is
likely to provide high impact in future; however, we believe that
this trait deserves greater attention in breeding cowpea for adap-
tation to climate change. Root architecture is important for plant
acquisition of nitrogen andwater (Lynch and Brown, 2001; Lynch,
2013), and of phosphorus, which is highly immobile and
commonly limiting. Considerable genetic diversity exists for
root traits that enhance growth in nutrient-poor and dry environ-
ments (Krasilnikoff et al., 2023). Root traits contributing to
efficient root architecture and improved productivity under
stressful (low soil fertility and drought) and optimal envi-
ronments have been identified in cowpea (Adu et al., 2019).
Significant genotypic variation and high heritability were
observed for phenotypes including primary root length (he
ritability = 0.77), basal root number (0.72), and taproot
branching density (0.67) (Mohammed et al., 2022). With the
development of high-throughput methods for phenotyping root
architecture, e.g., robotic imaging tools and analysis pipelines
to visualize, quantify, and analyze diverse root traits (Galkovskyi
et al., 2012), genetic diversity for root architecture could be
exploited in cowpea breeding.
Common bean (Phaseolus vulgaris)
The common bean expert survey identified resistance to emerging
pests and diseases, short cooking time (CKT), drought tolerance,
earlymaturity, andnutritionalbiofortificationas impactful future traits,
while CKT, nutritional biofortification, early vigor, and water use effi-
ciency were considered the most innovative traits for breeding
(Figure 1F). We discuss CKT and nutritional enhancement, and
include tolerance to poor soil fertility as a potentially overlooked
characteristic for bean (and likely for all six crops in this review).
Detailed survey results for common bean are summarized in
supplemental Figures 25–28 and supplemental Tables 38–43.
Beans are a major staple food in many parts of Africa; however,
long CKT is a disincentive to consumption since it demands large
amounts of water, fuel, and time (Shellie-Dessert and Hosfield,
1990). Women constitute more than 60% of bean producers
across Africa (Nchanji, 2021) and benefit from improved
common bean varieties with shorter CKT (Nakazi et al., 2017).
Over 85% of the rural and urban poor use wood or charcoal as
fuel to cook beans, which has environmental impact due to
deforestation. Research on ‘‘cookability’’ in common bean
began in the 1960s, and CKT and rate of water absorption were
later shown to be unique traits, with a low phenotypic
correlation between them and relatively small genotype byMolecenvironment interaction for both traits (Jackson and Varriano-
Marston, 1981; Shellie and Hosfield, 1991). Wide genotypic
variability associated with CKT exists in both Andean and
Mesoamerican bean accessions (Ribeiro et al., 2014, 2021;
Cichy et al., 2015). Variation in CKT has been associated with
seed qualities including color, size, and seed coat thickness
(Reyes-Moreno and Paredes-López, 1993; Klasener et al.,
2019; Bassett et al., 2021). In breeding for reduced CKT, care
must be taken to maintain protein content and quality. Studies
indicate that few QTLs contribute to CKT in beans, and high
narrow-sense heritability of CKT in beans (h2 = 0.74) has been re-
ported (Jacinto-Hernandez et al., 2003; Cichy et al., 2015). Using
an African bean panel of 358 genotypes, it was recently reported
that genomic selection with optimal contribution selection can
accelerate breeding of high yielding, biofortified, and rapid
cooking common bean cultivars (Saradadevi et al., 2021).
In many African homes, beans are an accessible source of Fe and
Zn, which are essential to the health and well-being of women and
children, and of protein which is essential for the entire household.
Inabio-efficacy trial amongcollege-agewomen inRwanda,highFe
beans improved Fe status and enhanced cognitive ability, brain
function, and work efficiency (Murray-Kolb et al., 2017). The
opportunity exists to improve the health of women and children
through increased consumption of rapid-cooking beans with high
and bioavailable Fe and Zn content. Genetic variation exists for
nutritional composition of cooked bean, including Zn, P, K, Ca,
and Fe in the Andean Diversity Panel (Katuuramu et al., 2018) and
in varieties released by Pan Africa Bean Research Alliance
(PABRA) programs (Amongi et al., 2018; Mukankusi et al., 2019).
Future breeding efforts may focus on improving the bioavailability
of Fe and Zn by incorporating mechanisms such as non- or slow-
darkening grain, or low phytate mutants (Beebe, 2020). However,
a homeostatic mechanism that regulates Fe and Zn uptake has
been found to impede biofortification progress and breeders may
need to cross between gene pools to achieve higher levels of Fe
and Zn uptake; using sister species that have evolved in Fe-poor
environments and are more receptive to Fe uptake could also be
a viable strategy (Beebe, 2020).
Common beans exhibit considerable genetic variability for specific
single or multiple edaphic stress tolerances including lowN, low P,
and soil aciditywith associatedAl and/orMn toxicities (Lunze et al.,
2012). Research on root phenotypes and their role in enhanced soil
exploration and P acquisition has been ongoing for a long time,
leading to better understanding of these traits (Lynch, 2011).
Several traits such as greater root branching and longer root hairs
(Lynch, 2011), percentage of N derived from atmosphere (Rao
et al., 2016), BNI (Subbarao et al., 2015), receptor kinases,
transmembrane transporters, and transcription factors (Kamfwa
et al., 2017) have been employed to select for tolerance to
specific mineral deficiencies. However, developing varieties that
are adapted to multiple soil mineral deficiencies occurring in
combination with abiotic stresses such as drought, heat, and
waterlogging common under farmers’ conditions has made little
progress. Definition of target population of environments has
mainly focused on climatic factors with less emphasis on soil
characteristics and deficiencies, which could guide variety testing
for low soil fertility tolerance. Gaps in breeding for multiple
edaphic stress tolerance include inadequate mapping of soil
deficiencies, poor understanding of the genetic basis of toleranceular Plant 16, 1590–1611, October 2 2023 ª 2023 The Author. 1599
Molecular Plant Redesigning crop varieties for changed climate
Figure 2. Source germplasm types for trait discovery to serve a core breeding pipeline.
(A) Four trait discovery and deployment quadrants, Qa, Qb, Qc, and Qd, separate potential trait donor germplasm sources along two axes, one focused
on the adaptation of the potential source germplasm to the target population of environments that the core breeding pipeline is serving, and the other axis
indicating the competitiveness of the germplasm compared with elite performance.
(B) The relative technical difficulty, cost, and probability of finding and deploying novel variation from each of the quadrants.to multiple soil mineral deficiencies, difficulties in developing
suitable screening protocols, and limited cooperation between
breeders and soil scientists.Innovative methods for mining genetic diversity
The extensive expert surveys reported herein propose traits with
high potential value for future crop varieties, some of which are
innovative in the sense that they are not currently prioritized by
breeding programs. Initiating breeding work for such desirable1600 Molecular Plant 16, 1590–1611, October 2 2023 ª 2023 The Author essential future traits relies on theavailability of genetic diversity
and the ability to accurately phenotype the trait or linked second-
ary trait(s). When useful diversity is not available within the elite,
adapted breeding germplasmpool, trait discovery in exotic germ-
plasm is necessary, and breeding teams must balance the bene-
fits from incorporating the desired genetic variation with the link-
age drag effects from less-desired variation from the same
donor. Therefore, breeding programs seeking trait variation not
found in the immediate elite breeding pool (Figure 2A, quadrant
Qa), generally initially explore elite germplasm from outside theor.
Redesigning crop varieties for changed climate Molecular Plantadaptation target zone (Figure 2A, quadrant Qb). This approach
avoids the most deleterious impacts of linkage drag and
minimizes the difficulty, cost, and time of developing new,
competitive, and adapted germplasm (Figure 2B). Despite these
advantages, the challenge faced when exploring elite
unadapted (Qb) germplasm as potential sources of ‘‘new’’ traits
is their relatively limited variation (Figure 2B). This limitation
drives many teams to consider adapted landraces (Qc) and
non-adapted landraces and wild relatives (Qd) as sources of ge-
netic variation novel to the elite pools. Despite challenges of
using landrace and wild relatives as trait donors, there are
numerous examples of successful trait identification and
deployment in modern breeding from these sources (Kilian
et al., 2021). Common challenges of using exotic germplasm
include sorting through many thousands of potential sources,
little relevant information to aid germplasm selections,
difficulties applying elite-breeding-based phenotyping assays to
often heterogeneous and very diverse materials, and the
inevitable linkage drag observed when breeding from these
germplasm sources.
Over the last 15 years, genomics has begun to open the black box
of genetic diversity through the evolution and application of cheap,
fast, and precise DNA sequencing technology. Unprecedented
scales of crop genetic resource genomic characterization, such
as those conducted in the 3000 genomes work in rice (Wang
et al., 2018) and for maize and wheat at CIMMYT (Sansaloni
et al., 2020), leveraged sequencing technology advances to
understand genetic resources. This genomic framework, while
powerful, required relevant phenotypic data to conduct primary
discovery activities through genome-wide association study
(GWAS) and genomic prediction approaches (Crossa et al., 2016;
Romero Navarro et al., 2017; Singh et al., 2018). Exploration of
the use of other variables, specifically germplasm collection site
enviro-climatic variables such as precipitation, temperature, soil
pH, etc., has facilitated a step-change in our ability to quickly iden-
tify (1) novel genetic variants of potential value for pre-breeding and
(2) the germplasm bank accessions most enriched in the desired
genetic variants (Forester et al., 2016; Mosca et al., 2016; Yu
et al., 2016; Romero Navarro et al., 2017; De La Torre et al., 2019;
Gates et al., 2019; Lasky et al., 2023).
Environmental GWAS (EnvGWAS) and environment-based predic-
tionuseclimate variablesaloneor incombinationsas responsevari-
ables replacing phenotype(s) used in classical GWAS. This ‘‘allele
mining’’ paradigm offers a new scale of experimentation because
isolationofenvironmental variables fromgeoreferencedgermplasm
collections is many orders of magnitude cheaper than phenotyping
the same material. EnvGWAS therefore avails all germplasm bank
accessions with genomic data and georeference data for their
collection site. These large and diverse germplasm panels offer
powerful resources toexploreadaptation to featuresstrongly repre-
sented in theenvironmental data, suchas tolerance todrought, high
temperature, flooding, and low soil pH.Where historic and endemic
disease and pest distributions arewell documented, these can also
be used for EnvGWAS analyses (Bellis et al., 2020). This paradigm
does not extend well when the features of interest are poorly
represented in environmental data, for example poor data on
disease distribution, poor spatial resolution of variables such as
salinity, or limited ranges for a feature of interest, e.g., freezing
temperatures among maize collections.MolecFurthermore, using genomic data per se, comparison of landrace
withmodern cultivars can help identify genomic regions where di-
versity in elite materials is narrow or fixed compared with land-
races. While this assessment and comparison of diversity does
not provide an understanding of direct benefit or cost of using
exotic diversity, it provides a structured approach to sample
and test exotic diversity in regions of the genome where breeding
bottlenecks have arisen (Sansaloni et al., 2020).Gene editing to develop climate-resilient crops
Forward breeding, which has been andwill continue to be amain-
stay of crop improvement, requires crossing of genotypes with
complementary traits followed by selection of desirable recombi-
nants in the target environments, often takingmore than a decade
to develop an improved cultivar. In contrast, introduction of high-
value traits such as herbicide tolerance and insect resistance us-
ing biotechnology has contributed substantially to food produc-
tion over the last two and a half decades (Klu€mper and Qaim,
2014). The impact of these products has been limited by
onerous regulatory approval processes, and opposition to
transgenic plants in many countries. CRISPR-Cas, which was
introduced as a tool for genome editing a decade ago, enables
altering of genes directly in crop plants without permanently intro-
ducing foreign geneticmaterial (Wang andDoudna, 2023).Myriad
examples of modifying genes using this technology to improve
crop plants have already been reported (Nascimento et al., 2023).
Success of gene editing in any crop plant is contingent on the
transformation and editing efficiencies. In rice and maize, for
example, almost any gene can be edited, whereas in difficult-
to-transform crop plants, including pearl millet, none or very
few examples are known (Nascimento et al., 2023). Two
common scenarios in gene editing with CRISPR-Cas are: (1)
repair of the Cas-catalyzed double-stranded DNA break by
non-homologous end joining (NHEJ), which deletes or introduces
nucleotides, often leading to frameshift mutations, and (2)
template-directed repair, referred to as homology-directed repair
(HDR), which allows introduction of targeted changes. HDR is
used for precise replacement or deletion of specific nucleotides
and insertion or replacement of large DNA segments (Anzalone
et al., 2020; Wang and Doudna, 2023). Other methods that can
produce results like HDR include base editing and prime
editing, which provide value where HDR is difficult to perform,
for example, in non-dividing cells. In plants, although all the
various CRISPR-Cas-mediated methods of gene editing have
been reported, NHEJ and HDR suffice to introduce any type of
the aforementioned changes (Anzalone et al., 2020). The
CRISPR-Cas system has been demonstrated to introduce
random mutations (NHEJ), change or replace specific
nucleotides (HDR), and replace or insert DNA segments (HDR)
in commercial crops (Svitashev et al., 2015; Shi et al., 2017).
Mutant libraries could be useful for the discovery and validation of
genetic diversity for use in breeding. The CRISPR-Cas system
was used to generate a library of mutations of the coding genes
in rice, which is a useful resource for gene discovery, similar to
TILLING and transposon-tagged populations (Slade et al., 2005;
McCarty and Meeley, 2009; Liu et al., 2023). For example,
mutations in genes for plant architecture and stalk strength were
isolated from a mu-tagged maize population (Gallavotti et al.,ular Plant 16, 1590–1611, October 2 2023 ª 2023 The Author. 1601
Molecular Plant Redesigning crop varieties for changed climate2004; Ching et al., 2006; McCarty and Meeley, 2009). Similarly, a
TILLING population of wheat was screened to isolate mutants of
all three homeoalleles of the powdery mildew resistance locus
(Slade et al., 2005; Acevedo-Garcia et al., 2017).
CRISPR-Cas can be a useful tool in validating the effect of
selected gene candidates from field or laboratory screening, or
which may be predicted by other methods, for example,
EnvGWAS and bioinformatic analyses, as long as a knockout
provides the requisite information. However, HDR would be
required if the objective is to measure the effect of a functional
candidate gene or genetic region on plant performance in the
target environment. CRISPR-Cas technology allows the insertion
of large pieces of DNA spanning several to many kilobases into
the genome (Anzalone et al., 2020). The resources required to
accomplish this would be extensive, though, first to perform
HDR, the frequency of which is an order to two orders of
magnitude lower than that of NHEJ, and to subsequently test
the individual coding sequences in the candidate interval. Gene
editing where HDR is required would preferably be reserved, in
practice, for the narrowed genetic intervals that have been
proven with high confidence to confer yield or performance
advantage in a target environment. Furthermore, the selected
genetic interval would ideally contain only a few genes to allow
rapid identification of the causal gene. Yet, there is no dearth of
desirable traits where an inactive gene results in a favorable
phenotype, or where the specific polymorphisms are known to
improve the performance of a plant. Gene editing, thus, can
certainly contribute to crop improvement.
Tostudy the effectofmultiple genesona trait, insteadof combining
individual, edited genes by crossing and selection, a multiplex
approach to edit the multiple target genes simultaneously in the
same line would be more efficient. Mutant maize populations for
various combinations of 48 growth-related genes were generated
via multiplexing (Lorenzo et al., 2023). Several loci in wild tomato
were altered to increase fruit size and quality characteristics
(Zhang et al., 2020). These types of studies are useful in
advancing knowledge but, for expedited product development, if
a combination of three or more genes results in a measurable
effect on the desired trait, it would be preferable to create it
afresh in each target cultivar instead of crossing and selection.
A major advantage of editing a gene to improve a trait is that it can
be performed directly in a commercial cultivar or elite line, elimi-
nating traditional pre-breeding stepsofbackcrossingandselection
for the parental genetic background and genetic drag that inevi-
tably accompanies these steps (Dhugga, 2022; Li et al., 2022;
Pixley et al., 2022; Biswal et al., 2023). Furthermore, it reduces
the time to develop an improved cultivar by nearly two-thirds rela-
tive to forward breeding (Dhugga, 2022). In themany countries that
have approved guidelines to consider gene-edited crops as non-
transgenic, improvedcrop varieties incur no costs for deregulation,
and the costs andprocedures for registration are similar to the can-
didates developed by traditional methods.Pre-breeding approaches
Our expert survey identified several traits for pearl millet, sorghum,
maize, groundnut, bean, and cowpea that will be impactful in miti-
gatingandadapting toclimatechange.Therehasbeen limitedwork1602 Molecular Plant 16, 1590–1611, October 2 2023 ª 2023 The Authfor several of these traits, particularly in someof these six crop spe-
cies. Therefore, there is an immediate need to intensify research to
better understand the inheritance and genetics toward developing
population improvement strategies and breeding tools.
New machine learning algorithms facilitate the identification of
candidate genes (Sun et al., 2020). Growing understanding of
structural variations in genomic regions, and comparative
genomics in related species, enabled by the availability of pan-
genomes, have further enhanced our ability to discover, validate,
and implement such knowledge in breeding programs (Ruperao
et al., 2021; Petereit et al., 2022; Yan et al., 2023). Gene editing
also provides tremendous opportunities for simple or oligogenic
traits with known causative gene information to rapidly deliver
improved germplasm where regulatory frameworks permit
(Pixley et al., 2022; Rock et al., 2023). For traits with simple or
oligogenic inheritance, these technological advances allow fast
and cost-effective genetic mapping of traits, and rapid forward
and backcross breeding using speed breeding techniques
(Ghosh et al., 2018; Wanga et al., 2021) and MAS (Bankole
et al., 2017; Baloch et al., 2023).
For complex traits, the impact of genomic selection in acceler-
ating genetic gain in crop breeding has been facilitated by
cheaper costs of mid-density genotyping, the availability of
computing power, new and novel algorithms, and rapid recycling
of elite material through doubled-haploid and speed-breeding
methods (Jeon et al., 2023). Genomic selection will be
appropriate for improving many of the traits identified in surveys.
Over the last decade, there have been several successful uses of
high-throughput phenotyping tools, such as drone- and satellite-
based images to rapidly screen thousands of breeding plots with
higher accuracy. There are several options already available to
deploy in breeding programs and active areas of research. These
technologies combined with machine learning algorithms have
significantly improved our ability to measure traits reliably and
consistently and allowed us to measure component traits, which
were previously unthinkable due to labor costs or other con-
straints (Gill et al., 2022). Such technologies can be used to
dissect genetics and reliably measure component traits at
higher scale, accuracy, and precision in breeding programs.
Despite tremendous technological advancements for breeding
crop varieties, their use is often limited by genotype-by-
environment or genetic background effects, and availability of
digital platforms to integrate genetic information in decision mak-
ing. Most of the investments are in model species, in developed
countries (Marks et al., 2023), and targeting commercial traits,
crops, and cropping systems (Pixley et al., 2019, 2022). This
disproportional investment in crops and geographies is
concerning and challenges efforts to upscale the use of
technologies equitably to benefit farmers and societies where
agriculture is most vulnerable to changing climate.BREEDING FOR FUTURE CROPPING
SYSTEMS
The demand exerted by a rising middle class and growing popula-
tion will continue to put pressure on agriculture to intensify.or.
Redesigning crop varieties for changed climate Molecular PlantNutritionally dense food and feed are expected to be in demand,
which will require breeding attention to novel traits as predicted
by survey respondents (Figure 1). On the other hand, our survey
did not explore additional, post-farm societal demands such as
innovative plant protein products to reduce meat consumption, or
environmental services, e.g., net carbonsequestration,biodiversity
conservation, and others (Kuyah et al., 2023). All of these growing
demands require transdisciplinary efforts, where plant breeders
work closely with diverse experts.
Intensified cropping systemswill take a range of forms, frommono-
cultures to double and triple cropping systems, to relay and inter-
crop arrangements. Cropping calendars will shift with changing
climate, and cropping options will adapt based onmanagement in-
novations, access to appropriate inputs (including varieties with
novel traits), and market forces. Mechanization, for example, is ex-
pected to increaseover timeandspace, supportinganddemanding
the use of different varieties to tolerate new stresses, e.g., sowing in
wetter soils or higher plant population density, and opportunities
such as dual-purpose, or bird-resistant, or avoiding varieties.
Increased use of hybrids is predicted by our survey to be of primary
importance in cereal crops,whichwill requireplant architecture that
is compatible with close spacing (Richards et al., 2019), and
increased levels of drought, disease, and pest tolerance expected
in such intensive planting systems (Ando et al., 2007).
Novel cropping systems will offer new stress-coping and produc-
tivity- or profit-maximizing options requiring system-optimizing
management practices and crop varieties. Complementary archi-
tectural and growth traits are already utilized in intercrop systems
such as cereal–legume associations and legume–legume systems
(Kuyah et al., 2021). For example, farmerparticipatory researchhas
shown that farmers in Rwanda select for ideotypes of beans that
perform well when intercropped with maize (Isaacs et al., 2016).
Architectural traits can be selected to facilitate complementarity,
such as slow growth aboveground, with a retarded rate of
branching in one crop, combined with selecting for rapid growth
in a complementary crop that is also selected for shade
tolerance. Maize and pigeonpea are a widely grown example of
such complementarity of plant phenotypes, which could be
enhanced through deliberate selection (Snapp et al., 2019).
Belowground competition could be minimized by developing
crops with steep root angles to reduce root overlap at the surface
(Bonser et al., 1996; Lynch et al., 2022).
As highlighted by respondents in this study, heat- and drought-
tolerant varieties will be very important to the success of future
cropping systems. Drought avoidance has been widely relied
upon historically and, as confirmed by our survey, will continue
to be important through selection for early maturing and rapid
growth types (Snowdon et al., 2021). In addition, a wide range
of plant physiological characteristics can enhance adaptation to
water deficiency and heat stress; these will need to be selected
as stand-alone traits and in combination (see maize section,
above). Crops with exceptional heat and drought tolerance
attributes, notably pearl millet, are expected to achieve further
progress in climate change adaptation traits, and some of these
traits will be extendable to related cereal crops through studies
of genomic synteny and application of modern breeding
technologies. Breeding for these traits will provide varieties for
novel cropping systems and to allow continued cultivation ofMoleccrops in their traditional agro-ecologies as climate change alters
the weather associated with them.
The ability of crops to tolerate nutrient-deficient soils is expected
to be of future importance and is highly complementary to
drought tolerance. This includes both belowground and above-
ground traits, as nutrient acquisition, allocation, and efficiency
of use are all involved (Liu et al., 2022). The plasticity of roots
and related factors that lead to large genotype by environment
interaction effects have historically complicated and slowed
progress in breeding for tolerance to low nutrient status, but the
advent of molecular and statistical tools could lead to
breakthroughs in this field. Progress in improving nutrient
acquisition and use efficiency will provide crop types that are
expected to improve the performance of conservation,
sustainable, and restorative agricultural systems.
Future scenarios that may vary widely are those driven by global-
ization, altering land use, farming systems, and market demand.
These could include greater integration of crop and livestock sys-
tems, which will increase the demand for crop types that are dual
use for fodder and food (Thornton and Herrero, 2014). Forage
quality and quantity of stover are very important in such
systems (Melesse et al., 2021). This is an area where
respondents predict rapid progress can be made. A much
longer-term project would be to breed for perennial and semi-
perennial grain crops, the prototypes of which have shown to pro-
vide a wide range of environmental services such as reduced loss
of nitrogen to the environment (Culman et al., 2013), although
others caution that perennial crops may be highly vulnerable to
pests and diseases. More specifically, enhanced soil carbon
gain has been proposed in a dual-use crop type through selection
for enhanced suberin and related biochemical properties in roots
of cereal and pulse crops (Eckardt et al., 2023). BNI is another
example of an environmentally friendly service that can
enhance crop performance in an intensive cropping system,
well suited to cereal crop genetic improvement (Subbarao
et al., 2021).
CONCLUDING REMARKS
Climate change will affect agriculture in every corner of the world.
Our survey respondents echoed predictions that temperatures
will increase, rainfall distribution will be less predictable, and
pest and disease ranges will change (Table 1). Not all changes
will be negative. Warmer temperatures will accelerate crop
development, enabling use of longer-duration and higher-
yielding varieties, or novel or intensified cropping systems
(Table 2). Optimal options for relay cropping may change in
regions where this practice is already common, such as
Indonesia, Vietnam, and India (Swastika et al., 2004; Thanh Ha
et al., 2004; Jat et al., 2020), and new opportunities may arise
in areas where only one crop was previously possible, for
example, in parts of West Africa predicted to become hotter
and wetter (Zhai et al., 2021).
Changing cropping systems will expose crops to new environ-
ments that may require or benefit from characteristics that are
not valuable in today’s varieties. Relay cropping may force crops
out from their optimal monocrop or current relay crop season,
exposing them to wetter or drier than optimal soils at planting,ular Plant 16, 1590–1611, October 2 2023 ª 2023 The Author. 1603
Molecular Plant Redesigning crop varieties for changed climatesunnier or cloudier conditions during vegetative growth, hotter or
cooler temperatures during grain fill, fewer or different insect pests,
etc. Short turn-around time between crops may incentivize rede-
signing of crop varieties, for example to facilitate mechanization
of harvest orplanting, and toprioritize rapid emergence, early vigor,
quick dry-down, and early and enhanced accumulation of nutri-
tional components in grain (e.g., protein, Fe, Zn, and provitamins
A) (Figure 1 and Table 4). Dual-purpose varieties, suitable for
grain and fodder production, may be increasingly valued for
averting the risk of crop failure during seasons when grain
production is poor or fails. For crops that will be intercropped,
traits related to growth architecture (e.g., erect leaves, branch
angle, plant height) and growth habit (e.g., early vigor, spreading
habit, determinate vs. indeterminate) will play important roles.
Breeding crop varieties for intercropping or relay crop systems
may require selection at early stages in breeding programs to
consider general and specific mixing ability (GMA and SMA),
assessing the suitability for use in multiple or specific systems
(Moore et al., 2022, 2023).
The expert surveyprioritized very few future-essential traits that are
not already targeted in current breeding programs (Table 3 and
supplemental information). These were mainly water use
efficiency in pearl millet, groundnut, and cowpea, adaptation to
cropping systems for pearl millet and maize, and suitability for
mechanization in groundnut. This finding is consistent with recent
surveys in 19 low- and middle-income countries that concluded
that changing climate has resulted in greater urgency and intensi-
fied breeding work on traits that already had high priority (Galluzzi
et al., 2020). While smarter and faster breeding for currently
important traits is essential, we suggest blind spots and
potentially large, missed opportunities from relying entirely on this
approach. We describe recent advances in diverse fields of
science that make or could soon make it feasible to breed for: (1)
optimized rhizosphere microbiome, with impacts on P, N, and
water use efficiency, (2) optimized performance across or in
specific cropping systems, (3) decreased nighttime respiration,
(4) improved stover quality, (5) increased early vigor, and (6)
improved heat tolerance. Each of these traits would be valuable
in most or all crops’ adaptation and resilience to climate change.
Survey respondents perceived a low likelihood of adoption of
sustainable agriculture approaches including reduced tillage,
increased soil cover, increased vegetative yield, and increased
use of precision machinery in agriculture to maximize efficiency
of fertilizer and other inputs (Table 2). This is a surprising result
given worldwide soil health concerns, conservation agriculture
being on the rise, and marked competition in uses for crop
residues. A strong case can be made for designing crops with
traits that are key to successful conservation farming, such as
vigorous early growth for improved performance under mulch.
The views documented here highlight a perception challenge,
suggesting that many experts view conservation farming
practices and precision agriculture narrowly, limited to
approaches that require a high degree of mechanization, which
may contribute to skepticism about adoption potential.
Breeding varieties that are redesigned for agriculture under
changed climate will require innovative phenotyping approaches
and transdisciplinary teams with expertise in agronomy, soil sci-
ence, microbiology, biochemistry, physiology, genomics, data sci-1604 Molecular Plant 16, 1590–1611, October 2 2023 ª 2023 The Authence, andmore. These teamsmust be bold enough to tackle traits
found only in exotic germplasm (see Figure 2) and for which
selection methods must be developed, validated, and optimized.
As described herein, recent and emerging methods for gene
discovery, allele mining, and plant breeding offer unprecedented
opportunities for precision, accuracy, and speed in developing
new varieties. By consequence, the greatest challenge to
developing crop varieties that win the race between climate
change and food security might be our innovativeness and
boldness in defining the future traits we breed for today.
SUPPLEMENTAL INFORMATION
Supplemental information is available at Molecular Plant Online.
AUTHOR CONTRIBUTIONS
K.V.P., project concept and lead author. J.E.C., S.L.-R., and C.O.O., co-
ordinated the sections: M.A.D. and I.D., pearl millet; T.M. and B.N., sor-
ghum; J.E.C. and G.A., maize; B.D., H. Daudi, and H. Desmae, groundnut;
B.J.B. and O.B., cowpea; C.T.M.M. and S.T.N., bean; S.J.H., allele min-
ing, including the figure; K.S.D., genome editing; H.G., pre-breeding;
S.S., breeding for cropping systems; S.L.R. and E.A.Z.-V., survey anal-
ysis, and figures and tables. All authors contributed to manuscript plan-
ning, and reviewed and approved the final manuscript.
ACKNOWLEDGMENTS
We thank all respondents of the survey who gave their valuable time and
shared their expertise, often enthusiastically and appreciative of the op-
portunity to benefit the global scientific community. We acknowledge
Dr. Roi Ben David, Institute of Plant Sciences, ARO-Volcani Center, Bet
Dagan, Israel, whose contributions to concepts and methods used in a
survey for wheat during his sabbatical visit to CIMMYT during 2018–
2019were useful in designing our survey.We also acknowledge the Excel-
lence in Breeding Platform trait team, in particular Dr. Mike Olsen, whose
initial concept of framing of germplasm trait sources along adaptation and
eliteness axes was foundational to the model presented in the allele min-
ing section. No conflict of interest declared.
Received: June 4, 2023
Revised: August 17, 2023
Accepted: September 3, 2023
Published: September 7, 2023
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