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Journal of Crop Improvement

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Genetic and genomic resources for finger millet
improvement: opportunities for advancing
climate-smart agriculture

Wilber Wambi, Gloria Otienno, Wycliffe Tumwesigye & John Mulumba

To cite this article: Wilber Wambi, Gloria Otienno, Wycliffe Tumwesigye & John Mulumba
(2021) Genetic and genomic resources for finger millet improvement: opportunities for
advancing climate-smart agriculture, Journal of Crop Improvement, 35:2, 204-233, DOI:
10.1080/15427528.2020.1808133

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Group.

Published online: 13 Sep 2020.

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Genetic and genomic resources for finger millet 
improvement: opportunities for advancing climate-smart 
agriculture
Wilber Wambia,b, Gloria Otiennoc, Wycliffe Tumwesigyea,d, and John Mulumbae

aAfrican Centre of Excellence for Climate-Smart Agriculture and Biodiversity Conservation, Haramaya 
University, Dire Dawa, Ethiopia; bNational Agricultural Research Organization, Bulindi Zonal Agricultural 
Research and Development Institute, Crops and Natural Resources department, Hoima, Uganda; cThe Alliance 
of Bioversity International-CIAT, Kampala, Uganda; dDepartment of agriculture, agribusiness, and 
environmental sciences, Bishop Stuart University, Mbarara, Uganda; eNational Agricultural Research 
Organization, National Agricultural Research Laboratories, Plant Genetic Resources Centre, Entebbe, Uganda

ABSTRACT
Finger millet (FM; Eleusine coracana (L.) Gaertn.) is becoming increas
ingly vulnerable to various climate-induced stresses, because of 
which the genetic and genomic resources will be important for 
improving the crop in the 21st century. Currently, sizable-untapped 
genetic resources exists that offer promise for FM improvement to 
biotic and abiotic stresses. Also, earlier reports elaborate on the 
potential FM genomic resources, such as molecular markers, genetic 
maps, and DNA sequence, but the data are scanty to support the 
efficient and accelerated delivery of the climate-smart FM varieties. 
This is partly attributable to the delayed availability of complete 
genome sequence (CGS) of FM. Following the latest developments 
in FM genomic research, based on the CGS, a diversity of genomic 
resources have been reported. The review, therefore, provided 
a detailed analysis on the FM genetic and genomic resources- 
aided interventions that could contribute to the three pillars of 
Climate-smart agriculture (CSA) for addressing FM production chal
lenges under changing climate. Exceptionally, it presented enriched 
information on additional useful sources of variation within FM 
genetic resources that have been screened for improving FM toler
ance to various climate-induced stresses. Also, it presents the novel 
opportunities for CSA that could come as a result of the recent 
availability of CGS data for revolutionizing the development of 
cutting-edge-molecular breeding tools. Specifically, emphasis was 
placed on genome-wide-based technologies, such as genomic 
selection (GS), gene pyramiding, and gene expression with 
the second-generation genomic biotechnologies, such as TILLING 
and EcoTILLING that are wanting and have received little attention.

ARTICLE HISTORY
Received 30 July 2019  
Accepted 6 August 2020  

KEYWORDS
Climate-induced stresses; 
climate-smart breeding; 
climate-smart varieties; 
Eleusine coracana; finger 
millet germplasm; orphan 
crop

Introduction

Finger Millet (FM) (Eleusine coracana (L.) Gaertn.) is a C4 crop that is 
envisioned to play a key role in CSA and boost food production in the face 

CONTACT Wilber Wambi wambiwilber@yahoo.com African Centre of Excellence for Climate-Smart 
Agriculture and Biodiversity Conservation, Haramaya University, Dire Dawa, Ethiopia 
This article has been republished with minor changes. These changes do not impact the academic content of the article.

JOURNAL OF CROP IMPROVEMENT
2021, VOL. 35, NO. 2, 204–233
https://doi.org/10.1080/15427528.2020.1808133

© 2020 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group. 
This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial-NoDerivatives 
License (http://creativecommons.org/licenses/by-nc-nd/4.0/), which permits non-commercial re-use, distribution, and reproduction 
in any medium, provided the original work is properly cited, and is not altered, transformed, or built upon in any way.

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of climate change, especially in the developing world (Goron et al. 2015; 
Gupta et al. 2012; Bandyopadhyay, Muthamilarasan, and Prasad 2017). This 
low-input orphan crop (Goron et al. 2015; Bandyopadhyay, 
Muthamilarasan, and Prasad 2017) has evolved across 5000 years with 
subsistence farmers majorly in Africa and Asia (Dida and Devos 2006; 
Fuller and Hildebrand 2013). It serves as a food-security crop because of 
its high nutritional value and excellent storage qualities (Chandra, Chandra, 
and Sharma 2016; Ramashia et al. 2018). Finger millet grain is gluten-free, 
rich in calcium, fiber, iron, and methionine, tryptophan, and other essential 
amino acids, with excellent malting qualities, and has a low glycemic index 
(Chandra, Chandra, and Sharma 2016; Pandian et al. 2017). More impor
tantly, FM grain contains higher calcium than other cereals (Kumar et al. 
2016), and it is also endowed with abundant phytochemicals, with distin
guished health beneficial properties, making the crop a reservoir of health- 
giving nutrients (Chandra, Chandra, and Sharma 2016).

Cumulative evidence shows that the growth and productivity of FM is 
becoming gradually vulnerable to various climate-induced biotic (pest, 
pathogens) and abiotic (solar radiation, drought, temperature, salinity) stres
ses (Gupta et al. 2017; Pavan et al. 2018). Climate change is happening so 
quickly on a global scale, and it is evident that in the last few decades, global 
agriculture has experienced increasing vulnerability because of erratic 
weather patterns, especially increased temperature and water stress (FAO 
2011; IPCC 2014, 2018). The rising CO2, coupled with other GHGs, majorly 
resulting from anthropogenic activities, is estimated to have caused approxi
mately 1.5°C of global warming above the pre-industrial levels (IPCC 2018). 
In the future, the warming is likely to range between 3.7 and 4.8°C by 2100 
(IPCC 2014), and further exacerbate agricultural production risks (IPCC 
2014; Pavan et al. 2018).

Studies affirm that with a temperature rise of 2°C or more, without 
mitigation, production of the cereal crops will be negatively affected in the 
tropics (Niang et al. 2014; IPCC 2014). According to Jena and Kalli (2018), 
like any other crop, most biological processes in FM are also temperature- 
sensitive. Plant growth could diminish in situations where the temperature is 
below 8°C or above 36°C. Additionally, the rising CO2 indirectly impacts 
plant performance through its effect on air temperature and water stress as 
well as directly by affecting plant metabolism through its role in photosynth
esis (Kanwal et al. 2014; Abebe et al. 2016). In general, climate change is 
already influencing the distribution of land suitable for cultivating many 
crops, thus significantly contributing to decreased productivity of most 
agricultural systems, especially for the resource-poor farmers (Adhikari 
et al., 2015). Furthermore, considerable evidence shows that the amount of 
land suitable for cereal crop production, including FM, will decline across the 

JOURNAL OF CROP IMPROVEMENT 205



world because of exacerbating abiotic stresses, in particular drought, salinity, 
and heat (Maqsood and Ali 2007; FAO 2015; Sudan, Negi, and Arora 2015).

Coping with the intensifying climatic challenges will necessitate adaption 
of new crop varieties that are tolerant to drought, high temperatures, flood
ing, salinity, and other environmental extremes. Consequently, the vital 
diverse FM genetic and genomic resources will become the core for strength
ening the crop’s resilience to the adverse climatic conditions through cli
mate-smart plant breeding in the 21st century (FAO 2015; Bandyopadhyay, 
Muthamilarasan, and Prasad 2017). The article, therefore, provides the latest 
knowledge on how the FM genetic and genomic resources could contribute 
to a transition to CSA to ensure increased and sustainable FM production in 
the face of climate change. It is intended to provide improved information on 
the additional screened FM germplasm base that is available for climate- 
smart breeding. Also, an updated detail on cross-compatibility, distribution, 
and genetic diversity of FM genetic resources for climate-smart breeding has 
been provided. Furthermore, expanded knowledge has been provided on the 
putative strategies for the implementation of genome-wide breeding research 
under the availability of the high-quality FM CGS data within the framework 
of CSA.

Climate-smart agriculture

Ensuring increased and sustainable FM production in the face of climate 
change requires a transition to agricultural production systems that are 
resilient to climate risks and shocks. Additionally, they should contribute 
to climate change mitigation and preservation of the vital ecosystem services 
(FAO 2011; Tumwesigye et al. 2019). Climate-Smart Agriculture (CSA) is the 
latest approach built on the grounds and experience of sustainable develop
ment that has attained recognition in addressing agricultural challenges 
under changing climate (Amin et al. 2015; Tumwesigye et al. 2019). This is 
achieved through its three dimensions namely; 1) Sustainable increase of 
agricultural productivity and incomes while conserving biodiversity, 2) 
Adapting and building resilience to climate change, and 3) Climate change 
mitigation – reducing greenhouse gas emissions (Amin et al. 2015).

Plant genetic resources constitute the base materials for crop improvement 
to withstand climate-induced biotic and abiotic stresses (FAO 2015). In 
contrast, genomic resources are genome-aided tools that accelerate the crea
tion of climate-smart crop varieties (Bandyopadhyay, Muthamilarasan, and 
Prasad 2017; Ceasar et al. 2018). Utilization of the FM genetic and genomic 
resources is one of the pathways to the CSA approach that could provide 
sustainable and cost-effective options that are crucial for increasing long- 
term crop productivity. Since FM is grown at subsistence level in marginal 
areas, this could lead to the required adaptation and mitigation options that 

206 W. WAMBI ET AL.



could ensure sustainable food and income security while preserving the agro- 
ecosystem services.

Finger millet gene pool and distribution of genetic diversity for 
climate-smart breeding

Amid increasing and unpleasant climatic conditions, next-generation breeding 
for climate-resilient cultivars of FM will rely largely on wide-scale identification 
of adaptation traits available in diverse populations and germplasm collections. 
The cultivated FM (Eleusine coracana subsp. coracana; 2 n = 4x = 36) is a likely 
product from the selection and domestication of a large-grained mutant of the 
wild E. coracana subsp. Africana, which is native to Africa but exhibits wider 
distribution to semi-arid parts of the world, especially Asia and South America 
(Dida et al., 2008; Fuller et al. 2011; Fuller and Hildebrand 2013; Dida and 
Devos, 2006). Hence, the continued existence of landraces, together with wild 
relatives, in diverse agro-ecosystems, presents the opportunity for immense and 
distinct evolutionary adaptive genetic variations. This could offer huge oppor
tunities for either selection or development of climate-resilient cultivars with 
stable yields and adaptation to abiotic (e.g., drought) and biotic (e.g., pests and 
diseases) stresses.

The national and international breeding programs are already seeking to 
develop new FM varieties that will be well adapted to climate-induced 
stresses. This is likely to increase the demand for a range of millet germ
plasm, including those of the crop wild relatives. The natural distribution of 
the wild relatives is restricted to two centers of diversity with sufficient 
variations, which include the highly variable primary center of origin in 
Africa and a secondary center in India (Fuller and Hildebrand 2013; 
Onziga, 2015; Tesfaye and Mengistu, 2018). Both the wild E. africana 
(2 n = 4x = 36; AABB genome) and cultivated FM E. coracana 
(2 n = 4x = 36; AABB genome) are important from the standpoint of 
germplasm collection and conservation, as they form the primary gene 
pool that is freely cross-compatible. Similarly, the cultivated FM is cross- 
compatible with another allotetraploid, E. kigeziensis (2 n = 4x = 38; AADD 
genome), which is also confined to the African continent with high endemi
city in eastern Africa (Dramadri. 2015). The cross-compatible diploid wild 
species E. indica (2 n = 2x = 18; AA genome), E. floccifolia (2 n = 18; BB 
genome), E. tristachya (2 n = 18; AA genome), and E. intermedia (2 n = 18; 
AB genome) form the secondary gene pool. The tertiary gene pool comprises 
diploid species E. jaegeri (2 n = 2x = 20; DD genome), E. multiflora 
(2 n = 2x = 16; CC genome), and E. verticillata (2 n = 2x = 18). 
Additionally, it has been comprehensively established that the diploid 
E. indica (wild goosegrass) is the source of the A genome in FM, but wanting 
evidence still exists on the source of B genome (Devarumath et al. 2005; Liu 

JOURNAL OF CROP IMPROVEMENT 207



et al., 2014; Hatakeyama et al. 2018; Zhang et al. 2019). Nevertheless, research 
on those species could bring novel genes that can be introgressed into the 
cultivable FM to develop high-yielding and stress-tolerant varieties, particu
larly against extreme drought, heat, salinity, low nutrients, and the devastat
ing FM blast disease, all exacerbated by climate change.

Sources of finger millet germplasm that confer tolerance to climatic 
stresses

More than 34,675 FM accessions are available in the major gene banks at 
various international and national research organizations worldwide 
(Dwivedi et al. 2012). More importantly, many of these are cross- 
compatible with the domesticated species, which offer greater opportunities 
for improvement for tolerance to the climatic stresses (Dwivedi et al. 2012; 
Saha et al. 2019; Gupta et al. 2017).

Unfortunately, the size of the collection with a promising genetic diversity 
has limited uses because of the costs associated with screening all accessions 
for traits that could be used in crop improvement programs. However, to 
maximize the usefulness of the conserved germplasm, preliminary screening 
attempts have been initiated by scientists. Core collections of 622 
(Upadhyaya et al. 2005), and a mini-core collection of 80 accessions 
(Upadhyaya et al. 2010; Babu et al. 2013) have been developed based on 
phenotypic characterization and multi-locational evaluation data recorded 
for quantitative traits.

The evaluations have identified useful variations, leading to availability of 
germplasm that is early maturing, high yielding, blast-resistant. In addition, 
a few drought- and salinity-tolerant accessions have been identified, which 
can be utilized in hybridization programs for strengthening FM resilience to 
climatic stresses. The blast-resistant accessions belonged to one wild 
(E. africana) and four cultivated (E. Coracana) races (vulgaris, plana, elon
gate, and compacta), and also possessed significant diversity for agronomic 
traits, such as maturity period, plant height, and panicle type. Similarly, many 
accessions with grains having high protein, calcium (Ca), iron (Fe), and zinc 
(Zn) were also identified that can be used to enrich the cultivated FM and 
other crops with increased nutrient levels (Babu et al. 2013).

In addition to the core and mini-core evaluations, in the last few years, 
gradual research attempts commenced at various research institutions to 
identify or develop FM genotypes with tolerance to climatic stresses 
(Table 1). So far, a few classical breeding programs in countries, such as 
India, Malawi, Zimbabwe, Kenya, Tanzania, and Ethiopia, have bred and 
released varieties with improved yield and tolerance to climatic stresses 
(Lenne et al. 2007; Mgonja et al. 2011; Sreenivasaprasad et al. 2004). 
These improved genotypes and screened materials could provide additional 

208 W. WAMBI ET AL.



useful sources of variation to the existing hub of germplasm in gene banks 
that confer tolerance to various climatic stresses for climate-smart breeding.

Furthermore, exploitation of the induced and natural mutant lines in the 
future could lead to the broadening of the genetic base for FM improvement 
against multiple climatic stresses. However, the mutant genetic resources 
available for FMs are negligible (Saha et al. 2016), which require additional 
attention. Generally, little has been done concerning the identification of 
sources of tolerance to abiotic stresses, such as drought, salinity, aluminum 
toxicity, nutrient starvation, waterlogging, and heat stress in FM. Besides, 
most of the reported screening trials were generally based on phenotypic 
data. Thus, the recent development in FM genomics research is expected to 
provide vibrant support for accurate and accelerated screening of the avail
able FM genetic resources for tolerance to various stresses. Ultimately, this 
will enhance the breeding efficiency of research programs, and hasten the 
creation and provision of climate-smart FM varieties for CSA.

Table 1. Screened finger millet germplasm base available for climate-smart breeding.
Traits and accessions Country Reference

Blast resistance trait
NW Himalayan, VHC3997, VHC3996 and VHC3930, 

IE-4795, VL-149, DM-7, PR-202, GPU-76, VR-948, 
BR-2, TNAU-1063, RAU-8, TNAU-1066, GPU-67, 
OEB-532, PPR-2885, and IE-4709

India Babu et al. (2014); Ramakrishnan et al. 
(2016); Ganesha et al. (2018); Saha et al. 
(2019)

KNE 688, KNE 814, KNE 1149, P 224 (Pese 1), 
Seremi 1, Seremi 2, Gulu E, SX8, SEC 915, KNE 
409, KNE 1098, KNE 409, and 1098

Kenya 
Ethiopia 
Uganda

Lenne et al. (2007); Mgonja et al. (2011); 
Sreenivasaprasad et al. (2004)

Drought and salt tolerance traits
ML 181, ML-365, IE 4797, PR202, MR1, GPU28, and 

Trichy 1
India Hittalmani et al. (2017); Rahman et al. 

(2014); 
Hatakeyama et al. (2018) 
Singh et al. (2014b)

High proteins, calcium, iron and zinc level traits
GE-6834-1, VL-384, GE-728, VR-1034; JWM-1, VR- 

1034, OUAT-2, TNEC-1234, GPU-71, VR-936, 
GPHCPB45, GPHCPB44, IE2957 and IE6537, GP- 
45 
GPHCPB-17, GPHCPB-20, GPHCPB-21, GPHCPB- 
26, GPHCPB-33, GPHCPB-35, GPHCPB-36, 
GPHCPB-37, GPHCPB-40, GPHCPB-42, GPHCPB- 
44, GPHCPB-45, and GPHCPB-52

India Saritha (2015); 
Yadav., Kumar., and Thakur (2017); Akbar 
et al. (2018); 
Panwar et al. (2010); Chinchole et al. 
(2017)

Phosphorus starvation tolerance traits
GPU45, IE5201, IE2871, IE7320, GPU66, HOSUR1, 

TCUM1, IE2034, SVK1, RAU8, VR708, and IE3391
India Ramakrishnan et al. (2017)

Nitrogen starvation tolerance traits
GE-3885 India Gaur et al. (2018); 

Kanwal et al. (2014); 
Gupta et al. (2018)

Aluminum toxicity tolerance trait
Gute and Degu Ethiopia Brhane et al. (2017)

JOURNAL OF CROP IMPROVEMENT 209



Genomic resources available for enhancing finger millet resilience to 
climatic stresses

Based on the NCBI database (https://www.ncbi.nlm.nih.gov/), in general 
FM has narrow genomic resources as compared with other major cereals, 
which hamper further improvement of this crop. As reported by Ceasar 
et al. (2018), FM has only 1934 ESTs associated with drought, salinity, and 
disease-tolerance traits. These are approximately 662.4, 1046.3, and 434.5 
times less compared with rice, maize, and barley, respectively. Nevertheless, 
within grasses, comparative genomics has been well studied, and can con
tribute considerably to marker-assisted selection efforts for tolerance to 
numerous climatic stresses in FM (Yadav et al. 2014; Ramakrishnan et al. 
2016, 2017; Hittalmani et al. 2017; Pandian et al. 2018). The EST projects 
have yielded a vast amount of sequence data for other grasses that are 
publicly available at the NCBI Genbank database. With the help of bioinfor
matics tools, SSRs could be mined through in-silico synteny analysis across 
the grass genomes.

Studies have also revealed high transferability of genic SSR markers 
associated with tolerance to climatic stresses and superior agronomic 
traits, such as blast tolerance, Ca, and yield among grasses, including 
FM (Yadav et al. 2014; Ramakrishnan et al. 2016). Such transferability 
of genomic resources from other well-studied grasses to FM, supported by 
the extensive gene-level synteny shared between the grass genomes, could 
be useful for improving the less-studied orphan crop for many complex 
climatic stresses.

Using Roche 454 and Illumina Next Generation Sequencing (NGS) tech
nologies, 10,327 SSRs, and 23,285 non-homeologous first SNPs were reported 
in FM (Gimode et al. 2016). Furthermore, following the recent whole- 
genome research development for FM (Hittalmani et al. 2017), ample geno
mic resources with numerous opportunities for CSA have been reported. 
This wealth of high-quality genomic data that include among others 114,083 
SSRs, 1766 R-genes, 2866 drought-responsive genes, 146 C4-pathway genes, 
56 families of transcription factors (TFs), and 330 calcium transport and 
accumulation-related genes also exists at the NCBI Genbank database for 
public use. Possibly, it could serve as a reference for modernizing FM 
molecular research in the future.

Prospects for the development of climate-smart finger millet varieties 
using genome-aided tools

Even though conventional breeding approaches have continued to contri
bute to genetic improvement of important traits in FM, their efficiency can 
be increased considerably by supplementation with genome-aided breeding 

210 W. WAMBI ET AL.

https://www.ncbi.nlm.nih.gov/


tools. However, the absence of FM CGS hampered the needed paradigm 
shift with respect to molecular-marker development, diversity assessment, 
linkage-map construction and quantitative trait locus/loci (QTL) mapping 
(Upadhyaya et al. 2010; Dwivedi et al. 2012; Saha et al. 2019; Gupta et al. 
2017). As a result, the breeding progress, for improving tolerance to 
climatic stresses, has been slow and difficult for this orphan crop. 
Nevertheless, comparative genomic studies within grasses, have contribu
ted primarily to the development of molecular marker systems that could 
be exploited for climate-smart breeding in FM. Thus, we update on the 
available potential key markers/QTL and candidate genes that could sup
port climate-smart molecular breeding.We also highlight the prospects for 
the implementation of genome-wide breeding research under the avail
ability of the high-quality FM CGS data in the context of CSA.

Potential molecular tools for genetic diversity and population 
structure analysis for enhancing climate-smart breeding in FM

Development of climate-smart cultivars could require introgressing stress- 
tolerance traits into various genetic backgrounds. Therefore, accurate 
assessment of genetic diversity and population structure for the vast 
amount of FM germplasm maintained in gene banks worldwide is crucial 
for genetic resource management, trait mapping, and crop improvement. 
A few studies have attempted to exploit molecular tools for the analysis of 
genetic diversity and structure in the landraces, collections, and wild 
germplasm accessions of this orphan crop (Table 2). The findings provide 
foundation knowledge about the level of polymorphism exhibited by the 
different markers for discerning useful variation among FM genotypes that 
could be exploited in breeding programs against various climatic stresses. 
For instance, various FM genotypes from cultivated and wild germplasm 
have been identified as most diverse parents that could generate high-vigor 
cultivars through hybridization. The genotypes harbor novel genes that 
hold potential for improving FM for Ca accumulation, variable seed-coat 
color, high grain-nutrient content, blast-resistance and drought-tolerance 
traits (Gupta et al. 2010; Panwar et al. 2010; Babu et al. 2014; Dramadri. 
2015; Saha et al. 2019). These genotypes could be exceptionally used as 
parental lines for developing climate-smart cultivars.

In general, almost all the past diversity-assessment studies were based on 
PCR and EST markers that were mined through in-silico analysis (Table 2). 
These markers could have some limitations, as the development of accurate 
primers, in the absence of complete genomic information, is quite difficult 
(Garibyan and Avashia 2013: Khar and Saini 2016). Additionally, a limited 
number of genotypes have been analyzed for a few traits, and the number of 
markers available for diversity analysis is still small. Application of the raw 

JOURNAL OF CROP IMPROVEMENT 211



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212 W. WAMBI ET AL.



data of the current genome is expected to explode and modernize 
a systematic and accurate analysis of the diversity existing within cultivated 
and wild FM germplasm. To this end, the complete genome will provide 
a strong platform for mining highly informative genomic markers, such as 
SSRs and SNPs. These could be increasingly used as next-generation markers 
of choice for accurate genotype identification and diversity analysis in FM, as 
done in other major cereals (Samayoa et al., 2015; Zhang et al. 2016; Pavan 
et al. 2018). Actually, this will help to inform sound breeding programs and 
define suitable genotypes with superior alleles that meet the breeding 
demands.

Identification of QTL associated with climatic stress tolerance traits

The majority of the traits that confer tolerance to climatic stresses such as 
disease, drought, salinity, nutrient starvation tolerance are complex and 
governed by QTL (Ceasar et al. 2018; Ramakrishnan et al. 2016, 2017; 
Serba and Yadav 2016; Sharma et al. 2014; Yadav, Sehgal, and Vadez 2011; 
Yadav et al. 2014). Hence, genetic improvement of such traits can be 
achieved through marker-assisted breeding once the QTL are identified and 
mapped.

At present, largely, the resistance genes (R-genes) are not yet mapped in 
FM. A few studies have, however, mapped R-genes for blast disease that were 
based on in-silico analysis (Table 3). According to Babu et al. (2014), four 
QTL for finger blast resistance and one for neck blast resistance were 
reported through association mapping using 104 SSRs to screen 190 FM 
genotypes via the general linear model (GLM) approach. Likewise, via the 
mixed linear model (MLM) approach, seven markers were associated with 
QTL for blast disease resistance; 3 with leaf, 1 with neck, and 3 with finger 
blast. Both the GLM and MLM approaches revealed three common markers, 
i.e., RM262, FMBLEST32, and UGEP18 that were linked to blast disease 
resistance QTL. The markers explained 5–13% phenotypic variance (R2), and 
were concentrated on chromosomes 1B, 2A, 3B, 4B and 6B of FM. Probably, 
these represent the major hub of finger blast and neck blast resistance genes. 
In a subsequent association mapping study using 87 genomic SSR markers, 
128 FM germplasm collections, originating from major diversity centers both 
in India and abroad, were analyzed. A total of seven QTL were found to be 
associated with various agronomic traits, including leaf blast resistance 
(Ramakrishnan et al. 2016). Two markers (UGEP101 and UGEP95) were 
strongly associated with leaf blast resistance QTL, and explained 21.05 and 
8.95% phenotypic variation respectively.

This preliminary information on blast resistance QTL, along with the 
associated markers, could be useful for the development of climate-resilient 
genotypes with high resistance to blast disease and acceptable agronomically 

JOURNAL OF CROP IMPROVEMENT 213



superior traits through marker-assisted QTL introgression. However, the 
markers were developed through in-silico analysis using primers designed 
from the Magnaporthe grisea (rice blast fungus) genes and several cloned rice 
blast Pi genes (Babu et al. 2014). Therefore, for the next-generation breeding, 
the arrival of the complete FM genome is expected to be a resource for fine 
mapping and validation of these QTL, along with the associated genic 
markers. Indeed, it will shorten the breeding for climate-smart cultivars, 
especially with high resistance to blast disease and acceptable agronomic 
traits. Resistance to the devastating blast disease exacerbated by climate 
change could minimize chemical use and lead to reduced emission of 
GHGs as well.

Finger millet is specifically Ca-rich compared to other cereals (Kumar 
et al. 2016). It is also a locally well-adapted semi-arid crop that is expected 
to drive food security for the developing world under climatic change-related 

Table 3. Details of markers associated with climatic stress-tolerance and superior agronomic 
traits for climate-smart breeding.

Trait Marker

Phenotypic variance 
explained (%) 

(R2) Chromosome Reference

Finger blast RM262 5–10 2A Babu et al. (2014)
FMBLEST32 4.5–8 6B
UGEP81 7.50 6B
UGEP53 10.50 -
UGEP24 8.00 3B

Leaf blast FMBLEST35 10.00 4B
FMBLEST15 8.00 4B
RM23842 11.00 6B

Neck blast UGEP18 11–13 1B
Leaf blast UGEP101 21.05 Ramakrishnan et al. 

(2016)UGEP95 8.95
Plant height UGEP50 6.69
Number of tillers UGEP98 9.53

UGEP65 11.72
Number of 

productive tillers
UGEP98 7.00
UGEP65 7.00
SSR01 6.51

Number of fingers UGEP104 6.85
UGEP75 6.31

Length of root UGEP9 8.12
UGEP57 6.28

Seed yield UGEP9 10.71
UGEP19 7.63
UGEP80 6.78

Ca accumulation UGEP78 
UGEP60

1B Yadav., Kumar., and 
Thakur (2017)

LRDW† UGEP19 9.5–14.3 Ramakrishnan et al. 
(2017)UGEP68 6.5–10.6

HSDW‡ UGEP13 12.7
HRL§ UGEP90 9.2

214 W. WAMBI ET AL.



stresses. Hence, the identification of QTL controlling nutrient signaling and 
Ca accumulation traits will be essential for improving FM shortly and 
enriching other cereals with elevated Ca levels. A total of 9 QTL associated 
with Ca content were identified in 113 genotypes of FM using 14 anchored- 
SSR markers that were designed from calcium transporters and sensors 
(Kumar et al. 2015). Through association analysis, using a global collection 
of 238 genotypes, and 85 genic and non-genic (SSR) markers, two genomic 
SSR markers (UGEP78 and UGEP60) were reported to be significantly 
associated with grain calcium content (GCC) (Yadav., Kumar., and Thakur 
2017). UGEP60 marker is linked to QTL for GCC that belongs to linkage 
group 1B of finger millet, which is also syntenous with rice chromosome 1 
harboring a QTL for calcium content. Though the identified QTL/markers 
could kick-start the genetic improvement of calcium content in finger millet, 
the availability of the complete genome is expected to contribute to the next 
generation advancement for fine mapping QTL associated with this trait. 
This could enhance successful genetic improvement of low-Ca FM genotypes 
and the other cereals under the stresses associated with climate change.

It has already been established that under extreme drought, uptake of 
nutrients, such as nitrogen (N) and phosphorous (P), in plants will be 
adversely affected (Goron et al. 2015; Gupta et al. 2012; Ramakrishnan 
et al. 2017; Bista et al. 2018). However, nutrient signaling breeding in FM 
has not yet been exploited partly because of the scanty molecular information 
about the QTL governing nutrient-uptake mechanisms. Based on association 
mapping of 128 FM genotypes from 18 countries two QTL (qLRDW.1 and 
qLRDW.2) were found to be associated with root dry weight, under low P, 
using 72 SSR markers (Ramakrishnan et al. 2017). The same authors reported 
two other QTL, viz., qHSDW.1 and qHRL.1, under P-sufficient conditions, 
which affected shoot dry weight and root length. The four reported QTL, viz., 
qLRDW.1, qLRDW.2, qHSDW.1, and qHRL.1, were linked to UGEP19, 
UGEP68, UGEP13, and UGEP90 markers, respectively (Table 3).

So far, a few QTL mapping studies related to nutrient signaling and 
accumulation have been conducted in FM (Ramakrishnan et al. 2017; 
Kumar et al. 2016). Under the changing climate scenario, a detailed under
standing of nutrient deficiency QTL will be important for the development of 
low-nutrient-tolerant FM cultivars. Therefore, the complete-genome-aided 
research is expected to help in the precise detection of nutrient-starvation- 
tolerance QTL for MAS. Eventually, it will facilitate the selection of either 
cultivars for areas where nutrient deficiency is noticeable or germplasm lines 
that could be used as donors for nutrient-starvation-tolerance genes. Thus, 
this will help to enhance productivity and resilience of resource-poor farm
ers, especially with low purchasing power for expensive fertilizers, and 
simultaneously reduce GHG emissions through minimal fertilizer 
application.

JOURNAL OF CROP IMPROVEMENT 215



Even though the highlighted foundation studies inform about the 
genetic loci associated with various climatic stresses, it is typically difficult 
to isolate candidate genes based on such few QTL-mapping experiments. 
The availability of the recent CGS will be instrumental in rapid validation, 
discovery, and fine mapping of QTL associated with complex stress- 
tolerance traits. The resultant high-density maps based on genome-wide 
next generation markers, such as SNPs and SSRs, could precisely facilitate 
the identification of genes, gene cloning, and gene pyramiding for 
improving traits that determine yield or/and confer tolerance to multiple 
climatic stresses in FM.

Linkage and association mapping are the two most common methods used 
for identifying QTL conditioning complex traits; through these methods 
genes/QTL have been identified in different plant species (Yang et al. 2011; 
Zhang et al. 2016; Lule et al. 2018; Sharma et al. 2018). Since the development 
of bi-parental mapping populations for small millets is a difficult, the classi
cal linkage analysis of QTL for traits associated with climatic stresses is 
limited. Also, large mapping populations are required to achieve high- 
resolution maps. It could be presumed that the genome-wide association 
studies (GWAS) and genotyping-by-sequencing in FM could be ignited by 
the advent of the CGS. These could evolve as powerful second-generation 
biotechnological tools for high-resolution QTL mapping and SNP discovery 
in FM, as in other well-studied cereals, such as maize (Cappa et al., 2013; 
Samayoa et al., 2015; Zhang et al. 2016). Accordingly, this could lead to 
overcoming limitations associated with the traditional QTL-analysis 
approach.

In addition, the availability of genome-wide high-density markers that 
cover the whole genome could further provide opportunities to increase 
genetic gains for complex traits through genomic selection (GS). With the 
continuous decline in sequencing costs, coupled with the availability of high- 
throughput sequencing platforms, the next-generation marker technology 
could provide hope for the selection of superior FM genotypes based on 
accurate breeding values. Hence, these could constitute foundation breeding 
populations for developing climate-smart FM cultivars at a low cost under 
the current climate-change scenario.

Functional characterization of key genes associated with 
climate-change-induced stresses

Under the present situation, it has been understood that climate-change- 
induced stresses, such as diseases, drought, salinity, and aluminum toxicity, 
have a serious effect on nutrient uptake, assimilation, and carbon metabo
lism in plants (Maqsood and Ali 2007; Goron et al. 2015; Bista et al. 2018). 
These effects are expected to further exacerbate agricultural production risks 

216 W. WAMBI ET AL.



in the future. Therefore, considerable research attention, focusing on the 
identification of the candidate genes associated with climatic stresses for 
enhancing FM resilience, could contribute to the required adaptation 
strategies.

Finger millet, a C4 crop, has a higher calcium content than some other 
cereals (Kumar et al. 2016), and it is likely to have evolved unique mechan
isms that permit the plant to perform well under low nitrogen and adapt to 
a wide range of environmental stresses, such as drought, salinity, aluminum 
toxicity, and diseases (Goron et al. 2015; N. Gupta et al. 2012; 
Bandyopadhyay, Muthamilarasan, and Prasad 2017). It is suggested that the 
genes underlying these complex mechanisms are driven by strong promoters, 
transcription factors, and regulatory proteins (Gaur et al. 2018; Pudake et al. 
2017; Rahman et al. 2016; Ramakrishna et al. 2018; Ramegowda et al. 2012; 
Sharma et al. 2017; Singh et al. 2014a, 2015). However, a lack of compre
hensive understanding of these underlying mechanisms, unlike in other well- 
studied cereals, such as rice, has been a bottleneck, especially because of 
availability of scanty genomic information. Nevertheless, based on model 
crops and comparative genomics, opening studies have been reported on the 
expression profile of some genes associated with stress tolerance, which could 
be used for climate-smart breeding (Table 4).

Most plants, including FM, obtain their mineral nutrients from the soil 
and transport them using nutrient-uptake proteins located in the cellular 
membranes of roots and shoots (Pudake et al. 2017; Sharma et al. 2017; Singh 
et al. 2014a, 2015). For instance, ammonium is taken up by the high-affinity 
AMT1family, while nitrate uptake is associated with members of the NRT1 
and NRT2 families of transporters with low-affinity NO3

− transporters at 
high N levels and high-affinity NO3

− transporters at low N levels, respectively 
(Dechorgnat et al. 2010; Xu, Fan, and Miller 2012). Similarly, phosphorus (P) 
is taken up by roots via the activity of PHT1-type transport proteins (Varma 
et al., 2017; Pudake et al. 2017). Most of the genes expressed in roots are up- 
regulated in P-stressed plant for this PHT1 family (Smith et al. 2003). Three 
ATP-binding cassette (ABC) (LOC_ Os11g39020, LOC_Os02g32690, 
LOC_Os01g24010) transporters and KUP (potassium uptake permease) 
potassium type transporters were reported by Rahman et al. (2014). The 
same authors reported several other transporters involved in the transport of 
various cations and anions, including metal cation transporter 
(LOC_Os03g46470) and proton antiporter-2 family (LOC_Os11g42790). 
These were significantly up-regulated in response to salinity stress in 
a tolerant FM genotype. This initial understanding of transport proteins 
forms a promising basis for crop improvement. In the future, their genetic 
manipulation under availability of FM CGS could be important in enhancing 
wide adaptation to soil nutritional, drought, and salinity stresses. For 
instance, wide-scale genome-aided alteration of sodium or potassium 

JOURNAL OF CROP IMPROVEMENT 217



Ta
bl

e 
4.

 C
an

di
da

te
 g

en
es

 a
ss

oc
ia

te
d 

w
ith

 s
tr

es
s 

to
le

ra
nc

e 
av

ai
la

bl
e 

fo
r 

fin
ge

r 
m

ill
et

 (
FM

) 
im

pr
ov

em
en

t.

Ca
nd

id
at

e 
ge

ne
s

Ex
pr

es
si

on
 r

eg
io

n
Po

te
nt

ia
l 

so
ur

ce
s

O
pp

or
tu

ni
ty

 f
or

 c
lim

at
e-

sm
ar

t 
ag

ric
ul

tu
re

Re
fe

re
nc

e

N
 u

pt
ak

e 
an

d 
as

si
m

ila
tio

n
Ec

H
N

RT
2,

 E
cL

N
RT

1,
 E

cN
AD

H
-N

R,
 E

cG
S,

 E
cF

d-
G

O
G

AT
, a

nd
 E

cD
of

1
Al

l i
nd

uc
ed

 in
 le

av
es

 E
xc

ep
t 

Ec
H

N
RT

2 
w

hi
ch

 in
du

ce
d 

in
 r

oo
t

FM
D

ev
el

op
m

en
t 

of
 N

U
E 

va
rie

tie
s

G
up

ta
 e

t 
al

. 
(2

01
3)

Ec
α-

pr
ol

am
in

 g
en

e
Ro

ot
, s

te
m

, l
ea

ve
s 

an
d 

se
ed

lin
g 

st
ag

e
FM

 
Ba

rle
y

D
ev

el
op

m
en

t 
of

 N
U

E 
va

rie
tie

s
G

au
r 

et
 a

l. 
(2

01
8)

G
en

es
 In

vo
lv

ed
 in

 C
a 

Tr
an

sp
or

t
CA

X1
, T

PC
1,

 
Ca

M
-s

tim
ul

at
ed

 t
yp

e 
IIB

 C
a2

+
 A

TP
as

e 
an

d 
tw

o 
Ca

M
 d

ep
en

de
nt

 
pr

ot
ei

n 
ki

na
se

 (
Ca

M
K1

 a
nd

 2
)

Ro
ot

 
st

em
 s

pi
ke

FM
 

W
he

at
 

Ri
ce

 
Ba

rle
y 

M
ai

ze
 

So
rg

hu
m

En
ha

nc
in

g 
Ca

 u
pt

ak
e 

an
d 

de
ve

lo
pm

en
t 

of
 c

al
ci

um
 b

io
fo

rt
ifi

ed
 c

ro
ps

M
irz

a 
et

 a
l. 

(2
01

4)

Ca
 s

en
so

r 
ge

ne
s 

fa
m

ily
 

Ca
M

 a
nd

 C
aM

Ls
, C

BL
s, 

CI
PK

s, 
CR

Ks
, P

EP
RK

s, 
CD

PK
s, 

Ca
M

Ks
, a

nd
 

CC
aM

K.

sp
ik

es
FM

 R
ic

e 
So

rg
hu

m
 

M
ai

ze

D
ev

el
op

in
g 

Ca
-b

io
fo

rt
ifi

ed
 c

ro
ps

Si
ng

h 
et

 a
l. 

(2
01

4b
)

Ca
 t

ra
ns

po
rt

er
 g

en
es

 in
cl

ud
in

g 
Ca

2+
 A

TP
as

es
, C

a2
+

/c
at

io
n 

ex
- 

ch
an

ge
rs

 a
nd

 C
a2

+
 c

ha
nn

el
Se

ed
FM

 
Ri

ce
D

ev
el

op
in

g 
Ca

-b
io

fo
rt

ifi
ed

 c
ro

ps
Si

ng
h 

et
 a

l. 
(2

01
5)

CI
Pk

24
ro

ot
, s

ho
ot

, l
ea

f 
an

d 
de

ve
lo

pi
ng

 
sp

ik
e 

tis
su

es
FM

 G
P-

45
 

Ri
ce

En
ha

nc
in

g 
Ca

 u
pt

ak
e 

an
d 

de
ve

lo
pi

ng
 

Ca
-b

io
fo

rt
ifi

ed
 c

ro
ps

Ch
in

ch
ol

e 
et

 a
l. 

(2
01

7)
G

en
es

 in
vo

lv
ed

 in
 c

ar
bo

n 
(C

) 
m

et
ab

ol
is

m
Ca

b,
 R

BC
S,

 P
EP

C,
 P

PD
K,

 P
EP

C-
k,

 M
E,

 S
PS

, P
K,

 1
4-

3-
3 

an
d 

Sn
RK

1
Le

av
es

 o
f 

se
ed

lin
gs

FM
 

M
ai

ze
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ar
le

y 
Ri

ce
 

W
he

at
 

So
rg

hu
m

Se
le

ct
io

n 
of

 g
en

ot
yp

es
 f

or
 b

et
te

r 
ag

ro
no

m
ic

 p
er

fo
rm

an
ce

 a
nd

 
En

ha
nc

in
g 

ne
t 

CO
2 

as
si

m
ila

tio
n 

in
 t

he
 n

ea
r 

fu
tu

re
.

Ka
nw

al
 e

t 
al

. 
(2

01
4)

G
en

es
 in

vo
lv

ed
 in

 p
ho

sp
ha

te
 t

ra
ns

po
rt

Fo
ur

 p
ho

sp
ha

te
 t

ra
ns

po
rt

er
 g

en
es

 (
Ec

PT
1 

to
 E

cP
T4

)
ro

ot
s 

an
d 

le
av

es
 o

f 
se

ed
lin

g
FM

 
Ri

ce
 

M
ai

ze

Im
pr

ov
in

g 
FM

 t
ol

er
an

ce
 t

o 
P 

st
ar

va
tio

n
Pu

da
ke

 e
t 

al
. 

(2
01

7)

G
en

es
 In

vo
lv

ed
 in

 d
ro

ug
ht

 S
tr

es
s 

To
le

ra
nc

e
Ec

D
eh

yd
rin

7
Se

ed
lin

g
FM

D
ev

el
op

m
en

t 
of

 t
ol

er
an

t 
dr

ou
gh

t 
an

d 
he

at
 c

ro
ps

Si
ng

h 
et

 a
l. 

(2
01

4b
)

(C
on

tin
ue

d
)

218 W. WAMBI ET AL.



Ta
bl

e 
4.

 (
Co

nt
in

ue
d)

. 

Ca
nd

id
at

e 
ge

ne
s

Ex
pr

es
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on
 r

eg
io

n
Po

te
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l 

so
ur

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or

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t 
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ric
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fe

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2,
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 R
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P,
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YP
FM

 
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ai
ze

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ov
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CI
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31
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FM
 

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xt

ai
l m

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ev

el
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ht

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t 
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s

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ar
ju

na
 

et
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l. 
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01
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en

es
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lv

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al

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ity

 t
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er
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ce
Va

sc
ul

ar
 A

TP
 s

yn
th

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e 

ge
ne

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 L
O

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O

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O

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ua

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rin

 p
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te
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ng
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en
es

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O

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O

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er

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O

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L_

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AK

_D
U

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6 

LO
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O
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79
0

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av

es
 a

nd
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ho
ot

s
FM

 
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ce
Im

pr
ov

in
g 

to
le

ra
nc

e 
to

 s
al

in
ity

Ra
hm

an
 e

t 
al

. 
(2

01
4)

Bi
P,

 P
D

IL
, a

nd
 C

RT
1

le
af

, s
ho

ot
, r

oo
t, 

pa
ni

cl
e,

 a
nd

 
ge

rm
in

at
ed

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ee

dl
in

g
To

ba
cc

o 
FM

 
M

ai
ze

 
Ri

ce

D
ev

el
op

m
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t 
of

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al

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ity

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ol

er
an

t 
cr

op
s

Ra
m

ak
ris

hn
a 

et
 a

l. 
(2

01
8)

; 
Li

u 
an

d 
H

ow
el

l 
(2

01
0)

LE
A1

4,
 r

d2
9A

, r
d2

9B
, S

O
D

, A
PX

, A
D

H
1,

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SP

70
 a

nd
 P

P2
C

se
ed

lin
gs

FM
 

So
rg

hu
m

 
To

ba
cc

o

D
ev

el
op

m
en

t 
of

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ra

ns
ge

ni
c 

cr
op

s 
w

ith
 

to
le

ra
nc

e 
to

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iv

er
se

 s
tr

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se

s.
Ba

bi
th

a 
et

 a
l. 

(2
01

5)

JOURNAL OF CROP IMPROVEMENT 219



transporters to improve tolerance to salinity, aluminum (Al) transporters to 
increase tolerance to Al toxicity, and nitrogen and phosphorus transporters 
for enhancing nutrient-starvation tolerance could contribute to the develop
ment of climate-resilient FM genotypes.

Additionally, the expression patterns of genes involved in nutrient 
signaling and response to abiotic stresses, such as drought and salinity, 
are primarily regulated at the transcriptional level by the promoter and 
several motifs recognized by plant-specific transcription factors (Table 5). 
These largely regulate the expression of multiple downstream target genes 
under stress conditions (Rahman et al. 2014). Preliminary reports on 
a few transcription factors (TFs) associated with climatic stresses in FM 
are listed in Table 5. In addition, the current published complete FM 
genome sequence possesses numerous transcription factors involved in 
nutrient signaling and response to abiotic stresses (Hittalmani et al. 
2017). Consequently, the wealth of TFs housed by the currently released 
CGS could provide additional potential tools for manipulating stress 
tolerance in FM. These could further enhance studies to identify impor
tant pathways for the accumulation of diverse protective osmolytes, such 
as proline, associated with physiological response to osmotic stress caused 
by drought or salinity (Aleksza et al. 2017; Khatoon and Singh 2016). For 
instance, under adverse conditions, proline, which is regulated by the 
MYB type transcription factors PHR1 and PHR1-LIKE1 (PHL1), acts as 
an osmoprotectant, stabilizing cellular structures and enzymes, scavenging 
reactive oxygen species (ROS), and maintaining redox equilibrium (Sudan, 
Negi, and Arora 2015; Aleksza et al. 2017). Indeed, such benefits could 
shrink GHG emissions from fossil fuel-dependent agricultural activities, 
such as irrigation, and inorganic fertilizer production. (Table 6)

In general, most of the previous expression-profiling studies for FM were 
based on model crops, such as Arabidopsis thaliana, rice, and tobacco. The 
introduction of CGS data could serve as an anchor resource that could 
stimulate similar studies as those on model plants. It is expected to provide 
novel opportunities for the rapid translation of genetic information through 
comparative genomic analysis between FM and closely related crops or other 
less-studied cereals. This will ultimately contribute to the required adapta
tions through crop diversification.

With the advent of complete genome raw data, gene-analysis studies could 
be aided with reverse genetic mutagenesis-based second-generation genomics 
biotechnologies including TILLING (Kashtwari, Wani, and Rather 2019), 
EcoTILLING (Bajaj et al. 2016), and other cutting-edge scientific tools, 
such as CRISPR/Cas9 (Miglani 2017). These non-transgenic reverse- 
genetics approaches are expected to have a broader application to plant 
species regardless of ploidy level or genome size (Barkley and Wang 2008). 
In the near future, they could serve as climate-smart high-throughput 

220 W. WAMBI ET AL.



Ta
bl

e 
5.

 T
ra

ns
cr

ip
tio

n 
fa

ct
or

s 
as

so
ci

at
ed

 w
ith

 s
tr

es
s 

to
le

ra
nc

e 
av

ai
la

bl
e 

fo
r 

fin
ge

r 
m

ill
et

 im
pr

ov
em

en
t.

Tr
an

sc
rip

tio
n 

fa
ct

or
s

Ex
pr

es
si

on
 s

ite
s

So
ur

ce
 o

f 
ge

ne
O

pp
or

tu
ni

ty
 f

or
 C

SA
Re

fe
re

nc
e

Ec
D

of
 g

en
es

ro
ot

, s
te

m
, l

ea
f, 

an
d 

de
ve

lo
pm

en
ta

l 
st

ag
es

 o
f 

sp
ik

es
FM

 
So

rg
hu

m
 

Ri
ce

D
ev

el
op

m
en

t 
of

 n
itr

og
en

 u
se

 e
ffi

ci
en

t 
(N

U
E)

, 
bi

of
or

tif
ie

d 
va

rie
tie

s,
 a

nd
 t

ho
se

 a
do

pt
ed

 u
nd

er
 in

cr
ea

si
ng

 C
o 2

 

fo
r 

yi
el

d 
in

 t
he

 n
ea

r 
fe

at
ur

e

Ka
nw

al
 e

t 
al

. (
20

14
); 

G
up

ta
 e

t 
al

. (
20

18
)

O
PA

Q
U

E2
 (

O
2)

 li
ke

 T
F

Ro
ot

, s
te

m
, l

ea
ve

s,
 a

nd
 s

ee
dl

in
g 

st
ag

e
FM

 
Ba

rle
y

D
ev

el
op

m
en

t 
of

 N
U

E 
va

rie
tie

s 
an

d 
bi

of
or

tif
ie

d 
cr

op
s

G
au

r 
et

 a
l. 

(2
01

8)

Ec
TA

F6
Sh

oo
t, 

Ro
ot

, 
se

ed
lin

g

FM
 

Ri
ce

im
pr

ov
ed

 
sa

lin
ity

 a
nd

 d
ro

ug
ht

 t
ol

er
an

ce
s

Pa
rv

at
hi

 e
t 

al
. (

20
19

)

Ec
bH

LH
57

le
av

es
FM

 
So

rg
hu

m
D

ev
el

op
m

en
t 

of
 s

al
in

ity
 a

nd
 d

ro
ug

ht
 s

tr
es

s 
cr

op
s

Ba
bi

th
a 

et
 a

l. 
(2

01
5)

Ec
N

AC
67

 T
F

le
av

es
, r

oo
t, 

an
d 

sh
oo

t 
tis

su
es

FM
 

Ri
ce

Im
pr

ov
ed

 
sa

lin
ity

 a
nd

 d
ro

ug
ht

 t
ol

er
an

ce
s

Ra
hm

an
 e

t 
al

. (
20

16
)

Ec
G

BF
3

FM
 

M
ai

ze
Im

pr
ov

ed
 t

ol
er

an
ce

 o
f 

pl
an

ts
 t

o 
os

m
ot

ic
 s

tr
es

s,
 d

ro
ug

ht
, a

nd
 

sa
lin

ity
Ra

m
eg

ow
da

 e
t 

al
. (

20
17

)

Ec
N

AC
1

Le
av

es
FM

 
Ri

ce
 

So
rg

hu
m

Im
pr

ov
ed

 t
ol

er
an

ce
 o

f 
pl

an
ts

 t
o 

os
m

ot
ic

 s
tr

es
s,

 d
ro

ug
ht

, a
nd

 
sa

lin
ity

Ra
m

eg
ow

da
 e

t 
al

. (
20

12
)

N
AC

 6
7,

 b
ZI

P,
 W

RK
Y2

9 
AP

2,
 M

YB
 a

nd
 N

AM
 f

am
ily

 
tr

an
sc

rip
tio

n 
fa

ct
or

s

le
av

es
 a

nd
 s

ho
ot

s
FM

 
Ri

ce
Im

pr
ov

ed
 t

ol
er

an
ce

 o
f 

pl
an

ts
 t

o 
os

m
ot

ic
 s

tr
es

s,
 d

ro
ug

ht
, a

nd
 

sa
lin

ity
Ra

hm
an

 e
t 

al
. (

20
14

)

Ec
bZ

IP
17

le
af

, s
ho

ot
, r

oo
t, 

pa
ni

cl
e,

 a
nd

 
ge

rm
in

at
ed

 s
ee

dl
in

g
FM

 
Ri

ce
 

M
ai

ze

D
ev

el
op

m
en

t 
of

 s
al

in
ity

 a
nd

 h
ea

t 
st

re
ss

-t
ol

er
an

t 
cr

op
s

Ra
m

ak
ris

hn
a 

et
 a

l. 
(2

01
8)

bH
LH

 (
TF

)
Ro

ot
Br

ac
hy

po
di

um
 

di
st

ac
hy

on
 

Ri
ce

 F
ox

ta
il 

m
ill

et

D
ev

el
op

m
en

t 
of

 P
-s

ta
rv

at
io

n-
 

to
le

ra
nt

 g
en

ot
yp

es
Ra

m
ak

ris
hn

an
 e

t 
al

. (
20

17
)

W
RK

Y 
(T

F)
Ro

ot
Br

ac
hy

po
di

um
 

di
st

ac
hy

on
 

Ri
ce

 
Fo

xt
ai

l m
ill

et

D
ev

el
op

m
en

t 
of

 P
-s

ta
rv

at
io

n-
 

to
le

ra
nt

 g
en

ot
yp

es
Ra

m
ak

ris
hn

an
 e

t 
al

. (
20

17
)

JOURNAL OF CROP IMPROVEMENT 221



breeding tools for developing either stress-tolerant FM mutant parental lines 
or varieties on a short-time scale and at a low cost for CSA.

Largely, the recent advances in FM genomic research could guide or 
support genome-wide transcript profiling, functional diversity studies, and 
validation of candidate genes associated with climatic stresses; especially 
so, those involved in different nutrient signaling pathways, such as cal
cium, phosphorous, and nitrogen uptake genes, nitrogen and carbon 
metabolism genes, and abiotic stresses (drought, salinity). As FM is richer 
in calcium content compared to other cereals (Kumar et al. 2016), the 
identified calcium genes of the complete genome will help in exploring 
FM germplasm for calcium uptake, translocation, and accumulation in 
various tissues, and enrichment of other cereals with this vital nutrient.

Genetic transformation

Under the adverse climatic conditions, genetic transformation will be central 
to most crop improvement programs to address complex climate-induced 
stresses, as conventional methods could be hindered by limited genetic 
variability among cross-compatible germplasm. For FM, the exploitation of 
genetic transformation for climate-smart breeding is still in infancy, majorly 
because of impairments that have been associated with the lack of ample 
genomic resources (Hittalmani et al. 2017). So far, few transformation studies 
have been attempted to transfer genes associated with tolerance to leaf blast 
disease, drought, and salinity in FM. This has been mainly because of the 
nonexistence of optimal transformation protocols for generating mutant lines 
in FM based on an Agrobacterium-mediated versatile method of gene deliv
ery (Ceasar and Ignacimuthu 2014). Likewise, most previous transformation 
studies relied on Biolistic-mediated gene delivery and were limited to marker 
gene expression assessments using model plants (Latha, Rao, and Reddy 
2005; Ceasar and Ignacimuthu 2014). In contrast, for other well-studied 
cereals, such as rice, Agrobacterium-mediated transformation has registered 
tremendous progress (Beyer et al. 2002; Zhang et al. 2016). Outspreading 
these efforts to FM within a short time under the genomic era is 

Table 6. Cloned functional genes associated with stress tolerance traits in finger millet.
Genotype Gene name† Promoter/reporter Purpose Reference

GPU28 PgNHX1 and 
AVP1

CaMV35S GUS‡ Salinity tolerance. Jayasudha et al. (2014)

GPU28 mtlD CaMV35S GUS Drought/Salinity 
tolerance.

Hema et al. (2014)

GPU 45 chi11 Maize ubiquitin 
promoter

Leaf blast disease 
resistance

Ignacimuthu and Ceasar 
(2012)

20 genotypes were 
used

pPin 35S CaMVs35S Leaf blast disease 
resistance

Latha, Rao, and Reddy 
(2005)

222 W. WAMBI ET AL.



a requirement to ensure improved food and economic security, as the crop is 
mainly grown by resource-poor farmers, mostly in semi-arid areas.

The availability of the complete genome assembly for FM is expected to 
enhance the Agrobacterium-mediated transformation protocols for the devel
opment of climate-resilient FM transgenic varieties. This is particularly so in 
equipping T-DNA with plant-specific promoters and terminators for cases 
where the genes of interest are from prokaryotes or non-plant eukaryotes. In 
general, the recent resources of the CGS for this orphan crop will serve as 
a reference for efficient, large-scale identification and cloning of additional 
foreign stress-tolerance genes from mutations based on SNPs in various 
transformation studies for enhancing FM resilience to multiple climatic 
stresses.

Conclusion

Finger millet is vulnerable to the intensifying climatic risks, though it has 
been considered a climate-resilient crop that could drive food production for 
the developing world in the 21st century. Ensuring increased and sustainable 
FM production in the face of climate change requires a transition to CSA 
production systems that are resilient to climate risks. Wise use of FM genetic 
and genomic resources through climate-smart breeding is one pathway that 
could significantly contribute to transition to CSA. Therefore, research 
initiatives should focus on trait-specific screening of the abundant FM 
genetic resources. This could aid in the identification of genotypes with 
superior alleles that meet the breeding demands attributable to increasing 
climate-induced stresses. Specifically, redesigning the climate-smart breeding 
research based on the recent wealth of the high-quality CGS data for FM is 
expected to revolutionize the discovery of high-throughput molecular breed
ing tools, such as SNPs on a large scale. The genome-wide-aided tools will 
support accurate diversity assessment, fine-mapping studies, genomic selec
tion, and GWAS for enhancing marker-assisted breeding in FM. In addition, 
they could offer novel opportunities to enrich genetic transformation studies, 
and gene expression with second-generation genomic biotechnologies, such 
as TILLING, EcoTILLING, and CRISPR/Cas9, for developing climate-smart 
FM varieties. In general, assimilation of these genomic inputs could enhance 
the utilization of the assembled genetic resources and shorten the breeding 
time for climate-smart cultivars. Adoption of such climate-resilient FM 
cultivars for CSA will enhance long-term crop productivity while preserving 
the vital ecosystem services. Likewise, it could buffer crop production from 
the effects of greater climate variability and extreme events by reducing GHG 
emissions from direct and indirect agricultural activities that are heavily 
reliant on fossil fuels. Ultimately, this will lead to viable adaptation and 

JOURNAL OF CROP IMPROVEMENT 223



mitigation options, especially for the smallholder farmers with limited capa
city to adapt under the current climate-change scenario.

Abbreviations

ABC ATP-binding cassette
ADH1 Alcohol dehydrogenase 1
Al Aluminum
AMT1 Ammonium transporter 1
AP2 APETALA 2 gene farmily
APX Ascorbate peroxidase
AVP1 Arabidopsis vacuolar pyrophosphatase1
BiP Binding protein
Bzip Basic leucine zipper gene family
Ca Calcium
Cab Chlorophyll a/b binding protein
CaM Calmodulin gene
CaM35S Cauliflower mosaic virus 35s
CaMKs Calmodulin-dependent protein kinases
CaMLs CaM-like genes
CAX1= Cation exchanger 1;
CBLs Calcium sensors calcineurin B-like
CCaMK Ca2+/calmodulin-dependent protein kinase
CDPKs Ca2+ dependent protein kinases
CGS Complete genome sequence
chi11 Rice chitinase
CIPKs CBL-interacting protein kinases
CRISPR/Cas9 Clustered regularly interspaced short palindromic 

repeat)-Cas9
CRKs Cysteine-rich receptor-like kinases
CSA Climate-smart agriculture
DBH Dead/Death box helicase
Dof DNA binding with one finger
DUF26 Domain of unknown function 26
EcbHLH57 Basic helix-loop-helix trancription factor 57
EcDof =DNA binding with one finger from finger 

millet
EcGBF3 G-box-binding factor 3 from finger millet,
EcNAC1 NAM, ATAF1/2 and CUC2 domain protein transcription 

factor 1
EcNAC67 NAM, ATAF1/2 and CUC2 domain protein transcription 

factor 67
EcoTILLING Ecotype Targeting Induced Local Lesions IN Genomes
EcPT1 to EcPT4 Phosphate transporters genes 1-4
EcTAF6 TATA-box binding protein associated Factor 6
ESTs Expressed sequence tags
ESTs Expressed sequence tags
Fe Iron
FM Finger millet
GBF3 G-Box binding factor3
GHGs Greenhouse gases
GLM General linear model
GS Genomic selection
GWAS Genome-wide association studies
HRL Root length under P-sufficient level
HSDW Shoot dry weight under P-sufficient

(Continued )

224 W. WAMBI ET AL.



Acknowledgments

This work was implemented as part of the CGIAR Research Program on Climate Change, 
Agriculture and Food Security (CCAFS), which is carried out with support from the 
CGIAR Trust Fund and through bilateral funding agreements. For details please visit 
https://ccafs.cgiar.org/donors. The views expressed in this document cannot be taken to 
reflect the official opinions of these organizations.

(Continued). 

HSP70 Heat shock protein 70
HYP Hypothetical protein
ICRISAT International Crops Research Institute for Semi-Arid 

Tropics
IRAK Interleukin-1receptor-associated kinase_
ISSR Inter simple sequence repeat
KUP Potassium uptake permease
LEA14= Late embryogenesis abundant protein
LRDW Root dry weight under P-deficiency level.
MAS Marker-assisted selection
ME Malic enzyme
MLM Mixed linear model
MtlD Mannitol-1-phosphate dehydrogenase
MYB myeloblastosis
NAM No apical meristem
NCBI National Center for Biotechnology Information
NUE Nitrogen use efficient
PCR Polymerase chain reaction
PDIL Protein disulfide isomerase-like gene
PEPC-k Phosphoenol pyruvate carboxykinase
PEPRKs Proline-rick extension-like receptor kinase
PgNHX1 Pennisetum glaucum sodium hydrogen exchanger
PHL1 PHR1-like1
PHR1 Phosphate starvation response1
PK Pyruvate dikinase
PP2C Protein phosphatase 2C.
PPDK Pyruvate dikinase
pPin 35S Antifungal protein
QTL Quantitative trait locus/loci
RAPD Random amplified polymorphic DNA
RBCS Rubisco; PEPC, Phosphoenol pyruvate carboxylase
rd29A Desiccation-responsive protein 29A
rd29B Desiccation-responsive protein 29B
RGAP2 Rho GTase activating protein 2
RSLP RNase S-like protein precursor
SNP Single nucleotide polymorphism;
SnRK1 Sucrose-nonfermentation1-related protein kinase1
SOD Superoxide dismutase
SPS Sucrose phosphate synthase
SRAP Sequence-related amplified polymorphism
SSR Simple sequence repeat
TFs Transcription factors
TILLING Targeting Induced Local Lesions IN Genomes
TKL Transketolase proteins
TPC1 Two pore calcium channel protein 1
Zn Zinc

JOURNAL OF CROP IMPROVEMENT 225

https://ccafs.cgiar.org/donors


Disclosure statement

No potential conflict of interest was reported by the authors.

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JOURNAL OF CROP IMPROVEMENT 233

https://doi.org/10.1007/s00606-014-0982-3

	Abstract
	Introduction
	Climate-smart agriculture
	Finger millet gene pool and distribution of genetic diversity for climate-smart breeding
	Sources of finger millet germplasm that confer tolerance to climatic stresses
	Genomic resources available for enhancing finger millet resilience to climatic stresses
	Prospects for the development of climate-smart finger millet varieties using genome-aided tools
	Potential molecular tools for genetic diversity and population structure analysis for enhancing climate-smart breeding in FM
	Identification of QTL associated with climatic stress tolerance traits
	Functional characterization of key genes associated with climate-change-induced stresses
	Genetic transformation
	Conclusion
	Abbreviations
	Acknowledgments
	Disclosure statement
	References