Underutilized Climate-smart Nutrient rich Small Millets for Food and Nutritional Security by HD Upadhyaya, ICRISAT - Regional Expert Consultation on Underutilized Crops for Food and Nutritional Security in Asia and the Pacific November 13-15, 2017, Bangkok

1. Hari D Upadhyaya
ICRISAT, India
Underutilized Climate-smart
Nutrient Rich Small Millets for
Food and Nutritional Security
Presented at
“Regional Expert Consultation on Underutilized Crops for Food and
Nutritional Security in Asia and the Pacific”, November 13-15, 2017, Bangkok

2. Our Vision
A prosperous, food secure and resilient dryland tropics
Our Mission
About ICRISAT

3. Specialization in crops suitable
for the drylands
Sorghum Pearl millet Groundnut Chickpea Pigeonpea
ICRISAT Mandate crops
Finger millet

4. ICRISAT Locations

5. Genebank Diversity
Helps ICRISAT produce
improved varieties that
Fight malnutrition Improve productivity Meet climate change
Genebank diversity

6. ICRISAT Genebank
• The ICRISAT genebank
conserves 125, 050 accession,
of six mandate crops and five
small millets, originating from
144 countries
• Distributed 1.47 million seed
samples to 148 countries
• Safely duplicated 110,818
accessions at Svalbard Global
Seed Vault, Norway

7. Germplasm distribution and Impact
• Developed germplasm diversity
representative subsets such as core,
mini core collections
• Distributed 339 germplasm diversity
representative subsets to 36 countries
• 104 germplasm accessions directly
released as 137 cultivars in 51
countries
• 1019 cultivars released in 81 countries
from germplasm and breeding
material
ICRISAT Genebank

8. Small millets
• Small millets are considered as climate-smart and nutrient rich crops
• Globally grown in a limited acreage, and are used as food, feed and
fodder purposes
Crop Botanical name Region of cultivation
Finger millet Eleusine coracana (L.) Gaertn. India, Uganda, Nepal, China, Myanmar, Sri
Lanka, Kenya, Eritrea, Sudan, Zimbabwe
Zambia, Malawi, Madagascar, Rwanda, Burundi
Foxtail millet Setaria italica (L.) P. Beauv. Asia, Europe, North America, Australia,
North Africa
Proso millet Panicum miliaceum L. Asia, Australia, North America, Europe, Africa
Little millet Panicum sumatrense Roth. India, Sri Lanka, Pakistan, Myanmar
Kodo millet Paspalum scrobiculatum L. India
Barnyard millet Echinochloa crus-galli &
Echinochloa colona
India, Japan, Korea, China, Nepal

9. • Play an important role in food and nutritional security in rural
households
• Nutritionally, they are characterized by high micronutrient content,
particularly rich in calcium and iron, and high dietary fibre
• Small millets have several agronomic advantages, including diverse
adaptation, less affected by biotic and abiotic stresses, short-duration,
high water use efficiency, drought tolerance, etc.
• Small millets are under-utilized and under-researched crops, and
continued to be neglected in terms of support for production,
promotion, research and development
• Their presence in the food basket has been declining over the years
• Currently there is an increasing recognition of small millets’ nutrient
composition and benefits as healthy food
Small millets

10. Finger millet
• Domesticated about 5000 years B.C. in
Eastern Africa (Ethiopia)
• Introduced into India about 3000 years ago
• Staple food in parts of Eastern and Central
Africa and India
• The major finger millet producing countries
are Uganda, India, Nepal and China
• In India, finger millet was grown in about
1.13 m ha with a production of 1.88 m t
during 2014
• In Nepal, finger millet is the fourth major
cereal crop, cultivated in 0.27 m ha with
an annual production of 0.31 m t

11. • Domesticated in China and Europe, and grown
since >10500 years ago in China
• Cultivated in Asia, Europe, North America,
Australia, and North Africa for grains or forage,
and an essential food for human consumption in
China, India, Korea, and Japan
• Valued for its drought tolerance, short duration,
and grains are nutritionally superior to other
cereals including rice and wheat
• China ranks top in foxtail millet production with
1.81 million tons from 0.72 m ha during 2014
• In India, foxtail millet is cultivated mostly in the
states such as Telangana, Andhra Pradesh,
Karnataka, Rajasthan, Madhya Pradesh, Tamil
Nadu and Chhattisgarh
Foxtail millet

12. Proso millet
• Domesticated in China and Europe
(Harlan 1975)
• Grown in Asia, Australia, North America,
Europe and Africa
• Used for feeding birds and as livestock
feed in the developed countries and for
food in some parts of Asia
• The U.S. is among the top producers of
proso millet (~ 0.20 million ha), and most
of the proso millet crop is utilized for
birdfeed and in cattle-fattening rations

13. Little millet
• Little millet was domesticated in
India particularly in the Eastern
Ghats of India, where it forms an
important part of tribal
agriculture
• Grown in India, Sri Lanka, Nepal,
western Burma

14. • Kodo millet was domesticated in
India about 3000 years ago
• Cultivated by tribal people in small
areas throughout India, from Kerala
and Tamil Nadu in the south, to
Rajasthan, Uttar Pradesh and West
Bengal in the North
• It occurs in moist or shady places
across the tropics and subtropics of
the Old World
Kodo millet

15. • E. crusgalli domesticated in Japan
4000 years ago
• E. colona domesticated in India
• Barnyard millet are fastest growing
of all millets
• Produces a crop in six weeks
Barnyard millet

16. Grain nutritional composition & potential uses
• Good sources for micro and macro nutrients with
high nutraceutical and antioxidant properties
• Rich in protein, fat, crude fiber, iron and other
minerals and vitamins, compared to other major
cereals
– Finger millet contains over >10 fold higher calcium
(350 mg per 100 g)
– Barnyard, little and foxtail millet are rich in crude
fiber (6.7 to 13.6%)
– Little and barnyard millets are rich in iron (9.3 to
18.6 mg per 100 g)
– Proso, foxtail and barnyard millets are rich in
protein (11 to 12.5%)
– Foxtail and little millets are rich in fat (4.0 to 5.2%)
• Small millets are used as an ingredient in
multigrain and gluten-free cereal products
• Serves as a major food component for various
traditional foods and beverages

17. Germplasm Resources: Global status
• Large numbers of small millets germplasm accessions
conserved ex situ globally are available to scientific
community
– Foxtail millet > 46,000 accessions
– Finger millet > 37,000 accessions
– Proso millet > 29,000 accessions
– Barnyard millet > 8,000 accessions
– Kodo millet > 8,000 accessions
– Little millet > 3,000 accessions

18. Finger millet germplasm at ICRISAT genebank
• Represents all four races
(compacta, vulgaris, elongata
and plana), and ten subraces
of finger millet
• Majority of accessions from
race vulgaris (63%) followed
by race plana (20%)
• 7186 accessions originating from
26 countries

19. Foxtail millet germplasm at ICRISAT genebank
• Represents all three races (Indica,
65%; Maxima 15%; Moharia 16%),
and ten subraces of foxtail millet
• Majority of accessions from race
Indica originates mostly from
India
• Maxima from China, Korea, India
• Moharia from Syria, Soviet union,
Lebanon, Pakistan
• 1542 originating from 26 countries
• Two wild species: Setaria viridis (17) and S. pumila (39)

20. • Proso millet: 849 accessions, originating from 30 countries;
mostly from Russian Federation (14%) and India (9%) and
Korea (9%)
• Little millet: 473 accessions originating from 5 countries;
mostly from India (98.5%)
• Kodo millet: 665 accessions originating from India (99.7%)
and Sri Lanka (0.3%)
• Barnyard millet: 749 accessions originated from 9 countries;
mostly from India (453 acc.) and Japan (164 acc.)
Proso, little, Kodo and barnyard millets

21. Crop Cultivated Wild Total
Finger millet 6981 205 7186 (25)
Foxtail millet 1488 54 1542 (26)
Proso millet 849 - 849 (30)
Little millet 473 - 473 (5)
Kodo millet 665 - 665 (2)
Barnyard millet 749 - 749 (9)
Total 11,205 259 11,464
Small millets germplasm at ICRISAT genebank
* Figures in parenthesis indicates the number of countries

22. Crop No. of samples
Finger millet 40,164 (56)
Foxtail millet 15,035 (52)
Proso millet 6,796 (41)
Little millet 2,557 (30)
Kodo millet 2,652 (27)
Barnyard millet 4,075 (30)
Total 71,279 (56)
Small millets germplasm distribution
* Figures in parenthesis indicates the number of countries

23. Germplasm use in crop improvement
• Very small proportion of germplasm has been
used in crop improvement
• This is mainly due to lack of reliable information
on large collections (considering crops)
• Need to reduce size without loosing diversity
• Overcome size induced low use of germplasm
• Developing core collection - an option

24. • Not really…..
• Reasons - size of core, if number of accessions in entire
collection is large, is still unwieldy for convenient exploitation
by the breeders (2247 in sorghum, 2094 in pearl millet, 1956
in chickpea, 1704 in groundnut)
• What is the remedy…..?
• Mini core (Upadhyaya and Ortiz 2001)
• - 10 % of core collection (1% of entire collection)
Does it help to develop core collections?

25. Germplasm diversity representative subsets –
ICRISAT small millets germplasm collection
Crop Germplasm subsets No. of
accessions
used
No. of
traits/
SSRs
used
No. of
accessions
in subset
Reference
Finger millet Core collection 5940 14 622 Upadhyaya et al. (2006a)
Mini core collection 622 20 80 Upadhyaya et al. (2010)
Composite collection - - 1000 Upadhyaya et al. (2005)
Reference set 1000 19 SSRs 300 Upadhyaya (2008a)
Foxtail millet Core collection 1474 23 155 Upadhyaya et al. (2008)
Mini core collection 155 21 35 Upadhyaya et al. (2011b)
Composite collection - - 500 Upadhyaya et al. (2006b)
Reference set 500 20 SSRs 200 Upadhyaya (2008b)
Proso millet Core collection 833 20 106 Upadhyaya et al. (2011c)
Barnyard millet Core collection 736 21 89 Upadhyaya et al. (2014)
Little millet Core collection 460 20 56 Upadhyaya et al. (2014)
Kodo millet Core collection 656 20 75 Upadhyaya et al. (2014)

26. Trait specific germplasm sources
identification using core and
mini core collections

27. • Biotic stress - Blast resistance
• Abiotic stress - Drought and salinity tolerance
• Grain nutritional traits - High Fe, Zn, Ca and Protein
• Agronomic traits - Early maturity, high grain yield
Finger millet core and mini core collection
Germplasm sources identified for important traits

28. Finger millet: Blast resistant accessions
from mini core collection
• Blast caused by Pyricularia grisea is
an economically important and
widespread disease of finger millet in
the world
• Sixty six of the 80 mini core
accessions showed combined
resistance to leaf, neck and finger
blast in two seasons of field
screening
• These resistant accessions
represented one wild (africana) and
four cultivated races (vulgaris, plana,
elongate and compacta) of finger
millet that originated from 13
countries in Asia and Africa

29. Finger millet: Grain nutrients rich
accessions from core collection
• Finger millet is a promising source of
micronutrients and protein besides
energy
• Contribute to the alleviation of iron
(Fe), zinc (Zn) and protein
malnutrition affecting women and
preschool children in African and
south-east Asian countries
• Substantial variability for
− Fe: 21.71 – 65.23 mgkg−1
− Zn: 16.58 – 25.33 mgkg−1
− Calcium: 1.84 – 4.89 g kg−1
− Protein: 6.00 – 11.09 %
• Grain nutrients rich germplasm
– 15 accessions each for Fe, Zn, Ca and
Protein
– 24 accessions for two or more grain
nutrients

30. Finger millet: Drought tolerant accessions
identified in mini core collection
• In the African and southern Asian
environments, finger millet is affected more
by the intermittent drought followed by the
terminal drought affecting the reproductive
growth
• A part of finger millet mini core collection
(n = 69) evaluated in mini-lysimeters for the
variation in total water use (T) and
transpiration efficiency (TE) under both
terminal drought-stress (DS) and well-
watered (WW) environments.
• Contribution of T to shoot biomass under
drought was minor but that of TE was large
and positive. Both T and TE positively
influenced the shoot biomass production.
• Identified 11 accessions having high TE

31. • The mini core finger millet
germplasm (n = 80) was screened
for grain yield performance in a
soil saturated with NaCl solution
of100 or 125 mM
• Salinity delayed phenology,
marginally reduced shoot biomass
and grain yield
• There was a large range of genotypic variation in grain yield under
salinity and other traits
• The yield loss was higher in accessions with prolific growth and grain
yield potential was associated with grain yield under saline yields.
• 21 accessions were identified as salinity tolerant based on grain yield
under saline conditions
Finger millet: Salinity tolerant accessions
identified in mini core collection

32. Foxtail millet core collection
as a source of trait specific germplasm
to meet needs of crop improvement
• Biotic stress - Blast resistance
• Abiotic stress - Drought and salinity tolerance
• Grain nutritional traits - High Fe, Zn, Ca and Protein
• Agronomic traits - Early maturity, high grain yield

33. • Blast, caused by Pyricularia grisea is a serious disease affecting both
forage and grain production in foxtail millet in India
• Foxtail millet core collection screening against four isolates P. grisea
(blast) collected in India under field and glasshouse conditions
• Identified 15 accessions resistance to sheath, neck and head blast
• Mostly accessions of maxima (8) showed resistant to blast disease
indicating importance of maxima for identifying blast resistant sources
Foxtail millet: Sources for blast resistance

34. • Foxtail millet core collection (n = 155)
evaluated in mini lysimeters under both
terminal drought stress (DS) and well-
watered (WW) environments
• The contribution of total water use (T) to
grain yield under drought was minor;
contribution of transpiration efficiency
(TE) was positive and harvest index (HI)
was negative
• Crop duration, T and TE positively
influenced, and HI negatively influenced
shoot biomass production
• Identified 16 accessions having high TE
• Accessions of Indica showed high T and TE,
and maxima and moharia high HI
Foxtail millet: Sources for drought tolerance

35. • Accessions screened in a soil saturated once with 100mM NaCl and in
a non-saline control in a partly controlled environment using Alfisol
• Salinity delayed panicle emergence and maturity, and reduced shoot
biomass by 24–41% and grain yield by 7–30%
• The yield loss by salinity was associated with duration of crop growth,
and grain yield loss was highest in the early-maturing accessions
• Identified 10 accessions as tolerant to salinity. All the identified
accessions belong to race Indica
Foxtail millet: Sources for salinity tolerance
• Soil salinization is an increasing
problem, with 23% of the global
cultivated land already affected
• Foxtail millet has potential as a
crop for salt affected soils, with
its high tolerance to salinity

36. • Large variation for grain nutritional traits (range Fe 24 to 68 mg kg−1;
Zn 34 to 74 mg kg−1; Ca 90 to 289 mg kg−1; Protein 10.7 to 18.5%)
• Identified 21 accessions each as sources for
– High Fe (58 to 68 mg kg-1)
– High Zn (55 to 74 mg kg-1)
– High Calcium (171 to 289 mg mg kg-1)
– High Protein (15.6 to 18.5%)
Foxtail millet: Sources for grain nutritional traits
• Foxtail millet core
collection evaluated for
21 traits at five agro-
ecologically diverse
locations in India
Foxtailmillet

37. • Core collection had
wide range of variation
for grain yield (485 to
1118 Kg ha-1) and days
to 50% flowering (36–
78 DAS)
Foxtail millet : Sources for early maturity
and high grain yield
• Identified 21 accessions each as sources for
– Earliness (36 to 43 days to 50% flowering)
– High grain yield (981 to 1118 kg ha-1)

38. Foxtail millet: Multiple trait specific
accessions identified in core collection
• Early maturity + high Fe, Zn, Ca and Protein - 1 accession
• Early maturity + High Fe and Zn + Blast resistant - 1 accession
• High grain yield + high Fe and Zn - 1 accession
• High grain yield + drought tolerant - 5 accessions
• High grain yield + salinity tolerant - 4 accessions
• High grain yield + salinity tolerant + drought - 1 accession
• Salinity and drought tolerant - 1 accession
Desirable combinations of multi-trait specific sources

39. Proso, kodo and little millets
• 200 accessions each of proso millet, kodo millet
and little millets were assessed for phenotypic
performance for grain yield and grain nutritional
contents
• A large variability was observed in each crop for
grain, Fe, Zn, Ca and Protein content
• Identified germplasm sources for high yield and
high grain nutrients content

40. Genomic resources in small millets
• Two reference genome sequences are available for foxtail
millet (Bennetzen et al., 2012; Zhang et al., 2012)
• Recently, Hittalmani et al. (2017) have reported genome and
transcriptome sequence of finger millet
• Genetic linkage map is available in proso millet (Rajput et al.
2016)
• ICRISAT and Cornel University collaborative project
– Sequenced about 200 accessions each of foxtail, proso,
kodo, little and barnyard millets following genotyping-by-
sequencing approach

41. • 190 accessions including 155 accessions of core
collection and 17714 high quality SNPs
• Genetic structure revealed that foxtail millet
germplasm accessions are structured along both
on the basis of races and geographic origin
• The maximum proportion of variation was due to
among individuals within populations
• Genome-wide linkage disequilibrium (LD) analysis
showed on an average LD extends up to ~150 kbp
and varied with individual chromosomes
Indica
Maxima
Moharia
Population structure of foxtail millet
germplasm characterized using 17,714 single
nucleotide polymorphisms assessed through
ADMIXTURE program;
(a) k = 4 & (b) k = 6

42. Genome-Wide Association Mapping
• Plant pigmentation (on chromosome 4)
We found the gene ID: Si006495m.g located on chromosome 4
(Position 7,189,103 to 7,195,068 bp), which encodes Chalcone-
flavanone isomerase, a major enzyme for flavonoid biosynthesis
pathway that leads to production of secondary metabolites
including anthocyanins, which gives color to the plant organs
• Flowering time (on chromosome 6, 7 and 8)
The SNP locus located at 34,568,483 bp on chromosome 6 located
on gene ID: Si015213m.g has a protein family called MYC type bHLH
domain, reported to have biological function of floral organ
formation (GO: 0048449), regulation of flower development (GO:
0009909), leaf morphogenesis (GO: 0009965)
Upadhyaya et al. 2015, The Plant Genome 8(3), 10.3835/plantgenome2015.07.0054
GWAS using foxtail millet core collection identified
several SNP loci associated with

43. Small millets improvement
• Very limited research attention for small millets improvement
• Majority of cultivars released globally were through pure line
selection from landraces
• India
– AICRP - Small Millets (1986) : Plan, coordinate and execute the
research programs in six small millets
– 245 varieties in 6 small millets have been released
– Majority of cultivars released were following pure line selection.
– Two ICRISAT germplasm accessions,
• Barnyard millet, IEc 542 originated from Japan was released as PRJ 1 in India (2003)
• Proso millet, IPm 2769 originated from Ukraine was released as DHPM 2769 in India
during 2015
– Finger millet varieties yields up to 5 to 6 tons/ha, and cultivars other
small millets yields up to 2.5 to 3 tons/ha under optimum
management conditions

44. • Africa:
– Finger millet is an important food crop, particularly in Eastern
Africa (Uganda, Ethiopia, Tanzania and Kenya)
– Systematic breeding efforts are very limited in Africa; resulted in
majority of cultivars grown were either landraces or direct
introduction
– The ICRISAT-HOPE project in collaboration with Department of
Research and Development (DRD), Tanzania, released cultivars
such as P 224 and U 15 in Tanzania, Kenya and Uganda
– Three ICRISAT finger millet germplasm accessions were directly
released in Zambia (IE 2929 as Lima and IE 2947 as FMV 287
during 1987) and Kenya (IE 4115 as KAK-WIMBI 2 during 2016)
Small millets improvement

45. • China
– Foxtail millet is one of the important crops
– About 870 cultivars were released since 1950
– Research using heterosis for foxtail millet began in the 1960s with
the development of male sterile lines by various approaches
– For example, Zhangzagu 5, a high yielding hybrid cultivar, released
by Zhangjiakou Academy of Agricultural Sciences, Hebei Province,
China, and yields up to 12000 kg/ha versus conventional cultivars
ranging from 4500 to 6000 kg/ha in 2007 (Liu et al., 2014)
– The development of herbicide resistant foxtail millet cultivars has
made the use of foxtail millet heterosis a reality by us of herbicide
resistant varieties as the restorer line (Diao 2017)
Small millets improvement

46. • The United States
– Proso millet is an important crop, used for birdfeed and in
cattle-fattening rations
– The focused breeding program for proso millet productivity
improvement was started in the year 1972 under the
alternative crops breeding program at Panhandle Research
and Extension Centre (PHREC), and released several cultivars
such as Sunup, Dawn, Cerise, Rise, Early bird, Hutsman,
Sunrise and Horizon
– There are 15 cultivars of proso millet available to growers,
and nine of these were selections from adapted landraces,
and six were developed through hybridization (Habiyaremye
et al. 2017)
Small millets improvement

47. • There is an increasing recognition of small millets’ nutrient composition
and benefits as healthy food
• Alternate/supplement crop to widen food basket to ensure food, feed
and nutritional security
• Considerable number of germplasm accessions conserved in genebanks
globally
• Core and mini core collections representing germplasm diversity
available for searching new source of variation and trait specific sources
identified
• More research efforts on
– Germplasm collecting, conserving, evaluating and utilizing, and
– Developing high yielding cultivars, processing and utilization technologies,
– Policy innervations
To promote small millets cultivation, and for food and nutritional
security of vulnerable population under climate change scenario
Conclusions

48. Thank You