Opportunities from the genetic diversity of the ILRI
genebank forage germplasm collection
Alieu Mortuwah Sartie, Alemayehu Teressa Negawo, Ermias Habte, Meki Shehabu Muktar,
Abel Teshome, Jean Hanson, Habib Olumide Akinmade, Ki-Won Lee and Chris S. Jones
27 Annual Conference of the Ethiopian Society of Animal Production (ESAP)
EIAR, Addis Ababa, 29–31 August 2019

Germplasm
Characterization
and evaluation
Promising
genotypes
Variety
registration
Basic seed
production
Delivery to
producers
ILRI Feed and forage, discovery to delivery
Public and
private sector
Farmers
fields
On-station
trials
Laboratory

Composition of forage Genebank at ILRI
Genera 381
Species 1,712
Accessions 18,664
Accession
type
Total
accessions
Total
accessions
under
Treaty
Number of
accessions
of Annex 1
species
Number of
accessions
of
named
cultivars
Number of
forage
cultivars
Browse 3458 3458 155 18 17
Grasses 4395 4390 1066 315 257
Legumes 10547 10521 2655 277 231
Others 264 264 41 30 1
Total 18664 18633 3917 640 506
The species range from short-lived annuals to long-lived perennial trees, small
herbaceous to large woody plants adapted to the tropics and Mediterranean areas
 Most of the collection was acquired from different regions, in partnership with and the consent of
national genebanks
 Others were donations from other institutes, notably the Commonwealth and Scientific Industrial
Research Organization (CSIRO) in Australia

Prioritisation of forages
Prioritisation categories and their definition
Category
Definition/explanation of species’
category
1
Species of known high value,
included in the Tropical forages
database (www.tropicalforages.info)
or commercially useful somewhere
2
Identified as high potential for
further development towards
commercial use or emerging as one
of high value somewhere
3
Often thought of as being interesting,
but never with enough value to
advance to category 1 or 2
4
Recognized anywhere as being of
importance through its taxonomic
affinity to (even minor) crop species
(crop wild relatives, CWR)
5
Widely recognized as being of low
value for forage or environmental use
A Global Tropical and Sub-Tropical Forages (TSTF) Strategy developed in 2015 based on a survey of major TSTF national
and international genebanks and input from genebank managers and forage specialists

Species type
Total species
conserved
Total # species
never
distributed
% species never
distributed
Legumes 631 233 36.9
Grasses 528 314 59.5
Browses 447 186 41.6
Others 106 60 56.6

Germplasm characterisation
Forage value
• Yield Quantity (High dry matter)
• Feed Quality
o Nutrition and digestibility
o Metabolizable Energy
o Hay and silage production
o Milk production
o Meat/beef production
o Presence of antinutritional or toxic compounds, e.g., Peramine and Lolitrem B
in perennial ryegrass that cause staggers in animals
 Characterise ILRI genebank germplasm collection to identify high value
forages based on:

Germplasm characterisation cont.
Resistance/tolerance to biotic and
abiotic factors
• Diseases – especially those that are
common in Africa
• Pests - especially those that are common in
Africa
• Drought (high WUE)
Adaptation and performance in
different agro-ecologies
• High lands
• Low lands
• Acid soil
• Alkaline soil
• Low fertility (high NUE)
Environmental integrity
• Greenhouse gas (Methane) emission
Mode of reproduction and genome
organisation
• Apomixis
• Ploidy
Soil management (Legumes only?)
• Legume / Rhyzobium relationship
o Nodulation and nodule numbers
o Presence of compounds (flavonoids) in root
nodules that attract rhyzobia

Genetic diversity in forage germplasm collections
Genotyping-by-sequencing (GBS) approach
 Combines genome complexity reduction using a combination of
restriction enzymes and next-generation sequencing
• allows the simultaneous discovery and genotyping of markers
• produces thousands of high-quality genome-wide genetic
markers that are suitable for diversity analysis, marker-trait
associations and genomic prediction
• applicable in species for which no reference genome is available
GBS using DArTseq platform (Kilian et al., 2012)

Markers generated GBS studies in forage crops and percentage of the
markers mapped onto the selected reference genomes.
Species
Number of
accessions
genotyped
Number of markers Number of Mapped markers (%) Reference
genomeSilico DArT SNP Silico DArT SNP
Cenchrus
purpureus
105 116,190 85,452 17% 33%
Penissetum
glaucum (pearl
millet)
Cenchrus ciliaris 185 111,917 93,501 7.20% 16.30%
Setaria italica
(foxtail millet)
Chloris gayana 94 93,128 65,529
0.23% 2.07%
Setaria italica
(foxtail millet)
0.74% 5.86%
Eragrostis tef
(teff)
0.56% 5.13%
Zoysia matrella
(Manila grass)
Sesbania sesban 41 (171) 34,798 47,609 3.36% 5.17%
Glycine max
(Soybean)
Lablab
purpureus
142 64,793 38,824 Not yet Not yet

Napier grass (Cenchrus purpureus)
The major forage species for
smallholder dairy in East Africa
– Five times more biomass than
natural pastures in Tanzania1
– Yield (≤23 t DM/ha/yr) under
irrigation increases by intercropping
with legumes in Ethiopia2
– Smut and stunt disease resistant
lines from the ILRI collection being
adopted by farmers
– Marker Assisted Selection for
performance under drought
1Lukuyu et al. High yielding improved forages. 7th Multi-Stakeholder Partnership Meeting of the Global Agenda for Sustainable Livestock, Addis Ababa, May 2017.
2Adie et al. Experiences of producing irrigated forages. Feed the Future Innovation Lab for Small Scale Irrigation Stakeholders Consultation Meeting, Addis Ababa,
May 2018.
Accessions
Total dry
weight
(t/ha/yr)
Crude
protien
(%)
Neutral
detergent
fibre (%)
Metabolizable
energy
(MJ/ha/yr)
16791 62.04 13.08 70.40 489.50
BAGCE 30 54.51 12.44 71.82 423.54
16819 52.08 13.55 69.07 406.74
BAGCE 90 48.99 12.87 70.84 383.59
16802 48.06 12.64 71.15 378.23
BAGCE 34 45.48 11.05 72.20 349.29
CNPGL 00-1-1 43.17 13.60 67.12 343.63
BAGCE 100 44.22 12.22 70.88 341.38
CNPGL 92-198-7 43.74 12.75 70.11 340.73
15357 41.85 13.07 71.66 336.06
Mean of the
collection 26.09 12.66 69.88 201.80
Standard error 6.11 0.75 0.74 47.01
Ranges: TDW 0.36-62.04; CP 10.95-15.03 and; NDF 66.7-73.4
Soil moisture 20 % Soil moisture 10 %

Genetic diversity and population structure of Napier
grass collection
Clusters of the 104 Napier grass accessions using 980 selected SNPs. (A) UPGMA tree showing seven groups; (B)
PCA plot for PC1 and PC2; (C) The delta K suggesting two major groups and up to 5 subgroups; (D) Bar plots based
on the admixture model in STRUCTURE, for K = 2 and K = 5. The colours are according to the STRUCTURE k = 5
(Muktar et al., et al., 2019)
A B
C D

Diversity in forage quality of Napier grass
PCA biplot showing feed quality traits of Napier grass accessions: Acid detergent fibre (ADF); Neutral
detergent fibre (NDF); Acid detergent lignin (ADL); Metabolizable energy (Me); Organic matter (OM); Dry
matter (DM); Total nitrogen Crude protein (CP); In vitro organic matter digestibility (IVOMD)

Genetic diversity and population structure of Buffel
grass (Cenchrus ciliaris) collection
Origin of buffelgrass collection (Jorge et al.
2008)
Buffel grass
• One of the best Tropical and Sub-
Tropical forages
• An apomictic perennial C4 grass
• Candidate for drought tolerance
• Helps to prevent soil erosion
Population structure of Buffel grass using 1,000 selected SNP markers with (a)
cluster analysis of the 185 accessions and; (b) bar plots showing the suggested
subpopulations.

Agronomic and nutritional characteristics of
Buffel grass
Wet Season
Group I
(49)
Group II
(11)
Group III
(25)
Group IV
(23)
Group V
(7)
Group VI
(10)
Y (kg/ha) 2378 3789 4831 2743 2328 4540
PH 71 94 102 84 84 114
LL (cm) 24 34 36 26 24 34
CP (%) 13.5 11.0 12.0 12.8 11.6 9.9
NDF (%) 69.2 70.2 71.4 71.0 72.3 73.9
ADF (%) 38.3 40.4 41.7 41.1 42.6 45.2
IVOMD (%) 72.6 65.6 70.2 71.5 66.3 63.0

Genetic diversity of Rhodes grass (Chloris gayana)
collection
Ponsens (2009)
Rhodes grass,
• A major forage in the tropics and subtropics.
• Cross-pollinating C4 with diploid and tetraploid
forms, usually propagated by seed
• Wide adaptability and ease of establishment
Cluster analysis of the 94 Rhodes grass accessions using SNP
markers clearly showing two differentiated groups

Genetic diversity in Sesbania sesban collection
Preliminary cluster analysis of 41 accessions of Sesbania sesban
using SNP markers
• 171 accessions
• 15 plants /accession genotyped

Diversity between and within accessions of
Lablab purpureus
52788
6479
755 491 465 462 610 2743 0 0
52616
6468
825 412 372 338 312 277 398 2775
0
10000
20000
30000
40000
50000
60000
0.05-
0.09
0.10-
0.14
0.15-
0.19
0.20-
0.24
0.25-
0.29
0.30-
0.34
0.35-
0.39
0.40-
0.44
0.45-
0.49
0.5
FREQUENCY
RANGE
PIC He
32481
3015
643 470 383 396 553 883 0 0
32232
3189
598 406 339 275 256 261 358 910
0
5000
10000
15000
20000
25000
30000
35000
FREQUENCY
RANGE
PIC He
Distribution of polymorphic information content (PIC) and heterozygosity
(He) for the silicoDArT (A) and SNP (B) markers in germplasm collection of
Lablab purpureus
A
B
• 142 accessions
• 15 plants /accession genotyped

Subsets identification
Optimal water Water-deficit
NAME Species Origin Collection NAME Species Origin Collection
ILRI_1026* C. purpureus Burundi ILRI ILRI_1026* C. purpureus Burundi ILRI
ILRI_16840*
C. purpureus x
P. glaucum Zimbabwe ILRI ILRI_14389 C. purpureus Nigeria ILRI
ILRI_14982
C. purpureus x
P. glaucum USA ILRI ILRI_14983 C. purpureus USA ILRI
ILRI_14984 C. purpureus USA ILRI ILRI_16811 C. purpureus USA ILRI
ILRI_16793* C. purpureus Cuba ILRI ILRI_16791 C. purpureus Swaziland ILRI
ILRI_16794 C. purpureus Mozambique ILRI ILRI_16793* C. purpureus Cuba ILRI
ILRI_16814* C. purpureus USA ILRI ILRI_16816 C. purpureus USA ILRI
ILRI_16839 C. purpureus Zimbabwe ILRI ILRI_16796 C. purpureus Zimbabwe ILRI
ILRI_16819 C. purpureus USA ILRI ILRI_16806* C. purpureus USA ILRI
ILRI_16797 C. purpureus Zimbabwe ILRI ILRI_16782 C. purpureus Tanzania ILRI
ILRI_16806* C. purpureus USA ILRI ILRI_16814* C. purpureus USA ILRI
ILRI_16822 C. purpureus Malawi ILRI ILRI_16840*
C. purpureus
x P. glaucum Zimbabwe ILRI
BAGCE_30* C. purpureus Brazil EMBRAPA BAGCE_30* C. purpureus Brazil EMBRAPA
BAGCE_97* C. purpureus Brazil EMBRAPA BAGCE_97* C. purpureus Brazil EMBRAPA
Napier grass subsets for irrigated and water deficit conditions (Muktar et al., 2019)
*accession selected in both subsets
Subsets were identified based on a combined analysis of GBS and phenotypic data

Some members of ILRI Genebank team

This presentation is licensed for use under the Creative Commons Attribution 4.0 International Licence.
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