Global diversity analysis identifies ample space for 
using CIMMYT and ICARDA’s wheat germplasm 
collections in breeding programs
Carolina Sansaloni1 *, Jorge Franco2, Bruno Santos3, Mario Caccamo3, Sukhwinder Singh1, Cesar Petroli1, Thomas Payne1, David Marshall4, Benjamin Kilian5, 
Carolina Saint Pierre1, José Crosa1, Andrzej Kilian6, Peter Wenzl7, Mohamed Fawzy Nawar8, Kai Sonder1, Jaime Campos1, Prashant Vikram1, Kevin Pixley1
1 CIMMYT- International Wheat and Maize Improvement Center, Mexico; 2Universidad de la República del Uruguay, Uruguay; 3 NIAB- National Institute of Agricultural Botany, UK; 4 James Hutton Institute, UK; 5 The Crop Trust, Germany; 6 
Diversity Arrays Technology, Australia; 7 CIAT- International Center for Tropical Agriculture; 8 ICARDA- International Center for Agricultural Research in the Dry Areas. 
* c.sansaloni@cgiar.org
ABSTRACT
Climate change and the growing human population trigger the demand to explore
and use genetic resources. Wheat’s undomesticated wild species, crop wild
relatives, and landraces have survived extreme environmental challenges and
continuous cycles of natural selection, and therefore offer a wealth of variation for
cultivar improvement.
CIMMYT’s Seeds of Discovery (SeeD)i initiative characterized more than 100,000
CIMMYT and ICARDA germplasm bank accessions with 130,000-450,000 molecular
markers. Diversity analyses successfully grouped 4,206 wild relatives according to A B Original set: 20000    Core subset: 4000
species and sub-species. Elite breeder lines and cultivars were mostly tightly
clustered and were much less diverse than landraces and unimproved accessions
both among 20,000 tetraploid (AB genome), and 60,000 hexaploid (ABD genome)
accessions.
This detailed analysis enabled the formation of core sub-sets that encompass the
total diversity of the germplasm bank collections while greatly reducing the numbers
of materials that researchers must evaluate in search of needed diversity. This work
is likely the largest crop genotyping effort to date, generating resources to underpin
the breakthroughs necessary to develop the crops for the future.
RESULTS C D Original set: 60000    Core subset: 12000
Diversity analyses: Figure 2 . Diversity study representation of A) 20,000 tetraploid cultivated accessions with B) the core subset
collection, and C) 60,000 hexaploid cultivated accessions with D) the core subset collection.
• Wild relatives: 3D representation of the multidimensional scaling (using DArTseq B C
SNPs) clearly identified (clustered) species and even subspecies (Fig. 1A). Diversity study Novel alleles and allele Bridging germplasm
• Tetraploids: although breeding programs visibly reduced diversity, a few elite donors
breeding lines appear to maintain a wide range of the diversity found among
landrace materials (Fig. 2A).
• Hexaploids: Landraces, elite breeding lines and synthetic derivatives formed
genetically distinct groups (Fig. 2C).
Figure 3 . Scheme showing the utilization of genetic resource strategy
CONCLUSION
Diversity analyses revealed that tetraploid, and especially hexaploid elite wheat
breeding lines and cultivars, are genetically narrow and encompass a small portion
of the total genetic diversity relative to their respective landraces and unimproved
germplasm. This suggests ample potential to explore germplasm bank accessions
for useful diversity to enrich the elite germplasm pools, particularly to address new
challenges to production.
The curated data, as well as links to passport and characterization/evaluation data,
are or will be available (www.seedsofdiscovery.org) for use by the larger community.
A B Original set: 4206    Core subset: 819 We are keen to partner with interested researchers and genebanks to further
Figure 1 . Multidimensional scaling representation of A) 4,206 Wild relatives wheat accessions; B) Core subset with leverage the value of existing data, and to generate new data, knowledge and value
819 accessions.
for breeding programs.
Core germplasm sub-sets:
METHODS
Understanding the global diversity is key to developing core sub-sets that capture
• The CIMMYT and ICARDA wheat germplasm bank collections were divided into three groups for diversity analyses:
most of the allele richness and genetic diversity of the overall germplasm groups. ➢ Wild relatives (WR): 4,206 accessions from 30 species with 20 genomes: A, B, D, C, M, S, U, N, T, UC, DN, GA, AB,
Core sub-sets are a valuable starting point for researchers searching for novel UM, DM, DC, MU, SU, UMX, DMS, DMU, GAA.
➢ Tetraploids (domesticated species): 20,000 accessions from 10 species; most of them Tritucum turgidum subsp
diversity, donor germplasm for pre-breeding programs (Fig. 1B, 2B and 2D). durum, but also Tritucum turgidum subsp turgidum, dicoccon, carthlicum, turanicum, polonicum, paleocolchicum
The use of genetic resources stored in germplasm banks requires an extensive, and Triticum aethiopicum
➢ Hexaploids (domesticated species): 60,000 accessions from 7 species; most of them are Triticum aestivum L.
long-term, scientific and financial commitment, involving (Fig. 3): aestivum, but also, T. aestivum L. spelta, compactum sphaerococcum, macha, Triticoaegilops and Triticosecale.
TM
• Studying the global genetic diversity of the germplasm bank accessions, as • DArTseq technology revealed 450,000, 130,000 and 200,000 high-quality SNP and SilicoDArT
(presence/absence variations) markers for WR, tetraploid and hexaploid sets respectively.
reported herein, • All markers were aligned to the IWGSC v0.4 reference genomeii and against the DArT consensus mapiii.
• Identifying novel diversity for traits of economic importance, and • Core sub-sets containing 20% of the accessions in each germplasm group were formed based exclusively on
• Introgressing useful, novel diversity into elite cultivars via germplasm genetic information.
enhancement programs.
These two last points are pursued by SeeD’s pre-breeding program.
Acknowledgements
This work was conducted under the Seeds of Discovery Project supported by SAGARPA (La Secretaría de Agricultura, Ganadería, Desarrollo Rural, Pesca y Alimentación), 
i ii iii Mexico under the MasAgro (Sustainable Modernization of Traditional Agriculture) initiative (CIMMYT accession and pre-breeding genotyping) and by the WHEAT CRP (ICARDA References: http://seedsofdiscovery.org, https://urgi.versailles.inra.fr/download/iwgsc/, www.diversityarrays.com and CIMMYT genebank genotyping).