Vol.

5 Issue- 1, September 2024 (e-ISSN: 2582-8223)

Concept of Core collections of Plant Genetic Resources

*S.Sheelamary, K.Lakshmi, K.Dhanapal and R.Vivek Kumar
Division of Crop Improvement, ICAR-Sugarcane Breeding Institute, Coimbatore

. ARTICLE ID: 09
Abstract
Worldwide efforts to breed plants are dependent on the genetic diversity that exists in
current cultivars and germplasm banks. In order to preserve valuable material before it
vanished, breeding programs prioritized germplasm collection activities throughout the mid-
to late 1900s. This led to the formation of the several vast germplasm resources that are
currently available in various nations. Risks to the preservation of genetic resources have
increased, along with a notable decline in the amount of expenditure spent on germplasm
collection explorations, a rise in international biosecurity regulations and restrictions on
breeders to freely exchange commercial germplasm. Plant breeders' capacity to use germplasm
is limited by the size of most genebank collections, as well as issues related to germplasm
passport data and the physical or genetic characterization of the accessions in collections. Core
collection is a representative subset of the entire germplasm collection has grown in favor as a
means of getting around these limitations. By including highly defined germplasm that tries to
capture the majority of the variation in a collection as a whole, core collections seek to increase
the usage of germplasm.
Key words: Core collection, quality evaluation, types and uses
Introduction
Under various environmental and climatic situations, plant genetic resources (PGR) are
the cornerstone of sustainable agriculture and global food security and stability. One of the
main issues causing the underutilization of material is the inadequate evaluation and
characterization of germplasm conserved in genebanks, which also has an adverse effect on
funding efforts and future opportunities. Plant breeding organizations use the germplasm stored
in genebanks, frequently on a global scale, and breeding program depend on the genetic
diversity that is available (Rajesekharan,2015). Elite crop cultivars are less able to adapt to
environmental changes because they are typically bred from a limited genetic base and intended
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for high input, intensive agricultural production. In order to achieve future breeding targets that
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Vol. 5 Issue- 1, September 2024 (e-ISSN: 2582-8223)

are climate resilient more work needs to be put into utilizing the germplasm found in
genebanks.
At NBPGR national gene bank conserves as per the gene bank standards as base
collections at -18o C. The current germplasm holdings in the National Gene Bank in the form
of orthodox seeds are 3, 96,189 including released varieties and genetic stocks representing
1,584 species (http://www.nbpgr.ernet.in). However, the varieties released represent only a
small proportion of the total variation. This is largely due to the negative effects of linkage
drag, unfavourable alleles and the breakdown of the coadapted gene complexes that can be
introduced from wild germplasm. Unless there is an extreme need, the breeders avoid adding
highly unadopted germplasm into their breeding programs.
What is core collection?
The core collection is a small subset that minimizes genetic redundancy while
preserving the maximum genetic diversity of the entire population. In order to represent the
genetic diversity of the full germplasm resource with the fewest possible resources, core
collection refers to the process of choosing a portion of the entire germplasm pool using certain
techniques. The hierarchical structure model of genetic variety and the notion of neutral
mutations provide the theoretical underpinnings for this idea. Germplasm resources are
essential for genetic research because they provide a basic material and facilitate the
identification and use of genes and traits with ecological and economic significance. Therefore,
the preservation and utilization of germplasm resources are of significant importance for the
development of new crop varieties, and a large number of germplasm banks have been
established. But the diversity that has been gathered may not be completely and efficiently used
because of their abundance, diversity, and lack of complete information about germplasm
resources.
3. What makes the Core collection good?
• A good core collection should have no redundant entries. In the absence of significant
differentiation among accessions, they can be considered as drawn from the same
population, and hence be regarded redundant. Combining such material into a single
accession is one of the possibilities to reduce the amount of redundancy in a collection,
and to improve the composition thereof.
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• Represent maximum the whole collection with regards to species, subspecies and
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geographical regions. Maximising the representativeness of genetic diversity implies

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Vol. 5 Issue- 1, September 2024 (e-ISSN: 2582-8223)

also the inclusion of broadly adapted and heterotic materials containing ‘generalist’
alleles in a core collection. It may represent the full range of variation present in the
whole collection or maximising the representativeness of the pattern of variation
present in the whole collection.
• Should be small enough to be easily managed.
• Data completeness: The primary cause of the limited utilization of germplasm in crop
improvement initiatives is the dearth of data on a vast number of accessions, especially
for economically significant traits that exhibit high genotype × environment (G x E)
interaction and necessitate multilocation assessment. Creating a "core collection," or
roughly 10% of the total collection, has been suggested as a solution to the size-related
collection problem. This collection would represent the genetic variability of the entire
collection.
• Utilization: The fact that crop improvement scientists were not using genebanks to their
full potential was evident from the rise in accession numbers within the collections and
the lack of a corresponding increase in their use (Marshall, 1989). There is a huge
discrepancy between the materials' actual use and their availability. This was valid for
both national and international programs, including the CGIAR institutes. Similarly, in
the national programs, the germplasm lines used in breeding programs are very limited
(Upadhyaya et al.,2008).
Types of core collection
Based on the purposes for which they are formed core collections can generally be
classified into three types or categories i.e. core collections representing (1) individual
accessions; (2) extremes; and (3) distribution of accessions in the whole collection.
Type I: A core collection that stand in for each of the collection’s individual accessions
(CC-I). In this instance, every item in the core collection stands in for one or more
accessions that taken together comprise the entire collection. The entry in the core that
most closely resembles each accession throughout the entire collection serves as its
representation.
Type II: The goal of a core collection of type CC-X is to accurately represent the
genotypes, allele and phenotypic ranges of the entire collection. Entries in a good core
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collection of type CC-X are as dissimilar from one another as feasible.

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Type III: A core collection that shows how the accessions for the entire collection are
distributed (CC-D).In this instance, it is important to make sure that the proportion of
accessions within a core collection accurately represents the numerical contributions
made by the various regions or categories to the collection as a whole. For instance, the
core collection ought to appropriately represent the significance of a particular
geographic region if the bulk of the accessions originate from that area.
Common methods used for evaluating core collections
Several types of information can be used for selecting core collections. The most
common type of data is (i) passport data (ii) agronomic data (iii) molecular marker data.
Passport data: The identity, origin, and taxonomic classification of an accession, along
with related information about domestication, distribution, breeding history, cropping
patterns, and use, are all included in passport data. Examples of passport information
include the origin nation, crop type (such as winter or summer wheat), and lineage.
Agronomic data: Data related to agriculture can be categorical, discrete or continuous.
Continuous variables include things like plant height, leaf area, and grain yield. Counts,
such as the number of fruits or seeds in a pod, are dealt with by discrete variables.
According to Crossa and Franco (2004), categorical variables can be classified as
nominal (such as an organ's color or shape), ordinal (a visual scale set up to represent
intensity, color, or size), or binary (presence or absence of a particular characteristic).
Environmental factors and multiple genes are typically responsible for controlling
agronomic traits.
Molecular data: Data from molecular or biochemical marker systems can be treated
as either continuous or categorical. Single nucleotide polymorphism (SNP), amplified
fragment polymorphism (AFLP), random amplified polymorphic DNA (RAPD), and
simple sequence repeats (SSR) are a few common types of molecular data (Odong et
al.,2012).
Criteria used for evaluation of quality of core collections
Criteria General comments
Summary statistics Agronomic: Mean, range, variance, phenotypic correlation
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coefficients)
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Vol. 5 Issue- 1, September 2024 (e-ISSN: 2582-8223)

Molecular: gene diversity, heterozygosity, PIC, major allele

frequency
Plot of the coordinates of the entries on main PCs to show spatial
PCA/ PCoA
distribution of entries
Diversity index Highest when uniform distribution and to be compared with the
eg. SDI, Nei max possible value (logn)
The highest value (100%) is obtained when all the categories are
Class coverage
represented in the core
Goodness of Fit To test frequency distributions of important categorical traits.

Core collection developed at NBPGR, New Delhi

Crop Entire collection Core collection (Mini core)
Moong bean 1532 152
Sesame 3129 362

Brinjal 1798 181

Wheat 22469 2208 (224)
Rice (NEH) 6984 701
Lentil (wild) 405 96
(Source : NBPGR, New Delhi)
Use of Core Collection
Genomic Study and Marker Development
Molecular markers have broad prospects for application in the core collection, which
can promote the protection and utilization of germplasm resources through evaluation of
genetic diversity, help identify the species and varieties of core collections that are difficult to
distinguish morphologically, an construct genetic maps of germplasm resources, which help
understand their genetic structure and evolutionary history, providing a basis for comparative
genomics research and the novel molecular markers derived from functional genes play a
crucial role in improving agronomic characteristics such as yield, quality, disease resistance,
and abiotic stress tolerance. Collectively, these novel molecular markers provide an effective
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approach for classifying germplasm resources, conducting genetic research, identifying the
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Vol. 5 Issue- 1, September 2024 (e-ISSN: 2582-8223)

specific genes affecting important traits, and facilitating marker-assisted breeding ( Gu et al.,
2023).
Identification of Disease or Pest Resistance
Core collections, which represent the entire genetic diversity of germplasm resources,
have been shown to improve the efficiency of identifying disease or pest-resistant accessions
or genes which can greatly aid in disease-resistance breeding efforts and may even lead to gene
editing and the introduction of novel alleles for single or multiple disease resistance in various
crops.
Gene Discovery and Allele Mining
Core collections are valuable genetic resources for the identification of elite genes and
mining alleles. Functional genes or markers can improve the efficiency and precision of
selecting desirable traits and aid in accumulating favorable alleles for high-yield crop breeding.
It is further necessary to work on mining of more underlying genes, manipulating the desired
traits.
Conclusion
Integration of phenotypic and molecular data needs to be addressed more effectively
and scientifically. It is necessary to improve phenotyping tools to enhance the efficiency of
phenotyping. Optimizing the sampling strategy, The development of core collections for timber
trees and bamboo and also the endangered forest species, is a top priority for the near future.
We should make full use of genome sequencing information to develop molecular markers and
gene discovery based on the core collection.
Reference
Gu, R, Fan, S, Wei, S, Li, J, Zheng, S, Liu, G. (2023). Developments on Core Collections of
Plant Genetic Resources: Do We Know Enough? Forests. 14, 926.
https://doi.org/10.3390/f14050926
http://www.nbpgr.ernet.in
Marshall, D.R. (1989). Limitations to the use of germplasm collections. p. 105-120. In: The
use
Odong, T.L, Jansen, J, van Eeuwijk, F.A, van Hintum, T.J. (2013). Quality of core collections
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for effective utilisation of genetic resources review, discussion and interpretation.

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Theor Appl Genet. 126(2):289-305. doi: 10.1007/s00122-012-1971-y.

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of plant genetic resources [Brown AHD, Frankel OH, Marshall DR and Williams JT
(eds)]. New York:Cambridge University Press.
Rajasekharan, P. (2015). “Gene banking for ex situ conservation of plant genetic resources,”
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Delhi: Springer; ), 445–459
Upadhyaya,H.D, Gowda, C.L.L and Sastry, DVSSR (2008). Management of Germplasm
Collections and Enhancing Their Use by Mini Core and Molecular Approaches. APEC-
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