Core Collection
Upcoming SlideShare
Loading in...5
×

Like this? Share it with your network

Share
  • Full Name Full Name Comment goes here.
    Are you sure you want to
    Your message goes here
    Be the first to comment
    Be the first to like this
No Downloads

Views

Total Views
155
On Slideshare
155
From Embeds
0
Number of Embeds
0

Actions

Shares
Downloads
0
Comments
0
Likes
0

Embeds 0

No embeds

Report content

Flagged as inappropriate Flag as inappropriate
Flag as inappropriate

Select your reason for flagging this presentation as inappropriate.

Cancel
    No notes for slide

Transcript

  • 1. Core CollectionCore Collection A. Manivannan Scientist(Genetics) DMR New Delhi
  • 2. ?
  • 3. BASE COLLECTION CORE COLLECTION RESERVE COLLECTION MINI CC
  • 4.  It is difficult to get an overview of the collection and thus to decide what should be a added or could be removed  It is difficult to chose material since there is so much material to chose  It is difficult to focus; knowing very much about a relatively few accessions can be better than knowing relatively little about very many accessions. Problems in Maintaining GermplasmCollection
  • 5. Frankel and Brown (1984) suggested that greater use of germplasm in crop improvement is possible if a small collection representing diversity of well characterized accessions is made available to researchers. Frankel (1984) coined the term “core collection” to sample representative variability from the entire collection. A core collection contains a subset of accessions from the entire collection that captures most of available diversity in the species (Brown 1989a). The core collection thus formed can be evaluated extensively and the information derived could be used to guide more efficient utilization of the entire collection (Brown 1989b). Core Collection – An Introduction
  • 6. • The entire collection is a large collection with a taxonomic entity • The core collection has a reduced size • The core is a representative sample of the entire collection • Like the entire collection, core too is a diverse set of germplasm. The guiding principles to constitute a core collection
  • 7. Global core collection: A core collection developed from these global germplasm collections could be termed as global core collection. Regional core collection: Ecological environments influence adaptation of germplasm accessions For example, groundnut is cultivated in over 113 countries, but it is an important crop in 25 countries in the Asian continent. The core developed from the accessions involving accessions from these countries might be more beneficial to users in Asia than a global core collection. Trait-specific core collection: Some research programs might have special focus on developing a trait-specific core collection, for example, early maturity. high heritability and are least affected by G x E interaction. Types of Core Collection
  • 8. 200 accessions 20 accessions Increase the balance between types of material in a relatively small selection of accessions.
  • 9. Definition of the domain: The first step in creating a core collection is defining the material that should be represented, i.e. the domain of the core collection. Division in groups: The second step is dividing the domain in groups, which should be genetically as distinct as possible. Allocation of entries: The size of the core collection has to be determined, and the choice of number of entries per group has to be made. Choice of accessions: The last step is the choice of accessions from each group that are to be included in the core. General methodology for creating a core collection
  • 10. Definition of the Domain
  • 11. Division in Groups
  • 12. Allocation of Entries
  • 13. Choice of Accessions
  • 14. Entire collection(EC) in genebank. Characterize and evaluate EC for complete data set.STEP1 Form groups( using Taxonomic, Morphological & Geographic data; Accessions from smaller and adjacent countries with similar agro-climatic conditions could be grouped together) STEP2 STEP3 Group1 Group2 - - - - - - - - - - - -- - Group n-1 Group n Clusters Clusters Clusters clusters Clusters15
  • 15. Analyse the standardized data sets within each group separately.Use standard clustering produce to group accessions in clusters in each groups. Select 10% of accessions from each cluters, minimum 1 acccessions if < 10 accessions in a cluster to contribute core (CC) Compare CC with EC to determine the representiveness in terms of mean variance, diversity, frequency distributions.etc.CC is representative of EC if these parameters did not differ significantly between the two sets(CC) STEP4 step5
  • 16. 1.Identify the material (collection) that will be represented.
  • 17. 2. Decide on the size of the core collection.
  • 18. 3. Divide the set of material used into distinct groups.
  • 19. 4. Decide on the number of entries per group.
  • 20. 5. Choose the entries from each group that will be included in the core.
  • 21. Seminal two-stage strategy for selecting mini core collections with minimum loss of variability. the core collection as a basis for developing a mini core collection, which consists of ~10% accessions of the core collection (~1% of the entire collection). The first stage in constituting a mini core collection involves developing a representative core collection (about 10%) from the entire collection using the available information on origin, characterization and evaluation data. The second stage involves evaluation of the core collection for various morphological, agronomic and grain quality traits, and selecting a further set of about 10% accessions from the core collection. At both the stages, standard clustering procedures were used to create groups of similar accessions Mini core Upadhyaya and Ortiz (2001)
  • 22. Entire collection(EC) in genebank. Characterize and evaluate EC for complete data set.STEP1 Form groups( using Taxonomic, Morphological & Geographic data; Accessions from smaller and adjacent countries with similar agro-climatic conditions could be grouped together) STEP2 STEP3 Group1 Group2 - - - - - - - - - - - -- - Group n-1 Group n Clusters Clusters Clusters clusters Clusters24
  • 23. Analyse the standardized data sets within each group separately.Use standard clustering produce to group accessions in clusters in each groups. Select 10% of accessions from each cluters, minimum 1 acccessions if < 10 accessions in a cluster to contribute core (CC) Compare CC with EC to determine the representiveness in terms of mean variance, diversity, frequency distributions.etc.CC is representative of EC if these parameters did not differ significantly between the two sets(CC) Evaluate the representative CC in replicated multilocation trial for morphological, agronomical and quality traits to identify parents for use. Use unreplicated data for making subgroups and developing mini core collection(MCC) if the size of CC is too large Repeat step 3 and 4 to select MCC there represent CC. Follow step5 to confirm representativeness of MCC with CC. Mini-core ready for use. STEP4 step5 STEP6 STEP7
  • 24. The principles and methodologies for appropriate sampling proportions and the choice of individual accessions from basic collections are yet controversial. Stratified sampling and M (maximization) strategies are preferred by most researchers (Peeters and Martinelli 1989; Charmet and Balfourier 1995; Spagnoletti and Qualset 1993; Schoen and Brown 1993, Zhang, 2010) Principles and Methodologies for Sampling Strategies
  • 25. Stratified sampling strategies
  • 26. (1) C—constant number (2) G—proportional to Nei’s gene diversity index of the group in basic collection**** (3) L—proportional to the logarithmic group size in the basic collection, (4) P—proportional to the group size in the basic collection, (5) S—proportional to the square-root of the group size in the basic collection (Li et al. 2002) Group Based Sampling Strategies **** use of markers in core collections
  • 27. (1) by EZ (2) by sub-species (SS) (3) by population structure (PS)
  • 28. An increasing number of germplasm collections are being genotyped for marker loci such as allozymes, RFLPs,RAPD and SSR markers. Schoen and Brown (1993) proposed two strategies that can use marker diversity to allocate sampling effort for the construction of the core collection. The H strategy seeks to maximize the total number of alleles in the core collection by sampling accessions from groups in pro portion to their within-group genetic diversity. Use of Markers in Core Collection AA AA bbbb CCCCdddd EEEE ffff GGGG hhh h A C fb G h
  • 29. The M strategy examines all possible core collections and singles out those that maximize the number of observed alleles at the marker loci. These can then be chosen as final candidates for the core. The expected superiority of this marker-based method is based on the correlation between observed allelic richness at the marker loci and allelic richness on other loci. Such a correlation (or linkage disequilibrium between marker and target alleles) is expected on theoretical grounds either because of (1) shared coancestry of populations, (2) the mating system of the species considered, or (3) episodes of selection whereby selected (target) and neutral (marker) alleles become associated through hitchhiking.
  • 30. Association analysis Case (30%) Control (50%)
  • 31. Spurious associations due to population structure Case (50%) Population 1 20% Population 2 80% Control (65%) Higher proportion of a causal SNP allele in the subgroup; Higher penetrance of the causal genotype in the subgroup due to environment; Ascertainment bias.
  • 32. Sample Marker 1 Marker 2 Marker 3 A1 A2 A3 A4 A5 A6 S1 1 0 0 1 0 0 S2 1 0 1 0 1 0 S3 1 0 0 1 0 1 S4 1 0 1 0 1 0 S5 1 0 0 1 1 0 S6 1 0 0 1 0 1 Example of selection of core sub set based on marker data
  • 33. Power Core
  • 34. Zhang et al.,2011
  • 35. Retention of SSR alleles (RT) in each core set developed by 225 group- based sampling
  • 36. Nei’s gene diversity index (He) in each core set developed by 225 group-based sampling schemes
  • 37. The M strategy aims at selecting the highest diversity among subsets and is expected to perform well in marker based grouping. The MSTRAT program was able to implement the M strategy, providing the opportunity not only to determine an optimal CC size, but also to choose the representative individuals for a given sized CC (Gouesnard et al. 2001) MSTRAT- M(Maximizing) Strategies
  • 38. Once a core collection has been established, an important question for genebank managers is the extent to which it meets its original objectives in terms of the representation of diversity and lack of repetition. The principal component score strategy(Noirot et al. (1996)) tends to select entries with extreme expressions of character states used. With this method, entries with median expressions may be under-represented. Test for Redundency (Ortiz.,et al.,1999) Biochemical and molecular markers have been suggested core collections of about 10% should possess about 70% of the alleles found in the whole collection. Validating the core collection
  • 39. Analysis with statistical indicators The search using the Power Core was heuristic Approach. Mean Difference % Variance Difference % Me: Mean of entire collection Mc: Mean of core collection Statistical Parameters Involved Ve: Variance of entire collection, Vc: Variance of core collection
  • 40. Re: Range of entire collection Rc: Range of core collection CVe: coefficient of variation of entire collection CVc: coefficient of variation of core collection m: number of traits Confidence Ratio % Variable Rate % Coverage % De: Classes in entire collection Dc: Classes in core collection m: number of traits
  • 41. FUNCTIONS OF A CORE COLLECTION Addition of new accessions Conservation Characterisation Evaluation Germplasm enhancement Germplasm distribution The core collection provides a reference set. A gene bank are worth adding to the collection. The core collection provides a reference set. A gene bank are worth adding to the collection.
  • 42. THE FUNCTIONS OF A CORE COLLECTION Addition of new accessions Conservation Characterisation Evaluation Germplasm enhancement Germplasm distribution The core contains material of highest priority for conservation. The core contains material of highest priority for conservation.
  • 43. FUNCTIONS OF A CORE COLLECTION Addition of new accessions Conservation Characterisation Evaluation Germplasm enhancement Germplasm distribution The core is the suitable material for developing an adequate list of descriptors The core is the suitable material for developing an adequate list of descriptors
  • 44. FUNCTIONS OF A CORE COLLECTION Addition of new accessions Conservation Characterisation Evaluation Germplasm enhancement Germplasm distribution Two-step procedure to be carried out in sampling 1.Expensive or complex traits. 2.Focusing evaluation on a restricted set of accessions, the core assists the development of a multivariate database. Two-step procedure to be carried out in sampling 1.Expensive or complex traits. 2.Focusing evaluation on a restricted set of accessions, the core assists the development of a multivariate database.
  • 45. THE FUNCTIONS OF A CORE COLLECTION Addition of new accessions Conservation Characterisation Evaluation Germplasm enhancement Germplasm distribution The core forms a reduced set of representative accessions. The core forms a reduced set of representative accessions.
  • 46. THE FUNCTIONS OF A CORE COLLECTION Addition of new accessions Conservation Characterisation Evaluation Germplasm enhancement Germplasm distribution Representative germplasm on a reduced scale. Representative germplasm on a reduced scale.
  • 47. aAAAABBBB dCCCCCDDDDEEEE FFFGGGHHH aAABB dCCCDDEE FFGGHHH aABCD EFGHH aABCD EFGH Applied 1 Applied 2 . . . . . . Applied 6 Primary core-collection Core-collection (100) ~ 10% of Base Collection Mini core-collection(10) ~ 1% of Base Collection ~ 10% of Core Collection Applied core-collection Basic Collection (1000) Structure of a Core Collection
  • 48. Algorithms for Core Collection Core Hunter Power Core MSTART Power Marker STRUCTURE
  • 49. Core Selector "core from the core”
  • 50. Core collection Authors Year Reported Ballforieru Fodder 2005 GRACE Hu J Rice 2000 TAG Diwan Medicago 1995 TAG Thome, J Cassava 1999 IPGRI Bhattachariayajee,R Pearl millet 2007 Euphytica Upadhyaya,HD Groundnu t 2002 GRACE Upadhyaya,HD Chickpea 2001 TAG Li, Y2005 Maize 2005 GRACE Hot Papers on Core Collection of Different Crops
  • 51. Cereals 4 amaranth, barley, maize (4)† , wheat Pulses 8 bean (2), chickpea, cowpea, greengram (3), peanut Oilseeds 3 safflower, sesame (2), soyabean Industrial crops 3 beet, hops, rubber Fruits 12 blueberries, citrus, currants, dates, grape (2), hazelnut, persimmon, pear, pecan, plum, raspberries, strawberry Vegetables 6 brassica (2), capsicum, eggplant, lettuce (2), okra (2), potato Beverages, herbs and spices 4 coffee, garlic, mint, mountain mint Forages 11 alfalfa, annual medics, berseem clover, Kentucky bluegrass, red clover, ryegrass (3), shaftal clover, subclover, sweet clover, trefoil, white clover Numbers of core collections of various crop types,(IPGRI Survey † The number in parentheses is the number of different core collection for that crop.
  • 52. Core Collection at Cross Roads (Today)
  • 53. 1.vulnerability of the reserve collection 2.bias towards diversity rather than usefulness; 3.inflexibility of core entries; and 4.lack of validity in sampling variation. Threaten the size of the total collection. Core Collection at Cross Roads (Today)
  • 54. These objections can be grouped under four headings: 1.vulnerability of the reserve collection; 2.bias towards diversity rather than usefulness 3.inflexibility of core entries; and 4.lack of validity in sampling variation. A suboptimal sample. Ignores the relative ease of making the crosses needed to use a character in breeding. Core Collection At Cross Roads
  • 55. These objections can be grouped under four headings: 1.vulnerability of the reserve collection; 2.bias towards diversity rather than usefulness; 3.inflexibility of core entries; and 4.lack of validity in sampling variation. The diversity of a collection that is itself changing. Reduced scope for studying interactions among attributes of all kinds that accrue. . Core Collection At Cross Roads
  • 56. These objections can be grouped under four headings: 1.vulnerability of the reserve collection; 2.bias towards diversity rather than usefulness; 3.inflexibility of core entries; and 4.lack of validity in sampling variation. Available knowledge of genetic diversity in any crop may be insufficient. No explicit account of polymorphism within accessions Core Collection At Cross Roads
  • 57. Uses of Core collections Several new sources of variation for use in crop improvement programs. Allele mining Duplicate conservation (Black Box arrangement) Limited size of the core is the key reason for its overall manageability Reference set of accessions for the whole collection Pre Breeding Programs Greater information value of the collection, reduced costs and increased efficiency in evaluation (1) Comprehensive synthetic core collections for a whole species, (2) Clonal core collections (3) Core collections in glacie or DNA banks (4) Core collections for in situ conservation.
  • 58. JCGlaszmann,2010 Base collection Core collection Existing diversity Reference Set A set of genetic stocks that are representative of the genetic resources of the crop and are used by the scientific community as a reference for an integrated characterization of its biological diversity.(50-500)
  • 59. Common set of reference materials to help R.E.A.D. R-Represent existing diversity E- Enter the whole collection A-Assess phenotypic variation D-Dissect trait–gene associations Germplasm through concerted efforts within the research community. R.E.A.D.
  • 60. SINGER  Documentation is essential in good genebank management to allow efficient and effective use of germplasm.  CGIAR’s System-wide Information Network for Genetic Resources (SINGER).  This searchable database has information on the identity, origin, and characteristics of the accessions in CGIAR genebank http://singer.grinfo.net.