This article provides notes on germplasm core set.
Emphasis on germplasm collection and conservation has resulted into huge collections in different crops including vegetables. Mostly these germplasm lines have been characterized by the germplasm curators/botanists on the basis of qualitative descriptors. However, replicated trial evaluation for economically important and quantitative traits requiring considerable time and resources has become rather difficult.
Recognizing this O. H. Frankel in 1984 proposed that entire collection be reduced to a manageable sample or “core set” that would represent the genetic diversity of the crop and its relatives with minimum repetition.
The core set would serve as a working collection and enable easy retrieval of germplasm and related information needed in various research programmes thereby facilitating better assembly, management, and use of genetic resources by the gene bank curator.
This would also allow plant breeders to extensively examine the genome for not only specific alleles but also desirable gene blocks. In addition, the core set can provide an indication of the group(s) that should be examined in detail for particular descriptors. The accessions not included in the core set are designated as reserve collection.
O. H. Frankel and A. H. D. Brown in 1984 and A. H. D. Brown in 1989 modified the concept further and suggested a procedure for identifying a core set using information on the origin and characteristics, van T. J. L. Hintum in 1999 described various steps for the development of a core collection. The details of the references for these investigations are available in Gangopadhyay (2010).
The issues that need to be looked into while forming a core set are:
1. The size of the core set
2. The grouping of accessions in the entire collection
3. The number of accessions to be selected from a group
4. The sampling theory
Brown (1989) used the sampling theory of selectively neutral alleles and advocated that if about 10% of germplasm accessions are drawn randomly from the entire collection, about 70% of the allelic variation of the collection would be retained.
The second issue relating to formation of non-overlapping groups in the entire collection based on similarities among accessions has been addressed to by Spagnoletti-Zeuli and Qualset, 1987.
In this approach, the hierarchy of grouping is based on the following:
1. Major geographical groups
2. Morpho-agronomic groups
3. Agro-ecological region groups
The clustering within a broad group could be on the basis of cytological, biochemical, and molecular markers. A germplasm collection with abundant discriminating data would require multivariate clustering to discern groups of similar accessions.
The third issue deals with the number of accessions to be selected within a group. The strategy to be followed here is that a good core set should capture maximum genetic diversity with a minimal number of genotypically redundant accessions from the entire collection. While doing so, it must be kept in mind that the core set should remain small enough to be managed properly as stated by Brown (1989).
The last issue involves using a suitable sampling procedure for selecting accessions within a group. As mentioned by Ganogopadhyay (2010), it is worth mentioning that Maria (2000) and Gounesnard (2001) have developed core set using algorithm technique.
There are reports that efficacy of sampling for allocation of accessions to different groups could be immensely improved by using a diversity-dependent strategy. For access to the source literature in this regard, Ganogopadhyay (2010) should be referred.
As mentioned by Ganogopadhyay (2010), concept of core set has been successfully used in several crop species such as soybean, lentil, peanut, chickpea, alfalfa, cassava, common bean, coffee, barley, okra, mungbean, sesame, sweet potato, chilli, pigeonpea, safflower, finger- millet, and eggplant.
Gangopadhyay (2010) carried out a study to develop a core set of cultivated eggplant (Solanum melongena) using geographical distribution and 14 qualitative and 14 quantitative morphological descriptors at NBPGR, New Delhi.
The material comprised 1798 accessions where 1503 were indigenous collections and 295 were exotic ones. The exotic collections included 252 from Asia, 3 from Africa, 4 from Europe, 35 from north America, and 1 from Australia.
The experiment was conducted in an augmented block design with 40 blocks. Each block had 45 accessions and 7 controls except last block which had 43 accessions and these were randomized within blocks.
Observations from 10 randomly selected plants were recorded for 14 qualitative and 14 quantitative morphological descriptors following the descriptors list developed by International Board of Plant Genetic Resources and NBPGR.
The 14 qualitative morphological descriptors, recorded visually, were petiole colour, leaf blade lobing, leaf blade tip angle, leaf colour distribution, calyx colour, calyx spininess, corolla colour, Fruit colour, fruit colour distribution, fruit shape, fruit curvature, fruit apex shape, fruit length-breadth ratio, and seediness.
The 14 quantitative descriptors were plant height (cm), plant spread (cm), number of primary branches, petiole length (cm), leaf blade length (cm), leaf blade width (cm), number of days to 50% flowering, peduncle length (cm), fruit length (cm), fruit width (cm), fruit weight (g), number of fruits/plant, number of days to 50% fruit harvest, and fruit yield/plant (kg).
The petiole length, petiole colour, leaf blade length, leaf blade width, leaf blade lobbing, leaf blade tip angle, and leaf colour were recorded on the fifth leaf from the top at full foliage stage. The calyx colour, calyx spininess, and corolla colour were recorded at peak flowering stage.
Plant height, plant spread, and number of primary branches were recorded at peak fruiting stage. The total number of fruits and fruit yield across 8 harvestings were divided by the number of plants to compute the number of fruits/plant and fruit yield/plant.
The core set was developed using Shannon-Wiener Diversity Index (H’) and the principal component score strategy (PCSS). The accessions were classified into 15 groups based on regions and continents. Following A. D. H. Brown, a core set (10% of entire collection) of 181 accessions was fixed in advance. In every group, H’ was calculated for each qualitative descriptor.
The total diversity in each group was determined by pooling Hs’ across all qualitative descriptors. The number of accessions in each group was then determined by proportional strategy (proportion to the total diversity in each group). Further, accessions from each group were selected using PCSS. Groups with less than 5 accessions had all their accessions directly added to the core set.
A comparison of means, variances and phenotypic correlations for quantitative descriptors and the Shannon-Wiener Diversity Index (H’) for qualitative descriptors indicated that the genetic variation for these descriptors was conserved in the core set.
This core set can be evaluated for agronomic/horticultural traits including resistance to biotic and abiotic stresses to identify accessions with desirable traits for use in eggplant breeding research and genomic studies.