Sorghum Core

Genetic diversity in ICRISAT sorghum collection using random vs non-random sampling procedures. A large collection, such as the sorghum [Sorghum bicolor (L.) Moench] landrace collection held at the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), represents a challenge for the maintenance of both the accessions of and the information documented for the germplasm collection. The accessibility and knowledge of the landrace collection are the essential factors for an efficient utilization of the genetic resources by both breeders and farmers.

Hence, the large size of the sorghum landrace collection maintained by ICRISAT led to the establishment of a core collection. The core collection concept has used to define a limited set of accessions derived from an existing germplasm collection, chosen to represent the genetic spectrum in the whole collection. The core should contain the maximum genetic diversity available in the collection. Accessions in the core should be chosen primarily to be representative of the whole collection, to be ecologically or genetically distinct from one another, and to maximize genetic diversity. The core collection serves as an entry point to the whole collection. Identification of core collections also simplifies the process of multiplication and distribution to potential users by substantially reducing the number of accessions that need to be maintained in active collections. Core collections can be formed on the basis of characterization information available on germplasm accessions, which can be further used to determine cluster groups of similar accessions together. A series of investigations, reported below, were under taken to define sorghum core collections and to compare each of their sampling procedures.

During this research, an assessment was also made, according to geographic and taxonomic classification, to determine the diversity pattern maintained in the landrace collection and its adequacy. This assessment indicates that the sorghum collection held in trust at ICRISAT was under represented for the race bicolor and for accessions from China. Furthermore, this assessment highlighted redundancies especially in races caudatum and durra, as well as in the germplasm acquired from East Africa and the Indian subcontinent.

Morpho-agronomic and passport data

Different sampling strategies, either random or non-random, were proposed to obtain subsets of reduced size (core collection) of sorghum accessions held in trust at ICRISAT. Three subsets were established following (i) a random sampling within a stratified collection (logarithmic strategy: L), (ii) a sample based upon morpho-agronomic diversity (principal component score strategy: PCS), and (iii) a sample based upon an empirical knowledge of sorghum (taxonomic strategy: T). click here to search the data Comparisons of these three samples for morpho-agronomic characterization and passport information were assessed to determine their impact on phenotypic diversity (Grenier et al. 2000a). For their overall diversity, the three subsets did not differ, as shown with the two-dimensional representation of the morpho-agronomic diversity and the Shannon-Weaver diversity indices. When comparisons for morpho-agronomic and passport data were considered, the PCS subset looked similar to the entire landrace collection. The L subset showed differences for characters associated with the photoperiod reaction that was considered in the stratification of the collection. The T subset was the most distinct from the entire landrace collection as it over-represented the landraces selected by farmers for specific uses and covered the widest range of geographical adaptation and morpho-agronomic characteristics.

Molecular markers

Microsatellite markers are used in crops to differentiate among genotypes and as tools in marker-aided selection and gene introgression. Early research with the sorghum world collection showed significant variation in the five microsatellite markers examined: 2.4 was the average number of alleles per locus within accessions and 19.2. in the whole sample of 25 accessions (Djè et al. 2000). This sorghum collection seems to be highly structured genetically with about 70% of genetic diversity accounted for among accessions. In contrast, morphologically defined races of sorghum, or the geographic origins accounted for below 15% of the total genetic diversity. This result shows that microsatellites are useful in the identification of individual accessions with a high relative contribution to the overall allelic diversity of the collection. Therefore, microsatellite markers were used to quantify the genetic diversity in each of the sampling procedures (PCS, L, T) using the polymorphisms at 15 microsatellite loci (Grenier et al. 2000b). The landraces of each subset were genotyped with three multiplex polymerase chain reactions (PCRs) of five fluorescent primer-pairs each with semi-automated allele sizing. The average allelic richness for each subset was equivalent (16.1, 16.3 and 15.4 alleles per locus for the subsets PCS, L, and T, respectively). The average genetic diversity was also comparable for the three subsets (0.81, 0.77 and 0.80 for the subsets PCS, L, and T, respectively). Allelic frequency distribution for each subset was compared with a chi-square test but few significant differences were observed. A high percentage of rare alleles (71 to 76% of 206 total rare alleles) was maintained in the three subsets. The global molecular diversity retained in each subset was not affected by a sampling procedure based upon phenotypic characters.