Characterization and mapping of sequence-tagged microsatellite sites in the chickpea (Cicer arietinum L.) genome

A size-selected genomic library comprising 280,000 colonies and representin g approximate to 18% of the chickpea genome, was screened for (GA)(n), (GAA )(n) and (TAA)(n) microsatellite-containing clones, of which 389 were seque nced. The majority (similar to 75%) contained perfect repeats; interrupted, interrupted compound and compound repeats were only present in 6%-9% of ca ses. (TAA)-microsatellites contained the longest repeats, with unit numbers from 9 to 131. For 218 loci primers could be designed and used for the det ection of microsatellite length polymorphisms in six chickpea breeding cult ivars, as well as in C. reticulatum and C. echinospermum, wild, intercrossa ble relatives of chickpea. A total of 174 primer pairs gave interpretable b anding patterns, 137 (79%) of which revealed at least two alleles on native polyacrylamide gels. A total of 120 sequence-tagged microsatellite site (S TMS) markers were genetically mapped in 90 recombinant lines from an inter- species cross between C. reticulatum and the chickpea cultivar ICC 4958. Ma rkers could be arranged in 11 linkage groups (at a LOD score of 4) covering 613 cM. Clustering as well as random distribution of loci was observed. Se gregation of 46 markers (39%) deviated significantly (P greater than or equ al to 0.05) from the expected 1:1 ratio, The majority of these loci (73%) w ere located in three distinct regions of the genome. The present STMS marke r map represents the most advanced co-dominant DNA marker map of the chickp ea genome.