Highly informative genic and genomic SSR markers to facilitate molecular breeding in cultivated groundnut (Arachis hypogaea)

Abstract

With an objective of identification of highly informative set of SSR markers in cultivated groundnut (Arachis hypogaea L.), a total of 4485 markers were used for screening using a set of 20 parental genotypes of 15 mapping populations. Although 3582 (79.9%) markers provided scorable amplification, only 1351 (37.3%) markers showed polymorphism. Polymorphism information content (PIC) value ranged from 0.10 (GM742) to 0.89 (S009) with an average of 0.31. Similarly, number of alleles ranged from 2 to 14 with an average of 3.2 alleles. In general, the SSR markers based on dinucleotide repeats displayed higher PIC value and number of alleles. Based on these polymorphism features, 199 markers with >0.50 PIC values have been identified. Polymorphism features of these markers along with the primer sequences, for the first time, for a total of 946 SSR markers have been provided. It is anticipated that the identified set of highly informative markers, instead of starting from the random set of SSR markers, should be very useful to initiate molecular genetics and breeding studies in cultivated groundnut