Development of SSR and ILP markers in horsegram (Macrotyloma uniflorum), their characterization, cross-transferability and relevance for mapping

Simple sequence repeat (SSR) and intron length polymorphism (ILP) primers were developed and characterized from public sequence data in horsegram. All characterized primers amplified alleles in a range of 1–8 with an average of 2.64 alleles per primer. Polymorphism information content ranged from 0.048 for primers MUMS-24, MUMST-21, MUMST-26 and MUMST-29 to 0.755 in MUMS-10 with an average of 0.360. Dendrogram and principal component analysis showed that newly characterized SSR and ILP markers developed in this study distinguished horsegram germplasm lines into two groups and revealed two genetic stocks for characterized germplasm. Cross-amplification of these developed markers was tested across 12 related legume species. Nineteen primers pairs showed a maximum of 100 % cross-transferability, while a minimum of 8.3 % transferability was shown by 27 primers. As no genomic resources are available in horsegram, these newly developed markers can advance molecular breeding research in this crop species and can be helpful in germplasm characterization, diversity studies, mapping and in comparative genomic studies.