Development of eSSR-Markers in Setaria italica and Their Applicability in Studying Genetic Diversity, Cross-Transferability and Comparative Mapping in Millet and Non-Millet Species

• DOI: 10.1371/journal.pone.0067742
• Publication Date: 2013-06-21T21:12:38Z
• Authors: Kajal Kumari; Mehanathan Mutham...; Gopal Misra; Sarika Gupta; Alagesan Subramanian; Swarup Kumar Parida; Debasis Chattopad...; Manoj Prasad
• Keywords: Genetic Markers; 0301 basic medicine; DNA, Plant; Science; Setaria Plant; Zea mays; Chromosomes, Plant; 03 medical and health sciences; Databases, Genetic; Phylogeny; Sorghum; Expressed Sequence Tags; 2. Zero hunger; Base Sequence; Q; R; Chromosome Mapping; Genetic Variation; Oryza; Sequence Analysis, DNA; 15. Life on land; Seeds; Medicine; Sequence Alignment; Research Article; Microsatellite Repeats

Foxtail millet (Setariaitalica L.) is a tractable experimental model crop for studying functional genomics of millets and bioenergy grasses. But the limited availability of genomic resources, particularly expressed sequence-based genic markers is significantly impeding its genetic improvement. Considering this, we attempted to develop EST-derived-SSR (eSSR) markers and utilize them in germplasm characterization, cross-genera transferability and in silico comparative mapping. From 66,027 foxtail millet EST sequences 24,828 non-redundant ESTs were deduced, representing ~16 Mb, which revealed 534 (~2%) eSSRs in 495 SSR containing ESTs at a frequency of 1/30 kb. A total of 447 pp were successfully designed, of which 327 were mapped physically onto nine chromosomes. About 106 selected primer pairs representing the foxtail millet genome showed high-level of cross-genera amplification at an average of ~88% in eight millets and four non-millet species. Broad range of genetic diversity (0.02-0.65) obtained in constructed phylogenetic tree using 40 eSSR markers demonstrated its utility in germplasm characterizations and phylogenetics. Comparative mapping of physically mapped eSSR markers showed considerable proportion of sequence-based orthology and syntenic relationship between foxtail millet chromosomes and sorghum (~68%), maize (~61%) and rice (~42%) chromosomes. Synteny analysis of eSSRs of foxtail millet, rice, maize and sorghum suggested the nested chromosome fusion frequently observed in grass genomes. Thus, for the first time we had generated large-scale eSSR markers in foxtail millet and demonstrated their utility in germplasm characterization, transferability, phylogenetics and comparative mapping studies in millets and bioenergy grass species.