Genetic diversity of foxtail millet (Setaria italica) as determined by Microsatellite Markers

Abstract

Foxtail millet (Setariaitalica) is an annual crop and easily cultivated cereal grain belonging to Setaria genus of Poaceae family and subfamily Panicoideae. Foxtail millet is a C4 plant and autogamous species with ploidy level 2n=2x=18 and relatively has small genome size of ~ 515 Mb.Foxtail millet is an important grain crop in temperate, subtropical, tropical Asia and parts of southern Europe. China, India and Japan are the major foxtail millet growing countries in the world. With the rapid development and spreading of maize and other crops, foxtail millet has gradually become a minor crop in the last 80 years but still widely cultivated in Asia, Europe, North America, Australia and North Africa as food grain and forage. China ranks first in the area and production of foxtail millet in the world.In India the crop is cultivated in states of Andhra Pradesh, Karnataka, Tamil Nadu, Rajasthan, Uttar Pradesh, Madhya Pradesh, Maharashtra, Gujarat and North Eastern states. Molecular markers are now used to track loci and genome regions of agronomic traits and diseases resistance traits in major crop species. Multilocus SSR-based molecular markers have great potential for genotyping, fingerprinting and establishing genetic relationships between cultivars and wild accessions. This study is to evaluate the genetic diversity among 26 accessions foxtail millet using five SSR or microsatellite based markers in order to assess the potential application of SSR-based marker system.The seed for study were collected from National Institute of Plant Genome Research, New Delhi. Five SSR primers namely SIGMS2443, SIGMS12819, SIGMS2541, SIGMS2303 and SIGMS4692 amplified 30 SSR marker loci. Out of 30 bands amplified, 22 were found to be polymorphic and 8 were monomorphic.Of the 26 pair wise combinations generated by foxtail millet (Setaria italica) accessions, the smallest G.S value (0.500) was observed between D57 and GS478, GS485 and GS461, GS478 and GS485 genotypes, which appear to be the most dissimilar accessions and distantly related, which shows the presence of extensive diversity in this species.Average numbers of band per primer was 6 while, average numbers of polymorphic band per primer was 3.67. Highest PIC value was 0.560 of SIGMS4296 which has 6 alleles among the 26 genotypes, while the lowest PIC value was obtained for SIGMS2303is 0.372.The maximum resolving power was calculated as 9.916 which was exhibited by SIGMS12819 and the lowest resolving power was calculated as 2.076 by SIGMS2541.The average resolving power was 7.180. The highest polymorphism was shown by primer SIGMS2443 which was around 85%. Genetic similarities were calculated using the Nei-Li similarity co-efficient. Significant genetic variation was found among all foxtail millet (Setaria italica) accessions with the GS value ranging from 0.500 to 0.954. The UPGMA cluster tree analysis led to the grouping of 26 accessions in two major groups.