Genetic diversity of foxtail millet (Setaria italica) as determined by Transposable Element Copia Markers

Abstract

Foxtail millet (Steria italica (L.) Beauv.) belongs to grass family Poaceae, and sub family Panicoideae. Foxtail is C4 plant and autogamous species with polidy level 2n=2x=18 with genome size ~515 Mb. Domesticated in China about 8700 years ago. And rank second in the worlds, production. In India it is commonly known asnavane (Kannada), korullu (Telegu), tenia (Tamil) and kangani (Gujarati and Hindi). Foxtail millet grains are rich in protein, fibre, β carotene and minerals. In India the crop is cultivated in states of Andhra Pradesh, Karnatka, Tamil Nadu, Rajasthan, Uttar Pradesh, Madhya Pradesh, Maharastra, 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 transposon-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 three transposable element based markers in order assess the potential application of transposons- based markers system. The seed for study were collected from National Institute of Plant Genome Research, New Delhi. Three primers Gypsy101, Gypsy1003 and Gypsy1159 amplified 27 loci. Out of 27 alleles, 26 were found to be polymorphic and only 1 monomorphic. On an average, 9 alleles per primer loci were found and 8.667 average polymorphic alleles. A high level of polymorphism (96.29%) indicated the presence of high variability in foxtail millet (S. italica) accessions. Polymorphism information content (PIC) was estimated for each of the 3 TE Copia markers. PIC values ranged from 0.518 (GYPSY1003) to .0890 (GYPSY 1159 primer) with an average of 0.701. Highest PIC value 0.890 was observed for GYPSY101. Lowest PIC value 0.518 was obtained for GYPSY1003. The primer GYPSY1159 was observed to be highly polymorphic (PIC value of 9.067). The resolving power (RP) varied between 4.532 (GYPSY 101) and 10.798 (GYPSY 1159) with an average value of 7.980. The highest resolving power shown by GYPSY1159 which is 10.798 and the lowest was 4.532 by GYPSY101. The average R.P. was 7.980. While GYPSY1003 showed 85.71% polymorphism. Genetic similarities were calculated using the Nei-Li similarity co-efficient. Significant genetic variation was found among all foxtail millet accessions with the GS value ranging from (0.407) to (0.962). The UPGMA cluster tree analysis led to the grouping of 26 accessions in two major groups.