In-Silico Identification of EST Based Microsatellite Markers and Snps, and Comparative Genomic Analysis of Ests in Barnyard Millet for their Omics Applications

B. Kalyana Babu¹ *, Rashmi Chauhan²

¹ICAR - Vivekananda Parvatiya Krishi Anusanthan Sansthan, Almora, Uttarakhand, India.

²ICAR - Indian Institute of Oil Palm Research, Pedavegi, West Godavari (Dt), Andhra Pradesh, India.

Corresponding Author Email: kalyan_biotek@yahoo.co.in

DOI : http://dx.doi.org/10.12944/CARJ.5.3.03

Abstract:

Barnyard millet belongs to the family poaceae, having good nutritional properties and is also effective for diabetic patients because of its ability to reduce the blood glucose levels. The research on genomics in barnyard millet lagging behind other millets and cereals, where there is a need of more focus towards identification of microsatellite markers. The availability of EST sequences given possibility to develop and explore the EST based SSRs and SNPs. Hence, the present study was conducted at ICAR-Vivekananda Parvateeya Krishi Anusanthan Sansthan, Almora, Uttarakhand in the year 2014-2015. In the present study, the barnyard millet EST sequences (41) were downloaded in FASTA format to find the microsatellite type, distribution, frequency and developed a total of 22 primer pairs from the ESTs. The most frequent SSR repeats found to be tetra- nucleotide repeats (50 percent) followed by the penta- and hexa- nucleotide repeats. Among the dimeric SSRs, GT was found to be the most common repeat motif, AGG was the most common repeat motif in trimeric repeat motifs. The most common tetra-, penta- and hexa nucleotide repeat motifs were AGA, CAAA, TGTTT, AGACGA respectively. The SNP mining of barnyard millet ESTs found to have 1 potential SNP and 1 reliable SNP and two haplotypes. Comparative analysis of barnyard millet EST sequences with the rice genome database showed that they were homology to the rice chromosomal regions of 2, 5, 6, 8, 9 and 12, however with maize genome showed homology with respect to Zea mays Waxy gene. Thus the identified twenty two microsatellite markers and SNPs can be effectively used for barnyard millet genomics applications to study diversity, and mapping aspects.

Keywords:

Barnyard millet; Comparative genomics; ESTs; Microsatellite markers; Single nucleotide polymorphism

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