Expressed Sequence Tags (ESTs) with comprehensive transcript information are valuable resources for development of molecular
markers as they are derived from conserved genic regions. The present study highlights the mining of EST database to deduce the
class I hyper variable SSRs in A. sativum. From 21694 garlic EST sequences, 642 non-redundant SSRs were identified with an
average frequency of 1 per 14.9 kb of garlic transcriptome. The most abundant SSR motifs were the mononucleotides (32.86%)
followed by trinucleotides (28.50%) and dinucleotides (13.39%). Among the individual SSRs, (A/T)n accounted for the highest
number (137; 21.33%) followed by (G/C)n (74; 11.52%) and (AAG)n (63;9.81%). Primers designed from a robust set of 7 AsESTSSRs
resulted in the amplification of 63 polymorphic alleles in 14 accessions of garlic. The resolving power of the markers varied
from 4.286 (AsSSR7) to 18.143 (AsSSR13) while the average marker index (MI) was 5.087. These EST-SSRs markers for garlic could
be useful for the improvement of garlic linkage map and could be used for evaluating genetic variation and comparative genomics
studies in Allium species.
Plant NBS-LRR R-genes recognizes several pathogen associated molecular patterns (PAMPs) and limit pathogen infection through
a multifaceted defense response. CzR1, a coiled-coil-nucleotide-binding-site-leucine-rich repeat R-gene isolated from Curcuma
zedoaria L exhibit constitutive resistance to different strains of P. aphanidermatum. Majority of the necrotrophic oomycetes are
characterized by the presence of carbohydrate PAMPs β-glucans in their cell walls which intercat with R-genes. In the present
study, we predicted the 3D (three dimensional) structure of CzR1 based on homology modeling using the homology module of
Prime through the Maestro interface of Schrodinger package ver 2.5. The docking investigation of CzR1 with β-glucan using the
Glide software suggests that six amino acid residues, Ser186, Glu187, Ser263, Asp264, Asp355 and Tyr425 act as catalytic residues
and are involved in hydrogen bonding with ligand β-(1,3)-D-Glucan. The calculated distance between the carboxylic oxygen atoms
of Glu187–Asp355 pair is well within the distance of 5Å suggesting a positive glucanase activity of CzR1. Elucidation of these
molecular characteristics will help in in silico screening and understanding the structural basis of ligand binding to CzR1 protein
and pave new ways towards a broad spectrum rhizome rot resistance development in the cultivated turmeric.
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