Browsing by Author "Manju, K.P."

Now showing 1 - 4 of 4
  • Thumbnail Image
    Item
    Bioinformatic prediction of SNP markers in WRKY sequences of palms
    (2011) Manju, K.P.; Arunachalam, V.
    WRKY transcription factors are unique to plants and performs many imperative functions mainly disease resistance. In the present study we have analyzed the WRKY transcription factor gene sequences to assess the variation at single nucleotide level. We have retrieved 525 sequences of WRKY genes of palms of 334 Kb size. The sequences were purified by employing EST trimmer and were clustered into 31 contigs using CAP3. Single nucleotide Polymorph isms (SNP) and insertion/deletions (indels) were detected in contigs using the AUTOSNP software. Alternatively candidate SNP containing contigs were aligned by Clustal X to locate the SNPs. Results from these two methods were compared and false SNPs were eliminated. Finally, about 568 SNPs were found including 250 transitions, 120 transversions and 198 indels. The SNPs were seen at a frequency of 2.84/l00bp in the WRKY sequences of palms. Primers were designed flanking to SNP/ indel sites with potential as markers in palms. We could obtain two novel WRKY-SNP markers (WRKY 7 and WRKY 12) which are not reported before in palms.
  • Thumbnail Image
    Item
    Biotechnology and Genomics in Palms
    (2013) Manimekalai, R.; Rajesh, M.K.; Manju, K.P.
  • Thumbnail Image
    Item
    Microsatellites in palm (Arecaceae) sequences
    (2011) Manju, K.P.; Manimekalai, R.; Arunachalam, V.
    Microsatellites are the most promising co-dominant markers, widely distributed throughout the genome. Identification of these repeating genomic subsets is a tedious and iterative process making computational approaches highly useful for solving this biological problem. Here 38,083 microsatellites were localized in palm sequences. A total of 2, 97,023 sequences retrieved from public domains were used for this study. The sequences were unstained using the tool Seqclean and consequently clustered using CAP3. SSRs are located in the sequences using the microsatellite search tool, MISA. Repeats were detected in 33,309 sequences and more than one SSR had appeared in 3,943 sequences. In the present study, dinucleotide repeats (49%) were found to be more abundant followed by mononucleotide (30%) and trinucleotide (19%). Also among the dinucleotides, AG/GA/TC/CT motifs (55.8%) are predominantly repeating within the palm sequences. Thus in future this study will lead to the development of specific algorithm for mining SSRs exclusively for palms.
  • Thumbnail Image
    Item
    Molecular marker-based genetic variability among Yellow Leaf Disease (YLD) resistant and susceptible arecanut (Areca catechu. L.) genotypes
    (2012-12) Manimekalai, R.; Deeshma, K.P.; Manju, K.P.; Soumya, V.P.; Sunaiba, M.; Smita Nair; Ananda, K.S.
    Yellow Leaf Disease (YLD) is a lethal disease affecting the arecanut palms of south India causing heavy yield loss. Presently, there is no cure for this disease and breeding for resistance is the only solution. Disease-free palms identified in hotspot areas (i.e., heavily disease affected regions), may harbour special gene family. The present study aimed to differentiate YLD resistant areca palms with susceptible palms using three different marker systems, i.e., RAPD, ISSR and resistant gene based markers. Amplification of arecanut genomic DNA using these marker systems yielded a total of 248 fragments, that could be scored, of which 130 were polymorphic between YLD resistant and susceptible individuals. Among these markers, RAPD generated greater polymorphic fragments (61.6%) than ISSR (34.9%) and resistant gene specific markers (40.7%). The primers, UBC 321, OPAF 15, and OPE13 produced distinct banding patterns for resistant and susceptible palms. The average genetic similarity coefficient for pair-wise comparison of individuals ranged from 0.73 to 0.88. The average similarity between the YLD resistant palms was found to be 0.79 and that of susceptible was 0.80. The highest similarity coefficient, 0.88 was observed between the YLD resistant individuals (R1 and R2). It has been found that the resistant and susceptible areca palms show relatively less genetic diversity and are skewed towards their phenotype. The results of this molecular characterization may provide starting points for map-based cloning of the YLD resistant genes.