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Amity University, Noida (2019)

Development of Indian wild Rice Database and DNA Markers for the Identification of wild Oryza Species

Tripathy, Kabita

Titre : Development of Indian wild Rice Database and DNA Markers for the Identification of wild Oryza Species

Auteur : Tripathy, Kabita

Université de soutenance : Amity University, Noida

Grade : Doctor of Philosophy (PhD) Biotechnology 2019

Résumé
Wild rice growth is naturally spreading in rice growing habitats. These are survivor of natural calamities from thousands of years and adapted to range of climatic situations like drought, water-logging and salty soil. For this reason, it is likely to have desirable resistance alleles for extreme calamity and various diseases. Collection of wild rice genotypes was initiated from different Indian climatic zones consisting of photographs, videos and basic passport data for the present study. In addition to this, the collected wild rice germplasm is evaluated at IARI field to generate morphological information of the single line. The chloroplast genome based techniques can be used as important tools in cataloguing and identification of wild rice species. For this study, 58 sequences of chloroplast genome from twenty two wild species of Oryza genus belonging to nine different genome types were downloaded from NCBI nucleotide database. The chloroplast DNA length varied from 134,401bp to 136,133bp. The nucleotide variations showed total 126,271 monomorphic sites and 8829 gaps. Total number of variable sites are 4017 that includes 512 singleton variable sites. Total numbers of mutations are 4137. Haplotype analysis revealed 50 SNP haplotypes representing 23 species of Oryza with haplotype diversity of 0.995. Haplotype analysis of InDels revealed 49 haplotypes covering 8912 InDels with haplotype diversity of 0.985. From 8912 InDels, 24 InDels were identified as species specific based on continuous InDels with size varying from 4bp to 40bp. Further analyzing these 24 InDels, 16 were capable of differentiating 22 Oryza species and therefore used as PCR based markers. These markers differentiate individual Oryza genome as well as species within the genome type based on their PCR amplicon size differences. These InDel and SNP markers can be used for inter-specific comparison, species identification and analysis of their phylogenetic relationship.

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