DNA Barcoding and ITS2 Secondary Structure Predictions in Taro (Colocasia esculenta L. Schott) from the North Eastern Hill Region of India

Abstract

Taro (Colocasia esculenta L. Schott, Araceae), an ancient root and tuber crop, is highly polygenic, polyphyletic, and polygeographic in nature, which leads to its rapid genetic erosion. To prevent the perceived loss of taro diversity, species discrimination and genetic conservation of promising taro genotypes need special attention. Reports on genetic discrimination of taro at its center of origin are still untapped. We performed DNA barcoding of twenty promising genotypes of taro indigenous to the northeastern hill region of India, deploying two chloroplast-plastid genes, matK and rbcL, and the ribosomal nuclear gene ITS2. The secondary structure of ITS2 was determined and molecular phylogeny was performed to assess genetic discrimination among the taro genotypes. The matK and rbcL genes were highly efficient (>90%) in amplification and sequencing. However, the ITS2 barcode region achieved significant discrimination among the tested taro genotypes. All the taro genotypes displayed most similar sequences at the conserved matK and rbcL loci. However, distinct sequence lengths were observed in the ITS2 barcode region, revealing accurate discriminations among the genotypes. Multiple barcode markers are unrelated to one another and change independently, providing different estimations of heritable traits and genetic lineages; thus, they are advantageous over a single locus in genetic discrimination studies. A dynamic programming algorithm that used base-pairing interactions within a single nucleic acid polymer or between two polymers transformed the secondary structures into the symbol code data to predict seven different minimum free energy secondary structures. Our analysis strengthens the potential of the ITS2 gene as a potent DNA barcode candidate in the prediction of a valuable secondary structure that would help in genetic discrimination between the genotypes while augmenting future breeding strategies in taro.

Deciphering phenotyping, DNA barcoding, and RNA secondary structure predictions in eggplant wild relatives provide insights for their future breeding strategies

“…The barcode gaps were manually edited in a pairwise alignment view using BLAST 42 . To obtain their respective accession numbers, the acquired Kim matK and ITS barcode sequences of each eggplant genotype were submitted to the BlankIt submission portal ( https://submit.ncbi.nlm.nih.gov/subs/genbank/ ) and Genbank ( https://submit.ncbi.nlm.nih.gov/ ) submission portal, respectively 43 . Around ten closest matches of the sequences were aligned with the query sequences by using Cluster Omega, and the resulting alignments were used to construct the phylogenetic tree by the neighbor–joining method.…”

“…RNA secondary structure represents the list of nucleotide bases paired by hydrogen bonding within its nucleotide sequence, and these base pairs form the scaffold driving the folding of RNA two– and three–dimensional structures. The knowledge of the RNA secondary structure is essential for modelling RNA structures and understanding their functional mechanism 43 . Target RNA structure is an important consideration in the design of small interfering RNAs and antisense DNA oligonucleotides.…”