“Overview of Sequencing Platforms and Their Role in Crop Improvement” ( Seminar Synopsis)

UNIVERSITY OF AGRICULTURAL SCIENCES, BANGALORE

DEPARTMENT OF GENETICS AND PLANT BREEDING

“Overview of Sequencing Platforms and Their Role in Crop Improvement”

DNA sequencing platforms have transformed the field of genomics by allowing the rapid and precise decoding of genetic information. These technologies serve as a cornerstone in molecular biology, genetics, and biotechnology by providing insights into the genetic architecture of organisms. By facilitating the identification of genes, detection of genetic variations, and analysis of trait-associated loci, sequencing has significantly advanced our understanding of the molecular basis underlying various traits of interest. The first widely adopted sequencing method was Sanger sequencing, which operates on the principle of chain termination using ddNTP and capillary electrophoresis for fragment separation.

Second-generation or Next-Generation Sequencing (NGS) platforms emerged in the mid-2000s, offering massive parallel sequencing at significantly reduced costs. Among these, Illumina technology is the most widely adopted. It uses sequencing-by-synthesis with fluorescently labelled nucleotides and enables high throughput with short read lengths (usually 150–300 bp).

Third-generation sequencing platforms introduced single-molecule, real-time (SMRT) sequencing, which offers longer read lengths, crucial for resolving complex genomic regions. Pacific Biosciences (PacBio) utilizes SMRT technology, producing average read lengths of 10–25 kb with high consensus accuracy, useful for de novo genome assembly and structural variation analysis. Another prominent third-generation platform, Oxford Nanopore Technologies (ONT), uses nanopore-based sequencing, where DNA strands pass through protein nanopores embedded in membranes, and sequence data is derived by measuring changes in ionic current.

A Genome-wide association study (GWAS) was conducted using a panel of 305 re-sequenced diverse indica accessions, comprising approximately 2.4 million SNPs predominantly enriched in genic regions. A major hotspot region associated with intermediate-to-high grain quality index (GI) variation was identified on chromosome 6, designated as GI6.1, encompassing 26 candidate genes. Notably, this region includes the gene GBSSI, which plays a key role in amylose biosynthesis.

DNA sequencing technology plays a crucial role in crop improvement by identifying genes responsible for desirable traits like yield, disease resistance, and drought tolerance. It enables precise selection and genetic modification, accelerating breeding programs. This technology enhances crop quality, productivity, and resilience, contributing significantly to sustainable agriculture and food security.

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REFERENCES

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3. Anacleto, R., Badoni, S., Parween, S., Butardo Jr, V.M., Misra, G., Cuevas, R.P., Kuhlmann, M., Trinidad, T.P., Mallillin, A.C., Acuin, C., and Bird, A.R. (2019). Integrating a genome-wide association study with a large-scale transcriptome analysis to predict genetic regions influencing the glycemic index and texture in rice. Plant Biotechnol. J., 17(7): 1261-1275.