Status and Prospects of Next Generation Sequencing Technologies in Crop Plants

Abstract

The history of DNA sequencing dates back to 1970s. During this period the two first generation nucleotide sequencing techniques were developed. Subsequently the Sanger's dideoxy method of sequencing gained popularity over Maxam and Gilbert's chemical method of sequencing. However, in the last decade, we have observed revolutionary changes in DNA sequencing technologies leading to the emergence of next-generation sequencing (NGS) techniques. NGS technologies have enhanced the throughput and speed of sequencing combined with bringing down the overall cost of the process over a time. The major applications of NGS technologies being genome sequencing and resequencing, transcriptomics, metagenomics in relation to plant-microbe interactions, exon and genome capturing, development of molecular markers and evolutionary studies. In this review, we present a broader picture of evolution of NGS tools, its various applications in crop plants, and future prospects of the technology for crop improvement.

Resequencing core accessions of a pedigree identifies derivation of genomic segments and key agronomic trait loci during cotton improvement

“…Using these genome sequences as precise references, it is now relatively straightforward to detect SNPs in many crop species (Rafalski, ). Next‐generation sequencing (NGS) technology has greatly reduced the labour and costs associated with resequencing studies (Sharma et al ., ). The dN/dS ratio, phylogenetic branch points, zero diversity segments, genetic diversity and linkage disequilibrium were often used as indicators of artificial selection during evolution (Lai et al ., ; Lam et al ., ; Zhou et al ., ).…”

De Novo Domestication: An Alternative Route toward New Crops for the Future

“…This is partially due to the better conservation of cereals in the fossil record, in part due to the research effort expended on the various species and largely due to the genetic tractability of the species in question. Nevertheless, genomics has revolutionized even our understanding of the evolution of crops that have historically been characterized only poorly (Olsen and Wendel, 2013;Sharma et al, 2018). Two aspects have been particularly instrumental in this endeavor: the advent of nextgeneration sequencing (Sharma et al, 2018) and techniques that use broad natural allelic variance for assessing the genetic architecture of traits (Zamir, 2001;Olsen and Wendel, 2013;Huang and Han, 2014).…”

“…Nevertheless, genomics has revolutionized even our understanding of the evolution of crops that have historically been characterized only poorly (Olsen and Wendel, 2013;Sharma et al, 2018). Two aspects have been particularly instrumental in this endeavor: the advent of nextgeneration sequencing (Sharma et al, 2018) and techniques that use broad natural allelic variance for assessing the genetic architecture of traits (Zamir, 2001;Olsen and Wendel, 2013;Huang and Han, 2014). A new species can be shaped in multiple ways including selection of specific organs (1, described in Osnas, 2012), allopolyploidy among subspecies (2, described in Griffiths et al, 1999), or absorbing new alleles through introgression from nearby species (3, described in Arnold et al, 2016).…”

Iso-Seq analysis of the Taxus cuspidata transcriptome reveals the complexity of Taxol biosynthesis

“…Transcriptome analysis-based next-generation sequencing (NGS) technology is a powerful and economical way to obtain genetic information on a large scale and has been widely used to uncover genes involved in the biosynthesis of secondary metabolites [24, 25]. Although NGS has the advantages of high sequencing depth and low cost, the short read length generated may restrict correct sequence assembly and annotation [25]. Third-generation sequencing (TGS) technology, single-molecule real-time (SMRT) sequencing developed by the PacBio company, offers an alternative method for overcoming these limitations.…”