title: Improvements in Genomic Technologies: Application to Crop Genomics.
abstract: Second-generation sequencing (SGS) has advanced the study of crop genomes and has provided insights into diversity and evolution. However, repetitive DNA sequences in crops often lead to incomplete or erroneous assemblies because SGS reads are too short to fully resolve these repeats. To overcome some of these challenges, long-read sequencing and optical mapping have been developed to produce high-quality assemblies for complex genomes. Previously, high error rates, low throughput, and high costs have limited the adoption of long-read sequencing and optical mapping. However, with recent improvements and the development of novel algorithms, the application of these technologies is increasing. We review the development of long-read sequencing and optical mapping, and assess their application in crop genomics for breeding improved crops.
authors.affiliation: School of Plant Biology, the University of Western Australia, Perth, WA, Australia.
authors.forename: Yuxuan
authors.initials: Y
authors.lastname: Yuan
authors.affiliation: School of Plant Biology, the University of Western Australia, Perth, WA, Australia.
authors.forename: Philipp E
authors.initials: PE
authors.lastname: Bayer
authors.affiliation: School of Plant Biology, the University of Western Australia, Perth, WA, Australia.
authors.forename: Jacqueline
authors.initials: J
authors.lastname: Batley
authors.affiliation: School of Plant Biology, the University of Western Australia, Perth, WA, Australia. Electronic address: dave.edwards@uwa.edu.au.
authors.forename: David
authors.initials: D
authors.lastname: Edwards
mesh_terms: D000465:Algorithms; D018556:Crops, Agricultural / Q000235:genetics*; D018745:Genome, Plant; D023281:Genomics / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*