Application of next-generation sequencing in plant breeding

Abstract

In the past decade, next-generation sequencing (NGS) platforms have changed the impact of sequencing on our knowledge of crop genomes and gene regulation. These techniques are today acquiring a great potential in metagenomic and agrigenomic research while showing prospects for their utilization in plant breeding. We can now obtain new and beneficial information about gene regulation on the cellular as well as whole-plant level through RNA-sequencing and subsequent expression analyses of genes participating in plant defence reactions to pathogens and in abiotic stress tolerance. NGS has facilitated the development of methods to genotype very large numbers of single-nucleotide polymorphisms. Genotyping-by-sequencing and whole-genome resequencing can lead to the development of molecular markers suited to studies of genetic relationships among breeding materials, creation of detailed genetic mapping of targeted genes and genome-wide association studies. Plant genotyping can benefit plant breeding through selection of individuals resistant to climatic stress and to pathogens causing substantial losses in agriculture.

Next Generation Sequencing Based Forward Genetic Approaches for Identification and Mapping of Causal Mutations in Crop Plants: A Comprehensive Review

“…These editing approaches enable site directed mutagenesis to improve economically useful traits by involving modification in targeted locus. Sequence-specific nucleases, such as zinc finger nucleases (ZFN), transcription activator-like effector nucleases (TALEN) and CRISPR/Cas9 system can be exploited for the same ( Figure 9 ) [ 194 ]. Using diverse irradiation methods to generate mutants and their characterization by refined NGS pipelines would become more popular in future studies.…”

Advances in Integrating Genomics and Bioinformatics in the Plant Breeding Pipeline

“…However, there are important limitations of NGS, such as inherent biases and ambiguous alignment of repetitive elements, which leads to highly fragmented draft genome assemblies and complicates the study of hidden indels and structural variants [20]. The emergence of third generation sequencing, including Pacific Biosciences (PacBio) single-molecule real-time sequencing and Oxford Nanopore Technologies (ONT) sequencing, has enabled the generation of long reads and allowed production of more accurate and contiguous genome assemblies [30][31][32]. Third generation sequencing helps generate high-quality whole genome de novo assemblies, using reads spanning complex regions such as those with high levels of repetitive sequence and shed light on the remaining complex of repeat sequences and other structural variants.…”

Characterization of genetic determinants of the resistance to phylloxera, Daktulosphaira vitifoliae, and the dagger nematode Xiphinema index from muscadine background

“…For grapevine, the development and application of SSR (Simple Sequence Repeat) markers are considered as a key step of the construction of molecular maps [21,28,29]. Next-generation sequencing (NGS) has then facilitated the development of methods to genotype very large numbers of SNP (Single Nucleotide Polymorphism) markers [30,31]. Genotyping-by-sequencing (GBS) has been developed as a rapid and robust approach to sequencing of multiplexed samples [32,33].…”