Genetic Transformation and Genomic Resources for Next-Generation Precise Genome Engineering in Vegetable Crops

Abstract

In the frame of modern agriculture facing the predicted increase of population and general environmental changes, the securement of high quality food remains a major challenge to deal with. Vegetable crops include a large number of species, characterized by multiple geographical origins, large genetic variability and diverse reproductive features. Due to their nutritional value, they have an important place in human diet. In recent years, many crop genomes have been sequenced permitting the identification of genes and superior alleles associated with desirable traits. Furthermore, innovative biotechnological approaches allow to take a step forward towards the development of new improved cultivars harboring precise genome modifications. Sequence-based knowledge coupled with advanced biotechnologies is supporting the widespread application of new plant breeding techniques to enhance the success in modification and transfer of useful alleles into target varieties. Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 system, zinc-finger nucleases, and transcription activator-like effector nucleases represent the main methods available for plant genome engineering through targeted modifications. Such technologies, however, require efficient transformation protocols as well as extensive genomic resources and accurate knowledge before they can be efficiently exploited in practical breeding programs. In this review, we revise the state of the art in relation to availability of such scientific and technological resources in various groups of vegetables, describe genome editing results obtained so far and discuss the implications for future applications.

Efficient genome editing using CRISPR‐Cas‐mediated homology directed repair in the ascidian Ciona robusta

“…The ability to precisely edit the genomes of a variety of organisms has greatly expanded the usefulness of these systems as models for human development and disease (Cardi, D'Agostino, & Tripodi, ; Chen et al, ; Singh, Braddick, & Dhar, ). Ascidians are gaining prominence as excellent models for examining a wide variety of biological problems including regeneration (Spina, Guzman, Zhou, Kosik, & Smith, ), Alzheimer's studies (Virata & Zeller, ), and climate change research (Lopez et al, ).…”

Expression of Single Chain Variable Fragment (scFv) Molecules in Plants: A Comprehensive Update

“…Among the methods employed for transformation of plant cells for scFv expression, Agrobacterium-mediated gene transfer tops the list with more than 95% of representation in the reports. Transformation along with the genome editing techniques to modify the genome of the host plant to facilitate the protein expression in a tailor-made fashion has been the subject for a number of recent reviews [59][60][61][62]. In general, Agrobacterium tumefaciens transfer the T-DNA region from its Ti plasmid into the genome of the host plant, with the help of its vir gene products.…”

NGS-Based Genotyping, High-Throughput Phenotyping and Genome-Wide Association Studies Laid the Foundations for Next-Generation Breeding in Horticultural Crops

“…A non-exhaustive but extensive list of genome editing approaches applied to vegetable crops is reported in a recently published review we co-authored [36].…”

“…The release into the public domain of complete, near-complete or partial genome sequence of the most important vegetable crops [36], the development of SNP detection assays [48,49] and high-density genotyping arrays [50][51][52] caused a shift from small-/medium-scale to large-scale SNP genotyping.…”