Special Issue "TILLING and CRISPR to design the varieties of tomorrow"

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Plant Genetics and Genomics".

Deadline for manuscript submissions: 30 October 2019.

Special Issue Editor

Prof. Abdelhafid Bendahmane
E-Mail
Guest Editor
Universite Paris-Sud XI, INRA, Orsay, France

Special Issue Information

Dear Colleagues,

The 2016 report of the Department of Economic and Social Affairs of the United Nations, states, in Sustainable Development Goal 2, that food production will need to increase by 50 percent globally to meet the growing human population demand. Since the green revolution in the 1960s, classical breeding has been the main driving force of yield increase in major crops. However, in the course of the last few decades, new threats, all human-made, have emerged as bottlenecks for today’s agriculture and traditional breeding is struggling to solve them.  

The scientific community is not standing idly by. Huge progress has been made in the understanding of the molecular mechanisms controlling biological processes, and every day new discoveries are published. For instance, the genes controlling growth and development as well as resistance to biotic and abiotic stresses have been identified and characterized. Unfortunately, the translation of the findings in leader alleles that breeders can use to develop the varieties of tomorrow have not matched that progress. Consequently, the exploitation of the wealth of information available to modify output traits in crops is still below our expectations.

Nevertheless, the development of reverse genetics strategies, where one first identifies a target gene based on its sequence identity and then proceeds with the phenotypic characterization of mutant alleles, open new opportunities in the field of translational research. TILLING and CRISPR-Cas9 are two technologies that could readily translate fundamental data into leader alleles. TILLING stands for targeted induced local lesions in the genome. CRISPR-Cas9 stands for Clustered regularly inter spaced short palindromic repeats associated Cas9. Both techniques provide an easy and cost-effective way to saturate a genome with mutations. In this Special Issue, we would like to invite researchers to describe their ideas and works relating to allele engineering, using TILLING and CRISPR, in the optic to create new traits.

Prof. Abdelhafid Bendahmane
Guest Editor

Manuscript Submission Information

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Keywords

  • TILLING
  • CRISPR
  • allele engineering
  • new traits
  • translational research
  • mutant collections
  • genetic screens
  • biosensors

Published Papers (3 papers)

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Research

Open AccessArticle
Multiplex CRISPR Mutagenesis of the Serine/Arginine-Rich (SR) Gene Family in Rice
Genes 2019, 10(8), 596; https://doi.org/10.3390/genes10080596 - 07 Aug 2019
Cited by 1
Abstract
Plant growth responds to various environmental and developmental cues via signaling cascades that influence gene expression at the level of transcription and pre-mRNA splicing. Alternative splicing of pre-mRNA increases the coding potential of the genome from multiexon genes and regulates gene expression through [...] Read more.
Plant growth responds to various environmental and developmental cues via signaling cascades that influence gene expression at the level of transcription and pre-mRNA splicing. Alternative splicing of pre-mRNA increases the coding potential of the genome from multiexon genes and regulates gene expression through multiple mechanisms. Serine/arginine-rich (SR) proteins, a conserved family of splicing factors, are the key players of alternative splicing and regulate pre-mRNA splicing under stress conditions. The rice (Oryza sativa) genome encodes 22 SR proteins categorized into six subfamilies. Three of the subfamilies are plant-specific with no mammalian orthologues, and the functions of these SR proteins are not well known. The clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) system is a genome engineering tool that cleaves the target DNA at specific locations directed by a guide RNA (gRNA). Recent advances in CRISPR/Cas9-mediated plant genome engineering make it possible to generate single and multiple functional knockout mutants in diverse plant species. In this study, we targeted each rice SR locus and produced single knockouts. To overcome the functional redundancy within each subfamily of SR genes, we utilized a polycistronic tRNA-gRNA multiplex targeting system and targeted all loci of each subfamily. Sanger sequencing results indicated that most of the targeted loci had knockout mutations. This study provides useful resource materials for understanding the molecular role of SR proteins in plant development and biotic and abiotic stress responses. Full article
(This article belongs to the Special Issue TILLING and CRISPR to design the varieties of tomorrow)
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Open AccessArticle
Identification and Characterization of a Thermotolerant TILLING Allele of Heat Shock Binding Protein 1 in Tomato
Genes 2019, 10(7), 516; https://doi.org/10.3390/genes10070516 - 07 Jul 2019
Cited by 1
Abstract
The identification of heat stress (HS)-resilient germplasm is important to ensure food security under less favorable environmental conditions. For that, germplasm with an altered activity of factors regulating the HS response is an important genetic tool for crop improvement. Heat shock binding protein [...] Read more.
The identification of heat stress (HS)-resilient germplasm is important to ensure food security under less favorable environmental conditions. For that, germplasm with an altered activity of factors regulating the HS response is an important genetic tool for crop improvement. Heat shock binding protein (HSBP) is one of the main negative regulators of HS response, acting as a repressor of the activity of HS transcription factors. We identified a TILLING allele of Solanum lycopersicum (tomato) HSBP1. We examined the effects of the mutation on the functionality of the protein in tomato protoplasts, and compared the thermotolerance capacity of lines carrying the wild-type and mutant alleles of HSBP1. The methionine-to-isoleucine mutation in the central heptad repeats of HSBP1 leads to a partial loss of protein function, thereby reducing the inhibitory effect on Hsf activity. Mutant seedlings show enhanced basal thermotolerance, while mature plants exhibit increased resilience in repeated HS treatments, as shown by several physiological parameters. Importantly, plants that are homozygous for the wild-type or mutant HSBP1 alleles showed no significant differences under non-stressed conditions. Altogether, these results indicate that the identified mutant HSBP1 allele can be used as a genetic tool in breeding, aiming to improve the thermotolerance of tomato varieties. Full article
(This article belongs to the Special Issue TILLING and CRISPR to design the varieties of tomorrow)
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Open AccessArticle
EcoTILLING Reveals Natural Allelic Variations in Starch Synthesis Key Gene TaSSIV and Its Haplotypes Associated with Higher Thousand Grain Weight
Genes 2019, 10(4), 307; https://doi.org/10.3390/genes10040307 - 18 Apr 2019
Abstract
Wheat is a staple food commodity grown worldwide, and wheat starch is a valuable source of energy and carbon that constitutes 80% of the grain weight. Manipulation of genes involved in starch synthesis significantly affects wheat grain weight and yield. TaSSIV plays an [...] Read more.
Wheat is a staple food commodity grown worldwide, and wheat starch is a valuable source of energy and carbon that constitutes 80% of the grain weight. Manipulation of genes involved in starch synthesis significantly affects wheat grain weight and yield. TaSSIV plays an important role in starch synthesis and its main function is granule formation. To mine and stack more favorable alleles, single nucleotide polymorphisms (SNPs) of TaSSIV-A, B, and D were investigated across 362 wheat accessions by Ecotype-Targeting Induced Local Lesions IN Genome (EcoTILLING). As a result, a total of 38 SNPs in the amplified regions of three TaSSIV genes were identified, of which 10, 15, and 13 were in TaSSIV-A, B, and D, respectively. These 38 SNPs were evaluated by using KASP and six SNPs showed an allele frequency >5% whereas the rest were <5%, i.e., considered to be minor alleles. In the Chinese mini core collection, three haplotypes were detected for TaSSIV–A and three for TaSSIV–B. The results of an association study in the Chinese mini core collection with thousand grain weight (TGW) and spike length (SPL) showed that Hap-2-1A was significantly associated with TGW and Hap-3-1B with SPL. Allelic frequency and geographic distribution indicated that the favored haplotype (Hap-2-1A) has been positively selected in Chinese wheat breeding. These results suggested that the Kompetitive Allele Specific PCR (KASP) markers can be applied in starch improvement to ultimately improve wheat yield by marker assisted selection in wheat breeding. Full article
(This article belongs to the Special Issue TILLING and CRISPR to design the varieties of tomorrow)
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