Single-tube genotyping for small insertion/deletion mutations: simultaneous identification of wild type, mutant and heterozygous alleles

Mutation Knock-in Methods Using Single-Stranded DNA and Gene Editing Tools in Zebrafish

Introduction or knock-in of precise genomic modifications remains one of the most important applications of CRISPR/Cas9 in all model systems including zebrafish. The most widely used type of donor template containing the desired modification is single-stranded DNA (ssDNA), either in the form of single-stranded oligodeoxynucleotides (ssODN) (<150 nucleotides (nt)) or as long ssDNA (lssDNA) molecules (up to about 2000 nt). Despite the challenges posed by DNA repair after DNA double-strand breaks, knock-in of precise mutations is relatively straightforward in zebrafish. Knock-in efficiency can be enhanced by careful donor template design, using lssDNA as template or tethering the donor template DNA to the Cas9-guide RNA complex. Other point mutation methods such as base editing and prime editing are starting to be applied in zebrafish and many other model systems. However, these methods may not always be sufficiently accessible or may have limited capacity to perform all desired mutation knock-ins which are possible with ssDNA-based knock-in methods. Thus, it is likely that there will be complementarity in the technologies used for generating precise mutants. Here, we review and describe a suite of CRISPR/Cas9 knock-in procedures utilizing ssDNA as the donor template in zebrafish, point out the potential challenges and suggest possible approaches for their solution ultimately leading to successful generation of precise mutant lines.

Phenotypic and genotypic characterization of dog tick Rhipicephalus sanguineus sensu lato (Acari: Ixodidae) resistance to deltamethrin in Benin

The aim of this study was to evaluate the phenotypic and genotypic resistance of Rhipicephalus sanguineus sensu lato to deltamethrin in dogs in the municipality of Natitingou in Benin. In this study, the collection and identification of ticks, Larval Packet Test and specific allele PCR were the main methods used. A total of 41 dogs were examined and 420 ticks were collected in six areas which includes: Tchrimina, Yokossi, Boriyoure, Berécingou, Péporiyakou and Perma. Three species of ticks were identified and they include: R. sanguineus s.l., Rhipicephalus microplus and Haemaphysalis spp. However, R. sanguineus s.l. was the most abundant tick species (9.85) and had the highest parasitic intensity (10.36). The results of the Larval Packet Test showed that the larvae of R. sanguineus s.l. developed a phenotypic resistance against deltamethrin, particularly in the Bérécingou area where resistance ratios of LC50 and LC95 of R. sanguineus s.l. compared to a susceptible strain were 1.591 (1.025-3.054) and 65.339 (20.235-579.825) respectively. The molecular study of the sodium channel gene revealed three genotypes namely the susceptible genotype (SS), the heterozygous genotype (SR) and the resistant genotype (RR), which correlates with the phenotypic results. This information is fundamental to improve monitoring and resistance management strategies of R. sanguineus s.l. ticks to pyrethroids.

Marker-Assisted Selection for Pollen-Free Somatic Plants of Sugi (Japanese Cedar, Cryptomeria japonica): A Simple and Effective Methodology for Selecting Male-Sterile Mutants With ms1-1 and ms1-2

Pollen allergy caused by sugi (Japanese cedar, Cryptomeria japonica) is a serious problem in Japan. One of the measures against pollinosis is the use of male-sterile plants (MSPs; pollen-free plants). In this context, the development of a novel technique for the efficient production of sugi MSPs, which combines marker-assisted selection (MAS) with somatic embryogenesis (SE), was recently reported by our research group. To improve the efficiency of MSP production, in this paper we report improved MAS for male-sterile individuals from embryogenic cells, cotyledonary embryos, and somatic plants of sugi using a newly developed marker in the form of the causative mutation of MS1 itself, selecting individuals with ms1-1 and ms1-2 male-sterile mutations. We also describe simplified methods for extracting DNA from different plant materials and for MAS using LAMP diagnostics. Finally, we show that MAS can be efficiently performed using the one-step indel genotyping (ING) marker developed in this study and using InstaGene for DNA extraction. The combination of SE and 100% accurate marker selection during the embryogenic cell stage enables the mass production of MS1 male-sterile sugi seedlings.