Somatic mutation detection in plants: a critical evaluation through simulations and reanalyses

Mutation, the source of genetic diversity, is the raw material of evolution; however, it remains an understudied process in plants. Using simulations, we demonstrate that generic variant callers, commonly used to detect mutations in plants, are outperformed by methods developed for cancer research. Reanalysis of published data identified up to 7x more somatic mutations than initially reported, advocating the use of cancer research callers to boost mutation research in plants.

webSalvador, a Web Tool for the Luria-Delbrük Experiment

ABSTRACT Existing Web tools for the Luria-Delbrück fluctuation experiment do not offer many desirable capabilities that are vital to mutation research. webSalvador offers these capabilities via a user interface that allows researchers to access most of the functions in the R package rSalvador without having to learn the R language.

Soybean breeding through induced mutation in Vietnam.

In Vietnam, soybean is one of the traditional crops and plays an important role in crop rotation, soil improvement and meeting the nutritional needs of humans and livestock. With the aim of generating genetic variability in soybean and creating new soybean varieties to meet the needs of production, induced mutation research has been carried out since the 1980s and has gained outstanding achievements. Induction of modified traits and their incorporation into an ideal genotype was achieved by judicious use of the induced mutation technique. So far, outstanding soybean varieties such as DT84, DT90, DT99, DT2008 and several promising lines have been developed in Vietnam by incorporating desirable traits like high and stable yield (2.0-3.5 t/ha), good quality, drought tolerance, disease resistance (rust, powdery mildew, downy mildew), short growth duration (70-100 days), wide adaptability and suitability for cropping systems and ecological regions in the whole country. The most outstanding variety, DT84, occupies over 50% of the total production area and 80% in Central and North Vietnam (about 70,000-80,000 ha/year). These varieties have also been used as materials for developing several additional improved soybean varieties. Thus, induced mutation research has played an important role in improving soybean varieties in Vietnam.

Epigenetic synthetic lethality approaches in cancer therapy

The onset and development of malignant tumors are closely related to epigenetic modifications, and this has become a research hotspot. In recent years, a variety of epigenetic regulators have been discovered, and corresponding small molecule inhibitors have been developed, but their efficacy in solid tumors is generally poor. With the introduction of the first synthetic lethal drug (the PARP inhibitor olaparib in ovarian cancer with BRCA1 mutation), research into synthetic lethality has also become a hotspot. High-throughput screening with CRISPR-Cas9 and shRNA technology has revealed a large number of synthetic lethal pairs involving epigenetic-related synthetic lethal genes, such as those encoding SWI/SNF complex subunits, PRC2 complex subunits, SETD2, KMT2C, and MLL fusion proteins. In this review, we focus on epigenetic-related synthetic lethal mechanisms, including synthetic lethality between epigenetic mutations and epigenetic inhibitors, epigenetic mutations and non-epigenetic inhibitors, and oncogene mutations and epigenetic inhibitors.