A large-scale whole-exome sequencing mutant resource for functional genomics in wheat

Stem lodging Resistance-1 controls stem strength by positively regulating the biosynthesis of cell wall components in Capsicum annuum L

Lodging presents a significant challenge in cultivating high-yield crops with extensive above-ground biomass, yet the molecular mechanisms underlying this phenomenon in the Solanaceae family remain largely unexplored. In this study, we identified a gene, CaSLR1 (Capsicum annuum Stem Lodging Resistance 1), which encodes a MYELOBLASTOSIS (MYB) family transcription factor, from a lodging-affected C. annuum EMS mutant. The suppression of CaSLR1 expression in pepper led to notable stem lodging, reduced thickness of the secondary cell wall, and decreased stem strength. A similar phenotype was observed in tomato with the knockdown of SlMYB61, the orthologous gene to CaSLR1. Further investigations demonstrated that CaNAC6, a gene involved in secondary cell wall (SCW) formation, is co-expressed with CaSLR1 and acts as a positive regulator of its expression, as confirmed through yeast one-hybrid, dual-luciferase reporter assays, and electrophoretic mobility shift assays. These findings elucidate the CaNAC6-CaSLR1 module that contributes to lodging resistance, emphasizing the critical role of CaSLR1 in the lodging resistance regulatory network.

A fully sequenced collection of homozygous EMS mutants for forward and reverse genetic screens in Arabidopsis thaliana

Genetic screens are powerful tools for biological research and are one of the reasons for the success of the thale cress Arabidopsis thaliana as a research model. Here, we describe the whole-genome sequencing of 871 Arabidopsis lines from the Homozygous EMS Mutant (HEM) collection as a novel resource for forward and reverse genetics. With an average 576 high-confidence mutations per HEM line, over three independent mutations altering protein sequences are found on average per gene in the collection. Pilot reverse genetics experiments on reproductive, developmental, immune and physiological traits confirmed the efficacy of the tool for identifying both null, knockdown and gain-of-function alleles. The possibility of conducting subtle repeated phenotyping and the immediate availability of the mutations will empower forward genetic approaches. The sequence resource is searchable with the ATHEM web interface (https://lipm-browsers.toulouse.inra.fr/pub/ATHEM/), and the biological material is distributed by the Versailles Arabidopsis Stock Center.

Comparison of Mutations Induced by Different Doses of Fast-Neutron Irradiation in the M1 Generation of Sorghum (Sorghum bicolor)

Sorghum is an important C4 crop with various food and nonfood uses. Although improvements through hybridization and selection have been exploited, the introduction of genetic variation and the development of new genotypes in sorghum are still limited. Fast-neutron (FN) mutagenesis is a very effective method for gene functional studies and to create genetic variability. However, the full spectrum of FN-induced mutations in sorghum is poorly understood. To address this, we generated an FN-induced mutant population from the inbred line 'BTx623' and sequenced 40 M1 seedlings to evaluate the mutagenic effects of FNs on sorghum. The results show that each line had an average of 43.7 single-base substitutions (SBSs), 3.7 InDels and 35.15 structural variations (SVs). SBSs accounted for approximately 90.0% of the total number of small mutations. Among the eight treatment groups, FN irradiation at a dose of 19 Gy generated the highest number of mutations. The ratio of transition/transversion ranged from 1.77 to 2.21, and the G/C to A/T transition was the most common substitution in all mutant lines. The distributions of the identified SBSs and InDels were similar and uneven across the genome. An average of 3.63 genes were mutated in each mutant line, indicating that FN irradiation resulted in a suitable density of mutated genes, which can be advantageous for improving elite material for one specific or a few traits. These results provide a basis for the selection of the suitable dose of mutagen and new genetic resources for sorghum breeding.

Genomic view of heavy-ion-induced deletions associated with distribution of essential genes in Arabidopsis thaliana

Heavy-ion beam, a type of ionizing radiation, has been applied to plant breeding as a powerful mutagen and is a promising tool to induce large deletions and chromosomal rearrangements. The effectiveness of heavy-ion irradiation can be explained by linear energy transfer (LET; keV µm-1). Heavy-ion beams with different LET values induce different types and sizes of mutations. It has been suggested that deletion size increases with increasing LET value, and complex chromosomal rearrangements are induced in higher LET radiations. In this study, we mapped heavy-ion beam-induced deletions detected in Arabidopsis mutants to its genome. We revealed that deletion sizes were similar between different LETs (100 to 290 keV μm-1), that their upper limit was affected by the distribution of essential genes, and that the detected chromosomal rearrangements avoid disrupting the essential genes. We also focused on tandemly arrayed genes (TAGs), where two or more homologous genes are adjacent to one another in the genome. Our results suggested that 100 keV µm-1 of LET is enough to disrupt TAGs and that the distribution of essential genes strongly affects the heritability of mutations overlapping them. Our results provide a genomic view of large deletion inductions in the Arabidopsis genome.

A platform for whole-genome speed introgression from Aegilops tauschii to wheat for breeding future crops

Breeding new and sustainable crop cultivars of high yields and desirable traits has been a major challenge for ensuring food security for the growing global human population. For polyploid crops such as wheat, introducing genetic variation from wild relatives of its subgenomes is a key strategy to improve the quality of their breeding pools. Over the past decades, considerable progress has been made in speed breeding, genome sequencing, high-throughput phenotyping and genomics-assisted breeding, which now allows us to realize whole-genome introgression from wild relatives to modern crops. Here, we present a standardized protocol to rapidly introgress the entire genome of Aegilops tauschii, the progenitor of the D subgenome of bread wheat, into elite wheat backgrounds. This protocol integrates multiple modern high-throughput technologies and includes three major phases: development of synthetic octaploid wheat, generation of hexaploid A. tauschii-wheat introgression lines (A-WIs) and homozygosis of the generated A-WIs. Our approach readily generates stable introgression lines in 2 y, thus greatly accelerating the generation of A-WIs and the introduction of desirable genes from A. tauschii to wheat cultivars. These A-WIs are valuable for wheat-breeding programs and functional gene discovery. The current protocol can be easily modified and used for introgressing the genomes of wild relatives to other polyploid crops.

Omics-driven exploration and mining of key functional genes for the improvement of food and fiber crops

The deployment of omics technologies has obtained an incredible boost over the past few decades with the advances in next-generation sequencing (NGS) technologies, innovative bioinformatics tools, and the deluge of available biological information. The major omics technologies in the limelight are genomics, transcriptomics, proteomics, metabolomics, and phenomics. These biotechnological advances have modernized crop breeding and opened new horizons for developing crop varieties with improved traits. The genomes of several crop species are sequenced, and a huge number of genes associated with crucial economic traits have been identified. These identified genes not only provide insights into the understanding of regulatory mechanisms of crop traits but also decipher practical grounds to assist in the molecular breeding of crops. This review discusses the potential of omics technologies for the acquisition of biological information and mining of the genes associated with important agronomic traits in important food and fiber crops, such as wheat, rice, maize, potato, tomato, cassava, and cotton. Different functional genomics approaches for the validation of these important genes are also highlighted. Furthermore, a list of genes discovered by employing omics approaches is being represented as potential targets for genetic modifications by the latest genome engineering methods for the development of climate-resilient crops that would in turn provide great impetus to secure global food security.

Genome-wide characterization of two homeobox families identifies key genes associated with grain-related traits in wheat

Homeodomain proteins encoded by BEL1- and KNAT1-type genes are ubiquitously distributed across plant species and play important roles in growth and development, whereby a comprehensive investigation of their molecular interactions and potential functions in wheat is of great significance. In this study, we systematically investigated the phylogenetic relationships, gene structures, conserved domains, and cis-acting elements of 34 TaBEL and 34 TaKNAT genes in the wheat genome. Our analysis revealed these genes evolved under different selective pressures and showed variable transcript levels in different wheat tissues. Subcellular localization analysis further indicated the proteins encoded by these genes were either exclusively located in the nucleus or both in the nucleus and the cytoplasm. Additionally, a comprehensive protein-protein interaction network was constructed with representative genes in which each TaBEL or TaKNAT proteins interact with at least two partners. The evaluation of wheat mutants identified key genes, including TaBEL-5B, TaBEL-4A.4, and TaKNAT6, which are involved in grain-related traits. Finally, haplotype analysis suggests TaKNAT-6B is associated with grain-related traits and is preferentially selected among a large set of wheat accessions. Our study provides important information on BEL1- and KNAT1-type gene families in wheat, and lays the foundation for functional research in the future.