Inferring defense-related gene families in Arabidopsis and wheat

Arabidopsis as a model for translational research

Arabidopsis thaliana is currently the most-studied plant species on earth, with an unprecedented number of genetic, genomic, and molecular resources having been generated in this plant model. In the era of translating foundational discoveries to crops and beyond, we aimed to highlight the utility and challenges of using Arabidopsis as a reference for applied plant biology research, agricultural innovation, biotechnology, and medicine. We hope that this review will inspire the next generation of plant biologists to continue leveraging Arabidopsis as a robust and convenient experimental system to address fundamental and applied questions in biology. We aim to encourage lab and field scientists alike to take advantage of the vast Arabidopsis datasets, annotations, germplasm, constructs, methods, molecular and computational tools in our pursuit to advance understanding of plant biology and help feed the world's growing population. We envision that the power of Arabidopsis-inspired biotechnologies and foundational discoveries will continue to fuel the development of resilient, high-yielding, nutritious plants for the betterment of plant and animal health and greater environmental sustainability.

Resistance of Modern Russian Winter Wheat Cultivars to Yellow Rust

Over the last decade, the significance of yellow rust caused by Puccinia striiformis (Pst) has substantially increased worldwide, including in Russia. The development and cultivation of resistant genotypes is the most efficient control method. The present study was conducted to explore the yellow rust resistance potential of modern common winter wheat cultivars included in the Russian Register of Breeding Achievements in 2019-2022 using the seedling tests with an array of Pst races and molecular markers linked with Yr resistance genes. Seventy-two winter wheat cultivars were inoculated with five Pst isolates differing in virulence and origin. Molecular markers were used to identify genes Yr2, Yr5, Yr7, Yr9, Yr10, Yr15, Yr17, Yr18, Yr24, Yr25 and Yr60. Thirteen cultivars were resistant to all Pst isolates. The genes Yr5, Yr10, Yr15 and Yr24 that are effective against all Russian Pst races in resistant cultivars were not found. Using molecular methods, gene Yr9 located in translocation 1BL.1RS was detected in 12 cultivars, gene Yr18 in 24, gene Yr17 in 3 and 1AL.1RS translocation with unknown Yr gene in 2. While these genes have lost effectiveness individually, they can still enhance genetic diversity and overall yellow rust resistance, whether used in combination with each other or alongside other Yr genes.

Decipher the molecular evolution and expression patterns of Cupin family genes in oilseed rape

Cupin proteins are involved in plant growth and development as well as in response to various stresses. Here, a total of 173 Cupin genes were identified in Brassica napus, and their molecular evolution and expression patterns were analyzed. These genes were classified into ten groups. Motif and exon-intron structure indicated a high degree of conservation within each group during evolution. BnaCupins were distributed on 19 chromosomes and their expansion is mainly contributed by whole-genome duplication (WGD) and segmental duplication events. BnaCupins have undergone severe purifying selection during a long evolutionary process. Meanwhile, some positive selection sites were identified. Expression patterns and cis-element analysis indicated that BnaCupins play significant roles in plant growth and stress responses. In addition, the expression levels of some BnCupins were significantly altered when treated with different conditions (cold, salt, drought, IAA, ABA, and 6-BA). Some BnaCupin interacting proteins, such as glycosyl hydrolase5 (GHs5), carbohydrate kinase (CHKs), ATP-dependent 6-phosphofructokinase (ATP-PFK), S-adenosylmethionine synthase (S-MAT), and aldolase class II (ALD II), were identified by the protein-protein interaction network. It will contribute to enriching our knowledge of the Cupin gene family in B. napus and provide a basis for further studies of their functions.

Appraising the Genetic Architecture of Kernel Traits in Hexaploid Wheat Using GWAS

Kernel morphology is one of the major yield traits of wheat, the genetic architecture of which is always important in crop breeding. In this study, we performed a genome-wide association study (GWAS) to appraise the genetic architecture of the kernel traits of 319 wheat accessions using 22,905 single nucleotide polymorphism (SNP) markers from a wheat 90K SNP array. As a result, 111 and 104 significant SNPs for Kernel traits were detected using four multi-locus GWAS models (mrMLM, FASTmrMLM, FASTmrEMMA, and pLARmEB) and three single-locus models (FarmCPU, MLM, and MLMM), respectively. Among the 111 SNPs detected by the multi-locus models, 24 SNPs were simultaneously detected across multiple models, including seven for kernel length, six for kernel width, six for kernels per spike, and five for thousand kernel weight. Interestingly, the five most stable SNPs (RAC875_29540_391, Kukri_07961_503, tplb0034e07_1581, BS00074341_51, and BobWhite_049_3064) were simultaneously detected by at least three multi-locus models. Integrating these newly developed multi-locus GWAS models to unravel the genetic architecture of kernel traits, the mrMLM approach detected the maximum number of SNPs. Furthermore, a total of 41 putative candidate genes were predicted to likely be involved in the genetic architecture underlining kernel traits. These findings can facilitate a better understanding of the complex genetic mechanisms of kernel traits and may lead to the genetic improvement of grain yield in wheat.

Variation Patterns of NLR Clusters in Arabidopsis thaliana Genomes

The nucleotide-binding domain and leucine-rich repeat (NLR) gene family is highly expanded in the plant lineage with extensive sequence and structure polymorphisms. To survey the landscape of NLR expansion, we mined the published long-read data generated by the resistance gene enrichment sequencing of 64 diverse Arabidopsis thaliana accessions. We found that the hot spots of massive multi-gene NLR cluster expansion did not typically span the whole cluster; instead, they were restricted to a handful of, or only one, dominant radiation(s). All sequences in such a radiation were distinct from other genes in the cluster but not from each other in the clade, making it difficult to assign trustworthy reference-based orthologies when multiple reference genes were present in the radiation. Consequently, NLR genes can be broadly divided into two types: radiating or high-fidelity, where high-fidelity genes are well conserved and well separated from other clades. A similar distinction could be made for NLR clusters, depending on whether cluster size was determined primarily by extensive radiation or the presence of numerous high-fidelity genes. We also identified groups of well-conserved NLR clades that were missing from the Columbia-0 reference genome. This suggests that the classification of NLRs using gene IDs from a single reference accession can rarely capture all major paralogs in a cluster accurately and representatively and that a reference-agnostic perspective is required to properly characterize these additional variations. Finally, we present a quantitative visualization method for differentiating these situations in a given clade of interest.

Identification of induced mutations in hexaploid wheat genome using exome capture assay

Wheat is a staple food crop of many countries. Improving resilience to biotic and abiotic stresses remain key breeding targets. Among these, rust diseases are the most detrimental in terms of depressing wheat production. In the present study, chemical mutagenesis was used to induce mutations in the wheat variety NN-Gandum-1. This cultivar is moderately resistant to leaf and yellow rust. The aim of mutagenesis was to improve resistance to the disease as well as to study function of genes conferring resistance to the disease. In the present investigation, a 0.8% EMS dose was found optimum for supporting 45-55% germination of NN-Gandum-1. A total of 3,634 M2 fertile plants were produced from each of the M1 plant. Out of these, 33 (0.91%) and 20 plants (0.55%) showed absolute resistance to leaf and yellow rust, respectively. While 126 (3.46%) and 127 plants (3.49%) exhibited high susceptibility to the leaf and yellow rust, respectively. In the M4 generation, a total of 11 M4 lines (nine absolute resistant and two highly susceptible) and one wild type were selected for NGS-based exome capture assay. A total of 104,779 SNPs were identified that were randomly distributed throughout the wheat sub genomes (A, B and D). Induced mutations in intronic sequences predominated. The highest total number of SNPs detected in this assay were mapped to chr.2B (14,273 SNPs), which contains the highest number of targeted base pairs in the assay. The average mutation density across all regions interrogated was estimated to be one mutation per 20.91 Mb. The highest mutation frequency was found in chr.2D (1/11.7 kb) and the lowest in chr.7D (1/353.4 kb). Out of the detected mutations, 101 SNPs were filtered using analysis criteria aimed to enrich for mutations that may affect gene function. Out of these, one putative SNP detected in Lr21 were selected for further analysis. The SNP identified in chimeric allele (Lr21) of a resistant mutant (N1-252) was located in a NBS domain of chr.1BS at 3.4 Mb position. Through computational analysis, it was demonstrated that this identified SNP causes a substitution of glutamic acid with alanine, resulting in a predicted altered protein structure. This mutation, therefore, is a candidate for contributing to the resistance phenotype in the mutant line. Based on this work, we conclude that the wheat mutant resource developed is useful as a source of novel genetic variation for forward-genetic screens and also as a useful tool for gaining insights into the important biological circuits of different traits of complex genomes like wheat.