Genetic diversity of disease resistance genes in foxtail millet (Setaria italica L.)

Multi-omics intervention in Setaria to dissect climate-resilient traits: Progress and prospects

Millets constitute a significant proportion of underutilized grasses and are well known for their climate resilience as well as excellent nutritional profiles. Among millets, foxtail millet (Setaria italica) and its wild relative green foxtail (S. viridis) are collectively regarded as models for studying broad-spectrum traits, including abiotic stress tolerance, C₄ photosynthesis, biofuel, and nutritional traits. Since the genome sequence release, the crop has seen an exponential increase in omics studies to dissect agronomic, nutritional, biofuel, and climate-resilience traits. These studies have provided first-hand information on the structure, organization, evolution, and expression of several genes; however, knowledge of the precise roles of such genes and their products remains elusive. Several open-access databases have also been instituted to enable advanced scientific research on these important crops. In this context, the current review enumerates the contemporary trend of research on understanding the climate resilience and other essential traits in Setaria, the knowledge gap, and how the information could be translated for the crop improvement of related millets, biofuel crops, and cereals. Also, the review provides a roadmap for studying other underutilized crop species using Setaria as a model.

Population genomic structure of Eurasian and African foxtail millet landrace accessions inferred from genotyping-by-sequencing

Foxtail millet [Setaria italica (L.) P. Beauv.] is the second most important millet species globally and is adapted to cultivation in diverse environments. Like its wild progenitor, green foxtail [S. viridis (L.) P. Beauv.], it is a model species for C4 photosynthetic pathways and stress tolerance genes in related bioenergy crops. We addressed questions regarding the evolution and spread of foxtail millet through a population genomic study of landraces from across its cultivated range in Europe, Asia, and Africa. We sought to determine population genomic structure and the relationship of domesticated lineages relative to green foxtail. Further, we aimed to identify genes involved in environmental stress tolerance that have undergone differential selection between geographical and genetic groups. Foxtail millet landrace accessions (n = 328) and green foxtail accessions (n = 12) were sequenced by genotyping-by-sequencing (GBS). After filtering, 5,677 single nucleotide polymorphisms (SNPs) were retained for the combined foxtail millet-green foxtail dataset and 5,020 for the foxtail millet dataset. We extended geographic coverage of green foxtail by including previously published GBS sequence tags, yielding a 4,515-SNP dataset for phylogenetic reconstruction. All foxtail millet samples were monophyletic relative to green foxtail, suggesting a single origin of foxtail millet, although no group of foxtail millet was clearly the most ancestral. Four genetic clusters were found within foxtail millet, each with a distinctive geographical distribution. These results, together with archaeobotanical evidence, suggest plausible routes of spread of foxtail millet. Selection scans identified nine candidate genes potentially involved in environmental adaptations, particularly to novel climates encountered, as domesticated foxtail millet spread to new altitudes and latitudes.

Biotechnological approaches to dissect climate-resilient traits in millets and their application in crop improvement

'Small millets' is a generic term that includes all the millets except pearl millet and sorghum. These small or minor millets constitute eleven species that are marginally cultivated and consumed worldwide. These small millets possess excellent agronomic-, climate-resilient, and nutritional traits, although they lack popularity. Small millets withstand a broad spectrum of environmental stresses and possess better water-use and nitrogen-use efficiencies. Of note, small millets are five- to seven-fold nutritionally rich in terms of protein, bioactive compounds, micro- and macro-nutrients as compared to major cereals. Irrespective of these merits, small millets have received little research attention compared to major millets and cereals. However, the knowledge generated from such studies is significant for the improvement of millets per se and for translating the information to improve major cereals through breeding and transgene-based approaches. Given this, the review enumerates the efforts invested in dissecting the climate-resilient traits in small millets and provides a roadmap for deploying the information in crop improvement of millets as well as cereals in the scenario of climate change.

Wheat Disease Resistance Genes and Their Diversification Through Integrated Domain Fusions

Plants are in a constant evolutionary arms race with their pathogens. At the molecular level, the plant nucleotide-binding leucine-rich repeat receptors (NLRs) family has coevolved with rapidly evolving pathogen effectors. While many NLRs utilize variable leucine-rich repeats (LRRs) to detect effectors, some have gained integrated domains (IDs) that may be involved in receptor activation or downstream signaling. The major objectives of this project were to identify NLR genes in wheat (Triticum aestivum L.) and assess IDs associated with immune signaling (e.g., kinase and transcription factor domains). We identified 2,151 NLR-like genes in wheat, of which 1,298 formed 547 gene clusters. Among the non-toll/interleukin-1 receptor NLR (non-TNL)-like genes, 1,552 encode LRRs, 802 are coiled-coil (CC) domain-encoding (CC-NBS-LRR or CNL) genes, and three encode resistance to powdery mildew 8 (RPW8) domains (RPW8-NBS-LRR or RNL). The expansion of the NLR gene family in wheat is attributable to its origin by recent polyploidy events. Gene clusters were likely formed by tandem duplications, and wheat NLR phylogenetic relationships were similar to those in barley and Aegilops. We also identified wheat NLR-ID fusion proteins as candidates for NLR functional diversification, often as kinase and transcription factor domains. Comparative analyses of the IDs revealed evolutionary conservation of more than 80% amino acid sequence similarity. Homology assessment indicates that these domains originated as functional non-NLR-encoding genes that were incorporated into NLR-encoding genes through duplication events. We also found that many of the NLR-ID genes encode alternative transcripts that include or exclude IDs, a phenomenon that seems to be conserved among species. To verify this, we have analyzed the alternative transcripts that include or exclude an ID of an NLR-ID from another monocotyledon species, rice (Oryza sativa). This indicates that plants employ alternative splicing to regulate IDs, possibly using them as baits, decoys, and functional signaling components. Genomic and expression data support the hypothesis that wheat uses alternative splicing to include and exclude IDs from NLR proteins.

Oleochemical Properties for Different Fractions of Foxtail Millet Bran

Foxtail millet (FM) is one of the oldest cultivated grain crops with a variety of nutritions, and foxtail millet bran (FMB), a by-product of FM milling process, is also rich in variety of nutrient substance. There are four classifications of FMB, namely coarse bran (FMCB), skin bran (FMSB), polished bran (FMPB) and mixed bran (FMMB). Because these nutrients are distributed within the different fractions of FMB, we compared some chemical composition and its oleochemical properties of four FMB samples. Results showed that the oil extracted from FMB is high value-added plant oil. It contains abundant unsaturated fatty acid (UFA), with the main UFAs were linoleic acid (65%~69%) and oleic acid (12~17%), which accounted for more than 80% of the lipids. The main triacylglycerols were trilinolein (LLL) and oleodilinolein (OLL). There were no evident difference on fatty acid, triacylglycerol and sterols profiles for FMSB, FMPB and FMMB, but the contents of amino acids, tocols, squalene and oryzanol were different.

Evolutionary Divergence of TNL Disease-Resistant Proteins in Soybean (Glycine max) and Common Bean (Phaseolus vulgaris)

Disease-resistant genes (R genes) encode proteins that are involved in protecting plants from their pathogens and pests. Availability of complete genome sequences from soybean and common bean allowed us to perform a genome-wide identification and analysis of the Toll interleukin-1 receptor-like nucleotide-binding site leucine-rich repeat (TNL) proteins. Hidden Markov model (HMM) profiling of all protein sequences resulted in the identification of 117 and 77 regular TNL genes in soybean and common bean, respectively. We also identified TNL gene homologs with unique domains, and signal peptides as well as nuclear localization signals. The TNL genes in soybean formed 28 clusters located on 10 of the 20 chromosomes, with the majority found on chromosome 3, 6 and 16. Similarly, the TNL genes in common bean formed 14 clusters located on five of the 11 chromosomes, with the majority found on chromosome 10. Phylogenetic analyses of the TNL genes from Arabidopsis, soybean and common bean revealed less divergence within legumes relative to the divergence between legumes and Arabidopsis. Syntenic blocks were found between chromosomes Pv10 and Gm03, Pv07 and Gm10, as well as Pv01 and Gm14. The gene expression data revealed basal level expression and tissue specificity, while analysis of available microRNA data showed 37 predicted microRNA families involved in targeting the identified TNL genes in soybean and common bean.

Genome-Wide Identification of NBS-Encoding Resistance Genes in Sunflower (Helianthus annuus L.)

Nucleotide Binding Site—Leucine-Rich Repeat (NBS-LRR) genes encode disease resistance proteins involved in plants’ defense against their pathogens. Although sunflower is affected by many diseases, only a few molecular details have been uncovered regarding pathogenesis and resistance mechanisms. Recent availability of sunflower whole genome sequences in publicly accessible databases allowed us to accomplish a genome-wide identification of Toll-interleukin-1 receptor-like Nucleotide-binding site Leucine-rich repeat (TNL), Coiled Coil (CC)-NBS-LRR (CNL), Resistance to powdery mildew8 (RPW8)-NBS-LRR (RNL) and NBS-LRR (NL) protein encoding genes. Hidden Markov Model (HMM) profiling of 52,243 putative protein sequences from sunflower resulted in 352 NBS-encoding genes, among which 100 genes belong to CNL group including 64 genes with RX_CC like domain, 77 to TNL, 13 to RNL, and 162 belong to NL group. We also identified signal peptides and nuclear localization signals present in the identified genes and their homologs. We found that NBS genes were located on all chromosomes and formed 75 gene clusters, one-third of which were located on chromosome 13. Phylogenetic analyses between sunflower and Arabidopsis NBS genes revealed a clade-specific nesting pattern in CNLs, with RNLs nested in the CNL-A clade, and species-specific nesting pattern for TNLs. Surprisingly, we found a moderate bootstrap support (BS = 50%) for CNL-A clade being nested within TNL clade making both the CNL and TNL clades paraphyletic. Arabidopsis and sunflower showed 87 syntenic blocks with 1049 high synteny hits between chromosome 5 of Arabidopsis and chromosome 6 of sunflower. Expression data revealed functional divergence of the NBS genes with basal level tissue-specific expression. This study represents the first genome-wide identification of NBS genes in sunflower paving avenues for functional characterization and potential crop improvement.

Comparative Genomics of Non-TNL Disease Resistance Genes from Six Plant Species

Disease resistance genes (R genes), as part of the plant defense system, have coevolved with corresponding pathogen molecules. The main objectives of this project were to identify non-Toll interleukin receptor, nucleotide-binding site, leucine-rich repeat (nTNL) genes and elucidate their evolutionary divergence across six plant genomes. Using reference sequences from Arabidopsis, we investigated nTNL orthologs in the genomes of common bean, Medicago, soybean, poplar, and rice. We used Hidden Markov Models for sequence identification, performed model-based phylogenetic analyses, visualized chromosomal positioning, inferred gene clustering, and assessed gene expression profiles. We analyzed 908 nTNL R genes in the genomes of the six plant species, and classified them into 12 subgroups based on the presence of coiled-coil (CC), nucleotide binding site (NBS), leucine rich repeat (LRR), resistance to Powdery mildew 8 (RPW8), and BED type zinc finger domains. Traditionally classified CC-NBS-LRR (CNL) genes were nested into four clades (CNL A-D) often with abundant, well-supported homogeneous subclades of Type-II R genes. CNL-D members were absent in rice, indicating a unique R gene retention pattern in the rice genome. Genomes from Arabidopsis, common bean, poplar and soybean had one chromosome without any CNL R genes. Medicago and Arabidopsis had the highest and lowest number of gene clusters, respectively. Gene expression analyses suggested unique patterns of expression for each of the CNL clades. Differential gene expression patterns of the nTNL genes were often found to correlate with number of introns and GC content, suggesting structural and functional divergence.

Data on the genome-wide identification of CNL R-genes in Setaria italica (L.) P. Beauv

We report data associated with the identification of 242 disease resistance genes (R-genes) in the genome of Setaria italica as presented in “Genetic diversity of disease resistance genes in foxtail millet (Setaria italica L.)” (Andersen and Nepal, 2017) [1]. Our data describe the structure and evolution of the Coiled-coil, Nucleotide-binding site, Leucine-rich repeat (CNL) R-genes in foxtail millet. The CNL genes were identified through rigorous extraction and analysis of recently available plant genome sequences using cutting-edge analytical software. Data visualization includes gene structure diagrams, chromosomal syntenic maps, a chromosomal density plot, and a maximum-likelihood phylogenetic tree comparing Sorghum bicolor, Panicum virgatum, Setaria italica, and Arabidopsis thaliana. Compilation of InterProScan annotations, Gene Ontology (GO) annotations, and Basic Local Alignment Search Tool (BLAST) results for the 242 R-genes identified in the foxtail millet genome are also included in tabular format.