Genome-Wide Investigation of Spliceosomal SM/LSM Genes in Wheat (Triticum aestivum L.) and Its Progenitors

The SSM/SLSM (spliceosomal Smith (SM)/SM-like (LSM)) genes are the central components of the spliceosome in eukaryotes, which play an important role in regulating RNA splicing, participating in diverse biological processes. Although it has been detected in Arabidopsis and rice etc. plants, the members and significance of the SSM/SLSM gene family in wheat are still not reported. In this study, we identified the SSM/SLSM genes in wheat and its progenitors at genome-scale, where 57 SSM/SLSM genes were identified in wheat, together with 41, 17and 19 found in Triticum dicoccoides, Triticum urartu, and Aegilops tauschii. Furthermore, their phylogenetic relationship, gene structures, conserved motifs, and cis-regulatory elements were systematically analyzed. By synteny analysis, good collinearity of SSM/SLSM genes was found among bread wheat and its progenitors’ genomes, and the distribution of SMD2 genes in wheat chromosome 5A, 4B and 4D located in the 4AL-5AL-7BS chromosome model, due to the translocation. Then, the positively selected genes were further investigated based on the non-synonymous to synonymous (dN/dS) analysis of the orthologous pairs. Finally, the expression profiles of the SSM/SLSM genes were detected using RNA-seq datasets, and eight stress-responsive candidate genes were selected to validate their expression through qPCR (real-time quantitative polymerase chain reaction). According to the co-expression network analysis, the correlation between the LSM7-7A gene and related genes was illustrated through Gene Ontology (GO) enrichment analysis. Furthermore, the LSM7-7A gene was related to the Arabidopsis homologous salt tolerance gene RCY1. This investigation systematically identified the complete candidates of SSM/SLSM genes and their characters in wheat and its progenitors, and provided clues to a better understanding of their contribution during the wheat polyploidy process.

Characterization of Potential Candidate Genes for Grain Size in Wild Emmer Wheat Triticum Dicoccoides

There is an incessant need to address food security in staple crops, and the crop yield is positively correlated with grain weight. Grain size, determined by grain length and width, is an essential component of final grain weight in cereals. Wheat wild relatives are the goldmine to harness any trait of interest, including the component traits of grain size. It is crucial to understand the detailed mechanism of grain size formation and unravel underlying genes controlling grain size in these species for their proper utilization in wheat improvement. In this study, gene expression analysis was performed on developing grain in wild tetraploid progenitor Triticum dicoccoides (AABB) to identify candidate genes involved in determining grain size. Four T. dicoccoides accessions were selected, two (pau5228 and pau5322) with higher grain length and weight and two (pau14703 and pau14756) with comparatively smaller grains.Six genes out of the eight genes selected for expression study, viz., GL7, TaGL3, TaGS5, GS3, SRS3, and TaGASR7, were upregulated from 8 days post-anthesis (DPA) to 20 DPA in both the large grain accessions, while TaGW2 gene was upregulated in both small grain accessions. TGW6 was downregulated in all the accessions at all stages of grain development. The results indicated that the selected genes play an essential role in grain size formation by controlling individual morphometric components of grain length and width. Targeted introgression genes controlling grain size components will eventually aid in improving grains yield.

Global patterns of subgenome evolution in organelle-targeted genes of six allotetraploid angiosperms

Whole-genome duplications (WGDs), in which the number of nuclear genome copies is elevated as a result of autopolyploidy or allopolyploidy, are a prominent process of diversification in eukaryotes. The genetic and evolutionary forces that WGD imposes upon cytoplasmic genomes are not well understood, despite the central role that cytonuclear interactions play in eukaryotic function and fitness. Cellular respiration and photosynthesis depend upon successful interaction between the 3000+ nuclear-encoded proteins destined for the mitochondria or plastids and the gene products of cytoplasmic genomes in multi-subunit complexes such as OXPHOS, organellar ribosomes, Photosystems I and II, and Rubisco. Allopolyploids are thus faced with the critical task of coordinating interactions between nuclear and cytoplasmic genes that were inherited from different species. Because cytoplasmic genomes share a more recent history of common descent with the maternal nuclear subgenome than the paternal subgenome, evolutionary "mismatches" between the paternal subgenome and the cytoplasmic genomes in allopolyploids might lead to accelerated rates of evolution in the paternal homoeologs of allopolyploids, either through relaxed purifying selection or strong directional selection to rectify these mismatches. We tested this hypothesis in maternal vs. paternal copies of organelle-targeted genes in six allotetraploids: Brachypodium hybridum, Chenopodium quinoa, Coffea arabica, Gossypium hirsutum, Nicotiana tabacum, and Triticum dicoccoides. We report evidence that allopolyploid subgenomes exhibit unequal rates of protein-sequence evolution, but we did not observe global effects of cytonuclear incompatibilities on paternal homoeologs of organelle-targeted genes. Analyses of gene content revealed mixed evidence for whether organelle-targeted genes re-diploidize more rapidly than non-organelle-targeted genes. Together, these global analyses provide insights into the complex evolutionary dynamics of allopolyploids, showing that allopolyploid subgenomes have separate evolutionary trajectories despite sharing the same nucleus, generation time, and ecological context.

Genome-wide member identification, phylogeny and expression analysis of PEBP gene family in wheat and its progenitors

The phosphatidylethanolamine binding protein (PEBP) family comprises ancient proteins found throughout the biosphere that play an important role in plant growth and development, flowering, seed development and dormancy. However, not all PEBP genes have been identified or analyzed in common wheat (Triticum aestivum L.) and its progenitors. In this study, we identified the PEBP genes in common wheat, Triticum dicoccoides, Triticum urartu and Aegilops tauschii by searching whole genome sequences, and characterized these genes by phylogenetic and transcriptome analyses. A total of 76, 38, 16 and 22 PEBP genes were identified in common wheat, T. dicoccoides, T. urartu and Ae. tauschii, respectively. Phylogenetic analysis classified the PEBP genes into four subfamilies (PEBP-like, MFT-like, TFL-like and FT-like); the PEBP-like subfamily was identified as a new subfamily with genes in this subfamily were conserved in plants. Group 2, 3 and 5 chromosomes of common wheat and its progenitors contained more PEBP genes than other chromosomes. The PEBP genes were conserved in wheat during evolution, and tandem duplication played a more important role in the amplification of PEBP genes than segmental duplication. Furthermore, transcriptome analysis revealed that PEBP genes showed tissue/organ-specific expression profiles and some PEBP genes were induced to express by biotic stresses. Quantitative real-time PCR (qRT-PCR) analysis revealed that seven randomly selected PEBP genes expressed differently during seed germination under cold, drought, flood, heat and salt stress treatments, and five of these genes (TaPEBP1, TaPEBP5, TaPEBP9, TaPEBP66 and TaPEBP69) showed significantly higher expression under different stress treatments, indicating that these genes play important roles during seed germination under stress conditions.

Genome-wide Identification and Expression Profiling Analysis of WOX Family Proteins Encoded Genes in Triticeae Plant Species

Background: Genotype dependence of plant regeneration is an important factor restricting the genetic improvement of Triticeae plant species. The WUSCHEL-related homeobox (WOX) is a group of plant specific transcription factor, which play an important role in plant growth and development, and cell division and differentiation. Recent studies revealed that the application of regeneration-related genes such as WOX and BABY BOOM (BBM) could improve plant regeneration. The application of WOX genes is one of the ways to improve the genetic transformation system of Triticeae and other species, but there are rare studies in this area.Results: From the available genome sequence database, in total 136 WOX transcripts were identified for the Triticeae plants, including 43 in Triticum aestivum, 30 in Triticum turgidum, 25 in Triticum dicoccoides, 17 in Hordeum vulgare, 13 in Aegilops tauschii, and 8 in Triticum urartu. All of the WOX family genes were distributed on the chromosomes of homologous groups 1 to 5 in the six Triticeae species, part of which were confirmed by their specific PCR markers using a set of T. durum-T. aestivum genome D substitution lines. All of the WOX proteins in the six Triticeae species could be grouped into three clades, similar to those in rice (Oryza sativa L.) and Arabidopsis. WOX family members were conserved among these Triticeae plants, all of them contained the conserved HOX DNA-binding homeodomain, and WUS clade members contained the characteristic WUS motif, while only TaWUS and TaWOX9 in all the six Triticeae plant species contained the ERF-associated amphiphilic repression (EAR) motif. The expression profiles of TaWOX genes by quantitative real-time PCR (qPCR) showed obvious difference among WOX family members.Conclusions: Totally 130 WOX genes were identified in the six Triticeae plant species. The WOX family genes were located on the chromosomes in the five homologous groups except groups 6 and 7 in the Triticeae species, and their expression profiles were different in different tissues, indicating that each of them had diverse function. The findings in this study could provide a basis for evolution and functional investigation and practical application of the WOX family genes in Triticeae plant species.

Discovery of a Promising Susceptibility Factor for Fusarium Head Blight in Wheat

Fusarium head blight (FHB) disease of wheat caused by Fusarium spp. deteriorates both quantity and quality of the crop. Manipulation of susceptibility factors, the genes facilitating disease development in plants, offers a novel and alternative strategy for enhancing FHB resistance in plants. In this study, a major effect susceptibility gene for FHB was identified on the short arm of chromosome 7A (7AS). Nullisomic-tetrasomic lines for homoeologous group-7 of wheat revealed dosage effect of the gene, with tetrasomic 7A being more susceptible than control Chinese Spring wheat, qualifying it as a bonafide susceptibility factor. The gene locus was conserved in six chromosome 7A inter-varietal wheat substitution lines of diverse origin and a tetraploid Triticum dicoccoides genotype. The susceptibility gene was named as SF7ASFHB and mapped on chromosome 7AS to 48.5-50.5 Mb peri-centromeric region between del7AS-3 and del7AS-8. Our results showed that deletion of SF7ASFHB imparts ~ 50-60% type 2 FHB resistance (against the spread of the fungal pathogen) and its manipulation may lead to enhanced resistance against FHB in wheat.HighlightDiscovery and mapping of a conserved susceptibility factor located on the short arm of wheat chromosome 7A whose deletion makes plants resistant to Fusarium Head Blight.

Seed-Derived Microbial Colonization of Wild Emmer and Domesticated Bread Wheat (Triticum dicoccoides and T. aestivum) Seedlings Shows Pronounced Differences in Overall Diversity and Composition

ABSTRACT The composition of the plant microbiota may be altered by ecological and evolutionary changes in the host population. Seed-associated microbiota, expected to be largely vertically transferred, have the potential to coadapt with their host over generations. Strong directional selection and changes in the genetic composition of plants during domestication and cultivation may have impacted the assembly and transmission of seed-associated microbiota. Nonetheless, the effect of plant speciation and domestication on the composition of these microbes is poorly understood. Here, we have investigated the composition of bacteria and fungi associated with the wild emmer wheat (Triticum dicoccoides) and domesticated bread wheat (Triticum aestivum). We show that vertically transmitted bacteria, but not fungi, of domesticated bread wheat species T. aestivum are less diverse and more inconsistent among individual plants compared to those of the wild emmer wheat species T. dicoccoides. We propagated wheat seeds under sterile conditions to characterize the colonization of seedlings by seed-associated microbes. Hereby, we show markedly different community compositions and diversities of leaf and root colonizers of the domesticated bread wheat compared to the wild emmer wheat. By propagating the wild emmer wheat and domesticated bread wheat in two different soils, we furthermore reveal a small effect of plant genotype on microbiota assembly. Our results suggest that domestication and prolonged breeding have impacted the vertically transferred bacteria, but only to a lesser extent have affected the soil-derived microbiota of bread wheat. IMPORTANCE Genetic and physiological changes associated with plant domestication have been studied for many crop species. Still little is known about the impact of domestication on the plant-associated microbiota. In this study, we analyze the seed-associated and soil-derived bacterial and fungal microbiota of domesticated bread wheat and wild emmer wheat. We show a significant difference in the seed-associated, but not soil-derived, bacterial communities of the wheat species. Interestingly, we find less pronounced effects on the fungal communities. Overall, this study provides novel insight into the diversity of vertically transmitted microbiota of wheat and thereby contributes to our understanding of wheat as a “metaorganism.” Insight into the wheat microbiota is of fundamental importance for the development of improved crops.