Raju Datla

Global Institute for Food Security

Einkorn (Triticum monococcum) was the first domesticated wheat species, and was central to the birth of agriculture and the Neolithic Revolution in the Fertile Crescent around 10,000 years ago1,2. Here we generate and analyse 5.2-Gb genome assemblies for wild and domesticated einkorn, including completely assembled centromeres. Einkorn centromeres...

Key Message This work reports the physical mapping of an important gene affecting spike compactness located in a low-recombination region of hexaploid wheat. This work paves the way for the eventual isolation and characterization of the factor involved but also opens up possibilities to use this approach to precisely map other wheat genes located o...

Mapping wheat genes, in the centromeric and pericentromeric regions (~2/3 rd of a given chromosome), poses a formidable challenge due to highly suppressed recombination. Using an example of compact spike locus ( C-locus) , this study provides an approach to precisely map wheat genes in the pericentromeric and centromeric regions that house ~30% of...

Lentil (Lens culinaris Medik.) is a nutritious legume, with seeds rich in protein, minerals and an array of diverse specialized metabolites. The formation of a seed requires regulation and tight coordination of developmental programs to form the embryo, endosperm and seed coat compartments, which determines the structure and composition of mature s...

Pea (Pisum sativum L.) is an important legume crop providing a good source of protein, vitamins, minerals and bioactive compounds with health benefits for humans. In this study, an improved method for simultaneous analysis of multiple phytoestrogens among 100 pea accessions was developed. Ipriflavone, (a synthetic isoflavone), was used as an intern...

The target of rapamycin (TOR) protein phosphorylates its downstream effector p70kDa ribosomal protein S6 kinases (S6K1) for ribosome biogenesis and translation initiation in eukaryotes. However, the molecular mechanism of TOR-S6K1-ribosomal protein (RP) signaling is not well understood in plants. In the present study, we report the transcriptional...

Production of viable progeny from interploid crosses requires precise regulation of gene expression from maternal and paternal chromosomes, yet the transcripts contributed to hybrid seeds from polyploid parent species have rarely been explored. To investigate the genome-wide maternal and paternal contributions to polyploid grain development, we ana...

In plants, the actin cytoskeleton plays a critical role in defense against diverse pathogens. The formation of actin patches is essential for the intracellular transport of organelles and molecules toward pathogen penetration sites and the formation of papillae for an early cellular response to powdery mildew attack in Arabidopsis thaliana. This re...

Seed development in angiosperms produces three genetically and developmentally distinct sub-compartments: the embryo, endosperm, and seed coat. The maternally derived seed coat protects the embryo and interacts closely with the external environment especially during germination and seedling establishment. Seed coat is a key contributor to seed comp...

Flax (Linum usitatissimum L.) is an important multipurpose crop widely grown for oil and fiber. Despite recent advances in genomics, detailed gene activities during the important reproductive phase of its development are not well defined. In this study, we employed high-throughput RNA-sequencing methods to generate in-depth transcriptome profiles o...

Although photosynthetic multiprotein complexes have received major attention, our knowledge about the assembly of these proteins into functional complexes in plants is still limited. In the present study, we have identified a chlorophyll‐deficient mutant, pale‐green leaf 1 (pgl1), in rice that displays abnormally developed chloroplasts. Map‐based c...

Introduction: Biofungicides with low toxicity and high efficiency are a global priority for sustainable agricultural development. Phytohormone salicylic acid (SA) is an ancient medicine against various diseases in humans and activates the immune system in plants, but little is known of its function as a biofungicide. Objectives: Here, Fusarium o...

The programs associated with embryonic roots (ERs), primary roots (PRs), lateral roots (LRs), and adventitious roots (ARs) play crucial roles in the growth and development of roots in plants. The root functions are involved in diverse processes such as water and nutrient absorption and their utilization, the storage of photosynthetic products, and...

The economically valuable Brassica species include the six related members of U’s Triangle. Despite the agronomic and economic importance of these Brassicas, the impacts of evolution and relatively recent domestication events on the genetic landscape of seed development have not been comprehensively examined in these species. Here we present a 3D t...

Key message Developmental and transcriptomic analysis of Brachypodium embryogenesis and comparison with Arabidopsis identifies conserved and divergent phases of embryogenesis and reveals widespread heterochrony of developmental gene expression. Abstract Embryogenesis, transforming the zygote into the mature embryo, represents a fundamental process...

Fusarium oxysporum is the causal agent of the devastating Fusarium wilt by invading and colonizing the vascular system in various plants, resulting in substantial economic losses worldwide. Target of rapamycin (TOR) is a central regulator that controls intracellular metabolism, cell growth, and stress responses in eukaryotes, but little is known ab...

The actin cytoskeleton regulates an array of diverse cellular activities that support the establishment of plant-microbe interactions and plays a critical role in the execution of plant immunity. However, molecular and cellular mechanisms regulating the assembly and rearrangement of actin filaments at plant-pathogen interaction sites remain largely...

The Target of Rapamycin (TOR) is a conserved multifunctional Serine/ Threonine protein kinase present in all eukaryotes, which controls several important signaling pathways related to growth and development. In the present investigation, we report that TOR overexpressing Arabidopsis plants ATR-1.4.27, and ATR-3.7.32 exhibit enhanced tolerance to os...

Key message This work reports a quick method that integrates RH mapping and genetic mapping to map the dominant Mov-1 locus to a 1.1-Mb physical interval with a small number of candidate genes. Abstract Bread wheat is an important crop for global human population. Identification of genes and alleles controlling agronomic traits is essential toward...

Fatty acids in crop seeds are a major source for both vegetable oils and industrial applications. Genetic improvement of fatty acid composition and oil content is critical to meet the current and future demands of plant-based renewable seed oils. Addressing this challenge can be approached by network modeling to capture key contributors of seed met...

Embryogenesis, transforming the zygote into the mature embryo, represents a fundamental process for all flowering plants. Current knowledge of cell specification and differentiation during plant embryogenesis is largely based on studies of the dicot model plant Arabidopsis thaliana . However, the major crops are monocots and the transcriptional pro...

Phytophthora infestans and Plasmodium are extremely harmful and economically important pathogens. Although they belong to distinct groups and infect very different hosts, P. infestans and Plasmodium display some common similarities. Such as they are closely related phylogenetically and have similarities in the strategies they use for the evasion or...

Among polyploid species with complex genomic architecture, variations in the regulation of alternative splicing (AS) provide opportunities for transcriptional and proteomic plasticity and the potential for generating trait diversities. However, the evolution of AS and its influence on grain development in diploid grass and valuable polyploid wheat...

Embryonic development represents an important reproductive phase of sexually reproducing plant species. The fusion of egg and sperm produces the plant zygote, a totipotent cell that through cell division and cell identity specification in early embryogenesis establishes the major cell lineages and tissues of the adult plant. The subsequent morphoge...

Background The recent release of the reference genome sequence assembly of flax, a self-pollinated crop with 15 chromosome pairs, into chromosome-scale pseudomolecules enables the characterization of gene families. The ABC transporter and HMA gene families are important in the control of cadmium (Cd) accumulation in crops. To date, the genome-wide...

Background Flax (Linum usitatissimum L.) is a self-pollinated crop and diversified into two morphotypes for its stem fibre and seed oil. The availability of the flax reference genome sequence, previously assembled into 15 pseudomolecules, enables the characterization of important gene families. The ABC transporter and HMA gene families are consider...

Background The recent release of the reference genome sequence assembly of flax, a self-pollinated crop with 15 chromosome pairs, into chromosome-scale pseudomolecules enables the characterization of gene families. The ABC transporter and HMA gene families are important in the control of cadmium (Cd) accumulation in crops. To date, the genome-wide...

Background The recent release of the reference genome sequence assembly of flax, a self-pollinated crop with 15 chromosome pairs, into chromosome-scale pseudomolecules enables the characterization of gene families. The ABC transporter and HMA gene families are important in the control of cadmium (Cd) accumulation in crops. To date, the genome-wide...

Different phosphoinositides enriched at the membrane of specific subcellular compartments within plant cells contribute to organelle identity, ensuring appropriate cellular trafficking and function. During the infection of plant cells, biotrophic pathogens such as powdery mildews enter plant cells and differentiate into haustoria. Each haustorium i...

A novel gene, At1g77960 , from Arabidopsis thaliana was characterized. At1g77960 transcripts accumulate to very high levels in plants ectopically overexpressing the Golden2-like1 ( GLK1 ) transcription factor and is designated as a R esponse to G LK1 O verexpression ( RGO ) gene. RGO encodes a protein with domains of tandem QH and QN repeats. Trans...

Flax seed has become consumers’ choice for not only polyunsaturated alpha-linolenic fatty acid but also nutraceuticals such as lignans and soluble fiber. There is, however, a major drawback of flax as a source of functional food since the seeds contain significant level of cyanogenic glucosides. The final step of cyanogenic glucoside biosynthesis i...

Previous studies have alternately supported and discounted the hypothesis that the maternal genome plays a predominant role in early embryogenesis in plants. We used 24 embryo defective (emb) mutants of Arabidopsis thaliana to test for maternal and paternal effects in early embryogenesis. 5 emb mutants had equal maternal and paternal effects, 5 sho...

The Target of Rapamycin (TOR) protein kinase reprograms cellular metabolism under various environmental stresses. The overexpression of TOR in Arabidopsis resulted in increased plant growth including yield and biomass when compared with the wild type under both controlled and limited water conditions. In the present investigation, we report that Ar...

In the original publication [1], the copyright line was incorrectly published as “© The Author(s) 2019”. The corrected copyright line should read as “© Her Majesty the Queen in Right of Canada as represented by the Minister of Agriculture and Agri-Food Canada, 2019”. The original article has been corrected.

Background: Targeted genome editing using the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas9 system has been applied in a large number of plant species. Using a gene-specific single guide RNA (sgRNA) and the CRISPR/Cas9 system, small editing events such as deletions of few bases can be obtained. However larger deletions ar...

Modern wheat production comes from two polyploid species, Triticum aestivum and Triticum turgidum (var durum), which putatively arose from diploid ancestors Triticum urartu, Aegilops speltoides, and Aegilops tauschii. How gene expression during embryogenesis and grain development in wheats has been shaped by the differing contributions of diploid g...

Flax is an important domesticated crop that is farmed for the production of linen textiles and for its oil seeds that contain many important human health-promoting compounds. Flax is one of the earliest domesticated crops, yet progress in genetic, genomic, and transcriptomic analysis of important agricultural traits has been relatively slow. Major...

The ability to create desirable gene variants through targeted changes offers tremendous opportunities for the advancement of basic and applied plant research. Gene editing technologies have opened new avenues to perform such precise gene modifications in diverse biological systems. These technologies use sequence-specific nucleases, such as homing...

From scientific advances in medical research to the plethora of anti-aging products available, our obsession with slowing the aging process and increasing lifespan is indisputable. A large research effort has been levied towards this perpetual search for the fountain of youth, yet the molecular mechanisms governing an organism’s lifespan and the ca...

Embryogenesis represents a critical phase in the life cycle of flowering plants. Here, we characterize transcriptome landscapes associated with key stages of embryogenesis by combining an optimized method for the isolation of developing Arabidopsis embryos with high-throughput RNA-seq. The resulting RNA-seq datasets identify distinct overlapping pa...

Land plants reproduce sexually by developing an embryo from a fertilized egg cell. However, embryos can also be formed from other cell types in many plant species. Thus, a key question is how embryo identity in plants is controlled, and how this process is modified during nonzygotic embryogenesis. The Arabidopsis (Arabidopsis thaliana) zygote divid...

UBC 13 is required for Lys63‐linked polyubiquitination and innate immune responses in mammals, but its functions in plant immunity remain to be defined. Here we used genetic and pathological methods to evaluate roles of Arabidopsis UBC 13 in response to pathogens and environmental stresses. Loss of UBC 13 failed to activate the expression of numero...

Insights from the annotated wheat genome Wheat is one of the major sources of food for much of the world. However, because bread wheat's genome is a large hybrid mix of three separate subgenomes, it has been difficult to produce a high-quality reference sequence. Using recent advances in sequencing, the International Wheat Genome Sequencing Consort...

An annotated reference sequence representing the hexaploid bread wheat genome in 21 pseudomolecules has been analyzed to identify the distribution and genomic context of coding and noncoding elements across the A, B, and D subgenomes. With an estimated coverage of 94% of the genome and containing 107,891 high-confidence gene models, this assembly e...

In most plants, the female germline starts with the differentiation of one megaspore mother cell (MMC) in each ovule that produces four megaspores through meiosis, one of which survives to become the functional megaspore (FM). The FM further develops into an embryo sac. Little is known regarding the control of MMC formation to one per ovule and the...

Genotyping of WT, septuple mutant and complementation lines with a genomic ICK7 fragment. An ICK7 genomic fragment was introduced into the septuple mutant. Many transformants (6/40) with normal silique length were observed and the analysis of two independent transformants (1243–4 and 1243–23) is shown here. PCR was used to determine the genotypes o...

Phenotyping of WT, ick12567 and septuple mutant plants. (A) Seedlings of WT, ick12567 and septuple mutants at 26 days after planting in soil. (B) Fresh seedling weight of 21-day-old WT, ick12567 and septuple mutants. For each line, 3 pots each with 5 plants were used in the analysis. The averages and standard deviations are shown. (C—E) Leaf area (...

Genotyping of WT, septuple mutant and complementation lines with a genomic ICK4 fragment. An ICK4 genomic fragment (including 2040 bp before ATG, 1028 bp of the coding region and 717 bp of the region after the STOP codon) was introduced into the septuple mutant. Multiple independent lines were identified that showed complementation of the silique l...

RT-PCR and phenotyping of WT, ick4, ick467, ick123467 and septuple mutants. (A) Analysis of ICK transcripts in the WT (the first lane), ick4 (the second lane), ick467 (the third lane), ick123467 (the fourth lane) and septuple mutant (the fifth lane), with WT genomic DNA as a control (the last lane). Gene-specific primers were used for amplifying th...

Identification of megaspore mother cells (MMCs) in meiosis by ASY1 immunostaining. Developing ovules were prepared and immunostained with an antibody against ASY1, which is specifically expressed during meiosis. (A—C) WT ovules at MMC (A), meiosis (B) and FG1 (C) stages. (D—I) Mutant ovules at MMC (D), meiosis (E—H) and FG1 (I) stages. One to four...

Early megagametogenesis in WT and ick septuple mutant. WT (A) and septuple (B—D) ovules at FG2 stage. The WT ovule had one pair of nuclei. The mutant ovules had two (B), three (C) and four (D) pairs of nuclei, with each pair likely derived from a functional megaspore. The two nuclei in each pair are close to each other and have similar appearance....

Observation of female gametes in mature embryo sacs in the WT and ick septuple mutant. The flower buds just before opening were emasculated and left for 1 day. Ovules (from about 15 gynoecia for each line) were prepared and observed under a microscope with DIC optics. If one central cell (secondary) nucleus and one egg nucleus, usually close to eac...

Genotyping and RT-PCR of ick3 and ick4 T-DNA insertion mutants. (A) Genotyping of ick3 (SALK_053533) and ick4 (Sail_548_B03) single mutants with WT as a control. For both genes, a pair of gene-specific primers was used for amplifying the full-length WT coding sequence of ICK3 or ICK4 while a T-DNA left border primer and a gene specific primer were...

Crosses used to produce various ick mutants from ICK single mutants and ick12567 mutant. (PDF)

Genotyping and RT-PCR of ick septuple mutant. (A) Gene-specific primers for ICK1, ICK2, ICK3, ICK4, ICK5, ICK6 and ICK7 were used to confirm the genotype of ICK septuple mutant with WT genomic DNA as a control. (B) Analysis of ICK transcripts in the WT (first lane) and septuple mutant (second lane), with WT genomic DNA as a control (third lane). Ge...

Reciprocal crosses to determine the transmission of the short silique phenotype through the parents. Reciprocal crosses (indicated as female X male) were made between the WT and septuple mutant. The length of fully-elongated siliques was measured. In each treatment, four plants with 4 siliques for each plant were used. The averages and standard dev...

RT-PCR and phenotyping of WT, septuple mutant and complementation lines with a genomic ICK4 fragment. (A) ICK4 transcript analysis. cDNAs synthesized from total RNAs were used to detect the ICK4 transcripts in WT, septuple mutant and two complementation lines (T2 generation). Actin (ACT8) was amplified as a control. (B) Silique length of WT, septup...

RT-PCR and phenotyping of WT, septuple mutant and transformants with ICK7. (A) ICK7 transcript analysis. cDNAs synthesized from total RNAs were used to detect the ICK7 transcripts in WT, septuple mutant and two transformants with ICK7 genomic fragment. Actin (ACT8) was amplified as a control. (B) Silique length of WT, septuple mutant and the two tr...

Analysis of surviving megaspores in WT and septuple mutant ovules with one MMC. Ovules with a single MMC were identified based on callose staining with aniline blue and DIC microscopy. For each ovule, the callose fluorescence image is shown at the top and the DIC image at the bottom. The numbers in the images indicate the 1st to 4th megaspore posit...

Analysis of mature pollen grains in WT and ick septuple mutant. Mature pollen grains from ten nascent flowers each line were collected and stained with DAPI. Vegetative and sperm cell nuclei were observed and counted under a fluorescence microscope (Leica DM2500) with a 63× (NA = 1.40) oil lens. (PDF)

Development of functional megaspore (FM) in ovules of the WT and ick septuple mutant. The ovules were checked and those at functional megaspore stage were included in the analysis. They were observed under a microscope with DIC optics. The presence and number of functional megaspores in ovules (from about 15 gynoecia) were counted. (PDF)

Frequency of twin seedlings in the WT and ick septuple mutant. WT and septuple mutant seeds were plated on ½ MS plates. Four days after plating, seedlings were screened under a dissecting microscope for the occurrence of twin seedlings. (PDF)

Genotyping of WT, ick4, ick467, ick123467 and septuple mutants. Gene-specific primers for ICK1, ICK2, ICK3, ICK4, ICK5, ICK6 and ICK7 genes, and a T-DNA left border primer were used to confirm the genotypes of WT, ick4, ick467, ick123467 and septuple mutants. (PDF)

Number of megaspore mother cells determined by DIC, DMC1 immunostaining and callose deposition patterns. (A) WT and septuple ovules at stage 2-II were surveyed under a DIC microscope and determined for the number of enlarged MMC-like cells prior to meiosis. Number of ovules counted: WT = 129 and mutant = 149. (B) Number of MMCs undergoing meiosis a...

Analysis of endosperm development and presence of extra central cells after fertilization in the WT and ick septuple mutant. Three days after flowers opened, ovules were collected and prepared for DIC observation. Only the ovules containing at least one developing embryo were included (about 20 gynoecia from each line used). All the WT ovules had o...

Genomic imprinting is an epigenetic regulatory mechanism that operates through expression of certain genes from maternal or paternal in a parent-of-origin-specific manner. Imprinted genes have been identified in diverse biological systems that are implicated in some human diseases and in embryonic and seed developmental programs in plants. The mole...