Beat the heat: Breeding, genomics, and gene editing for high nighttime temperature tolerance in rice.

High nighttime temperature (HNT) is a major obstacle in rice production worldwide. It severely impacts spikelet fertility and induces grain chalk, the two undesirable factors leading to yield and quality decline in rice. Recently, major efforts have been undertaken to understand the genetic mechanisms underlying HNT tolerance.

Targeted mutagenesis of the vacuolar H translocating pyrophosphatase gene reduces grain chalkiness in rice.

Grain chalkiness is a major concern in rice production because it impacts milling yield and cooking quality, eventually reducing market value of the rice. A gene encoding vacuolar H translocating pyrophosphatase (V-PPase) is a major quantitative trait locus in indica rice, controlling grain chalkiness. Higher transcriptional activity of this gene is associated with increased chalk content.

Effect of Interfacial Schemes on the Optical and Structural Properties of InAs/GaSb Type-II Superlattices.

Incorporating an intentional strain compensating InSb interface (IF) layer in InAs/GaSb type-II superlattices (T2SLs) enhances device performance. But there is a lack of studies that correlate this approach's optical and structural quality, so the mechanisms by which this improvement is achieved remain unclear. One critical issue in increasing the performance of InAs/GaSb T2SLs arises from the lattice mismatch between InAs and GaSb, leading to interfacial strain in the structure.

Phenotypic and transcriptomic analysis reveals early stress responses in transgenic rice expressing Arabidopsis DREB1a.

Overexpression of Arabidopsis dehydration response element binding 1a () is a well-known approach for developing salinity, cold and/or drought stress tolerance. However, understanding of the genetic mechanisms associated with expression in rice is generally limited. In this study, -associated early responses were investigated in a transgenic rice line harboring cold-inducible at a gene stacked locus.

Field-Evolved from Palmer Amaranth Confers Pre-emergence Tolerance to PPO-Inhibitors in Rice and .

Resistance to protoporphyrinogen IX oxidase (PPO)-inhibitors in Amaranthus palmeri and Amaranthus tuberculatus is mainly contributed by mutations in the PPO enzyme, which renders herbicide molecules ineffective. The deletion of glycine210 (ΔG210) is the most predominant PPO mutation. ΔG210-ppo2 is overexpressed in rice (Oryza sativa c.

Targeting TOR and SnRK1 Genes in Rice with CRISPR/Cas9.

Genome targeting with CRISPR/Cas9 is a popular method for introducing mutations and creating knock-out effects. However, limited information is currently available on the mutagenesis of essential genes. This study investigated the efficiency of CRISPR/Cas9 in targeting rice essential genes: the singleton TARGET OF RAPAMYCIN (OsTOR) and the three paralogs of the Sucrose non-fermenting-1 (SNF1)-related kinase 1 (OsSnRK1α), OsSnRK1αA, OsSnRK1αB and OsSnRK1αC.

Multigene Transformation Through Cre-lox Mediated Site-Specific Integration in Rice.

Plant transformation with multiple genes is a major challenge, rendering multi-trait engineering extremely difficult in crop plants. One of the hurdles in multigene transformation is the uncontrolled integration process that leads to low quality transgenic lines that are unsuitable for practical application. Recombinase-mediated site-specific integration has been tested and validated for developing high quality transgenic lines expressing one, two, or multiple genes.

Genotype-dependent and heat-induced grain chalkiness in rice correlates with the expression patterns of starch biosynthesis genes.

Starch biosynthesis is a complex process underlying grain chalkiness in rice in a genotype-dependent manner. Coordinated expression of starch biosynthesis genes is important for producing translucent rice grains, while disruption in this process leads to opaque or chalky grains. To better understand the dynamics of starch biosynthesis genes in grain chalkiness, six rice genotypes showing variable chalk levels were subjected to gene expression analysis during reproductive stages.

Suppression of ERECTA Signaling Impacts Agronomic Performance of Soybean ( (L) Merril) in the Greenhouse.

The ERECTA (ER) family of genes, encoding leucine-rich repeat receptor-like kinase (RLK), influences complex morphological and physiological aspects of plants. Modulation of ER signaling leads to abiotic stress tolerance in diverse plant species. However, whether the gain in stress tolerance is accompanied with desirable agronomic performance is not clearly known.

SNF1-related protein kinase 1: the many-faced signaling hub regulating developmental plasticity in plants.

The Snf1-related protein kinase 1 (SnRK1) is the plant homolog of the heterotrimeric AMP-activated protein kinase/sucrose non-fermenting 1 (AMPK/Snf1), which works as a major regulator of growth under nutrient-limiting conditions in eukaryotes. Along with its conserved role as a master regulator of sugar starvation responses, SnRK1 is involved in controlling the developmental plasticity and resilience under diverse environmental conditions in plants. In this review, through mining and analyzing the interactome and phosphoproteome data of SnRK1, we are highlighting its role in fundamental cellular processes such as gene regulation, protein synthesis, primary metabolism, protein trafficking, nutrient homeostasis, and autophagy.

FLP-Mediated Site-Specific Gene Integration in Rice.

Enabling precise gene integration is important for installing traits in the plants. One of the practical methods of achieving precise gene integration is by using the yeast FLP-FRT recombination system that is efficient in directing DNA integration into the "engineered" genomic sites. The critical parameters of this method include the use of the thermostable version of FLP protein and the promoter trap design to select site-specific integration clones.

Recombinase-mediated integration of a multigene cassette in rice leads to stable expression and inheritance of the stacked locus.

Unlabelled: Efficient methods for multigene transformation are important for developing novel crop varieties. Methods based on random integrations of multiple genes have been successfully used for metabolic engineering in plants. However, efficiency of co-integration and co-expression of the genes could present a bottleneck.

Modification of soybean growth and abiotic stress tolerance by expression of truncated ERECTA protein from Arabidopsis thaliana.

ERECTA gene family encodes leucine-rich repeat receptor-like kinases that control major aspects of plant development such as elongation of aboveground organs, leaf initiation, development of flowers, and epidermis differentiation. To clarify the importance of ERECTA signaling for the development of soybean (Glycine max), we expressed the dominant-negative ERECTA gene from Arabidopsis thaliana that is truncated in the kinase domain (AtΔKinase). Expression of AtΔKinase in soybean resulted in the short stature, reduced number of leaves, reduced leaf surface area and enhanced branching in the transgenic plants.

Heat-shock-inducible CRISPR/Cas9 system generates heritable mutations in rice.

Transient expression of CRISPR/Cas9 is an effective approach for limiting its activities and improving its precision in genome editing. Here, we describe the heat-shock-inducible CRISPR/Cas9 for controlled genome editing, and demonstrate its efficiency in the model crop, rice. Using the soybean heat-shock protein gene promoter and the rice promoter to express Cas9 and sgRNA, respectively, we developed the heat-shock (HS)-inducible CRISPR/Cas9 system, and tested its efficacy in targeted mutagenesis.

Utility of I-SceI and CCR5-ZFN nucleases in excising selectable marker genes from transgenic plants.

Objectives: Removal of selection marker genes from transgenic plants is highly desirable for their regulatory approval and public acceptance. This study evaluated the use of two nucleases, the yeast homing endonuclease, I-SceI, and the designed zinc finger nuclease, CCR5-ZFN, in excising marker genes from plants using rice and Arabidopsis as the models.

Results: In an in vitro culture assay, both nucleases were effective in precisely excising the DNA fragments marked by the nuclease target sites.

Dual-targeting by CRISPR/Cas9 leads to efficient point mutagenesis but only rare targeted deletions in the rice genome.

The present study investigated the efficiency of CRISPR/Cas9 in creating genomic deletions as the basis of its application in removing selection marker genes or the intergenic regions. Three loci, representing a transgene and two rice genes, were targeted at two sites each, in separate experiments, and the deletion of the defined fragments was investigated by PCR and sequencing. Genomic deletions were found at a low rate among the transformed callus lines that could be isolated, cultured, and regenerated into plants harboring the deletion.

Generation of a selectable marker free, highly expressed single copy locus as landing pad for transgene stacking in sugarcane.

A selectable marker free, highly expressed single copy locus flanked by insulators was created as landing pad for transgene stacking in sugarcane. These events displayed superior transgene expression compared to single-copy transgenic lines lacking insulators. Excision of the selectable marker gene from transgenic sugarcane lines was supported by FLPe/FRT site-specific recombination.

Gene Stacking in Plants Through the Application of Site-Specific Recombination and Nuclease Activity.

Biotechnology methods for inserting genes one by one or as a block of fragment into plant genomes are needed to introduce valuable traits into crop varieties. Insertion of multiple genes into a single site, called as molecular stacking, is important to allow co-inheritance of the genes into the progeny. Generally, two approaches are available for creating gene stacks: nuclease-induced targeted gene integration into native sites and recombinase-mediated gene integration into the engineered sites.

Association analysis of salt tolerance in cowpea (Vigna unguiculata (L.) Walp) at germination and seedling stages.

This is the first report on association analysis of salt tolerance and identification of SNP markers associated with salt tolerance in cowpea. Cowpea (Vigna unguiculata (L.) Walp) is one of the most important cultivated legumes in Africa.

Effect of gene order in DNA constructs on gene expression upon integration into plant genome.

Several plant biotechnology applications are based on the expression of multiple genes located on a single transformation vector. The principles of stable expression of foreign genes in plant cells include integration of full-length gene fragments consisting of promoter and transcription terminator sequences, and avoiding converging orientation of the gene transcriptional direction. Therefore, investigators usually generate constructs in which genes are assembled in the same orientation.

Gene stacking in plant cell using recombinases for gene integration and nucleases for marker gene deletion.

Background: Practical approaches for multigene transformation and gene stacking are extremely important for engineering complex traits and adding new traits in transgenic crops. Trait deployment by gene stacking would greatly simplify downstream plant breeding and trait introgression into cultivars. Gene stacking into pre-determined genomic sites depends on mechanisms of targeted DNA integration and recycling of selectable marker genes.

Gene stacking by recombinases.

Efficient methods of stacking genes into plant genomes are needed to expedite transfer of multigenic traits to crop varieties of diverse ecosystems. Over two decades of research has identified several DNA recombinases that carryout efficient cis and trans recombination between the recombination sites artificially introduced into the plant chromosome. The specificity and efficiency of recombinases make them extremely attractive for genome engineering.

Simplifying transgene locus structure through Cre-lox recombination.

Transgene silencing is often associated with multicopy integrations, which occur frequently during plant transformation. Transgene expression can be restored in a number of multicopy loci by converting them to single copy. This chapter describes a plant transformation protocol based on use of the Cre-lox system, which allows conversion of a multicopy transgene locus into single copy.

Physiological and molecular basis of acetolactate synthase-inhibiting herbicide resistance in barnyardgrass (Echinochloa crus-galli).

Barnyardgrass biotypes from Arkansas (AR1 and AR2) and Mississippi (MS1) have evolved cross-resistance to imazamox, imazethapyr, and penoxsulam. Additionally, AR1 and MS1 have evolved cross-resistance to bispyribac-sodium. Studies were conducted to determine if resistance to acetolactate synthase (ALS)-inhibiting herbicides in these biotypes is target-site or non-target-site based.