Genome-Wide Association Study to Identify Marker-Trait Associations for Seed Color in Colored Wheat (Triticum aestivum L.).

This study conducted phenotypic evaluations on a wheat F3 population derived from 155 F2 plants. Traits related to seed color, including chlorophyll a, chlorophyll b, carotenoid, anthocyanin, L*, a*, and b*, were assessed, revealing highly significant correlations among various traits. Genotyping using 81,587 SNP markers resulted in 3969 high-quality markers, revealing a genome-wide distribution with varying densities across chromosomes. A genome-wide association study using fixed and random model circulating probability unification (FarmCPU) and Bayesian-information and linkage-disequilibrium iteratively nested keyway (BLINK) identified 11 significant marker-trait associations (MTAs) associated with L*, a*, and b*, and chromosomal distribution patterns revealed predominant locations on chromosomes 2A, 2B, and 4B. A comprehensive annotation uncovered 69 genes within the genomic vicinity of each MTA, providing potential functional insights. Gene expression analysis during seed development identified greater than 2-fold increases or decreases in expression in colored wheat for 16 of 69 genes. Among these, eight genes, including transcription factors and genes related to flavonoid and ubiquitination pathways, exhibited distinct expression patterns during seed development, providing further approaches for exploring seed coloration. This comprehensive exploration expands our understanding of the genetic basis of seed color and paves the way for informed discussions on the molecular intricacies contributing to this phenotypic trait.

Identification and transcriptomic profiling of salinity stress response genes in colored wheat mutant.

Background: Salinity is a major abiotic stress that prevents normal plant growth and development, ultimately reducing crop productivity. This study investigated the effects of salinity stress on two wheat lines: PL1 (wild type) and PL6 (mutant line generated through gamma irradiation of PL1). Results: The salinity treatment was carried out with a solution consisting of a total volume of 200 mL containing 150 mM NaCl. Salinity stress negatively impacted germination and plant growth in both lines, but PL6 exhibited higher tolerance. PL6 showed lower Na+ accumulation and higher K+ levels, indicating better ion homeostasis. Genome-wide transcriptomic analysis revealed distinct gene expression patterns between PL1 and PL6 under salt stress, resulting in notable phenotypic differences. Gene ontology analysis revealed positive correlations between salt stress and defense response, glutathione metabolism, peroxidase activity, and reactive oxygen species metabolic processes, highlighting the importance of antioxidant activities in salt tolerance. Additionally, hormone-related genes, transcription factors, and protein kinases showed differential expression, suggesting their roles in the differential salt stress response. Enrichment of pathways related to flavonoid biosynthesis and secondary metabolite biosynthesis in PL6 may contribute to its enhanced antioxidant activities. Furthermore, differentially expressed genes associated with the circadian clock system, cytoskeleton organization, and cell wall organization shed light on the plant's response to salt stress. Conclusions: Understanding these mechanisms is crucial for developing stress-tolerant crop varieties, improving agricultural practices, and breeding salt-resistant crops to enhance global food production and address food security challenges.

Unveiling differential expression profiles of the wheat DOG1 gene family and functional analysis of the association between TaDOG1-1 and heat stress tolerance in transgenic Arabidopsis.

High temperatures can significantly impact wheat growth and grain yields during the grain-filling stage. In this study, we identified genes that respond to high-temperature stress during the grain-filling stage. We also identified and characterized 24 novel genes of the DOG1 gene family in hexaploid wheat. Motif analysis and conserved domain search revealed substantial similarities among TaDOG1 family members. Phylogenetic analysis demonstrated the evolutionary conservation of the TaDOG1 family across various plant species. Tissue-specific expression profiling indicated consistent patterns, with TaDOG1 genes predominantly expressed in stem tissues. Only TaDOG1-1 exhibited enhanced expression, particularly during hard dough and ripening stages. TaDOG1-1 and TaDOG1-7 exhibited increased expression under heat stress during the grain-filling stage, indicating their heat-responsive nature. Cis-element analysis revealed potential regulatory motifs, suggesting the involvement of TaDOG1-1 and TaDOG1-7 in stress tolerance mechanisms. Yeast two-hybrid screening revealed interacting proteins, including stress-responsive and grain development-associated proteins. To understand the biological function, we overexpressed TaDOG1-1 in Arabidopsis plants and observed enhanced thermotolerance under basal heat stress. Under heat stress, the transgenic plants exhibited increased biomass and elevated expression levels of heat-responsive genes. Furthermore, TaDOG1-1-overexpressing plants showed improved survival rates under soil heat stress, along with a greater accumulation of antioxidant enzymes in leaves. In this study, the identification and functions of the DOG1 gene family provide valuable insights for developing genetic engineering strategies aimed at improving wheat yield under high-temperature stress.

Oat AsDA1-2D enhances heat stress tolerance and negatively regulates seed-storage globulin.

The importance of oats has increased because of their high nutritional value and health benefits in the human diet. High-temperature stress during the reproductive growth period has a detrimental effect on grain morphology by changing the structure and concentration of several seed-storage proteins. DA1, a conserved ubiquitin-proteasome pathway component, plays an important role in regulating grain size by controlling cell proliferation in maternal integuments during the grain-filling stage. However, there have been no reports or studies on oat DA1 genes. In this study, we identified three DA1-like genes (AsDA1-2D, AsDA1-5A, and AsDA1-1D) using genome-wide analysis. Among these, AsDA1-2D was found to be responsible for high-temperature stress tolerance via a yeast thermotolerance assay. The physical interaction of AsDA1-2D with oat-storage-globulin (AsGL-4D) and a protease inhibitor (AsPI-4D) was observed using yeast two-hybrid screening. A subcellular localization assay revealed that AsDA1-2D and its interacting proteins are localized in the cytosol and plasma membrane. An in vitro pull-down assay showed that AsDA1-2D forms a complex with both AsPI-4D and AsGL-4D. An in vitro cell-free degradation assay showed that AsGL-4D was degraded by AsDA1-2D under high-temperature conditions and that AsPI-4D inhibited the function of AsDA1-2D. These results suggest that AsDA1-2D acts as a cysteine protease and negatively regulates oat-grain-storage-globulin under heat stress.

Molecular characterization of wheat floret development-related F-box protein (TaF-box2): Possible involvement in regulation of Arabidopsis flowering.

In wheat (Triticum aestivum L.), the floret development stage is an important step in determining grain yield per spike; however, the molecular mechanisms underlying floret development remain unclear. In this study, we elucidated the role of TaF-box2, a member of the F-box-containing E3 ubiquitin protein ligases, which is involved in floret development and anthesis of wheat. TaF-box2 was transiently expressed in the plasma membrane and cytoplasm of both tobacco and wheat. We also found that the SCFF-box2 (Skp1-Cul1-Rbx1-TaF-box2) ubiquitin ligase complex mediated self-ubiquitination activity. Transgenic Arabidopsis plants that constitutively overexpressed TaF-box2 showed markedly greater hypocotyl and root length than wild-type plants, and produced early flowering phenotypes. Flowering-related genes were significantly upregulated in TaF-box2-overexpressing Arabidopsis plants. Further protein interaction analyses such as yeast two-hybrid, in vitro pull-down, and bimolecular fluorescence complementation assays confirmed that TaF-box2 physically interacted with TaCYCL1 (Triticum aestivum cyclin-L1-1). Ubiquitination and degradation assays demonstrated that TaCYCL1 was ubiquitinated by SCFF-box2 and degraded through the 26S proteasome complex. The physiological functions of the TaF-box2 protein remain unclear; however, we discuss several potential routes of involvement in various physiological mechanisms which counteract flowering in transgenic Arabidopsis plants.

Wheat (Triticum aestivum L.) TaHMW1D Transcript Variants Are Highly Expressed in Response to Heat Stress and in Grains Located in Distal Part of the Spike.

High-temperature stress during the grain filling stage has a deleterious effect on grain yield and end-use quality. Plants undergo various transcriptional events of protein complexity as defensive responses to various stressors. The "Keumgang" wheat cultivar was subjected to high-temperature stress for 6 and 10 days beginning 9 days after anthesis, then two-dimensional gel electrophoresis (2DE) and peptide analyses were performed. Spots showing decreased contents in stressed plants were shown to have strong similarities with a high-molecular glutenin gene, TraesCS1D02G317301 (TaHMW1D). QRT-PCR results confirmed that TaHMW1D was expressed in its full form and in the form of four different transcript variants. These events always occurred between repetitive regions at specific deletion sites (5'-CAA (Glutamine) GG/TG (Glycine) or (Valine)-3', 5'-GGG (Glycine) CAA (Glutamine) -3') in an exonic region. Heat stress led to a significant increase in the expression of the transcript variants. This was most evident in the distal parts of the spike. Considering the importance of high-molecular weight glutenin subunits of seed storage proteins, stressed plants might choose shorter polypeptides while retaining glutenin function, thus maintaining the expression of glutenin motifs and conserved sites.