Cotton (Gossypium spp.) is the primary source of natural textile fiber in the U.S. and a major crop in the Southeastern U.S. Despite constant efforts to increase the cotton fiber yield, the yield gain has stagnated. Therefore, we undertook a novel approach to improve the cotton fiber yield by altering its growth habit from perennial to annual. In this effort, we identified genotypes with high-expression alleles of five floral induction and meristem identity genes (FT, SOC1, FUL, LFY, and AP1) from an Upland cotton mini-core collection and crossed them in various combinations to develop cotton lines with annual growth habit, optimal flowering time, and enhanced productivity. To facilitate the characterization of genotypes with the desired combinations of stacked alleles, we identified molecular markers associated with the gene expression traits via genome-wide association analysis using a 63 K SNP Array. Over 14,500 SNPs showed polymorphism and were used for association analysis. A total of 396 markers showed associations with expression traits. Of these 396 markers, 159 were mapped to genes, 50 to untranslated regions, and 187 to random genomic regions. Biased genomic distribution of associated markers was observed where more trait-associated markers mapped to the cotton D sub-genome. Many quantitative trait loci coincided at specific genomic regions. This observation has implications as these traits could be bred together. The analysis also allowed the identification of candidate regulators of the expression patterns of these floral induction and meristem identity genes whose functions will be validated.

Sensitivity to wheat and peanut proteins is widespread and is not restricted to geographical areas where wheat and peanuts are produced. It emphasizes the importance of these crops as a source of energy and proteins to populations globally. An uptick in the number of individuals diagnosed with celiac disease, an autoimmune disorder, and peanut allergy was observed in the last two decades. According to a recent estimate, ~1.4% of the world population is diagnosed with celiac disease, and ~2% of the Western population is diagnosed with peanut allergies. Unfortunately, there is no therapy available for these sensitivities other than an abstinent diet, with a need to maintain an immunogen-free environment to prevent sensitive individuals’ accidental exposure to the antigen. Given this knowledge, we focused our research on developing reduced-immunogenicity wheat and peanut genotypes that can significantly reduce the scope of severe reaction to accidental exposure to wheat/peanut proteins. Working in this direction, we undertook two approaches to develop reduced-immunogenicity wheat/peanut genotypes: (1) Use wheat/peanut germplasm screening for genotypes with reduced immunogen content, to crossbreed them to develop reduced to non-immunogenic wheat/peanut lines. (2) Use genetic engineering to silence genes encoding immunogenic proteins. To achieve the first objective, we screened wheat landraces/mutants and peanut-mini-core collections. Similarly, for gene silencing, RNA-interference constructs for the wheat DEMETER gene or guide RNAs from the wheat-gluten-gene sequences and the peanut Ara h1, Ara h2, Ara h3, and Ara h6 gene sequences were developed and assembled in single guide-RNA modules. The progress made towards the target is discussed below.

Soybean is the primary oilseed crop in the United States, with significant industrial value. Understanding the molecular mechanisms of heat stress tolerance in soybean plants is critical for developing stress-resistant cultivars. Current knowledge about the role of fatty acid desaturases (FADs) in modulating membrane fluidity under abiotic stress prompted this investigation into the impact of mutations in the FAD genes on seed germination from heat-stressed plants. In soybean plants, exposure to heat stress during anthesis is known to significantly reduce seed germination. In silico expression analysis indicated high expression levels of the soybean FAD2 and FAD3 genes in the leaves. Therefore, a detailed expression analysis of these genes was conducted using qRT-PCR from leaf tissue. Generally, downregulation of these genes was observed in the mutants; however, two genes, FAD3A and FAD2-3, showed a more than 2-fold increase in expression in six out of ten mutants under heat stress. This upregulation was particularly pronounced (7-fold) in the mutant S17CR-170. Correlation analysis revealed a positive correlation (up to 0.48) between the expression level of FAD3A, FAD3B, FAD3C, and FAD2-3 and the decline in germination from heat-stressed plants. This suggests these FAD genes may act as negative regulators of germination under heat stress conditions.

Soybean is the primary oilseed crop in the United States, with significant industrial value. Understanding the molecular mechanisms of heat stress tolerance in soybean is critical for developing stress-resistant cultivars. Current knowledge about the role of fatty acid desaturases (FADs) in modulating membrane fluidity under abiotic stress prompted this investigation into the impact of mutations in the FAD genes on seed germination from heat-stressed plants. In soybean, exposure to heat stress during anthesis is known to significantly reduce seed germination. In silico expression analysis indicated high levels of expression of the soybean FAD2 and FAD3 genes in leaves. Therefore, a detailed expression analysis of these genes was conducted using qRT-PCR from leaf tissue. Generally, downregulation of these genes was observed in the mutants; however, two genes, FAD3A and FAD2-3, showed a more than 2-fold increase in expression in six out of ten mutants under heat stress. This upregulation was particularly pronounced (7-fold) in mutant S17CR-170. Correlation analysis revealed a positive correlation (0.5) between the expression level of FAD3A, FAD3B, FAD3C, and FAD2-3 and the decline in germination from heat-stressed plants. This suggests these FAD genes may act as negative regulators of germination under heat stress conditions.