Tong Geon Lee

Evolution of non-specific lipid transfer protein (nsLTP) genes in the Poaceae family: their duplication and diversity.

Previously, the genes encoding non-specific lipid transfer proteins (nsLTPs) of the Poaceae family appear to evidence different genomic distribution and somewhat different shares of EST clones, which is suggestive of independent duplication(s) followed by functional diversity. To further evaluate the evolutionary fate of the Poaceae nsLTP genes, we have identified Ka/Ks values, conserved, mutated or lost cis-regulatory elements, responses to several elicitors, genome-wide expression profiles, and nsLTP gene-coexpression networks of both (or either) wheat and rice. The Ka/Ks values within each group and between groups appeared to be similar, but not identical, in both species. The conserved cis-regulatory elements, e.g. the RY repeat (CATGCA) element related to ABA regulation in group A, might be reflected in some degree of long-term conservation in transcriptional regulation postdating speciation. In group A, wheat nsLTP genes, with the exception of TaLTP4, evidenced responses similar to those of plant elicitors; however, the rice nsLTP genes evidenced differences in expression profiles, even though the genes of both species have undergone purifying selection, thereby suggesting their independent functional diversity. The expression profiles of rice nsLTP genes with a microarray dataset of 155 gene expression omnibus sample (GSM) plates suggest that subfunctionalization is not the sole mechanism inherent to the evolutionary history of nsLTP genes but may, rather, function in concert with other mechanism(s). As inferred by the nsLTP gene-coexpression networks, the functional diversity of nsLTP genes appears not to be randomized, but rather to be specialized in the direction of specific biological processes over evolutionary time.

A genome-wide analysis of transcripts in a 2BS.2RL wheat-rye translocation during Hessian fly infestation

The Hessian fly [Mayetiola destructor (Say)] biotype L is the most damaging pest to wheat (Triticum aestivum L.). The long arm of rye chromosome 2 (2RL) has been transferred to common wheat, in the form of 2BS.2RL wheat-rye translocations. 2RL carries gene(s) for resistance to Hessian fly (biotype L), representing a promising target for engineered resistance. The objective of this study was to examine changes in gene expression in near-isogenic lines (NILs) differing by the presence (resistant NIL) or absence (susceptible NIL) of 2RL under Hessian fly infestation. Gene expression was detected using an Affymetrix 3′ IVT wheat genome array. Separate comparisons of data sets generated from the array were performed to identify transcripts involved in the defense pathways. Diverse resistant NIL-specific transcripts including ethylene-responsive factor-like transcription factors and zinc-finger proteins were discovered. Evidence of the enrichment of gene ontologies associated with hydrolase was found in resistant NIL during Hessian fly infestation. The gene information identified in this study would be an important resource in growing our understanding of the resistance mechanisms and for cloning candidate genes.

Employment of hordein subunit polymorphisms in establishing selection criteria for high quality malting barley (Hordeum vulgare L.)

Cereal seed storage proteins are encoded by complex multigene families and their subunit profiles are highly related to end-use qualities. Each fraction of albumin and hordein was extracted and its subunit profile was evaluated in related to malt and grain quality parameters. The purpose of this study was to provide selection criteria for high quality malting barley using grain and malt quality parameters and biochemical-genetic information. Grain and malt quality of 13 local adaptability test (LAT) lines were evaluated for malting process. A total of 16 germplasm accessions of high or low seed storage protein content were also evaluated for biochemicalgenetic analysis. The correlation coefficients among quality parameters were analyzed. Several important quality parameters in brewing process showed significant positive or negative correlations. Seed storage protein subunits of albumin and hordein of all tested lines and accessions were evaluated using 12% 1D SDS-PAGE. Scored data of protein subunit’s presence or absence was applied to Agglomerative Hierarchical Clustering (AHC) for statistical analysis and showed specific grouping patterns among tested lines. Clustered lines with subunit information were highly related with agricultural performance and grain and malt qualities. Based on the profiles of seed storage protein subunits, association of hordein subunit of 38, 43, and 65 kDa with high malt scored lines was found. The obtained results would provide improved selection criteria for high quality malting barley in the malting barley breeding program.

Expressed sequence tags from wheat roots under hypoxia

Hypoxia due to waterlogging adversely affects agricultural crops in many parts of the world and severely impacts overall annual production levels. To evaluate the response of wheat roots to a controlled hypoxic environment at the level of transcription, a cDNA library was constructed using hypoxia-stressed wheat. A total of 1274 clones (94.8%) out of 1344 sequences were found to be at least 50 bp long. Phrap assembly using high quality sequences formed 879 sets of non-overlapping sequences. Based on BLASTx analysis against the nonredundant database, a total of 494 unigenes showed a high homology to the registered amino acid sequences of plant (E < e−10). A total of 112 unigenes, which were not matched to any wheat ESTs in the database, were detected. A functional classification of 118 clones whose transcript levels were evaluated under hypoxia was performed according to gene ontology. These results may provide useful information for further investigations to better understand the response of wheat roots to waterlogging.

Comparison of proteomes between wheat-rye translocations and their recurrent parents

Abstract2BS.2RL wheat-rye translocations have presented phenotypes of improved agronomic performance, such as Hessian fly resistance. The main objective of this work was to use two-dimensional electrophoresis to identify the proteomic differences between 2BS.2RL wheat-rye translocations and their recurrent parents. The investigation of seeds revealed line-specific protein spots, such as α-amylase inhibitor 0.19. More diverse expression patterns were observed in leaves than in seeds. Protein spots found specifically in 2BS.2RL, but not in non-2RL translocations were identified as β-glucosidase and vacuolar ATP synthase subunit B2, demonstrating the effects of translocated rye chromatin 2RL on common wheat genetic background. When the leaf protein spots were compared in the control and Hessian fly-infested near-isogenic line (NIL) (2BS.2RL), many down-regulated proteins and specific proteins, such as β-glucosidase, were detected in the latter.

Identification of genome-specific transcripts in wheat–rye translocation lines

Studying gene expression in wheat–rye translocation lines is complicated due to the presence of homeologs in hexaploid wheat and high levels of synteny between wheat and rye genomes (Naranjo and Fernandez-Rueda, 1991 [1]; Devos et al., 1995 [2]; Lee et al., 2010 [3]; Lee et al., 2013 [4]). To overcome limitations of current gene expression studies on wheat–rye translocation lines and identify genome-specific transcripts, we developed a custom Roche NimbleGen Gene Expression microarray that contains probes derived from the sequence of hexaploid wheat, diploid rye and diploid progenitors of hexaploid wheat genome (Lee et al., 2014). Using the array developed, we identified genome-specific transcripts in a wheat–rye translocation line (Lee et al., 2014). Expression data are deposited in the NCBI Gene Expression Omnibus (GEO) under accession number GSE58678. Here we report the details of the methods used in the array workflow and data analysis.