Hwa-Young Heo

Genome comparisons reveal a dominant mechanism of chromosome number reduction in grasses and accelerated genome evolution in Triticeae

Single-nucleotide polymorphism was used in the construction of an expressed sequence tag map of Aegilops tauschii, the diploid source of the wheat D genome. Comparisons of the map with the rice and sorghum genome sequences revealed 50 inversions and translocations; 2, 8, and 40 were assigned respectively to the rice, sorghum, and Ae. tauschii lineages, showing greatly accelerated genome evolution in the large Triticeae genomes. The reduction of the basic chromosome number from 12 to 7 in the Triticeae has taken place by a process during which an entire chromosome is inserted by its telomeres into a break in the centromeric region of another chromosome. The original centromere–telomere polarity of the chromosome arms is maintained in the new chromosome. An intrachromosomal telomere–telomere fusion resulting in a pericentric translocation of a chromosome segment or an entire arm accompanied or preceded the chromosome insertion in some instances. Insertional dysploidy has been recorded in three grass subfamilies and appears to be the dominant mechanism of basic chromosome number reduction in grasses. A total of 64% and 66% of Ae. tauschii genes were syntenic with sorghum and rice genes, respectively. Synteny was reduced in the vicinity of the termini of modern Ae. tauschii chromosomes but not in the vicinity of the ancient termini embedded in the Ae. tauschii chromosomes, suggesting that the dependence of synteny erosion on gene location along the centromere–telomere axis either evolved recently in the Triticeae phylogenetic lineage or its evolution was recently accelerated.

Nucleotide diversity maps reveal variation in diversity among wheat genomes and chromosomes.

BackgroundA genome-wide assessment of nucleotide diversity in a polyploid species must minimize the inclusion of homoeologous sequences into diversity estimates and reliably allocate individual haplotypes into their respective genomes. The same requirements complicate the development and deployment of single nucleotide polymorphism (SNP) markers in polyploid species. We report here a strategy that satisfies these requirements and deploy it in the sequencing of genes in cultivated hexaploid wheat (Triticum aestivum, genomes AABBDD) and wild tetraploid wheat (Triticum turgidum ssp. dicoccoides, genomes AABB) from the putative site of wheat domestication in Turkey. Data are used to assess the distribution of diversity among and within wheat genomes and to develop a panel of SNP markers for polyploid wheat.ResultsNucleotide diversity was estimated in 2114 wheat genes and was similar between the A and B genomes and reduced in the D genome. Within a genome, diversity was diminished on some chromosomes. Low diversity was always accompanied by an excess of rare alleles. A total of 5,471 SNPs was discovered in 1791 wheat genes. Totals of 1,271, 1,218, and 2,203 SNPs were discovered in 488, 463, and 641 genes of wheat putative diploid ancestors, T. urartu, Aegilops speltoides, and Ae. tauschii, respectively. A public database containing genome-specific primers, SNPs, and other information was constructed. A total of 987 genes with nucleotide diversity estimated in one or more of the wheat genomes was placed on an Ae. tauschii genetic map, and the map was superimposed on wheat deletion-bin maps. The agreement between the maps was assessed.ConclusionsIn a young polyploid, exemplified by T. aestivum, ancestral species are the primary source of genetic diversity. Low effective recombination due to self-pollination and a genetic mechanism precluding homoeologous chromosome pairing during polyploid meiosis can lead to the loss of diversity from large chromosomal regions. The net effect of these factors in T. aestivum is large variation in diversity among genomes and chromosomes, which impacts the development of SNP markers and their practical utility. Accumulation of new mutations in older polyploid species, such as wild emmer, results in increased diversity and its more uniform distribution across the genome.

Large-scale proteome investigation in wild relatives (A, B, and D genomes) of wheat

Large-scale proteomics of three wild relatives of wheat grain (A, B, and D genomes) were analyzed by using multidimensional protein identification technology coupled to liquid chromatography quadruple mass spectrometry. A total of 1568 (peptide match ≥1) and 255 (peptide match ≥2) unique proteins were detected and classified, which represents the most wide-ranging proteomic exploitation to date. The development of standard proteomes exhibiting all of the proteins involved in normal physiology will facilitate the delineation of disease/defense, metabolism, energy metabolism, and protein synthesis. A relative proteome exploration of the expression patterns indicates that proteins are involved in abiotic and biotic stress. Functional category analysis indicates that these differentially expressed proteins are mainly involved in disease/defense (15.38%, 21.26%, and 16.78%), metabolism (8.39%, 12.07%, and 14.09%), energy metabolism (11.19%, 11.49%, and 13.42%), protein synthesis (9.09%, 9.20%, and 8.72%), cell growth and division (9.09%, 4.60%, and 6.04%), cellular organization (4.20%, 5.75%, and 5.37%), development (6.29%, 2.87%, 3.36%), folding and stability (6.29%, 8.62%, and 8.05%), signal transduction (11.19%, 7.47%, and 8.05%), storage protein (4.20%, 1.72%, and 2.01%), transcription (5.59%, 5.17%, and 4.03%), and transport facilitation (1.40%, 1.15%, and 3.36%) in A, B, and D genomes, respectively. Here, we reported genome-specific protein interaction network using Cytoscape software, which provides further insight into the molecular functions and mechanism of biochemical pathways. We provide a promising understanding about the expressed proteins and protein functions. Our approach should be applicable as a marker to assist in breeding or gene transfer for quality and stress research of cultivated wheat.

Diversity of Novel Glutenin Subunits in Bread Wheat (Triticum aestivum L.)

Glutenin is a major determinant of baking performance and viscoelasticity, which are responsible for high-quality bread with a light porous crumb structure of a well-leavened loaf. We analyzed the diversity of glutenin genes from six wheat cultivars (Korean cvs. Keumgang and Jinpum, Chinese cvs. China-108 and Yeonnon-78, and Japanese cvs. Norin-61 and Kantou-107). Glutenins contain two types of isoforms such as high molecular weight glutenin subunit (HMW-GS) and low molecular weight glutenin subunit (LMW-GS). Glutenin fractions were extracted from wheat endosperm using Osborne solubility method. A total of 217 protein spots were separated on two-dimensional gel electrophoresis with isoelectric focusing (wide range of pH 3–10). The proteins spots were subjected to tryptic digestion and identified by matrix assisted laser desorption/ionization–time of flight mass spectrometry. HMW-GS (43 isoforms) and LMW-GS (seven isoforms) are directly responsible for producing high-quality bread and noodles. Likewise, all the seed storage proteins are digested to provide nutrients for the embryo during seed germination and seedling growth. We identified the diverse glutenin subunits in wheat cultivars and compared the gluten isoforms among different wheat cultivars according to quality. This work gives an insight on the quality improvement in wheat crop.

Phenotypic and Haplotype Diversity among Tetraploid and Hexaploid Wheat Accessions with Potentially Novel Insect Resistance Genes for Wheat Stem Sawfly

Haplotype diversity underlying Qss.msub.3BL solid‐stem QTL present among solid‐stem wheat landraces. Frequency and diversity of haplotypes vary among ploidy levels and geographical regions. New haplotypes potentially containing novel resistance alleles will augment WSS resistance. KASP markers can be used for marker assisted selection of the solid‐stem Qss.msub.3BL allele.

Identification of QTL for Grain Protein Content and Grain Hardness from Winter Wheat for Genetic Improvement of Spring Wheat

To utilize the favorable gene(s) from winter wheat for genetic improvement of spring wheat, this study was carried out to identify the quantitative trait loci (QTL) associated with grain protein content (GPC) and grain hardness (GH) by analysis of recombinant inbred lines (RILS) derived from a cross between spring wheat and spring version of winter wheat. A genetic map of 334 loci was constructed which covered 1575.30cM on all 21 chromosomes. Two QTLs on 3B and 5B chromosome were detected for GPC. A QTL identified barc77 on chromosome 3B had additive effect of 0.17 and the other QTL identified by gwm499 on chromosome 5B had additive effect of 0.19. There were two major QTLs for GH identified on Chromosome 1B and chromosome 5A. The QTL on 1B was localized within a 18.7cM region flanked by wmc719 and wmc367-1 with 1.75 additive effect. The QTL on chromosome 5A flanked by SNP markers, IWA6573 and IWA2363, had additive effect of 1.44.

Influence of amylose content on cooking time and textural properties of white salted noodles

White salted noodles were prepared from reconstituted flours of various amylose content to determine the effects of amylose content on noodle dough properties and texture of noodles cooked for optimum cooking time. With decrease of amylose content from 26.5 to 3. 0%, optimum water absorption of noodle dough increased from 39 to 49% and cooking time of noodles decreased from 16 to 7 min. Hardness of cooked noodles prepared from reconstituted flour consistently decreased with increase in proportion of waxy starch. Noodles less than 12.4% amylose content exhibited higher springiness and cohesiveness than noodles greater than 17.1% amylose content. Cohesiveness and springiness of noodles prepared with partial waxy starches, of which amylose content ranged from 16. 6 to 22. 7%, were comparable to those of noodles prepared from <12. 4% amylose content. Amylose content of starch was significantly correlated with hardness, springiness, and cohesiveness of cooked noodles prepared from reconstituted flours.

Wild Relatives of the Wheat Grain Proteome

We applied proteomics analysis to generate a map of the wild relatives of wheat grain proteins. These differentially expressed proteins are potentially involved in metabolism, stress responses, and other biological activities. Using two-dimensional electrophoresis, we detected 119, 134, and 193 reproducible spots on gels loaded with protein samples extracted from the A, B, and D genomes, respectively, of the mature grain. In all, 89, 53, and 54 distinct proteins, respectively, were found among these genomes through MALDI-TOF mass spectrometry. Of these, 26% (n = 52) proteins were considered distinct. They included 18.89% (n = 17) in the A, 28.30% (n = 15) in the B, and 37.04% (n = 20) in the D genome, all functioning in disease and defense roles. For example, the ABA-inducible protein PHVA1 can be induced by drought, cold, heat, and salinity, while the basic endochitinase confers protection against chitin-containing fungal pathogens. The diverse functional categories found here suggest different biological processes, such as disease/defense, energy metabolism, protein synthesis and storage, cellular organization, signal transduction, transcription, and the facilitation of transport. Our findings demonstrate that these functional proteins have important roles in stress tolerance and the maintenance of quality in mature grains. The interacting effects of genetics and environment on differential protein production may be partially mediated by a regulatory mechanism in those grains.

Characteristics of yellow alkaline noodles prepared from Korean wheat cultivar

Physicochemical properties of Korean wheat flours were evaluated to determine the effect of flour characteristics on yellow alkaline noodles by comparing commercial and imported wheat flours. Optimum water absorption, thickness, and color of noodle dough significantly correlated with protein content-related parameters of flour. Korean waxy wheats showed shorter cooking time (8 min) and softer texture of cooked noodles than other Korean wheats. Cooking time significantly correlated with protein content, optimum water absorption, and thickness of noodle dough. Hardness of cooked noodles positively correlated with protein content (r=0.614, p<0.01) and protein content related parameters. Cohesiveness of cooked noodles positively correlated with SDS-sedimentation based on a constant protein weight (r=0.437, p<0.05). Several Korean wheat cultivars showed comparable noodle making properties to commercial flour for yellow alkaline noodles despite of dark noodle color. Wheat cvs. Baekjoong, Jeokjoong, and Ol had softer and more elastic texture than other Korean wheats.