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Featured researches published by I. Dweikat.


Theoretical and Applied Genetics | 2004

Comparative analysis of seeded and vegetative biotype buffalograsses based on phylogenetic relationship using ISSRs, SSRs, RAPDs, and SRAPs

H. Budak; Robert C. Shearman; I. Parmaksiz; I. Dweikat

Buffalograss [Buchloe dactyloides (Nutt.) Englem.] is the only native grass that is being used extensively as a turfgrass in the Great Plains region. Its low-growth habit, drought resistance, and low-maintenance requirement make it attractive as a turfgrass species. Our objective was to obtain an overview on the genetic relatedness among and within seeded and vegetative biotype buffalograsses using inter-simple sequence repeats (ISSRs), random amplified polymorphic DNA (RAPDs), sequence-related amplified polymorphisms (SRAPs), and simple sequence repeats (SSRs) markers that were derived from related species (maize, pearl millet, sorghum, and sugarcane). Twenty individuals per cultivar were genotyped using 30 markers from each marker system. All buffalograss cultivars were uniquely fingerprinted by all four marker systems. Mean genetic similarities were estimated at 0.52, 0.51, 0.62, and 0.57 using SSRs, ISSRs, SRAPs, and RAPDs, respectively. Two main clusters separating the seeded-biotype from the vegetative-biotype cultivars were produced using UPGMA analysis. Further subgroupings were unequivocal. The Mantel test resulted in a very good fit (SRAP=0.92, ISSR=0.90) to good fit (RAPD=0.86, SSR=0.88) of cophenetic values. Comparing the four marker systems to each other, RAPD and SRAP similarity indices were highly correlated (r=0.73), while Spearman’s rank correlation coefficient between RAPDs and SSRs was r=0.24 and between ISSRs and SSRs was r=0.66. A genotype-assignment analytical approach might be useful for cultivar identification and property rights protection. Polymorphic SRAPs were abundant and demonstrated genetic diversity among closely related cultivars.


Theoretical and Applied Genetics | 2004

Transferability of SSR markers among wheat, rye, and triticale

C. Kuleung; P. S. Baenziger; I. Dweikat

Abstract Simple sequence repeat (SSR) markers are a valuable tool for many purposes, such as mapping, fingerprinting, and breeding. However, they are only available in some economically important crops because of the high cost and labor intensity involved in their development. Comparative mapping reveals a high degree of colinearity between closely related species, which allows the exchange of markers between them. Our objective was to examine the transferability of SSR markers among wheat (Triticum aestivum L.), rye (Secale cereale L.), and triticale (X Triticosecale Wittmack). One hundred forty-eight wheat and 28 rye SSR markers were used to amplify genomic DNA extracted from five lines each of wheat, rye, and triticale. Transferability of wheat SSR markers to rye was 17%, whereas 25% of rye markers were amplifiable in wheat. In triticale, 58% and 39% transferability was achieved for wheat and rye markers, respectively. Wheat markers gave an average of 2.6, 2.7, and 2.4 polymorphic bands in wheat, rye, and triticale, respectively, while rye markers gave an average of 2.0 in rye and none in wheat and triticale. These transferable markers can now be exploited for further genetic and breeding studies in these species.


Theoretical and Applied Genetics | 2004

Molecular characterization of Buffalograss germplasm using sequence-related amplified polymorphism markers

H. Budak; Robert C. Shearman; I. Parmaksiz; R. E. Gaussoin; Terrance P. Riordan; I. Dweikat

Buffalograss [Buchloe dactyloides (Nutt.) Englem] germplasm has a broad resource of genetic diversity that can be used for turfgrass, forage and conservation. Buffalograss is the only native grass that is presently used as a turfgrass in the Great Plains region of North America. Its low growth habit, drought tolerance and reduced requirement for fertilizer and pesticides contribute to interest in its use. The objectives of this study were to use sequence-related amplified polymorphism (SRAP) markers in the evaluation of genetic diversity and phenetic relationships in a diverse collection of 53 buffalograss germplasms, and to identify buffalograss ploidy levels using flow cytometry. Based on their DNA contents, buffalograss genotypes were grouped into four sets, corresponding to their ploidy levels. Thirty-four SRAP primer combinations were used. This is the first report of the detection of differentiating diploid, tetraploid, pentaploid and hexaploid buffalograss genotypes, representing diverse locations of origin, using SRAP markers. Cluster analysis by the unweighted pair-group method with arithmetic averages based on genetic similarity matrices indicated that there were eight clusters. The coefficients of genetic distance among the genotypes ranged from 0.33 up to 0.99 and averaged D=0.66. The genetic diversity estimate, He, averaged 0.35. These results demonstrated that genotypes with potential traits for turfgrass improvement could readily be distinguished, based on SRAP. The use of PCR-based technologies such as SRAP is an effective tool for estimating genetic diversity, identifying unique genotypes as new sources of alleles for enhancing turf characteristics, and for analyzing the evolutionary and historical development of cultivars at the genomic level in a buffalograss breeding program.


Euphytica | 2005

Comparison of phenotypic and molecular marker-based classifications of hard red winter wheat cultivars

H. Fufa; P. S. Baenziger; B. S. Beecher; I. Dweikat; Robert A. Graybosch; Kent M. Eskridge

Genetic diversity is the basis for successful crop improvement and can be estimated by different methods. The objectives of this study were to estimate the genetic diversity of 30 ancestral to modern hard red winter wheat (Triticum aestivum L.) cultivars adapted to the Northern Great Plains using pedigree information, morphological traits (agronomic measurements from six environments), end-use quality traits (micro-quality assays on 50 g grain or milled flour samples for the six environments), and molecular markers (seed storage proteins separated using SDS-PAGE, 51 SSRs, and 23 SRAP DNA markers), and to determine the relationships of genetic distance estimates obtained from these methods. Relationships among diversity estimates were determined using simple (Pearson) and rank (Spearman) correlation coefficients between distance estimates and by clustering cultivars using genetic-distances for different traits. All methods found a wide range in genetic diversity. The genetic distance estimates based on pedigree had the highest values due to possible over-estimation arising from model assumptions. The genetic diversity estimates based on seed storage protein were lowest because they were the major determinants of end-use quality, which is a highly selected trait. In general, the diversity estimates from each of the methods were positively correlated at a low level with the exceptions of SRAP diversity estimates being independent of morphologic traits (simple correlation), SDS-PAGE, and SSR diversity estimates (rank correlation). However, SSR markers, thought to be among the most efficient markers for estimating genetic diversity, were most highly correlated with seed storage proteins. The procedures used to accurately estimate genetic diversity will depend largely upon the tools available to the researcher and their application to the breeding scheme.


Molecular Breeding | 2008

Assessment of genetic diversity and relationship among a collection of US sweet sorghum germplasm by SSR markers

M. L. Ali; J. F. Rajewski; P. S. Baenziger; Kulvinder S. Gill; Kent M. Eskridge; I. Dweikat

Sweet sorghum (Sorghum bicolor L.) is a type of cultivated sorghums and has been recognized widely as potential alternative source of bio-fuel because of its high fermentable sugar content in the stalk. A substantial variation of sugar content and related traits is known to exist in US sweet sorghum. The objectives of the study were to assess the genetic diversity and relationship among the US sweet sorghum cultivars and lines using SSR markers and to examine the genetic variability within sweet sorghum accessions for sugar content. Sixty-eight sweet sorghum and four grain sorghum cultivars and lines were genotyped with 41 SSR markers that generated 132 alleles with an average of 3.22 alleles per locus. Polymorphism information content (PIC) value, a measure of gene diversity, was 0.40 with a range of 0.03–0.87. The genetic similarity co-efficient was estimated based on the segregation of the 132 SSR alleles. Clustering analysis based on the genetic similarity (GS) grouped the 72 sorghum accessions into 10 distinct clusters. Grouping based on clustering analysis was in good agreement with available pedigree and genetic background information. The study has revealed the genetic relationship of cultivars with unknown parentage to those with known parentage. A number of diverse pairs of sweet sorghum accessions were identified which were polymorphic at many SSR loci and significantly different for sugar content as well. Information generated from this study can be used to select parents for hybrid development to maximize the sugar content and total biomass, and development of segregating populations to map genes controlling sugar content in sweet sorghum.


Plant Cell Reports | 2006

Rapid and reproducible Agrobacterium-mediated transformation of sorghum

Arlene R. Howe; Shirley Sato; I. Dweikat; Mike Fromm; Thomas E. Clemente

A rapid and reproducible Agrobacterium-mediated transformation protocol for sorghum has been developed. The protocol uses the nptII selectable marker gene with either of the aminoglycosides geneticin or paromomycin. A screen of various A. tumefaciens strains revealed that a novel C58 nopaline chromosomal background carrying the chrysanthopine disarmed Ti plasmid pTiKPSF2, designated NTL4/Chry5, was most efficient for gene transfer to sorghum immature embryos. A NTL4/Chry5 transconjugant harboring the pPTN290 binary plasmid, which carries nptII and GUSPlusTM expression cassettes, was used in a series of stable transformation experiments with Tx430 and C2-97 sorghum genotypes and approximately 80% of these transformation experiments resulted in the recovery of at least one transgenic event. The transformation frequencies among the successful experiments ranged from 0.3 to 4.5%, with the average transformation frequency being approximately 1% for both genotypes. Over 97% of the transgenic events were successfully established in the greenhouse and were fully fertile. Co-expression of GUSPlusTM occurred in 89% of the transgenic T0 events. Seed set for the primary transgenic plants ranged from 145 to 1400 seed/plant. Analysis of T1 progeny demonstrated transmission of the transgenes in a simple Mendelian fashion in the majority of events.


Plant Physiology | 2012

The Chloroplast Triggers Developmental Reprogramming When MUTS HOMOLOG1 Is Suppressed in Plants

Ying-Zhi Xu; Roberto De la Rosa Santamaria; Kamaldeep S. Virdi; Maria P. Arrieta-Montiel; Fareha Razvi; Shaoqing Li; Guodong Ren; Bin Yu; Danny Alexander; Lining Guo; Xuehui Feng; I. Dweikat; Thomas E. Clemente; Sally A. Mackenzie

Multicellular eukaryotes demonstrate nongenetic, heritable phenotypic versatility in their adaptation to environmental changes. This inclusive inheritance is composed of interacting epigenetic, maternal, and environmental factors. Yet-unidentified maternal effects can have a pronounced influence on plant phenotypic adaptation to changing environmental conditions. To explore the control of phenotypy in higher plants, we examined the effect of a single plant nuclear gene on the expression and transmission of phenotypic variability in Arabidopsis (Arabidopsis thaliana). MutS HOMOLOG1 (MSH1) is a plant-specific nuclear gene product that functions in both mitochondria and plastids to maintain genome stability. RNA interference suppression of the gene elicits strikingly similar programmed changes in plant growth pattern in six different plant species, changes subsequently heritable independent of the RNA interference transgene. The altered phenotypes reflect multiple pathways that are known to participate in adaptation, including altered phytohormone effects for dwarfed growth and reduced internode elongation, enhanced branching, reduced stomatal density, altered leaf morphology, delayed flowering, and extended juvenility, with conversion to perennial growth pattern in short days. Some of these effects are partially reversed with the application of gibberellic acid. Genetic hemicomplementation experiments show that this phenotypic plasticity derives from changes in chloroplast state. Our results suggest that suppression of MSH1, which occurs under several forms of abiotic stress, triggers a plastidial response process that involves nongenetic inheritance.


BMC Genomics | 2014

Identification of differentially expressed genes between sorghum genotypes with contrasting nitrogen stress tolerance by genome-wide transcriptional profiling.

Malleswari Gelli; Yongchao Duo; Anji Reddy Konda; Chi Zhang; David R. Holding; I. Dweikat

BackgroundSorghum is an important cereal crop, which requires large quantities of nitrogen fertilizer for achieving commercial yields. Identification of the genes responsible for low-N tolerance in sorghum will facilitate understanding of the molecular mechanisms of low-N tolerance, and also facilitate the genetic improvement of sorghum through marker-assisted selection or gene transformation. In this study we compared the transcriptomes of root tissues from seven sorghum genotypes having differential response to low-N stress.ResultsIllumina RNA-sequencing detected several common differentially expressed genes (DEGs) between four low-N tolerant sorghum genotypes (San Chi San, China17, KS78 and high-NUE bulk) and three sensitive genotypes (CK60, BTx623 and low-NUE bulk). In sensitive genotypes, N-stress increased the abundance of DEG transcripts associated with stress responses including oxidative stress and stimuli were abundant. The tolerant genotypes adapt to N deficiency by producing greater root mass for efficient uptake of nutrients. In tolerant genotypes, higher abundance of transcripts related to high affinity nitrate transporters (NRT2.2, NRT2.3, NRT2.5, and NRT2.6) and lysine histidine transporter 1 (LHT1), may suggest an improved uptake efficiency of inorganic and organic forms of nitrogen. Higher abundance of SEC14 cytosolic factor family protein transcript in tolerant genotypes could lead to increased membrane stability and tolerance to N-stress.ConclusionsComparison of transcriptomes between N-stress tolerant and sensitive genotypes revealed several common DEG transcripts. Some of these DEGs were evaluated further by comparing the transcriptomes of genotypes grown under full N. The DEG transcripts showed higher expression in tolerant genotypes could be used for transgenic over-expression in sensitive genotypes of sorghum and related crops for increased tolerance to N-stress, which results in increased nitrogen use efficiency for sustainable agriculture.


Plant Biotechnology Journal | 2012

Modulation of kernel storage proteins in grain sorghum( Sorghum bicolor (L.) Moench)

Tejinder Kumar; I. Dweikat; Shirley Sato; Zhengxiang Ge; Natalya Nersesian; Han Chen; Thomas E. Elthon; Scott R. Bean; Brian P. Ioerger; Mike Tilley; Thomas E. Clemente

Sorghum prolamins, termed kafirins, are categorized into subgroups α, β, and γ. The kafirins are co-translationally translocated to the endoplasmic reticulum (ER) where they are assembled into discrete protein bodies that tend to be poorly digestible with low functionality in food and feed applications. As a means to address the issues surrounding functionality and digestibility in sorghum, we employed a biotechnology approach that is designed to alter protein body structure, with the concomitant synthesis of a co-protein in the endosperm fraction of the grain. Wherein perturbation of protein body architecture may provide a route to impact digestibility by reducing disulphide bonds about the periphery of the body, while synthesis of a co-protein, with known functionality attributes, theoretically could impact structure of the protein body through direct association and/or augment end-use applications of sorghum flour by stabilizing ß-sheet formation of the kafirins in sorghum dough preparations. This in turn may improve viscoelasticity of sorghum dough. To this end, we report here on the molecular and phenotypic characterizations of transgenic sorghum events that are down-regulated in γ- and the 29-kDa α-kafirins and the expression of a wheat Dy10/Dx 5 hybrid high-molecular weight glutenin protein. The results demonstrate that down-regulation of γ-kafirin alone does not alter protein body formation or impacts protein digestibility of cooked flour samples. However, reduction in accumulation of a predicted 29-kDa α-kafirin alters the morphology of protein body and enhances protein digestibility in both raw and cooked samples.


Theoretical and Applied Genetics | 2009

Substoichiometric shifting in the fertility reversion of cytoplasmic male sterile pearl millet

X. Feng; A. P. Kaur; Sally A. Mackenzie; I. Dweikat

Cytoplasmic male sterility (CMS) represents an important agricultural trait in pearl millet [Pennisetum glaucum (L.) R. Br.] with a value to the seed industry in facilitating economical hybrid seed production. Among the CMS systems available in millet, the A1 source is the most commonly used for hybrid production, but it can undergo low frequency reversion to fertility. Plant mitochondrial genomes are highly recombinogenic, becoming unstable and prone to ectopic recombination under conditions of tissue culture, somatic hybridization, or interspecific crossing. Similarly, CMS systems prone to spontaneous fertility reversion experience sporadic mitochondrial genome instability. We compared mitochondrial genome configurations between the male-sterile A1 line and fertile revertants of pearl millet to develop a model for millet mitochondrial genome reorganization upon reversion. Relative copy number of a subgenomic molecule containing the CoxI-1-2 junction region, a component of the recombination process for reversion, is amplified tenfold following reversion, relative to the CMS A1 line. We propose that increased copy number of this molecule in a small number of cells or at low frequency triggers a recombination cascade, likely during reproductive development. The proposed recombination process initiates with ectopic recombination through a 7-bp repeat to produce a novel CoxI-3-2 junction molecule and an unstable recombination intermediate. Subsequent intra-molecular recombination stabilizes the intermediate to form a new copy of CoxI accompanied by a deletion. This study furthers the argument that substoichiometric shifting within the plant mitochondrial genome plays an important role in the evolution of the mitochondrial genome and plant reproductive dynamics.

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P. S. Baenziger

University of Nebraska–Lincoln

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Kent M. Eskridge

University of Nebraska–Lincoln

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Kulvinder S. Gill

Washington State University

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Thomas E. Clemente

University of Nebraska–Lincoln

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P. Stephen Baenziger

University of Nebraska–Lincoln

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Robert C. Shearman

University of Nebraska–Lincoln

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Shirley Sato

University of Nebraska–Lincoln

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J. F. Rajewski

University of Nebraska–Lincoln

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Chi Zhang

University of Nebraska–Lincoln

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David R. Holding

University of Nebraska–Lincoln

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