Hikmet Budak

Arizona Western College

Introduction Wheat stem sawfly (WSS), Cephus cinctus Norton, is a major pest of common bread wheat (Triticum aestivum L.) and other cultivated cereals in North America. Planting of cultivars with solid stems has been the primary management strategy to prevent yield loss due to WSS infestation, however expression of this phenotype can vary depending...

This century is facing huge challenges such as climate change, water shortage, malnutrition, and food safety and security across the world. These challenges can only be addressed by (i) the deliberate application and utilization of cutting-edge technologies and (ii) combining/using interdisciplinary, multidisciplinary, and even transdisciplinary to...

Powdery mildew (PM), caused by the fungus, Blumeria graminis tritici is a devastating and notorious disease that is prevalent across the globe and causes up to 62% of yield losses in wheat. The well-known 68 PM resistance loci (Pm1 - Pm68) are not long-lasting and break down when new races of pathogens interact with host plants. The editing of thre...

Long noncoding RNAs (lncRNAs) are a diverse class of noncoding RNAs that are typically longer than 200 nucleotides but lack coding potentials. Advances in deep sequencing technologies enabled a better exploration of this type of noncoding transcripts. The poor sequence conservation, however, complicates the identification and annotation of lncRNAs...

Sulforaphane (SFN) is an isothiocyanate-type phytomolecule present in crucifers, which is mainly synthesized in response to biotic stress. In animals, SFN incorporated in the diet has anticancer properties among others. The mechanism of action and signaling are well described in animals; however, little is known in plants. The goal in the present s...

Recent technological advances in next-generation sequencing (NGS) technologies have dramatically reduced the cost of DNA sequencing, allowing species with large and complex genomes to be sequenced. Although bread wheat (Triticum aestivum L.) is one of the world’s most important food crops, efficient exploitation of molecular marker-assisted breedin...

Background G-quadruplexes (G4s), formed within guanine-rich nucleic acids, are secondary structures involved in important biological processes. Although every G4 motif has the potential to form a stable G4 structure, not every G4 motif would, and accurate energy-based methods are needed to assess their structural stability. Here, we present a decis...

High-yielding crop varieties will become critical in meeting the future food demand in the face of worsening weather extremes and threatening biotic stressors. The bread wheat cultivar Sonmez-2001 is a registered variety that is notable for its performance under low-irrigation conditions, which further improves upon irrigation. Additionally, Sonmez...

MADS-box gene family members play multifarious roles in regulating the growth and development of crop plants and hold enormous promise for bolstering grain yield potential under changing global environments. Bread wheat (Triticum aestivum L.) is a key stable food crop around the globe. Until now, the available information concerning MADS-box genes...

Objectives High-yielding crop varieties will become critical in meeting the future food demand in the face of worsening weather extremes and threatening biotic stressors. Bread wheat cultivar Sonmez-2001 is a registered variety that is notable for its performance under low irrigation conditions, which further improves upon irrigation. In order to e...

Food insecurity and malnutrition have reached critical levels with increased human population, climate fluctuations, water shortage; therefore, higher-yielding crops are in the spotlight of numerous studies. Abiotic factors affect the yield of staple food crops; among all, wheat stem sawfly (Cephus cinctus Norton) and orange wheat blossom midge (Si...

The highly challenging hexaploid wheat (Triticum aestivum) genome is becoming ever more accessible due to the continued development of multiple reference genomes, a factor which aids in the plight to better understand variation in important traits. Although the process of variant calling is relatively straightforward, selection of the best combinat...

- Online conference (Microsoft team) - Link: http://www.aun.edu.eg/faculty_agriculture/MGBS/index.php - Free attendance

Aegilops tauschii is the donor of the D subgenome of hexaploid wheat and an important genetic resource. The reference-quality genome sequence Aet v4.0 for Ae. tauschii acc. AL8/78 was therefore an important milestone for wheat biology and breeding. Further advances in sequencing acc. AL8/78 and release of the Aet v5.0 sequence assembly are reported...

The incredible success of crop breeding and agricultural innovation in the last century greatly contributed to the Green Revolution, which significantly increased yields and ensures food security, despite the population explosion. However, new challenges such as rapid climate change, deteriorating soil, and the accumulation of pollutants require mu...

Genome editing can be used to create new wheat varieties with enhanced performance. Clustered regularly interspaced short palindromic repeat (CRISPR) is a powerful tool for knockout generation, precise modification, multiplex engineering, and the activation and repression of target genes. Targeted mutagenesis via RNA-guided genome editing using typ...

Beyond the most crucial roles of RNA molecules as a messenger, ribosomal, and transfer RNAs, the regulatory role of many non-coding RNAs (ncRNAs) in plant biology has been recognized. ncRNAs act as riboregulators by recognizing specific nucleic acid targets through homologous sequence interactions to regulate plant growth, development, and stress r...

Pan-genomes are efficient tools for the identification of conserved and varying genomic sequences within lineages of a species. Investigating genetic variations might lead to the discovery of genes present in a subset of lineages, which might contribute into beneficial agronomic traits such as stress resistance or yield. The content of varying geno...

G-quadruplexes (G4s) are four-stranded nucleic acid structures with closely spaced guanine bases forming square planar G-quartets. Aberrant formation of G4 structures has been associated with genomic instability. However, most plant species are lacking comprehensive studies of G4 motifs. In this study, genome-wide identification of G4 motifs in bar...

Rye ( Secale cereale L.) is an exceptionally climate-resilient cereal crop, used extensively to produce improved wheat varieties via introgressive hybridization and possessing the entire repertoire of genes necessary to enable hybrid breeding. Rye is allogamous and only recently domesticated, thus giving cultivated ryes access to a diverse and expl...

Since it was first recognized in bacteria as a mechanism for innate viral immunity in the early 2010s, CRISPR/Cas has rapidly been developed into a robust, multifunctional genome editing tool with many uses. Following the discovery of the initial CRISPR/Cas-based system, the technology has been advanced to facilitate a multitude of different functi...

Recent technological advances in next-generation sequencing (NGS) technologies have dramatically reduced the cost of DNA sequencing, allowing species with large and complex genomes to be sequenced. Although bread wheat ( Triticum aestivum L.) is one of the world's most important food crops, until very recently efficient exploitation of molecular ma...

Following the elucidation of the critical roles they play in numerous important biological processes, long noncoding RNAs (lncRNAs) have gained vast attention in recent years. Manual annotation of lncRNAs is restricted by known gene annotations and is prone to false prediction due to the incompleteness of available data. However, with the advent of...

In 2008, we published the first set of guidelines for standardizing research in autophagy. Since then, this topic has received increasing attention, and many scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Thus, it is important to formulate on a regular basis updated guidelines for monit...

In 2008, we published the first set of guidelines for standardizing research in autophagy. Since then, this topic has received increasing attention, and many scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Thus, it is important to formulate on a regular basis updated guidelines for monit...

the PDF can be download freely on pubmed. https://pubmed.ncbi.nlm.nih.gov/33634751/

In 2008, we published the first set of guidelines for standardizing research in autophagy. Since then, this topic has received increasing attention, and many scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Thus, it is important to formulate on a regular basis updated guidelines for monit...

In 2008, we published the first set of guidelines for standardizing research in autophagy. Since then, this topic has received increasing attention, and many scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Thus, it is important to formulate on a regular basis updated guidelines for monit...

Genetic diversity is key to crop improvement. Owing to pervasive genomic structural variation, a single reference genome assembly cannot capture the full complement of sequence diversity of a crop species (known as the ‘pan-genome’1). Multiple high-quality sequence assemblies are an indispensable component of a pan-genome infrastructure. Barley (Ho...

Advances in genomics have expedited the improvement of several agriculturally important crops but similar efforts in wheat (Triticum spp.) have been more challenging. This is largely owing to the size and complexity of the wheat genome¹, and the lack of genome-assembly data for multiple wheat lines2,3. Here we generated ten chromosome pseudomolecul...

MADS-box gene family members play multifarious roles in regulating the growth and development of crop plants and hold enormous promise for bolstering grain yield potential under changing global environments. Bread wheat (Triticum aestivum L.) is a key stable food crop around the globe. Until now, the available information concerning MADS-box genes...

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Barley and wheat are the most important temperate cereal crops of the Triticeae. Although they ranked in terms of world production, fourth (barley 141 million tons (MT)) and second (wheat 749 MT), according to FAO (FAO, 2018), their large genomes prevented to be fully sequenced until recently. Nevertheless, advances in development of new high-throu...

Background: Photoperiod signals provide important cues by which plants regulate their growth and development in response to predictable seasonal changes. Phytochromes, a family of red and far-red light receptors, play critical roles in regulating flowering time in response to changing photoperiods. A previous study showed that loss-of-function mut...

Background Photoperiod signals provide important cues by which plants regulate their growth and development in response to predictable seasonal changes. Phytochromes, a family of red and far-red light receptors, play critical roles in regulating flowering time in response to changing photoperiods. A previous study showed that loss-of-function mutat...

The discovery of non-coding RNAs (ncRNAs), and the subsequent elucidation of their functional roles, was largely delayed due to the misidentification of non-protein-coding parts of DNA as “junk DNA,” which forced ncRNAs into the shadows of their protein-coding counterparts. However, over the past decade, insight into the important regulatory roles...

Wheat is an important staple crop cultivated throughout the world. It has a complex genome with multiple copies of a gene. Due to the growing world population and increasing food demand, it is the need of time to increase the production capability of wheat crop. Apart from that climate change with sudden floods and drought conditions, serious atten...

Research Topic Use of Barley and Wheat Reference Sequences: Downstream Applications in Breeding, Gene Isolation, GWAS and Evolution

Gene silencing exists in eukaryotic organisms as a conserved regulation of the gene expression mechanism. In general, small RNAs (sRNAs) are produced within the eukaryotic cells and incorporated into an RNA‐induced silencing complex (RISC) within cells. However, exogenous sRNAs, once delivered into cells, can also silence target genes via the same...

Tör, M., Bilir, Ozlem, Telli, Osman, John, Simon, Norman, Chris, Budak, H. and Hong, Yiguo (2019) Silencing Genes in Arabidopsis Downy Mildew Using Exogenously Applied Small RNAs. In: IS-MPMI XVIII Congress Annual Meeting, 14th - 16th July 2019, Glasgow, Scotland. (Unpublished) The interaction between Arabidopsis thaliana and diploid biotrophic oo...

In this report, we describe the selection of ssDNA aptamers targeting Fibroblast Growth Factor Receptor Binding Protein 3 K650E, which has roles in cell division, growth, and differentiation through the kinase cascade. The selection process was based on the label-free, real-time monitoring of binding interactions by surface plasmon resonance, allow...

The domestication of wild emmer wheat led to the selection of modern durum wheat, grown mainly for pasta production. We describe the 10.45 gigabase (Gb) assembly of the genome of durum wheat cultivar Svevo. The assembly enabled genome-wide genetic diversity analyses revealing the changes imposed by thousands of years of empirical selection and bree...

Wheat can adapt to most agricultural conditions across temperate regions. This success is the result of phenotypic plasticity conferred by a large and complex genome composed of three homoeologous genomes (A, B, and D). Although drought is a major cause of yield and quality loss in wheat, the adaptive mechanisms and gene networks underlying drought...

Background Whole genome shotgun re-sequencing of wheat is expensive because of its large, repetitive genome. Moreover, sequence data can fail to map uniquely to the reference genome making it difficult to unambiguously assign variation. Re-sequencing using target capture enables sequencing of large numbers of individuals at high coverage to reliabl...

To elucidate dynamic developmental processes in plants, live tissues and organs must be visualised frequently and for extended periods. The development of roots is studied at a cellular resolution not only to comprehend the basic processes fundamental to maintenance and pattern formation but also study stress tolerance adaptation in plants. Despite...

Figure S1 Sequences from chromosome assemblies associated with conserved and non‐conserved genes.

Figure S4 Numbers of putative miRNA families identified in chromosome assemblies.

Figure S5 Putative tRNA genes identified from repeat‐masked (top panel) and unmasked (bottom panel) chromosome assemblies.

Figure S6. A schematic representation of BTR alleles identified in the Zavitan genome and our chromosome assemblies.

Figure S7 Proposed model for autophagy induction in response to stress and developmental regulations.

Data S1 Selected agronomically important genes covered by chromosome assemblies.

Figure S2 Syntenic relationships between T. dicoccoides and related grasses Brachypodium (Bd), rice (Os) and sorghum (Sb).

Figure S3 Overview of the structural genome comparison between tetraploid wild wheat Zavitan and hexaploid bread wheat cv. Chinese Spring, aided by chromosome assemblies.

Table S5 Overview of annotated ATG proteins from tetraploid and hexaploid wheat.

Table S6 Simple Sequence Repeats (SSRs) and TE junctions found in chromosome assemblies that contain coding regions for selected agronomically important traits.

Table S2 Summary of the single nucleotide polymorphisms and small InDels between T. dicoccoides survey sequences and pseudomolecules from cv. Zavitan.

Table S4 lncRNAs commonly mapping to chromosome assemblies, in addition to Zavitan and T. aestivum genomes. Potential lncRNA‐miRNA interactions are also included.