Hikmet Budak received his Ph.D. degree from the University of Nebraska-Lincoln, USA, in 2002. He worked as a Coordinator, and led buffalograss genetics and breeding program at the same university, then returned to Turkey in 2004. In 2016, he returned to Montana State University, USA as Endowed Chair. He is currently working as a Chief Science Officer at Montana BioAg. Inc., USA. He also serves as and Adjunct Professor at the University of Nebraska-Lincoln, USA. Address: MT, USA
The complete reference genome of wheat was released in 2018 (IWGSC in Science 361:eaar7191, 2018)... more The complete reference genome of wheat was released in 2018 (IWGSC in Science 361:eaar7191, 2018), and since then many wheats genomic resources have been developed in a short period of time. These resources include resequencing of several hundred wheat varieties, exome capture from thousands of wheat germplasm lines, large-scale RNAseq studies, and complete genome sequences with de novo assemblies of 17 important cultivars. These genomic resources provide impetus for accelerated gene discovery and manipulation of genes for genetic improvement in wheat. The groundwork for this prospect includes the discovery of more than 200 genes using classical gene mapping techniques and comparative genomics approaches to explain moderate to major phenotypic variations in wheat. Similarly, QTL repositories are available in wheat which are frequently used by wheat genetics researchers and breeding communities for reference. The current wheat genome annotation is currently lagging in pinpointing the...
Plant and Animal Genome XXII Conference, Jan 13, 2014
ABSTRACT In this study, we aimed to introgress drought related genomic regions identified in two ... more ABSTRACT In this study, we aimed to introgress drought related genomic regions identified in two South Australian cultivars into five European elite cultivars. We performed all different possible combinations of crosses. We confirmed the successful introgression of the drought related key regions in seven F1 plants using linked SSR markers. These plants were backcrossed three times until BC3F2, which will be extensively characterized for their yield components and water use efficiency under water limited conditions. With this research, we aim to develop bread wheat cultivars with high field performance in drought prone environments. Keywords : drought, wheat, T. aestivum, drought tolerance, breeding, QTL , wheat improvement
MicroRNAs, small regulatory molecules with significant impacts on the transcriptional network of ... more MicroRNAs, small regulatory molecules with significant impacts on the transcriptional network of all living organisms, have been the focus of several studies conducted mostly on modern wheat cultivars. In this study, we investigated miRNA repertoires of modern durum wheat and its wild relatives, with differing degrees of drought tolerance, to identify miRNA candidates and their targets involved in drought stress response. Root transcriptomes of Triticum turgidum ssp. durum variety Kızıltan and two Triticum turgidum ssp. dicoccoides genotypes TR39477 and TTD-22 under control and drought conditions were assembled from individual RNA-Seq reads and used for in silico identification of miRNAs. A total of 66 miRNAs were identified from all species, across all conditions, of which 46 and 38 of the miRNAs identified from modern durum wheat and wild genotypes, respectively, had not been previously reported. Genotype- and/or stress-specific miRNAs provide insights into our understanding of the complex drought response. Particularly, miR1435, miR5024, and miR7714, identified only from drought-stress roots of drought-tolerant genotype TR39477, can be candidates for future studies to explore and exploit the drought response to develop tolerant varieties.
MADS-box gene family members play multifarious roles in regulating the growth and development of ... more 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 in the wheat genome has been insufficient. Here, a comprehensive genome-wide analysis identified 300 high confidence MADS-box genes from the publicly available reference genome of wheat. Comparative phylogenetic analyses with Arabidopsis and rice MADS-box genes classified the wheat genes into 16 distinct subfamilies. Gene duplications were mainly identified in subfamilies containing unbalanced homeologs, pointing towards a potential mechanism for gene family expansion. Moreover, a more rapid evolution was inferred for M-type genes, as compared with MIKC-type genes, indicating their significance in understanding the evolutionary history of ...
Objectives High-yielding crop varieties will become critical in meeting the future food demand in... more 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 explore and exploit the genomic potential of this elite variety, in 2015, we sequenced the modern elite cultivar Sonmez genome which represents a diverse genetic background. Data description Here, we provide a reference-guided whole genome sequence of Sonmez-2001, assembled into 21 chromosomes of the A, B and D genomes and totaling to 13.3 gigabase-pairs in length. Additionally, a de novo assembly, of an additional 1.05 gigabase-pairs, was generated that represents either Sonmez-specific sequences or sequences that considerably diverged between Sonmez and Chinese Spring. We identified up to 24 million sequence variants, of which up to 2.4% ...
Three subfamilies of grasses, the Erhardtoideae (rice), the Panicoideae (maize, sorghum, sugar ca... more Three subfamilies of grasses, the Erhardtoideae (rice), the Panicoideae (maize, sorghum, sugar cane and millet), and the Pooideae (wheat, barley and cool season forage grasses) provide the basis of human nutrition and are poised to become major sources of renewable energy. Here we describe the complete genome sequence of the wild grass Brachypodium distachyon (Brachypodium), the first member of the Pooideae subfamily to be completely sequenced. Comparison of the Brachypodium, rice and sorghum genomes reveals a precise sequence- based history of genome evolution across a broad diversity of the grass family and identifies nested insertions of whole chromosomes into centromeric regions as a predominant mechanism driving chromosome evolution in the grasses. The relatively compact genome of Brachypodium is maintained by a balance of retroelement replication and loss. The complete genome sequence of Brachypodium, coupled to its exceptional promise as a model system for grass research, wil...
The complete reference genome of wheat was released in 2018 (IWGSC in Science 361:eaar7191, 2018)... more The complete reference genome of wheat was released in 2018 (IWGSC in Science 361:eaar7191, 2018), and since then many wheats genomic resources have been developed in a short period of time. These resources include resequencing of several hundred wheat varieties, exome capture from thousands of wheat germplasm lines, large-scale RNAseq studies, and complete genome sequences with de novo assemblies of 17 important cultivars. These genomic resources provide impetus for accelerated gene discovery and manipulation of genes for genetic improvement in wheat. The groundwork for this prospect includes the discovery of more than 200 genes using classical gene mapping techniques and comparative genomics approaches to explain moderate to major phenotypic variations in wheat. Similarly, QTL repositories are available in wheat which are frequently used by wheat genetics researchers and breeding communities for reference. The current wheat genome annotation is currently lagging in pinpointing the...
Plant and Animal Genome XXII Conference, Jan 13, 2014
ABSTRACT In this study, we aimed to introgress drought related genomic regions identified in two ... more ABSTRACT In this study, we aimed to introgress drought related genomic regions identified in two South Australian cultivars into five European elite cultivars. We performed all different possible combinations of crosses. We confirmed the successful introgression of the drought related key regions in seven F1 plants using linked SSR markers. These plants were backcrossed three times until BC3F2, which will be extensively characterized for their yield components and water use efficiency under water limited conditions. With this research, we aim to develop bread wheat cultivars with high field performance in drought prone environments. Keywords : drought, wheat, T. aestivum, drought tolerance, breeding, QTL , wheat improvement
MicroRNAs, small regulatory molecules with significant impacts on the transcriptional network of ... more MicroRNAs, small regulatory molecules with significant impacts on the transcriptional network of all living organisms, have been the focus of several studies conducted mostly on modern wheat cultivars. In this study, we investigated miRNA repertoires of modern durum wheat and its wild relatives, with differing degrees of drought tolerance, to identify miRNA candidates and their targets involved in drought stress response. Root transcriptomes of Triticum turgidum ssp. durum variety Kızıltan and two Triticum turgidum ssp. dicoccoides genotypes TR39477 and TTD-22 under control and drought conditions were assembled from individual RNA-Seq reads and used for in silico identification of miRNAs. A total of 66 miRNAs were identified from all species, across all conditions, of which 46 and 38 of the miRNAs identified from modern durum wheat and wild genotypes, respectively, had not been previously reported. Genotype- and/or stress-specific miRNAs provide insights into our understanding of the complex drought response. Particularly, miR1435, miR5024, and miR7714, identified only from drought-stress roots of drought-tolerant genotype TR39477, can be candidates for future studies to explore and exploit the drought response to develop tolerant varieties.
MADS-box gene family members play multifarious roles in regulating the growth and development of ... more 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 in the wheat genome has been insufficient. Here, a comprehensive genome-wide analysis identified 300 high confidence MADS-box genes from the publicly available reference genome of wheat. Comparative phylogenetic analyses with Arabidopsis and rice MADS-box genes classified the wheat genes into 16 distinct subfamilies. Gene duplications were mainly identified in subfamilies containing unbalanced homeologs, pointing towards a potential mechanism for gene family expansion. Moreover, a more rapid evolution was inferred for M-type genes, as compared with MIKC-type genes, indicating their significance in understanding the evolutionary history of ...
Objectives High-yielding crop varieties will become critical in meeting the future food demand in... more 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 explore and exploit the genomic potential of this elite variety, in 2015, we sequenced the modern elite cultivar Sonmez genome which represents a diverse genetic background. Data description Here, we provide a reference-guided whole genome sequence of Sonmez-2001, assembled into 21 chromosomes of the A, B and D genomes and totaling to 13.3 gigabase-pairs in length. Additionally, a de novo assembly, of an additional 1.05 gigabase-pairs, was generated that represents either Sonmez-specific sequences or sequences that considerably diverged between Sonmez and Chinese Spring. We identified up to 24 million sequence variants, of which up to 2.4% ...
Three subfamilies of grasses, the Erhardtoideae (rice), the Panicoideae (maize, sorghum, sugar ca... more Three subfamilies of grasses, the Erhardtoideae (rice), the Panicoideae (maize, sorghum, sugar cane and millet), and the Pooideae (wheat, barley and cool season forage grasses) provide the basis of human nutrition and are poised to become major sources of renewable energy. Here we describe the complete genome sequence of the wild grass Brachypodium distachyon (Brachypodium), the first member of the Pooideae subfamily to be completely sequenced. Comparison of the Brachypodium, rice and sorghum genomes reveals a precise sequence- based history of genome evolution across a broad diversity of the grass family and identifies nested insertions of whole chromosomes into centromeric regions as a predominant mechanism driving chromosome evolution in the grasses. The relatively compact genome of Brachypodium is maintained by a balance of retroelement replication and loss. The complete genome sequence of Brachypodium, coupled to its exceptional promise as a model system for grass research, wil...
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