273 results on '"Ming-cheng Luo"'
Search Results
2. Aegilops tauschii genome assembly Aet v5.0 features greater sequence contiguity and improved annotation
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Le Wang, Tingting Zhu, Juan C Rodriguez, Karin R Deal, Jorge Dubcovsky, Patrick E McGuire, Thomas Lux, Manuel Spannagl, Klaus F X Mayer, Patricia Baldrich, Blake C Meyers, Naxin Huo, Yong Q Gu, Hongye Zhou, Katrien M Devos, Jeffrey L Bennetzen, Turgay Unver, Hikmet Budak, Patrick J Gulick, Gabor Galiba, Balázs Kalapos, David R Nelson, Pingchuan Li, Frank M You, Ming-Cheng Luo, and Jan Dvorak
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Genetics ,QH426-470 - Abstract
Abstract Aegilops tauschiiAe. tauschiiAe. tauschii
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- 2021
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3. An ancestral NB-LRR with duplicated 3′UTRs confers stripe rust resistance in wheat and barley
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Chaozhong Zhang, Lin Huang, Huifei Zhang, Qunqun Hao, Bo Lyu, Meinan Wang, Lynn Epstein, Miao Liu, Chunlan Kou, Juan Qi, Fengjuan Chen, Mengkai Li, Ge Gao, Fei Ni, Lianquan Zhang, Ming Hao, Jirui Wang, Xianming Chen, Ming-Cheng Luo, Youliang Zheng, Jiajie Wu, Dengcai Liu, and Daolin Fu
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Science - Abstract
Stripe rust is a serious threat to wheat production. Here, the authors reveal that the resistance gene, only present in the wheat progenitor Aegilops tauschii and its derived synthetic wheat, encodes a nucleotide oligomerization domain-like receptor and confers resistance in common wheat and barley.
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- 2019
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4. Sequencing a Juglans regia × J. microcarpa hybrid yields high-quality genome assemblies of parental species
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Tingting Zhu, Le Wang, Frank M. You, Juan C. Rodriguez, Karin R. Deal, Limin Chen, Jie Li, Sandeep Chakraborty, Bipin Balan, Cai-Zhong Jiang, Patrick J. Brown, Charles A. Leslie, Mallikarjuna K. Aradhya, Abhaya M. Dandekar, Patrick E. McGuire, Daniel Kluepfel, Jan Dvorak, and Ming-Cheng Luo
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Botany ,QK1-989 ,Plant culture ,SB1-1110 - Abstract
Crop genetics: lessons from hybrids The genetic sequence of a hybrid walnut tree sheds light on the evolution of the parental species and on some important traits. A study led by Ming-Cheng Luo and Jan Dvorak at the University of California Davis, USA, describes a new approach for producing high-quality genome assemblies of the parental species from interspecific hybrids. By applying long-read sequencing technology and optical mapping to a popular hybrid between cultivated Persian/English walnut and a wild relative that is native to North America they were able to completely assemble the genomes of these two species, gain insights into the evolution of their chromosomes and the distribution of disease-resistant genes. This approach could be used on other outcrossing crops to generate reference-quality genome assemblies and accelerate genetic improvements in commercially important crops.
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- 2019
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5. Aegilops tauschii Genome Sequence: A Framework for Meta-analysis of Wheat QTLs
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Jiale Xu, Xiongtao Dai, Ramesh K. Ramasamy, Le Wang, Tingting Zhu, Patrick E. McGuire, Chad M. Jorgensen, Hamid Dehghani, Patrick J. Gulick, Ming-Cheng Luo, Hans-Georg Müller, and Jan Dvorak
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QTL distribution ,meta-QTL ,QTL database ,probability ,Web portal ,recombination rate ,fusarium head blight ,Genetics ,QH426-470 - Abstract
Numerous quantitative trait loci (QTL) have been mapped in tetraploid and hexaploid wheat and wheat relatives, mostly with simple sequence repeat (SSR) or single nucleotide polymorphism (SNP) markers. To conduct meta-analysis of QTL requires projecting them onto a common genomic framework, either a consensus genetic map or genomic sequence. The latter strategy is pursued here. Of 774 QTL mapped in wheat and wheat relatives found in the literature, 585 (75.6%) were successfully projected onto the Aegilops tauschii pseudomolecules. QTL mapped with SNP markers were more successfully projected (92.2%) than those mapped with SSR markers (66.2%). The QTL were not distributed homogeneously along chromosome arms. Their frequencies increased in the proximal-to-distal direction but declined in the most distal regions and were weakly correlated with recombination rates along the chromosome arms. Databases for projected SSR markers and QTL were constructed and incorporated into the Ae. tauschii JBrowse. To facilitate meta-QTL analysis, eight clusters of QTL were used to estimate standard deviations (σ ^ ) of independently mapped QTL projected onto the Ae. tauschii genome sequence. The standard deviations σ ^ were modeled as an exponential decay function of recombination rates along the Ae. tauschii chromosomes. We implemented four hypothesis tests for determining the membership of query QTL. The hypothesis tests and estimation procedure for σ ^ were implemented in a web portal for meta-analysis of projected QTL. Twenty-one QTL for Fusarium head blight resistance mapped on wheat chromosomes 3A, 3B, and 3D were analyzed to illustrate the use of the portal for meta-QTL analyses.
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- 2019
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6. Improved Genome Sequence of Wild Emmer Wheat Zavitan with the Aid of Optical Maps
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Tingting Zhu, Le Wang, Juan C. Rodriguez, Karin R. Deal, Raz Avni, Assaf Distelfeld, Patrick E. McGuire, Jan Dvorak, and Ming-Cheng Luo
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Triticum dicoccoides ,Genome assembly ,DLS ,Pseudomolecules ,Genetics ,QH426-470 - Abstract
Wild emmer (Triticum turgidum ssp. dicoccoides) is the progenitor of all modern cultivated tetraploid wheat. Its genome is large (> 10 Gb) and contains over 80% repeated sequences. The successful whole-genome-shotgun assembly of the wild emmer (accession Zavitan) genome sequence (WEW_v1.0) was an important milestone for wheat genomics. In an effort to improve this assembly, an optical map of accession Zavitan was constructed using Bionano Direct Label and Stain (DLS) technology. The map spanned 10.4 Gb. This map and another map produced earlier by us with the Bionano’s Nick Label Repair and Stain (NLRS) technology were used to improve the current wild emmer assembly. The WEW_v1.0 assembly consisted of 151,912 scaffolds. Of them, 3,102 could be confidently aligned on the optical maps. Forty-seven were chimeric. They were disjoined and new scaffolds were assembled with the aid of the optical maps. The total number of scaffolds was reduced from 151,912 to 149,252 and N50 increased from 6.96 Mb to 72.63 Mb. Of the 149,252 scaffolds, 485 scaffolds, which accounted for 97% of the total genome length, were aligned and oriented on genetic maps, and new WEW_v2.0 pseudomolecules were constructed. The new pseudomolecules included 333 scaffolds (68.51 Mb) which were originally unassigned, 226 scaffolds (554.84 Mb) were placed into new locations, and 332 scaffolds (394.83 Mb) were re-oriented. The improved wild emmer genome assembly is an important resource for understanding genomic modification that occurred by domestication.
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- 2019
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7. Optical and physical mapping with local finishing enables megabase-scale resolution of agronomically important regions in the wheat genome
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Gabriel Keeble-Gagnère, Philippe Rigault, Josquin Tibbits, Raj Pasam, Matthew Hayden, Kerrie Forrest, Zeev Frenkel, Abraham Korol, B. Emma Huang, Colin Cavanagh, Jen Taylor, Michael Abrouk, Andrew Sharpe, David Konkin, Pierre Sourdille, Benoît Darrier, Frédéric Choulet, Aurélien Bernard, Simone Rochfort, Adam Dimech, Nathan Watson-Haigh, Ute Baumann, Paul Eckermann, Delphine Fleury, Angela Juhasz, Sébastien Boisvert, Marc-Alexandre Nolin, Jaroslav Doležel, Hana Šimková, Helena Toegelová, Jan Šafář, Ming-Cheng Luo, Francisco Câmara, Matthias Pfeifer, Don Isdale, Johan Nyström-Persson, IWGSC, Dal-Hoe Koo, Matthew Tinning, Dangqun Cui, Zhengang Ru, and Rudi Appels
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Wheat sequence finishing ,Megabase-scale integration ,Optical/physical maps Grain quality ,Yield ,Biology (General) ,QH301-705.5 ,Genetics ,QH426-470 - Abstract
Abstract Background Numerous scaffold-level sequences for wheat are now being released and, in this context, we report on a strategy for improving the overall assembly to a level comparable to that of the human genome. Results Using chromosome 7A of wheat as a model, sequence-finished megabase-scale sections of this chromosome were established by combining a new independent assembly using a bacterial artificial chromosome (BAC)-based physical map, BAC pool paired-end sequencing, chromosome-arm-specific mate-pair sequencing and Bionano optical mapping with the International Wheat Genome Sequencing Consortium RefSeq v1.0 sequence and its underlying raw data. The combined assembly results in 18 super-scaffolds across the chromosome. The value of finished genome regions is demonstrated for two approximately 2.5 Mb regions associated with yield and the grain quality phenotype of fructan carbohydrate grain levels. In addition, the 50 Mb centromere region analysis incorporates cytological data highlighting the importance of non-sequence data in the assembly of this complex genome region. Conclusions Sufficient genome sequence information is shown to now be available for the wheat community to produce sequence-finished releases of each chromosome of the reference genome. The high-level completion identified that an array of seven fructosyl transferase genes underpins grain quality and that yield attributes are affected by five F-box-only-protein-ubiquitin ligase domain and four root-specific lipid transfer domain genes. The completed sequence also includes the centromere.
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- 2018
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8. Molecular mapping of YrTZ2, a stripe rust resistance gene in wild emmer accession TZ-2 and its comparative analyses with Aegilops tauschii
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Zhen-zhong WANG, Jing-zhong XIE, Li GUO, De-yun ZHANG, Gen-qiao LI, Ti-lin FANG, Yong-xing CHEN, Jun LI, Qiu-hong WU, Ping LU, Miao-miao LI, Hai-bin WU, Huai-zhi ZHANG, Yan ZHANG, Wu-yun YANG, Ming-cheng LUO, Fahima Tzion, and Zhi-yong LIU
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Triticum dicoccoides ,Puccinia striiformis f. sp. tritici ,SNP ,comparative genomics ,Agriculture (General) ,S1-972 - Abstract
Wheat stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is a devastating disease that can cause severe yield losses. Identification and utilization of stripe rust resistance genes are essential for effective breeding against the disease. Wild emmer accession TZ-2, originally collected from Mount Hermon, Israel, confers near-immunity resistance against several prevailing Pst races in China. A set of 200 F6:7 recombinant inbred lines (RILs) derived from a cross between susceptible durum wheat cultivar Langdon and TZ-2 was used for stripe rust evaluation. Genetic analysis indicated that the stripe rust resistance of TZ-2 to Pst race CYR34 was controlled by a single dominant gene, temporarily designated YrTZ2. Through bulked segregant analysis (BSA) with SSR markers, YrTZ2 was located on chromosome arm 1BS flanked by Xwmc230 and Xgwm413 with genetic distance of 0.8 cM (distal) and 0.3 cM (proximal), respectively. By applying wheat 90K iSelect SNP genotyping assay, 11 polymorphic loci (consisting of 250 SNP markers) closely linked to YrTZ2 were identified. YrTZ2 was further delimited into a 0.8-cM genetic interval between SNP marker IWB19368 and SSR marker Xgwm413, and co-segregated with SNP marker IWB28744 (co-segregated with 28 SNP). Comparative genomics analyses revealed high level of collinearity between the YrTZ2 genomic region and the orthologous region of Aegilops tauschii 1DS. The genomic region between loci IWB19368 and IWB31649 harboring YrTZ2 is orthologous to a 24.5-Mb genomic region between AT1D0112 and AT1D0150, spanning 15 contigs on chromosome 1DS. The genetic and comparative maps of YrTZ2 provide a framework for map-based cloning and marker-assisted selection of YrTZ2.
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- 2018
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9. Wheat Ms2 encodes for an orphan protein that confers male sterility in grass species
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Fei Ni, Juan Qi, Qunqun Hao, Bo Lyu, Ming-Cheng Luo, Yan Wang, Fengjuan Chen, Shuyun Wang, Chaozhong Zhang, Lynn Epstein, Xiangyu Zhao, Honggang Wang, Xiansheng Zhang, Cuixia Chen, Lanzhen Sun, and Daolin Fu
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Science - Abstract
The dominant male-sterile geneMs2 has facilitated the release of hundreds of wheat-breeding lines and cultivars in China. Here Ni et al. describe the cloning of the Ms2 gene, which appears as an orphan gene in the Triticinae, and show that Ms2 can be used to confer male sterility in wheat, barley and Brachypodium.
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- 2017
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10. Computational Identification and Comparative Analysis of Conserved miRNAs and Their Putative Target Genes in the Juglans regia and J. microcarpa Genomes
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Le Wang, Tingting Zhu, Karin R. Deal, Jan Dvorak, and Ming-Cheng Luo
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homoeologous ,miRNA ,subgenome ,walnut ,Botany ,QK1-989 - Abstract
MicroRNAs (miRNAs) are important factors for the post-transcriptional regulation of protein-coding genes in plants and animals. They are discovered either by sequencing small RNAs or computationally. We employed a sequence-homology-based computational approach to identify conserved miRNAs and their target genes in Persian (English) walnut, Juglans regia, and its North American wild relative, J. microcarpa. A total of 119 miRNA precursors (pre-miRNAs) were detected in the J. regia genome and 121 in the J. microcarpa genome and miRNA target genes were predicted and their functional annotations were performed in both genomes. In the J. regia genome, 325 different genes were targets; 87.08% were regulated by transcript cleavage and 12.92% by translation repression. In the J. microcarpa genome, 316 different genes were targets; 88.92% were regulated by transcript cleavage and 11.08% were regulated by translation repression. Totals of 1.3% and 2.0% of all resistance gene analogues (RGA) and 2.7% and 2.6% of all transcription factors (TFs) were regulated by miRNAs in the J. regia and J. microcarpa genomes, respectively. Juglans genomes evolved by a whole genome duplication (WGD) and consist of eight pairs of fractionated homoeologous chromosomes. Within each pair, the chromosome that has more genes with greater average transcription also harbors more pre-miRNAs and more target genes than its homoeologue. While only minor differences were detected in pre-miRNAs between the J. regia and J. microcarpa genomes, about one-third of the pre-miRNA loci were not conserved between homoeologous chromosome within each genome. Pre-miRNA and their corresponding target genes showed a tendency to be collocated within a subgenome.
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- 2020
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11. Gene Duplication and Evolution Dynamics in the Homeologous Regions Harboring Multiple Prolamin and Resistance Gene Families in Hexaploid Wheat
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Naxin Huo, Shengli Zhang, Tingting Zhu, Lingli Dong, Yi Wang, Toni Mohr, Tiezhu Hu, Zhiyong Liu, Jan Dvorak, Ming-Cheng Luo, Daowen Wang, Jong-Yeol Lee, Susan Altenbach, and Yong Q. Gu
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wheat prolamins ,disease resistance genes ,gene family ,gene duplication ,genome evolution ,phylogeny ,Plant culture ,SB1-1110 - Abstract
Improving end-use quality and disease resistance are important goals in wheat breeding. The genetic loci controlling these traits are highly complex, consisting of large families of prolamin and resistance genes with members present in all three homeologous A, B, and D genomes in hexaploid bread wheat. Here, orthologous regions harboring both prolamin and resistance gene loci were reconstructed and compared to understand gene duplication and evolution in different wheat genomes. Comparison of the two orthologous D regions from the hexaploid wheat Chinese Spring and the diploid progenitor Aegilops tauschii revealed their considerable difference due to the presence of five large structural variations with sizes ranging from 100 kb to 2 Mb. As a result, 44% of the Ae. tauschii and 71% of the Chinese Spring sequences in the analyzed regions, including 79 genes, are not shared. Gene rearrangement events, including differential gene duplication and deletion in the A, B, and D regions, have resulted in considerable erosion of gene collinearity in the analyzed regions, suggesting rapid evolution of prolamin and resistance gene families after the separation of the three wheat genomes. We hypothesize that this fast evolution is attributed to the co-evolution of the two gene families dispersed within a high recombination region. The identification of a full set of prolamin genes facilitated transcriptome profiling and revealed that the A genome contributes the least to prolamin expression because of its smaller number of expressed intact genes and their low expression levels, while the B and D genomes contribute similarly.
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- 2018
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12. Introgression of the Aegilops speltoides Su1-Ph1 Suppressor into Wheat
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Hao Li, Karin R. Deal, Ming-Cheng Luo, Wanquan Ji, Assaf Distelfeld, and Jan Dvorak
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homoeologous chromosome pairing ,in situ hybridization ,MAS ,Ph1 ,ZIP4 ,Plant culture ,SB1-1110 - Abstract
Meiotic pairing between homoeologous chromosomes in polyploid wheat is inhibited by the Ph1 locus on the long arm of chromosome 5 in the B genome. Aegilops speltoides (genomes SS), the closest relative of the progenitor of the wheat B genome, is polymorphic for genetic suppression of Ph1. Using this polymorphism, two major suppressor loci, Su1-Ph1 and Su2-Ph1, have been mapped in Ae. speltoides. Su1-Ph1 is located in the distal, high-recombination region of the long arm of the Ae. speltoides chromosome 3S. Its location and tight linkage to marker Xpsr1205-3S makes Su1-Ph1 a suitable target for introgression into wheat. Here, Xpsr1205-3S was introgressed into hexaploid bread wheat cv. Chinese Spring (CS) and from there into tetraploid durum wheat cv. Langdon (LDN). Sequential fluorescence in situ hybridization and genomic in situ hybridization showed that an Ae. speltoides segment with Xpsr1205-3S replaced the distal end of the long arm of chromosome 3A. In the CS genetic background, the chromosome induced homoeologous chromosome pairing in interspecific hybrids with Ae. peregrina but not in progenies from crosses involving alien disomic substitution lines. In the LDN genetic background, the chromosome induced homoeologous chromosome pairing in both interspecific hybrids and progenies from crosses involving alien disomic substitution lines. We conclude that the recombined chromosome harbors Su1-Ph1 but its expression requires expression of complementary gene that is present in LDN but absent in CS. We suggest that it is unlikely that Su1-Ph1 and ZIP4-1, a paralog of Ph1 located on wheat chromosomes 3A and 3B and Ae. tauschii chromosome 3D, are equivalent. The utility of Su1-Ph1 for induction of recombination between homoeologous chromosomes in wheat is illustrated.
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- 2017
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13. A High-Density Genetic Map of Wild Emmer Wheat from the Karaca Dağ Region Provides New Evidence on the Structure and Evolution of Wheat Chromosomes
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Chad Jorgensen, Ming-Cheng Luo, Ramesh Ramasamy, Mathew Dawson, Bikram S. Gill, Abraham B. Korol, Assaf Distelfeld, and Jan Dvorak
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inversion ,single nucleotide polymorphism ,SNP ,translocation ,Triticum dicoccoides ,wheat evolution ,Plant culture ,SB1-1110 - Abstract
Wild emmer (Triticum turgidum ssp. dicoccoides) is a progenitor of all cultivated wheat grown today. It has been hypothesized that emmer was domesticated in the Karaca Dağ region in southeastern Turkey. A total of 445 recombinant inbred lines of T. turgidum ssp. durum cv. ‘Langdon’ x wild emmer accession PI 428082 from this region was developed and genotyped with the Illumina 90K single nucleotide polymorphism Infinium assay. A genetic map comprising 2,650 segregating markers was constructed. The order of the segregating markers and an additional 8,264 co-segregating markers in the Aegilops tauschii reference genome sequence was used to compare synteny of the tetraploid wheat with the Brachypodium distachyon, rice, and sorghum. These comparisons revealed the presence of 15 structural chromosome rearrangements, in addition to the already known 4A-5A-7B rearrangements. The most common type was an intra-chromosomal translocation in which the translocated segment was short and was translocated only a short distance along the chromosome. A large reciprocal translocation, one small non-reciprocal translocation, and three large and one small paracentric inversions were also discovered. The use of inversions for a phylogeny reconstruction in the Triticum–Aegilops alliance was illustrated. The genetic map was inconsistent with the current model of evolution of the rearranged chromosomes 4A-5A-7B. Genetic diversity in the rearranged chromosome 4A showed that the rearrangements might have been contemporary with wild emmer speciation. A selective sweep was found in the centromeric region of chromosome 4A in Karaca Dağ wild emmer but not in 4A of T. aestivum. The absence of diversity from a large portion of chromosome 4A of wild emmer, believed to be ancestral to all domesticated wheat, is puzzling.
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- 2017
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14. Genetic Diversity Revealed by Single Nucleotide Polymorphism Markers in a Worldwide Germplasm Collection of Durum Wheat
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Ming-Cheng Luo, Junhua Peng, Eviatar Nevo, Dongfa Sun, Yunliang Peng, Jirui Wang, Frank M. You, Liang Chen, Daokun Sun, and Jing Ren
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T. durum ,landrace ,cultivars ,molecular marker ,SNP ,genetic structure ,Biology (General) ,QH301-705.5 ,Chemistry ,QD1-999 - Abstract
Evaluation of genetic diversity and genetic structure in crops has important implications for plant breeding programs and the conservation of genetic resources. Newly developed single nucleotide polymorphism (SNP) markers are effective in detecting genetic diversity. In the present study, a worldwide durum wheat collection consisting of 150 accessions was used. Genetic diversity and genetic structure were investigated using 946 polymorphic SNP markers covering the whole genome of tetraploid wheat. Genetic structure was greatly impacted by multiple factors, such as environmental conditions, breeding methods reflected by release periods of varieties, and gene flows via human activities. A loss of genetic diversity was observed from landraces and old cultivars to the modern cultivars released during periods of the Early Green Revolution, but an increase in cultivars released during the Post Green Revolution. Furthermore, a comparative analysis of genetic diversity among the 10 mega ecogeographical regions indicated that South America, North America, and Europe possessed the richest genetic variability, while the Middle East showed moderate levels of genetic diversity.
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- 2013
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15. High-density genetic linkage map construction and QTL mapping of grain shape and size in the wheat population Yanda1817 × Beinong6.
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Qiu-Hong Wu, Yong-Xing Chen, Sheng-Hui Zhou, Lin Fu, Jiao-Jiao Chen, Yao Xiao, Dong Zhang, Shu-Hong Ouyang, Xiao-Jie Zhao, Yu Cui, De-Yun Zhang, Yong Liang, Zhen-Zhong Wang, Jing-Zhong Xie, Jin-Xia Qin, Guo-Xin Wang, De-Lin Li, Yin-Lian Huang, Mei-Hua Yu, Ping Lu, Li-Li Wang, Ling Wang, Hao Wang, Chen Dang, Jie Li, Yan Zhang, Hui-Ru Peng, Cheng-Guo Yuan, Ming-Shan You, Qi-Xin Sun, Ji-Rui Wang, Li-Xin Wang, Ming-Cheng Luo, Jun Han, and Zhi-Yong Liu
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Medicine ,Science - Abstract
High-density genetic linkage maps are necessary for precisely mapping quantitative trait loci (QTLs) controlling grain shape and size in wheat. By applying the Infinium iSelect 9K SNP assay, we have constructed a high-density genetic linkage map with 269 F 8 recombinant inbred lines (RILs) developed between a Chinese cornerstone wheat breeding parental line Yanda1817 and a high-yielding line Beinong6. The map contains 2431 SNPs and 128 SSR & EST-SSR markers in a total coverage of 3213.2 cM with an average interval of 1.26 cM per marker. Eighty-eight QTLs for thousand-grain weight (TGW), grain length (GL), grain width (GW) and grain thickness (GT) were detected in nine ecological environments (Beijing, Shijiazhuang and Kaifeng) during five years between 2010-2014 by inclusive composite interval mapping (ICIM) (LOD ≥ 2.5). Among which, 17 QTLs for TGW were mapped on chromosomes 1A, 1B, 2A, 2B, 3A, 3B, 3D, 4A, 4D, 5A, 5B and 6B with phenotypic variations ranging from 2.62% to 12.08%. Four stable QTLs for TGW could be detected in five and seven environments, respectively. Thirty-two QTLs for GL were mapped on chromosomes 1B, 1D, 2A, 2B, 2D, 3B, 3D, 4A, 4B, 4D, 5A, 5B, 6B, 7A and 7B, with phenotypic variations ranging from 2.62% to 44.39%. QGl.cau-2A.2 can be detected in all the environments with the largest phenotypic variations, indicating that it is a major and stable QTL. For GW, 12 QTLs were identified with phenotypic variations range from 3.69% to 12.30%. We found 27 QTLs for GT with phenotypic variations ranged from 2.55% to 36.42%. In particular, QTL QGt.cau-5A.1 with phenotypic variations of 6.82-23.59% was detected in all the nine environments. Moreover, pleiotropic effects were detected for several QTL loci responsible for grain shape and size that could serve as target regions for fine mapping and marker assisted selection in wheat breeding programs.
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- 2015
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16. Combinatorial pooling enables selective sequencing of the barley gene space.
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Stefano Lonardi, Denisa Duma, Matthew Alpert, Francesca Cordero, Marco Beccuti, Prasanna R Bhat, Yonghui Wu, Gianfranco Ciardo, Burair Alsaihati, Yaqin Ma, Steve Wanamaker, Josh Resnik, Serdar Bozdag, Ming-Cheng Luo, and Timothy J Close
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Biology (General) ,QH301-705.5 - Abstract
For the vast majority of species - including many economically or ecologically important organisms, progress in biological research is hampered due to the lack of a reference genome sequence. Despite recent advances in sequencing technologies, several factors still limit the availability of such a critical resource. At the same time, many research groups and international consortia have already produced BAC libraries and physical maps and now are in a position to proceed with the development of whole-genome sequences organized around a physical map anchored to a genetic map. We propose a BAC-by-BAC sequencing protocol that combines combinatorial pooling design and second-generation sequencing technology to efficiently approach denovo selective genome sequencing. We show that combinatorial pooling is a cost-effective and practical alternative to exhaustive DNA barcoding when preparing sequencing libraries for hundreds or thousands of DNA samples, such as in this case gene-bearing minimum-tiling-path BAC clones. The novelty of the protocol hinges on the computational ability to efficiently compare hundred millions of short reads and assign them to the correct BAC clones (deconvolution) so that the assembly can be carried out clone-by-clone. Experimental results on simulated data for the rice genome show that the deconvolution is very accurate, and the resulting BAC assemblies have high quality. Results on real data for a gene-rich subset of the barley genome confirm that the deconvolution is accurate and the BAC assemblies have good quality. While our method cannot provide the level of completeness that one would achieve with a comprehensive whole-genome sequencing project, we show that it is quite successful in reconstructing the gene sequences within BACs. In the case of plants such as barley, this level of sequence knowledge is sufficient to support critical end-point objectives such as map-based cloning and marker-assisted breeding.
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- 2013
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17. Rapid genome mapping in nanochannel arrays for highly complete and accurate de novo sequence assembly of the complex Aegilops tauschii genome.
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Alex R Hastie, Lingli Dong, Alexis Smith, Jeff Finklestein, Ernest T Lam, Naxin Huo, Han Cao, Pui-Yan Kwok, Karin R Deal, Jan Dvorak, Ming-Cheng Luo, Yong Gu, and Ming Xiao
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Medicine ,Science - Abstract
Next-generation sequencing (NGS) technologies have enabled high-throughput and low-cost generation of sequence data; however, de novo genome assembly remains a great challenge, particularly for large genomes. NGS short reads are often insufficient to create large contigs that span repeat sequences and to facilitate unambiguous assembly. Plant genomes are notorious for containing high quantities of repetitive elements, which combined with huge genome sizes, makes accurate assembly of these large and complex genomes intractable thus far. Using two-color genome mapping of tiling bacterial artificial chromosomes (BAC) clones on nanochannel arrays, we completed high-confidence assembly of a 2.1-Mb, highly repetitive region in the large and complex genome of Aegilops tauschii, the D-genome donor of hexaploid wheat (Triticum aestivum). Genome mapping is based on direct visualization of sequence motifs on single DNA molecules hundreds of kilobases in length. With the genome map as a scaffold, we anchored unplaced sequence contigs, validated the initial draft assembly, and resolved instances of misassembly, some involving contigs
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- 2013
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18. Correction: Rapid Genome Mapping in Nanochannel Arrays for Highly Complete and Accurate Sequence Assembly of the Complex Genome.
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Alex R. Hastie, Lingli Dong, Alexis Smith, Jeff Finklestein, Ernest T. Lam, Naxin Huo, Han Cao, Pui-Yan Kwok, Karin R. Deal, Jan Dvorak, Ming-Cheng Luo, Yong Gu, and Ming Xiao
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Medicine ,Science - Published
- 2013
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19. Insular organization of gene space in grass genomes.
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Andrea Gottlieb, Hans-Georg Müller, Alicia N Massa, Humphrey Wanjugi, Karin R Deal, Frank M You, Xiangyang Xu, Yong Q Gu, Ming-Cheng Luo, Olin D Anderson, Agnes P Chan, Pablo Rabinowicz, Katrien M Devos, and Jan Dvorak
- Subjects
Medicine ,Science - Abstract
Wheat and maize genes were hypothesized to be clustered into islands but the hypothesis was not statistically tested. The hypothesis is statistically tested here in four grass species differing in genome size, Brachypodium distachyon, Oryza sativa, Sorghum bicolor, and Aegilops tauschii. Density functions obtained under a model where gene locations follow a homogeneous Poisson process and thus are not clustered are compared with a model-free situation quantified through a non-parametric density estimate. A simple homogeneous Poisson model for gene locations is not rejected for the small O. sativa and B. distachyon genomes, indicating that genes are distributed largely uniformly in those species, but is rejected for the larger S. bicolor and Ae. tauschii genomes, providing evidence for clustering of genes into islands. It is proposed to call the gene islands "gene insulae" to distinguish them from other types of gene clustering that have been proposed. An average S. bicolor and Ae. tauschii insula is estimated to contain 3.7 and 3.9 genes with an average intergenic distance within an insula of 2.1 and 16.5 kb, respectively. Inter-insular distances are greater than 8 and 81 kb and average 15.1 and 205 kb, in S. bicolor and Ae. tauschii, respectively. A greater gene density observed in the distal regions of the Ae. tauschii chromosomes is shown to be primarily caused by shortening of inter-insular distances. The comparison of the four grass genomes suggests that gene locations are largely a function of a homogeneous Poisson process in small genomes. Nonrandom insertions of LTR retroelements during genome expansion creates gene insulae, which become less dense and further apart with the increase in genome size. High concordance in relative lengths of orthologous intergenic distances among the investigated genomes including the maize genome suggests functional constraints on gene distribution in the grass genomes.
- Published
- 2013
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20. Fine mapping of the Bsr1 barley stripe mosaic virus resistance gene in the model grass Brachypodium distachyon.
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Yu Cui, Mi Yeon Lee, Naxin Huo, Jennifer Bragg, Lijie Yan, Cheng Yuan, Cui Li, Sara J Holditch, Jingzhong Xie, Ming-Cheng Luo, Dawei Li, Jialin Yu, Joel Martin, Wendy Schackwitz, Yong Qiang Gu, John P Vogel, Andrew O Jackson, Zhiyong Liu, and David F Garvin
- Subjects
Medicine ,Science - Abstract
The ND18 strain of Barley stripe mosaic virus (BSMV) infects several lines of Brachypodium distachyon, a recently developed model system for genomics research in cereals. Among the inbred lines tested, Bd3-1 is highly resistant at 20 to 25 °C, whereas Bd21 is susceptible and infection results in an intense mosaic phenotype accompanied by high levels of replicating virus. We generated an F(6:7) recombinant inbred line (RIL) population from a cross between Bd3-1 and Bd21 and used the RILs, and an F(2) population of a second Bd21 × Bd3-1 cross to evaluate the inheritance of resistance. The results indicate that resistance segregates as expected for a single dominant gene, which we have designated Barley stripe mosaic virus resistance 1 (Bsr1). We constructed a genetic linkage map of the RIL population using SNP markers to map this gene to within 705 Kb of the distal end of the top of chromosome 3. Additional CAPS and Indel markers were used to fine map Bsr1 to a 23 Kb interval containing five putative genes. Our study demonstrates the power of using RILs to rapidly map the genetic determinants of BSMV resistance in Brachypodium. Moreover, the RILs and their associated genetic map, when combined with the complete genomic sequence of Brachypodium, provide new resources for genetic analyses of many other traits.
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- 2012
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21. Identification and development of crown gall-resistant walnut rootstocks
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Ali E. McClean, Jan Dvorak, Daniel A. Kluepfel, Ramesh K Ramasamy, Mallikarjuna K. Aradhya, Ming-Cheng Luo, Gregory T. Browne, C.A. Leslie, and Andreas Westphal
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Horticulture ,Crown (botany) ,Gall ,Identification (biology) ,Biology ,Rootstock - Published
- 2021
22. An Algorithm for Discrimination of Multiple-Fragment Peaks in Capillary Fingerprinting Chromatograms.
- Author
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Frank M. You, Ming-Cheng Luo, Yong Qiang Gu, Gerard R. Lazo, Jan Dvorak, and Olin D. Anderson
- Published
- 2008
23. Myb10‐D confers PHS‐3D resistance to pre‐harvest sprouting by regulating NCED in ABA biosynthesis pathway of wheat
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Lixuan Gui, Mengping Cheng, You-Liang Zheng, Xiaojiang Guo, Maolian Li, Tingting Zhu, Qiantao Jiang, Chao Tan, Pengfei Qi, Yingjin Yi, Linchuan Li, Yuxin Fu, Yujiao Liu, Ze-Hou Liu, Jirui Wang, Zhien Pu, Zhongxu Chen, Yongrui Wu, Dengcai Liu, Lianquan Zhang, Yuming Wei, Ming Hao, Ming-Cheng Luo, Jian Yang, Guoyue Chen, Jing Lang, Lin Huang, Yong Zhou, Min Deng, and Jian Ma
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Physiology ,Triticum aestivum ,Germination ,Plant Science ,functional analyses ,integrated omics ,Dioxygenases ,Transcriptome ,chemistry.chemical_compound ,Biosynthesis ,Metabolome ,Aegilops tauschii ,Cultivar ,Gene ,Abscisic acid ,Triticum ,Plant Proteins ,synthetic wheat ,biology ,Full Paper ,Research ,pre‐harvest sprouting ,food and beverages ,Full Papers ,biology.organism_classification ,presence–absence variation ,Horticulture ,grain color ,chemistry - Abstract
Summary Pre‐harvest sprouting (PHS), the germination of grain before harvest, is a serious problem resulting in wheat yield and quality losses.Here, we mapped the PHS resistance gene PHS‐3D from synthetic hexaploid wheat to a 2.4 Mb presence–absence variation (PAV) region and found that its resistance effect was attributed to the pleiotropic Myb10‐D by integrated omics and functional analyses.Three haplotypes were detected in this PAV region among 262 worldwide wheat lines and 16 Aegilops tauschii, and the germination percentages of wheat lines containing Myb10‐D was approximately 40% lower than that of the other lines. Transcriptome and metabolome profiling indicated that Myb10‐D affected the transcription of genes in both the flavonoid and abscisic acid (ABA) biosynthesis pathways, which resulted in increases in flavonoids and ABA in transgenic wheat lines. Myb10‐D activates 9‐cis‐epoxycarotenoid dioxygenase (NCED) by biding the secondary wall MYB‐responsive element (SMRE) to promote ABA biosynthesis in early wheat seed development stages.We revealed that the newly discovered function of Myb10‐D confers PHS resistance by enhancing ABA biosynthesis to delay germination in wheat. The PAV harboring Myb10‐D associated with grain color and PHS will be useful for understanding and selecting white grained PHS resistant wheat cultivars.
- Published
- 2021
24. Observation of the rotational Doppler shift of a spinning object based on an acoustic vortex with a Fresnel-spiral zone plate
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Zheng-Kun Cheng, Ming-Cheng Luo, Xiao-Yu Sun, Ming Chen, Yi Zhang, Sheng-Quan Li, and Xiao-Chun Zhu
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General Physics and Astronomy - Abstract
It has been demonstrated that sound waves carrying orbital angular momentum undergo frequency modulation after being reflected by a rotating object. In this paper, we, observed the rotational Doppler shift phenomenon of the acoustic vortex in an underwater environment by using a Fresnel-spiral zone plate for the construction of the focused acoustic vortex with controllable topological charge. The positive and negative rotation speeds of the spinning object are precisely determined with the rotational frequency shift and the acoustic vortex's topological charge. The rotational Doppler effect of acoustic vortex provides a possibility to improve the detection and recognition accuracy of Autonomous Underwater Vehicles with propellers.
- Published
- 2023
25. PIECE: a database for plant gene structure comparison and evolution.
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Yi Wang 0052, Frank M. You, Gerard R. Lazo, Ming-Cheng Luo, Roger Thilmony, Sean Gordon, Shahryar F. Kianian, and Yong Qiang Gu
- Published
- 2013
- Full Text
- View/download PDF
26. Population genomic analysis of Aegilops tauschii identifies targets for bread wheat improvement
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H. Randy Kutcher, Richard Horsnell, James Simmonds, Pierre Hucl, Ahmed Fawzy Elkot, Thomas Lux, Catherine Chinoy, Long Mao, Parveen Chhuneja, Guotai Yu, Vijay K. Tiwari, Annemarie Fejer Justesen, G. S. Brar, Shuyu Liu, Jan Dvorak, Kumar Gaurav, Brian J. Steffenson, Macarena Forner-Martínez, Sanu Arora, Raz Avni, Jitender Cheema, Beat Keller, Martin Mascher, Barbara Steiner, Oadi Matny, Mark A. Smedley, Catherine Gardener, Paula Silva, Dengcai Liu, Victoria Widrig, Ksenia V. Krasileva, Ngonidzashe Kangara, David M. Gilbert, Simon M. Tyrrell, W. John Raupp, Burkhard Steuernagel, Hermann Buerstmayr, Rizky Pasthika Kirana, Javier Sánchez-Martín, Evans Lagudah, Firuza Nasyrova, Xingdong Bian, Susanne Artmeier, Cristobal Uauy, Suzannah Pearce, Joshua Waites, Jackie C. Rudd, Ali A. Mehrabi, Aili Li, Shuangye Wu, Noam Chayut, Attilio Pascucci, Sadiye Hayta, Narinder Singh, Alison R. Bentley, Martin Simonsen, Ming-Cheng Luo, Steven S. Xu, Scott A. Boden, Sreya Ghosh, Brande B. H. Wulff, Paul Nicholson, Amber N. Hafeez, Tom O’Hara, Amir Sharon, Justin D. Faris, Jesús Quiroz-Chávez, Klaus F. X. Mayer, Wendy Harwood, Liangliang Gao, Leif Schauser, Sandip Kale, M. Patpour, Robert P. Davey, Nitika Sandhu, Jesse Poland, Jiaqian Liu, and Gina Brown-Guedira
- Subjects
0106 biological sciences ,Aegilops ,Population ,Biomedical Engineering ,Population genetics ,Bioengineering ,01 natural sciences ,Applied Microbiology and Biotechnology ,Genome ,03 medical and health sciences ,Genetics ,Aegilops tauschii ,education ,Association mapping ,Triticum ,030304 developmental biology ,2. Zero hunger ,0303 health sciences ,Genetic diversity ,education.field_of_study ,biology ,Human Genome ,food and beverages ,Bread ,Genomics ,biology.organism_classification ,ddc ,Plant Breeding ,Molecular Medicine ,Metagenomics ,Ploidy ,Plant immunity ,Genome-wide association studies ,Plant domestication ,Genome informatics ,Plant breeding ,010606 plant biology & botany ,Biotechnology - Abstract
Aegilops tauschii, the diploid wild progenitor of the D subgenome of bread wheat, is a reservoir of genetic diversity for improving bread wheat performance and environmental resilience. Here we sequenced 242 Ae. tauschii accessions and compared them to the wheat D subgenome to characterize genomic diversity. We found that a rare lineage of Ae. tauschii geographically restricted to present-day Georgia contributed to the wheat D subgenome in the independent hybridizations that gave rise to modern bread wheat. Through k-mer-based association mapping, we identified discrete genomic regions with candidate genes for disease and pest resistance and demonstrated their functional transfer into wheat by transgenesis and wide crossing, including the generation of a library of hexaploids incorporating diverse Ae. tauschii genomes. Exploiting the genomic diversity of the Ae. tauschii ancestral diploid genome permits rapid trait discovery and functional genetic validation in a hexaploid background amenable to breeding.
- Published
- 2022
27. RJPrimers: unique transposable element insertion junction discovery and PCR primer design for marker development.
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Frank M. You, Humphrey Wanjugi, Naxin Huo, Gerard R. Lazo, Ming-Cheng Luo, Olin D. Anderson, Jan Dvorak, and Yong Qiang Gu
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- 2010
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28. The clinical efficacy of neoadjuvant chemotherapy on urothelial carcinoma of the bladder: A retrospective analysis from a single-center in Taiwan
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Ming Cheng Luo, Ying-Hsu Chang, Cheng-Keng Chuang, See-Tong Pang, Po-Hung Lin, and Chung-Yi Liu
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Diseases of the genitourinary system. Urology ,RC870-923 - Published
- 2016
- Full Text
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29. Identification of candidate chromosome region of Sbwm1 for Soil-borne wheat mosaic virus resistance in wheat
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Feng Jin, Ming-Cheng Luo, Guihua Bai, Meng Lin, Dadong Zhang, Shubing Liu, Harold N. Trick, Liuling Yan, and Bin Tian
- Subjects
Genetic Markers ,0106 biological sciences ,0301 basic medicine ,Candidate gene ,Quantitative Trait Loci ,lcsh:Medicine ,Plant disease resistance ,Quantitative trait locus ,Polymorphism, Single Nucleotide ,01 natural sciences ,Article ,Plant breeding ,Chromosomes, Plant ,Plant Viruses ,03 medical and health sciences ,Genetic linkage ,Chromosome regions ,lcsh:Science ,Triticum ,Disease Resistance ,Plant Diseases ,Plant Proteins ,Genetics ,Multidisciplinary ,biology ,lcsh:R ,Intergenic SNP ,Chromosome Mapping ,food and beverages ,biology.organism_classification ,Phenotype ,030104 developmental biology ,Soil-borne wheat mosaic virus ,lcsh:Q ,Wheat mosaic virus ,Genome, Plant ,010606 plant biology & botany - Abstract
Soil-borne wheat mosaic virus (SBWMV) causes a serious viral disease that can significantly reduce grain yield in winter wheat worldwide. Using resistant cultivars is the only feasible strategy to reduce the losses caused by SBWMV. To fine map the resistance gene Sbwm1, 205 wheat accessions was genotyped using wheat Infinium iSelect Beadchips with 90 K SNPs. Association analysis identified 35 SNPs in 12 wheat genes and one intergenic SNP in the Sbwm1 region that showed a significant association with SBWMV resistance. Those SNPs were converted into Kompetitive Allele-Specific Polymerase assays (KASP) and analyzed in two F6-derived recombinant inbred line (RIL) populations derived from the crosses between two resistant cultivars ‘Wesley’ and ‘Deliver’ and a susceptible line ‘OK03825-5403-6’. Linkage analysis mapped this gene on chromosome 5D at intervals of 5.1 cM and 3.4 cM in the two populations, respectively. The two flanking markers in both populations delimited the gene to a 620 kb region where 19 genes were annotated. Comparative analysis identified a syntenic region of 660 kb in Ae. tauschii with 18 annotated genes and a syntenic region in chromosome 1 of B. distachyon. The candidate region includes several disease resistance related genes and we identified a PTI1-like tyrosine-protein kinase 1 gene as a putative candidate gene for Sbwm1. The two flanking SNPs for Sbwm1 can effectively separate the resistant and susceptible lines in a new diversity panel of 159 wheat germplasm. The results from this study lay a solid foundation for the cloning, functional characterization and marker-assisted selection of Sbwm1.
- Published
- 2020
30. A rare gain of function mutation in a wheat tandem kinase confers resistance to powdery mildew
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Yahui Li, Hongjie Li, Yang Lijun, Yan Zhang, Jan Dvorak, Zhenzhong Wang, Shi Wenqi, Zhiyong Liu, Cuimin Liu, Beibei Li, Miaomiao Li, Huaizhi Zhang, Li Guo, Yu Dazhao, Karin R. Deal, Dan Qiu, Lingli Dong, Jing Li, Naxin Huo, Yong Q. Gu, Panpan Zhang, Guanghao Guo, Ning Wang, Keyu Zhu, Qiuhong Wu, Ming-Cheng Luo, Ping Lu, Yongxing Chen, and Jingzhong Xie
- Subjects
0106 biological sciences ,0301 basic medicine ,China ,Science ,Protein domain ,Mutant ,General Physics and Astronomy ,Mutagenesis (molecular biology technique) ,Blumeria graminis ,Biology ,Genes, Plant ,01 natural sciences ,Article ,Plant breeding ,General Biochemistry, Genetics and Molecular Biology ,03 medical and health sciences ,Plant immunity ,Transformation, Genetic ,Ascomycota ,Protein Domains ,lcsh:Science ,Gene ,Triticum ,Disease Resistance ,Plant Diseases ,Plant Proteins ,2. Zero hunger ,Genetics ,Multidisciplinary ,Haplotype ,food and beverages ,Hydrogen Peroxide ,General Chemistry ,Plants, Genetically Modified ,biology.organism_classification ,Transformation (genetics) ,Natural variation in plants ,030104 developmental biology ,Mutagenesis ,Gain of Function Mutation ,lcsh:Q ,Protein Kinases ,Powdery mildew ,010606 plant biology & botany - Abstract
Powdery mildew, caused by Blumeria graminis f. sp. tritici (Bgt), is one of the most destructive diseases that pose a great threat to wheat production. Wheat landraces represent a rich source of powdery mildew resistance. Here, we report the map-based cloning of powdery mildew resistance gene Pm24 from Chinese wheat landrace Hulutou. It encodes a tandem kinase protein (TKP) with putative kinase-pseudokinase domains, designated WHEAT TANDEM KINASE 3 (WTK3). The resistance function of Pm24 was validated by transgenic assay, independent mutants, and allelic association analyses. Haplotype analysis revealed that a rare 6-bp natural deletion of lysine-glycine codons, endemic to wheat landraces of Shaanxi Province, China, in the kinase I domain (Kin I) of WTK3 is critical for the resistance function. Transgenic assay of WTK3 chimeric variants revealed that only the specific two amino acid deletion, rather than any of the single or more amino acid deletions, in the Kin I of WTK3 is responsible for gaining the resistance function of WTK3 against the Bgt fungus., Powdery mildew is a major threat to world wheat yields. Here the authors describe the map-based cloning of Pm24, a gain-of-function powdery mildew resistance allele that encodes a tandem kinase-pseudokinase protein with a deletion in a kinase domain that is endemic to certain wheat landraces.
- Published
- 2020
31. Genome-wide introgression from a bread wheat × Lophopyrum elongatum amphiploid into wheat
- Author
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Frank M. You, Tingting Zhu, Julia Malvick, Jiale Xu, Le Wang, Patrick E. McGuire, Ramesh K Ramasamy, Ming-Cheng Luo, Jan Dvorak, and Karin R. Deal
- Subjects
Genetic Markers ,0106 biological sciences ,Germplasm ,Introgression ,Chromosomal translocation ,Poaceae ,Polymorphism, Single Nucleotide ,01 natural sciences ,Genome ,Chromosomes, Plant ,Genetics ,Inbreeding ,Triticeae ,Gene ,Crosses, Genetic ,Triticum ,Ploidies ,biology ,food and beverages ,Bread ,General Medicine ,biology.organism_classification ,Ploidy ,Agronomy and Crop Science ,Genome, Plant ,010606 plant biology & botany ,Biotechnology ,SNP array - Abstract
We introgressed wheatgrass germplasm from the octoploid amphiploid Triticum aestivum× Lophopyrum elongatum into wheat by manipulating the wheat Ph1 gene and discovered and characterized 130 introgression lines harboring single or, in various combinations, complete and recombined L. elongatum chromosomes. Diploid wheatgrass Lophopyrum elongatum (genomes EE) possesses valuable traits for wheat genetics and breeding. We evaluated several strategies for introgression of this germplasm into wheat. To detect it, we developed and validated multiplexed sets of Sequenom MassARRAY single nucleotide polymorphism (SNP) markers, which differentiated disomic and monosomic L. elongatum chromosomes from wheat chromosomes. We identified 130 introgression lines (ILs), which harbored 108 complete and 89 recombined L. elongatum chromosomes. Of the latter, 59 chromosomes were recombined by one or more crossovers and 30 were involved in centromeric (Robertsonian) translocations or were telocentric. To identify wheat chromosomes substituted for or recombined with L. elongatum chromosomes, we genotyped the ILs with the wheat 90-K Infinium SNP array. We found that most of the wheat 90-K probes correctly detected their targets in the L. elongatum genome and showed that some wheat SNPs are ancient and had originated prior to the divergence of the wheat and L. elongatum lineages. Of the 130 ILs, 52% were homozygous for Ph1 deletion and thus are staged to be recombined further. We failed to detect in the L. elongatum genome the 4/5 reciprocal translocation that has been reported in Thinopyrum bessarabicum and several other Triticeae genomes.
- Published
- 2020
32. Aegilops tauschii genome assembly Aet v5.0 features greater sequence contiguity and improved annotation
- Author
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Pingchuan Li, Patrick J. Gulick, Tingting Zhu, Frank M. You, Hikmet Budak, Turgay Unver, Hongye Zhou, Katrien M. Devos, Thomas Lux, David R. Nelson, Ming-Cheng Luo, Gábor Galiba, Patrick E. McGuire, Balázs Kalapos, Naxin Huo, Patricia Baldrich, Jeffrey L. Bennetzen, Yong Q. Gu, Blake C. Meyers, Jorge Dubcovsky, Le Wang, Juan C Rodriguez, Klaus F. X. Mayer, Manuel Spannagl, Karin R. Deal, Jan Dvorak, and Dawe, R
- Subjects
Transposable element ,AcademicSubjects/SCI01140 ,disease resistance ,AcademicSubjects/SCI00010 ,Aegilops ,Sequence assembly ,Computational biology ,Biology ,QH426-470 ,Poaceae ,AcademicSubjects/SCI01180 ,Pacific Biosciences ,Disease Resistance ,Hc-sirna ,Mirna ,Optical Map ,Phasirna ,Trf ,Trna ,Transposable Elements ,Chromosome regions ,Genetics ,Aegilops tauschii ,tRF ,Molecular Biology ,Gene ,tRNA ,Genetics (clinical) ,Triticum ,miRNA ,Whole genome sequencing ,Genome ,Contig ,hc-siRNA ,Human Genome ,phasiRNA ,Plant ,biology.organism_classification ,Genome Report ,Plant Breeding ,Transfer RNA ,AcademicSubjects/SCI00960 ,transposable elements ,optical map ,Genome, Plant ,Biotechnology - Abstract
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 here. Two new optical maps were constructed and used in the revision of pseudomolecules. Gaps were closed with Pacific Biosciences long-read contigs, decreasing the gap number by 38,899. Transposable elements and protein-coding genes were reannotated. The number of annotated high-confidence genes was reduced from 39,635 in Aet v4.0 to 32,885 in Aet v5.0. A total of 2245 biologically important genes, including those affecting plant phenology, grain quality, and tolerance of abiotic stresses in wheat, was manually annotated and disease-resistance genes were annotated by a dedicated pipeline. Disease-resistance genes encoding nucleotide-binding site domains, receptor-like protein kinases, and receptor-like proteins were preferentially located in distal chromosome regions, whereas those encoding transmembrane coiled-coil proteins were dispersed more evenly along the chromosomes. Discovery, annotation, and expression analyses of microRNA (miRNA) precursors, mature miRNAs, and phasiRNAs are reported, including miRNA target genes. Other small RNAs, such as hc-siRNAs and tRFs, were characterized. These advances enhance the utility of the Ae. tauschii genome sequence for wheat genetics, biotechnology, and breeding.
- Published
- 2021
33. Optical maps refine the bread wheat Triticum aestivum cv. Chinese Spring genome assembly
- Author
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Le Wang, Frédéric Choulet, Juan C Rodriguez, Kellye Eversole, Hélène Rimbert, Martin Mascher, Yong Q. Gu, Rudi Appels, Tingting Zhu, Romain De Oliveira, Gabriel Keeble-Gagnère, Josquin Tibbits, Karin R. Deal, Jan Dvorak, Jane Rogers, Ming-Cheng Luo, UCDavis (UCD), Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Clermont Auvergne (UCA), Agriculture Victoria (AgriBio), International Wheat Genome Sequencing Consortium, Eau Claire (IWGS), United States Department of Agriculture (USDA), Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben] (IPK-Gatersleben), United States Department of Agriculture (USDA) : 2030-21430-014-00-D, National Science Foundation (NSF ) : IOS-1929053, and ANR-10-BTBR-0003,BREEDWHEAT,Développer de nouvelles variétés de blé pour une agriculture durable(2010)
- Subjects
0106 biological sciences ,0301 basic medicine ,Resource ,Chromosomes, Artificial, Bacterial ,[SDV]Life Sciences [q-bio] ,Sequence assembly ,gene collinearity ,Plant Science ,Computational biology ,Biology ,01 natural sciences ,Genome ,DNA sequencing ,Chromosomes, Plant ,03 medical and health sciences ,Hi-C ,Genetics ,RefSeq ,[SDV.BV]Life Sciences [q-bio]/Vegetal Biology ,Genome size ,direct label and stain ,Triticum ,2. Zero hunger ,Comparative genomics ,Whole genome sequencing ,Contig ,Hi‐C ,pseudomolecule ,Chromosome Mapping ,food and beverages ,Molecular Sequence Annotation ,Cell Biology ,transposable element ,030104 developmental biology ,DNA Transposable Elements ,Genome, Plant ,010606 plant biology & botany - Abstract
Summary Until recently, achieving a reference‐quality genome sequence for bread wheat was long thought beyond the limits of genome sequencing and assembly technology, primarily due to the large genome size and > 80% repetitive sequence content. The release of the chromosome scale 14.5‐Gb IWGSC RefSeq v1.0 genome sequence of bread wheat cv. Chinese Spring (CS) was, therefore, a milestone. Here, we used a direct label and stain (DLS) optical map of the CS genome together with a prior nick, label, repair and stain (NLRS) optical map, and sequence contigs assembled with Pacific Biosciences long reads, to refine the v1.0 assembly. Inconsistencies between the sequence and maps were reconciled and gaps were closed. Gap filling and anchoring of 279 unplaced scaffolds increased the total length of pseudomolecules by 168 Mb (excluding Ns). Positions and orientations were corrected for 233 and 354 scaffolds, respectively, representing 10% of the genome sequence. The accuracy of the remaining 90% of the assembly was validated. As a result of the increased contiguity, the numbers of transposable elements (TEs) and intact TEs have increased in IWGSC RefSeq v2.1 compared with v1.0. In total, 98% of the gene models identified in v1.0 were mapped onto this new assembly through development of a dedicated approach implemented in the MAGAAT pipeline. The numbers of high‐confidence genes on pseudomolecules have increased from 105 319 to 105 534. The reconciled assembly enhances the utility of the sequence for genetic mapping, comparative genomics, gene annotation and isolation, and more general studies on the biology of wheat., Significance Statement This new release of bread wheat cv. Chinese Spring reference genome sequence, IWGSC RefSeq v2.1, features correction of assembly errors affecting approximately 10% of the prior IWGSC RefSeq v1.0 release using genome‐wide optical maps and filling of gaps with single‐molecule long‐reads as well as incorporating re‐annotation of TEs and re‐computation of gene coordinates. These refinements enhance the sequence utility for breeding and research applications.
- Published
- 2021
34. Co-located quantitative trait loci mediate resistance to Agrobacterium tumefaciens, Phytophthora cinnamomi, and P. pini in Juglans microcarpa × J. regia hybrids
- Author
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Dianne Velasco, Jan Dvorak, Ramesh K Ramasamy, Mallikarjuna K. Aradhya, N. J. Ott, Ali E. McClean, Andreas Westphal, Patrick J. Brown, Charles A. Leslie, Abhaya M. Dandekar, Gregory T. Browne, Daniel A. Kluepfel, and Ming-Cheng Luo
- Subjects
Juglans microcarpa ,food and beverages ,Plant Science ,Agrobacterium tumefaciens ,Horticulture ,Biology ,Phytophthora cinnamomi ,biology.organism_classification ,Biochemistry ,Article ,Plant breeding ,Good Health and Well Being ,Plant hybridization ,Botany ,Genetics ,Gall ,Phytophthora ,Rootstock ,Biotechnology ,Hybrid ,Juglans - Abstract
Soil-borne plant pathogens represent a serious threat that undermines commercial walnut (Juglans regia) production worldwide. Crown gall, caused by Agrobacterium tumefaciens, and Phytophthora root and crown rots, caused by various Phytophthora spp., are among the most devastating walnut soil-borne diseases. A recognized strategy to combat soil-borne diseases is adoption of resistant rootstocks. Here, resistance to A. tumefaciens, P. cinnamomi, and P. pini is mapped in the genome of Juglans microcarpa, a North American wild relative of cultivated walnut. Half-sib J. microcarpa mother trees DJUG 31.01 and DJUG 31.09 were crossed with J. regia cv. Serr, producing 353 and 400 hybrids, respectively. Clonally propagated hybrids were genotyped by sequencing to construct genetic maps for the two populations and challenged with the three pathogens. Resistance to each of the three pathogens was mapped as a major QTL on the long arm of J. microcarpa chromosome 4D and was associated with the same haplotype, designated as haplotype b, raising the possibility that the two mother trees were heterozygous for a single Mendelian gene conferring resistance to all three pathogens. The deployment of this haplotype in rootstock breeding will facilitate breeding of a walnut rootstock resistant to both crown gall and Phytophthora root and crown rots.
- Published
- 2021
35. Recombination between homoeologous chromosomes induced in durum wheat by the Aegilops speltoides Su1-Ph1 suppressor
- Author
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Xiongtao Dai, Yun Zhou, Ming-Cheng Luo, Le Wang, Patrick E. McGuire, Assaf Distelfeld, Fang Nie, Jan Dvorak, Chun-Peng Song, and Hao Li
- Subjects
Aegilops ,Introgression ,Genes, Plant ,Chromosomes, Plant ,Gene mapping ,Meiosis ,Genetics ,medicine ,Plant breeding ,Triticum ,Recombination, Genetic ,biology ,medicine.diagnostic_test ,Chromosome Mapping ,food and beverages ,Chromosome ,General Medicine ,biology.organism_classification ,Aegilops speltoides ,Tetraploidy ,Plant Breeding ,Agronomy and Crop Science ,Recombination ,Biotechnology ,Fluorescence in situ hybridization - Abstract
Su1-Ph1, which we previously introgressed into wheat from Aegilops speltoides, is a potent suppressor of Ph1 and a valuable tool for gene introgression in tetraploid wheat. We previously introgressed Su1-Ph1, a suppressor of the wheat Ph1 gene, from Aegilops speltoides into durum wheat cv Langdon (LDN). Here, we evaluated the utility of the introgressed suppressor for inducing introgression of alien germplasm into durum wheat. We built LDN plants heterozygous for Su1-Ph1 that simultaneously contained a single LDN chromosome 5B and a single Ae. searsii chromosome 5Sse, which targeted them for recombination. We genotyped 28 BC1F1 and 84 F2 progeny with the wheat 90-K Illumina single-nucleotide polymorphism assay and detected extensive recombination between the two chromosomes, which we confirmed by non-denaturing fluorescence in situ hybridization (ND-FISH). We constructed BC1F1 and F2 genetic maps that were 65.31 and 63.71 cM long, respectively. Recombination rates between the 5B and 5Sse chromosomes were double the expected rate computed from their meiotic pairing, which we attributed to selection against aneuploid gametes. Recombination rate between 5B and 5Sse was depressed compared to that between 5B chromosomes in the proximal region of the long arm. We integrated ND-FISH signals into the genetic map and constructed a physical map, which we used to map a 172,188,453-bp Ph1 region. Despite the location of the region in a low-recombination region of the 5B chromosome, we detected three crossovers in it. Our data show that Su1-Ph1 is a valuable tool for gene introgression and gene mapping based on recombination between homoeologous chromosomes in wheat.
- Published
- 2019
36. A fine‐scale genetic linkage map reveals genomic regions associated with economic traits in walnut (Juglans regia)
- Author
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Dianne Velasco, Ming-Cheng Luo, Frank M. You, Jirui Wang, Mallikarjuna K. Aradhya, Jan Dvorak, C.A. Leslie, Ramesh K Ramasamy, and Abhaya M. Dandekar
- Subjects
Scale (ratio) ,biology ,Evolutionary biology ,Genetics ,Genetic linkage map ,Plant Science ,Marker-assisted selection ,biology.organism_classification ,Agronomy and Crop Science ,Juglans - Published
- 2019
37. Improved Genome Sequence of Wild Emmer Wheat Zavitan with the Aid of Optical Maps
- Author
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Jan Dvorak, Assaf Distelfeld, Raz Avni, Le Wang, Karin R. Deal, Juan C Rodriguez, Tingting Zhu, Ming-Cheng Luo, and Patrick E. McGuire
- Subjects
0106 biological sciences ,0301 basic medicine ,Optical Map ,DLS ,Sequence assembly ,Genomics ,Computational biology ,Biology ,QH426-470 ,01 natural sciences ,Genome ,03 medical and health sciences ,Genetics ,Molecular Biology ,Genetics (clinical) ,Triticum turgidum ,Triticum ,2. Zero hunger ,Whole genome sequencing ,Genome assembly ,Whole Genome Sequencing ,Triticum dicoccoides ,Genome Report ,030104 developmental biology ,Wild emmer wheat ,Pseudomolecules ,Genome, Plant ,010606 plant biology & botany - Abstract
Wild emmer (Triticum turgidum ssp. dicoccoides) is the progenitor of all modern cultivated tetraploid wheat. Its genome is large (> 10 Gb) and contains over 80% repeated sequences. The successful whole-genome-shotgun assembly of the wild emmer (accession Zavitan) genome sequence (WEW_v1.0) was an important milestone for wheat genomics. In an effort to improve this assembly, an optical map of accession Zavitan was constructed using Bionano Direct Label and Stain (DLS) technology. The map spanned 10.4 Gb. This map and another map produced earlier by us with the Bionano’s Nick Label Repair and Stain (NLRS) technology were used to improve the current wild emmer assembly. The WEW_v1.0 assembly consisted of 151,912 scaffolds. Of them, 3,102 could be confidently aligned on the optical maps. Forty-seven were chimeric. They were disjoined and new scaffolds were assembled with the aid of the optical maps. The total number of scaffolds was reduced from 151,912 to 149,252 and N50 increased from 6.96 Mb to 72.63 Mb. Of the 149,252 scaffolds, 485 scaffolds, which accounted for 97% of the total genome length, were aligned and oriented on genetic maps, and new WEW_v2.0 pseudomolecules were constructed. The new pseudomolecules included 333 scaffolds (68.51 Mb) which were originally unassigned, 226 scaffolds (554.84 Mb) were placed into new locations, and 332 scaffolds (394.83 Mb) were re-oriented. The improved wild emmer genome assembly is an important resource for understanding genomic modification that occurred by domestication.
- Published
- 2019
38. GenoProfiler: batch processing of high-throughput capillary fingerprinting data.
- Author
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Frank M. You, Ming-Cheng Luo, Yong Qiang Gu, Gerard R. Lazo, Karin Deal, Jan Dvorak, and Olin D. Anderson
- Published
- 2007
- Full Text
- View/download PDF
39. Computational Identification and Comparative Analysis of Conserved miRNAs and Their Putative Target Genes in the Juglans regia and J. microcarpa Genomes
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Jan Dvorak, Ming-Cheng Luo, Tingting Zhu, Karin R. Deal, and Le Wang
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0106 biological sciences ,0301 basic medicine ,walnut ,Plant Science ,01 natural sciences ,Genome ,subgenome ,Mirna target ,03 medical and health sciences ,Transcription (biology) ,microRNA ,Gene ,Transcription factor ,Ecology, Evolution, Behavior and Systematics ,miRNA ,Genetics ,Ecology ,biology ,Botany ,Chromosome ,biology.organism_classification ,030104 developmental biology ,QK1-989 ,010606 plant biology & botany ,Juglans ,homoeologous - Abstract
MicroRNAs (miRNAs) are important factors for the post-transcriptional regulation of protein-coding genes in plants and animals. They are discovered either by sequencing small RNAs or computationally. We employed a sequence-homology-based computational approach to identify conserved miRNAs and their target genes in Persian (English) walnut, Juglans regia, and its North American wild relative, J. microcarpa. A total of 119 miRNA precursors (pre-miRNAs) were detected in the J. regia genome and 121 in the J. microcarpa genome and miRNA target genes were predicted and their functional annotations were performed in both genomes. In the J. regia genome, 325 different genes were targets, 87.08% were regulated by transcript cleavage and 12.92% by translation repression. In the J. microcarpa genome, 316 different genes were targets, 88.92% were regulated by transcript cleavage and 11.08% were regulated by translation repression. Totals of 1.3% and 2.0% of all resistance gene analogues (RGA) and 2.7% and 2.6% of all transcription factors (TFs) were regulated by miRNAs in the J. regia and J. microcarpa genomes, respectively. Juglans genomes evolved by a whole genome duplication (WGD) and consist of eight pairs of fractionated homoeologous chromosomes. Within each pair, the chromosome that has more genes with greater average transcription also harbors more pre-miRNAs and more target genes than its homoeologue. While only minor differences were detected in pre-miRNAs between the J. regia and J. microcarpa genomes, about one-third of the pre-miRNA loci were not conserved between homoeologous chromosome within each genome. Pre-miRNA and their corresponding target genes showed a tendency to be collocated within a subgenome.
- Published
- 2020
- Full Text
- View/download PDF
40. Introgression of perennial growth habit from Lophopyrum elongatum into wheat
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Jiale Xu, Patrick E. McGuire, Jan Dvorak, Hamid Dehghani, Ming-Cheng Luo, Juliya Abbasi, and Karin R. Deal
- Subjects
0106 biological sciences ,Germplasm ,Genotype ,Population ,Introgression ,Locus (genetics) ,Biology ,Genes, Plant ,Poaceae ,01 natural sciences ,Genome ,Polymorphism, Single Nucleotide ,Chromosomes, Plant ,Polyploidy ,Genetics ,education ,Gene ,Triticum ,education.field_of_study ,food and beverages ,Chromosome ,Chromosome Mapping ,General Medicine ,Plant Breeding ,Chromosome Arm ,Agronomy and Crop Science ,010606 plant biology & botany ,Biotechnology - Abstract
A locus for perennial growth was mapped on Lophopyrum elongatum chromosome arm 4ES and introgressed into the wheat genome. Evidence was obtained that in addition to chromosome 4E, other L. elongatum chromosomes control perennial growth. Monocarpy versus polycarpy is one of the fundamental developmental dichotomies in flowering plants. Advances in the understanding of the genetic basis of this dichotomy are important for basic biological reasons and practically for genetic manipulation of growth development in economically important plants. Nine wheat introgression lines (ILs) harboring germplasm of the Lophopyrum elongatum genome present in the octoploid amphiploid Triticum aestivum cv. Chinese Spring (subgenomes AABBDD) × L. elongatum (genomes EE) were selected from a population of ILs developed earlier. These ILs were employed here in genomic analyses of post-sexual cycle regrowth (PSCR), which is a component of polycarpy in caespitose L. elongatum. Analyses of disomic substitution (DS) lines confirmed that L. elongatum chromosome 4E confers PSCR on wheat. The gene was mapped into a short distal region of L. elongatum arm 4ES and was tentatively named Pscr1. ILs harboring recombined chromosomes with 4ES segments, including Pscr1, incorporated into the distal part of the 4DS chromosome arm were identified. Based on the location, Pscr1 is not orthologous with the rice rhizome-development gene Rhz2 located on rice chromosome Os3, which is homoeologous with chromosome 4E, but it may correspond to the Teosinte branched1 (TB1) gene, which is located in the introgressed region in the L. elongatum and Ae. tauschii genomes. A hexaploid IL harboring a large portion of the E-genome but devoid of chromosome 4E also expressed PSCR, which provided evidence that perennial growth is controlled by genes on other L. elongatum chromosomes in addition to 4E.
- Published
- 2020
41. A rare single nucleotide variant in Pm5e confers powdery mildew resistance in common wheat
- Author
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Yahui Li, Hongjie Li, Sanzhen Liu, Ming-Cheng Luo, Yan Zhang, Li-li Wang, Yong Wang, Beibei Li, Karin R. Deal, Dan Qiu, Huaizhi Zhang, Tiezhu Hu, Naxin Huo, Keyu Zhu, Qiuhong Wu, Zhiyong Liu, Panpan Zhang, Guanghao Guo, Jingting Li, Miaomiao Li, Lingli Dong, Ping Lu, Yongxing Chen, Yong Q. Gu, and Jingzhong Xie
- Subjects
0106 biological sciences ,0301 basic medicine ,Nonsynonymous substitution ,Candidate gene ,China ,Physiology ,Population ,Plant Science ,Biology ,Genes, Plant ,01 natural sciences ,03 medical and health sciences ,Allele ,Common wheat ,education ,Gene ,Triticum ,Disease Resistance ,Plant Diseases ,Genetics ,education.field_of_study ,Nucleotides ,Haplotype ,food and beverages ,Plant Breeding ,030104 developmental biology ,Powdery mildew ,010606 plant biology & botany - Abstract
Powdery mildew poses severe threats to wheat production. The most sustainable way to control this disease is through planting resistant cultivars. We report the map-based cloning of the powdery mildew resistance allele Pm5e from a Chinese wheat landrace. We applied a two-step bulked segregant RNA sequencing (BSR-Seq) approach in developing tightly linked or co-segregating markers to Pm5e. The first BSR-Seq used phenotypically contrasting bulks of recombinant inbred lines (RILs) to identify Pm5e-linked markers. The second BSR-Seq utilized bulks of genetic recombinants screened from a fine-mapping population to precisely quantify the associated genomic variation in the mapping interval, and identified the Pm5e candidate genes. The function of Pm5e was validated by transgenic assay, loss-of-function mutants and haplotype association analysis. Pm5e encodes a nucleotide-binding domain leucine-rich-repeat-containing (NLR) protein. A rare nonsynonymous single nucleotide variant (SNV) within the C-terminal leucine rich repeat (LRR) domain is responsible for the gain of powdery mildew resistance function of Pm5e, an allele endemic to wheat landraces of Shaanxi province of China. Results from this study demonstrate the value of landraces in discovering useful genes for modern wheat breeding. The key SNV associated with powdery mildew resistance will be useful for marker-assisted selection of Pm5e in wheat breeding programs.
- Published
- 2020
42. BatchPrimer3: A high throughput web application for PCR and sequencing primer design.
- Author
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Frank M. You, Naxin Huo, Yong Qiang Gu, Ming-Cheng Luo, Yaqin Ma, Dave Hane, Gerard R. Lazo, Jan Dvorak, and Olin D. Anderson
- Published
- 2008
- Full Text
- View/download PDF
43. A CNL protein in wild emmer wheat confers powdery mildew resistance
- Author
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Yongxing Chen, Rongge Wang, Ping Lu, Wei Liu, Yiwen Li, Huaizhi Zhang, Tzion Fahima, Panpan Zhang, Beibei Li, Guanghao Guo, Z. Wang, Keyu Zhu, Lingli Dong, Dan Qiu, Zhiyong Liu, Yu Dazhao, Jingzhong Xie, Eviatar Nevo, Yahui Li, Hongjie Li, Miaomiao Li, Shi Wenqi, Yang Lijun, Yan Zhang, Ming-Cheng Luo, Chengguo Yuan, and Qiuhong Wu
- Subjects
0106 biological sciences ,0301 basic medicine ,Genetics ,Positional cloning ,biology ,Physiology ,food and beverages ,Blumeria graminis ,Plant Science ,biology.organism_classification ,Genes, Plant ,01 natural sciences ,03 medical and health sciences ,030104 developmental biology ,Ascomycota ,Cultivar ,Gene pool ,Common wheat ,Domestication ,Gene ,Powdery mildew ,Triticum ,010606 plant biology & botany ,Disease Resistance ,Plant Diseases - Abstract
Powdery mildew, a fungal disease caused by Blumeria graminis f. sp. tritici (Bgt), has a serious impact on wheat production. Loss of resistance in cultivars prompts a continuing search for new sources of resistance. Wild emmer wheat (Triticum turgidum ssp. dicoccoides, WEW), the progenitor of both modern tetraploid and hexaploid wheats, harbors many powdery mildew resistance genes. We report here the positional cloning and functional characterization of Pm41, a powdery mildew resistance gene derived from WEW, which encodes a coiled-coil, nucleotide-binding site and leucine-rich repeat protein (CNL). Mutagenesis and stable genetic transformation confirmed the function of Pm41 against Bgt infection in wheat. We demonstrated that Pm41 was present at a very low frequency (1.81%) only in southern WEW populations. It was absent in other WEW populations, domesticated emmer, durum, and common wheat, suggesting that the ancestral Pm41 was restricted to its place of origin and was not incorporated into domesticated wheat. Our findings emphasize the importance of conservation and exploitation of the primary WEW gene pool, as a valuable resource for discovery of resistance genes for improvement of modern wheat cultivars.
- Published
- 2019
44. Optical and physical mapping with local finishing enables megabase-scale resolution of agronomically important regions in the wheat genome
- Author
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Helena Toegelová, Hana Šimková, Andrew G. Sharpe, Benoit Darrier, Adam M. Dimech, Jan Šafář, Nathan S. Watson-Haigh, Pierre Sourdille, Zeev Frenkel, Matthew J. Hayden, Frédéric Choulet, Johan Nyström-Persson, Iwgsc, Dangqun Cui, Gabriel Keeble-Gagnère, Matthias Pfeifer, Sébastien Boisvert, Angéla Juhász, Jaroslav Doležel, Francisco Câmara, Simone Rochfort, Matthew Tinning, Colin Cavanagh, Kerrie Forrest, Paul Eckermann, Delphine Fleury, Ute Baumann, Aurélien Bernard, Ming-Cheng Luo, B. Emma Huang, Jen Taylor, Rudi Appels, Dal-Hoe Koo, Zhengang Ru, David Konkin, Raj K. Pasam, Philippe Rigault, Michael Abrouk, Don Isdale, Abraham B. Korol, Marc-Alexandre Nolin, Josquin Tibbits, Agriculture Victoria Research, Department of Economic Development, Jobs, Transport and Resources, AgriBio, GYDLE, Center for Organismal Studies, Heidelberg University, Institute of Evolution, University of Haifa [Haifa], CSIRO Plant Industrie, Desert Agriculture Initiati, King Abdullah University of Science and Technology (KAUST), Institute of Experimental Botany of the Czech Academy of Sciences (IEB / CAS), Czech Academy of Sciences [Prague] (CAS), Global Institute of Food Security, University of Saskatchewan [Saskatoon] (U of S), Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), School of Agriculture, Food and Wine, University of Adelaide, Veterinary and Agriculture, Murdoch University, Plant Genetics and Bioinformatics, Department of Plant Sciences [Univ California Davis] (Plant - UC Davis), University of California [Davis] (UC Davis), University of California (UC)-University of California (UC)-University of California [Davis] (UC Davis), University of California (UC)-University of California (UC), Bioinformatics and Genomics Program, Centre for Genomic Regulation (CRG), Universitat Pompeu Fabra [Barcelona] (UPF), Plant Genome and Systems Biology, Helmholtz Diabetes Center at Helmholtz Zentrum, GYB Akihabara, Wheat Genetics Resource Center and Department of Plant Pathology, Kansas State University, Australian Genome Research Facility, National Research Council of Canada, Henan Agricultural University, Australian Government Department of Industry, Innovation, Science, Research and Tertiary Education ACSRF00542, BioPlatforms Australia (BPA), Grains Research Development Corporation UMU00037, CSIRO Plant Industry, Australia, Agriculture Victoria Research, National Science Foundation (NSF) grant 1338897, INB ('Instituto National de Bioinformatica') Project (ISCIII - FEDER) PT13/0001/0021, Czech Ministry of Education Youth and Sports (National Program of Sustainability) LO1204, University of Saskatchewan, UC Davis Plant Sciences, University of Heidelberg, Institute of Experimental Botany (IEB), Czech Academy of Sciences [Prague] (ASCR), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Institut National de la Recherche Agronomique (INRA), Universitat Pompeu Fabra [Barcelona], and Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP)
- Subjects
0106 biological sciences ,0301 basic medicine ,Chromosomes, Artificial, Bacterial ,Optical Phenomena ,01 natural sciences ,Genome ,Megabase-scale integration ,570 Life sciences ,wheat ,chromosome ,lcsh:QH301-705.5 ,Paired-end tag ,Triticum ,2. Zero hunger ,0303 health sciences ,Vegetal Biology ,Physical Chromosome Mapping ,Agriculture ,Wheat Sequence Finishing ,Megabase-scale Integration ,Optical/physical Maps Grain Quality ,Yield ,restriction map ,Seeds ,Wheat sequence finishing ,Genome, Plant ,carte physique ,lcsh:QH426-470 ,Centromere ,Genomics ,Computational biology ,Biology ,Chromosomes, Plant ,DNA sequencing ,03 medical and health sciences ,blé ,[SDV.BV]Life Sciences [q-bio]/Vegetal Biology ,Optical/physical maps Grain quality ,030304 developmental biology ,Whole genome sequencing ,Bacterial artificial chromosome ,génome ,Research ,Chromosome ,Fructans ,lcsh:Genetics ,030104 developmental biology ,lcsh:Biology (General) ,Human genome ,Biologie végétale ,010606 plant biology & botany ,Reference genome - Abstract
GK-G, PR, JT contributed equally to experimental design, data analysis andinterpretation/writing of manuscript;, RP, MH, KF, RA genome analyses andinterpretation; ZF, AK data analysis and physical map construction; EH, CC, JTMAGIC map construction; MA rice-wheat phylogenomic; AS, DK, mate-pairlibraries; PS. BD, FC, PL, Chinese Spring x Renan molecular genetic map andannotation of genome sequence; NW-H, UB, PE, DF, AJ analysis of genespace and QTL, SB, M-AN, development of Bionano alignments and tools; JD,HŠ, JŠ, HT, flow sorting of chromosomes, BAC library construction andBionano maps; M-CL fingerprinting of BAC library; FC, MP gene annotation;DC, ZR, AK58 genome assembly, JN-P, genome assembly; DI in-housesoftware development; IWGSC, genome assembly network, D-HK, CENH3antibody cytology; RA, planning of experiments and writing of manuscript.All authors have read and approved the final manuscript.; Background: Numerous scaffold-level sequences for wheat are now being released and, in this context, we report on a strategy for improving the overall assembly to a level comparable to that of the human genome.Results: Using chromosome 7A of wheat as a model, sequence-finished megabase-scale sections of this chromosome were established by combining a new independent assembly using a bacterial artificial chromosome (BAC)-based physical map, BAC pool paired-end sequencing, chromosome-arm-specific mate-pair sequencing and Bionano optical mapping with the International Wheat Genome Sequencing Consortium RefSeq v1.0 sequence and its underlying raw data. The combined assembly results in 18 super-scaffolds across the chromosome. The value of finished genome regions is demonstrated for two approximately 2.5 Mb regions associated with yield and the grain quality phenotype of fructan carbohydrate grain levels. In addition, the 50 Mb centromere region analysis incorporates cytological data highlighting the importance of non-sequence data in the assembly of this complex genome region.Conclusions: Sufficient genome sequence information is shown to now be available for the wheat community to produce sequence-finished releases of each chromosome of the reference genome. The high-level completion identified that an array of seven fructosyl transferase genes underpins grain quality and that yield attributes are affected by five F-box-only-protein-ubiquitin ligase domain and four root-specific lipid transfer domain genes. The completed sequence also includes the centromere.
- Published
- 2018
45. Analysis of Brachypodium genomes with genome-wide optical maps
- Author
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Jan Dvorak, Zhiyong Liu, Karin R. Deal, Tingting Zhu, Ming-Cheng Luo, Juan C Rodriguez, Zhaorong Hu, and John P. Vogel
- Subjects
0301 basic medicine ,Sequence assembly ,Genome ,Chromosomes, Plant ,Evolution, Molecular ,Polyploidy ,Structural variation ,03 medical and health sciences ,Species Specificity ,Polyploid ,Genetic model ,Genetics ,Molecular Biology ,Phylogeny ,biology ,General Medicine ,biology.organism_classification ,Diploidy ,030104 developmental biology ,Evolutionary biology ,Brachypodium ,Brachypodium distachyon ,Ploidy ,Biotechnology - Abstract
Brachypodium distachyon (n = 5) is a diploid and has been widely used as a genetic model. Brachypodium stacei (n = 10) and B. hybridum (n = 15) are species that are related to B. distachyon, leading to an hypothesis that they are part of a polyploid series based on x = 5. Several lines of evidence suggest that this hypothesis is incorrect and that the genomes of the three taxa may have evolved by a more complex process. We constructed an optical whole-genome BioNano genome (BNG) map for each species and did pairwise alignment of the BNG maps. The maps showed that B. distachyon and B. stacei are both diploid, in spite of B. stacei having twice as many chromosomes as B. distachyon, and that B. hybridum is an allopolyploid formed from hybridization between B. distachyon and B. stacei. This study also demonstrated the use of BNG maps in the detection and quantification of structural variants among the genomes.
- Published
- 2018
46. Chromosome 3DL Arm Assembly and Annotation v1
- Author
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Fu-Hao Lu, Neil McKenzie, Laura-Jayne Gardiner, Ming-Cheng Luo, Anthony Hall, and Michael W Bevan
- Abstract
This protocol descriobed the detailed procedures how we made the chromosome 3D long arm pseudomolecule in hexaploid wheat (Triticum aestivum, AABBDD).
- Published
- 2019
47. Transcription Analyses v1
- Author
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Fu-Hao Lu, Neil McKenzie, Laura-Jayne Gardiner, Ming-Cheng Luo, Anthony Hall, and Michael W Bevan
- Abstract
This protocol describes how we preccessed the RNAseq data of wheat and Aegilops tauschii.
- Published
- 2019
48. Bisulphite Sequencing v1
- Author
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Fu-Hao Lu, Neil McKenzie, Laura-Jayne Gardiner, Ming-Cheng Luo, Anthony Hall, and Michael W Bevan
- Abstract
This protocol describes how we generated and processed the bisulphite sequencing data
- Published
- 2019
49. Assay for Transposase-Accessible Chromatin (ATAC) Sequencing v1
- Author
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Fu-Hao Lu, Neil McKenzie, Laura-Jayne Gardiner, Ming-Cheng Luo, Anthony Hall, and Michael W Bevan
- Abstract
This protocol describes how we generated and processed ATAC-seq data
- Published
- 2019
50. Chromosome-scale pseudomolecules refined by optical, physical and genetic maps in flax
- Author
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Xiue Wang, Gaofeng Jia, Sylvie Cloutier, Jin Xiao, Zhen Yao, Tingting Zhu, Liqiang He, Pingchuan Li, Frank M. You, Michael K. Deyholos, and Ming-Cheng Luo
- Subjects
0106 biological sciences ,0301 basic medicine ,Linum ,Bacterial artificial chromosome ,biology ,Contig ,Chromosome Mapping ,Chromosome ,Cell Biology ,Plant Science ,Computational biology ,biology.organism_classification ,01 natural sciences ,Genome ,Chromosomes, Plant ,DNA sequencing ,03 medical and health sciences ,030104 developmental biology ,Flax ,Genetics ,Ploidy ,Gene ,Genome, Plant ,Phylogeny ,010606 plant biology & botany - Abstract
Genomes of varying sizes have been sequenced with next-generation sequencing platforms. However, most reference sequences include draft unordered scaffolds containing chimeras caused by mis-scaffolding. A BioNano genome (BNG) optical map was constructed to improve the previously sequenced flax genome (Linum usitatissimum L., 2n = 30, about 373 Mb), which consisted of 3852 scaffolds larger than 1 kb and totalling 300.6 Mb. The high-resolution BNG map of cv. CDC Bethune totalled 317 Mb and consisted of 251 BNG contigs with an N50 of 2.15 Mb. A total of 622 scaffolds (286.6 Mb, 94.9%) aligned to 211 BNG contigs (298.6 Mb, 94.2%). Of those, 99 scaffolds, diagnosed to contain assembly errors, were refined into 225 new scaffolds. Using the newly refined scaffold sequences and the validated bacterial artificial chromosome-based physical map of CDC Bethune, the 211 BNG contigs were scaffolded into 94 super-BNG contigs (N50 of 6.64 Mb) that were further assigned to the 15 flax chromosomes using the genetic map. The pseudomolecules total about 316 Mb, with individual chromosomes of 15.6 to 29.4 Mb, and cover 97% of the annotated genes. Evidence from the chromosome-scale pseudomolecules suggests that flax has undergone palaeopolyploidization and mesopolyploidization events, followed by rearrangements and deletions or fusion of chromosome arms from an ancient progenitor with a haploid chromosome number of eight.
- Published
- 2018
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