20 results on '"Yaqin Ma"'
Search Results
2. Sequencing of 15 622 gene‐bearing BACs clarifies the gene‐dense regions of the barley genome
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Anders Falk, Jane Grimwood, Dave Kudrna, Nils Stein, Rod A. Wing, Ming-Cheng Luo, Matthew J. Moscou, Pascal Condamine, Kavitha Madishetty, Leila Feiz, Prasanna R. Bhat, Phil Bregitzer, Josh Resnik, Yaqin Ma, Jeremy Schmutz, Andris Kleinhofs, Hana Šimková, Roger P. Wise, Shane Heinen, Jaroslav Dolezel, Denisa Duma, Matthew Alpert, Lothar Altschmied, Rachid Ounit, Marco Beccuti, Andreas Graner, Peggy G. Lemaux, Muharrem Dilbirligi, Francesca Cordero, Perry Gustafson, Frank You, Timothy J. Close, Yonghui Wu, Tao Jiang, Jafar Mammadov, Gary J. Muehlbauer, Patrick M. Hayes, Heather Witt, Shiaoman Chao, Laurel Cooper, Jan T. Svensson, Steve Wanamaker, Hamid Mirebrahim, Jie Zheng, Serdar Bozdag, María Muñoz-Amatriaín, Stefano Lonardi, Edmundo Rodriguez, and Tom Blake
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Resource ,Chromosomes, Artificial, Bacterial ,gene distribution ,Molecular Sequence Data ,BAC sequencing ,Plant Science ,Genome ,Complete sequence ,Barley ,HarvEST:Barley ,Genetics ,centromere BACs ,Aegilops tauschii ,Gene ,Synteny ,2. Zero hunger ,Comparative genomics ,Bacterial artificial chromosome ,Hordeum vulgare L ,biology ,synteny ,food and beverages ,Hordeum ,Cell Biology ,biology.organism_classification ,recombination frequency ,Hordeum vulgare ,Genome, Plant - Abstract
Summary Barley (Hordeum vulgare L.) possesses a large and highly repetitive genome of 5.1 Gb that has hindered the development of a complete sequence. In 2012, the International Barley Sequencing Consortium released a resource integrating whole‐genome shotgun sequences with a physical and genetic framework. However, because only 6278 bacterial artificial chromosome (BACs) in the physical map were sequenced, fine structure was limited. To gain access to the gene‐containing portion of the barley genome at high resolution, we identified and sequenced 15 622 BACs representing the minimal tiling path of 72 052 physical‐mapped gene‐bearing BACs. This generated ~1.7 Gb of genomic sequence containing an estimated 2/3 of all Morex barley genes. Exploration of these sequenced BACs revealed that although distal ends of chromosomes contain most of the gene‐enriched BACs and are characterized by high recombination rates, there are also gene‐dense regions with suppressed recombination. We made use of published map‐anchored sequence data from Aegilops tauschii to develop a synteny viewer between barley and the ancestor of the wheat D‐genome. Except for some notable inversions, there is a high level of collinearity between the two species. The software HarvEST:Barley provides facile access to BAC sequences and their annotations, along with the barley–Ae. tauschii synteny viewer. These BAC sequences constitute a resource to improve the efficiency of marker development, map‐based cloning, and comparative genomics in barley and related crops. Additional knowledge about regions of the barley genome that are gene‐dense but low recombination is particularly relevant., Significance Statement We provide new genome sequence resources for barley and related species, to improve the efficiency of marker development, map‐based cloning, comparative genomics studies, and to provide insights into genome architecture. Notably, some of the gene‐rich islands in the barley genome deviate markedly from assumption that gene density and high recombination frequency are correlated.
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- 2015
3. Genome resources for climate-resilient cowpea, an essential crop for food security
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Francis Kusi, Christian Fatokun, Ibrahim Atokple, Steve Wanamaker, Hind Alhakami, Ming-Cheng Luo, Hamid Mirebrahim, Cindy Lawley, Mitchell R. Lucas, Frank M. You, Matthew Alpert, Ousmane Boukar, Jeffrey D. Ehlers, Jiajie Wu, María Muñoz-Amatriaín, Scott A. Jackson, Timothy J. Close, Yi-Ning Guo, Bao-Lam Huynh, Pei Xu, Noelle A. Barkley, Andrew Farmer, Stefano Lonardi, Ndiaga Cisse, Yong Q. Gu, Serdar Bozdag, Benoit Joseph Batieno, Philip A. Roberts, Yaqin Ma, Michael P. Timko, and Issa Drabo
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0106 biological sciences ,0301 basic medicine ,Germplasm ,Chromosomes, Artificial, Bacterial ,Climate ,Plant Biology ,BAC sequencing ,Plant Science ,01 natural sciences ,Genome ,Food Supply ,iSelect genotyping array ,Food security ,genetic anchoring ,consensus genetic map ,synteny ,Bacterial ,food and beverages ,WGS sequencing ,Artificial ,Zero Hunger ,Genome, Plant ,Biotechnology ,Crops, Agricultural ,Genotype ,Plant Biology & Botany ,Genomics ,Crops ,Biology ,Chromosomes, Plant ,Chromosomes ,03 medical and health sciences ,Vigna unguiculata L. Walp ,West Africa ,Genetics ,Plant breeding ,Synteny ,Genetic diversity ,Agricultural ,business.industry ,Vigna ,Phaseolus vulgaris L ,Cell Biology ,Plant ,cowpea ,030104 developmental biology ,Agriculture ,Biochemistry and Cell Biology ,business ,010606 plant biology & botany - Abstract
Summary Cowpea (Vigna unguiculata L. Walp.) is a legume crop that is resilient to hot and drought-prone climates, and a primary source of protein in sub-Saharan Africa and other parts of the developing world. However, genome resources for cowpea have lagged behind most other major crops. Here we describe foundational genome resources and their application to analysis of germplasm currently in use in West African breeding programs. Resources developed from the African cultivar IT97K-499-35 include a whole-genome shotgun (WGS) assembly, a bacterial artificial chromosome (BAC) physical map, and assembled sequences from 4,355 BACs. These resources and WGS sequences of an additional 36 diverse cowpea accessions supported the development of a genotyping assay for 51,128 SNPs, which was then applied to five biparental RIL populations to produce a consensus genetic map containing 37,372 SNPs. This genetic map enabled the anchoring of 100 Mb of WGS and 420 Mb of BAC sequences, an exploration of genetic diversity along each linkage group, and clarification of macrosynteny between cowpea and common bean. The SNP assay enabled a diversity analysis of materials from West African breeding programs. Two major subpopulations exist within those materials, one of which has significant parentage from South and East Africa and more diversity. There are genomic regions of high differentiation between subpopulations, one of which coincides with a cluster of nodulin genes. The new resources and knowledge help to define goals and accelerate the breeding of improved varieties to address food security issues related to limited-input small-holder farming and climate stress. This article is protected by copyright. All rights reserved.
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- 2017
4. Genome resources for climate-resilient cowpea, an essential crop for food security
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Ibrahim Atokple, Yong Q. Gu, Ndiaga Cisse, Francis Kusi, Hamid Mirebrahim, Cindy Lawley, Hind Alhakami, Bao-Lam Huynh, Ming-Cheng Luo, Michael P. Timko, María Muñoz-Amatriaín, Matthew Alpert, Pei Xu, Andrew Farmer, Ousmane Boukar, Mitchell R. Lucas, Scott A. Jackson, Timothy J. Close, Christian Fatokun, Yi-Ning Guo, Serdar Bozdag, Frank M. You, Jiajie Wu, Yaqin Ma, Stefano Lonardi, Issa Drabo, Steve Wanamaker, Jeffrey D. Ehlers, Benoit Joseph Batieno, and Philip A. Roberts
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2. Zero hunger ,0106 biological sciences ,Germplasm ,0303 health sciences ,Bacterial artificial chromosome ,Genetic diversity ,Food security ,business.industry ,food and beverages ,Genomics ,15. Life on land ,Biology ,01 natural sciences ,Genome ,Biotechnology ,Crop ,03 medical and health sciences ,Agriculture ,business ,030304 developmental biology ,010606 plant biology & botany - Abstract
SUMMARYCowpea (Vigna unguiculata L. Walp.) is a legume crop that is resilient to hot and drought-prone climates, and a primary source of protein in sub-Saharan Africa and other parts of the developing world. However, genome resources for cowpea have lagged behind most other major crop plants. Here we describe foundational genome resources and their application to analysis of germplasm currently in use in West African breeding programs. Resources developed from the African cultivar IT97K-499-35 include bacterial artificial chromosome (BAC) libraries and a BAC-based physical map, assembled sequences from 4,355 BACs, as well as a whole-genome shotgun (WGS) assembly. These resources and WGS sequences of an additional 36 diverse cowpea accessions supported the development of a genotyping assay for over 50,000 SNPs, which was then applied to five biparental RIL populations to produce a consensus genetic map containing 37,372 SNPs. This genetic map enabled the anchoring of 100 Mb of WGS and 420 Mb of BAC sequences, an exploration of genetic diversity along each linkage group, and clarification of macrosynteny between cowpea and common bean. The genomes of West African breeding lines and landraces have regions of marked depletion of diversity, some of which coincide with QTL that may be the result of artificial selection or environmental adaptation. The new publicly available resources and knowledge help to define goals and accelerate the breeding of improved varieties to address food security issues related to limited-input small-holder farming and climate stress.
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- 2016
- Full Text
- View/download PDF
5. Fine genetic mapping of greenbug aphid-resistance gene Gb3 in Aegilops tauschii
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Ming-Cheng Luo, Jackie C. Rudd, Perumal Azhaguvel, Yaqin Ma, and Yiqun Weng
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Genetic Markers ,Germplasm ,Chromosomes, Artificial, Bacterial ,Population ,Locus (genetics) ,Breeding ,Genes, Plant ,Poaceae ,Sequence-tagged site ,Gene mapping ,Cleaved amplified polymorphic sequence ,Genetics ,Animals ,Aegilops tauschii ,Amplified Fragment Length Polymorphism Analysis ,education ,Disease Resistance ,Plant Diseases ,Sequence Tagged Sites ,Expressed Sequence Tags ,education.field_of_study ,biology ,Chromosome Mapping ,food and beverages ,General Medicine ,biology.organism_classification ,Aphids ,Chromosomal region ,Agronomy and Crop Science ,Biotechnology - Abstract
The greenbug, Schizaphis graminum (Rondani), is an important aphid pest of small grain crops especially wheat (Triticum aestivum L., 2n = 6x = 42, genomes AABBDD) in many parts of the world. The greenbug-resistance gene Gb3 originated from Aegilops tauschii Coss. (2n = 2x = 14, genome D(t)D(t)) has shown consistent and durable resistance against prevailing greenbug biotypes in wheat fields. We previously mapped Gb3 in a recombination-rich, telomeric bin of wheat chromosome arm 7DL. In this study, high-resolution genetic mapping was carried out using an F(2:3) segregating population derived from two Ae. tauschii accessions, the resistant PI 268210 (original donor of Gb3 in the hexaploid wheat germplasm line 'Largo') and susceptible AL8/78. Molecular markers were developed by exploring bin-mapped wheat RFLPs, SSRs, ESTs and the Ae. tauschii physical map (BAC contigs). Wheat EST and Ae. tauschii BAC end sequences located in the deletion bin 7DL3-0.82-1.00 were used to design STS (sequence tagged site) or CAPS (Cleaved Amplified Polymorphic Sequence) markers. Forty-five PCR-based markers were developed and mapped to the chromosomal region spanning the Gb3 locus. The greenbug-resistance gene Gb3 now was delimited in an interval of 1.1 cM by two molecular markers (HI067J6-R and HI009B3-R). This localized high-resolution genetic map with markers closely linked to Gb3 lays a solid foundation for map based cloning of Gb3 and marker-assisted selection of this gene in wheat breeding.
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- 2011
6. BAC Libraries from Wheat Chromosome 7D: Efficient Tool for Positional Cloning of Aphid Resistance Genes
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Jan Šafář, Yaqin Ma, Frank M. You, Jan Bartoš, Hana Šimková, Ming-Cheng Luo, Junhua Peng, Marie Kubaláková, Jarmila Číhalíková, Perumal Azhaguvel, Nora L. V. Lapitan, Yiqun Weng, Heda Robert-Quatre, Pavla Suchánková, and Jaroslav Doležel
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Chromosomes, Artificial, Bacterial ,Article Subject ,Library ,Positional cloning ,lcsh:Biotechnology ,Health, Toxicology and Mutagenesis ,lcsh:Medicine ,Genes, Plant ,Polymerase Chain Reaction ,Chromosomes, Plant ,Fluorescence ,law.invention ,law ,lcsh:TP248.13-248.65 ,Genetics ,Animals ,Cloning, Molecular ,Molecular Biology ,Genome size ,Gene ,Triticum ,Polymerase chain reaction ,Plant Diseases ,Cloning ,biology ,lcsh:R ,Nucleic Acid Hybridization ,food and beverages ,Chromosome ,General Medicine ,biology.organism_classification ,Immunity, Innate ,Aphids ,Karyotyping ,Molecular Medicine ,Russian wheat aphid ,Microsatellite Repeats ,Research Article ,Biotechnology - Abstract
Positional cloning in bread wheat is a tedious task due to its huge genome size and hexaploid character. BAC libraries represent an essential tool for positional cloning. However, wheat BAC libraries comprise more than million clones, which makes their screening very laborious. Here, we present a targeted approach based on chromosome-specific BAC libraries. Such libraries were constructed from flow-sorted arms of wheat chromosome 7D. A library from the short arm (7DS) consisting of 49,152 clones with 113 kb insert size represented 12.1 arm equivalents whereas a library from the long arm (7DL) comprised 50,304 clones of 116 kb providing 14.9x arm coverage. The 7DS library was PCR screened with markers linked to Russian wheat aphid resistance geneDnCI2401, the 7DL library was screened by hybridization with a probe linked to greenbug resistance geneGb3. The small number of clones combined with high coverage made the screening highly efficient and cost effective.
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- 2011
7. Genome comparisons reveal a dominant mechanism of chromosome number reduction in grasses and accelerated genome evolution in Triticeae
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Jorge Dubcovsky, Devin Coleman-Derr, Yong Q. Gu, Frank M. You, Hwa-Young Heo, J. Hadam, Calvin O. Qualset, Eduard Akhunov, Nancy K. Blake, Patrick E. McGuire, E. Conley, Olin D. Anderson, Naxin Huo, Gerard R. Lazo, Marilyn L. Warburton, Bikram S. Gill, David E. Matthews, D. M. Toleno, C. C. Crossman, Jan Dvorak, Ming-Cheng Luo, D. A. Tabanao, Alina Akhunova, Chao Tian, Michael T. Clegg, Luther E. Talbert, Ken Deal, J. Renfro, Peter L. Morrell, James A. Anderson, Yaqin Ma, and Wenjun Zhang
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Translocation, Genetic ,dysploidy ,Models ,wheat ,Chromosome regions ,Triticeae ,Triticum ,Phylogeny ,Expressed Sequence Tags ,Genetics ,Genome ,Multidisciplinary ,biology ,Chromosome Mapping ,food and beverages ,Single Nucleotide ,Biological Sciences ,Telomere ,Genome, Plant ,Biotechnology ,Evolution ,Centromere ,Translocation ,Oryza sativa ,Poaceae ,Polymorphism, Single Nucleotide ,Synteny ,Chromosomes, Plant ,Chromosomes ,Evolution, Molecular ,Chromosome 16 ,Genetic ,Species Specificity ,Chromosome 19 ,Aegilops tauschii ,Polymorphism ,Sorghum ,Models, Genetic ,rice ,Human Genome ,Molecular ,Oryza ,Plant ,biology.organism_classification ,linkage map ,Chromosome 3 ,Chromosome Inversion ,Chromosome 21 - Abstract
Single-nucleotide polymorphism was used in the construction of an expressed sequence tag map of Aegilops tauschii , the diploid source of the wheat D genome. Comparisons of the map with the rice and sorghum genome sequences revealed 50 inversions and translocations; 2, 8, and 40 were assigned respectively to the rice, sorghum, and Ae. tauschii lineages, showing greatly accelerated genome evolution in the large Triticeae genomes. The reduction of the basic chromosome number from 12 to 7 in the Triticeae has taken place by a process during which an entire chromosome is inserted by its telomeres into a break in the centromeric region of another chromosome. The original centromere–telomere polarity of the chromosome arms is maintained in the new chromosome. An intrachromosomal telomere–telomere fusion resulting in a pericentric translocation of a chromosome segment or an entire arm accompanied or preceded the chromosome insertion in some instances. Insertional dysploidy has been recorded in three grass subfamilies and appears to be the dominant mechanism of basic chromosome number reduction in grasses. A total of 64% and 66% of Ae. tauschii genes were syntenic with sorghum and rice genes, respectively. Synteny was reduced in the vicinity of the termini of modern Ae. tauschii chromosomes but not in the vicinity of the ancient termini embedded in the Ae. tauschii chromosomes, suggesting that the dependence of synteny erosion on gene location along the centromere–telomere axis either evolved recently in the Triticeae phylogenetic lineage or its evolution was recently accelerated.
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- 2009
8. Structural characterization of Brachypodium genome and its syntenic relationship with rice and wheat
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Jan Dvorak, Yaqin Ma, Naxin Huo, Olin D. Anderson, Gerard R. Lazo, Ming-Cheng Luo, Frank M. You, Yong Q. Gu, John P. Vogel, and Stephanie McMahon
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Chromosomes, Artificial, Bacterial ,Genome evolution ,Colinearity ,DNA, Plant ,Genomics ,Plant Science ,Repetitive DNA elements ,Biology ,Genes, Plant ,Poaceae ,Synteny ,Genome ,Evolution, Molecular ,Gene density ,Genetics ,Conserved Sequence ,Triticum ,Expressed Sequence Tags ,Comparative genomics ,Brachypodium distachyon ,Plant Sciences ,Life Sciences ,food and beverages ,Oryza ,Sequence Analysis, DNA ,General Medicine ,Plant Pathology ,biology.organism_classification ,Biochemistry, general ,Brachypodium ,Sequence Alignment ,Agronomy and Crop Science ,Genome, Plant - Abstract
Brachypodium distachyon (Brachypodium) has been recently recognized as an emerging model system for both comparative and functional genomics in grass species. In this study, 55,221 repeat masked Brachypodium BAC end sequences (BES) were used for comparative analysis against the 12 rice pseudomolecules. The analysis revealed that approximately 26.4% of BES have significant matches with the rice genome and 82.4% of the matches were homologous to known genes. Further analysis of paired-end BES and approximately 1.0 Mb sequences from nine selected BACs proved to be useful in revealing conserved regions and regions that have undergone considerable genomic changes. Differential gene amplification, insertions/deletions and inversions appeared to be the common evolutionary events that caused variations of microcolinearity at different orthologous genomic regions. It was found that approximately 17% of genes in the two genomes are not colinear in the orthologous regions. Analysis of BAC sequences also revealed higher gene density (approximately 9 kb/gene) and lower repeat DNA content (approximately 13.1%) in Brachypodium when compared to the orthologous rice regions, consistent with the smaller size of the Brachypodium genome. The 119 annotated Brachypodium genes were BLASTN compared against the wheat EST database and deletion bin mapped wheat ESTs. About 77% of the genes retrieved significant matches in the EST database, while 9.2% matched to the bin mapped ESTs. In some cases, genes in single Brachypodium BACs matched to multiple ESTs that were mapped to the same deletion bins, suggesting that the Brachypodium genome will be useful for ordering wheat ESTs within the deletion bins and developing specific markers at targeted regions in the wheat genome.
- Published
- 2009
9. Phenolic Compounds and Antioxidant Activity of Extracts from Ultrasonic Treatment of Satsuma Mandarin (Citrus unshiu Marc.) Peels
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Yaqin Ma, Zhongxiang Fang, Jianchu Chen, Guihua Xu, Donghong Liu, and Xingqian Ye
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Citrus ,Hot Temperature ,Chromatography ,biology ,Food Handling ,Plant Extracts ,General Chemistry ,Phenolic acid ,biology.organism_classification ,Antioxidants ,Protocatechuic acid ,Citrus unshiu ,Ferulic acid ,Sonication ,chemistry.chemical_compound ,Phenols ,chemistry ,Biochemistry ,Fruit ,Maceration (wine) ,Vanillic acid ,Caffeic acid ,General Agricultural and Biological Sciences ,Chromatography, High Pressure Liquid - Abstract
Ultrasound-assisted extraction (UAE) was used to extract phenolic compounds from Satsuma mandarin ( Citrus unshiu Marc.) peels (SMP), and maceration extraction (ME) was used as a control. The effects of ultrasonic time (10, 20, 30, 40, 50, and 60 min), temperature (15, 30, and 40 degrees C), and ultrasonic power (3.2, 8, 30, and 56 W) on phenolic compounds were investigated. High-performance liquid chromatography (HPLC) coupled with a photodiode array (PDA) detector was used for the analysis of phenolic acids after alkaline hydrolysis (bound phenolic acids) and flavanone glycosides. The contents of seven phenolic acids (caffeic acid, p-coumaric acid, ferulic acid, sinapic acid, protocatechuic acid, p-hydroxybenzoic acid, and vanillic acid) and two flavanone glycosides (narirutin and hesperidin) in extracts obtained by ultrasonic treatment were significantly higher than in extracts obtained by the maceration method. Moreover, the contents of extracts increased as both treatment time and temperature increased. Ultrasonic power had a positive effect on the contents of extracts. However, the phenolic acids may be degraded by ultrasound at higher temperature for a long time. For example, after ultrasonic treatment at 40 degrees C for 20 min, the contents of caffeic acid, p-coumaric acid, ferulic acid, and p-hydroxybenzoic acid decreased by 48.90, 44.20, 48.23, and 35.33%, respectively. The interaction of ultrasonic parameters probably has a complex effect on the extracts. A linear relationship was observed between Trolox equivalent antioxidant capacity (TEAC) values and total phenolic contents (TPC); the correlation coefficient, R(2), is 0.8288 at 15 degrees C, 0.7706 at 30 degrees C, and 0.8626 at 40 degrees C, respectively. The data indicated that SMPs were rich sources of antioxidants. Furthermore, UAE techniques should be carefully used to enhance the yields of phenolic acids from SMPs.
- Published
- 2008
10. Sequencing of 15,622 gene-bearing BACs reveals new features of the barley genome
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Yaqin Ma, Hana Šimková, Rod A. Wing, Jan T. Svensson, Leila Feiz, Muharrem Dilbirligi, Josh Resnik, Roger P. Wise, Hamid Mirebrahim, Ming-Cheng Luo, Anders Falk, Jie Zheng, Patrick M. Hayes, Serdar Bozdag, Maŕ ia Mu ~noz-Amatriá, Dave Kudrna, Heather Witt, Steve Wanamaker, Pascal Condamine, Nils Stein, Jane Grimwood, Frank M. You, Perry Gustafson, Andreas Graner, Matthew Alpert, Gary J. Muehlbauer, Prasanna R. Bhat, Shane Heinen, Edmundo Rodriguez, Yonghui Wu, Tom Blake, Laurel Cooper, Jeremy Schmutz, Stefano Lonardi, Shiaoman Chao, Andris Kleinhofs, Jaroslav Doležel, Rachid Ounit, Marco Beccuti, Peggy G. Lemaux, Tao Jiang, Kavitha Madishetty, Phil Bregitzer, Francesca Cordero, María Muñoz-Amatriaín, Matthew J. Moscou, Jafar Mammadov, Denisa Duma, Timothy J. Close, and Lothar Altschmied
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0106 biological sciences ,2. Zero hunger ,Genetics ,0303 health sciences ,biology ,Introgression ,food and beverages ,Genomics ,biology.organism_classification ,01 natural sciences ,Genome ,03 medical and health sciences ,Complete sequence ,Aegilops tauschii ,Hordeum vulgare ,Gene ,030304 developmental biology ,010606 plant biology & botany ,Synteny - Abstract
Barley (Hordeum vulgareL.) possesses a large and highly repetitive genome of 5.1 Gb that has hindered the development of a complete sequence. In 2012, the International Barley Sequencing Consortium released a resource integrating whole-genome shotgun sequences with a physical and genetic framework. However, since only 6,278 BACs in the physical map were sequenced, detailed fine structure was limited. To gain access to the gene-containing portion of the barley genome at high resolution, we identified and sequenced 15,622 BACs representing the minimal tiling path of 72,052 physical mapped gene-bearing BACs. This generated about 1.7 Gb of genomic sequence containing 17,386 annotated barley genes. Exploration of the sequenced BACs revealed that although distal ends of chromosomes contain most of the gene-enriched BACs and are characterized by high rates of recombination, there are also gene-dense regions with suppressed recombination. Knowledge of these deviant regions is relevant to trait introgression, genome-wide association studies, genomic selection model development and map-based cloning strategies. Sequences and their gene and SNP annotations can be accessed and exported via http://harvest-web.org/hweb/utilmenu.wc or through the software HarvEST:Barley (download from harvest.ucr.edu). In the latter, we have implemented a synteny viewer between barley andAegilops tauschiito aid in comparative genome analysis.
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- 2015
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11. Cassava genome from a wild ancestor to cultivated varieties
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Nanna Heinz, Songbi Chen, Xincheng Zhou, Wenbin Liao, Wenbin Hu, Jinli Pei, Bin Liu, Weixiong Zhang, Zhicheng Wu, Luiz Joaquim Castelo Branco Carvalho, Jun Yang, Kevin Galens, Xin Chen, Anping Guo, Meili Chen, Jianchun Guo, Fu Yuhua, Peng Zhang, Changying Zeng, Haiyan Wang, Sandra Ott, Zhengwen Zhang, Gong Xiao, Zhiqiang Xia, Rubini Kannangara, Shujuan Wang, Shixiang Sun, Shengkui Zhang, Jiajie Wu, Mengbin Ruan, Pinghua Li, Henan Ceballos, Wenli Zhu, Songnian Hu, Chen Yeyuan, Silin Zhong, Meizhen Hu, Ping-An Ma, Guodao Liu, Jiaming Zhang, Shuigeng Zhou, Kirsten Jørgensen, Pablo D. Rabinowicz, Jingjing Xue, Luke J. Tallon, Meiling Zou, Jie Huang, Xiaojing Lu, Qingqun Yao, Yang Zhang, Kaimian Li, Guojiang Wu, Ming-Cheng Luo, Xinyue Liu, Frank M. You, Hong-Bin Zhang, Wenquan Wang, Qinghuang Wang, Birger Lindberg Møller, Qunfeng Lou, L. Augusto Becerra Lopez-Lavalle, Martin A. Fregene, Jing Xia, Jingfa Xiao, Hui Liu, Binxiao Feng, Zhengxu Li, Rebecca Louise Neale, Ming Peng, Wenjun Ou, Kun Pan, Mingfu Wen, Peng Ling, Maya Bonde, Yaqin Ma, Cheng Lu, Jingxing Liu, Jianqiu Ye, Feifei An, and Ying Wang
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Manihot ,Plant genetics ,Molecular Sequence Data ,General Physics and Astronomy ,Biology ,Genome ,General Biochemistry, Genetics and Molecular Biology ,Article ,Crop ,Evolution, Molecular ,Genetic variation ,Botany ,Photosynthesis ,Selection, Genetic ,Domestication ,Gene ,Phylogeny ,Plant Proteins ,Abiotic component ,Multidisciplinary ,food and beverages ,Genetic Variation ,Starch ,General Chemistry ,Cyanogenic Glucoside ,Genome, Plant - Abstract
Cassava is a major tropical food crop in the Euphorbiaceae family that has high carbohydrate production potential and adaptability to diverse environments. Here we present the draft genome sequences of a wild ancestor and a domesticated variety of cassava and comparative analyses with a partial inbred line. We identify 1,584 and 1,678 gene models specific to the wild and domesticated varieties, respectively, and discover high heterozygosity and millions of single-nucleotide variations. Our analyses reveal that genes involved in photosynthesis, starch accumulation and abiotic stresses have been positively selected, whereas those involved in cell wall biosynthesis and secondary metabolism, including cyanogenic glucoside formation, have been negatively selected in the cultivated varieties, reflecting the result of natural selection and domestication. Differences in microRNA genes and retrotransposon regulation could partly explain an increased carbon flux towards starch accumulation and reduced cyanogenic glucoside accumulation in domesticated cassava. These results may contribute to genetic improvement of cassava through better understanding of its biology., Cassava is a major source of food in tropical and subtropical regions. Here the authors sequence the genomes of wild and domesticated cassava varieties and identify genes that have been selected for and against during the evolution and domestication of this economically important crop.
- Published
- 2014
12. A 4-gigabase physical map unlocks the structure and evolution of the complex genome of Aegilops tauschii, the wheat D-genome progenitor
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Frank M. You, Gerard R. Lazo, Ming-Cheng Luo, Yong Q. Gu, Shiran Pasternak, Song Weining, Karin R. Deal, Patrick E. McGuire, W. Richard McCombie, Shiyong Chen, Wanlong Li, Shahryar F. Kianian, Yuqin Hu, Melissa Kramer, Sunish K. Sehgal, Naxin Huo, Chad M. Jorgensen, Jirui Wang, Doreen Ware, Jan Dvorak, Michael W. Bevan, Yong Zhang, Mihaela Martis, Bikram S. Gill, Jaroslav Doležel, Olin D. Anderson, Joshua C. Stein, Klaus F. X. Mayer, Yaqin Ma, Hana Šimková, and Yi Wang
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Genetic Markers ,Chromosomes, Artificial, Bacterial ,Genome evolution ,Centromere ,Genes, Plant ,Poaceae ,Polymorphism, Single Nucleotide ,Genome ,Chromosomes, Plant ,Single nucleotide polymorphism ,Synteny ,Gene density ,Oryza ,BAC contig coassembly ,Evolution, Molecular ,Contig Mapping ,Aegilops tauschii ,Triticum ,Recombination, Genetic ,Whole genome sequencing ,Genetics ,Multidisciplinary ,biology ,Shotgun sequencing ,food and beverages ,Sequence Analysis, DNA ,Genome project ,Biological Sciences ,biology.organism_classification ,Brachypodium distachyon ,Genome, Plant - Abstract
The current limitations in genome sequencing technology require the construction of physical maps for high-quality draft sequences of large plant genomes, such as that of Aegilops tauschii , the wheat D-genome progenitor. To construct a physical map of the Ae. tauschii genome, we fingerprinted 461,706 bacterial artificial chromosome clones, assembled contigs, designed a 10K Ae. tauschii Infinium SNP array, constructed a 7,185-marker genetic map, and anchored on the map contigs totaling 4.03 Gb. Using whole genome shotgun reads, we extended the SNP marker sequences and found 17,093 genes and gene fragments. We showed that collinearity of the Ae. tauschii genes with Brachypodium distachyon, rice, and sorghum decreased with phylogenetic distance and that structural genome evolution rates have been high across all investigated lineages in subfamily Pooideae, including that of Brachypodieae. We obtained additional information about the evolution of the seven Triticeae chromosomes from 12 ancestral chromosomes and uncovered a pattern of centromere inactivation accompanying nested chromosome insertions in grasses. We showed that the density of noncollinear genes along the Ae. tauschii chromosomes positively correlates with recombination rates, suggested a cause, and showed that new genes, exemplified by disease resistance genes, are preferentially located in high-recombination chromosome regions.
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- 2013
13. Comparative analysis of syntenic genes in grass genomes reveals accelerated rates of gene structure and coding sequence evolution in polyploid wheat
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Bikram S. Gill, Eduard Akhunov, Wanlong Li, Hanquan Liang, Deven R. See, Ming-Cheng Luo, Jaroslav Dolezel, Gaganpreet Kaur, Alina Akhunova, Sunish K. Sehgal, Shichen Wang, Matthew J. Hayden, Justin D. Faris, Kerrie Forrest, Yaqin Ma, and Hana Šimková
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Lineage (genetic) ,DNA, Plant ,Physiology ,Plant Science ,Biology ,Genome ,Synteny ,Chromosomes, Plant ,Evolution, Molecular ,Polyploidy ,Open Reading Frames ,Mutation Rate ,Gene duplication ,Databases, Genetic ,Gene Order ,Genetics ,Selection, Genetic ,Frameshift Mutation ,Gene ,Genome size ,Triticum ,Gene Expression Profiling ,food and beverages ,Exons ,biology.organism_classification ,Genes, Development, and Evolution ,Introns ,Alternative Splicing ,Codon, Nonsense ,Genetic redundancy ,Brachypodium distachyon ,Orthologous Gene ,Genome, Plant ,Pseudogenes ,Brachypodium - Abstract
Cycles of whole-genome duplication (WGD) and diploidization are hallmarks of eukaryotic genome evolution and speciation. Polyploid wheat (Triticum aestivum) has had a massive increase in genome size largely due to recent WGDs. How these processes may impact the dynamics of gene evolution was studied by comparing the patterns of gene structure changes, alternative splicing (AS), and codon substitution rates among wheat and model grass genomes. In orthologous gene sets, significantly more acquired and lost exonic sequences were detected in wheat than in model grasses. In wheat, 35% of these gene structure rearrangements resulted in frame-shift mutations and premature termination codons. An increased codon mutation rate in the wheat lineage compared with Brachypodium distachyon was found for 17% of orthologs. The discovery of premature termination codons in 38% of expressed genes was consistent with ongoing pseudogenization of the wheat genome. The rates of AS within the individual wheat subgenomes (21%–25%) were similar to diploid plants. However, we uncovered a high level of AS pattern divergence between the duplicated homeologous copies of genes. Our results are consistent with the accelerated accumulation of AS isoforms, nonsynonymous mutations, and gene structure rearrangements in the wheat lineage, likely due to genetic redundancy created by WGDs. Whereas these processes mostly contribute to the degeneration of a duplicated genome and its diploidization, they have the potential to facilitate the origin of new functional variations, which, upon selection in the evolutionary lineage, may play an important role in the origin of novel traits.
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- 2012
14. Feasibility of physical map construction from fingerprinted bacterial artificial chromosome libraries of polyploid plant species
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Bikram S. Gill, Jan Dvorak, Jan Šafář, Olin D. Anderson, David Kopecký, Jaroslav Doležel, Ming-Cheng Luo, Frank M. You, Yaqin Ma, Hana Šimková, and Patrick E. McGuire
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0106 biological sciences ,Chromosomes, Artificial, Bacterial ,DNA, Plant ,lcsh:QH426-470 ,lcsh:Biotechnology ,Computational biology ,Biology ,01 natural sciences ,Genome ,DNA sequencing ,Contig Mapping ,Polyploidy ,03 medical and health sciences ,Polyploid ,lcsh:TP248.13-248.65 ,Genetics ,Genomic library ,In Situ Hybridization, Fluorescence ,030304 developmental biology ,Gene Library ,0303 health sciences ,Bacterial artificial chromosome ,Contig ,food and beverages ,Sequence Analysis, DNA ,Plants ,DNA Fingerprinting ,lcsh:Genetics ,Ploidy ,Genome, Plant ,010606 plant biology & botany ,Biotechnology ,Research Article - Abstract
Background The presence of closely related genomes in polyploid species makes the assembly of total genomic sequence from shotgun sequence reads produced by the current sequencing platforms exceedingly difficult, if not impossible. Genomes of polyploid species could be sequenced following the ordered-clone sequencing approach employing contigs of bacterial artificial chromosome (BAC) clones and BAC-based physical maps. Although BAC contigs can currently be constructed for virtually any diploid organism with the SNaPshot high-information-content-fingerprinting (HICF) technology, it is currently unknown if this is also true for polyploid species. It is possible that BAC clones from orthologous regions of homoeologous chromosomes would share numerous restriction fragments and be therefore included into common contigs. Because of this and other concerns, physical mapping utilizing the SNaPshot HICF of BAC libraries of polyploid species has not been pursued and the possibility of doing so has not been assessed. The sole exception has been in common wheat, an allohexaploid in which it is possible to construct single-chromosome or single-chromosome-arm BAC libraries from DNA of flow-sorted chromosomes and bypass the obstacles created by polyploidy. Results The potential of the SNaPshot HICF technology for physical mapping of polyploid plants utilizing global BAC libraries was evaluated by assembling contigs of fingerprinted clones in an in silico merged BAC library composed of single-chromosome libraries of two wheat homoeologous chromosome arms, 3AS and 3DS, and complete chromosome 3B. Because the chromosome arm origin of each clone was known, it was possible to estimate the fidelity of contig assembly. On average 97.78% or more clones, depending on the library, were from a single chromosome arm. A large portion of the remaining clones was shown to be library contamination from other chromosomes, a feature that is unavoidable during the construction of single-chromosome BAC libraries. Conclusions The negligibly low level of incorporation of clones from homoeologous chromosome arms into a contig during contig assembly suggested that it is feasible to construct contigs and physical maps using global BAC libraries of wheat and almost certainly also of other plant polyploid species with genome sizes comparable to that of wheat. Because of the high purity of the resulting assembled contigs, they can be directly used for genome sequencing. It is currently unknown but possible that equally good BAC contigs can be also constructed for polyploid species containing smaller, more gene-rich genomes.
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- 2010
15. Analysis of gene-derived SNP marker polymorphism in US wheat (Triticum aestivum L.) cultivars
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Ming-Cheng Luo, Eduard Akhunov, Shiaoman Chao, Jamie D. Sherman, Wenjun Zhang, Jorge Dubcovsky, and Yaqin Ma
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Genetics ,Germplasm ,Crop and Pasture Production ,Human Genome ,Plant Biology & Botany ,food and beverages ,SNP ,Plant Biology ,Single-nucleotide polymorphism ,Plant Science ,Tag SNP ,Biology ,Genome ,SSR ,Minor allele frequency ,Genetic marker ,Wheat ,EST ,Common wheat ,Agronomy and Crop Science ,Molecular Biology ,Biotechnology - Abstract
In this study, we developed 359 detection primers for single nucleotide polymorphisms (SNPs) previously discovered within intron sequences of wheat genes and used them to evaluate SNP polymorphism in common wheat (Triticum aestivum L.). These SNPs showed an average polymorphism information content (PIC) of 0.18 among 20 US elite wheat cultivars, representing seven market classes. This value increased to 0.23 when SNPs were pre-selected for polymorphisms among a diverse set of 13 hexaploid wheat accessions (excluding synthetic wheats) used in the wheat SNP discovery project ( http://wheat.pw. usda.gov/SNP ). PIC values for SNP markers in the D genome were approximately half of those for the A and B genomes. D genome SNPs also showed a larger PIC reduction relative to the other genomes (P < 0.05) when US cultivars were compared with the more diverse set of 13 wheat accessions. Within those accessions, D genome SNPs show a higher proportion of alleles with low minor allele frequencies (
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- 2009
16. The nuclear genome of Brachypodium distachyon: analysis of BAC end sequences
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Yong Q. Gu, Gerard R. Lazo, Olin D. Anderson, Theresa Hill, Yaqin Ma, Naxin Huo, Ming-Cheng Luo, John P. Vogel, Daniel M. Hayden, Frank M. You, Devin Coleman-Derr, and Jan Dvorak
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Chromosomes, Artificial, Bacterial ,DNA, Plant ,Retroelements ,Molecular Sequence Data ,Retrotransposon ,Genomics ,Poaceae ,Genome ,Genetics ,Repeated sequence ,Triticeae ,Phylogeny ,Repetitive Sequences, Nucleic Acid ,Cell Nucleus ,Expressed Sequence Tags ,Bacterial artificial chromosome ,biology ,Base Sequence ,Terminal Repeat Sequences ,food and beverages ,General Medicine ,biology.organism_classification ,Brachypodium ,Brachypodium distachyon ,Genome, Plant ,Microsatellite Repeats - Abstract
Due in part to its small genome (approximately 350 Mb), Brachypodium distachyon is emerging as a model system for temperate grasses, including important crops like wheat and barley. We present the analysis of 10.9% of the Brachypodium genome based on 64,696 bacterial artificial chromosome (BAC) end sequences (BES). Analysis of repeat DNA content in BES revealed that approximately 11.0% of the genome consists of known repetitive DNA. The vast majority of the Brachypodium repetitive elements are LTR retrotransposons. While Bare-1 retrotransposons are common to wheat and barley, Brachypodium repetitive element sequence-1 (BRES-1), closely related to Bare-1, is also abundant in Brachypodium. Moreover, unique Brachypodium repetitive element sequences identified constitute approximately 7.4% of its genome. Simple sequence repeats from BES were analyzed, and flanking primer sequences for SSR detection potentially useful for genetic mapping are available at http://brachypodium.pw.usda.gov . Sequence analyses of BES indicated that approximately 21.2% of the Brachypodium genome represents coding sequence. Furthermore, Brachypodium BES have more significant matches to ESTs from wheat than rice or maize, although these species have similar sizes of EST collections. A phylogenetic analysis based on 335 sequences shared among seven grass species further revealed a closer relationship between Brachypodium and Triticeae than Brachypodium and rice or maize.
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- 2007
17. Combinatorial Pooling Enables Selective Sequencing of the Barley Gene Space
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Timothy J. Close, Yonghui Wu, Marco Beccuti, Yaqin Ma, Serdar Bozdag, Burair Alsaihati, Steve Wanamaker, Josh Resnik, Matthew Alpert, Denisa Duma, Ming-Cheng Luo, Prasanna R. Bhat, Gianfranco Ciardo, Stefano Lonardi, Francesca Cordero, and Miyano, Satoru
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0106 biological sciences ,Chromosomes, Artificial, Bacterial ,Pooling ,01 natural sciences ,Genome ,Mathematical Sciences ,Contig Mapping ,Models ,Genomic library ,Genome Sequencing ,Cloning, Molecular ,lcsh:QH301-705.5 ,Genetics ,Genomic Library ,0303 health sciences ,Ecology ,Bacterial ,food and beverages ,DNA sequencing theory ,Genomics ,Biological Sciences ,Physical Chromosome Mapping ,Computational Theory and Mathematics ,Modeling and Simulation ,Artificial ,Sequence Analysis ,Algorithms ,Research Article ,Biotechnology ,Genetic Markers ,Bioinformatics ,Sequence analysis ,Oryza sativa ,Hybrid genome assembly ,Computational biology ,Biology ,Genes, Plant ,Chromosomes ,DNA sequencing ,03 medical and health sciences ,Cellular and Molecular Neuroscience ,Species Specificity ,Genetic ,Information and Computing Sciences ,Computer Simulation ,Molecular Biology ,Ecology, Evolution, Behavior and Systematics ,030304 developmental biology ,Models, Genetic ,Discrete Mathematics ,Human Genome ,Molecular ,Computational Biology ,Hordeum ,Oryza ,Sequence Analysis, DNA ,DNA ,Plant ,Genes ,lcsh:Biology (General) ,Combinatorics ,Computer Science ,Generic health relevance ,Mathematics ,Cloning ,010606 plant biology & botany - 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., Author Summary The problem of obtaining the full genomic sequence of an organism has been solved either via a global brute-force approach (called whole-genome shotgun) or by a divide-and-conquer strategy (called clone-by-clone). Both approaches have advantages and disadvantages in terms of cost, manual labor, and the ability to deal with sequencing errors and highly repetitive regions of the genome. With the advent of second-generation sequencing instruments, the whole-genome shotgun approach has been the preferred choice. The clone-by-clone strategy is, however, still very relevant for large complex genomes. In fact, several research groups and international consortia have produced clone libraries and physical maps for many economically or ecologically important organisms and now are in a position to proceed with sequencing. In this manuscript, we demonstrate the feasibility of this approach on the gene-space of a large, very repetitive plant genome. The novelty of our approach is that, in order to take advantage of the throughput of the current generation of sequencing instruments, we pool hundreds of clones using a special type of “smart” pooling design that allows one to establish with high accuracy the source clone from the sequenced reads in a pool. Extensive simulations and experimental results support our claims.
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- 2013
18. A BAC-based physical map of Brachypodium distachyon and its comparative analysis with rice and wheat
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William Nelson, Frank M. You, Jan Dvorak, Yong Q. Gu, Carol Soderlund, John P. Vogel, Gerard R. Lazo, Ming-Cheng Luo, Olin D. Anderson, Naxin Huo, and Yaqin Ma
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Chromosomes, Artificial, Bacterial ,lcsh:QH426-470 ,lcsh:Biotechnology ,Genomics ,Computational biology ,Poaceae ,Genome ,Evolution, Molecular ,Contig Mapping ,lcsh:TP248.13-248.65 ,Genetics ,Genome size ,Triticum ,Whole genome sequencing ,Comparative genomics ,Expressed Sequence Tags ,biology ,food and beverages ,Oryza ,biology.organism_classification ,Physical Chromosome Mapping ,DNA Fingerprinting ,lcsh:Genetics ,Brachypodium ,Brachypodium distachyon ,Edible Grain ,Functional genomics ,Genome, Plant ,Biotechnology ,Research Article - Abstract
BackgroundBrachypodium distachyon(Brachypodium) has been recognized as a new model species for comparative and functional genomics of cereal and bioenergy crops because it possesses many biological attributes desirable in a model, such as a small genome size, short stature, self-pollinating habit, and short generation cycle. To maximize the utility ofBrachypodium as a model for basic and applied research it is necessary to develop genomic resources for it. A BAC-based physical map is one of them. A physical map will facilitate analysis of genome structure, comparative genomics, and assembly of the entire genome sequence.ResultsA total of 67,151BrachypodiumBAC clones were fingerprinted with the SNaPshot HICF fingerprinting method and a genome-wide physical map of theBrachypodiumgenome was constructed. The map consisted of 671 contigs and 2,161 clones remained as singletons. The contigs and singletons spanned 414 Mb. A total of 13,970 gene-related sequences were detected in the BAC end sequences (BES). These gene tags aligned 345 contigs with 336 Mb of rice genome sequence, showing thatBrachypodiumand rice genomes are generally highly colinear. Divergent regions were mainly in the rice centromeric regions. A dot-plot ofBrachypodiumcontigs against the rice genome sequences revealed remnants of the whole-genome duplication caused by paleotetraploidy, which were previously found in rice and sorghum.Brachypodiumcontigs were anchored to the wheat deletion bin maps with the BES gene-tags, opening the door toBrachypodium-Triticeae comparative genomics.ConclusionThe construction of theBrachypodiumphysical map, and its comparison with the rice genome sequence demonstrated the utility of the SNaPshot-HICF method in the construction of BAC-based physical maps. The map represents an important genomic resource for the completion ofBrachypodiumgenome sequence and grass comparative genomics. A draft of the physical map and its comparisons with rice and wheat are available athttp://phymap.ucdavis.edu/brachypodium/.
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- 2009
19. A high-throughput strategy for screening of bacterial artificial chromosome libraries and anchoring of clones on a genetic map constructed with single nucleotide polymorphisms
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Ming-Cheng Luo, Jan Dvorak, Karin R. Deal, Yaqin Ma, Kenong Xu, and Charles M Nicolet
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0106 biological sciences ,Genetic Markers ,Chromosomes, Artificial, Bacterial ,lcsh:QH426-470 ,DNA, Plant ,Genotype ,lcsh:Biotechnology ,Biology ,01 natural sciences ,Genome ,Polymorphism, Single Nucleotide ,03 medical and health sciences ,Gene mapping ,lcsh:TP248.13-248.65 ,Genetics ,Aegilops tauschii ,Genomic library ,Triticum ,030304 developmental biology ,Gene Library ,0303 health sciences ,Bacterial artificial chromosome ,Contig ,Methodology Article ,Chromosome Mapping ,food and beverages ,biology.organism_classification ,lcsh:Genetics ,Genetic marker ,DNA microarray ,Genome, Plant ,010606 plant biology & botany ,Biotechnology - Abstract
Background Current techniques of screening bacterial artificial chromosome (BAC) libraries for molecular markers during the construction of physical maps are slow, laborious and often assign multiple BAC contigs to a single locus on a genetic map. These limitations are the principal impediment in the construction of physical maps of large eukaryotic genomes. It is hypothesized that this impediment can be overcome by screening multidimensional pools of BAC clones using the highly parallel Illumina GoldenGate™ assay. Results To test the efficacy of the Golden Gate assay in BAC library screening, multidimensional pools involving 302976 Aegilops tauschii BAC clones were genotyped for the presence/absence of specific gene sequences with multiplexed Illumina GoldenGate oligonucleotide assays previously used to place single nucleotide polymorphisms on an Ae. tauschii genetic map. Of 1384 allele-informative oligonucleotide assays, 87.6% successfully clustered BAC pools into those positive for a BAC clone harboring a specific gene locus and those negative for it. The location of the positive BAC clones within contigs assembled from 199190 fingerprinted Ae. tauschii BAC clones was used to evaluate the precision of anchoring of BAC clones and contigs on the Ae. tauschii genetic map. For 41 (95%) assays, positive BAC clones were neighbors in single contigs. Those contigs could be unequivocally assigned to loci on the genetic map. For two (5%) assays, positive clones were in two different contigs and the relationships of these contigs to loci on the Ae. tauschii genetic map were equivocal. Screening of BAC libraries with a simple five-dimensional BAC pooling strategy was evaluated and shown to allow direct detection of positive BAC clones without the need for manual deconvolution of BAC clone pools. Conclusion The highly parallel Illumina oligonucleotide assay is shown here to be an efficient tool for screening BAC libraries and a strategy for high-throughput anchoring of BAC contigs on genetic maps during the construction of physical maps of eukaryotic genomes. In most cases, screening of BAC libraries with Illumina oligonucleotide assays results in the unequivocal relationship of BAC clones with loci on the genetic map.
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20. BatchPrimer3: A high throughput web application for PCR and sequencing primer design
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Naxin Huo, Frank M. You, Dave Hane, Olin D. Anderson, Gerard R. Lazo, Ming-Cheng Luo, Jan Dvorak, Yong Q. Gu, and Yaqin Ma
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0106 biological sciences ,Genetic Markers ,Molecular Sequence Data ,Biology ,Molecular Inversion Probe ,lcsh:Computer applications to medicine. Medical informatics ,01 natural sciences ,Polymerase Chain Reaction ,Polymorphism, Single Nucleotide ,Biochemistry ,DNA sequencing ,03 medical and health sciences ,Structural Biology ,Genotyping ,lcsh:QH301-705.5 ,Molecular Biology ,030304 developmental biology ,DNA Primers ,Genetics ,0303 health sciences ,Internet ,Base Sequence ,Applied Mathematics ,FASTA format ,food and beverages ,Genome project ,Sequence Analysis, DNA ,SNP genotyping ,Computer Science Applications ,lcsh:Biology (General) ,Microsatellite ,lcsh:R858-859.7 ,Primer (molecular biology) ,Software ,Algorithms ,010606 plant biology & botany ,Microsatellite Repeats - Abstract
BackgroundMicrosatellite (simple sequence repeat – SSR) and single nucleotide polymorphism (SNP) markers are two types of important genetic markers useful in genetic mapping and genotyping. Often, large-scale genomic research projects require high-throughput computer-assisted primer design. Numerous such web-based or standard-alone programs for PCR primer design are available but vary in quality and functionality. In particular, most programs lack batch primer design capability. Such a high-throughput software tool for designing SSR flanking primers and SNP genotyping primers is increasingly demanded.ResultsA new web primer design program, BatchPrimer3, is developed based on Primer3. BatchPrimer3 adopted the Primer3 core program as a major primer design engine to choose the best primer pairs. A new score-based primer picking module is incorporated into BatchPrimer3 and used to pick position-restricted primers. BatchPrimer3 v1.0 implements several types of primer designs including generic primers, SSR primers together with SSR detection, and SNP genotyping primers (including single-base extension primers, allele-specific primers, and tetra-primers for tetra-primer ARMS PCR), as well as DNA sequencing primers. DNA sequences in FASTA format can be batch read into the program. The basic information of input sequences, as a reference of parameter setting of primer design, can be obtained by pre-analysis of sequences. The input sequences can be pre-processed and masked to exclude and/or include specific regions, or set targets for different primer design purposes as in Primer3Web and primer3Plus. A tab-delimited or Excel-formatted primer output also greatly facilitates the subsequent primer-ordering process. Thousands of primers, including wheat conserved intron-flanking primers, wheat genome-specific SNP genotyping primers, andBrachypodiumSSR flanking primers in several genome projects have been designed using the program and validated in several laboratories.ConclusionBatchPrimer3 is a comprehensive web primer design program to develop different types of primers in a high-throughput manner. Additional methods of primer design can be easily integrated into future versions of BatchPrimer3. The program with source code and thousands of PCR and sequencing primers designed for wheat andBrachypodiumare accessible athttp://wheat.pw.usda.gov/demos/BatchPrimer3/.
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