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López de Heredia U, Mora-Márquez F, Goicoechea PG, Guillardín-Calvo L, Simeone MC, Soto Á. ddRAD Sequencing-Based Identification of Genomic Boundaries and Permeability in Quercus ilex and Q. suber Hybrids. FRONTIERS IN PLANT SCIENCE 2020; 11:564414. [PMID: 33013984 PMCID: PMC7498617 DOI: 10.3389/fpls.2020.564414] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 08/13/2020] [Indexed: 05/03/2023]
Abstract
Hybridization and its relevance is a hot topic in ecology and evolutionary biology. Interspecific gene flow may play a key role in species adaptation to environmental change, as well as in the survival of endangered populations. Despite the fact that hybridization is quite common in plants, many hybridizing species, such as Quercus spp., maintain their integrity, while precise determination of genomic boundaries between species remains elusive. Novel high throughput sequencing techniques have opened up new perspectives in the comparative analysis of genomes and in the study of historical and current interspecific gene flow. In this work, we applied ddRADseq technique and developed an ad hoc bioinformatics pipeline for the study of ongoing hybridization between two relevant Mediterranean oaks, Q. ilex and Q. suber. We adopted a local scale approach, analyzing adult hybrids (sensu lato) identified in a mixed stand and their open-pollinated progenies. We have identified up to 9,435 markers across the genome and have estimated individual introgression levels in adults and seedlings. Estimated contribution of Q. suber to the genome is higher, on average, in hybrid progenies than in hybrid adults, suggesting preferential backcrossing with this parental species, maybe followed by selection during juvenile stages against individuals with higher Q. suber genomic contribution. Most discriminating markers seem to be scattered throughout the genome, suggesting that a large number of small genomic regions underlie boundaries between these species. A noticeable proportion of the markers (26%) showed allelic frequencies in adult hybrids very similar to one of the parental species, and very different from the other; a finding that seems relevant for understanding the hybridization process and the occurrence of adaptive introgression. Candidate marker databases developed in this study constitute a valuable resource to design large scale re-sequencing experiments in Mediterranean sclerophyllous oak species and could provide insight in species boundaries and on adaptive introgression between Q. suber and Q. ilex.
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Affiliation(s)
- Unai López de Heredia
- G.I. Genética, Fisiología e Historia Forestal, Dpto. Sistemas y Recursos Naturales, ETSI Montes, Forestal y del Medio Natural, Universidad Politécnica de Madrid, Madrid, Spain
| | - Fernando Mora-Márquez
- G.I. Genética, Fisiología e Historia Forestal, Dpto. Sistemas y Recursos Naturales, ETSI Montes, Forestal y del Medio Natural, Universidad Politécnica de Madrid, Madrid, Spain
| | | | - Laura Guillardín-Calvo
- G.I. Genética, Fisiología e Historia Forestal, Dpto. Sistemas y Recursos Naturales, ETSI Montes, Forestal y del Medio Natural, Universidad Politécnica de Madrid, Madrid, Spain
| | - Marco C. Simeone
- Dipartimento di Scienze Agrarie e Forestali (DAFNE), Università degli Studi della Tuscia, Viterbo, Italy
| | - Álvaro Soto
- G.I. Genética, Fisiología e Historia Forestal, Dpto. Sistemas y Recursos Naturales, ETSI Montes, Forestal y del Medio Natural, Universidad Politécnica de Madrid, Madrid, Spain
- *Correspondence: Álvaro Soto,
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Pootakham W, Sonthirod C, Naktang C, Jomchai N, Sangsrakru D, Tangphatsornruang S. Effects of methylation-sensitive enzymes on the enrichment of genic SNPs and the degree of genome complexity reduction in a two-enzyme genotyping-by-sequencing (GBS) approach: a case study in oil palm ( Elaeis guineensis). MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2016; 36:154. [PMID: 27942246 PMCID: PMC5104780 DOI: 10.1007/s11032-016-0572-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 10/20/2016] [Indexed: 05/08/2023]
Abstract
Advances in next generation sequencing have facilitated a large-scale single nucleotide polymorphism (SNP) discovery in many crop species. Genotyping-by-sequencing (GBS) approach couples next generation sequencing with genome complexity reduction techniques to simultaneously identify and genotype SNPs. Choice of enzymes used in GBS library preparation depends on several factors including the number of markers required, the desired level of multiplexing, and whether the enrichment of genic SNP is preferred. We evaluated various combinations of methylation-sensitive (AatII, PstI, MspI) and methylation-insensitive (SphI, MseI) enzymes for their effectiveness in genome complexity reduction and enrichment of genic SNPs. We discovered that the use of two methylation-sensitive enzymes effectively reduced genome complexity and did not require a size selection step. On the contrary, the genome coverage of libraries constructed with methylation-insensitive enzymes was quite high, and the additional size selection step may be required to increase the overall read depth. We also demonstrated the effectiveness of methylation-sensitive enzymes in enriching for SNPs located in genic regions. When two methylation-insensitive enzymes were used, only 16% of SNPs identified were located in genes and 18% in the vicinity (± 5 kb) of the genic regions, while most SNPs resided in the intergenic regions. In contrast, a remarkable degree of enrichment was observed when two methylation-sensitive enzymes were employed. Almost two thirds of the SNPs were located either inside (32-36%) or in the vicinity (28-31%) of the genic regions. These results provide useful information to help researchers choose appropriate GBS enzymes in oil palm and other crop species.
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Affiliation(s)
- Wirulda Pootakham
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Pathum Thani, 12120 Thailand
| | - Chutima Sonthirod
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Pathum Thani, 12120 Thailand
| | - Chaiwat Naktang
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Pathum Thani, 12120 Thailand
| | - Nukoon Jomchai
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Pathum Thani, 12120 Thailand
| | - Duangjai Sangsrakru
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Pathum Thani, 12120 Thailand
| | - Sithichoke Tangphatsornruang
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Pathum Thani, 12120 Thailand
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Pootakham W, Ruang-Areerate P, Jomchai N, Sonthirod C, Sangsrakru D, Yoocha T, Theerawattanasuk K, Nirapathpongporn K, Romruensukharom P, Tragoonrung S, Tangphatsornruang S. Construction of a high-density integrated genetic linkage map of rubber tree (Hevea brasiliensis) using genotyping-by-sequencing (GBS). FRONTIERS IN PLANT SCIENCE 2015; 6:367. [PMID: 26074933 PMCID: PMC4444744 DOI: 10.3389/fpls.2015.00367] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Accepted: 05/09/2015] [Indexed: 05/18/2023]
Abstract
Construction of linkage maps is crucial for genetic studies and marker-assisted breeding programs. Recent advances in next generation sequencing technologies allow for the generation of high-density linkage maps, especially in non-model species lacking extensive genomic resources. Here, we constructed a high-density integrated genetic linkage map of rubber tree (Hevea brasiliensis), the sole commercial producer of high-quality natural rubber. We applied a genotyping-by-sequencing (GBS) technique to simultaneously discover and genotype single nucleotide polymorphism (SNP) markers in two rubber tree populations. A total of 21,353 single nucleotide substitutions were identified, 55% of which represented transition events. GBS-based genetic maps of populations P and C comprised 1704 and 1719 markers and encompassed 2041 cM and 1874 cM, respectively. The average marker densities of these two maps were one SNP in 1.23-1.25 cM. A total of 1114 shared SNP markers were used to merge the two component maps. An integrated linkage map consisted of 2321 markers and spanned the cumulative length of 2052 cM. The composite map showed a substantial improvement in marker density, with one SNP marker in every 0.89 cM. To our knowledge, this is the most saturated genetic map in rubber tree to date. This integrated map allowed us to anchor 28,965 contigs, covering 135 Mb or 12% of the published rubber tree genome. We demonstrated that GBS is a robust and cost-effective approach for generating a common set of genome-wide SNP data suitable for constructing integrated linkage maps from multiple populations in a highly heterozygous agricultural species.
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Affiliation(s)
- Wirulda Pootakham
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development AgencyPathum Thani, Thailand
| | - Panthita Ruang-Areerate
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development AgencyPathum Thani, Thailand
| | - Nukoon Jomchai
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development AgencyPathum Thani, Thailand
| | - Chutima Sonthirod
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development AgencyPathum Thani, Thailand
| | - Duangjai Sangsrakru
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development AgencyPathum Thani, Thailand
| | - Thippawan Yoocha
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development AgencyPathum Thani, Thailand
| | - Kanikar Theerawattanasuk
- Department of Agriculture, Rubber Research Institute of Thailand, Ministry of Agriculture and CooperativesBangkok, Thailand
| | - Kanlaya Nirapathpongporn
- Department of Agriculture, Rubber Research Institute of Thailand, Ministry of Agriculture and CooperativesBangkok, Thailand
| | - Phayao Romruensukharom
- Department of Agriculture, Rubber Research Institute of Thailand, Ministry of Agriculture and CooperativesBangkok, Thailand
| | - Somvong Tragoonrung
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development AgencyPathum Thani, Thailand
| | - Sithichoke Tangphatsornruang
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development AgencyPathum Thani, Thailand
- *Correspondence: Sithichoke Tangphatsornruang, National Center for Genetic Engineering and Biotechnology (BIOTEC), 113 Thailand Science Park, Phahonyothin Rd., Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand
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Grativol C, Regulski M, Bertalan M, McCombie WR, da Silva FR, Neto AZ, Vicentini R, Farinelli L, Hemerly AS, Martienssen RA, Ferreira PCG. Sugarcane genome sequencing by methylation filtration provides tools for genomic research in the genus Saccharum. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2014; 79:162-72. [PMID: 24773339 PMCID: PMC4458261 DOI: 10.1111/tpj.12539] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Revised: 04/03/2014] [Accepted: 04/08/2014] [Indexed: 05/21/2023]
Abstract
Many economically important crops have large and complex genomes that hamper their sequencing by standard methods such as whole genome shotgun (WGS). Large tracts of methylated repeats occur in plant genomes that are interspersed by hypomethylated gene-rich regions. Gene-enrichment strategies based on methylation profiles offer an alternative to sequencing repetitive genomes. Here, we have applied methyl filtration with McrBC endonuclease digestion to enrich for euchromatic regions in the sugarcane genome. To verify the efficiency of methylation filtration and the assembly quality of sequences submitted to gene-enrichment strategy, we have compared assemblies using methyl-filtered (MF) and unfiltered (UF) libraries. The use of methy filtration allowed a better assembly by filtering out 35% of the sugarcane genome and by producing 1.5× more scaffolds and 1.7× more assembled Mb in length compared with unfiltered dataset. The coverage of sorghum coding sequences (CDS) by MF scaffolds was at least 36% higher than by the use of UF scaffolds. Using MF technology, we increased by 134× the coverage of gene regions of the monoploid sugarcane genome. The MF reads assembled into scaffolds that covered all genes of the sugarcane bacterial artificial chromosomes (BACs), 97.2% of sugarcane expressed sequence tags (ESTs), 92.7% of sugarcane RNA-seq reads and 98.4% of sorghum protein sequences. Analysis of MF scaffolds from encoded enzymes of the sucrose/starch pathway discovered 291 single-nucleotide polymorphisms (SNPs) in the wild sugarcane species, S. spontaneum and S. officinarum. A large number of microRNA genes was also identified in the MF scaffolds. The information achieved by the MF dataset provides a valuable tool for genomic research in the genus Saccharum and for improvement of sugarcane as a biofuel crop.
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Affiliation(s)
- Clícia Grativol
- Laboratório de Biologia Molecular de Plantas, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho 373, CCS, Bl.L-29, Cidade Universitária 21941-599, Rio de Janeiro, RJ, Brazil
| | - Michael Regulski
- Cold Spring Harbor Laboratory, 1 Bungtown Rd, Cold Spring Harbor, NY 11724, USA
| | - Marcelo Bertalan
- Institute of Biological Psychiatry Mental Health Center, Sct. Hans MHS - Capital Region of Denmark Boserupvej, DK-4000 Roskilde, Denmark
| | - W. Richard McCombie
- Cold Spring Harbor Laboratory, 1 Bungtown Rd, Cold Spring Harbor, NY 11724, USA
| | - Felipe Rodrigues da Silva
- Embrapa Informática Agropecuária, Av. Andre Tosello, 209, Barão Geraldo 13.083-886, Campinas, SP, Brazil
| | - Adhemar Zerlotini Neto
- Embrapa Informática Agropecuária, Av. Andre Tosello, 209, Barão Geraldo 13.083-886, Campinas, SP, Brazil
| | - Renato Vicentini
- Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade Estadual de Campinas, Campinas, SP, Brazil
| | | | - Adriana Silva Hemerly
- Laboratório de Biologia Molecular de Plantas, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho 373, CCS, Bl.L-29, Cidade Universitária 21941-599, Rio de Janeiro, RJ, Brazil
| | - Robert A. Martienssen
- Cold Spring Harbor Laboratory, 1 Bungtown Rd, Cold Spring Harbor, NY 11724, USA
- Howard Hughes Medical Institute and Gordon and Betty Moore Foundation, Cold Spring Harbor Laboratory, Cold Spring Harbor NY11724, USA
| | - Paulo Cavalcanti Gomes Ferreira
- Laboratório de Biologia Molecular de Plantas, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho 373, CCS, Bl.L-29, Cidade Universitária 21941-599, Rio de Janeiro, RJ, Brazil
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D'Addario C, Dell'Osso B, Palazzo MC, Benatti B, Lietti L, Cattaneo E, Galimberti D, Fenoglio C, Cortini F, Scarpini E, Arosio B, Di Francesco A, Di Benedetto M, Romualdi P, Candeletti S, Mari D, Bergamaschini L, Bresolin N, Maccarrone M, Altamura AC. Selective DNA methylation of BDNF promoter in bipolar disorder: differences among patients with BDI and BDII. Neuropsychopharmacology 2012; 37:1647-55. [PMID: 22353757 PMCID: PMC3358733 DOI: 10.1038/npp.2012.10] [Citation(s) in RCA: 122] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/11/2011] [Revised: 12/21/2011] [Accepted: 12/23/2011] [Indexed: 01/08/2023]
Abstract
The etiology of bipolar disorder (BD) is still poorly understood, involving genetic and epigenetic mechanisms as well as environmental contributions. This study aimed to investigate the degree of DNA methylation at the promoter region of the brain-derived neurotrophic factor (BDNF) gene, as one of the candidate genes associated with major psychoses, in peripheral blood mononuclear cells isolated from 94 patients with BD (BD I=49, BD II=45) and 52 healthy controls. A significant BDNF gene expression downregulation was observed in BD II 0.53±0.11%; P<0.05), but not in BD I (1.13±0.19%) patients compared with controls (CONT: 1±0.2%). Consistently, an hypermethylation of the BDNF promoter region was specifically found in BD II patients (CONT: 24.0±2.1%; BDI: 20.4±1.7%; BDII: 33.3±3.5%, P<0.05). Of note, higher levels of DNA methylation were observed in BD subjects on pharmacological treatment with mood stabilizers plus antidepressants (34.6±4.2%, predominantly BD II) compared with those exclusively on mood-stabilizing agents (21.7±1.8%; P<0.01, predominantly BD I). Moreover, among the different pharmacological therapies, lithium (20.1±3.8%, P<0.05) and valproate (23.6±2.9%, P<0.05) were associated with a significant reduction of DNA methylation compared with other drugs (35.6±4.6%). Present findings suggest selective changes in DNA methylation of BDNF promoter in subjects with BD type II and highlight the importance of epigenetic factors in mediating the onset and/or susceptibility to BD, providing new insight into the mechanisms of gene expression. Moreover, they shed light on possible mechanisms of action of mood-stabilizing compounds vs antidepressants in the treatment of BD, pointing out that BDNF regulation might be a key target for their effects.
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Affiliation(s)
- Claudio D'Addario
- Department of Biomedical Sciences, University of Teramo, Teramo, Italy
| | - Bernardo Dell'Osso
- Department of Clinical Psychiatry, Università degli Studi di Milano, Fondazione IRRCS Cà Granda, Ospedale Maggiore Policlinico, Department of Mental Health, Department of Psychiatry, Milano, Italy
| | - Maria Carlotta Palazzo
- Department of Clinical Psychiatry, Università degli Studi di Milano, Fondazione IRRCS Cà Granda, Ospedale Maggiore Policlinico, Department of Mental Health, Department of Psychiatry, Milano, Italy
| | - Beatrice Benatti
- Department of Clinical Psychiatry, Università degli Studi di Milano, Fondazione IRRCS Cà Granda, Ospedale Maggiore Policlinico, Department of Mental Health, Department of Psychiatry, Milano, Italy
| | - Licia Lietti
- Department of Clinical Psychiatry, Università degli Studi di Milano, Fondazione IRRCS Cà Granda, Ospedale Maggiore Policlinico, Department of Mental Health, Department of Psychiatry, Milano, Italy
| | - Elisabetta Cattaneo
- Department of Clinical Psychiatry, Università degli Studi di Milano, Fondazione IRRCS Cà Granda, Ospedale Maggiore Policlinico, Department of Mental Health, Department of Psychiatry, Milano, Italy
| | - Daniela Galimberti
- Department of Neurological Sciences, Centro Dino Ferrari, Università degli Studi di Milano, Fondazione IRRCS Cà Granda, Ospedale Maggiore Policlinico, Department of Neurology, Milano, Italy
| | - Chiara Fenoglio
- Department of Neurological Sciences, Centro Dino Ferrari, Università degli Studi di Milano, Fondazione IRRCS Cà Granda, Ospedale Maggiore Policlinico, Department of Neurology, Milano, Italy
| | - Francesca Cortini
- Department of Neurological Sciences, Centro Dino Ferrari, Università degli Studi di Milano, Fondazione IRRCS Cà Granda, Ospedale Maggiore Policlinico, Department of Neurology, Milano, Italy
| | - Elio Scarpini
- Department of Neurological Sciences, Centro Dino Ferrari, Università degli Studi di Milano, Fondazione IRRCS Cà Granda, Ospedale Maggiore Policlinico, Department of Neurology, Milano, Italy
| | - Beatrice Arosio
- Geriatric Unit, Fondazione IRCCS Cà Granda Osp Maggiore Policlinico, University of Milan, Milano, Italy
| | | | | | | | | | - Daniela Mari
- Geriatric Unit, Fondazione IRCCS Cà Granda Osp Maggiore Policlinico, University of Milan, Milano, Italy
| | | | - Nereo Bresolin
- Department of Neurological Sciences, Centro Dino Ferrari, Università degli Studi di Milano, Fondazione IRRCS Cà Granda, Ospedale Maggiore Policlinico, Department of Neurology, Milano, Italy
| | - Mauro Maccarrone
- Department of Biomedical Sciences, University of Teramo, Teramo, Italy
- European Center for Brain Research (CERC)/Santa Lucia Foundation, Rome, Italy
| | - A Carlo Altamura
- Department of Clinical Psychiatry, Università degli Studi di Milano, Fondazione IRRCS Cà Granda, Ospedale Maggiore Policlinico, Department of Mental Health, Department of Psychiatry, Milano, Italy
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The physical and genetic framework of the maize B73 genome. PLoS Genet 2009; 5:e1000715. [PMID: 19936061 PMCID: PMC2774505 DOI: 10.1371/journal.pgen.1000715] [Citation(s) in RCA: 84] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2009] [Accepted: 10/12/2009] [Indexed: 11/19/2022] Open
Abstract
Maize is a major cereal crop and an important model system for basic biological research. Knowledge gained from maize research can also be used to genetically improve its grass relatives such as sorghum, wheat, and rice. The primary objective of the Maize Genome Sequencing Consortium (MGSC) was to generate a reference genome sequence that was integrated with both the physical and genetic maps. Using a previously published integrated genetic and physical map, combined with in-coming maize genomic sequence, new sequence-based genetic markers, and an optical map, we dynamically picked a minimum tiling path (MTP) of 16,910 bacterial artificial chromosome (BAC) and fosmid clones that were used by the MGSC to sequence the maize genome. The final MTP resulted in a significantly improved physical map that reduced the number of contigs from 721 to 435, incorporated a total of 8,315 mapped markers, and ordered and oriented the majority of FPC contigs. The new integrated physical and genetic map covered 2,120 Mb (93%) of the 2,300-Mb genome, of which 405 contigs were anchored to the genetic map, totaling 2,103.4 Mb (99.2% of the 2,120 Mb physical map). More importantly, 336 contigs, comprising 94.0% of the physical map (∼1,993 Mb), were ordered and oriented. Finally we used all available physical, sequence, genetic, and optical data to generate a golden path (AGP) of chromosome-based pseudomolecules, herein referred to as the B73 Reference Genome Sequence version 1 (B73 RefGen_v1). Maize has been a cultural icon and staple food crop of Americans since the discovery of the new world in 1492. Contemporary society is now faced with growing demands for food and fuel in the face of global climate change and the potential for increased disease pressure. To provide a comprehensive foundation to systematically understand maize biology with the goal of breeding higher yielding, disease-resistant, and drought-tolerant cultivars, our consortium sequenced the B73 genome of maize. In this study, we used a comprehensive physical and genetic framework map to develop a minimum tiling path (MTP) of over 16,000 BAC clones across the genome. The MTP was generated dynamically and integrated numerous data types, such as in-coming genome sequence, over 8,000 sequence-based genetic markers, and the maize optical map. This allowed us to genetically anchor, order, and orient the majority of the maize physical map and genome sequence to the genetic map. Post-genome sequencing, we constructed a golden path (AGP) of sequence-based pseudomolecules representing the ten chromosomes of the maize B73 genome (B73 RefGen_v1). This unprecedented integration of genetic, physical, and genomic sequence into one framework will greatly facilitate all aspects of plant biological research.
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