Extensive intraspecific gene order and gene structural. Using transcriptome sequencing of seedling rna from 503 maize zea mays inbred lines to characterize the maize pan genome, we identified 8681 representative transcript assemblies rtas1 with 16. Characterizing the pangenome of maize with pacbio smrt. Aug 20, 2015 northern corn leaf blight nclb caused by exserohilum turcicum is a destructive disease in maize. Nearly 85% of the genome is composed of hundreds of families of transposable elements, dispersed nonuniformly across the genome. Its genetic variation has been characterized by using molecular markers and by sequencing multiple alleles from selected loci 5,6. The maize genome is complex with striking intraspecific variation in gene order, repetitive dna content, and allelic content exceeding the levels observed between primate species. Genotypingbysequencing gbs is a one such method highly suited to nonhuman organisms. These were responsible for the capture and amplification of numerous gene fragments and affect the composition, sizes, and positions of centromeres. In addition to these maps, maize researchers now have access to genomic sequence of the b73 inbred lines genic regions schnable et al. We sequenced the maize genome using a diversity, and dynamics minimum tiling. The 63rd annual maize genetics conference will be held on march 1114, 2021, at the union station in st. Detailed analysis of a contiguous 22mb region of the maize genome.
Characterizing the population structure and genetic diversity. Characterizing the pan genome of maize with pacbio smrt sequencing author. Indeed, the maize reference genome, b73, carries only c. Improved maize reference genome with singlemolecule technologies.
Stein,6f fusheng wei,8f shiran pasternak,6 chengzhi liang,6 jianwei zhang,8 luanda fulton,7 tina a. The huangzaosi maize genome provides insights into. Centromeric retrotransposons cr are located almost exclusively at the centromeres of plant chromosomes. Retrotransposons with long terminal repeats ltrs are the most abundant transposable elements in plant genomes. Genome size diversity in angiosperms and its influence on. Beyond its considerable agricultural and economic value as a crop for food, feed and fuel, maize presents unparalleled biological attributes as a research model for genetic diversity and genome evolution 1, 2. Complexity, diversity, and dynamics science 326, 1112 2009, doi. The maize b73 reference genome has been revised four times since its initial release as a bacbybac assembly in 2009. Close split of sorghum and maize genome progenitors. To determine whether the maize pantranscriptome is open the size of pan genome grows continuously with the number of sequenced individuals increases or closed the size of pan genome reached a constant value with the number of sequenced individuals increases and to estimate the size of it. Lugenomewide characterization of nonreference transposable element insertion polymorphisms reveals genetic diversity in tropical and temperate maize. Complexity, diversity, and dynamics, abstract we report an improved draft nucleotide sequence of the 2. Authorized to april 30, includes plants for which units per mo radio equipment, units per mo shell fuze parts, units per mo anderson ind ware woolen co navy blankets and not reported 942 wis wollensak optical co telescope sights, not reported 542 completed l24l. Graves,7 patrick minx,7 amy denise reily,7 laura courtney,7 scott s.
A robust, simple genotypingbysequencing gbs approach for. Identification of structural variants in two novel genomes of. Among the 39 324 proteincoding genes predicted, the vast majority are untapped due to the lack of suitable highthroughput reverse genetic resources. Repetitive dna content in the maize genome is uncoupled from. Distribution, diversity, evolution, and survival of helitrons. The polychromatic helitron landscape of the maize genome pnas. Genomes at the species level are dynamic, with genes present in every individual core and genes in a subset of individuals dispensable that collectively constitute the pan genome. James holland and colleagues report a genome wide association study for resistance to southern leaf blight slb in the maize nested association mapping population. Maizegdb is a communityoriented, longterm, federally funded informatics service to researchers focused on the crop plant and model organism zea mays. Improved maize reference genome with singlemolecule. If you wish to distribute this article to others, you can order highquality copies for your following the guidelines here. Considering that maize line b73 is sensitive to glyphosate 30 for a more accurate prediction, the pool of snps and indels was narrowed to those occurring only in the tolerant line. Complexity, diversity, and dynamics article pdf available in science 3265956. The maize genome is complex with striking intraspecific.
Analysis of the bread wheat genome using whole genome. The 7% of the genome 170 mb that is not contained within the maize physical map accounts for 70% of the missing sequence. Schnable ps1, ware d, fulton rs, stein jc, wei f, pasternak s, liang c. The maize genetic pool includes a large natural diversity among both wild and cultivated relatives.
Specificity and evolutionary dynamics of small rnas in maize. Insights into the maize pangenome and pantranscriptome. Pdf the physical and genetic framework of the maize b73. Flexible and scalable genotypingbysequencing strategies. Genomewide association mapping reveals novel sources of. The 62nd annual maize genetics meeting will be held on march 1215, 2020, at the sheraton kona, kailuakona, hawai. The maize b73 representative reference genome the maize b73 reference genome has been revised four times since its initial release as a bacbybac assembly in 2009. However, this requires the identification and use of stable resistance genes that are effective across different environments. We isolated and sequenced large genomic fragments from the regions surrounding five. Reports long terminal repeat retrotransposons ltr retro the b73 maize genome.
For example, an analysis of the maize inbred line b73. We have taken a new approach to investigate the origin of the maize genome. The wheat variety chinese spring cs42 was selected for sequencing because of its wide use in genome studies 14,15. In maize it has been shown that svs influence thousands of genes e. The trimmed reads are mapped to the b73 maize genome agp v2 pseudomolecules using blastn run in parallel on the uf hpc computing cluster. A total of 1,930 intact helitrons from eight families 62 subfamilies and 20,000 helitron fragments were identified, accounting for. A 100kb window was selected in order to fall within the estimated 100kb window of linkage. The approximately 120bp snp probe sequences illumina, inc. In this way, we obtained a large number of variances table2. This pdf file includes materials and methods som text figs.
To obtain confidently mapped reads, reads were retained if they mapped uniquely in the genome. Many areas critical to agricultural production and research, such as the breeding and trait mapping in plants and livestock, require robust and scalable genotyping platforms. The availability of the b73 inbred reference genome sets the stage for highthroughput functional characterization of maize genes on a whole genome scale. Nov 24, 2009 homology and structurebased approaches were used to identify helitrons in the genome of maize inbred b73. The maize genome sequencing consortium publishes the b73. A study in 2005 demonstrated that half of the genome sequence and onethird of the gene content between two inbred lines of maize was not shared. Maize genome complexity is primarily driven by polyploidization and explosive amplification of ltr retrotransposons, with the counteracting effect of unequal and illegitimate crossover. Maizecode assayed up to five tissues from four maize strains b73, nc350, w22. Maize pantranscriptome provides novel insights into. This copy is for your personal, noncommercial use only. As of 2016, the maize nomenclature committee has adopted naming standards to accommodate multiple zea species, multiple accessions, and multiple versions. Maizegdb is a founding member of agbiodata, a consortuim of agriculturerelated online resources which is committed to making agriculturerelated research data fair. In the gbs protocol, genomic dna is fractionated via restriction digest, then reduced representation is achieved through.
Transposition of at least one of these families is ongoing, but the most prominent burst of amplification activity was. Pdf we report an improved draft nucleotide sequence of the 2. Reference chromosomes with physical fingerprint contigs as alternating gray and white bands. Genome size diversity in angiosperms and its influence on gene space. Tirlearner, a new ensemble pipeline for tir transposable element identification and annotation, was used to analyze tir elements in three sequence maize lines b73, mo17, and w22. Insights into the maize pan genome and pantranscriptome.
Genomewide association study of quantitative resistance. The genome sequence of a typical female line, b73, was previously released. Selection and evaluation of a panel of simple sequence. Maizecode assayed up to five tissues from four maize strains b73, nc350, w22, til11 by rnaseq, chipseq, rampage, and small rna sequencing. Extensive intraspecific gene order and gene structural variations. Its genetic variation has been characterized by using molecular markers and by sequencing multiple. Complexity, diversity, and dynamics science november 20, 2009 326. We report an improved draft nucleotide sequence of the 2.
The physical and genetic framework of the maize b73 genome. Using host resistance to minimize the detrimental effects of nclb on maize productivity is the most costeffective and appealing disease management strategy. A novel ltr retrotransposon named rtposon primarily occurs in. Ocean optical data from potential otec sites in the gulf of mexico. The editors note that the title of this summary was not intended to convey a connection between toc1 and the plant gene tic. Analysis of the emerging zea mays inbred b73 genome sequence revealed two novel subfamilies of cr elements of maize crm, bringing the total number of known crm subfamilies. Unveiling the complexity of the maize transcriptome by. Maize breeding germplasm used in southwest china has high complexity because of the diverse ecological features of this area. Nov 24, 2009 the maize genome sequence data used in the present analysis are reported in. Genomewide patterns of genetic variation among elite. In this study, the population structure, genetic diversity, and linkage disequilibrium decay distance of 362 important inbred lines collected from the breeding program of southwest china were characterized using the maizesnp50 beadchip with 56,110 single nucleotide. The top track shows positions of 2,522 gaps in the pseudomolecules, including 1,115 gaps in which the lengths were estimated using optical genome maps orange, whereas the remainder purple have undetermined lengths.
Genetic control of morphometric diversity in the maize. Complexity, diversity, and dynamics this copy is for your personal, noncommercial use only. Oct 24, 2010 the maize genome is large and complex 1,2,3,4. Complexity, diversity, and dynamics abstract we report an improved draft nucleotide sequence of the 2. Genomewide patterns of genetic variation among elite maize. The availability of the b73 reference genome sequence opens up new research possibilities. Maize is an important crop with a high level of genome diversity and heterosis. The physical and genetic framework of the maize b73 genome article pdf available in plos genetics 511. The gold standard maize genome is defined as containing the complete sequence and structures of all maize genes and their locations in linear order on both the genetic and physical maps of maize, using b73 as the reference genome. Structural diversity of a novel ltr retrotransposon.
Louis, missouri, usa the 62nd annual maize genetics meeting was cancelled due to covid19 and details about a virtual meeting will be forthcoming. Pdf improved maize reference genome with singlemolecule. Repetitive dna is a major component of plant genomes and is thought to be a. Schnable ps, ware d, fulton rs, stein jc, wei f, et al. Presumed centromeric positions are indicated by red bands. Genomewide association study identifies candidate genes. Bennetzen 2012 centromere retention and loss during the descent of maize from a tetraploid ancestor. Maize pantranscriptome provides novel insights into genome. The results identified abundant new tir transposable elements with markedly varying positions between lines, indicating the potential impact of tir elements on gene expression and genome evolution. Repetitive dna is a major component of plant genomes and is thought to be a driver of evolutionary novelty. The available genome sequence of the maize line b73 was used as the reference genome for candidate gene analyses schnable et al.