学会抄録

Genetic map file of consensus genotypes for each contig

Helianthus Genespace Est Assembly

All genotyping was performed using a custom Affymetrix GeneChip (Affymetrix, CA, USA) designed from Helianthus expressed-sequence tags (ESTs). A total of 283,605 Sanger ESTs from 7 sunflower species (GenBank numbers: AJ318230-AJ318330, AJ412174-AJ412667, AJ437699-AJ437975, AJ539583-AJ540226, AJ541055-AJ541795, AJ542101-AJ542392, AJ827751-AJ829440, BG734514-BG734530, BG874297-BG874313, BG891021-BG891022, BQ909263-BQ917261, BQ965129-BQ980049, BU015365-BU036497, BU671782-BU672110, CD845604-CD858495, CF076145-CF099271, CX943504-CX948070, DY903733-DY959228, EE605695-EE627562, EE628472-EE661299, EL412382-EL492411, EL511146-EL515442, EL772988) were assembled using TGICL [11]. These sequences included 94,017 ESTs from H. annuus; 35,704 from H. argophyllus; 21,589 from H. ciliaris; 33,959 from H. exilis; 30,504 from H. paradoxus; 27,479 from H. petiolaris; and 40,353 from H. tuberosus. The final assembly included 87,237 “unigenes” corresponding to 27,587 contigs and 59,650 singletons

C. palaestinus transcriptome assembly

Assembly is based on RNA extracted from leaves, florets, and ovules of PI 23566

Supplement 1: Thin film wavelength converters for photonic integrated circuits

Supplementary Material Originally published in Optica on 20 May 2016 (optica-3-5-531

SNP Discovery and Development of a High-Density Genotyping Array for Sunflower

<div><p>Recent advances in next-generation DNA sequencing technologies have made possible the development of high-throughput SNP genotyping platforms that allow for the simultaneous interrogation of thousands of single-nucleotide polymorphisms (SNPs). Such resources have the potential to facilitate the rapid development of high-density genetic maps, and to enable genome-wide association studies as well as molecular breeding approaches in a variety of taxa. Herein, we describe the development of a SNP genotyping resource for use in sunflower (<em>Helianthus annuus</em> L.). This work involved the development of a reference transcriptome assembly for sunflower, the discovery of thousands of high quality SNPs based on the generation and analysis of ca. 6 Gb of transcriptome re-sequencing data derived from multiple genotypes, the selection of 10,640 SNPs for inclusion in the genotyping array, and the use of the resulting array to screen a diverse panel of sunflower accessions as well as related wild species. The results of this work revealed a high frequency of polymorphic SNPs and relatively high level of cross-species transferability. Indeed, greater than 95% of successful SNP assays revealed polymorphism, and more than 90% of these assays could be successfully transferred to related wild species. Analysis of the polymorphism data revealed patterns of genetic differentiation that were largely congruent with the evolutionary history of sunflower, though the large number of markers allowed for finer resolution than has previously been possible.</p> </div

Development of an Ultra-Dense Genetic Map of the Sunflower Genome Based on Single-Feature Polymorphisms

<div><p>The development of ultra-dense genetic maps has the potential to facilitate detailed comparative genomic analyses and whole genome sequence assemblies. Here we describe the use of a custom Affymetrix GeneChip containing nearly 2.4 million features (25 bp sequences) targeting 86,023 unigenes from sunflower (<em>Helianthus annuus</em> L.) and related species to test for single-feature polymorphisms (SFPs) in a recombinant inbred line (RIL) mapping population derived from a cross between confectionery and oilseed sunflower lines (RHA280×RHA801). We then employed an existing genetic map derived from this same population to rigorously filter out low quality data and place 67,486 features corresponding to 22,481 unigenes on the sunflower genetic map. The resulting map contains a substantial fraction of all sunflower genes and will thus facilitate a number of downstream applications, including genome assembly and the identification of candidate genes underlying QTL or traits of interest.</p> </div

Marker density on genetic map.

<p>Marker density per cM across all 17 sunflower linkage groups. Bars represent the number of chip features mapped as SFPs using the Affymetrix technology.</p

Supplement 1: Dynamically reconfigurable integrated optical circulators

Supplementary material Originally published in Optica on 20 January 2017 (optica-4-1-23

Principal coordinates analysis plot.

<p>Plot of the first two principal coordinates for the 32 <i>H. annuus</i> individuals based on all SNPs with MAF ≥0.10. Each data point represents an accession with one of six groups: OPV/Landraces (OPV/LR), HA-oil, HA-nonoil (HA-NO), RHA-oil, RHA-nonoil (RHA-NO), and wild <i>H. annuus</i>.</p

Summary of DNA sequence data used in the reference assembly (above line) and SNP discovery (below line).

<p>*These sequence datasets were used for both the reference assembly and for SNP identification.</p