New Diversity Arrays Technology (DArT) markers for tetraploid oat (Avena magna Murphy et Terrell) provide the first complete oat linkage map and markers linked to domestication genes from hexaploid A. sativa L.

Oliver, Rebekah E.; Jellen, Eric N.; Ladizinsky, G.; Korol, Abraham B.; Kilian, Andrzej; Beard, John L.; Dumlupınar, Ziya; Wisniewski-Morehead, N. H.; Svedin, Elisabeth; Coon, Melissa; Redman, Rachel Rebecca; Maughan, Peter J.; Obert, D. E.; Jackson, Eric W.

doi:10.1007/s00122-011-1656-y

Cited by 29 publications

(30 citation statements)

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“…As noted in Background, some presumptive folds in the atrial wall were interpreted as evidence for atrial wall invagination in the formation of book lung lamellae in scorpion embryos, although a relationship between folds and lamellae was not shown [19,22]. The structures diagramed as folds may have been small widenings of the air sac entrance as observed in the book lungs of spider embryos.…”

Section: Resultsmentioning

confidence: 99%

“…This was considered as evidence of hypodermal invagination like that proposed for book gills [17,22,26] although the presumptive folds were not actually shown to be related to the formation of book lung lamellae.…”

Section: Introductionmentioning

confidence: 99%

“…This process was thought to be similar to the small amount of invagination that may occur along with outgrowth folds for book gill development at the posterior surface of branchial appendages in horseshoe crabs [2-10,18-22]. Slight widening of the air sac entrance at the atrial wall was interpreted as indications of hypodermal infolding.…”

Section: Introductionmentioning

confidence: 99%

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The ultrastructure of book lung development in the bark scorpion Centruroides gracilis (Scorpiones: Buthidae)

Farley

2011

Front Zool

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BackgroundNear the end of the nineteenth century the hypothesis was presented for the homology of book lungs in arachnids and book gills in the horseshoe crab. Early studies with the light microscope showed that book gill lamellae are formed by outgrowth and possibly some invagination (infolding) of hypodermis (epithelium) from the posterior surface of opisthosomal limb buds. Scorpion book lungs are formed near the bilateral sites of earlier limb buds. Hypodermal invaginations in the ventral opisthosoma result in spiracles and sac-like cavities (atria). In early histological sections of embryo book lungs, widening of the atrial entrance of some lamellae (air channels, air sacs, saccules) was interpreted as an indication of invagination as hypothesized for book gill lamellae. The hypodermal infolding was thought to produce the many rows of lamellar precursor cells anterior to the atrium. The ultrastructure of scorpion book lung development is compared herein with earlier investigations of book gill formation.ResultsIn scorpion embryos, there is ingression (inward migration) of atrial hypodermal cells rather than invagination or infolding of the atrial hypodermal layer. The ingressing cells proliferate and align in rows anterior to the atrium. Their apical-basal polarity results in primordial air channels among double rows of cells. The cuticular walls of the air channels are produced by secretion from the apical surfaces of the aligned cells. Since the precursor cells are in rows, their secreted product is also in rows (i.e., primordial air channels, saccules). For each double row of cells, their opposed basal surfaces are gradually separated by a hemolymph channel of increasing width.ConclusionsThe results from this and earlier studies show there are differences and similarities in the formation of book lung and book gill lamellae. The homology hypothesis for these respiratory organs is thus supported or not supported depending on which developmental features are emphasized. For both organs, when the epithelial cells are in position, their apical-basal polarity results in alternate page-like channels of hemolymph and air or water with outward directed hemolymph saccules for book gills and inward directed air saccules for book lungs.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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The ultrastructure of book lung development in the bark scorpion Centruroides gracilis (Scorpiones: Buthidae)

Farley

2011

Front Zool

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“…The authors outlined a rapid and effective high-throughput pipeline for SNP discovery and genotyping that could be used in other species with poorly-characterized genomes. Some of the SNPs developed were used to construct the first complete tetraploid oat linkage map [21]. …”

Section: Introductionmentioning

confidence: 99%

Analysis and annotation of the hexaploid oat seed transcriptome

Gutiérrez-González

Garvin

2013

BMC Genomics

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BackgroundNext generation sequencing provides new opportunities to explore transcriptomes. However, challenges remain for accurate differentiation of homoeoalleles and paralogs, particularly in polyploid organisms with no supporting genome sequence. In this study, RNA-Seq was employed to generate and characterize the first gene expression atlas for hexaploid oat.ResultsThe software packages Trinity and Oases were used to produce a transcript assembly from nearly 134 million 100-bp paired-end reads from developing oat seeds. Based on the quality-parameters employed, Oases assemblies were superior. The Oases 67-kmer assembly, denoted dnOST (de novo Oat Seed Transcriptome), is over 55 million nucleotides in length and the average transcript length is 1,043 nucleotides. The 74.8× sequencing depth was adequate to differentiate a large proportion of putative homoeoalleles and paralogs. To assess the robustness of dnOST, we successfully identified gene transcripts associated with the biosynthetic pathways of three compounds with health-promoting properties (avenanthramides, tocols, β-glucans), and quantified their expression.ConclusionsTo our knowledge, this study provides the first direct performance comparison between two major assemblers in a polyploid organism. The workflow we developed provides a useful guide for comparable analyses in other organisms. The transcript assembly developed here is a major advance. It expands the number of oat ESTs 3-fold, and constitutes the first comprehensive transcriptome study in oat. This resource will be a useful new tool both for analysis of genes relevant to nutritional enhancement of oat, and for improvement of this crop in general.

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“…These studies revealed low genetic diversity of Miscanthus 9 giganteus accessions used for bioenergy. More recently, Diversity Array Technology (DArT) has been successfully applied in genetic diversity analyses, linkage mapping, and surveying population structure of various crop species (Oliver et al 2011;Castillo et al 2013;Von Mark et al 2013). DArT is microarray-based method using DNA-DNA hybridisation (Jaccoud et al 2001).…”

Section: Introductionmentioning

confidence: 98%

DArT-based characterisation of genetic diversity in a Miscanthus collection from Poland

Tang

Daroch

Kilian

et al. 2015

Planta

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Analysis of 180 accessions of Miscanthus using a DArT platform revealed high diversity. The phylogenetic analysis revealed that M. × giganteus accessions fall into two genetically distinct groups. Miscanthus is a genus of perennial rhizomatous grasses that has emerged in last 20 years as a feedstock for bioenergy and biofuel production. Currently, the most widely used accession for bioenergy purposes is Miscanthus × giganteus, a sterile triploid hybrid between Miscanthus sinensis and Miscanthus sacchariflorus. However, previous reports have shown that genetic diversity of Miscanthus × giganteus is limited. Here, we report development of Diversity Arrays Technology platform for the analysis of genetic structure of a Miscanthus collection of 180 accessions. A total of 906 markers were obtained of which around 25.5% exhibited polymorphism information content value in the range of 0.40 and 0.50 and are considered particularly informative. Newly developed marker system will serve as an additional resource to assist crop improvement, germplasm preservation and genetic studies. Three types of analysis indicated that 180 accessions from the collection were well differentiated and presented high diversity. Interestingly, the analysis revealed that there are two separate groups of plants, significantly differing in genetic diversity, that are commercially available as M. × giganteus. We suggest that one of these groups is most likely mutants or somaclonal variants of original M. × giganteus. The other group is recent hybrids of Miscanthus of higher genetic diversity. This study indicates that the diversity of commercially available M. × giganteus is higher than commonly assumed. Development of the new marker system can significantly assist breeding of new commercial cultivars of Miscanthus for bioenergy use.

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New Diversity Arrays Technology (DArT) markers for tetraploid oat (Avena magna Murphy et Terrell) provide the first complete oat linkage map and markers linked to domestication genes from hexaploid A. sativa L.

Cited by 29 publications

References 59 publications

The ultrastructure of book lung development in the bark scorpion Centruroides gracilis (Scorpiones: Buthidae)

The ultrastructure of book lung development in the bark scorpion Centruroides gracilis (Scorpiones: Buthidae)

Analysis and annotation of the hexaploid oat seed transcriptome

DArT-based characterisation of genetic diversity in a Miscanthus collection from Poland

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