ERS3165690
SRA accession
Cardinal*3/3/Knox//CI 15329/CI 3984.
ancestory
DEVELOPED 2003 Indiana, United States by Ratcliffe, R., USDA-ARS; Ohm, H., Purdue University; Cambron, S., USDA-ARS; Patterson, F., Purdue University; Williams, C., USDA-ARS
collected by
bread wheat
common name
P921696
cultivar
exome sequences of ExomeCapture-DAS5-004540 - Soft red winter wheat with gene H31, located on chromosome 5BS close to marker Xupw4148, that confers resistance to Hessian fly (Mayetiola destructor) biotype L. CI3984, the donor of H31, has one gene for resistance to Hessian fly biotype L, determined by segregation analysis of 63 backcross F2 families in which 32 families were segregating and 31 families were susceptible, fitting a 1 gene genetic model by X2 analysis. The Hessian fly resistance of CI3984 was highly effective against Hessian fly populations collected from Maryland, Delaware, South Carolina, and Georgia, as well as biotype D in laboratory tests. This is a progeny from an F6 plant that resulted from plant selection for resistance to Hessian fly biotype L during inbreeding following the backcross to Cardinal, a Hessian fly susceptible soft red winter wheat cultivar. Typically, 15-30 progeny seedlings from F2, F3, F4, and F6 plants were infested and placed in a controlled chamber at 19 deg. C, similar to conditions described previously. Stems are hollow, anthocyanin is absent. Spikes awnless, fusiform, and lax. Glumes glabrous, long, midwide, and white at maturity. Anthers yellow. Kernels red, long, and elliptical; crease is midwide and middeep; cheeks rounded, brush mid-sized, midlong, and not collared.
description
2 week old
dev stage
F
ecotype
USA
geographic location (country and/or sea)
PI 633876
isolate
USDA Germplasm Resources Information Network
lab host
Triticum aestivum
organism
Triticum aestivum subsp. aestivum
scientific name
subsp. aestivum
sub species
The exome sequenced hexaploid wheat accessions were selected from a worldwide population of landraces and cultivars obtained from the USDA National Small Grains Collection and the Australian Grains Genebank (formally the Australian Winter Cereal Collection). The worldwide population comprised 3990 accessions from 106 countries that were genotyped using the Infinium iSelect 90K SNP wheat bead chip array40. The MCG method41 was used to select accessions for exome sequencing. This method uses a genetic relationship matrix calculated from genotype data to iteratively chose and arbitrary number of accessions (in the case of this study 20% of the accessions) that collectively explain the largest proportion of variance in genetic relationships among the whole set. Genomic DNA was extracted from leaf tissue for each accession using the Agencourt DNAdvance Genomic DNA Isolation Kit (Beckman Coulter) and subjected to sequence capture using the NimbleGen SeqCap EZ wheat whole genome assay12. In brief, 1 µg of DNA was fragmented with the Covaris S2 instrument to obtain an average fragment length of 300 bp. Shorter fragments were removed using Agencourt AMPure XP beads (Beckman Coulter). The KAPA Library Preparation Kit (Kapa Biosystems) and adapters supplied in the NimbleGen SeqCap EZ Reagent Kit Plus v2 (Roche) were used to prepare sample libraries for the capture assay, according to the KAPA protocol but excluding steps 8.1-8.22. The quality and yield of each sample library was assessed using an Agilent 2200 TapeStation (Agilent Technologies) before proceeding to the sequence capture assay following the Roche protocol. Each target capture sequence enriched sample library was sequenced on an Illumina HiSeq2000 instrument (Illumina) to generate about 30 million reads per accession.
submission description
GSB-711
submission identifier
Exome sequencing reveals the role of historic wild relative introgressions in shaping the adaptive landscape of the wheat genome
submission title
leaf
http://purl.obolibrary.org/obo/PO_0025034
tissue type
:P921696
variety