ExomeCapture-DAS5-004571
ERS3164749
SRA accession
selection from a composite population that was composed of the following F1 hybrids
ancestory
DEVELOPED 2001 New York, United States by Sorrells, M., Cornell University; Bergstrom, G., Cornell University; Benscher, D., Cornell University
collected by
bread wheat
common name
Richland
cultivar
exome sequences of ExomeCapture-DAS5-004571 - Grain yield similar to Caledonia and averaged 6% higher grain yield than Geneva in 5 yrs. of regional testing in New York site. Test weight similar to Geneva and averaged 78.1 kg h1, 1 kg/h1 above Caledonia over 5 yrs. Similar in height to Geneva and averages 11 cm taller than Caledonia. Lodging resistance and winter hardiness similar to Geneva and slightly superior to Caledonia. Milling and baking characteristics are among the best for soft white winter wheats as deteremined by the USDA Soft Wheat Quality Lab., Wooster, OH. Susceptible to preharvest sprouting. Days to heading and maturity similar to most soft white winter cvs. grown in New York except Geneva which is 2 days earlier to reach anthesis. Stems and leaves yellow-green at booting and hollow white stems at maturity. At booting the flag leaf is erect and twisted and the stems have a waxy bloom. Spikes dense, tapering, and awnletted. Glumes tan, medium long, wide and have a square shoulder and an obtuse beak. Kernels soft white, ovate, have rounded cheeks and short brush, and a narrow, shallow crease. The mass of 1000 kernels averages 35g. Moderately resistant to prevalent races of loose smut (Ustilago tritici) and highly resistant to prevalent races of Powdery mildew (Erysiphe graminis). Susceptible to fusarium head blight (Fusarium graminearum), and highly resistant to wheat spindle streak, mosaic virus and soil borne mosaic virus.
description
2 week old
dev stage
winter wheat
ecotype
USA
geographic location (country and/or sea)
PI 632399
isolate
USDA Germplasm Resources Information Network
lab host
Triticum aestivum subsp. aestivum
http://purl.obolibrary.org/obo/NCBITaxon_4565
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
:Richland;:NY88024-117
variety