Variants from "The role of deleterious substitutions in crop genomes"

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2013
2014

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2015

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Title

Variants from "The role of deleterious substitutions in crop genomes"

Published Date

2016-07-26T18:46:49Z

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Author Contact

Kono, Thomas J Y
konox006@umn.edu

Type

Dataset
Genomics Data

Abstract

SNP calls in protein coding regions were obtained from 15 barley and 8 soybean lines. Non synonymous SNPs were predicted to be deleterious or not using three approaches.

Description

There are two gzipped VCF (variant call format) files with variant calls for barley and soybean. A total of 652,797 SNPs were identified in the barley lines, which consisted of 13 cultivars and 2 wild accessions. For soybean, 7 cultivars and 1 wild accession were used, and 586,102 SNPs were called. Whether a variant is deleterious or not was determined using SIFT (http://sift.jcvi.org/), PolyPhen2 (http://genetics.bwh.harvard.edu/pph2/), and a likelihood ratio test of sequence conservation. Raw reads are available through the SRA accession numbers in Table S1 of Kono et al. 2016. The code used for this research, BAD_Mutations, is open source and freely available at https://github.com/MorrellLAB/BAD_Mutations.

Funding Information

USDA NIFA National Needs Fellowship (Appropriation No. 5430-21000-006-00D)
MnDrive 2014 Food Security Fellowship
Minnesota Agricultural Experiment Station Variety Development fund
United Soybean Board
U.S. NSF Plant Genome Program (BDI-1339393)

Referenced by

The method used to extract the genetic material from the plant samples is described in: Mascher M, Richmond TA, Gerhardt DJ, Himmelbach A, Clissold L, Sampath D, Ayling S, Steuernagel B, Pfeifer M, D'Ascenzo M, Akhunov ED, Hedley PE, Gonzales AM, Morrell PL, Kilian B, Blattner FR, Scholz U, Mayer KF, Flavell AJ, Muehlbauer GJ, Waugh R, Jeddeloh JA, Stein N. (2013). Barley whole exome capture: a tool for genomic research in the genus Hordeum and beyond. The Plant Journal, 2013, Vol.76(3), pp.494-505 doi: 10.1111/tpj.12294.
http://dx.doi.org/10.1111/tpj.12294
Published article: Thomas J. Y. Kono, Fengli Fu1, Mohsen Mohammadi, Paul J. Hoffman, Chaochih Liu, Robert M. Stupar, Kevin P. Smith, Peter Tiffin, Justin C. Fay and Peter L. Morrell. (2016). The Role of Deleterious Substitutions in Crop Genomes. Mol Biol Evol. doi: 10.1093/molbev/msw102
http://dx.doi.org/10.1093/molbev/msw102
Original preprint can be found in BioRxiv:
http://dx.doi.org/10.1101/033175

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Funding information

USDA NIFA National Needs Fellowship (Appropriation No. 5430-21000-006-00D)
MnDrive 2014 Food Security Fellowship
Minnesota Agricultural Experiment Station Variety Development fund
United Soybean Board
U.S. NSF Plant Genome Program (BDI-1339393)

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