scholarly journals Soybean Haplotype Map (GmHapMap): A Universal Resource for Soybean Translational and Functional Genomics

2019 ◽  
Author(s):  
Davoud Torkamaneh ◽  
Jérôme Laroche ◽  
Babu Valliyodan ◽  
Louise O’Donoughue ◽  
Elroy Cober ◽  
...  
Keyword(s):  
Glycine Max ◽  
Gene Function ◽  
Oil Content ◽  
Seed Oil ◽  
Sequence Data ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Loss Of Function ◽  
Seed Oil Content ◽  
Extensive Coverage

AbstractHere we describe the first worldwide haplotype map for soybean (GmHapMap) constructed using whole-genome sequence data for 1,007 Glycine max accessions and yielding 15 million variants. The number of unique haplotypes plateaued within this collection (4.3 million tag SNPs) suggesting extensive coverage of diversity within the cultivated germplasm. We imputed GmHapMap variants onto 21,618 previously genotyped (50K array/210K GBS) accessions with up to 96% success for common alleles. A GWAS performed with imputed data enabled us to identify a causal SNP residing in the NPC1 gene and to demonstrate its role in controlling seed oil content. We identified 405,101 haplotypes for the 55,589 genes and show that such haplotypes can help define alleles. Finally, we predicted 18,031 putative loss-of-function (LOF) mutations in 10,662 genes and illustrate how such a resource can be used to explore gene function. The GmHapMap provides a unique worldwide resource for soybean genomics and breeding.

scholarly journals MEN1 Mutations in Hürthle Cell (Oncocytic) Thyroid Carcinoma

2015 ◽  
Vol 100 (4) ◽  
pp. E611-E615 ◽  
Author(s):  
Katayoon Kasaian ◽  
Ana-Maria Chindris ◽  
Sam M. Wiseman ◽  
Karen L. Mungall ◽  
Thomas Zeng ◽  
...  
Keyword(s):  
Thyroid Carcinoma ◽  
Sequence Data ◽  
Whole Genome Sequence ◽  
Regulation Of Transcription ◽  
Whole Genome ◽  
Loss Of Function ◽  
Transcription Control ◽  
Thyroid Carcinomas ◽  
Normal Tissues ◽  
Hürthle Cell

Context and Objective: Oncocytic thyroid carcinoma, also known as Hürthle cell thyroid carcinoma, accounts for only a small percentage of all thyroid cancers. However, this malignancy often presents at an advanced stage and poses unique challenges to patients and clinicians. Surgical resection of the tumor accompanied in some cases by radioactive iodine treatment, radiation, and chemotherapy are the established modes of therapy. Knowledge of the perturbed oncogenic pathways can provide better understanding of the mechanism of disease and thus opportunities for more effective clinical management. Design and Patients: Initially, two oncocytic thyroid carcinomas and their matched normal tissues were profiled using whole genome sequencing. Subsequently, 72 oncocytic thyroid carcinomas, one cell line, and five Hürthle cell adenomas were examined by targeted sequencing for the presence of mutations in the multiple endocrine neoplasia I (MEN1) gene. Results: Here we report the identification of MEN1 loss-of-function mutations in 4% of patients diagnosed with oncocytic thyroid carcinoma. Whole genome sequence data also revealed large regions of copy number variation encompassing nearly the entire genomes of these tumors. Conclusion: Menin, a ubiquitously expressed nuclear protein, is a well-characterized tumor suppressor whose loss is the cause of MEN1 syndrome. Menin is involved in several major cellular pathways such as regulation of transcription, control of cell cycle, apoptosis, and DNA damage repair pathways. Mutations of this gene in a subset of Hürthle cell tumors point to a potential role for this protein and its associated pathways in thyroid tumorigenesis.

OAC Thames soybean

1998 ◽  
Vol 78 (4) ◽  
pp. 633-634
Author(s):  
J. W. Tanner ◽  
B. M. Luzzi ◽  
W. Montminy ◽  
P. Gostovic ◽  
D. J. Hume
Keyword(s):  
Glycine Max ◽  
Key Words ◽  
Plant Height ◽  
Oil Content ◽  
Seed Oil ◽  
Soybean Cultivar ◽  
Seed Oil Content ◽  
Glycine Max L ◽  
Cultivar Description ◽  
The Mean

Thames is a 3025 CHU soybean (Glycine max [L.] Merr.) cultivar that had slightly higher yields than the mean of the checks, similar plant height, low lodging and high seed oil content. Key words: Soybean, cultivar description

OAC Frontier soybean

1994 ◽  
Vol 74 (1) ◽  
pp. 143-144
Author(s):  
W. D. Beversdorf ◽  
J. W. Tanner ◽  
W. Montminy ◽  
P. Gostovic ◽  
D. J. Hume
Keyword(s):  
Glycine Max ◽  
Key Words ◽  
Oil Content ◽  
Seed Oil ◽  
Yield Potential ◽  
Maturity Group ◽  
Seed Oil Content ◽  
Early Maturity ◽  
Glycine Max L ◽  
Cultivar Description

OAC Frontier is an early Maturity Group 00 soybean (Glycine max [L.] Merr.) cultivar with excellent yield potential and high seed oil content. Key words: Soybean, cultivar description

OAC Eclipse soybean

1994 ◽  
Vol 74 (1) ◽  
pp. 141-142
Author(s):  
W. D. Beversdorf ◽  
J. W. Tanner ◽  
W. Montminy ◽  
P. Gostovic ◽  
D. J. Hume
Keyword(s):  
Glycine Max ◽  
Key Words ◽  
Oil Content ◽  
Seed Oil ◽  
Soybean Cultivar ◽  
Yield Potential ◽  
Maturity Group ◽  
Seed Oil Content ◽  
Glycine Max L ◽  
Cultivar Description

OAC Eclipse is a mid-Maturity Group 0 soybean (Glycine max [L.] Merr.) cultivar with excellent yield potential and high seed oil content. Key words: Soybean, cultivar description

scholarly journals Characterising the loss-of-function impact of 5’ untranslated region variants in whole genome sequence data from 15,708 individuals

2019 ◽  
Author(s):  
Nicola Whiffin ◽  
Konrad J Karczewski ◽  
Xiaolei Zhang ◽  
Sonia Chothani ◽  
Miriam J Smith ◽  
...  
Keyword(s):  
Human Disease ◽  
Large Scale ◽  
Sequence Data ◽  
Case Reports ◽  
Protein Translation ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Loss Of Function ◽  
Genetic Sequencing ◽  
Strong Negative Selection

AbstractUpstream open reading frames (uORFs) are important tissue-specific cis-regulators of protein translation. Although isolated case reports have shown that variants that create or disrupt uORFs can cause disease, genetic sequencing approaches typically focus on protein-coding regions and ignore these variants. Here, we describe a systematic genome-wide study of variants that create and disrupt human uORFs, and explore their role in human disease using 15,708 whole genome sequences collected by the Genome Aggregation Database (gnomAD) project. We show that 14,897 variants that create new start codons upstream of the canonical coding sequence (CDS), and 2,406 variants disrupting the stop site of existing uORFs, are under strong negative selection. Furthermore, variants creating uORFs that overlap the CDS show signals of selection equivalent to coding loss-of-function variants, and uORF-perturbing variants are under strong selection when arising upstream of known disease genes and genes intolerant to loss-of-function variants. Finally, we identify specific genes where perturbation of uORFs is likely to represent an important disease mechanism, and report a novel uORF frameshift variant upstream of NF2 in families with neurofibromatosis. Our results highlight uORF-perturbing variants as an important and under-recognised functional class that can contribute to penetrant human disease, and demonstrate the power of large-scale population sequencing data to study the deleteriousness of specific classes of non-coding variants.

OAC Sparta soybean

1998 ◽  
Vol 78 (4) ◽  
pp. 631-632
Author(s):  
J. W. Tanner ◽  
B. M. Luzzi ◽  
W. Montminy ◽  
P. Gostovic ◽  
D. J. Hume
Keyword(s):  
Glycine Max ◽  
Key Words ◽  
Plant Height ◽  
Oil Content ◽  
Seed Oil ◽  
Soybean Cultivar ◽  
Seed Oil Content ◽  
Lodging Resistance ◽  
Glycine Max L ◽  
Cultivar Description

OAC Sparta is a 3125 CHU soybean (Glycine max [L.] Merr.) cultivar that outyielded check cultivars, had greater plant height and higher seed oil content but less lodging resistance. Key words: Soybean, cultivar description

Registration of ‘NC-Miller’ Soybean with High Yield and High Seed-Oil Content

2012 ◽  
Vol 6 (3) ◽  
pp. 294-297 ◽  
Author(s):  
J. W. Burton ◽  
L. M. Miranda ◽  
T. E. Carter ◽  
D. T. Bowman
Keyword(s):  
Oil Content ◽  
Seed Oil ◽  
High Yield ◽  
Seed Oil Content
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