scholarly journals In-Depth Sequence Analysis of Bread Wheat VRN1 Genes

2021 ◽  
Vol 22 (22) ◽  
pp. 12284
Author(s):  
Beáta Strejčková ◽  
Zbyněk Milec ◽  
Kateřina Holušová ◽  
Petr Cápal ◽  
Tereza Vojtková ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Copy Number ◽  
Complete Sequence ◽  
Heading Time ◽  
Specific Expression ◽  
Promoter Sequences ◽  
Intron 1 ◽  
Vrn1 Gene ◽  
Number Variation ◽  
Specific Expression Pattern

The VERNALIZATION1 (VRN1) gene encodes a MADS-box transcription factor and plays an important role in the cold-induced transition from the vegetative to reproductive stage. Allelic variability of VRN1 homoeologs has been associated with large differences in flowering time. The aim of this study was to investigate the genetic variability of VRN1 homoeologs (VRN-A1, VRN-B1 and VRN-D1). We performed an in-depth sequence analysis of VRN1 homoeologs in a panel of 105 winter and spring varieties of hexaploid wheat. We describe the novel allele Vrn-B1f with an 836 bp insertion within intron 1 and show its specific expression pattern associated with reduced heading time. We further provide the complete sequence of the Vrn-A1b allele, revealing a 177 bp insertion in intron 1, which is transcribed into an alternative splice variant. Copy number variation (CNV) analysis of VRN1 homoeologs showed that VRN-B1 and VRN-D1 are present in only one copy. The copy number of recessive vrn-A1 ranged from one to four, while that of dominant Vrn-A1 was one or two. Different numbers of Vrn-A1a copies in the spring cultivars Branisovicka IX/49 and Bastion did not significantly affect heading time. We also report on the deletion of secondary structures (G-quadruplex) in promoter sequences of cultivars with more vrn-A1 copies.

Unusual genomic rearrangements in introns 1 and 22 of the F8 gene

2011 ◽  
Vol 31 (S 01) ◽  
pp. S69-S73 ◽  
Author(s):  
M. A. Zimmermann ◽  
J. Oldenburg ◽  
C. R. Müller ◽  
S. Rost
Keyword(s):  
Factor Viii ◽  
Copy Number ◽  
Copy Number Variations ◽  
Severe Phenotype ◽  
Factor Viii Gene ◽  
Intron 1 ◽  
Number Variation ◽  
Abnormal Band ◽  
Large Rearrangements

SummaryIntron 1 and intron 22 inversions, two large rearrangements of the factor VIII gene, are generally associated with a severe phenotype of haemophilia A and a high risk of inhibitor formation. In several haemophiliacs, diagnostic analyses for detection of these inversions revealed unusual band patterns. Upon further examination, different copy number variations were detected in the factor VIII gene of these patients by multiplex ligationdependent probe amplification (MLPA). Since these duplications or deletions alone could not sufficiently explain the abnormal band patterns of the first analyses, we assumed a combination of intron 1 or intron 22 inversions together with a copy number variation. Result We could confirm this hypothesis by specific long range PCRs but a detailed characterization of the breakpoints and the mechanisms for these complex rearrangements have yet to be elucidated.

scholarly journals Copy number variation of Ppd-B1 is the major determinant of heading time in durum wheat

BMC Genetics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Tobias Würschum ◽  
Matthias Rapp ◽  
Thomas Miedaner ◽  
C. Friedrich H. Longin ◽  
Willmar L. Leiser
Keyword(s):  
Copy Number Variation ◽  
Durum Wheat ◽  
Copy Number ◽  
Major Determinant ◽  
Heading Time ◽  
Number Variation

scholarly journals Copy Number Variation in Intron 1 of SOX5 Causes the Pea-comb Phenotype in Chickens

PLoS Genetics ◽  
2009 ◽  
Vol 5 (6) ◽  
pp. e1000512 ◽  
Author(s):  
Dominic Wright ◽  
Henrik Boije ◽  
Jennifer R. S. Meadows ◽  
Bertrand Bed'hom ◽  
David Gourichon ◽  
...  
Keyword(s):  
Copy Number Variation ◽  
Copy Number ◽  
Intron 1 ◽  
Number Variation

Identification of Novel Germline and Tumor-Specific Nucleotide Variants and Copy Number Variation in Clival Chordomas by Exome Sequencing

2015 ◽  
Vol 76 (S 01) ◽  
Author(s):  
Georgios Zenonos ◽  
Peter Howard ◽  
Maureen Lyons-Weiler ◽  
Wang Eric ◽  
William LaFambroise ◽  
...  
Keyword(s):  
Copy Number Variation ◽  
Exome Sequencing ◽  
Copy Number ◽  
Number Variation ◽  
Specific Nucleotide

The impact of paralog genes: detection of copy number variation in spinal muscle atrophy patients

BIOCELL ◽  
2018 ◽  
Vol 42 (3) ◽  
pp. 87-91 ◽  
Author(s):  
Sergio LAURITO ◽  
Juan A. CUETO ◽  
Jimena PEREZ ◽  
Mar韆 ROQU�
Keyword(s):  
Copy Number Variation ◽  
Muscle Atrophy ◽  
Copy Number ◽  
Number Variation ◽  
The Impact

Transcriptional profiling of iPSC-derived neurons with reciprocal monogenic CNV in 3p26.3 region

2020 ◽  
pp. 10-11
Author(s):  
М.Е. Лопаткина ◽  
В.С. Фишман ◽  
М.М. Гридина ◽  
Н.А. Скрябин ◽  
Т.В. Никитина ◽  
...  
Keyword(s):  
Gene Expression ◽  
Copy Number ◽  
System Development ◽  
Transcriptional Profiling ◽  
Global Gene Expression ◽  
Nervous System Development ◽  
Number Variation ◽  
The Central Nervous System ◽  
Cntn6 Gene ◽  
Copy Number Changes

Проведен анализ генной экспрессии в нейронах, дифференцированных из индуцированных плюрипотентных стволовых клеток пациентов с идиопатическими интеллектуальными нарушениями и реципрокными хромосомными мутациями в регионе 3p26.3, затрагивающими единственный ген CNTN6. Для нейронов с различным типом хромосомных аберраций была показана глобальная дисрегуляция генной экспрессии. В нейронах с вариациями числа копий гена CNTN6 была снижена экспрессия генов, продукты которых вовлечены в процессы развития центральной нервной системы. The gene expression analysis of iPSC-derived neurons, obtained from patients with idiopathic intellectual disability and reciprocal microdeletion and microduplication in 3p26.3 region affecting the single CNTN6 gene was performed. The global gene expression dysregulation was demonstrated for cells with CNTN6 copy number variation. Gene expression in neurons with CNTN6 copy number changes was downregulated for genes, whose products are involved in the central nervous system development.

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