Wheat in the Mediterranean revisited--tetraploid wheat landraces assessed with elite bread wheat Single Nucleotide Polymorphism markers

BMC Genetics
Hugo R OliveiraMartin K Jones

Abstract

Single Nucleotide Polymorphism (SNP) panels recently developed for the assessment of genetic diversity in wheat are primarily based on elite varieties, mostly those of bread wheat. The usefulness of such SNP panels for studying wheat evolution and domestication has not yet been fully explored and ascertainment bias issues can potentially affect their applicability when studying landraces and tetraploid ancestors of bread wheat. We here evaluate whether population structure and evolutionary history can be assessed in tetraploid landrace wheats using SNP markers previously developed for the analysis of elite cultivars of hexaploid wheat. We genotyped more than 100 tetraploid wheat landraces and wild emmer wheat accessions, some of which had previously been screened with SSR markers, for an existing SNP panel and obtained publically available genotypes for the same SNPs for hexaploid wheat varieties and landraces. Results showed that quantification of genetic diversity can be affected by ascertainment bias but that the effects of ascertainment bias can at least partly be alleviated by merging SNPs to haplotypes. Analyses of population structure and genetic differentiation show strong subdivision between the tetraploid wheat subspe...Continue Reading

References

Dec 1, 1973·Proceedings of the National Academy of Sciences of the United States of America·M Nei
May 3, 2000·Genome Génome / Conseil National De Recherches Canada·X HuangVolker Mohler
Jun 4, 2002·Nature Reviews. Genetics·Francesco SalaminiWilliam Martin
May 24, 2005·PLoS Biology·Magnus NordborgJoy Bergelson
Oct 13, 2006·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Mona AkbariAndrzej Kilian
Oct 24, 2006·Nature Genetics·Donald F ConradJonathan K Pritchard
Feb 24, 2007·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·M-C LuoJan Dvorak
Apr 20, 2007·Molecular Biology and Evolution·A HaudryJ David
Jul 17, 2007·Genome Génome / Conseil National De Recherches Canada·Daryl J SomersCurt McCartney
Apr 26, 2008·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Zvi PelegTzion Fahima
May 19, 2009·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Eduard AkhunovJan Dvorak
Jan 12, 2010·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Delphine Van InghelandtBenjamin Stich
Jun 19, 2010·Molecular Biology and Evolution·Anders AlbrechtsenRasmus Nielsen
Nov 3, 2010·Journal of Experimental Botany·Marco MaccaferriRoberto Tuberosa
May 26, 2011·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Daniele TrebbiRoberto Tuberosa
Jan 20, 2012·Molecular Ecology·Sariel HübnerKarl J Schmid
Mar 2, 2012·The Journal of Heredity·Jan DvorakHamid Dehghani
Feb 23, 2013·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Tobias WürschumJochen C Reif
May 1, 2013·Proceedings of the National Academy of Sciences of the United States of America·Colin R CavanaghEduard Akhunov

Citations

Jan 21, 2016·BMC Plant Biology·Jenny HagenbladMatti W Leino
Jan 1, 2015·Nature Plants·Graham Moore
Dec 22, 2017·BMC Genetics·Maria LundströmJenny Hagenblad
Jan 23, 2020·PloS One·Hugo R OliveiraTerence A Brown
Mar 21, 2019·International Journal of Molecular Sciences·Cyrine RobbanaAhmed Amri
Nov 24, 2020·BMC Plant Biology·Kamal KhadkaAlireza Navabi

Methods Mentioned

BETA
genotyping
PCA
PCAs

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Spatio-Temporal Regulation of DNA Repair

DNA repair is a complex process regulated by several different classes of enzymes, including ligases, endonucleases, and polymerases. This feed focuses on the spatial and temporal regulation that accompanies DNA damage signaling and repair enzymes and processes.

Glut1 Deficiency

Glut1 deficiency, an autosomal dominant, genetic metabolic disorder associated with a deficiency of GLUT1, the protein that transports glucose across the blood brain barrier, is characterized by mental and motor developmental delays and infantile seizures. Follow the latest research on Glut1 deficiency with this feed.

Hereditary Sensory Autonomic Neuropathy

Hereditary Sensory Autonomic Neuropathies are a group of inherited neurodegenerative disorders characterized clinically by loss of sensation and autonomic dysfunction. Here is the latest research on these neuropathies.

Separation Anxiety

Separation anxiety is a type of anxiety disorder that involves excessive distress and anxiety with separation. This may include separation from places or people to which they have a strong emotional connection with. It often affects children more than adults. Here is the latest research on separation anxiety.

Neural Activity: Imaging

Imaging of neural activity in vivo has developed rapidly recently with the advancement of fluorescence microscopy, including new applications using miniaturized microscopes (miniscopes). This feed follows the progress in this growing field.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.