Association genetics studies on frost tolerance in wheat (Triticum aestivum L.) reveal new highly conserved amino acid substitutions in CBF-A3, CBF-A15, VRN3 and PPD1 genes

BMC Genomics
Steve BabbenDragan Perovic

Abstract

Understanding the genetic basis of frost tolerance (FT) in wheat (Triticum aestivum L.) is essential for preventing yield losses caused by frost due to cellular damage, dehydration and reduced metabolism. FT is a complex trait regulated by a number of genes and several gene families. Availability of the wheat genomic sequence opens new opportunities for exploring candidate genes diversity for FT. Therefore, the objectives of this study were to identity SNPs and insertion-deletion (indels) in genes known to be involved in frost tolerance and to perform association genetics analysis of respective SNPs and indels on FT. Here we report on the sequence analysis of 19 candidate genes for FT in wheat assembled using the Chinese Spring IWGSC RefSeq v1.0. Out of these, the tandem duplicated C-repeat binding factors (CBF), i.e. CBF-A3, CBF-A5, CBF-A10, CBF-A13, CBF-A14, CBF-A15, CBF-A18, the vernalisation response gene VRN-A1, VRN-B3, the photoperiod response genes PPD-B1 and PPD-D1 revealed association to FT in 235 wheat cultivars. Within six genes (CBF-A3, CBF-A15, VRN-A1, VRN-B3, PPD-B1 and PPD-D1) amino acid (AA) substitutions in important protein domains were identified. The amino acid substitution effect in VRN-A1 on FT was confirm...Continue Reading

References

Dec 1, 1977·Proceedings of the National Academy of Sciences of the United States of America·F SangerA R Coulson
Aug 22, 1997·Science·S D Tanksley, S R McCouch
Dec 10, 1998·Nucleic Acids Research·K HigoT Korenaga
Mar 15, 2000·Journal of Molecular Biology·E Santelli, T J Richmond
Sep 21, 2000·The Plant Journal : for Cell and Molecular Biology·B L OrvarR S Dhindsa
Jun 13, 2002·Proceedings of the National Academy of Sciences of the United States of America·Shaoxing HuangPiotr Gornicki
Jul 24, 2002·Nucleic Acids Research·Kazutaka KatohTakashi Miyata
Apr 4, 2003·Genes & Development·Viswanathan ChinnusamyJian-Kang Zhu
May 6, 2003·Proceedings of the National Academy of Sciences of the United States of America·L YanJ Dubcovsky
Oct 15, 2003·Proceedings of the National Academy of Sciences of the United States of America·Ben TrevaskisElizabeth S Dennis
Oct 25, 2003·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·E FranciaN Pecchioni
Nov 11, 2003·Biochemistry. Biokhimii︠a︡·Ch R AllagulovaV A Vakhitov
May 29, 2004·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·John E KoemelEdward L Smith
Oct 29, 2004·Bioinformatics·Sergei L Kosakovsky PondSpencer V Muse
Jan 22, 2005·Nucleic Acids Research·Kazutaka KatohTakashi Miyata
Oct 4, 2005·Molecular Genetics and Genomics : MGG·Attila VágújfalviLuigi Cattivelli
Dec 20, 2005·Molecular Genetics and Genomics : MGG·Andrea K MillerJorge Dubcovsky
Jan 5, 2006·Genome Génome / Conseil National De Recherches Canada·Patrick J GulickFathey Sarhan
Dec 13, 2006·Proceedings of the National Academy of Sciences of the United States of America·L YanJ Dubcovsky
Apr 18, 2007·Plant Molecular Biology·Antonio F MonroyPatrick J Gulick
Jun 15, 2007·The Plant Journal : for Cell and Molecular Biology·Eric J StockingerNicola Pecchioni
Jun 26, 2007·Bioinformatics·Peter J BradburyEdward S Buckler
Mar 5, 2008·Plant Molecular Biology·Andrea K KnoxJorge Dubcovsky
Jan 9, 2009·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Yihua ChenLiuling Yan
Jan 20, 2009·Bioinformatics·Andrew M WaterhouseGeoffrey J Barton
May 8, 2009·Molecular Genetics and Genomics : MGG·Chiara CampoliD Brian Fowler
Feb 25, 2010·Molecular Genetics and Genomics : MGG·Gábor KocsyNils Stein
Mar 10, 2010·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Andrea K KnoxEric J Stockinger

❮ Previous
Next ❯

Citations

Jun 10, 2019·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Yi ChenAlireza Navabi
Jul 18, 2020·BMC Bioinformatics·Alexander Coulton, Keith J Edwards
Nov 30, 2019·Plant Science : an International Journal of Experimental Plant Biology·Lavinia MareriEnrico Francia
Sep 12, 2021·BMC Plant Biology·Matías SchierenbeckAndreas Börner
Nov 4, 2021·Journal of Agricultural and Food Chemistry·Kankan PengJing Cang

❮ Previous
Next ❯

Methods Mentioned

BETA
Genome Sequencing
genotyping
chip
PCR
amplicon sequencing
PCA
electrophoresis

Software Mentioned

BLASTX
Jalview
BLASTn
Pal2Nal
CLC
R
BLAST
Quantity One® 1 - D
HyPhy
MEGA

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.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

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.

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.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

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.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.