Genome Synteny Has Been Conserved Among the Octoploid Progenitors of Cultivated Strawberry Over Millions of Years of Evolution

Frontiers in Plant Science
Michael A HardiganSteven J Knapp

Abstract

Allo-octoploid cultivated strawberry (Fragaria × ananassa) originated through a combination of polyploid and homoploid hybridization, domestication of an interspecific hybrid lineage, and continued admixture of wild species over the last 300 years. While genes appear to flow freely between the octoploid progenitors, the genome structures and diversity of the octoploid species remain poorly understood. The complexity and absence of an octoploid genome frustrated early efforts to study chromosome evolution, resolve subgenomic structure, and develop a single coherent linkage group nomenclature. Here, we show that octoploid Fragaria species harbor millions of subgenome-specific DNA variants. Their diversity was sufficient to distinguish duplicated (homoeologous and paralogous) DNA sequences and develop 50K and 850K SNP genotyping arrays populated with co-dominant, disomic SNP markers distributed throughout the octoploid genome. Whole-genome shotgun genotyping of an interspecific segregating population yielded 1.9M genetically mapped subgenome variants in 5,521 haploblocks spanning 3,394 cM in F. chiloensis subsp. lucida, and 1.6M genetically mapped subgenome variants in 3,179 haploblocks spanning 2,017 cM in F. × ananassa. These st...Continue Reading

References

May 28, 2003·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·E Lerceteau-KöhlerB Denoyes-Rothan
May 29, 2004·Genetics·John M BurkeLoren H Rieseberg
Nov 24, 2005·Nature Reviews. Genetics·Luca Comai
Aug 1, 2007·Hereditas·G R A MargaridoA A F Garcia
Aug 21, 2007·Proceedings of the National Academy of Sciences of the United States of America·Colin E HughesC Donovan Bailey
Apr 26, 2008·Science·A R Leitch, I J Leitch
May 8, 2009·Genome Research·Xuehui HuangBin Han
Nov 17, 2009·The New Phytologist·Marta CifuentesEric Jenczewski
Dec 17, 2009·The New Phytologist·Robert T Gaeta, J Chris Pires
Dec 24, 2009·The New Phytologist·S C Le ComberA R Leitch
May 7, 2010·The Journal of Heredity·Rachel B SpiglerTia-Lynn Ashman
Dec 28, 2010·Nature Genetics·Vladimir ShulaevKevin M Folta
Mar 4, 2011·Proceedings of the National Academy of Sciences of the United States of America·James C SchnableMichael Freeling
Apr 12, 2011·Nature·Yuannian JiaoClaude W dePamphilis
Aug 26, 2011·American Journal of Botany·Allison J Miller, Briana L Gross
Nov 30, 2011·Nature Reviews. Genetics·Todd J Treangen, Steven L Salzberg
Jan 6, 2012·Nucleic Acids Research·Yupeng WangAndrew H Paterson
Jan 10, 2012·Proceedings of the National Academy of Sciences of the United States of America·Michael ChesterDouglas E Soltis
Mar 28, 2012·The Plant Journal : for Cell and Molecular Biology·John P Hamilton, C Robin Buell
Jun 5, 2012·Nature Genetics·Matthew B HuffordJeffrey Ross-Ibarra
Sep 18, 2012·Molecular Phylogenetics and Evolution·Wambui NjugunaNahla Bassil
Oct 5, 2012·The New Phytologist·C E GroverJ F Wendel
Mar 5, 2013·Annual Review of Plant Biology·Candice N Hirsch, C Robin Buell
Aug 28, 2013·G3 : Genes - Genomes - Genetics·Justin T PageJoshua A Udall
Feb 1, 1995·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·D V Shaw
Nov 19, 2013·Nature Reviews. Genetics·Rachel S Meyer, Michael D Purugganan
Nov 28, 2013·DNA Research : an International Journal for Rapid Publication of Reports on Genes and Genomes·Hideki HirakawaSachiko N Isobe
Apr 24, 2014·The New Phytologist·Douglas E SoltisMatthew A Gitzendanner
Apr 29, 2014·Genetics·Jessica G BarbJohn M Burke
Jun 25, 2014·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Pamela S SoltisDouglas E Soltis
Aug 6, 2014·American Journal of Botany·Simon Renny-Byfield, Jonathan F Wendel
Aug 27, 2014·American Journal of Botany·Sarah B Yakimowski, Loren H Rieseberg
Oct 19, 2014·American Journal of Botany·Aaron ListonTia-Lynn Ashman
Apr 17, 2015·American Journal of Botany·Rajanikanth GovindarajuluTia-Lynn Ashman
May 2, 2015·Evolution; International Journal of Organic Evolution·Mario Vallejo-MarínJoshua R Puzey

❮ Previous
Next ❯

Citations

Feb 11, 2021·Genome Biology and Evolution·Itay Mayrose, Martin A Lysak
Dec 10, 2020·Current Opinion in Plant Biology·Lei GuoZhongchi Liu
Feb 11, 2021·G3 : Genes - Genomes - Genetics·Jonathan R NelsonVance M Whitaker
Jan 29, 2021·Molecular Biology and Evolution·Michael A HardiganSteven J Knapp
Mar 28, 2021·G3 : Genes - Genomes - Genetics·Dominique D A PincotSteven J Knapp
Mar 23, 2021·Frontiers in Plant Science·Eiji YamamotoSachiko Isobe
Jun 22, 2021·Chromosome Research : an International Journal on the Molecular, Supramolecular and Evolutionary Aspects of Chromosome Biology·Manman QuYonghua Han
Oct 13, 2021·American Journal of Botany·Kevin A BirdPatrick P Edger

❮ Previous
Next ❯

Datasets Mentioned

BETA
SRR1513873
PRJNA578384

Methods Mentioned

BETA
genotyping
Illumina sequencing
PCR

Software Mentioned

MCScan
MCScan Toolkit
BatchMap
BLAST
iStraw
ALLMAPS
Affymetrix
Picard Tools
Axiom Suite
PhaseLD

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.