Genetic diversity and structure of wild and cultivated Amorphophallus paeoniifolius populations in southwestern China as revealed by RAD-seq

Scientific Reports
Yong GaoLizhou Tang

Abstract

Amorphophallus paeoniifolius, is a commercially important vegetable crop because of its high production potential. In this study, we generated a total of 166 Gb of genomic data from 16 wild and 20 cultivated A. paeoniifolius individuals in southwestern China using restriction site associated DNA sequencing (RAD-seq). We compared the genome-wide variations between the wild and cultivated populations. Wild populations exhibited higher genetic diversity than did cultivated populations based on private allele number, expected heterozygosity, observed heterozygosity and nucleotide diversity. STRUCTURE analysis, principal component analysis (PCA) and a maximum likelihood (ML) tree indicated that A. paeoniifolius populations could be divided into three groups (a cultivated group and two wild groups) with significant genetic differentiation. The low genetic diversity and shallow genetic differentiation found within cultivated populations are likely caused by continuous selection and the clonal propagation methods used during domestication. The significant differentiation between the wild populations may suggest strong genetic drift due to small populations and human disturbance. The genome-wide single nucleotide polymorphisms (SNPs) id...Continue Reading

References

Aug 4, 2004·Genome Research·Matthew R NelsonAndreas Braun
Apr 2, 2005·Proceedings of the National Academy of Sciences of the United States of America·Marie VoisinFrédérique Viard
Dec 28, 2006·Cell·John F DoebleyBruce D Smith
Jan 31, 1975·Science·D Zohary, P Spiegel-Roy
Jan 30, 2008·Bioinformatics·Ruiqiang LiJun Wang
Mar 20, 2008·Genome Research·Daniel R Zerbino, Ewan Birney
Dec 1, 2009·Current Opinion in Plant Biology·Haibao TangAndrew H Paterson
Dec 17, 2009·BMC Bioinformatics·Christiam CamachoThomas L Madden
Mar 6, 2010·The New Phytologist·Doyle McKeyAnne Duputié
Aug 28, 2010·Proceedings of the National Academy of Sciences of the United States of America·Kevin J EmersonChristina M Holzapfel
May 14, 2011·Molecular Ecology Resources·Laurent Excoffier, Heidi E L Lischer
May 17, 2011·Nature Biotechnology·Manfred G GrabherrAviv Regev
May 25, 2013·Molecular Ecology·Julian CatchenWilliam A Cresko

❮ Previous
Next ❯

Methods Mentioned

BETA
genotyping
PCA
RAD-seq
deamination

Software Mentioned

Trinity
Arlequin
STRUCTURE
Blast2GO
R adegenet package
AMOVA
GenGis
STRUCTURE HARVESTER
BLASTX
SNPhylo

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.