Reconstruction of the Largest Pedigree Network for Pear Cultivars and Evaluation of the Genetic Diversity of the USDA-ARS National Pyrus Collection.

G3 : Genes - Genomes - Genetics
Sara MontanariDavid B Neale

Abstract

The USDA-ARS National Clonal Germplasm Repository (NCGR) in Corvallis, Oregon, maintains one of the world's largest and most diverse living Pyrus collection. A thorough genetic characterization of this germplasm will provide relevant information to optimize the conservation strategy of pear biodiversity, support the use of this germplasm in breeding, and increase our knowledge of Pyrus taxonomy, evolution, and domestication. In the last two decades simple sequence repeat (SSR) markers have been used at the NCGR for cultivar identification and small population structure analysis. However, the recent development of the Applied Biosystems Axiom Pear 70K Genotyping Array has allowed high-density single nucleotide polymorphism (SNP)-based genotyping of almost the entire collection. In this study, we have analyzed this rich dataset to discover new synonyms and mutants, identify putative labeling errors in the collection, reconstruct the largest pear cultivar pedigree and further elucidate the genetic diversity of Pyrus.

References

Oct 5, 1990·Journal of Molecular Biology·S F AltschulD J Lipman
Feb 22, 2002·Current Opinion in Plant Biology·Antoni Rafalski
Oct 12, 2010·Bioinformatics·Ani ManichaikulWei-Min Chen
Sep 20, 2011·Bioinformatics·Thibaut Jombart, Ismaïl Ahmed
Nov 15, 2012·Genome Research·Jun WuShaoling Zhang
Jun 14, 2013·BMC Genomics·Satish KumarRichard K Volz
Apr 5, 2014·PloS One·David ChagnéRiccardo Velasco
Aug 3, 2014·BMC Bioinformatics·Paul D ShawDavid F Marshall
Aug 26, 2014·SpringerPlus·Ramesh Krishnan RamasamyV Girish Naik
Jun 13, 2018·Genome Biology·Jun WuShaoling Zhang
Jan 4, 2020·BMC Plant Biology·Hélène MurantyCharles-Eric Durel
Mar 17, 2020·Phytopathology·Jason D ZurnNahla V Bassil

❮ Previous
Next ❯

Citations


❮ Previous
Next ❯

Methods Mentioned

BETA
genotyping
PCA

Software Mentioned

R package network
R package
SNPRelate
R package SNPRelate
plink
Clumpp
Affymetrix
R package adegenet
Helium
Structure Plot

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.