Reconstruction of the largest pedigree network for pear cultivars and evaluation of the genetic diversity of the USDA-ARS national Pyrus collection

Authors: MONTANARI, SARA - University Of California, Davis; POSTMAN, JOSEPH - Former ARS Employee; Bassil, Nahla; NEALE, DAVID - University Of California, Davis

Submitted to: G3, Genes/Genomes/Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/14/2020
Publication Date: 9/1/2020
Citation: Montanari, S., Postman, J., Bassil, N.V., Neale, D. 2020. 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. 10:3285-3297. https://doi.org/10.1534/g3.120.401327.
DOI: https://doi.org/10.1534/g3.120.401327

Interpretive Summary: The USDA-ARS National Clonal Germplasm Repository (NCGR) in Corvallis, Oregon, maintains the world’s largest and most diverse collection of pear. A thorough genetic characterization of this germplasm would provide relevant information to optimize the conservation strategy of pear biodiversity, support the use of this germplasm in breeding, and increase our knowledge of pear taxonomy, evolution and domestication. The recent development of a high throughput Genotyping Array has allowed high-density genotyping of almost the entire collection. In this study, we have analyzed this rich dataset to discover new synonyms and mutants and identify putative labelling errors in the collection, reconstruct the largest pedigree of pear cultivars and further elucidate the genetic diversity of pear. This is the first study that genetically characterized the entire pear germplasm collection held at the National Clonal Germplasm Repository in Corvallis, OR, the largest pear repository in the world.

Technical Abstract: The USDA-ARS National Clonal Germplasm Repository (NCGR) in Corvallis, Oregon, maintains the world’s largest and most diverse collection of Pyrus. A thorough genetic characterization of this germplasm would 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 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 and identify putative labelling errors in the collection, reconstruct the largest pedigree of pear cultivars and further elucidate the genetic diversity of Pyrus. This is the first study that genetically characterized the entire Pyrus germplasm collection held at the National Clonal Germplasm Repository in Corvallis, OR, the largest pear repository in the world.