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

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.

Montanari S ，Postman J ，Bassil NV ，Neale DB ... -  《G3-Genes Genomes Genetics》

Development of a highly efficient Axiom™ 70 K SNP array for Pyrus and evaluation for high-density mapping and germplasm characterization.

Montanari S ，Bianco L ，Allen BJ ，Martínez-García PJ ，Bassil NV ，Postman J ，Knäbel M ，Kitson B ，Deng CH ，Chagné D ，Crepeau MW ，Langley CH ，Evans K ，Dhingra A ，Troggio M ，Neale DB ... -  《BMC GENOMICS》

Development of an integrated 200K SNP genotyping array and application for genetic mapping, genome assembly improvement and genome wide association studies in pear (Pyrus).

Pear (Pyrus; 2n = 34), the third most important temperate fruit crop, has great nutritional and economic value. Despite the availability of many genomic resources in pear, it is challenging to genotype novel germplasm resources and breeding progeny in a timely and cost-effective manner. Genotyping arrays can provide fast, efficient and high-throughput genetic characterization of diverse germplasm, genetic mapping and breeding populations. We present here 200K AXIOM® PyrSNP, a large-scale single nucleotide polymorphism (SNP) genotyping array to facilitate genotyping of Pyrus species. A diverse panel of 113 re-sequenced pear genotypes was used to discover SNPs to promote increased adoption of the array. A set of 188 diverse accessions and an F1 population of 98 individuals from 'Cuiguan' × 'Starkrimson' was genotyped with the array to assess its effectiveness. A large majority of SNPs (166 335 or 83%) are of high quality. The high density and uniform distribution of the array SNPs facilitated prediction of centromeric regions on 17 pear chromosomes, and significantly improved the genome assembly from 75.5% to 81.4% based on genetic mapping. Identification of a gene associated with flowering time and candidate genes linked to size of fruit core via genome wide association studies showed the usefulness of the array in pear genetic research. The newly developed high-density SNP array presents an important tool for rapid and high-throughput genotyping in pear for genetic map construction, QTL identification and genomic selection.

Li X ，Singh J ，Qin M ，Li S ，Zhang X ，Zhang M ，Khan A ，Zhang S ，Wu J ... -  《-》

Genome-wide characterization of simple sequence repeats in Pyrus bretschneideri and their application in an analysis of genetic diversity in pear.

Xue H ，Zhang P ，Shi T ，Yang J ，Wang L ，Wang S ，Su Y ，Zhang H ，Qiao Y ，Li X ... -  《BMC GENOMICS》

Identification of Pyrus single nucleotide polymorphisms (SNPs) and evaluation for genetic mapping in European pear and interspecific Pyrus hybrids.

Montanari S ，Saeed M ，Knäbel M ，Kim Y ，Troggio M ，Malnoy M ，Velasco R ，Fontana P ，Won K ，Durel CE ，Perchepied L ，Schaffer R ，Wiedow C ，Bus V ，Brewer L ，Gardiner SE ，Crowhurst RN ，Chagné D ... -  《PLoS One》