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 ... -  《-》

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》

High-resolution genetic linkage map of European pear (Pyrus communis) and QTL fine-mapping of vegetative budbreak time.

Gabay G ，Dahan Y ，Izhaki Y ，Faigenboim A ，Ben-Ari G ，Elkind Y ，Flaishman MA ... -  《BMC PLANT BIOLOGY》

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》

Integrated high-density consensus genetic map of Pyrus and anchoring of the 'Bartlett' v1.0 (Pyrus communis) genome.

Genetic maps are essential tools for pear genetics and genomics research. In this study, we first constructed an integrated simple sequence repeat (SSR) and single nucleotide polymorphism (SNP)-based consensus genetic map for pear based on common SSR markers between nine published maps. A total of 5,085 markers, including 1,232 SSRs and 3,853 SNPs, were localized on a consensus map spanning 3,266.0 cM in total, with an average marker interval of 0.64 cM, which represents the highest density consensus map of pear to date. Using three sets of high-density SNP-based genetic maps with European pear genetic backgrounds, we anchored a total of 291.5 Mb of the 'Bartlett' v1.0 (Pyrus communis L.) genome scaffolds into 17 pseudo-chromosomes. This accounted for 50.5% of the genome assembly, which was a great improvement on the 29.7% achieved originally. Intra-genome and inter-genome synteny analyses of the new 'Bartlett' v1.1 genome assembly with the Asian pear 'Dangshansuli' (Pyrus bretschneideri Rehd.) and apple (Malus × domestica Borkh.) genomes uncovered four new segmental duplication regions. The integrated high-density SSR and SNP-based consensus genetic map provided new insights into the genetic structure patterns of pear and assisted in the genome assembly of 'Bartlett' through further exploration of different pear genetic maps.

Li L ，Deng CH ，Knäbel M ，Chagné D ，Kumar S ，Sun J ，Zhang S ，Wu J ... -  《-》