title: Integrated high-density consensus genetic map of Pyrus and anchoring of the 'Bartlett' v1.0 (Pyrus communis) genome.
abstract: 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.
authors.affiliation: State Key Laboratory of Crop Genetics and Germplasm Enhancement, Centre of Pear Engineering Technology Research, Nanjing Agricultural University, Nanjing, China.
authors.forename: Leiting
authors.initials: L
authors.lastname: Li
authors.affiliation: The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research), New Zealand.
authors.forename: Cecilia H
authors.initials: CH
authors.lastname: Deng
authors.affiliation: The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research), New Zealand.
authors.forename: Mareike
authors.initials: M
authors.lastname: Knäbel
authors.affiliation: The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research), New Zealand.
authors.forename: David
authors.initials: D
authors.lastname: Chagné
authors.affiliation: The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research), New Zealand.
authors.forename: Satish
authors.initials: S
authors.lastname: Kumar
authors.affiliation: State Key Laboratory of Crop Genetics and Germplasm Enhancement, Centre of Pear Engineering Technology Research, Nanjing Agricultural University, Nanjing, China.
authors.forename: Jiangmei
authors.initials: J
authors.lastname: Sun
authors.affiliation: State Key Laboratory of Crop Genetics and Germplasm Enhancement, Centre of Pear Engineering Technology Research, Nanjing Agricultural University, Nanjing, China.
authors.forename: Shaoling
authors.initials: S
authors.lastname: Zhang
authors.affiliation: State Key Laboratory of Crop Genetics and Germplasm Enhancement, Centre of Pear Engineering Technology Research, Nanjing Agricultural University, Nanjing, China.
authors.forename: Jun
authors.initials: J
authors.lastname: Wu
mesh_terms: D002874:Chromosome Mapping; D032461:Chromosomes, Plant; D019143:Evolution, Molecular; D018745:Genome, Plant; D023281:Genomics; D018895:Microsatellite Repeats; D020641:Polymorphism, Single Nucleotide; D031989:Pyrus / Q000235:genetics*
keywords: SNP; SSR; genetic map; genome assembly; pear