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

Publication Overview
TitleDevelopment of an integrated 200K SNP genotyping array and application for genetic mapping, genome assembly improvement and GWAS in pear (Pyrus)
AuthorsLi X, Singh J, Qin M, Li S, Zhang X, Zhang M, Khan A, Zhang S, Wu J
TypeJournal Article
Journal NamePlant biotechnology journal
Volume8
Issue5
Year2019
CitationLi X, Singh J, Qin M, Li S, Zhang X, Zhang M, Khan A, Zhang S, Wu J. Development of an integrated 200K SNP genotyping array and application for genetic mapping, genome assembly improvement and GWAS in pear (Pyrus). Plant biotechnology journal. 2019;17(8):1582‐1594

Abstract

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.
Features
This publication contains information about 200,481 features:
Feature NameUniquenameType
pco_AX-171890995pco_AX-171890995genetic_marker
pco_AX-171891525pco_AX-171891525genetic_marker
pco_AX-171891810pco_AX-171891810genetic_marker
pco_AX-171891892pco_AX-171891892genetic_marker
pco_AX-171891964pco_AX-171891964genetic_marker
pco_AX-171892172pco_AX-171892172genetic_marker
pco_AX-171892273pco_AX-171892273genetic_marker
pco_AX-171892293pco_AX-171892293genetic_marker
pco_AX-171892490pco_AX-171892490genetic_marker
pco_AX-171893205pco_AX-171893205genetic_marker
pco_AX-171893574pco_AX-171893574genetic_marker
pco_AX-171893775pco_AX-171893775genetic_marker
pco_AX-171893817pco_AX-171893817genetic_marker
pco_AX-171894182pco_AX-171894182genetic_marker
pco_AX-171894334pco_AX-171894334genetic_marker
pco_AX-171894726pco_AX-171894726genetic_marker
pco_AX-171894764pco_AX-171894764genetic_marker
pco_AX-171895459pco_AX-171895459genetic_marker
pco_AX-171896103pco_AX-171896103genetic_marker
pco_AX-171896931pco_AX-171896931genetic_marker
pco_AX-171896991pco_AX-171896991genetic_marker
pco_AX-171897037pco_AX-171897037genetic_marker
pco_AX-171897065pco_AX-171897065genetic_marker
pco_AX-171897390pco_AX-171897390genetic_marker
pco_AX-171898438pco_AX-171898438genetic_marker

Pages

Featuremaps
This publication contains information about 1 maps:
Map Name
Pear-Cuiguan/Starkrimson-F1
Libraries
This publication contains information about 1 libraries:
Library NameUnique NameOrganism
200K AXIOM PyrSNP200K AXIOM PyrSNPPyrus sp.
Stocks
This publication contains information about 1 stocks:
Stock NameUniquenameType
Cuiguan/Starkrimson-F1Cuiguan/Starkrimson-F1population