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-179359174pco_AX-179359174genetic_marker
pco_AX-179359175pco_AX-179359175genetic_marker
pco_AX-179359176pco_AX-179359176genetic_marker
pco_AX-179359177pco_AX-179359177genetic_marker
pco_AX-179359178pco_AX-179359178genetic_marker
pco_AX-179359179pco_AX-179359179genetic_marker
pco_AX-179359180pco_AX-179359180genetic_marker
pco_AX-179359181pco_AX-179359181genetic_marker
pco_AX-179359182pco_AX-179359182genetic_marker
pco_AX-179359183pco_AX-179359183genetic_marker
pco_AX-179359184pco_AX-179359184genetic_marker
pco_AX-179359185pco_AX-179359185genetic_marker
pco_AX-179359186pco_AX-179359186genetic_marker
pco_AX-179359187pco_AX-179359187genetic_marker
pco_AX-179359188pco_AX-179359188genetic_marker
pco_AX-179359189pco_AX-179359189genetic_marker
pco_AX-179359190pco_AX-179359190genetic_marker
pco_AX-179359191pco_AX-179359191genetic_marker
pco_AX-179359192pco_AX-179359192genetic_marker
pco_AX-179359193pco_AX-179359193genetic_marker
pco_AX-179359194pco_AX-179359194genetic_marker
pco_AX-179359195pco_AX-179359195genetic_marker
pco_AX-179359196pco_AX-179359196genetic_marker
pco_AX-179359197pco_AX-179359197genetic_marker
pco_AX-179359198pco_AX-179359198genetic_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