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

Xiaolong Li,Awais Khan,Mingyue Zhang,Mengfan Qin,Siwei Li,Jun Wu,Shaoling Zhang,Jugpreet Singh,Xun Zhang

doi:10.1111/pbi.13085

Abstract

SummaryPear (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.

Highlights

The development and application of molecular markers in plant genetics and breeding has seen great progress in recent years (Rasheed et al, 2017)
single nucleotide polymorphism (SNP) markers have been widely utilized in genetic diversity studies, high density genetic linkage map constructions and identification of loci or genes associated with the complex traits in many plant species (Chen et al, 2014; Khan et al, 2012; Mccouch et al, 2002; Unterseer et al, 2014; Winfield et al, 2016)
SNP arrays have been increasingly adopted for genome-wide genotyping, QTL mapping, genome wide association studies (GWAS) and genomic selection in both model and non-model plant species like maize (Unterseer et al, 2014), wheat (Winfield et al, 2016), rice (Chen et al, 2014; Yu et al, 2014), barley (Bayer et al, 2017), soybean (Lee et al, 2015; Wang et al, 2015), tomato (Sim et al 2012), potato (Vos et al, 2015) and peanut (Clevenger et al, 2017)

Summary

Introduction

The development and application of molecular markers in plant genetics and breeding has seen great progress in recent years (Rasheed et al, 2017). SNP-based chips or arrays, once developed, can significantly reduce time and cost of genotyping new populations for efficient plant breeding (Rasheed et al, 2017). SNP arrays have been increasingly adopted for genome-wide genotyping, QTL mapping, genome wide association studies (GWAS) and genomic selection in both model and non-model plant species like maize (Unterseer et al, 2014), wheat (Winfield et al, 2016), rice (Chen et al, 2014; Yu et al, 2014), barley (Bayer et al, 2017), soybean (Lee et al, 2015; Wang et al, 2015), tomato (Sim et al 2012), potato (Vos et al, 2015) and peanut (Clevenger et al, 2017)

Methods

Results

Conclusion