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

Abstract

Summary Pear ( Pyrus ; 2 n = 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 ® Pyr SNP , 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 SNP s to promote increased adoption of the array. A set of 188 diverse accessions and an F 1 population of 98 individuals from ‘Cuiguan’ × ‘Starkrimson’ was genotyped with the array to assess its effectiveness. A large majority of SNP s (166 335 or 83%) are of high quality. The high density and uniform distribution of the array SNP s 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.

Construction of a high-density SNP-based genetic map and identification of fruit-related QTLs and candidate genes in peach [Prunus persica (L.) Batsch]

“…SLAF-seq is a cost-effective technology for SNP discovery and genotyping and has been applied for genetic map construction and QTL detection in many plant species [ 24 – 29 ]. In addition, the high-density SNP array also was used in high-throughput genotyping, genetic map construction and genome-wide association study of fruit traits [ 30 ]. The IPSC 9 K SNP array was commercially available for peach [ 31 ].…”

Peer Review #2 of "RIdeogram: drawing SVG graphics to visualize and map genome-wide data on the idiograms (v0.1)"

“…For instance, the chromosomal regions adjacent to the centromeres are gene-poor in chromosome 1, 9 and 16 while those are gene-rich in chromosome 11, 14 and 17. This function can be applied to many different situations, such as single nucleotide polymorphism (SNP) density and candidate markers ( Figure S1 & Data S1, original data see (Li et al 2019)), DNA methylation dynamics and potential activated genes ( Figure S2 & Data S2, original data see (Huang et al 2019)) and transcription factor (TF) binding sites and candidate target genes ( Figure S3 & Data S3, original data see (Shamimuzzaman & Vodkin 2013)).…”

Effects of Metaxenia on Stone Cell Formation in Pear (Pyrus bretschneideri) Based on Transcriptomic Analysis and Functional Characterization of the Lignin-Related Gene PbC4H2

“…'Yali' and 'Cuiguan' belong to P. bretschneideri and P. pyrifolia, respectively [27][28][29]. These varieties are often used as pollen parents in Dangshan County, Anhui Province, China.…”