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Article|23 Jun 2022|OPEN
Construction of a high-density bin-map and identification of fruit quality-related quantitative trait loci and functional genes in pear
Meng-Fan Qin1 ,† , Lei-Ting Li1 ,† , Jugpreet Singh2 , Man-Yi Sun1 , Bing Bai1 , Si-Wei Li1 , Jiang-Ping Ni1 , Jia-Ying Zhang1 , Xun Zhang1 , Wei-Lin Wei1 , Ming-Yue Zhang1 , Jia-Ming Li1 , Kai-Jie Qi1 , Shao-Ling Zhang1 , Awais Khan2 , and Jun Wu,1 ,
1College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
2Plant Pathology and Plant-Microbe Section, Cornell University, Geneva, NY 14456, USA
*Corresponding author. E-mail: awais.khan@cornell.edu,wujun@njau.edu.cn
Both authors contributed equally to the study.

Horticulture Research 9,
Article number: uhac141 (2022)
doi: https://doi.org/10.1093/hr/uhac141
Views: 85

Received: 01 Jan 2022
Accepted: 13 Jun 2022
Published online: 23 Jun 2022

Abstract

Pear (Pyrus spp.) is one of the most common fruit crops grown in temperate regions worldwide. Genetic enhancement of fruit quality is a fundamental goal of pear breeding programs. The genetic control of pear fruit quality traits is highly quantitative, and development of high-density genetic maps can facilitate fine-mapping of quantitative trait loci (QTLs) and gene identification. Bin-mapping is a powerful method of constructing high-resolution genetic maps from large-scale genotyping datasets. We performed whole-genome sequencing of pear cultivars ‘Niitaka’ and ‘Hongxiangsu’ and their 176 F1 progeny to identify genome-wide single-nucleotide polymorphism (SNP) markers for constructing a high-density bin-map of pear. This analysis yielded a total of 1.93 million SNPs and a genetic bin-map of 3190 markers spanning 1358.5 cM, with an average adjacent interval of 0.43 cM. This bin-map, along with other high-density genetic maps in pear, improved the reference genome assembly from 75.5 to 83.7% by re-anchoring the scaffolds. A quantitative genetic analysis identified 148 QTLs for 18 fruit-related traits; among them, QTLs for stone cell content, several key monosaccharides, and fruit pulp acids were identified for the first time in pear. A gene expression analysis of six pear cultivars identified 399 candidates in the identified QTL regions, which showed expression specific to fruit developmental stages in pear. Finally, we confirmed the function of PbrtMT1, a tonoplast monosaccharide transporter-related gene responsible for the enhancement of fructose accumulation in pear fruit on linkage group 16, in a transient transformation experiment. This study provides genomic and genetic resources as well as potential candidate genes for fruit quality improvement in pear.