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. The bin-mapping is a powerful method to construct 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 (SCC), 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 LG16 by transient transformation experiment. This study provides genomic and genetic resources as well as potential candidate genes for fruit quality improvement in pear.

中文翻译：

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梨果实品质相关数量性状位点和功能基因的高密度Bin-map构建及鉴定

梨 (Pyrus spp) 是全球温带地区最常见的水果作物之一。果实品质的遗传增强是梨育种计划的基本目标。梨果实品质性状的遗传控制是高度定量的，高密度遗传图谱的开发可以促进数量性状位点（QTL）的精细定位和基因鉴定。bin-mapping 是一种从大规模基因分型数据集中构建高分辨率遗传图谱的强大方法。我们对梨品种“Niitaka”和“Hongxiangsu”及其176个F1后代进行了全基因组测序，以确定全基因组单核苷酸多态性（SNP）标记，以构建梨的高密度bin-map。该分析产生了总共 193 万个 SNP 和 3190 个标记的遗传 bin-map，跨越 1358.5 cM，平均相邻间隔为 0.43 cM。该 bin-map 与梨中的其他高密度遗传图谱一起，通过重新锚定支架将参考基因组组装从 75.5% 提高到 83.7%。定量遗传分析确定了 18 个果实相关性状的 148 个 QTL；其中，首次在梨中鉴定出石细胞含量（SCC）、几种关键单糖和果肉酸的QTL。对 6 个梨品种的基因表达分析在已确定的 QTL 区域中确定了 399 个候选品种，显示出梨果实发育阶段特有的表达。最后，我们通过瞬时转化实验证实了 PbrtMT1 的功能，PbrtMT1 是一种液泡膜单糖转运蛋白相关基因，负责在 LG16 上增强梨果实中的果糖积累。