Abstract
Pear (Pyrus spp) is an important fruit crop, grown in all temperate regions of the world, with global production ranked after grape and apples among deciduous tree crops. A high-density linkage map is a valuable tool for fine mapping quantitative trait loci (QTL) and map-based gene cloning. In this study, we firstly constructed a high-density linkage map of pear using SNPs integrated with SSRs, developed by the rapid and robust technology of restriction-associated DNA sequencing (RADseq). The linkage map consists of 3143 SNP markers and 98 SSRs, 3241 markers in total, spanning 2243.4 cM, with an average marker distance of 0.70 cM. Anchoring SSRs were able to anchor seventeen linkage groups to their corresponding chromosomes. Based on this high-density integrated pear linkage map and two years of fruit phenotyping, a total of 32 potential QTLs for 11 traits, including length of pedicel (LFP), single fruit weight (SFW), soluble solid content (SSC), transverse diameter (TD), vertical diameter (VD), calyx status (CS), flesh colour (FC), juice content (JC), number of seeds (NS), skin colour (SC), and skin smooth (SS), were identified and positioned on the genetic map. Among them, some important fruit-related traits have for the first time been identified, such as calyx status, length of pedicel, and flesh colour, and reliable localization of QTLs were verified repeatable. This high-density linkage map of pear is a worthy reference for mapping important fruit traits, QTL identification, and comparison and combination of different genetic maps.
Highlights
Pear (Pyrus spp.) is one of the most important and popular fruits in Europe, East Asia, and North America, with a cultivation history of up to 3000 years (Lombard and Westwood, 1987)
After identifying barcodes in the start of each read and trimming raw data into the same read length of 41 bp, the total number of reads was reduced to 1.12 billion, and valid sequence decreased to 45.8 Gb
The number of reads for each individual affected the capability of SNP calling
Summary
Pear (Pyrus spp.) is one of the most important and popular fruits in Europe, East Asia, and North America, with a cultivation history of up to 3000 years (Lombard and Westwood, 1987). The following published pear linkage maps used either AFLP or SSR markers, with marker number of ranging from 154–447 (Yamamoto et al, 2002c; Dondini et al, 2005; Yamamoto et al, 2007; Terakami et al, 2009). This low marker density, along with the time and labour required, and the high costs of the marker type makes most of them unsuitable for fine mapping of traits of interest and for full use for breeding purposes. An SNP-based map was first tried with 857 polymorphic markers (Montanari et al, 2013); this is still not dense and saturated enough to be a desirable and fine map for QTL localization
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