SNP-based high-density linkage map construction and QTL mapping of black spot disease resistance in Chinese sand pear

Black spot disease (PBS) caused by Alternaria alternata is an economic disease of pear (Pyrus pyrifolia Nakai). Developing cultivars with durable PBS resistance traits is an important research objective for improving pear germplasm. The Desh-engxiang is a popular pear variety in China and resistant to PBS. This study aimed to detect quantitative trait loci (QTL) associated with PBS resistance trait in pear and determine closely linked molecular markers by specific locus amplified fragment sequencing (SLAF-seq). F1 population resulting from a cross between Deshengxiang (female) and Guiguan, a susceptible (male) variety, was developed and evaluated in 2016 and 2017. SLAF technology was used to discover SNPs in the F1 individuals and subsequently a high-density genetic linkage map for PBS resistance was constructed which contained 17,604 SNP markers. Based on the linkage map, the markers were distributed into 17 linkage groups, spanning 1548.48 cM, with a mean marker distance of 0.09 cM, representing the densest genetic map of the genus Pyrus. QTL analysis of PBS resistance identified a locus strongly related to PBS resistance at 77.68 similar to 112.99 cM on linkage group 15, which was further narrowed down to 93.79 similar to 112.99 cM. Two markers, Marker94293 and Marker94206, located at 97.47 and 102.93 cM, were closely associated with PBS resistance, with a Delta (SNP index) value of 0.46. Co-localization of QTL interval, bioinformatics analysis, and functional annotation revealed PBS putative candidate genes. Overall, the high-density pear linkage map is a suitable reference for mapping PBS resistance trait, QTL, and genes identified in this study contribute information that could be useful for PBS improvement in pear.

Automated summary

In this study, a high-density genetic linkage map for pear black spot (PBS) resistance was constructed using SLAF-seq technology, and quantitative trait loci (QTL) associated with PBS resistance were identified. Two closely associated markers with PBS resistance were also identified. The results provide valuable information for improving PBS resistance in pear.