QTL analysis and development of HRM markers associated with fruit shape in interspecific pears (Pyrus pyrifolia x P. bretschneideri)

Fruit shape is one of the important quantitative traits in pear (Pyrus spp.) breeding program, thus genetic study related to fruit shape could be beneficial to pear breeding. Quantitative trait loci (QTL) analysis was carried out using Whangkeumbae' (P. pyrifolia, round) x Tali' (P. bretschneideri, pyriform) and high-resolution melting (HRM) markers were developed. The genetic linkage map of Whangkeumbae' x Tali' was constructed using single nucleotide polymorphisms (SNPs) derived from Axiom Pear 70 K Genotyping Array and simple sequence repeats. The integrated genetic linkage map of 'Whangkeumbae' x Tali' showed similar to 90% of genome coverage, a total genetic distance of 998.2 cM, and a marker density of 1.6 cM. F-1 progenies of Whang-keumbae' x Tali' showed normal distribution of fruit length (L), diameter (D), and L/D ratio. Three QTLs located in linkage group (LG) 6, 7, and 12 were identified with LOD thresholds of 2.8-3.0. Six HRM markers were developed using array-SNPs anchored in the QTLs and predicted fruit shape with 28.6-65.3% accuracy. Notably, accuracy was increased by similar to 90% using an HRM marker combination consisting of CBp06sn02, CBp07sn01, and CBp12sn03. These results could provide a better understanding of the genetic mechanism of fruit shape development and reducing pear breeding period.

Automated summary

This study conducted genetic analysis on fruit shape in pear using QTL analysis and HRM markers, providing valuable information for pear breeding.