## 2 Materials and Methods
### Genotyping by Sequencing  
Collection of test materials: A total of 10 trees were selected from each of the YB and CK groups, and 10 tender leaves were collected from each tree as samples. The samples were numbered YB1-YB10 and CK1-CK10. The leaves were placed in a sealed bag and stored with a silica gel desiccant. DNA extraction was performed using a DNA kit produced by Kangwei Century Biological Company (Beijing, China) according to the instructions. Construction and library inspection of GBS gene library [47; 48]: The extracted DNA samples were commissioned by Novo Bioinformatics Technology Co., Ltd. (Beijing, China) for sequencing and database construction. First, one or more of the enzymes Mse I, Nla III, Hae II, Hae III, Msp I, and EcoR I were used for digestion evaluation. After evaluation, the first DNA digestion was performed, and Mse I enzyme was also used. Solexa P1 and P2 adapters were added at both ends of the digested fragment (which could recognize the Mse I restriction enzyme site and complement the enzyme digestion end). Then, the second enzyme selected in advance was used for combined enzyme digestion (adjusting the number of tags). The sequences containing P1 and P2 adaptors at both ends were amplified by PCR, and the DNA bands were recovered by electrophoresis. The PCR products were purified by AMPure XP beads to obtain the GBS library. After the construction of the library was completed, the preliminary quantification was performed using a Qubit2.0 Fluorometer, and the library was diluted to 1.5 ng/uL. Subsequently, Agilent 2100 bioanalyzer (Beijing Longyue Biotechnology Development Co., Ltd., Beijing, China) was used to detect the insert size of the library. After the insert size was in line with expectations, the effective concentration of the library was accurately quantified by qRT-PCR to ensure the quality of the library. On-machine sequencing: After the library inspection was qualified, different libraries were pooled according to the effective concentration and the target offline data volume requirements, and the sequencing was completed on the Illumina platform, thereby generating 150 bp paired-end readings. SNP detection: The original data were filtered to filter out the reads containing the adaptor sequence. When the N content in the single-end sequencing read exceeded 10% of  
Figure 3: Korla fragment pear young fruit 2.5\(\times\) objective lens picture and the corresponding tissue structure picture. the read length ratio, the paired reads were removed. When the number of low-quality bases (quality value q \(\leq\) 5) contained in the single-end sequencing read exceeded 50% of the read length ratio, this pair of paired reads was removed. After strict filtering of the sequencing data, high-quality clean data were finally obtained. Comparison of reference genome: Chinese white pear ([[https://www.ncbi.nlm.nih.gov/genome/7](https://www.ncbi.nlm.nih.gov/genome/7) Term=Pyrus+bretschneideri]([https://www.ncbi.nlm.nih.gov/genome/7](https://www.ncbi.nlm.nih.gov/genome/7) Term=Pyrus+bretschneideri). Accessed on 7 October 2022) was used as the reference genome. Through the comparison software BWA (version 0.7.17) [49], the effective high-quality sequences filtered from each sample were compared with the reference genome, and the parameter was set to mem-t4-k32-M. At the same time, SAMTOOLS (version 1.17) [50] software was used to detect the SNP of 20 samples. After filtering the SNP sites detected by SAMTOOLS software, high-quality SNP sites were finally obtained for subsequent analysis. Phylogenetic tree analysis: In order to evaluate the phylogenetic evolution of 20 pear resources, we used TreeBest ([[http://treesoft.sourceforge.net/treebest.shtml](http://treesoft.sourceforge.net/treebest.shtml)]([http://treesoft.sourceforge.net/treebest.shtml](http://treesoft.sourceforge.net/treebest.shtml)). Accessed on 26 October 2022) software to calculate the distance matrix based on SNP genotyping results.