Genetic analysis of local pear varieties in Weixian county, Hebei province based on whole-genome resequencing and chloroplast DNA sequences by QI Dan, DONG Xingguang, LI Zhenjiang, CAO Yufen, LU Lu, TIAN Luming, LI Junxi, ZHANG Ying, HUO Hongliang, MIAO Xiuchen, XU Jiayu, LIU Chao, LI Jinling, ZHU Ruiying

“…The clean reads were aligned to the reference genome Yunhong No.1 using BWA v0.7.15 software for whole-genome alignment; SNP detection and filtering were performed using GATK v4.2.5.0 software; Population structure analysis was conducted using Admixture v1.3.0 and principal component analysis was carried out using GCTA v1.93.2 software; Treebest v1.9.2 software was used to calculate the distance matrix, and a phylogenetic tree was constructed using the neighbor-joining method. The chloroplast DNA sequencing results were aligned and manually corrected using the software MEGA X; the genetic parameters of chloroplast DNA sequence fragments were calculated using the software DnaSP 5.1; the evolutionary relationship between haplotypes was analyzed using the software NetWork 10. …”
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