Genetic analysis of local pear varieties in Weixian county, Hebei province based on whole-genome resequencing and chloroplast DNA sequences

【Objective】Weixian has a long pear cultivation history with approximately 20 unique local pear cultivars, including the most famous Weixian Yali. Researchers have made significant progress in the collection, preservation and phenotypic evaluation on pear germplasm resources in Weixian, but the genetic relationship and background of these pears remain largely unexplored. To provide a theory basis for the efficient utilization of Weixian pears and the sustainable development of pear industry, it is needed to elucidate the genetic relationship and background of Weixian pear accessions.【Methods】Twenty local pear cultivars from Weixian and 10 representative local pear cultivars from other regions within Hebei province were selected as research materials. Based on the whole-genome resequencing data and chloroplast DNA variation, we investigated the genetic relationship and background of local pear cultivars in Weixian. 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 usingGATK 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.【Results】By comparing the resequencing data of 30 materials with the reference genome, a total of 30 041, 877 SNP loci were identified. We performed principal component analysis, population genetic structure and phylogenetic tree based on these SNPs. The results showed that local pear cultivars in Weixian exhibited a clear population genetic structure, which could be divided into two groups: Group 1 consisted of 9 materials including Weixian Hongli, Youqiu, Xiaohongmian, Baidunzili, Baihongli, Dunzili, Jinfeng Yali, Kaixinmian and Suanjiuli; Group 2 comprised the remaining 11 materials from Weixian, including Xiaobaimian, Xuehua, Wu'an Youqiu, Dabaimian, Yayamian, Teda Baimian, Baixuehua, Yinbai, Yali, Teda Yali, Meixiang Yali and Xiaobaimian, which can be further divided into two subgroups. Additionally, Group 2 included 10 local pear cultivars from northern Hebei, like Anli and Baihuaguan, indicating a close genetic relationship between Weixian pears in Group 2 and northern pear cultivars. In contrast, Weixian Hongli in Group 1 belonged to the Chinese Sand Pears, suggesting a closer genetic relationship between Weixian pears in Group 1 and southern pear cultivars. The sequencing results of the non-coding region of chloroplast DNA showed that three more evolved haplotypes were detected in Weixian pears. The haplotype of most Weixian pears was haplotype H_3, while Weixian Hongli exhibited the haplotype H_2. Additionally, Xuehua and the Yali group, with the exception of Jinfeng Yali, displayed the haplotype H_1. By analyzing the genetic relationship and haplotype categories, we identified the genetic background of bud sport mutations and hybrids of Weixian pears. Jinfeng Yali belonged to the Yali group and had the characteristic of high self-fertility. Whole-genome resequencing analysis and chloroplast haplotype results showed that Yali, Meixiang Yali and Teda Yali belonged to the same branch and had the same haplotype. The clustering results and haplotype of Jinfeng Yali were different from these three Yali pear varieties. Jinfeng Yali was more closely related to Suanjiuli, and both had the same chloroplast haplotype, indicating that Jinfeng Yali was not a bud sport of Yali but possibly a selection from Yali seedlings. Dunzili and Baidunzili had a close genetic relationship and shared the same haplotype, suggesting Baidunzili may be a bud sport of Dunzili. The chloroplast haplotypes of Baihongli and Weixian Hongli were inconsistent, but they had a close relationship, suggesting that Weixian Hongli was more likely to be its paternal variety. Kaixinmian and Xiaohongmian shared the same chloroplast haplotype, and Xiaohongmian and Dunzili were in the same group, suggesting that Kaixinmian was a hybrid between Xiaohongmian and Dunzili. There was a distinct genetic difference between Youqiu and Wu'an Youqiu, despite their similar names.【Conclusion】In this study, based on the information of single nucleotide polymorphisms (SNPs) revealed by whole-genome resequencing and chloroplast DNA variation, we clarified the genetic relationship and background of Weixian pears. This result provides valuable references for protection and rational utilization of Weixian pear germplasm resources, further aiding in advancing the genetic understanding of pear cultivation in the region. Additionally, it enriches the cultural significance of pear culture in Weixian and offers cultural support for rural revitalization efforts.