Durian has high economic and nutritional value. In China, the durian industry is highly dependent on imports. The durian industry in Hainan Province is in its infancy, characterized by limited acreage, low yield, complete reliance on introduced varieties, lack of self-sufficiency, and insufficient supporting cultivation techniques. These issues lead to a stark contrast between high market demand and a weak industry. There is an urgent need for the collection, identification, and evaluation of durian germplasm resources. In this study, DNA was extracted from 99 durian germplasm resources. Libraries were constructed, and second-generation whole-genome sequencing was performed. Bioinformatic analyses, including quality control of sequencing data, variant site discovery and annotation, and population evolution studies, were conducted on the sequencing data. The total amount of sequencing data was 1.62 Tb, yielding 54,974,697 variant sites, including SNPs, insertions (INS), and deletions (DEL), with SNPs being the most prevalent. On average, there is one variant site per 13 bases in the durian genome. These variant sites are mainly located in intergenic regions, with fewer in gene exons and introns. The 99 durian resources can be divided into three subgroups. The distance at which the LD coefficient decays to half its maximum value is only 0.1-0.2 kb, indicating rich genetic diversity. This study provides genome sequencing data and variant site information for 99 durian germplasm resources, offering fundamental data support for durian genetics, breeding methods, and breeding theory research. This will aid in the selection and breeding of durian varieties in Hainan and worldwide.

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