Genome resequencing reveals the population structure and genetic diversity of almond in Xinjiang, China

Almonds are widely grown and a commercially important species in the Xinjiang region. However, weakened resistance and poor quality can occur during the production of almonds. Therefore, the development of a reserve of superior lines of almond and selection of lines suitable for diversified consumption are key to current breeding efforts. In this study, genotyping by sequencing (GBS) was used to sequence the native germplasm and superior cultivars of Xinjiang almonds. A total of 108,481 high-quality single nucleotide polymorphisms were obtained, and almond cultivars could be classified into four groups based on the evolutionary tree and PCA results. The genetic structure was also divided into two groups, three of which were grouped together, and gene exchange has occurred between the various groups. Fst analysis and ROD analysis were carried out on selective signals, and the Fst values and genetic distances indicated some degree of genetic differentiation between almond populations in Xinjiang, probably due to some geographical barriers and different management levels. A total of 82 selection windows (top 5% of ROD and Fst) were screened, and 306 selected genes were enriched. Based on the annotation results, we identified a range of candidate genes related to growth, stress and hormones, and the almond cultivars differed in terms of metabolic processes and oil content. In this study, genome sequencing was used to find differential genes associated with resistance and quality, laying a foundation for subsequent variety substitutions.