Sapindus germplasm re-sequencing in China: diversity, genetic structure, evolution, and GWAS analysis

J.M. Liu, L.M. Jia, Z. Chen, J. Salojärvi

State Key Laboratory of Efficient Production of Forest Resources, Beijing Forestry University, 35 E Qinghua Rd., Beijing 100083, PR China

National Energy R&D Center for Non-food Biamass, Beijing Forestry University, Beijing 100083, PR China

School of Biological Sciences, Nanyang Technological University, 637551 Singapore, Singapore

Sapindus is an important forest tree genus with utilization in biodiesel, biomedicine, biochemical, and multifunctional economic forest species. Here we report a whole-genome resequencing experiment of 100 Sapindus core populations. Genetic structure analysis reveals Sapindus can be divided into six subgroups: S. delavayi subgroup, S. rarak subgroup, northern subgroup, Southeast subgroup, Guizhou subgroup, and hybrids subgroup. We found that S. delavayi and S. rarak were not diploid but potentially tetraploid or hexaploid, and proposed hypotheses for the differentiation of each subgroup. Selective sweep analysis identified fixed alleles of the genes CYP716A, CAMTA, and HD-ZIP to be involved in triterpenoid saponin biosynthesis and stress response. In addition, GWAS analysis revealed the KCS, FAD, and FAB homologous genes participated in kernel fatty acid biosynthesis. Our findings elucidated the genetic structure of Sapindus in China and provided targets and materials for genetic improvement of Sapindus.