Scoring Mating System of a Natural Population of Neolamarckia cadamba with Genome Resequencing Data

N. cadamba is a fast-growing and economically important tree species with significant industrial and medicinal values. Its spherical capitulum comprises hundreds of sessile florets densely aggregated on a receptacle. How this unique floral structure shapes the mating system of this species remains unknown, as this structure enhances the probabilities of both selfing and outcrossing. Here we clarify this question by investigating a natural population. We randomly sampled 11 half-sib families and 6 progenies per half-sib family and assayed samples with whole-genome resequencing. Population genomic analysis indicated that about 93.09% of 4,876,674 high-quality SNPs were under Hardy–Weinberg equilibrium, with a mean inbreeding coefficient of 0.0614 in the sample. Genome-wide nucleotide diversity (π) was 0.0024 on average. The linkage disequilibria (r2) decayed by half at approximately 2.31 kb between sites across genomes. Principal component analysis showed clear family structure among all samples. Analysis with independent SNPs and MLTR (Program for estimating multilocus outcrossing rate) showed that the multilocus outcrossing rate (tm) and single-locus outcrossing rate (ts) were 1.028 ± 0.048 and 1.015 ± 0.060, respectively, with an estimated difference between tm and ts of 0.013 ± 0.022. Analysis with BORICE (Bayesian outcrossing rate and inbreeding coefficient estimation) showed an outcrossing rate (t) of 0.948 ± 0.029 and an inbreeding coefficient (F) of 0.012 ± 0.010. Collectively, these results imply that N. cadamba could be essentially outcrossing, without selfing and biparental inbreeding. The potentially outcrossing system of N. cadamba implies differences from its close relative N. macrophylla (a mixed-mating system) in population structure, genome evolution, and natural geographical distribution. This finding also provided a useful reference for breeding and genetic improvement of this “miracle tree”.