Schima superba (Theaceae) is a popular woody tree in China. The obscure chromosomal characters of this species are a limitation in the development of high-density genetic linkage maps, which are valuable resources for molecular breeding and functional genomics. We determined the chromosome number and the karyotype of S. superba as 2n = 36 = 36 m, which is consistent with the tribe Schimeae (n = 18). A high-density genetic map was constructed using genotyping by sequencing (GBS). A F1 full-sib with 116 individuals and their parents (LC31 × JO32) were sequenced on the Illumina HiSeq™ platform. Overall, 343.3 Gb of raw data containing 1,191,933,474 paired-end reads were generated. Based on this, 99,966 polymorphic SNP markers were developed from the parents, and 2209 markers were mapped onto the integrated genetic linkage map after data filtering and SNP genotyping. The map spanned 2076.24 cM and was distributed among 18 linkage groups. The average marker interval was 0.94 cM. A total of 168 quantitative trait loci (QTLs) for 14 growth traits were identified. The chromosome number and karyotype of S. superba was 2n = 36 = 36 m and a linkage map with 2209 SNP markers was constructed to identify QTLs for growth traits. Our study provides a basis for molecular-assisted breeding and genomic studies, which will contribute towards the future research and genetic improvement of S. superba.

Schima superba Gardn. et Champ. is a perennial, evergreen tree valued for its eco-protection and commercial values in China. In this study, we investigate the breeding system, reproductive ecology and pollination biology of S. superba in a seed orchard. The flowers are hermaphrodite and protogynous. The viability of the pollen is inactivated rapidly, and the stigma maintains a high receptivity within the flower lifespan. Flowers typically offer pollen and nectar to visitors. The flowers possess a typical insect pollination syndrome, and three visitors (Apis cerana cerana Fabricius, Protaetia brevitarsis Lewis, and Popillia mutans Newman) are observed on flowers during the study period. The visitation frequency per minute and capability of pollen removal and deposition of A. cerana are significantly higher than P. brevitarsis and P. mutans, although the pollinator efficiency is lower than those shown by the two beetles. Fruit set (28.27%) and seed set (6.57%) percentages resulting from open-pollination are significantly lower than those resulting from cross-pollination (fruit/seed set, 43.73%/11.66%), and the pollen limitation index (L) was 0.34, suggesting that seed production is pollen-limited in the seed orchard. The pollen/ovule ratio (P/O) and outcrossing index (OCI) values are 6686.67 and 4, respectively. The self-incompatibility index (ISI) was estimated to be 0.95. Results from hand-pollination, pollen tube growth experiments and the ISI value show that S. superba is late-acting self-incompatible. The synthetic results indicate that A. cerana is the most efficient pollinator of S. superba, and seed production is frequently limited by pollinators, fruit abortion, and pollen quality.