Genetic diversity and population structure of four Trapa species from the Yangtze River and Amur River basins, China

Water chestnuts ( Trapa L.) are annual floating-leaved macrophytes with significant economic and ecological values. Genetic information assessment of wild germplasm resources is essential to the effective utilization and cultivation breeding of this genus. Here, Expressed Sequence Tag-Simple sequence repeat (EST-SSR) markers were developed and used to evaluate the genetic diversity and population structure of the four common wild Trapa species from the two diversity centers of Trapa in China: the Yangtze River Basin (YRB) and the Amur River Basin (ARB). For the 12,178 EST-SSRs, the dinucleotide (55.3 %) was the predominant type. Using 19 primers, higher levels of genetic variation were detected in the two Trapa species from YRB ( T. bispinosa : H e= 0.530; T. quadrispinosa : H e=0.498) than that of the species from ARB ( T. manshurica : H e = 0.279; T. maximowiczii : H e=0.415). This might be attributed to the smaller population size and lower hydrological connectivity among populations for the two species of ARB. Correspondingly, the population differentiation levels within the two Trapa species in ARB ( T. manshurica : F ST =0.383; T. maximowiczii : F ST =0.239) were higher than that of the species in YRB ( T. bispinosa : F ST =0.169; T. quadrispinosa : F ST =0.124). The clustering analyses (UPGMA, PCoA and SRUCTURE) consistently showed that all the individuals were divided into three branches: the accessions from T. maximowiczii and T. manshurica were clustered based on their species origins; the same genetic group was shared by the individuals from T. bispinosa and T. quadrispinosa , which possessed similar fruit morphological characteristics in addition to the number of waist horns . Findings of this study suggested the Trapa populations with high genetic diversity should be prioritized for conservation in YRB, while each population should be equally protected because of obvious genetic differentiation among populations in ARB. • Nineteen EST-SSRs first developed based on the transcriptome. • Genetic diversity evaluated for four common Trapa species. • Higher genetic variation in Yangtze River than that of Amer River. • Habitat differences in two rivers leading to different genetic structure. • Conservation strategies developed for each river basin.