Moderate Genetic Diversity and Genetic Differentiation in the Relict Tree Liquidambar formosana Hance Revealed by Genic Simple Sequence Repeat Markers

Abstract

Chinese sweetgum (Liquidambar formosana) is a relatively fast-growing ecological pioneer species. It is widely used for multiple purposes. To assess the genetic diversity and genetic differentiation of the species, genic SSR markers were mined from transcriptome data for subsequent analysis of the genetic diversity and population structure of natural populations. A total of 10645 potential genic SSR loci were identified in 80482 unigenes. The average frequency was one SSR per 5.12 kb, and the dinucleotide unit was the most abundant motif. A total of 67 alleles were found, with a mean of 6.091 alleles per locus and a mean polymorphism information content of 0.390. Moreover, the species exhibited a relatively moderate level of genetic diversity (He = 0.399), with the highest was found in population XY (He = 0.469). At the regional level, the southwestern region displayed the highest genetic diversity (He = 0.435) and the largest number of private alleles (n = 5), which indicated that the Southwestern region may be the diversity hot spot of L. formosana. The AMOVA results showed that variation within populations (94.02%) was significantly higher than among populations (5.98%), which was in agreement with the coefficient of genetic differentiation (Fst = 0.076). According to the UPGMA analysis and principal coordinate analysis and confirmed by the assignment test, 25 populations could be divided into three groups, and there were different degrees of introgression among populations. No correlation was found between genetic distance and geographic distance (P > 0.05). These results provided further evidence that geographic isolation was not the primary factor leading to the moderate genetic differentiation of L. formosana. As most of the genetic diversity of L. formosana exists among individuals within a population, individual plant selection would be an effective way to use natural variation in genetic improvement programs. This would be helpful to not only protect the genetic resources but also attain effective management and exploit genetic resources.

Phylogeographical Structure of Liquidambar formosana Hance Revealed by Chloroplast Phylogeography and Species Distribution Models

“…The higher cpDNA chloroplast genetic variation was inconsistent with the moderate SSR genetic variation reported by a previous study [18]. This may have been caused by pollen and seed mediating gene flow.…”

“…L. formosana is a pioneer and fast-growing deciduous tree species. Its natural distribution across Southern China, north from Qinling and Dabieshan Mountains, west to Sichuan and Guizhou, south to Hainan, and east to Taiwan [18]. This species occurs across a broad elevational range (100 m-1600 m) and environments.…”

“…A previous study based on four chloroplast markers and two nuclear makers indicated that L. formosana and Liquidambar acalycina may have multiple glacial refugia in East, South, and Southwest China, but the phylogeographic structure was weak [19]. Population genetic analysis based on simple sequence repeat (SSR)and inter simple sequence repeat (ISSR) markers showed a moderate genetic diversity and moderate level of population differentiation [18,20]. However, the information on the evolutionary history of the species was limited by small sample size and a narrow sampling range.…”

Development and Characterization of Simple Sequence Repeat Markers for, and Genetic Diversity Analysis of Liquidambar formosana

“…Of the 32 pairs of polymorphic primers developed, 16 pairs that did not show non-specific amplification were selected. Additionally, the four SSR pairs developed by Sun et al [18] were employed; these exhibited high-level capacity to detect polymorphisms and were well-amplified. A total of 20 SSRs were thus used for PCR amplification of 53 plus L. formosana individuals.…”

“…For estimation of genetic advantage, EST-SSRs have been developed for many trees and crops (including Gossypium, Populus, and the Leguminosae) [25][26][27]; these have been used to create high-quality genetic maps, to perform comparative genomic studies, and to facilitate MAS. For L. formosana, the 14 currently available EST-SSRs pairs are inadequate for detailed genetic research [18]. Consequently, a set of polymorphic EST-SSR markers for L. formosana based on transcriptome data is urgently needed.…”