Shao-Qing Tang

Effect of sampling strategy on estimation of fine-scale spatial genetic structure in Androsace tapete （Primulaceae）, an alpine plant endemic to Qinghai-Tibetan Plateau

Abstract  The fine‐scale spatial genetic structure (SGS) of alpine plants is receiving increasing attention, from which seed and pollen dispersal can be inferred. However, estimation of SGS may depend strongly on the sampling strategy, including the sample size and spatial sampling scheme. Here, we examined the effects of sample size and three spatial schemes, simple‐random, line‐transect, and random‐cluster sampling, on the estimation of SGS in Androsace tapete, an alpine cushion plant endemic to Qinghai‐Tibetan Plateau. Using both real data and simulated data of dominant molecular markers, we show that: (i) SGS is highly sensitive to sample strategy especially when the sample size is small (e.g., below 100); (ii) the commonly used SGS parameter (the intercept of the autocorrelogram) is more susceptible to sample error than a newly developed Sp statistic; and (iii) the random‐cluster scheme is susceptible to obvious bias in parameter estimation even when the sample size is relatively large (e.g., above 200). Overall, the line‐transect scheme is recommendable, in that it performs slightly better than the simple‐random scheme in parameter estimation and is more efficient to encompass broad spatial scales. The consistency between simulated data and real data implies that these findings might hold true in other alpine plants and more species should be examined in future work.

Molecular systematics and biogeography of Wisteria inferred from nucleotide sequences of nuclear and plastid genes

Previous molecular phylogenetic studies of Fabaceae indicated that species of Wisteria, an intercontinental disjunct genus between eastern Asia and eastern North America, formed a clade derived from within Callerya. However, interspecific relationships were not well resolved or supported. In this study, we used sequences of the nuclear ribosomal DNA internal transcribed spacer region and the chloroplast gene matK to examine interspecific relationships and explore implications of the phylogeny for the systematics and biogeography of Wisteria. Our results showed that Wisteria with deciduous leaves and racemose inflorescences formed a strongly supported clade derived from within the paraphyletic Callerya. Afgekia was also found to be included within Callerya. Therefore, our data support the merger of Afgekia, Callerya, and Wisteria. The phylogenetic pattern suggested that the deciduousness in Wisteria may be a derived trait likely in response to temperate climate, and the racemose inflorescences in the Afgekia–Callerya–Wisteria clade may have evolved from panicles. Our study also provided strong support for the sister relationship of the North American and eastern Asian species of Wisteria. In the Asian clade, Wisteria brachybotrys Siebold & Zucc. of Japan was sister to the clade containing W. floribunda (Willd.) DC of Japan and Korea, and W. sinensis (Sims) Sweet of China. However, our data offered weak support for the sister relationship of W. floribunda and W. sinensis. Our divergence time and biogeographic analyses suggested that the eastern Asian–North American disjunction in Wisteria may have occurred through a dispersal event in the middle Miocene (13.4 Mya) from the Old World to the New World across the Bering land bridge followed by vicariance in the late Miocene (6.8 Mya). This study added another example to the “out of Asia” migration for the eastern Asian–eastern North American disjunction.

Development and characterization of sixteen microsatellite primers in Abies chensiensis and A. fargesii (Pinaceae)

Abies chensiensis is a vulnerable species and has been included in the checklist of State Protection Category II in China. Sixteen microsatellite loci were developed in A. chensiensis and Abies fargesii (Pinaceae) to facilitate studies of population genetic structure and genetic diversity. All of these loci showed polymorphism, and the number of alleles per locus ranged from 1 to 21 from two wild populations. The observed and expected heterozygosities ranged from 0.172 to 1.000 and from 0.250 to 0.935, respectively. These markers will be useful in the research on the population genetic structure and genetic diversity of A. chensiensis, A. fargesi and other Abies species.

Development of microsatellite markers in Kmeria septentrionalis (Magnoliaceae), an endangered Chinese tree

PREMISE OF THE STUDY Microsatellite markers were developed in an endangered plant, Kmeria septentrionalis, to investigate its population genetic structure, gene flow, and mating systems. METHODS AND RESULTS Using the combined biotin capture method, 14 microsatellite primer sets were isolated and characterized. All of these markers showed polymorphism, and the number of alleles per locus ranged from 3 to 15 across 60 individuals from two populations. The observed and expected heterozygosities ranged from 0.2692 to 0.9667 and from 0.3271 to 0.8881, respectively. CONCLUSIONS These markers will facilitate further studies on the genetic diversity and mating systems of K. septentrionalis.

Microsatellite Markers for the Invasive Species Bidens alba (Asteraceae)

Premise of the study: Microsatellite markers were developed in the invasive species Bidens alba (Asteraceae) to assess its population structure and to facilitate tracking its expansion in China. Methods and Results: Using 454 pyrosequencing, 20 microsatellite primer sets were developed for B. alba. The markers were tested on one population of B. alba (30 individuals) and one population of the closely related B. pilosa (30 individuals) in China. For B. alba, all of the markers were polymorphic, and the number of alleles per locus ranged from three to 32. The expected heterozygosity values were from 0.3787 to 0.9284, and the Shannon–Wiener index was from 0.6796 to 2.8401. Conclusions: These markers will be useful for investigating the genetic structure, genetic diversity, and invasion dynamics of B. alba and will also be useful in studies of B. pilosa.

Assessment of genetic diversity and relationships of upland rice accessions from southwest China using microsatellite markers

Abstract Upland rice (UR) is a unique rice ecotype that can be grown on upland fields without surface water accumulation in cultivation. Although UR has long been recognised as an important genetic resource for breeding of drought‐tolerant rice varieties, it is facing the risk of genetic erosion due to the rapid spread of high‐yielding modern rice strains. In this study, genetic diversity and relationships among 221 UR accessions collected from southwest China were evaluated using microsatellite (i.e. simple sequence repeat, SSR) markers. A total of 269 alleles were detected using 28 pairs of SSR primers, and the number of alleles per locus ranged from 2 to 20, with an average of 9.6. The polymorphism information content value, a measure of gene diversity, was 0.63 with a range of 0.25–0.89. Clustering analysis showed that all 236 accessions fell into two groups corresponding to indica and japonica. More than 75% of UR accessions were identified as japonica. We detected no clear relationship between genetic similarity and geographical distances, which may be partially due to the frequent seed exchange by local farmers. Our study revealed relatively high levels of genetic diversity in the Chinese UR germplasm, which could provide invaluable genetic resources for improving economically important traits in rice, such as tolerance to drought stress.

Population Genetic Structure and Phylogeography of Camellia flavida (Theaceae) Based on Chloroplast and Nuclear DNA Sequences

Camellia flavida is an endangered species of yellow camellia growing in limestone mountains in southwest China. The current classification of C. flavida into two varieties, var. flavida and var. patens, is controversial. We conducted a genetic analysis of C. flavida to determine its taxonomic structure. A total of 188 individual plants from 20 populations across the entire distribution range in southwest China were analyzed using two DNA fragments: a chloroplast DNA fragment from the small single copy region and a single-copy nuclear gene called phenylalanine ammonia-lyase (PAL). Sequences from both chloroplast and nuclear DNA were highly diverse; with high levels of genetic differentiation and restricted gene flow. This result can be attributed to the high habitat heterogeneity in limestone karst, which isolates C. flavida populations from each other. Our nuclear DNA results demonstrate that there are three differentiated groups within C. flavida: var. flavida 1, var. flavida 2, and var. patens. These genetic groupings are consistent with the morphological characteristics of the plants. We suggest that the samples included in this study constitute three taxa and the var. flavida 2 group is the genuine C. flavida. The three groups should be recognized as three management units for conservation concerns.

Development and characterization of 38 microsatellite markers for Camellia flavida based on transcriptome sequencing

Camellia flavida is an endangered and valuable ornamental plant species with yellow flower. Here we isolated and characterized 38 polymorphic microsatellite loci for C. flavida using transcriptome sequencing. The markers were tested on one population of C. flavida and one population of closely related C. nitidissima. For C. fladviia, all of these loci showed polymorphism, and the number of alleles per locus ranged from 2 to 8. The observed and expected heterozygosities ranged from 0.250 to 0.900 and from 0.250 to 0.789, respectively. These markers will be useful in the research on the genetic diversity and population genetic structure of C. flavida. These loci can also be used for other related Camellia species.

Microsatellite primers in luohanguo (Siraitia grosvenorii, Cucurbitaceae), an economically important plant species

PREMISE OF THE STUDY Microsatellite markers were developed in an economically important plant, Siraitia grosvenorii, to evaluate its genetic diversity. METHODS AND RESULTS Using the combined biotin capture method, 15 microsatellite primer sets were isolated and characterized. All of these markers showed polymorphism, and the number of alleles per locus ranged from two to 12 across 98 individuals from cultivars and a wild population. The observed and expected heterozygosities ranged from 0.000 to 0.905 and from 0.000 to 0.845, respectively. CONCLUSIONS These markers will facilitate the breeding and further study of the genetic diversity of S. grosvenorii.