Yupeng Geng

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.

Epigenetic Flexibility Underlying Phenotypic Plasticity

Phenotypic plasticity refers to the ability of an organism to produce different phenotypes under different environmental circumstances. The mechanisms underlying phenotypic plasticity received considerable attention in recent years. It has become widely acknowledged that plastic variation in phenotypes mostly take place by altering gene expression and eventually altering ontogenetic trajectory in response to environmental changes. Epigenetic modifications provide a plausible mechanism for the putative link between environmental variation and alterations in gene expression. While much attention is being paid to heritable epigenetic changes, little attention is being paid to swift and reversible epigenetic alternations, which mediate rapid plastic responses of the organism to environmental perturbation. This mechanism is particularly important to allow organisms with no/low genetic diversity to adapt to different environments, and is likely to be a favorable evolutionary response when organisms are exposed to stress periods that last shorter than a single life span. Studying epigenetic complexes in the real environment would allow us to get greater insights into the molecular machinery that interfaces the genotype and the environment.

Microsatellite markers for the cushion rock jasmine, Androsace tapete (Primulaceae), a species endemic to the Qinghai-Tibetan Plateau

UNLABELLED PREMISE OF THE STUDY Microsatellite markers were developed in an alpine plant endemic to the Qinghai-Tibetan Plateau, Androsace tapete, to investigate its spatial genetic structure, gene flow, and mating patterns. • METHODS AND RESULTS Using the combined biotin capture method, 16 microsatellite primer sets were isolated and characterized. Fifteen of these markers showed polymorphism, and the number of alleles per locus ranged from three to 13 across 56 individuals from six Tibetan populations. • CONCLUSIONS These markers provide a useful tool to investigate the spatial genetic structure, gene flow, and mating system of A. tapete.

Variation of genome size and the ribosomal DNA ITS region of Alternanthera philoxeroides (Amaranthaceae) in Argentina, the USA, and China

Alligator weed, Alternanthera philoxeroides (Mart.) Griseb., is one of the worst invasive weeds in the world. In the present study, the genome size of seven forms/biotypes of alligator weed from Argentina (native area), the USA (introduced area), and China (introduced area) was analyzed using flow cytometers; the ribosomal DNA internal transcribed spacer region (ITS) was cloned and sequenced. We found that the genome size of A. philoxeroides ranged from 5.72 to 8.50 pg/2C nucleus, consisting of four levels of genome and three kinds of ploidy. Among them, three levels and two kinds (tetraploid and hexaploid) were found in samples from Argentina, two levels and one kind (pentaploid) in US samples, and one level and one kind (hexaploid) in samples from China. Contrary to the significant variation in genome size, we found that the intraspecific differentiation of the ITS sequences in the seven forms/biotypes was extremely low, and that six of them shared ITS sequences with no or one single substitution. These results show that the change of genome size played a major role in the differentiation of A. philoxeroides, and that forms/biotypes with higher ploidy seem to have stronger invasive ability. Furthermore, the differences of A. philoxeroides in ploidy between samples from the USA and China showed that alligator weeds from these two invaded areas certainly have different native progenitors.

Development of microsatellite markers for the invasive weed Parthenium hysterophorus (Asteraceae).

PREMISE OF THE STUDY Microsatellite primers were developed for Parthenium hysterophorus to investigate its genetic structure and genetic diversity. METHODS AND RESULTS Using the combined biotin capture method, 15 microsatellite primer sets were isolated and characterized. All markers showed polymorphism, and the number of alleles per locus ranged from two to nine across 60 individuals from two populations. The observed and expected heterozygosities ranged from 0.117 to 0.750 and from 0.182 to 0.835, respectively. CONCLUSIONS These markers will be useful for investigating the invasion history of this weed globally and to help characterize its invasiveness.

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.

Differentially Expressed microRNAs and Target Genes Associated with Plastic Internode Elongation in Alternanthera philoxeroides in Contrasting Hydrological Habitats

Phenotypic plasticity is crucial for plants to survive in changing environments. Discovering microRNAs, identifying their targets and further inferring microRNA functions in mediating plastic developmental responses to environmental changes have been a critical strategy for understanding the underlying molecular mechanisms of phenotypic plasticity. In this study, the dynamic expression patterns of microRNAs under contrasting hydrological habitats in the amphibious species Alternanthera philoxeroides were identified by time course expression profiling using high-throughput sequencing technology. A total of 128 known and 18 novel microRNAs were found to be differentially expressed under contrasting hydrological habitats. The microRNA:mRNA pairs potentially associated with plastic internode elongation were identified by integrative analysis of microRNA and mRNA expression profiles, and were validated by qRT-PCR and 5′ RLM-RACE. The results showed that both the universal microRNAs conserved across different plants and the unique microRNAs novelly identified in A. philoxeroides were involved in the responses to varied water regimes. The results also showed that most of the differentially expressed microRNAs were transiently up-/down-regulated at certain time points during the treatments. The fine-scale temporal changes in microRNA expression highlighted the importance of time-series sampling in identifying stress-responsive microRNAs and analyzing their role in stress response/tolerance.