• Dynamic changes of DNA methylation during wild strawberry (Fragaria nilgerrensis) tissue culture

      Cao, Qiang; Feng, Yuxi; Dai, Xiongwei; Huang, Lin; Li, Jiamin; Tao, Pang; Crabbe, M. James C.; Zhang, Ti-Cao; Qiao, Qin; Yunnan University; et al. (Frontiers, 2021-11-30)
      Tissue culture is an important tool for asexual propagation and genetic transformation of strawberry plants. In plant tissue culture, variation of DNA methylation is a potential source of phenotypic variation in regenerated plants. However, the genome wide dynamic methylation patterns of strawberry tissue culture remain unclear. In this study, we used whole-genome bisulfite sequencing (WGBS) to study genomic DNA methylation changes of a wild strawberry Fragaria nilgerrensis at six stages: from explants of shoot tips to outplanting and acclimation. Global methylation levels showed that CG sites exhibited the highest methylation level in all stages with an average of 49.5%, followed by CHG (33.2%) and CHH (12.4%). Although CHH accounted for the lowest proportion of total cytosine methylation, it showed the most obvious methylation change and the most of these changes occurred in the transposable element regions. The overall methylation levels alternately decreased and increased during the entire tissue culture process and the distribution of DNA methylation was non-uniform among different genetic regions. Furthermore, much more differentially methylated regions (DMRs) were detected in dedifferentiation and redifferentiation stages and most of them were transposable elements, suggesting these processes involved activating or silencing of amounts of transposons. The functional enrichment of the DMR-related genes indicated that genes involved in hormone metabolic processes, plant development and the stress response changed methylation throughout the tissue culture process. Finally, the quantitative real-time PCR (qRT-PCR) was conducted to examine the association of methylation and gene expression of a set of different methylated genes. Our findings give deeper insight into the epigenetic regulation of gene expression during the plant tissue cultures process, which will be useful in the efficient control of somaclonal variations and in crop improvement.
    • Evaluation of genetic diversity and population structure of Fragaria nilgerrensis using EST-SSR markers

      Liu, Jie; Zhang, Yichen; Diao, Xia; Yu, Kun; Dai, Xiongwei; Qu, Peng; Crabbe, M. James C.; Zhang, Ti-Cao; Qiao, Qin; Yunnan University; et al. (Elsevier, 2021-06-25)
      Fragaria nilgerrensis is a diploid wild strawberry widely distributed in Southwest China. Its white color and “peach-like” fragrance of fruits are valuable characters for the genetic improvement of cultivated strawberry plants. Its strong biotic and abiotic resistance and tolerance also enable it to survive in different habitats in the field. In this study, we evaluated the level of genetic variation within and between 16 populations with 169 individuals of F. nilgerrensis using 16 newly developed EST-SSR (expressed sequence tag-simple sequence repeats) markers. The results show that the genetic diversity of this species was high, based on Nei’s genetic diversity (0.26) and polymorphic loci (0.41), although it is self-compatible and has clonal propagation. Significant genetic differentiation among populations was also detected by AMOVA analysis (Fst = 0.34), which could be indicative of little gene flow (Nm = 0.43) in F. nilgerrensis. The phylogenetic tree indicates that most of individuals from the same population have clustered together. These populations were not grouped based on the geographical distance, consistent with the Mantel test result (R2 = 0.0063, P > 0.05). All the populations were assigned into two ancestral groups, with some individuals admixed, suggesting ancestral gene flow had occurred between these two groups. Our developed EST-SSR markers as well as the genetic diversity and population structure analysis of F. nilgerrensis are important for genetic improvement in the breeding process. Moreover, the populations that contain high genetic diversity would be a priority for collection and conservation.
    • Genomic analysis of field pennycress (Thlaspi arvense) provides insights into mechanisms of adaptation to high elevation

      Geng, Yu-peng; Guan, Yabin; Qiong, La; Lu, Shugang; An, Miao; Crabbe, M. James C.; Qi, Ji.; Zhao, Fangqing; Qiao, Qin; Zhang, Ti-Cao; et al. (Springer Nature, 2021-07-22)
      Background: Understanding how organisms evolve and adapt to extreme habitats is of crucial importance in evolutionary ecology. Altitude gradients are an important determinant of the distribution pattern and range of organisms due to distinct climate conditions at different altitudes. High-altitude regions often provide extreme environments including low temperature and oxygen concentration, poor soil, and strong levels of ultraviolet radiation, leading to very few plant species being able to populate elevation ranges greater than 4000 m. Field pennycress (Thlaspi arvense) is a valuable oilseed crop and emerging model plant distributed across an elevation range of nearly 4500 m. Here, we generate an improved genome assembly to understand how this species adapts to such different environments. Results: We sequenced and assembled de novo the chromosome-level pennycress genome of 527.3 Mb encoding 31,596 genes. Phylogenomic analyses based on 2495 single-copy genes revealed that pennycress is closely related to Eutrema salsugineum (estimated divergence 14.32–18.58 Mya), and both species form a sister clade to Schrenkiella parvula and genus Brassica. Field pennycress contains the highest percentage (70.19%) of transposable elements in all reported genomes of Brassicaceae, with the retrotransposon proliferation in the Middle Pleistocene being likely responsible for the expansion of genome size. Moreover, our analysis of 40 field pennycress samples in two highand two low-elevation populations detected 1,256,971 high-quality single nucleotide polymorphisms. Using three complementary selection tests, we detected 130 candidate naturally selected genes in the Qinghai-Tibet Plateau (QTP) populations, some of which are involved in DNA repair and the ubiquitin system and potential candidates involved in high-altitude adaptation. Notably, we detected a single base mutation causing loss-of-function of the FLOWERING LOCUS C protein, responsible for the transition to early flowering in high-elevation populations. Conclusions: Our results provide a genome-wide perspective of how plants adapt to distinct environmental conditions across extreme elevation differences and the potential for further follow-up research with extensive data from additional populations and species.
    • Spatial genetic and epigenetic structure of Thlaspi arvense (field pennycress) in China

      Guan, Yabin; Qu, Peng; Lu, Shugang; Crabbe, M. James C.; Zhang, Ti-Cao; Geng, Yu-peng; Yunnan University; Oxford University; Shanxi University; University of Bedfordshire; et al. (Genetics Society of Japan, 2020-11-11)
      (Received 13 May 2020, accepted 15 July 2020; J-STAGE Advance published date: 11 November 2020) Thlaspi arvense (field pennycress) is widespread in temperate regions of the northern hemisphere. We estimated the genetic and epigenetic structure of eight T. arvense populations (131 individuals) in China using amplified fragment length polymorphism and methylation-sensitive amplified polymorphism molecularmarker techniques. We detected low diversity at both genetic (mean = 0.03; total = 0.07) and epigenetic (mean = 0.04; total = 0.07) levels, while significant genetic (FST = 0.42, P < 0.001) and epigenetic (FST = 0.32, P < 0.001) divergence was found across the distribution range. Using Mantel testing, we found spatial genetic and epigenetic differentiation, consistent with isolation-by-distance models. We also identified a strong correlation between genetic and epigenetic differentiation (r = 0.7438, P < 0.001), suggesting genetic control of the epigenetic variation. Our results indicate that mating system, natural selection and gene flow events jointly structure spatial patterns of genetic and epigenetic variation. Moreover, epigenetic variation may serve as a basis of natural selection and ecological evolution to enable species to adapt to heterogeneous habitats. Our study provides novel clues for the adaptation of T. arvense.