Retrotransposon-based molecular markers for assessment of genomic diversity

Deciphering the genetic diversity and population structure of Turkish bread wheat germplasm using iPBS-retrotransposons markers

BACKGROUND

Research activities aiming to investigate the genetic diversity are very crucial because they provide information for the breeding and germplasm conservation activities. Wheat is one of the most important cereal crops globally by feeding more than a third of the human population around the world.

METHODS AND RESULTS

During present investigation, a total of 74 Turkish bread wheat accessions (54 landraces and 20 cultivars) were used as plant material and iPBS-retrotransposons marker system was used for the molecular characterization. 13 polymorphic primers used for molecular characterization resulted a total of 152 bands. Range of calculated diversity indices like polymorphism information content (0.11-0.702), effective numbers of alleles (1.026-1.526), Shannon's information index (0.101-0.247) and gene diversity (0.098-0.443) confirmed higher genetic variations in studied germplasm. Bread wheat landraces reflected higher genetic variations compared to commercial cultivars. Analysis of molecular variance resulted that higher (98%) genetic variations are present within populations. The model-based structure algorithm separated 74 bread wheat accessions in to two populations. Diversity indices based on structure evaluated population's revealed population B as a more diverse population. The principal coordinate analysis and neighbor-joining analysis separated 74 bread wheat accessions according to their collection points. Genetic distance for 74 Turkish bread wheat accessions explored Bingol and Asure accessions as genetically diverse that can be used as parents for breeding activities.

CONCLUSIONS

The extensive diversity of bread wheat in Turkish germplasm might be used as genetic resource for the exhaustive wheat breeding program. For instance, accessions Bingol and Asure were found genetically diverse and can be used as parents for future breeding activities.

Genetic analysis and population structure of wild and cultivated wishbone flower (Torenia fournieri Lind.) lines related to specific floral color

Background

The wishbone flower or Torenia fournieri Lind., an annual from tropical Indochina and southern China, is a popular ornamental plant, and many interspecific (T. fournieri × T. concolor) hybrid lines have been bred for the international market. The cultivated lines show a pattern of genetic similarity that correlates with floral color which informs on future breeding strategies. This study aimed to perform genetic analysis and population structure of cultivated hybrid lines comparing with closely related T. concolor wild populations.

Methods

We applied the retrotransposon based iPBS marker system for genotyping of a total of 136 accessions from 17 lines/populations of Torenia. These included 15 cultivated lines of three series: Duchess (A, B, C); Kauai (D, E, F, G, H, I, J); Little Kiss (K, L, M, N, P) and two wild T. concolor populations (Q and R). PCR products from each individual were applied to estimate the genetic diversity and differentiation between lines/populations.

Results

Genotyping results showed a pattern of genetic variation differentiating the 17 lines/populations characterized by their specific floral colors. The final PCoA analysis, phylogenetic tree construction, and Bayesian population structural bar plot all showed a clear subdivision of lines/populations analysed. The 15 cultivated hybrid lines and the wild population Q that collected from a small area showed the lowest genetic variability while the other wild population R which sampled from a larger area had the highest genetic variability.

Discussion

The extremely low genetic variability of 15 cultivated lines indicated that individual line has similar reduction in diversity/heterozygosity from a bottleneck event, and each retained a similar (but different from each other) content of the wild genetic diversity. The genetic variance for the two wild T. concolor populations could be due to our varied sampling methods. The two wild populations (Q, R) and the cultivated hybrid lines (I, K, M, N, P) are genetically more closely related, but strong positive correlations presented in cultivated lines A, C, E, M, and N. These results could be used to guide future Torenia breeding.

Conclusions

The genetic variation and population structure found in our study showed that cultivated hybrid lines had similar reduction in diversity/heterozygosity from a bottleneck event and each line retained a similar (but different from each other) content of the wild genetic diversity, especially when strong phenotypic selection of floral color overlaps. Generally, environmental factors could induce transposon activation and generate genetic variability which enabled the acceleration of the evolutionary process of wild Torenia species. Our study revealed that wild Torenia populations sampled from broad geographic region represent stronger species strength with outstanding genetic diversity, but selective breeding targeting a specific floral color decreased such genetic variability.

Draft genome sequence of the pulse crop blackgram [Vigna mungo (L.) Hepper] reveals potential R-genes

Blackgram [Vigna mungo (L.) Hepper] (2n = 2x = 22), an important Asiatic legume crop, is a major source of dietary protein for the predominantly vegetarian population. Here we construct a draft genome sequence of blackgram, for the first time, by employing hybrid genome assembly with Illumina reads and third generation Oxford Nanopore sequencing technology. The final de novo whole genome of blackgram is ~ 475 Mb (82% of the genome) and has maximum scaffold length of 6.3 Mb with scaffold N50 of 1.42 Mb. Genome analysis identified 42,115 genes with mean coding sequence length of 1131 bp. Around 80.6% of predicted genes were annotated. Nearly half of the assembled sequence is composed of repetitive elements with retrotransposons as major (47.3% of genome) transposable elements, whereas, DNA transposons made up only 2.29% of the genome. A total of 166,014 SSRs, including 65,180 compound SSRs, were identified and primer pairs for 34,816 SSRs were designed. Out of the 33,959 proteins, 1659 proteins showed presence of R-gene related domains. KIN class was found in majority of the proteins (905) followed by RLK (239) and RLP (188). The genome sequence of blackgram will facilitate identification of agronomically important genes and accelerate the genetic improvement of blackgram.

Moving through the Stressed Genome: Emerging Regulatory Roles for Transposons in Plant Stress Response

The recognition of a positive correlation between organism genome size with its transposable element (TE) content, represents a key discovery of the field of genome biology. Considerable evidence accumulated since then suggests the involvement of TEs in genome structure, evolution and function. The global genome reorganization brought about by transposon activity might play an adaptive/regulatory role in the host response to environmental challenges, reminiscent of McClintock's original 'Controlling Element' hypothesis. This regulatory aspect of TEs is also garnering support in light of the recent evidences, which project TEs as "distributed genomic control modules." According to this view, TEs are capable of actively reprogramming host genes circuits and ultimately fine-tuning the host response to specific environmental stimuli. Moreover, the stress-induced changes in epigenetic status of TE activity may allow TEs to propagate their stress responsive elements to host genes; the resulting genome fluidity can permit phenotypic plasticity and adaptation to stress. Given their predominating presence in the plant genomes, nested organization in the genic regions and potential regulatory role in stress response, TEs hold unexplored potential for crop improvement programs. This review intends to present the current information about the roles played by TEs in plant genome organization, evolution, and function and highlight the regulatory mechanisms in plant stress responses. We will also briefly discuss the connection between TE activity, host epigenetic response and phenotypic plasticity as a critical link for traversing the translational bridge from a purely basic study of TEs, to the applied field of stress adaptation and crop improvement.