Development and Deployment of High-Throughput Retrotransposon-Based Markers Reveal Genetic Diversity and Population Structure of Asian Bamboo

Abstract

Bamboo, a non-timber grass species, known for exceptionally fast growth is a commercially viable crop. Long terminal repeat (LTR) retrotransposons, the main class I mobile genetic elements in plant genomes, are highly abundant (46%) in bamboo, contributing to genome diversity. They play significant roles in the regulation of gene expression, chromosome size and structure as well as in genome integrity. Due to their random insertion behavior, interspaces of retrotransposons can vary significantly among bamboo genotypes. Capitalizing this feature, inter-retrotransposon amplified polymorphism (IRAP) is a high-throughput marker system to study the genetic diversity of plant species. To date, there are no transposon based markers reported from the bamboo genome and particularly using IRAP markers on genetic diversity. Phyllostachys genus of Asian bamboo is the largest of the Bambusoideae subfamily, with great economic importance. We report structure-based analysis of bamboo genome for the LTR-retrotransposon superfamilies, Ty3-gypsy and Ty1-copia, which revealed a total of 98,850 retrotransposons with intact LTR sequences at both the ends. Grouped into 64,281 clusters/scaffold using CD-HIT-EST software, only 13 clusters of retroelements were found with more than 30 LTR sequences and with at least one copy having all intact protein domains such as gag and polyprotein. A total of 16 IRAP primers were synthesized, based on the high copy numbers of conserved LTR sequences. A study using these IRAP markers on genetic diversity and population structure of 58 Asian bamboo accessions belonging to the genus Phyllostachys revealed 3340 amplicons with an average of 98% polymorphism. The bamboo accessions were collected from nine different provinces of China, as well as from Italy and America. A three phased approach using hierarchical clustering, principal components and a model based population structure divided the bamboo accessions into four sub-populations, PhSP1, PhSP2, PhSP3 and PhSP4. All the three analyses produced significant sub-population wise consensus. Further, all the sub-populations revealed admixture of alleles. The analysis of molecular variance (AMOVA) among the sub-populations revealed high intra-population genetic variation (75%) than inter-population. The results suggest that Phyllostachys bamboos are not well evolutionarily diversified, although geographic speciation could have occurred at a limited level. This study highlights the usability of IRAP markers in determining the inter-species variability of Asian bamboos.

Genetic diversity of Alternaria species associated with black point in wheat grains

“…However, DNA profiling applications based on retrotransposons are limited by a paucity of knowledge about nucleotide sequences of LTR retrotransposons in species without a sequenced genome. In particular, phytopathogenic fungi have a small genome, so the development of genetic markers based on retrotransposons is difficult relative to species with a large genome (e.g., green plants and animals; Mandoulakani et al, 2015;Doungous et al, 2015;Ghonaim et al, 2020;Leigh et al, 2003;Li et al, 2020;Teo et al, 2005;Vukich et al, 2009;Vuorinen et al, 2018). However, the Inter-primer Binding Site (iPBS) amplification technique has proved to be a powerful DNA fingerprinting method that does not require information about retrotransposon sequences (Kalendar et al, 2010).…”

Inter-primer binding site (iPBS) markers reveal the population genetic diversity and structure of tropical climbing Cissampelopsis (Asteraceae) in Thailand

“…Only reproducible DNA bands were designated for data analysis. The polymorphic information content (PIC) values were assessed employing the method suggested by Li et al (2020). The agroupment analysis was run in PAST 3.14 software (Hammer et al 2001), using Unweighted Pair-group Method with Arithmetic Average (UPGMA) and Principal Coordinate Analysis (PCoA), grouping based on the resulting similarity values of all Cissampelopsis accessions.…”

Genetics and genomics of moso bamboo (Phyllostachys edulis): Current status, future challenges, and biotechnological opportunities toward a sustainable bamboo industry

“…Particularly, Ty3‐gypsy and Ty1‐copia are found to have the highest copy numbers (Peng, Lu, et al, 2013; Zhao, Gao, et al, 2018). Given that LTR retrotransposons play significant roles in bamboo genome evolution (Li, Ramakrishnan, et al, 2020), Ty3‐gypsy and Ty1‐copia elements are thought to be responsible for enlarging the genome size of moso bamboo (Zhou, Hu, & Zhu, 2017; Zhou, Zhong, Zhang, Tang, & Tang, 2010). Moreover, the LTRs produce more than 30% of small interfering RNAs (siRNA) in the moso bamboo (Zhou, Zhu, Bai, Hänninen, & Meng, 2017) that might contribute to diversification of gene regulatory network.…”