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Open AccessArticle

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

1
State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin’an, Hangzhou 311300, China
2
Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
3
Department of Agricultural Sciences, Viikki Plant Science Centre and Helsinki Sustainability Centre, University of Helsinki, P.O. Box 27 (Latokartanonkaari 5), FI-00014 Helsinki, Finland
4
RSE, National Center for Biotechnology, 13/5, Kurgalzhynskoye road, Nur-Sultan 010000, Kazakhstan
5
Department of Forest Sciences, University of Helsinki, 00014 Helsinki, Finland
6
Zhejiang Provincial Collaborative Innovation Center for Bamboo Resources and High-Efficiency Utilization, Zhejiang A&F University, Lin’an, Hangzhou 311300, China
*
Author to whom correspondence should be addressed.
These authors contributed equally to this article.
Forests 2020, 11(1), 31; https://doi.org/10.3390/f11010031
Received: 31 October 2019 / Revised: 14 December 2019 / Accepted: 17 December 2019 / Published: 24 December 2019
(This article belongs to the Special Issue Genetics and Improvement of Forest Trees)
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. View Full-Text
Keywords: LTR-retrotransposon; Ty3-gypsy; Ty1-copia; IRAP; molecular markers; bamboo; Phyllostachys; genetic diversity; populations structure; AMOVA LTR-retrotransposon; Ty3-gypsy; Ty1-copia; IRAP; molecular markers; bamboo; Phyllostachys; genetic diversity; populations structure; AMOVA
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MDPI and ACS Style

Li, S.; Ramakrishnan, M.; Vinod, K.K.; Kalendar, R.; Yrjälä, K.; Zhou, M. Development and Deployment of High-Throughput Retrotransposon-Based Markers Reveal Genetic Diversity and Population Structure of Asian Bamboo. Forests 2020, 11, 31.

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