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.
Highlights
Bamboo, a monocot and a major grass genera, is a group of evergreen flowering plants belonging to the subfamily Bambusoideae of the family Poaceae [1]
We report, for the first time, the development of several inter-retrotransposon amplified polymorphism (IRAP) markers based on the moso bamboo genome and the use of these markers to assess the IRAP-based genetic diversity and population structure of Phyllostachys bamboo
Our study further proved that, model based and principal component analysis (PCA) based approaches were significantly better for resolving the population structure of bamboo, in the event of having a few polymorphic IRAP markers, that has produced significantly good number for highly polymorphic alleles
Summary
A monocot and a major grass genera, is a group of evergreen flowering plants belonging to the subfamily Bambusoideae of the family Poaceae [1]. Flowering intervals are long and vary between species, ranging from several to hundreds of years [2,3,4]. More than 1642 bamboo species from 75 genera are known (https://www.inbar.int), among which 100 species are commercially cultivated over 30 million hectares worldwide, in Asia. Several members of the bamboo, including Asian bamboo, are recognised as fast-growing plants, growing up to a height of 35–50 m and up to 30 cm in diameter (https://www.inbar.int). The Asian bamboo can grow at a maximum rate of 100 cm a day and produces huge biomass [5]
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