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. 2018 Nov 12;18(1):276.
doi: 10.1186/s12870-018-1509-9.

Development of novel EST-SSR markers in the macaúba palm (Acrocomia aculeata) using transcriptome sequencing and cross-species transferability in Arecaceae species

Bárbara Regina Bazzo  1 , Lucas Miguel de Carvalho  1 , Marcelo Falsarella Carazzolle  1 , Gonçalo Amarante Guimarães Pereira  2 , Carlos Augusto Colombo  3
Affiliations

Development of novel EST-SSR markers in the macaúba palm (Acrocomia aculeata) using transcriptome sequencing and cross-species transferability in Arecaceae species

Bárbara Regina Bazzo et al. BMC Plant Biol. .

Abstract

Background: The macaúba palm is a novel feedstock for oil production suitable for multiple uses, including as biodiesel and in the food and cosmetic industries. As an efficient alternative, the macaúba palm has limited genomic resources, particularly expressed sequence tag (EST) markers. We report a comprehensive set of validated EST-simple sequence repeat (SSR) markers by using transcriptome sequencing, its application in genetic diversity analysis and cross transferability in other palm trees with environmental and economic importance.

Results: In this study, a total of 418 EST-SSRs were identified to be unique for one transcript and region; 232 EST-SSRs were selected, with trinucleotide repeats being the most frequent motif, representing 380 (90.9%), followed by composited (4.5%), di- (3.6%), and hexanucleotides (3.6%). A total of 145 EST-SSRs (62.5%) were validated for consistent amplification in seventeen macaúba palm samples, and 100 were determined to be polymorphic with PIC values ranging from 0.25 to 0.77. Genetic diversity analysis was performed with the 20 most informative EST-SSR markers showing a distinct separation of the different groups of macaúba palm. Additionally, these 145 markers were transferred in six other palm species resulting in transferability rates of 99% (144) in Acrocomia intumescens, 98% (143) in Acrocomia totai, 80.7% (117 EST-EST) in African oil palm (Elaeis guineensis) and peach palm (Bactris gasipaes) samples, 70% (102) in the juçara palm (Euterpe edulis) and 71.7% (104) in the hat palm (Sabal causiarum). Analysis of genetic distance showed a high separation in accordance with geographic location, establishing distinct groups by genera.

Conclusions: The EST markers identified in our study are a valuable resource and provide a genomic tool for genetic mapping and further genetic studies, as well as evaluation of co-location between QTLs and functionally associated markers.

Keywords: Genetic diversity; Genic molecular markers; Macaúba palm; Polymorphism; RNA-Seq; Transcript sequences.

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Competing interests

The authors declare that they have no competing interests.

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Figures

Fig. 1
Fig. 1
Acrocomia aculeata PCoA analysis. Two-dimensional plot of principal coordinate analysis (PCoA) based on the Nei distance of Acrocomia aculeata samples from different locations for the 20 more discriminating EST-SSRs
Fig. 2
Fig. 2
Arecaceae family PCoA analysis. Two-dimensional plot of principal coordinate analysis (PCoA) based on the Nei distance of Arecaceae samples for 145 EST-SSR data
See this image and copyright information in PMC

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