Expressed sequence tag simple sequence repeats (EST-SSRs) mining and marker development from Leucaena leucocephala root transcriptome

Abstract

Leucaena leucocephala is a nitrogen-fixing legume and a fast-growing species used for various purposes, including food, medicine, and most recently, energy-source wood. Compared to other commonly planted legumes, this species has a high-stress tolerance, and only one recorded insect infestation. The transcriptome analysis revealed genes involved in the production of stress tolerance compounds in the root. In this study, we attempted to extract simple sequence repeats (SSRs) from the transcriptome data of L. leucocephala root to establish molecular markers. The SSRs mined from L. leucocephala transcriptome deposited in NCBI with accession number GDRZ00000000. We used Krait v.1.3.3 to extract the SSRs and developed the primers. The SSRs cover 0.3% of the total transcriptome sequence, with 21.321 perfect SSRs found and relative density 2908.63 (bp/Mb). The most abundant type of SSRs was found in mononucleotide (39.85%), followed by dinucleotide (33.49%) and trinucleotide (24.75). However, for tetra, penta, and hexanucleotide, the percentage was lower than 2%. The number of primers generated was 8137 primers, with 3969 dinucleotides, 3947 trinucleotides, 150 tetranucleotides, 21 pentanucleotides, and 50 hexanucleotide SSR primers. This finding may help to accelerate stress-tolerant legume improvement in the future.