Welcome to Chinese Agricultural Science Bulletin,

Chinese Agricultural Science Bulletin ›› 2019, Vol. 35 ›› Issue (28): 38-43.doi: 10.11924/j.issn.1000-6850.casb18050026

Special Issue: 生物技术

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Bioinformatic Analysis of Simple Sequence Repeat (SSR) Loci in Banana (Musa acuminata L.) Root Transcriptome

  

  • Received:2018-05-08 Revised:2019-09-04 Accepted:2018-07-24 Online:2019-10-14 Published:2019-10-14

Abstract: In order to establish new molecular markers and design SSR primers, the SSR motifs were identified based on the root transcriptome sequencing of Musa acuminata. SSR loci in unigene sequences were identified with the MISA software. A total of 4,663 SSRs were identified from 25,158 banana root unigene sequences, and these SSRs were distributed in 3,820 unigenes in the examined sequences. The frequency of SSRs accounted for 18.53% of all unigenes, and the average distribution distance of SSRs was 7.77 kb. Fifty-eighty kinds of repeat motifs were found. Among them, the most abundant motifs were the di-, and tri-nucleotide repeats, accounting for 40.50% and 40.63% of all SSRs, respectively. AG/CT and AGG/CCT are the superior repeat motifs of di-, and tri-nucleotide, accounting for 88.03% and 30.83%, respectively. Most of the repeat numbers of the SSRs were from 5 to 9, and the length of the motifs mainly ranged from 12 to 20 bp, with the average of 18.80 bp. The SSR loci in the banana root transcriptome had high frequency, and density of distribution, and various types, which can be applied in genetic diversity and marker-assisted breeding in banana.