SSR and SNP/InDel Characteristics of Fruit Transcriptomic Data of <i>Canarium album</i>
Welcome to Chinese Journal of Tropical Crops,

Chinese Journal of Tropical Crops ›› 2023, Vol. 44 ›› Issue (4): 681-688.DOI: 10.3969/j.issn.1000-2561.2023.04.003

• Omics & Biotechnology • Previous Articles     Next Articles

SSR and SNP/InDel Characteristics of Fruit Transcriptomic Data of Canarium album

LAI Ruilian, SHEN Chaogui, FENG Xin, CHEN Yiting, WEI Xiaoxia, WU Rujian()   

  1. Fruit Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian 350013, China
  • Received:2022-07-01 Revised:2022-07-18 Online:2023-04-25 Published:2023-05-11
  • Contact: *WU Rujian, E-mail: wurujian@126.com.

Abstract:

Simple sequence repeats (SSR) and single nucleotide polymorphism (SNP) markers have been confirmed to be high sensitivity and specificity. Development of molecular markers related to different types of fruit quality traits of Canarium album (Lour.) Raeusch. can provide reference for its molecular assisted breeding to a considerable extent. The fully mature fruits of C. album cv. Changying and Huiyuan were collected to use as materials. After total RNA extraction and cDNA library construction, the transcriptome was sequenced on the Illumina Novaseq platform, and the SSR, SNP and InDel loci characteristics of the transcriptome were analyzed by MISA 1.0 and GATK3 software. Results showed that a total of 13 935 SSR loci were identified from 10 124 unigenes of C. album fruit transcriptome, the average 1 kb sequence appeared 0.25 SSR loci, the frequency and average length was 22.98% and 14.34 bp, respectively. Among them, the single base repeat type had the largest number of SSR loci (accounting for 66.80%), with a length of 10-64 bp, and an average length of 12.85 bp, the repeat times of repeat motifs were concentrated in 9-12, and the motif with the highest frequency was A/T (accounting for 66.67%). The number of SSR loci of six base repeat motif type was the least (0.47%), the length was 30-54 bp, which average length was 31.76 bp, the number of motif repeats was concentrated in 5-8 times, and the motif with the highest frequency was AGATGG/ATCTCC (0.04%). A total of 284 992 SNP loci were detected in the transcriptome of C. album fruit, the average 1 kb sequence contained 5.21 SNP loci; Among them, the number of SNP loci of transformation type was 166 162, including C/T and A/G. The number of SNP loci of transversion type was 118 830, including A/T, A/C, T/G and C/G. In addition, 18 548 InDel loci were found in the transcriptome of C. album fruit, the average 1 kb sequence existed 2.95 InDel loci. The number of unigenes containing one InDel locus was the largest. It was predicted that the unigene containing the most InDel loci might be the callose synthase gene. These results showed that SSR and SNP/InDel markers could be effectively developed through RNA-seq. The SSR loci and SNP/InDel loci were widely distributed in C. album fruits with different quality traits. The results would provide a data basis for the development of identification markers of C. album fruit traits.

Key words: Canarium album, transcriptome, simple sequence repeats, single nucleotide polymorphism, InDel

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