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Acta Agronomica Sinica ›› 2019, Vol. 45 ›› Issue (1): 10-17.doi: 10.3724/SP.J.1006.2019.84072


Evaluation and characteristic analysis of SSRs from the whole genome of jute (Corchorus capsularis)

Jia-Yu YAO1(),Li-Wu ZHANG1,2(),Jie ZHAO1,Yi XU1,2,Jian-Min QI1,Lie-Mei ZHANG1,*()   

  1. 1 Key Laboratory for Genetics, Breeding and Multiple Utilization of Crops of Ministry of Education / Fujian Key Laboratory for Crop Breeding by Design / College of Crop Science, Fuzhou 350002, Fujian, China
    2 Center for Genomics and Biotechnology of Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
  • Received:2018-05-18 Accepted:2018-08-20 Online:2018-09-14 Published:2018-09-14
  • Contact: Lie-Mei ZHANG E-mail:3533551417@qq.com;lwzhang@fafu.edu.cn;zhangliemei@126.com
  • Supported by:
    This study was supported by the National Natural Science Foundation of China(31771369);the China Agriculture Research System(CARS-19-E06);the Experiment Station of Jute and Kenaf in Southeast China (Nongkejiaofa 2011), and the Construction of Germplasm Resources Platform for Bast Fiber Crops in Fujian, China.(2010N2002)


Jute is one of the most important natural bast fiber crops worldwide. However, the lack of SSR markers limits the genetic improvement of jute. In this study, simple sequence repeats (SSRs) were identified from the genome, genes, CDS and cDNA of CVL-1, a sequenced variety in Corchorus capsularis. SSR loci was called using SSR Primer software and the characteristics of SSR loci were analyzed. The 153,242 genomic SSRs were called based on the genomic sequence with an average density of 467.20 SSRs Mb -1. Based on the cDNA sequence, we called 10,747 SSRs were developed with an average density of 260.85 SSRs Mb -1. The majority of repeat types were di- to tetra-nucleotides, accounting for 76.91%. Among them, the tri-nucleotide repeat types were the highest abundance repeat types in the cDNA_SSRs while the di-nucleotide repeat types were the highest abundance repeat types in the genomic SSRs. For different SSR repeat types, the genomic and cDNA-SSR frequency decreased dramatically as repeat times increased. Identification of SSR markers in the whole genome can not only enrich the number of molecular markers, but also lay a foundation for the analysis of genetic basis of important agronomic traits in jute.

Key words: jute (Corchorus capsularis), genome, cDNA, SSRs

Table 1

Distribution features of SSR classes identified in jute"

Sequence type
GC content (%)
(SSR Mb-1)
(SSR Mb-1)
(SSR Mb-1)
cDNA 41.20 57.79 1251 30.36 9496 230.49 10747 260.85
CDS 29.80 59.33 592 19.87 4862 163.15 5454 183.02
Gene 96.30 54.39 7865 81.67 28428 295.20 36293 376.87
Genome 330.00 54.03 38917 118.65 114325 348.55 153242 467.20

Fig. 1

Freguency distribution of SSRs in the genome-wide and cDNA by the repeat length of total SSRs (a), class II SSRs (b), and class I SSRs (c), respectively"

Fig. 2

Frequency distribution of total SSRs (a), class II SSRs (b), and class I SSRs (c) according to the length of repeat motif in cDNA, CDS, genes and the whole genome, respectively"

Fig. 3

Frequency distribution of mean motif length and repeat types in SSRs identified from cDNA and the whole genome of jute"

Table 2

Comparison of frequencies of SSRs repeat types in the whole genome sequences of jute and other plant species"

Sequence type
Density of SSRs in other plant species (SSR Mb-1)
Number of SSRs
Mean repeat number
(SSR Mb-1)
Oryza sativa (Os)
Sorghum bicolor (Sb)
拟南芥Arabidopsis thaliana (At) 黄瓜
Cucumis sativus (Cs)
Di- 1082 10.07 7.99 26.26 57.9 52.1 54.8 40.7
Tri- 5862 54.55 5.12 142.28 485.7 366.3 179.7 108.4
Tetra- 1674 15.58 3.47 40.63 107.3 125.5 69.3 53.3
Penta- 729 6.78 3.56 17.69 41.6 44.1 23.3 17.4
Hexa- 1400 13.03 3.64 33.98 44.6 56.5 36.1 22.1
Total/mean 10747 100.00 23.78 260.85 737.1 644.5 363.2 241.9
Di- 40863 26.67 10.38 124.58 100.1 51.6 78.7 146.0 117.2
Tri- 36836 24.04 5.35 112.30 220.1 108.5 146.6 141.1 115.8
Tetra- 40144 26.20 3.61 122.39 132.7 105.4 93.2 164.2 171.3
Penta- 18098 11.81 3.61 55.18 45.8 22.5 32.0 54.4 58.0
Hexa- 17301 11.29 3.64 52.75 27.4 27.5 13.6 31.0 29.3
Total/mean 153242 100.00 26.59 467.20 526.1 315.5 364.1 536.7 491.6

Fig. 4

Frequency distribution of predominant repeat motifs for di- and tri-nucleotide SSRs in jute"

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