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

• CROP GENETICS & BREEDING·GERMPLASM RESOURCES·MOLECULAR GENETICS • Previous Articles     Next Articles

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)

Abstract:

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"

序列类型
Sequence type
大小
Size
(Mb)
GC含量
GC content (%)
I类SSR Class I SSR II类SSR Class II SSR 总SSR Total SSR
数目
Number
密度
Density
(SSR Mb-1)
数目
Number
密度
Density
(SSR Mb-1)
数目
Number
密度
Density
(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"

序列类型
Sequence type
黄麻
Jute
其他植物物种的SSR密度
Density of SSRs in other plant species (SSR Mb-1)
识别SSR数
Number of SSRs
identified
相对频率
Relative
frequency
(%)
平均重复次数
Mean repeat number
密度
(SSR Mb-1)
水稻
Oryza sativa (Os)
高粱
Sorghum bicolor (Sb)
拟南芥Arabidopsis thaliana (At) 黄瓜
Cucumis sativus (Cs)
葡萄
Vitis
vinifera
(Vv)
cDNA
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
Genome
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"

[1] 熊和平 . 麻类作物育种学. 北京: 中国农业科学技术出版社, 2008. pp 208-296.
Xiong H P. Breeding Sciences of Bast and Leaf Fiber Crops. Beijing: China Agricultural Science and Technology Press, 2008. pp 208-296(in Chinese).
[2] 祁建民, 李维明, 吴为人 . 黄麻的起源与进化研究. 作物学报, 1997,23:677-682.
Qi J M, Li W M, Wu W R . Studies on origin and evolution of jute. Acta Agron Sin, 1997,23:677-682 (in Chinese with English abstract).
[3] Islam M S, Saito J A, Emdad E M, Ahmed B, Islam M M, Halim A, Hossen Q M M, Hossain M Z, Ahmed R, Hossain M S, Kabir S M T, Khan M S A, Khan M M, Hasan R, Aktar N, Honi U, Islam R, Rashid M M, Wan X H, Hou S B, Haque T, Azam M S, Moosa M M, Elias S M., Hasan A M M, Mahmood N, Shafiuddin M, Shahid S, Shommu N S, Jahan S, Roy S, Chowdhury A, Akhand A I, Nisho G M, Uddin K S, Rabeya T, Hoque S M E, Snigdha A R, Mortoza S, Matin S A, Islam M K, Lashkar M Z H, Zaman M, Yuryev A, Uddin M K, Rahman M S, Haque M S, Alam M M, Khan H, Alam M . Comparative genomics of two jute species and insight into fibre biogenesis. Nat Plants, 2017,3:16223-16230.
doi: 10.1038/nplants.2016.223 pmid: 28134914
[4] Basu A, Ghosh M, Meyer R, Powell W, Basak S L, Sen S K . Analysis of genetic diversity in cultivated jute determined by means of SSR markers and AFLP profiling. Crop Sci, 2004,44:678-685.
doi: 10.2135/cropsci2004.6780
[5] Nishat S, Haseena K, Nadim A, Sharkar M T K . Construction of an intraspecific linkage map of jute. Asian J Plant Sci, 2006,5:758-762.
doi: 10.3923/ajps.2006.758.762
[6] Das M, Banerjee S, Dhariwal R, Vyas S, Mir R, Topdar N, Kundu A, Khurana J, Tyagi A, Sarkar D, Sinha M, Balyan H, Gupta P . Development of SSR markers and construction of a linkage map in jute. J Genet, 2012,91:21-31.
doi: 10.1007/s12041-012-0151-9
[7] Biswas C, Dey P, Karmakar P G, Satpathy S . Discovery of large-scale SNP markers and construction of linkage map in a RIL population of jute (Corchorus capsularis). Mol Breed, 2015,35:1-10.
doi: 10.1007/s11032-015-0311-8
[8] Kundu A, Chakraborty A, Mandal N, Das D, Karmakar P G, Singh N K, Sarkar D . A restriction-site-associated DNA (RAD) linkage map, comparative genomics and identification of QTL for histological fibre content coincident with those for retted bast fibre yield and its major components in jute (Corchorus olitorius L., Malvaceae s. l.). Mol Breed, 2015,35:1-17.
doi: 10.1007/s11032-015-0249-x
[9] Tao A, Huang L, Wu G, Afshar R K, Qi J M, Xu J T, Fang P P, Lin L H, Zhang L W, Lin P Q . High-density genetic map construction and QTLs identification for plant height in white jute (Corchorus capsularis L.) using specific locus amplified fragment (SLAF) sequencing. BMC Genomics, 2017,18:355-376.
doi: 10.1186/s12864-017-3712-8 pmid: 28482802
[10] Zhang L W, Li S P, Chen L, Yang G S . Identification and mapping of a major dominant quantitative trait locus controlling seeds per silique as a single Mendelian factor in Brassica napus L. Theor Appl Genet, 2012,125:695-705.
doi: 10.1007/s00122-012-1861-3 pmid: 22487878
[11] Temnykh S, DeClerck G, Lukashova A, Lipovich L, Cartinhour S, McCouch S . Computational and experimental analysis of microsatellitess in rice (Oryza sativa L.): frequency, length variation, transposon associations, and genetic marker potential. Genome Res, 2001,11:1441-1452.
[12] Russell J, Fuller J, Macaulay M, Hatz B, Jahoor A, Powell W, Waugh R . Direct comparison of levels of genetic variation among barley accessions detected by RFLPs, AFLPs, SSRs and RAPDs. Theor Appl Genet, 1997,95:714-722.
doi: 10.1007/s001220050617
[13] Pejic I, Ajmone-Marsan P, Morgante M, Kozumplick V, Castiglioni P, Taramino G, Motto M . Comparative analysis of genetic similarity among maize inbred lines detected by RFLPs, RAPDs, SSRs and AFLPs. Theor Appl Genet, 1998,97:1248-1255.
doi: 10.1007/s001220051017
[14] Cheng X, Xu J, Xia S, Gu J, Yang Y, Fu J, Qian X, Zhang S C, Wu J S, Liu K . Development and genetic mapping of microsatellite markers from genome survey sequences in Brassica napus. Theor Appl Genet, 2009,118:1121-1131.
doi: 10.1007/s00122-009-0967-8 pmid: 19190889
[15] Li H, Chen X, Yang Y, Xu J S, Gu J X, Fu J, Qian X J, Zhang S C, Wu J S, Liu K . Development and genetic mapping of microsatellite markers from whole genome shotgun sequences in Brassica oleracea. Mol Breed, 2010,28:585-596.
doi: 10.1007/s11032-010-9509-y
[16] Xu J, Qian X, Wang X, Li R, Cheng X, Yang Y, Fu J, Zhang S C, King G J, Wu J S, Liu K . Construction of an integrated genetic linkage map for the A genome of Brassica napus using SSR markers derived from sequenced BACs in B. rapa. BMC Genomics, 2010,11:594-603.
doi: 10.1186/1471-2164-11-594 pmid: 3091739
[17] Karaoglu H, Lee C M Y, Meyer W . Survey of simple sequence repeats in completed fungal genomes. Mol Biol Evol, 2005,22:639-649.
doi: 10.1093/molbev/msi057 pmid: 15563717
[18] 张立武, 袁民航, 何雄威, 徐建堂, 祁建民, 刘星, 方平平, 林荔辉, 陶爱芬 . 基于GenBank黄麻EST-SSR标记的开发及其通用性评价. 作物学报, 2014,40:1028-1034.
Zhang L W, Yuan M H, He X W, Xu JT, Qi J M, Liu X, Fang P P, Lin L H, Tao A F . Development and universality evaluation of EST-SSR markers in jute (Corchorus spp.) from GenBank database. Acta Agron Sin, 2014,40:1028-1034.
[19] Hong C, Piao Z, Kang T, Batley J, Yang T, Hur Y K, Bhak J, Park B S, Edwards D, Lim Y P . Genomic distribution of simple sequence repeats in Brassica rapa. Mol Cells, 2007,23:349-356.
[20] Goff S, Ricke D, Lan T, Presting G, Wang R, Dunn M, Glazebrook J, Sessions A, Oeller P, Varma H, Hadley D, Hutchison D, Martin C, Katagiri F, Lange M, Moughamer T, Xia Y, Budworth P, Zhong J, Miguel T, Paszkowski U, Zhang S, Colbert M, Sun W, Chen L, Cooper B, Park S, Charles T, Mao L, Quail P, Wing R, Dean R, Yu Y, Zharkikh A, Shen R, Sahasrabudhe S, Thomas A, Cannings R, Gutin A, Pruss D, Reid J, Tavtigian S, Mitchell J, Eldredge G, Scholl T, Miller R M, Bhatnagar S, Adey N, Rubano T, Tusneem N, Robinson R, Feldhaus R, Macalma T, Oliphant A, Briggs S . A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science, 2002,296:92-100.
[21] Morgante M, Hanafey M, Powell W . Microsatellites are preferentially associated with nonrepetitive DNA in plant genomes. Nat Genet, 2002,30:194-200
doi: 10.1063/1.363554 pmid: 11799393
[22] Huo N, Lazo G, Vogel J, You F M, Ma Y, Hayden D M, Coleman-Derr D, Hill A, Dvorak J, Anderson O D, Luo M C, Gu Y Q . The nuclear genome of Brachypodium distachyon: analysis of BAC end sequences. Funct Integr Genom, 2008,8:135-147.
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