欢迎访问作物学报，今天是
作物学报

作物学报 ›› 2019, Vol. 45 ›› Issue (1): 10-17.doi: 10.3724/SP.J.1006.2019.84072

• 作物遗传育种·种质资源·分子遗传学 • 上一篇    下一篇

黄麻全基因组SSR鉴定与特征分析

姚嘉瑜1(),张立武1,2(),赵捷1,徐益1,2,祁建民1,张列梅1,*()   

  1. 1福建农林大学作物遗传育种与综合利用教育部重点实验室 / 福建省作物设计育种重点实验室 / 作物科学学院, 福建福州 350002
    2福建农林大学海峡联合研究院基因组与生物技术中心, 福建福州 350002
  • 收稿日期:2018-05-18 接受日期:2018-08-20 出版日期:2018-09-14 网络出版日期:2018-09-14
  • 通讯作者: 张列梅
  • 基金资助:
    本研究由国家自然科学基金项目(31771369);国家现代农业产业技术体系建设专项(CARS-19-E06);农业部东南黄红麻实验观测站(农科教发2011)和福建省麻类种质资源共享平台资助(2010N2002)

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 Published:2018-09-14 Published online:2018-09-14
  • Contact: Lie-Mei ZHANG
  • 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)

RichHTML

27

PDF

609

摘要：

黄麻是世界上重要的天然韧皮部纤维作物之一。然而, SSR标记的缺乏限制了黄麻的遗传改良。本研究从圆果种黄麻测序品种CVL-1的基因组、基因、CDS和cDNA中挖掘SSR信息, 利用SSR Primer软件查找SSR位点, 并分析其分布特征。结果表明, 基于基因组序列共开发了153,242个基因组SSR, 平均密度为467.20个SSR Mb -1; 基于cDNA序列开发了10,747个SSR, 平均密度为260.85 SSR Mb -1。大部分重复基元为二至四核苷酸, 占76.91%, 其中cDNA序列SSR中三核苷酸重复基元数量较多而基因组SSR中二核苷酸重复基元数量较多。对于不同类型的SSR重复基元, 随着重复单元数量的增加, 其基因组和cDNA的SSR分布频率呈现逐步降低特征。黄麻全基因组SSR标记鉴定, 不仅可以丰富黄麻分子标记的数量, 而且为剖析黄麻重要农艺性状的遗传机制奠定基础。

关键词: 黄麻, 基因组, cDNA, SSR

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

表1

黄麻SSR的分布特征"

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

图1

黄麻SSR重复序列长度的频率分布"

图2

黄麻基因组、基因、CDS和cDNA的SSR重复基元的频率分布"

图3

黄麻基因组和cDNA的SSR重复基元及平均重复序列长度的频率分布"

表2

黄麻与不同物种间SSR重复类型的频率分布比较"

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

图4

黄麻SSR二核苷酸和三核苷酸序列的优势重复基元的频率分布"

[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.
[1] 陈玲玲, 李战, 刘亭萱, 谷勇哲, 宋健, 王俊, 邱丽娟. 基于783份大豆种质资源的叶柄夹角全基因组关联分析[J]. 作物学报, 2022, 48(6): 1333-1345.
[2] 孙思敏, 韩贝, 陈林, 孙伟男, 张献龙, 杨细燕. 棉花苗期根系分型及根系性状的关联分析[J]. 作物学报, 2022, 48(5): 1081-1090.
[3] 陈小红, 林元香, 王倩, 丁敏, 王海岗, 陈凌, 高志军, 王瑞云, 乔治军. 基于高基元SSR构建黍稷种质资源的分子身份证[J]. 作物学报, 2022, 48(4): 908-919.
[4] 张霞, 于卓, 金兴红, 于肖夏, 李景伟, 李佳奇. 马铃薯SSR引物的开发、特征分析及在彩色马铃薯材料中的扩增研究[J]. 作物学报, 2022, 48(4): 920-929.
[5] 刘丹, 周彩娥, 王晓婷, 吴启蒙, 张旭, 王琪琳, 曾庆东, 康振生, 韩德俊, 吴建辉. 利用集群分离分析结合高密度芯片快速定位小麦成株期抗条锈病基因YrC271[J]. 作物学报, 2022, 48(3): 553-564.
[6] 杨昕, 林文忠, 陈思远, 杜振国, 林杰, 祁建民, 方平平, 陶爱芬, 张立武. 黄麻双生病毒CoYVV的分子鉴定和抗性种质筛选[J]. 作物学报, 2022, 48(3): 624-634.
[7] 郭艳春, 姚嘉瑜, 张镕斌, 陈思远, 何青垚, 陶爱芬, 方平平, 祁建民, 张列梅, 张立武. 中国黄麻炭疽病病原菌的分离鉴定及系统发育分析[J]. 作物学报, 2022, 48(3): 770-777.
[8] 渠建洲, 冯文豪, 张兴华, 徐淑兔, 薛吉全. 基于全基因组关联分析解析玉米籽粒大小的遗传结构[J]. 作物学报, 2022, 48(2): 304-319.
[9] 张艳波, 王袁, 冯甘雨, 段慧蓉, 刘海英. 棉籽油分和3种主要脂肪酸含量QTL分析[J]. 作物学报, 2022, 48(2): 380-395.
[10] 赵海涵, 练旺民, 占小登, 徐海明, 张迎信, 程式华, 楼向阳, 曹立勇, 洪永波. 水稻协优9308重组自交系群体白叶枯病抗性的全基因组关联分析[J]. 作物学报, 2022, 48(1): 121-137.
[11] 王艳朋, 凌磊, 张文睿, 王丹, 郭长虹. 小麦B-box基因家族全基因组鉴定与表达分析[J]. 作物学报, 2021, 47(8): 1437-1449.
[12] 张旺, 冼俊霖, 孙超, 王春明, 石丽, 于为常. CRISPR/Cas9编辑花生FAD2基因研究[J]. 作物学报, 2021, 47(8): 1481-1490.
[13] 耿腊, 黄业昌, 李梦迪, 谢尚耿, 叶玲珍, 张国平. 大麦籽粒β-葡聚糖含量的全基因组关联分析[J]. 作物学报, 2021, 47(7): 1205-1214.
[14] 马娟, 曹言勇, 李会勇. 玉米穗轴粗全基因组关联分析[J]. 作物学报, 2021, 47(7): 1228-1238.
[15] 王琰琰, 王俊, 刘国祥, 钟秋, 张华述, 骆铮珍, 陈志华, 戴培刚, 佟英, 李媛, 蒋勋, 张兴伟, 杨爱国. 基于SSR标记的雪茄烟种质资源指纹图谱库的构建及遗传多样性分析[J]. 作物学报, 2021, 47(7): 1259-1274.
Viewed
Full text


Abstract

Cited
  Shared   
  Discussed   
No Suggested Reading articles found!
京ICP备15008789号-2