欢迎访问作物学报，今天是
作物学报

作物学报 ›› 2020, Vol. 46 ›› Issue (7): 987-996.doi: 10.3724/SP.J.1006.2020.94158

• 作物遗传育种·种质资源·分子遗传学 • 上一篇    下一篇

基于黄麻转录组序列SNP位点的CAPS标记开发与验证

陶爱芬1,2,游梓翊2,徐建堂2,林荔辉2,张立武2,祁建民2,*(),方平平2,*()   

  1. 1 福建农林大学金山学院, 福建福州 350002
    2 福建农林大学教育部作物遗传育种与综合利用重点实验室 / 福建省分子设计育种实验室, 福建福州 350002
  • 收稿日期:2019-10-23 接受日期:2020-03-24 出版日期:2020-07-12 网络出版日期:2020-04-16
  • 通讯作者: 祁建民,方平平
  • 作者简介:E-mail: 281770126@qq.com, Tel: 0591-83789483
  • 基金资助:
    国家现代农业产业技术体系建设专项(CARS-19-E06)

Development and verification of CAPS markers based on SNPs from transcriptome of jute (Corchorus L.)

TAO Ai-Fen1,2,YOU Zi-Yi2,XU Jian-Tang2,LIN Li-Hui2,ZHANG Li-Wu2,QI Jian-Min2,*(),FANG Ping-Ping2,*()   

  1. 1 Jinshan College, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
    2 Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops / Key Laboratory of Crops by Design, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
  • Received:2019-10-23 Accepted:2020-03-24 Published:2020-07-12 Published online:2020-04-16
  • Contact: Jian-Min QI,Ping-Ping FANG
  • Supported by:
    China Agriculture Research System(CARS-19-E06)

RichHTML

22

PDF

667

摘要：

黄麻CAPS分子标记的开发, 可以为黄麻遗传多样性分析、种质资源鉴定和分子标记辅助选择等研究提供有效方法。本试验以黄麻179和爱店野生种为材料, 采用Illumina HiSeq 4000测序技术进行转录组测序, 对其SNP位点进行分析, 设计了与木质素合成基因4CL、COMT及转录因子MYB相关的SNP引物, 在此基础上, 应用dCAPS Finder2.0软件开发了CAPS标记, 并对其有效性进行了验证。结果表明: (1)组装后的黄麻unigene序列共72,674条, 序列总长度为29,705,997 bp, 检测到的SNP位点总数为67,567个, 平均每440 bp有1个SNP。(2)获得了39对分别与4CL、COMT和MYB相关的SNP引物, 从中筛选获得26对CAPS标记引物, 开发成功率为66.7%, 其中11对CAPS标记具有多态性, 多态性比例为43.2%。(3)开发的CAPS标记能较好地将12份不同类型的黄麻种质区分开来, 表明CAPS是适用于黄麻研究的较理想的分子标记方法, 为黄麻遗传基础研究提供了可靠工具。

关键词: 黄麻, 转录组, SNP位点, CAPS标记, 开发

Abstract:

Developing CAPS markers can provide a new and effective tool for genetic diversity analysis, germplasm identification and marker-assistant selection of jute. The transcriptional sequence analysis was carried out by Illumina HiSeq 4000 with jute 179 and the wild species in Aidian. Furthermore, the SNP loci were screened and primers related to lignin synthesis genes 4CL, COMT and transcription factor MYB were developed. CAPS markers were screened based on above SNP primers using dCAPS Finder2.0 and their polymorphism was verified. A total of 72,674 unigene sequences were got in jute transcriptome by assembly, with a length of 29,705,997 bp, a number of SNP loci of 67,567, and an average of 1 SNP per 440 bp. Thirty-nine pairs of SNP primers related to 4CL, COMT, and MYB were designed by Oligo8, of which 26 pairs of CAPS primers were screened, with a developing rate of 66.7%. Among the 26 pairs of CAPS markers, 11 pairs were polymorphic, with a polymorphic ratio of 43.2%. The screened CAPS markers could effectively distinguish 12 different accessions of jute germplasm, indicating CAPS is an ideal molecular marker which can lie a reliable tool used in genetic research of jute.

Key words: jute, transcriptome, SNP loci, CAPS markers, development

表1

用于CAPS引物多态性验证的黄麻品种名称和类型"

编号
Number		 名称
Name		 品种类型
Type of accessions
1 梅峰4号 Meifeng 4 圆果种 Corchorus capsularis
2 越南圆果 Yuenanyuanguo 圆果种 Corchorus capsularis
3 广东独尾麻 Guangdongduweima 圆果种 Corchorus capsularis
4 中黄麻1号 Zhonghuangma 1 圆果种 Corchorus capsularis
5 日本大分青皮 Japanese Dafenqingpi 圆果种 Corchorus capsularis
6 福农1号 Funong 1 长果种 Corchorus olitoris
7 马里野生种 Maliyeshengzhong 长果种 Corchorus olitoris
8 广西长果 Guangxichangguo 长果种 Corchorus olitoris
9 日本5号 Japanese 5 长果种 Corchorus olitoris
10 翠绿 Cuilyu 长果种 Corchorus olitoris
11 龙溪长果 Longxichangguo 长果种 Corchorus olitoris
12 台湾加利麻 Taiwanjialima 圆果种 Corchorus capsularis

图1

黄麻unigene中SNP位点分布的趋势图 横坐标为SNP的密度, 即每kb基因序列上的SNP数目; 纵坐标为拥有对应密度的unigene数目。"

表2

黄麻unigene中SNP位点的分布密度表"

SNP位点的数目
Number of SNP loci		 对应unigene序列的数目
Corresponding number of unigenes		 所占比例
Ratio of SNP (%)
0-1 66,525 91.53
1-2 2092 2.88
2-3 1277 1.76
3-4 948 1.30
4-5 735 1.01
5-6 258 0.35
6-7 234 0.32
7-8 174 0.24
>8 431 0.59

表3

39对SNP引物的编号、名称及序列"

引物名称
Primer name		 正向引物序列
Forward primer sequence (5′-3′)		 反向引物序列
Reverse primer sequence (5′-3′)
4CL SNP1-1 GTGCTTTTCATCGGTGGTTT TGTCGTAAAACTGCTGCTGG
4CL SNP1-2 CGATTTTCATCTCGGCATTT GCCACCCATAGTTTTGGCTA
4CL SNP2-1 AGCTCCCATGAAAGCAAAGA AGCTCCCATGAAAGCAAAGA
4CL SNP2-2 AGCTCCCATGAAAGCAAAGA CGATTTTCATCTCGGCATTT
4CL SNP3-1 GAGCTTAGCGCGAGAAGTGT TGTCGTAAAACTGCTGCTGG
4CL SNP3-2 TCTCGGCATTTCTAACCACC GCCACCCATAGTTTTGGCTA
COMT SNP1F1 CACCGTTTTCCGTTGTTCTT GTTGGAAAGCTAGCCAAACG
COMT SNP1F2 ACACTCCATCTTGGTTTGGC GCTACCCATGGCGTTAAAAA
COMT SNP1F3 CCAGGTTTTCAACACTGCAA GCATCTCCATTGGGAACACT
COMT SNP1F4 TGAAGATGACAATAAAGCGAAAA GTGGACAATCAGTGTGTGGC
COMT SNP1F5 ATGCAAGAAAGCCGAGTTTG GCAGGATTCCAAGGTTTCAA
COMT SNP2F1 AAGGTGATAGAAACACGCCG GTTGGAAAGCTAGCCAAACG
COMT SNP2F2 ACTCCATCTTGGTTTGGCAC GCTACCCATGGCGTTAAAAA
引物名称
Primer name		 正向引物序列
Forward primer sequence (5′-3′)		 反向引物序列
Reverse primer sequence (5′-3′)
COMT SNP2F3 GCTTAACCGGGTTGTTGATG GCATCTCCATTGGGAACACT
COMT SNP2F4 TGAAGATGACAATAAAGCGAAAA GCATCTCCATTGGGAACACT
COMT SNP2F5 ATGCAAGAAAGCCGAGTTTG TTGATTGCATCATGTTGGCT
COMT SNP3F1 AATTTCACCGTTTTCCGTTG GTTGGAAAGCTAGCCAAACG
COMT SNP3F2 ACTCCATCTTGGTTTGGCAC AAAAACTGCGGTGGAGATTG
COMT SNP3F3 GCTTAACCGGGTTGTTGATG CCATTGTCTGGAATGGCTTT
COMT SNP3F4 TGAAGATGACAATAAAGCGAAAA TGGACAATCAGTGTGTGGCT
COMT SNP3F5 ATGCAAGAAAGCCGAGTTTG CATAATCCGGGTGGAAAAGA
MYB SNP F1 TTGCAATGGATTTGTGCAAT GATTCCCAGCAAATGGAAGA
MYB SNP F2 TGCCTTGTCCTCTCACTAAGC TTGAGGCCACATGTTCTAATTG
MYB SNP F3 CCTTGCTATCATTGCCCATT TTTATGGCCCTCAAAACTGG
MYB SNP F4 CAAAAGCTCATCCTCTTCCG CAAACTGCTTGGCTCATCAA
MYB SNP F5 AAGTGTTCAAAGAGAAGCAGCA TTATAGATGGCGATGGAGGC
MYB SNP F6 AAGCAGAAGCAAAATCCCAA AAGTAGCCATGGAGGTGTGG
MYB SNP F7 GGCCATGAGTTTCAACGACT GACGGGAAGAGAAAACCCTT
MYB SNP F8 CTGCGTTTGTAACCCCAGAT GCTTCCTCTTCTGCTTCTCG
MYB SNP F9 CGACTCTTTCGGGACTCAAG TCGTCGGCGTTTAAGAAGTT
MYB SNP F10 TTACACCACCGTAACCGACA AGATGTGGATCGGATCAAGG
MYB SNP F11 AAGGAAGCCATGGAAGGACT ATGCTTCTACCAATGCCAGG
MYB SNP F12 TCGATCATCAGCAACCAAAA GCATTGAATTTTCCGTGGTT
MYB SNP F13 CCTGATCTTAAGCGTGGCTC TTTGGTGACGGAGTTGATGA
MYB SNP F14 GGCCATTGGAAAACTCAAAA TGGATGAAGAGCCTTTCACA
MYB SNP F15 ATCTTTGCCCAAAAATGCTG GCAATTACCTGCTTCCCAAA
MYB SNP F16 GAGAAGGGAAATGGCATCAA CTTTGGTGGAACTGGAAGGA
MYB SNP F17 TTCTTCAGCTCTCCAACGCT GGCTTGTGGTATTGTGAGCA
MYB SNP F18 CCCTTTCTAGCATATGGGCA AACATCCCTCCATATTCATGTGT

表4

CAPS引物名称、对应的unigene编号及内切酶名称"

序号
Code		 引物名称
Primer name		 unigene编号
unigene code		 内切酶的名称
Endonuclease name
1 4CL CAPS1-1 unigene_17597 Ssp I
2 4CL CAPS2-1 unigene_17597 Ssp I
3 4CL CAPS3-1 unigene_17597 Ssp I
4 COMT CAPS1-1 unigene_04800 Cla I
5 COMT CAPS1-3 unigene_09002 Bsi YI
6 COMT CAPS1-5 unigene_08713 Ava III
7 COMT CAPS2-1 unigene_04800 Cla I
8 COMT CAPS2-3 unigene_09002 Bsi YI
9 COMT CAPS2-5 unigene_08713 Ava III
10 COMT CAPS3-1 unigene_04800 Cla I
11 COMT CAPS3-3 unigene_09002 Bsi YI
12 COMT CAPS3-5 unigene_08713 Ava III
13 MYB CAPS1 unigene_47261 Psi I
14 MYB CAPS2 unigene_17018 Mse I
序号
Code		 引物名称
Primer name		 unigene编号
unigene code		 内切酶的名称
Endonuclease name
15 MYB CAPS3 unigene_53709 Mbo II
16 MYB CAPS5 unigene_64377 Mnl I
17 MYB CAPS6 unigene_10508 Mbo I
18 MYB CAPS7 unigene_21631 Mfe I
19 MYB CAPS8 unigene_31305 Sec I
20 MYB CAPS9 unigene_16840 Hpy99 I
21 MYB CAPS11 unigene_02399 Alu I
22 MYB CAPS12 unigene_02162 Asu I
23 MYB CAPS13 unigene_46122 Sec I
24 MYB CAPS14 unigene_10460 Tsp RI
25 MYB CAPS17 unigene_59879 Rsa I
26 MYB CAPS18 unigene_49512 Mae I

图2

COMT CAPS1-3引物扩增和酶切结果 M: marker; 1~12表示试验所用的12份黄麻种质资源的代号。"

图3

12份黄麻品种基于CAPS标记的聚类图"

[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 156-157.
Xiong H P. Breeding Science of Bast and Leaf Fiber Crops. Beijing: Chinese Agricultural Science and Technology Press, 2008. pp 156-157(in Chinese).
[2] 兰红艳, 张延辉. 麻类纤维的性能及其应用. 上海毛麻科技, 2009, ( 3):1-5.
Lan H Y, Zhang Y H. The properties and applications of bast fibers. Shanghai Hemp Technol, 2009, ( 3):1-5 (in Chinese with English abstract).
[3] 孔华, 郭安平, 郭运玲, 刘恩平, 贺立卡. 木质素生物合成及转基因调控研究进展. 热带农业工程, 2009,33(5):47-53.
Kong H, Guo A P, Guo Y L, Liu E P, He L K. Advances in study of lignin biosynthesis and its genetic manipulation. Trop Agric Engineer, 2009,33(5):47-53 (in Chinese with English abstract).
[4] Li J, Han G, Sun C, Sui N. Research advances of MYB transcription factors in plant stress resistance and breeding. Plant Signal Behav, 2019,14:1613131. doi: 10.1080/15592324.2019.16131 31.
doi: 10.1080/15592324.2019.1613131 pmid: 31084451
[5] 李利斌, 牛佳玉, 王永强, 杨宗辉, 杨桂兰, 侯丽霞, 刘淑梅, 曹齐卫, 孟昭娟. 分子标记技术在黄瓜农艺性状基因定位上的应用. 植物生理学报, 2019,55:1-13.
Li L B, Niu J Y, Wang Y Q, Yang Z H, Yang G L, Hou L X, Liu S M, Cao Q W, Meng Z J. Application of molecular markers in gene localization of cucumber (Cucumis sativus) agronomic. J Plant Physiol, 2019,55:1-13 (in Chinese with English abstract).
[6] 张明飞, 于卓, 于肖夏, 李景伟, 马艳红, 吴国芳, 王颖. 四倍体马铃薯SRAP分子遗传连锁图谱的构建. 草业学报, 2019,28(9):190-199.
Zhang M F, Yu Z, Yu X X, Li J W, Ma Y H, Wu G F, Wang Y. Construction of a genetic linkage map for tetraploid potato based on SRAP markers. Acta Pratac Sin, 2019,28(9):190-199 (in Chinese with English abstract).
[7] Yang X, Zhang Y, Cheng Y F, Chen X H. Transcriptome analysis reveals multiple signal network contributing to the Verticillium wilt resistance in eggplant. Sci Hortic, 2019,256. doi: 10.1016/j.scienta.2019.108576.
[8] Zhang Z H, Cao B L, Li N, Chen Z J, Xu K. Comparative transcriptome analysis of the regulation of ABA signaling genes in different rootstock grafted tomato seedlings under drought stress. Environ Exp Bot, 2019,166. doi: 10.1016/j.envexpbot.2019. 103814.
[9] 贾昌路, 张瑶, 朱玲, 张锐. 转录组测序技术在生物测序中的应用研究进展. 分子植物育种, 2015,13:2388-2394.
Jia C L, Zhang Y, Zhu L, Zhang R. Application progress of transcriptome sequencing technology in biological. Mol Plant Breed, 2015,13:2388-2394 (in Chinese with English abstract).
[10] 王尧龙, 黄璐琦, 袁媛, 查良平. 药用植物转录组研究进展. 中国中药杂志, 2015,11:2055-2061.
Wang Y L, Huang L Q, Yuan Y, Zha L P. Research advances on analysis of medicinal plants transcriptome. Chin J Chin Mater Med, 2015,11:2055-2061 (in Chinese with English abstract).
[11] 肖炳光, 邱杰, 曹培健, 桂毅杰, 卢秀萍, 李永平, 樊龙江. 利用基因组简约法开发烟草SNP 标记及遗传作图. 作物学报, 2014,40:397-404.
doi: 10.3724/SP.J.1006.2014.00397
Xiao B G, Qiu J, Cao P J, Gui Y J, Lu X P, Li Y P, Fan L J. Development and genetic mapping of SNP markers via genome complexity reduction in tobacco. Acta Agron Sin, 2014,40:397-404 (in Chinese with English abstract).
doi: 10.3724/SP.J.1006.2014.00397
[12] Tao A F, Huang L, Wu G F, Reza K A, 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.
doi: 10.1186/s12864-017-3712-8 pmid: 28482802
[13] Hayden M J, Tabone T, Mather D E. Development and assessment of simple PCR markers for SNP genotyping in barley. Theor Appl Genet, 2009,119:939-951.
pmid: 19597725
[14] 束永俊, 李勇, 柏锡, 才华, 纪巍, 朱延明. 基于基因重测序信息的大豆基因靶向CAPS标记开发. 作物学报, 2009,35:2015-2021.
Shu Y J, Li Y, Bai X, Cai H, Ji W, Zhu Y M. Development of soybean gene-driven functional CAPS markers based on gene re-sequencing. Acta Agron Sin, 2009,35:2015-2021 (in Chinese with English abstract).
[15] 杨广阔, 陈子强, 陈在杰, 苏军, 陈松彪, 王锋. 基于二代测序数据开发以93-11为亲本的水稻SNP-dCAPS 标记的研究实例. 分子植物育种, 2014,12:1288-1295.
Yang G K, Chen Z Q, Chen Z J, Su J, Chen S B, Wang F. Developing rice SNP-dCAPS markers based on next generation re-sequencing data of 93-11 as parental line, a case study. Mol Plant Breed, 2014,12:1288-1295 (in Chinese with English abstract).
[16] 王彩芬, 刘冬成, 马晓玲, 安永平, 张文银, 马静. 水稻耐盐基因SKC1 特异性CAPS 标记的开发与验证. 分子植物育种, 2015,13:2437-2440.
Wang C F, Liu D C, Ma X L, An Y P, Zhang W Y, Ma J. Development and validation of the specific CAPS markers of rice salt tolerant gene. Mol Plant Breed, 2015,13:2437-2440 (in Chinese with English abstract).
[17] 司文洁, 吴林楠, 郭利建, 周梦蝶, 刘香利, 马猛, 赵惠贤. 小麦粒重相关基因TaCYP78A5功能标记开发及验证. 作物学报, 2019,12:1905-1911.
Si W J, Wu L N, Guo L J, Zhou M D, Liu X L, Ma M, Zhao H X. Development and validation of the functional marker of grain weight-related gene TaCYP78A5 in wheat (Triticum aestivum L.). Acta Agron Sin, 2019,12:1905-1911 (in Chinese with English abstract).
[18] 雷天刚, 何永睿, 彭爱红, 许兰珍, 刘小丰, 姚利晓, 邹修平, 江东, 陈善春. 柑橘CAPS标记和AS-PCR引物的开发. 园艺学报, 2012,39:1027-1034.
Lei T G, He Y R, Peng A H, Xu L Z, Liu X F, Yao L X, Zou X P, Jiang D, Chen S C. Development of CAPS markers and allele-specific PCR primers in citrus. Acta Hortic Sin, 2012,39:1027-1034 (in Chinese with English abstract).
[19] 阚帅帅. 玉米主效抗丝黑穗病候选基因预测及dCAPS标记开发. 东北农业大学硕士学位论文, 黑龙江哈尔滨, 2012.
Kan S S. Major Resistance Candidate Gene Prediction and dCAPS Markers Development of Head Smut in Maize. MS Thesis of Northeast Agriculture University, Harbin, Heilongjiang, China, 2012 (in Chinese with English abstract).
[20] 朱文文, 徐建飞, 李广存, 段绍光, 刘杰, 卞春松, 庞万福, Walter D J, 金黎平. 马铃薯块茎形状基因CAPS 标记的开发与验证. 作物学报, 2015,41:1529-1536.
Zhu W W, Xu J F, Li G C, Duan S G, Liu J, Bian C S, Pang W F, Walter D J, Jin L P. Development and verification of a CAPS marker linked to tuber shape gene in potato. Acta Agron Sin, 2015,41:1529-1536 (in Chinese with English abstract).
[21] 尚小红, 周慧文, 严华兵, 肖亮, 陈新. 木薯块根肉质颜色基因CAPS标记的开发与验证. 分子植物育种, 2018,16:873-879.
Shang X H, Zhou H W, Yan H B, Xiao L, Chen X. Development and verification of a CAPS marker for color gene in cassava tuber. Mol Plant Breed, 2018,16:873-879 (in Chinese with English abstract).
[22] 陶爱芬, 徐建堂, 祁建民, 吴建梅, 粟建光, 林培清, 李爱青, 李木兰, 方平平, 林荔辉. SRAP和ISSR及两种方法结合在分析黄麻属起源与演化上的比较. 作物学报, 2011,37:2277-2284.
Tao A F, Xu J T, Qi J M, Wu J M, Su J G, Lin P Q, Li A Q, Li M L, Fang P P, Lin L H. Method comparison of using SRAP and ISSR and combination of both in origin and evolution of jute. Acta Agron Sin, 2011,37:2277-2284 (in Chinese with English abstract).
[23] 陶爱芬, 祁建民, 李木兰, 方平平, 林荔辉, 徐建堂. SRAP 结合ISSR 方法分析黄麻属的起源与演化. 中国农业科学, 2012,45:16-25.
Tao A F, Qi J M, Li M L, Fang P P, Lin L H, Xu J T. Origin and evolution of jute analysed by SRAP and ISSR methods. Sci Agric Sin, 2012,45:16-25 (in Chinese with English abstract).
[24] 巫桂芬, 徐鲜均, 徐建堂, 陶爱芬, 张立武, 魏丽真, 潘漠, 方平平, 林荔辉, 祁建民. 利用SRAP、ISSR、SSR标记绘制黄麻基因源分子指纹图谱. 作物学报, 2015,41:367-377.
Wu G F, Xu X J, Xu J T, Tao A F, Zhang L W, Wei L Z, Pan M, Fang P P, Lin L H, Qi J M. Construction of molecular fingerprinting map in gene pool of jute with SRAP, ISSR, and SSR markers. Acta Agron Sin, 2015,41:367-377 (in Chinese with English abstract).
[25] Kundu A, Chakraborty A, Mandal N A, 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, 2015,35:19.
[26] Topdar N, Kundu A, Sinha M K, Sarkar D, Das M, Banerjee S, Kar C S, Satya P, Balyan H S, Mahapatra B S. A complete genetic linkage map and QTL analyses for bast fibre quality traits, yield and yield components in jute (Corchorus olitorius L.). Cytol Genet, 2013,47:129-137.
[27] 张立武, 袁民航, 何雄威, 刘星, 方平平, 林荔辉, 陶爱芬, 徐建堂, 祁建民. GenBank数据库中黄麻EST-SSR标记的开发及其通用性评价. 作物学报, 2014,40:1213-1219.
Zhang L W, Yuan M H, He X W, Liu X, Fang P P, Lin L H, Tao A F, Xu J T, Qi J M. Development and universality evaluation of EST-SSR markers from GenBank in jute. Acta Agron Sin, 2014,40:1213-1219 (in Chinese with English abstract).
[28] Das M, Banerjee S, Dhariwal R, Vyas S, Mir R R, Topdar N, Kundu A, Khurana J P, Tyagi A K, Sarkar D, Sinha M K, Balyan H S, Gupta P K. Development of SSR markers and construction of a linkage map in jute. J Genet, 2012,91:21-31.
pmid: 22546823
[29] 陶爱芬, 陈婉婷, 祁建民, 徐建堂, 林荔辉, 林培清, 张立武, 方平平. 基于转录组测序的黄麻SSR分子标记开发与初步验证. 中国农业大学学报, 2018,23(6) : 24-33.
Tao A F, Chen W T, Qi J M, Xu J T, Lin L H, Lin P Q, Zhang L W, Fang P P. Development and identification of SSR molecular markers based on transcriptome sequences of jute (Corchorus capsularis L.). J China Agric Univ, 2018,23(6):24-33 (in Chinese with English abstract).
[30] 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, 2015,35:119.
[31] 陶爱芬, 谢丽丽, 祁建民, 方平平, 林荔辉, 徐建堂, 张立武, 林培清. 与黄麻炭疽病抗性相关的SSR分子标记筛选及新型SNP标记开发. 福建农林大学学报(自然科学版), 2017,46(1):27-33.
Tao A F, Xie L L, Qi J M, Fang P P, Lin L H, Xu J T, Zhang L W, Lin P Q. Screening of SSR markers and developing of newly SNP markers associated with anthracnose resistance in Corchorus capsularis. J Fujian Agric For Univ(Nat Sci Edn), 2017,46(1):27-33 (in Chinese with English abstract).
[32] Zhao Y, Wang K, Wang W L, Yin T T, Dong W Q, Xu C J. A high-throughput SNP discovery strategy for RNA-seq data. BMC Genomics, 2019,20:160. doi: 10.1186/s12864-019-5533-4.
pmid: 30813897
[33] Nei M, Li W H. Mathematical model for studying genetic variation in terms of restriction endonucleases. Proc Natl Acad Sci USA, 1979,76:5269-5273.
doi: 10.1073/pnas.76.10.5269 pmid: 291943
[34] 王振玉, 李威, 周晓箭, 裴小雨, 刘艳改, 周克海, 张文生, 孟清芹, 王海风, 葛勇, 李莹, 刘俊芳, 马雄风, 杨代刚. 棉花单核苷酸多态性标记研究进展. 棉花学报, 2016,28:399-406.
doi: 10.11963/issn.1002-7807.201604012
Wang Z Y, Li W, Zhou X J, Pei X Y, Liu Y G, Zhou K H, Zhang W S, Meng Q Q, Wang H F, Ge Y, Li Y, Liu J F, Ma X F, Yang D G. Review of single nucleotide polymorphism markers in cotton. Cotton Sci, 2016,28:399-406 (in Chinese with English abstract).
doi: 10.11963/issn.1002-7807.201604012
[35] 郭海洋. 基于HRM技术的水稻全基因组SNP标记开发及其初步应用. 华南农业大学硕士学位论文, 广东广州, 2016.
Guo H Y. Development of Rice SNP Marker Based on HRM Technology and Its Application in Gene Location. MS Thesis of South China Agricultural University, Guangzhou, Guangdong, China, 2016 (in Chinese with English abstract).
[36] Ching A, Caldwell K S, Jung M, Dolan M, Smith O S, Tingey S, Morgante M, Rafalskiet A J. SNP frequency, haplotype structure and linkage disequilibrium in elite maize inbred lines. BMC Genet, 2002,3:19.
doi: 10.1186/1471-2156-3-19 pmid: 12366868
[37] Lam H M, Xu X, Liu X. Resequencing of 31 wild and cultivated soybean genomes identifies patterns of genetic diversity and selection. Nat Genet, 2010,42:1053-1059.
doi: 10.1038/ng.715 pmid: 21076406
[38] 张成才. 茶树SNP标记的开发与应用. 中国农业科学院硕士学位论文, 北京, 2012.
Zhang C C. The Development and Applications of SNP Markers in Tea Plants (Camellia sinensis). MS Thesis of Chinese Academy of Agricultural Sciences, Beijing, China, 2012 (in Chinese with English abstract).
[39] Lopez C, Piegu B, Cooke R, Delseny M, Tohme J, Verdier V. Using cDNA and genomic sequences as tools to develop SNP strategies in cassava (Manihot esculenta Crantz). Theor Appl Genet, 2005,110:425-431.
doi: 10.1007/s00122-004-1833-3 pmid: 15650816
[40] Alencar S, Silva J O, Togawa R. SNP discovery in apple cultivars using next generation sequencing. BMC Proce, 2011,5:42.
[41] Thakur S, Singh P K, Rathour R, Variar M, Prashanthi S K, Gopalakrishnan S, Singh A K, Singh U D, Chand D, Singh N K, Sharma T R. Genotyping and development of single-nucleotide polymorphism (SNP) markers associated with blast resistance genes in rice using Golden Gate assay. Mol Breed, 2014,34:1449-1463.
doi: 10.1007/s11032-014-0129-9
[42] 潜宗伟, 陈海丽, 崔彦玲. 菠菜转录组SSR位点分析及其分子标记的开发. 农业生物技术学报, 2016,24:1688-1697.
Qian Z W, Chen H L, Cui Y L. Analysis of the SSR Loci and development of molecular markers in Spinacia oleracea transcriptome. Chin J Agric Biotechol, 2016,24:1688-1697 (in Chinese with English abstract).
[1] 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.
[2] 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.
[3] 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.
[4] 李玲红, 张哲, 陈永明, 尤明山, 倪中福, 邢界文. 普通小麦颖壳蜡质缺失突变体glossy1的转录组分析[J]. 作物学报, 2022, 48(1): 48-62.
[5] 汪颖, 高芳, 刘兆新, 赵继浩, 赖华江, 潘小怡, 毕晨, 李向东, 杨东清. 利用WGCNA鉴定花生主茎生长基因共表达模块[J]. 作物学报, 2021, 47(9): 1639-1653.
[6] 曹亮, 杜昕, 于高波, 金喜军, 张明聪, 任春元, 王孟雪, 张玉先. 外源褪黑素对干旱胁迫下绥农26大豆鼓粒期叶片碳氮代谢调控的途径分析[J]. 作物学报, 2021, 47(9): 1779-1790.
[7] 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.
[8] 黄文功, 姜卫东, 姚玉波, 宋喜霞, 刘岩, 陈思, 赵东升, 吴广文, 袁红梅, 任传英, 孙中义, 吴建忠, 康庆华. 亚麻响应低钾胁迫转录谱分析[J]. 作物学报, 2021, 47(6): 1070-1081.
[9] 马贵芳, 满夏夏, 张益娟, 高豪, 孙朝霞, 李红英, 韩渊怀, 侯思宇. 谷子穗发育期转录组与叶酸代谢谱联合分析[J]. 作物学报, 2021, 47(5): 837-846.
[10] 李鹏程, 毕真真, 孙超, 秦天元, 梁文君, 王一好, 许德蓉, 刘玉汇, 张俊莲, 白江平. DNA甲基化参与调控马铃薯响应干旱胁迫的关键基因挖掘[J]. 作物学报, 2021, 47(4): 599-612.
[11] 王瑞莉, 王刘艳, 雷维, 吴家怡, 史红松, 李晨阳, 唐章林, 李加纳, 周清元, 崔翠. 结合RNA-seq分析和QTL定位筛选甘蓝型油菜萌发期与铝毒胁迫相关的候选基因[J]. 作物学报, 2021, 47(12): 2407-2422.
[12] 张欢, 罗怀勇, 李威涛, 郭建斌, 陈伟刚, 周小静, 黄莉, 刘念, 晏立英, 雷永, 廖伯寿, 姜慧芳. 花生全基因组抗病基因鉴定及其对青枯菌侵染的响应分析[J]. 作物学报, 2021, 47(12): 2314-2323.
[13] 曾健, 徐先超, 徐昱斐, 王秀成, 于海燕, 冯贝贝, 邢光南. 利用动态转录组学挖掘大豆百粒重候选基因[J]. 作物学报, 2021, 47(11): 2121-2133.
[14] 郭艳春, 张力岚, 陈思远, 祁建民, 方平平, 陶爱芬, 张列梅, 张立武. 黄麻应用核心种质的DNA分子身份证构建[J]. 作物学报, 2021, 47(1): 80-93.
[15] 秦天元, 孙超, 毕真真, 梁文君, 李鹏程, 张俊莲, 白江平. 基于WGCNA的马铃薯根系抗旱相关共表达模块鉴定和核心基因发掘[J]. 作物学报, 2020, 46(7): 1033-1051.
Viewed
Full text


Abstract

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