Welcome to Acta Agronomica Sinica，

Acta Agronomica Sinica ›› 2019, Vol. 45 ›› Issue (2): 316-321.doi: 10.3724/SP.J.1006.2019.82037

• RESEARCH NOTES • Previous Articles    

Development of molecular markers polymorphic between Dongxiang wild rice and Geng rice cultivar ‘Nipponbare’

Xiao-Ding MA1,Jiang-Hong TANG2,Jia-Ni ZHANG2,Di CUI1,Hui LI3,Mao-Mao LI3,*(),Long-Zhi HAN1,*()   

  1. 1 National Key Facility for Crop Gene Resources and Genetic Improvement / Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
    2 Chongqing Normal University, Chongqing 401331, China
    3 Rice Research Institute, Jiangxi Academy of Agricultural Sciences, Nanchang 330200, Jiangxi, China
  • Received:2018-07-09 Accepted:2018-10-08 Online:2019-02-12 Published:2018-11-06
  • Contact: Mao-Mao LI,Long-Zhi HAN E-mail:lmm3056@163.com;hanlongzhi@caas.cn
  • Supported by:
    This study was supported by the National Key Research and Development Program of China(2016YFD0100101);This study was supported by the National Key Research and Development Program of China(2016YFD0100301);the National Natural Science Foundation of China(31501287);the National Natural Science Foundation of China(31671664);the National Key Technology Support Program of China(2015BAD01B01-1);the Agricultural Science and Technology Innovation Program of CAAS;the National Crop Germplasm Conservation Project(2017NWB036-01);the National Crop Germplasm Conservation Project(2017NWB036-12-2);and the National Crop Germplasm Resources Platform Project(NICGR2017-001)

RichHTML343

17

PDF

345

Abstract:

Dongxiang wild rice is a type of common wild rice (Oryza rufipogon) that has the northernmost natural distribution of any wild rice species. The genome of Dongxiang wild rice differs from that of modern cultivated rice varieties (Oryza sativa). At present, a set of molecular markers that covers the entire genome of Dongxiang wild rice is lacking. In this study, we used Dongxiang wild rice and the Geng rice variety “Nipponbare” as research materials. By screening the existing collection of 1017 SSR and InDel markers and the 217 InDel markers which were designed using Dongxiang wild rice genome resequencing information, we obtained a set of 203 markers polymorphic between Dongxiang wild rice and ‘Nipponbare’, which were relatively uniformly distributed on the 12 rice chromosomes, and basically covered the entire genome, with an average inter-locus distance of 1.9 Mb. Through the genotyping of five Xian and five Geng varieties, we concluded that those 203 polymorphic molecular markers have a high application value in genotype analysis of Dongxiang wild rice and Geng rice offspring population. These results provide a powerful tool for exploring beneficial genes from Dongxiang wild rice as well as marker-assisted breeding and selection.

Key words: InDel marker, genome re-sequencing, Geng rice

Fig. 1

Screening of polymorphic molecular markers 1: Dongxiang wild rice; 2: Nipponbare; 3: artificial F1 hybrid between Dongxiang wild rice and Nipponbare; M: DNA size marker."

Table 1

Distribution of polymorphic molecular marker loci on 12 rice chromosomes"

染色体
Chromosome		 染色体长度
Chromosome length (kb)		 标记数量
Number of marker		 平均标记间隔
Mean interval
(kb)
1 43270 23 1881
2 35937 22 1633
3 36413 30 1213
4 35502 17 2088
5 29958 16 1872
6 31248 18 1736
7 29697 16 1856
8 28443 13 2187
9 23012 14 1643
10 23207 9 2578
11 29021 13 2232
12 27531 12 2294

Fig. 2

Distribution of polymorphic molecular marker loci on rice chromosomes The numbers to the left of each chromosome indicate the physical locations of the marker loci in Mb."

Fig. 3

Genotyping of Xian and Geng cultivars by polymorphic molecular markers 1: Dongxiang wild rice; 2: Nipponbare; 3: Liaoyan 241; 4: Songgeng 8; 5: Jigeng 88; 6: Huaidao 9; 7: Hexi 6; 8: Huanghuazhan; 9: Baiyusimiao; 10: Yangdao 6; 11: Xiangwanxian 12; 12: Ezhong 5."

Table 2

Consensus analysis of genotype identification of Xian and Geng cultivars using the polymorphic molecular markers"

亚种
Subspecies		 鉴定总数
Number of
identification		 东乡野生稻基因型数目
Number of Dongxiang wild rice genotype		 日本晴基因型数目
Number of Nipponbare genotype		 杂合基因型数目
Number of heterozygous genotype		 其他基因型数目
Number of others
genotype
粳 295 (5×59) 34 (11.6%) 250 (84.7%) 6 (2.0%) 5 (1.7%)
籼 295 (5×59) 218 (73.9%) 40 (13.5%) 5 (1.7%) 32 (10.9%)
[1] 邬柏梁, 何国成, 白国章, 吴蔼如 . 我省东乡县一带发现野生稻. 江西农业科技, 1979, ( 2):6-7.
Wu B L, He G C, Bai G Z, Wu A R . Wild rice found in Dongxiang County in our province. Jiangxi Agric Sci & Technol, 1979, ( 2):6-7 (in Chinese with English abstract).
[2] 潘熙淦, 饶宪章 . 东乡野生稻观察及特征鉴定报告. 江西农业科技, 1982, ( 7):5-9.
Pan X G, Rao X Z . Report of Dongxiang wild rice observation and characterization. Jiangxi Agric Sci & Technol, 1982, ( 7):5-9 (in Chinese with English abstract).
[3] 黄依南, 黄国勤 . 东乡野生稻的发现、价值与保护. 农业资源与环境学报, 2012,29:13-15.
doi: 10.3969/j.issn.1005-4944.2012.01.004
Huang Y N, Huang G Q . The discovery, value and protection of Dongxiang wild rice. J Agric Resour Environ, 2012,29:13-15 (in Chinese with English abstract).
doi: 10.3969/j.issn.1005-4944.2012.01.004
[4] 刘丹, 孙玉友, 魏才强, 解忠, 李洪亮, 张巍巍, 程杜娟, 孙国宏, 徐德海 . InDel分子标记及其在水稻研究中的应用. 种子, 2017, ( 9):47-52.
doi: 10.16590/j.cnki.1001-4705.2017.09.047
Liu D, Sun Y Y, Wei C Q, Xie Z, Li H L, Zhang W W, Cheng D J, Sun G H, Xu D H . InDel molecular marker and its application in rice (Oryza sativa) research. Seed, 2017, ( 9):47-52 (in Chinese with English abstract).
doi: 10.16590/j.cnki.1001-4705.2017.09.047
[5] Shen Y J, Jiang H, Jin J P, Zhang Z B, Xi B, He Y Y, Wang G, Qian L L, Li X, Yu Q B, Liu H J, Chen D H, Gao J H, Huang H, Shi T L, Yang Z N . Development of genome-wide DNA polymorphism database for map-based cloning of rice genes. Plant Physiol, 2004,135:1198-1205.
doi: 10.1104/pp.103.038463 pmid: 15266053
[6] 冯芳君, 罗利军, 李荧, 周立国, 徐小艳, 吴金, 陈宏伟, 陈亮, 梅捍卫 . 水稻InDel和SSR标记多态性的比较分析. 分子植物育种, 2005,3:725-730.
doi: 10.3969/j.issn.1672-416X.2005.05.024
Feng F J, Luo L J, Li Y, Zhou L G, Xu X Y, Wu J, Chen H W, Chen L, Mei H W . Comparative analysis of polymorphism of InDel and SSR markers in rice. Mol Plant Breed, 2005,3:725-730 (in Chinese with English abstract).
doi: 10.3969/j.issn.1672-416X.2005.05.024
[7] 初志战, 郭海滨, 曾栋昌, 刘耀光 . 籼粳稻基因组295个InDel 标记的开发. 作物学报, 2016,42:932-941.
doi: 10.3724/SP.J.1006.2016.00932
Chu Z Z, Guo H B, Zeng D C, Liu Y G . Development of 295 InDel markers for indica and japonica rice. Acta Agron Sin, 2016, 42:932-941 (in Chinese with English abstract).
doi: 10.3724/SP.J.1006.2016.00932
[8] Taillon-Miller P, Gu Z J, Li Q, Hillier L, Kwok P Y . Overlapping genomic sequences: a treasure trove of single nucleotide polymorphisms. Genome Res, 1998,8:748-754.
doi: 10.1051/gse:19980406 pmid: 9685323
[9] 唐立群, 肖层林, 王伟平 . SNP分子标记的研究及其应用进展. 中国农学通报, 2012,28(12):154-158.
doi: 10.3969/j.issn.1000-6850.2012.12.028
Tang L Q, Xiao C L, Wang W P . Research and application progress of SNP markers. Chin Agric Sci Bull, 2012,28(12):154-158 (in Chinese with English abstract).
doi: 10.3969/j.issn.1000-6850.2012.12.028
[10] Yu H H, Xie W B, Wang J, Xing Y Z, Xu C G, Li X H, Xiao J H, Zhang Q F . Gains in QTL detection using an ultra-high density SNP map based on population sequencing relative to traditional RFLP/SSR markers. PLoS One, 2011,6:e17595.
doi: 10.1371/journal.pone.0017595
[11] Abyzov A, Urban A E, Snyder M, Gerstein M . CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing. Genome Res, 2011,21:974-984.
doi: 10.1101/gr.114876.110 pmid: 21324876
[12] 李德军 . 江西东乡普通野生稻渗入系的构建及高产QTL定位. 中国农业大学博士学位论文,北京, 2003.
doi: 10.7666/d.y558395
Li D J . Development of Introgression Lines of Common Wild Rice (O. rufipogon Griff.) from Dongxiang in Jiangxi Province and Mapping QTLs for Improving Yield. PhD Dissertation of China Agricultural University, Beijing,China, 2003 (in Chinese with English abstract).
doi: 10.7666/d.y558395
[13] Li H, Durbin R . Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics, 2009,25:1754-1760.
doi: 10.1093/bioinformatics/btp324 pmid: 19451168
[14] Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R . The Sequence Alignment/ Map format and SAMtools. Bioinformatics, 2009,25:2078-2079.
doi: 10.1046/j.1440-1665.1999.0178e.x pmid: 19505943
[15] Wang K, Li M, Hakonarson H . ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucl Acids Res, 2010,38:e164.
doi: 10.1093/nar/gkq603
[16] Murray M G, Thompson W F . Rapid isolation of high molecular weight plant DNA. Nucl Acids Res, 1980,8:4321-4325.
doi: 10.1093/nar/8.19.4321
[17] Bassam B J, Caetano-Anollés G, Gresshoff P M . Fast and sensitive silver staining of DNA in polyacrylamide gels. Anal Biochem, 1991,196:80-83.
doi: 10.1016/0003-2697(91)90120-I pmid: 1716076
[1] WANG Rui, CHEN Xue, GUO Qing-Qing, ZHOU Rong, CHEN Lei, LI Jia-Na. Development of linkage InDel markers of the white petal gene based on whole-genome re-sequencing data in Brassica napus L. [J]. Acta Agronomica Sinica, 2022, 48(3): 759-769.
[2] XU Ting-Ting, WANG Qiao-Ling, ZOU Shu-Qiong, DI Jia-Chun, YANG Xin, ZHU Yin, ZHAO Han, YAN Wei. Development and application of InDel markers based on high throughput sequencing in barley [J]. Acta Agronomica Sinica, 2020, 46(9): 1340-1350.
[3] Mi WU,Nian WANG,Chao SHEN,Cong HUANG,Tian-Wang WEN,Zhong-Xu LIN. Development and evaluation of InDel markers in cotton based on whole-genome re-sequencing data [J]. Acta Agronomica Sinica, 2019, 45(2): 196-203.
[4] Qing-Ying ZHAO, Rui-Juan ZHANG, Rui-Liang WANG, Jian-Hua GAO, Yuan-Huai HAN, Zhi-Rong YANG, Xing-Chun WANG. Genome-wide Identification of Molecular Markers Based on Genomic Re-sequencing of Foxtail Millet Elite Cultivar Jingu 21 [J]. Acta Agronomica Sinica, 2018, 44(05): 686-696.
[5] CHU Zhi-Zhan,GUO Hai-Bin,ZENG Dong-Chang,LIU Yao-Guang. Development of 295 InDel Markers for Indica andJapanicaRice [J]. Acta Agron Sin, 2016, 42(06): 932-941.
[6] NAN Hai-Yang,LI Ying-Hui,CHANG Ru-Zhen,QIU Li-Juan. Development and Identification of InDel Marker Based on rhg1 Gene for Resistance to Soybean Cyst Nematode(Heterodera glycines Ichinohe) [J]. Acta Agron Sin, 2009, 35(7): 1236-1243.
Viewed
Full text


Abstract

Cited
  Shared   
  Discussed   
No Suggested Reading articles found!
Add: No.12 Zhongguancun South Street, Beijing 100081,China Email:xbzw@chinajournal.net.cn
Supported by Beijing Magtech Co.Ltd