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Application of SV markers developed from Dongxiang common wild rice in analysis of cultivated rice

Published online by Cambridge University Press:  08 May 2019

Fantao Zhang*
Affiliation:
College of Life Sciences, Jiangxi Normal University, Nanchang 330022, People's Republic of China
Yuan Luo
Affiliation:
College of Life Sciences, Jiangxi Normal University, Nanchang 330022, People's Republic of China
Bin Ai
Affiliation:
College of Life Sciences, Jiangxi Normal University, Nanchang 330022, People's Republic of China
Yong Chen
Affiliation:
College of Life Sciences, Jiangxi Normal University, Nanchang 330022, People's Republic of China
Weidong Qi
Affiliation:
College of Life Sciences, Jiangxi Normal University, Nanchang 330022, People's Republic of China
Jiankun Xie*
Affiliation:
College of Life Sciences, Jiangxi Normal University, Nanchang 330022, People's Republic of China
*
*Corresponding author. E-mail: zhang84004@163.com and xiejiankun11@163.com
*Corresponding author. E-mail: zhang84004@163.com and xiejiankun11@163.com

Abstract

Dongxiang common wild rice (Oryza rufipogon Griff., DXWR) is an important genetic resource for the improvement of cultivated rice. For the past three decades, great achievements have been made in the field of molecular marker development. Although structural variations (SVs) had been studied between DXWR and Nipponbare (Oryza sativa L. ssp. japonica), the development and application of SV markers in DXWR has not been reported. In this study, based on the genome-wide SV loci, we developed and synthesized a total of 195 SV markers that were evenly distributed across the 12 rice chromosomes. Then, these markers were tested for their stabilities and polymorphisms. Of these 195 markers, 147 (75.4%) were successfully amplified and displayed abundant polymorphisms between DXWR and Nipponbare. Meanwhile, through the genotyping of 20 rice varieties from 13 countries and areas, we concluded that these SV markers have a wide application prospect in the analysis of cultivated rice. Therefore, these molecular markers greatly enrich the number of markers available for DXWR, which will facilitate genomic research and molecular breeding for this important and endangered germplasm resource.

Type
Short Communication
Copyright
Copyright © NIAB 2019 

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References

Abdel-Latif, A and Osman, G (2017) Comparison of three genomic DNA extraction methods to obtain high DNA quality from maize. Plant Methods 13: 1.Google Scholar
Davey, JW, Hohenlohe, PA, Etter, PD, Boone, JQ, Catchen, JM and Blaxter, ML (2011) Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Nature Reviews Genetics 12: 499510.Google Scholar
Eren, AM, Vineis, JH, Morrison, HG and Sogin, ML (2013) A filtering method to generate high quality short reads using illumina paired-end technology. PLoS One 8: e66643.Google Scholar
Hayashi, K, Hashimoto, N, Daigen, M and Ashikawa, I (2004) Development of PCR-based SNP markers for rice blast resistance genes at the Piz locus. Theoretical and Applied Genetics 108: 12121220.Google Scholar
Kaur, S, Panesar, PS, Bera, MB and Kaur, V (2015) Simple sequence repeat markers in genetic divergence and marker-assisted selection of rice cultivars: a review. Critical Reviews in Food Science and Nutrition 55: 4149.Google Scholar
Li, YR, Zheng, HC, Luo, RB, Wu, HL, Zhu, HM, Li, RQ, Cao, HZ, Wu, BX, Huang, SJ, Shao, HJ, Ma, HZ, Zhang, F, Feng, SJ, Zhang, W, Du, HL, Tian, G, Li, JX, Zhang, XQ, Li, SG, Bolund, L, Kristiansen, K, de Smith, AJ, Blakemore, AI, Coin, LJ, Yang, HM, Wang, J and Wang, J (2011) Structural variation in two human genomes mapped at single-nucleotide resolution by whole genome de novo assembly. Nature Biotechnology 29: 723730.Google Scholar
Mao, DH, Yu, L, Chen, DZ, Li, LY, Zhu, YX, Xiao, YQ, Zhang, DC and Chen, CY (2015) Multiple cold resistance loci confer the high cold tolerance adaptation of Dongxiang wild rice (Oryza rufipogon Griff.) to its high-latitude habitat. Theoretical and Applied Genetics 128: 13591371.Google Scholar
Ren, Y, Zhao, H, Kou, QH, Jiang, J, Guo, SG, Zhang, HY, Hou, WJ, Zou, XH, Sun, HH, Gong, GY, Levi, A and Xu, Y (2012) A high resolution genetic map anchoring scaffolds of the sequenced watermelon genome. PLoS ONE 7: e29453.Google Scholar
Untergasser, A, Cutcutache, I, Koressaar, T, Ye, J, Faircloth, BC, Remm, M and Rozen, SG (2012) Primer3 -- new capabilities and interfaces. Nucleic Acids Research 40: e115.Google Scholar
Wang, W, Chen, BZ, Zhang, L, Yan, JJ, Lu, YP, Zhang, XY, Jiang, YJ, Wu, TJ, van Peer, AF, Li, SJ and Xie, BG (2015) Structural variation (SV) markers in the Basidiomycete Volvariella volvacea and their application in the construction of a genetic map. International Journal of Molecular Sciences 16: 1666916682.Google Scholar
Xu, X, Liu, X, Ge, S, Jensen, JD, Hu, FY, Li, X, Dong, Y, Gutenkunst, RN, Fang, L, Huang, L, Li, JX, He, WM, Zhang, GJ, Zheng, XM, Zhang, FM, Li, YR, Yu, C, Kristiansen, K, Zhang, XQ, Wang, J, Wright, M, McCouch, S, Nielsen, R, Wang, J and Wang, W (2011) Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes. Nature Biotechnology 30: 105111.Google Scholar
Yadav, MK, Aravindan, S, Ngangkham, U, Shubudhi, HN, Bag, MK, Adak, T, Munda, S, Samantaray, S and Jena, M (2017) Use of molecular markers in identification and characterization of resistance to rice blast in India. PLoS ONE 12: e0176236.Google Scholar
Zhang, X, Zhou, S, Fu, Y, Su, Z, Wang, X and Sun, C (2006) Identification of a drought tolerant introgression line derived from Dongxiang common wild rice (Oryza rufipogon Griff.). Plant Molecular Biology 62: 247259.Google Scholar
Zhang, FT, Zhang, LX, Cui, FL, Luo, XD, Zhou, Y and Xie, JK (2015) Identification of novel insertion-deletion markers for Dongxiang wild rice (Oryza rufipogon griff.) using highthroughput sequencing technology. Journal of Genetics 94: e51e55.Google Scholar
Zhang, FT, Xu, T, Mao, LY, Yan, SY, Chen, XW, Wu, ZF, Chen, R, Luo, XD, Xie, JK and Gao, S (2016) Genome-wide analysis of Dongxiang wild rice (Oryza rufipogon Griff.) to investigate lost/acquired genes during rice domestication. BMC Plant Biology 16: 103.Google Scholar
Zhang, FT, Zhou, Y, Zhang, M, Luo, XD and Xie, JK (2017) Effects of drought stress on global gene expression profile in leaf and root samples of Dongxiang wild rice (Oryza rufipogon). Bioscience Reports 37: 3.Google Scholar
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