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Development of a set of InDel markers for characterizing three japonica rice (Oryza sativa L.) varieties

Published online by Cambridge University Press:  06 March 2023

Hongmei Wang Open the ORCID record for Hongmei Wang [Opens in a new window] ,
Yue Zhu ,
Chujian Xiao ,
Jianming Yuan ,
Yaoguang Liu  and
Qunyu Zhang
Hongmei Wang
Affiliation:
State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
Yue Zhu
Affiliation:
State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
Chujian Xiao
Affiliation:
State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
Jianming Yuan
Affiliation:
State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
Yaoguang Liu
Affiliation:
State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
Qunyu Zhang*
Affiliation:
State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China Main Campus Teaching & Research Base, South China Agricultural University, Guangzhou, 510642, China
*
Author for correspondence: Qunyu Zhang, E-mail: zqy@scau.edu.cn
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Abstract

The use of molecular markers is one of the most sensitive, powerful technologies for genetic purity assessment of seed lots. In this study, we aimed to develop a set of insertion and deletion (InDel) markers, through bioinformatics approaches, that may effectively distinguish three representative japonica rice (Oryza sativa L.) varieties, Nipponbare, Taichung 65 and Zhonghua11. The published whole-genome sequences of these varieties were aligned using BWA-MEM, followed by manual inspection for InDels of more than ten base pairs in size with the tview function of SAMtools. A set of ten InDel markers were thus identified and then validated by PCR in the three japonica rice varieties and their intercross F1 hybrids. Results showed that the InDel markers developed in this study could reliably distinguish these three japonica rice varieties. These molecular markers together with the detection method developed here can be applied to DNA-based genetic purity evaluation in rice breeding.

Keywords

Genetic purity testingInDelmolecular markerrice
Type
Short Communication
Information
Plant Genetic Resources , Volume 20 , Issue 4 , August 2022 , pp. 304 - 307
Copyright
Copyright © The Author(s), 2023. Published by Cambridge University Press on behalf of NIAB

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References

Adedze, YMN, Lu, X, Xia, YC, Sun, QY, Nchongboh, CG, Alam, MA, Liu, MH, Yang, X, Zhang, WT, Deng, ZJ, Li, WH and Si, LT (2021) Agarose-resolvable InDel markers based on whole genome re-sequencing in cucumber. Scientific Reports 11, 3872–3884.CrossRefGoogle ScholarPubMed
Arai-Kichise, Y, Shiwa, Y, Nagasaki, H, Ebana, K, Yoshikawa, H, Yano, M and Wakasa, K (2011) Discovery of genome-wide DNA polymorphisms in a landrace cultivar of japonica rice by whole-genome sequencing. Plant and Cell Physiology 52, 274–282.CrossRefGoogle Scholar
Bassam, BJ, Caetano-Anollés, G and Gresshoff, PM (1991) Fast and sensitive silver staining of DNA in polyacrylamide gels. Analytical Biochemistry 196, 80–83.CrossRefGoogle ScholarPubMed
Baveja, A, Muthusamy, V, Panda, KK, Zunjare, RU, Das, AK, Chhabra, R, Mishra, SJ, Mehta, BK, Saha, S and Hossain, F (2021) Development of multinutrient-rich biofortified sweet corn hybrids through genomics-assisted selection of shrunken2, opaque2, lcyE and crtRB1 genes. Journal of Applied Genetics 62, 419–429.CrossRefGoogle ScholarPubMed
Cheon, KS, Jeong, YM, Oh, H, Oh, J, Kang, DY, Kim, N, Lee, E, Baek, J, Kim, SL and Choi, I (2020) Development of 454 new Kompetitive Allele-Specific PCR (KASP) markers for temperate japonica rice varieties. Plants 9, 1531–1542.CrossRefGoogle ScholarPubMed
Gull, S, Haider, Z, Gu, H, Raza Khan, RA, Miao, J, Tan, WC, Uddin, S, Ahmad, I and Liang, GH (2019) InDel marker based estimation of multi-gene allele contribution and genetic variations for grain size and weight in rice (Oryza sativa L.). International Journal of Molecular Sciences 20, 4824–4850.CrossRefGoogle ScholarPubMed
Hechanova, SL, Bhattarai, K, Simon, EV, Clave, G, Karunarathne, P, Ahn, EK, Li, CP, Lee, JS, Kohli, A, Hamilton, NRS, Hernandez, JE, Gregorio, GB, Jena, KK, An, G and Kim, SR (2021) Development of a genome-wide InDel marker set for allele discrimination between rice (Oryza sativa L.) and the other seven AA-genome Oryza species. Scientific Reports 11, 8962–8962.CrossRefGoogle Scholar
Li, H (2013) Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. p arXiv:1303.3997. Available at https://ui.adsabs.harvard.edu/abs/2013arXiv1303.3997L (Last accessed 1 March 2013).Google Scholar
Li, XK, Wu, L, Wang, JH, Sun, J, Xia, XH, Geng, X, Wang, XH, Xu, ZJ and Xu, Q (2018) Genome sequencing of rice subspecies and genetic analysis of recombinant lines reveals regional yield-and quality-associated loci. BMC Biology 16, 102–114.CrossRefGoogle ScholarPubMed
Liu, J, Li, JW, Qu, JT and Yan, SY (2015) Development of genome-wide insertion and deletion polymorphism markers from next-generation sequencing data in rice. Rice (N Y) 8, 63.Google ScholarPubMed
Liu, WH, Zeng, S, Wu, GJ, Li, H and Chen, FF (2021) Rice seed purity identification technology using hyperspectral image with LASSO logistic regression model. Sensors (Basel, Switzerland) 21, 4384–4403.CrossRefGoogle ScholarPubMed
Mao, D, Xin, Y, Tan, Y, Hu, X, Bai, J, Liu, ZY, Yu, Y, Li, L, Peng, C, Fan, T, Zhu, Y, Guo, YL, Wang, S, Lu, D, Xing, Y, Yuan, L and Chen, C (2019) Natural variation in the HAN1 gene confers chilling tolerance in rice and allowed adaptation to a temperate climate. Proceedings of the National Academy of Sciences, USA 116, 3494–3501.CrossRefGoogle ScholarPubMed
Rozen, S and Skaletsky, H (2000) Primer3 on the WWW for general users and for biologist programmers. Methods in Molecular Biology 132, 365–386.Google ScholarPubMed
Sohn, HB, Kim, SJ, Hwang, TY, Park, HM, Lee, YY, Markkandan, K, Lee, D, Lee, S, Hong, SY, Song, YH, Koo, BC and Kim, YH (2017) Glycine maxBarcode system for genetic identification of soybean [(L.) Merrill] cultivars using InDel markers specific to dense variation blocks. Frontiers in Plant Science 8, 520–532.CrossRefGoogle ScholarPubMed
Steele, KA, Quinton Tulloch, MJ, Amgai, RB, Dhakal, R, Khatiwada, SP, Vyas, D, Heine, M and Witcombe, JR (2018) Accelerating public sector rice breeding with high-density KASP markers derived from whole genome sequencing of indica rice. Molecular Breeding 38, 38–42.CrossRefGoogle ScholarPubMed
Sun, HY, Gu, WW, Wang, SY, Xu, GM, Luo, B, Yang, ZG, Shen, ZG and Duanmu, YX (2014) Identification of seed purity on hybrid japonica rice ‘Changyou 1’ using SSR markers. Molecular Plant Breeding 12, 1128–1132.Google Scholar
Wang, HN, Chu, ZZ, Ma, XL, Li, RQ and Liu, YG (2013) A high through-put protocol of plant genomic DNA preparation for PCR. Acta Agronomica Sinica 39, 1200–1205.Google Scholar
Wang, WS, Mauleon, R, Hu, ZQ, Chebotarov, D, Tai, SS, Wu, ZC, Li, M, Zheng, TQ, Fuentes, RR, Zhang, F, Mansueto, L, Copetti, D, Sanciangco, M, Palis, KC, Xu, JL, Sun, C, Fu, BY, Zhang, HL, Gao, YM, Zhao, XQ, Shen, F, Cui, X, Yu, H, Li, ZC, Chen, ML, Detras, J, Zhou, YL, Zhang, XY, Zhao, Y, Kudrna, D, Wang, CC, Li, R, Jia, B, Lu, JY, He, XC, Dong, ZT, Xu, JB, Li, YH, Wang, M, Shi, JX, Li, J, Zhang, DB, Lee, S, Hu, WS, Poliakov, A, Dubchak, I, Ulat, V, Borja, F, Mendoza, J, Ali, J, Li, J, Gao, Q, Niu, YC, Yue, Z, Naredo, M, Talag, J, Wang, XQ, Li, JJ, Fang, XD, Yin, Y, Glaszmann, J, Zhang, JW, Li, JY, Hamilton, R, Wing, R, Ruan, J, Zhang, GY, Wei, CC, Alexandrov, N, McNally, K, Li, ZK and Leung, H (2018) Genomic variation in 3,010 diverse accessions of Asian cultivated rice. Nature 557, 43–49.CrossRefGoogle ScholarPubMed
Wu, DH, Wu, HP, Wang, CS, Tseng, HY and Hwu, KK (2013) Genome-wide InDel marker system for application in rice breeding and mapping studies. Euphytica 192, 131–143.CrossRefGoogle Scholar
Yamamoto, T, Nagasaki, H, Yonemaru, J-i, Ebana, K, Nakajima, M, Shibaya, T and Yano, M (2010) Fine definition of the pedigree haplotypes of closely related rice cultivars by means of genome-wide discovery of single-nucleotide polymorphisms. BMC Genomics 11, 267–281.CrossRefGoogle ScholarPubMed
Yashitola, J, Thirumurugan, T, Sundaram, RM, Naseerullah, MK and Ramesha, MS (2002) Assessment of purity of rice hybrids using microsatellite and STS markers. Crop Science 42, 1369–1373.CrossRefGoogle Scholar
Yuan, HR, Yang, WL, Zou, JN, Cheng, MX, Fan, FF, Liang, T, Yu, YJ, Qiu, RH, Li, SQ and Hu, J (2021) InDel markers based on 3k whole-genome re-sequencing data characterise the subspecies of rice (Oryza sativa L.). Agriculture 11, 655–661.CrossRefGoogle Scholar
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