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Identifying the Grain Chalkiness Gene Using Molecular Marker Techniques in Rice (Oryza sativa L.)

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Chalkiness is a major constraint on rice production because it is one of the key factors determining grain quality (appearance, processing, milling, storing, eating, and cooking quality) and price. In this study, we conducted grain chalkiness gene identification using co-dominant insertion/deletion (INDEL) markers and SSR marker combination on 50 different varieties. The application results in 7 InDel markers and SSR marker on chromosome 7 were recorded. Three primers, InDel 5, InDel 14 and RM21938, associated with grain chalkiness. For the InDel 5 primer, the amplification product was 100%. Use of primer InDel 5 in detection and evaluation of genotype to the chalkiness trait of rice grain on 50 rice varieties indicated the suitability level with phenotypic evaluation was 86% and the unsuitability level was 14%. For the InDel 14 primer, the amplification products were 100%. The suitability with phenotypic assessment was 84% and the unsuitability was 16%. For the RM21938 primer, the amplification product was 94%. The suitability with phenotypic assessment was 76% and the unsuitability was 24%. Thirteen of the selected varieties had grain chalkiness gene both InDel 5, InDel 14 and RM21938. Total 13 varieties were detected from InDel 5, InDel 14 and RM12938 primer combinations also showed high efficiency of the InDel technique in identifying chalkiness gene in rice grain. A cluster analysis was performed and a dendrogram was constructed which evinced the nature of phylogenetic classification among the genotypes of the varieties. These markers could be used for developing quality of rice in breeding program.


International Letters of Natural Sciences (Volume 63)
N. Thi Lang et al., "Identifying the Grain Chalkiness Gene Using Molecular Marker Techniques in Rice (Oryza sativa L.)", International Letters of Natural Sciences, Vol. 63, pp. 18-26, 2017
Online since:
May 2017

[1] L.J. Zhou et al., Fine mapping of the grain chalkiness QTL qPGWC-7 in rice (Oryza sativa L. ), Theor. Appl. Genet. 118 (2009) 581–590.


[2] Q.S. Jin, B.Q. Qiu, Optical determination of rice grain chalkiness, Int. Rice Res. Newslett. 13(2) (2) (1988) 8.

[3] A.R. Del Rosario et al., Composition and endosperm structure of developing and mature rice kernel, Cereal Chem. 45 (1968) 225–235.

[4] X.P. Yi, F.Y. Cheng, A study on genetic effect of cytoplasm on quality character of indica hybrid rice. I. The analysis of out looking characters and contents of amino acids, J. Guangxi Agric. College. 10(1) (1991) 25–32.

[5] L. Zhou et al., Analysis on grain quality traits of the national authorized indica hybrid rice varieties during 2003 - 2013, Hybrid Rice. 30 (2015) 76–80.

[6] W.Q. Sun et al., Identification of genomicregions and the isoamylase gene for reduced grain chalkiness in rice, PLos One. 10(3) (2015).

[7] S. Yamaki et al., Development of INDEL markers to discriminate all genome types rapidly in the genus Oryza, Breed. Sci. 63 (2013) 246–254.


[8] D.I. Pacurar et al., A collection of INDEL markers for map-based cloning in seven Arabidopsis accessions, J. Exp. Bot. 63 (2012) 2491–2501.


[9] N. Dela Cruz, G.S. Khush, Rice grain quality evaluation procedures, in: Aromatic rice, R.K. Singh, U.S. Singh, G.S. Khush (Eds), Oxford & IBH Publishing Co. Pvt. Ltd, New Delhi, India, 2000, p.16–28.

[10] N. T. Lang, Basic methods in biotechnology research, Agricultural Publisher, Ho Chi Minh City, (2002).

[11] Genome Sequencing Project (IRGSP) on http: /www. rgp. dna. affrc. go. jp/IRGSP/index. html.

[12] Gramene database on http: /www. gramene. org.

[13] M. Nei, W.H. Li, Mathematical model for studying genetically variation in terms of restriction endonucleases, Proceedings of the National Academy of Sciences of the United States of America. 76(10) (1979) 5269–5273.


[14] F.J. Rohlf. NTSYS-PC: Numerical taxonomy and multivariate analysis system, version 1. 75, Applied Biostatistics Inc, New York, USA, (1990).

[15] F. Wang, F. Cheng, G. Zhang, Impact of cultivar variation in grain density of rice panicle on grain weight and quality, Journal of the Science of Food and Agriculture. 88 (2008) 897–903.


[16] Z. J Xu et al., Genetical and physiological basis of plant type model of erect and large panicle japonica super rice in Northern China, Agricultural Sciences in China. 9 (2010) 457–462.


[17] L. Zhou et al., Factors affecting head rice yield and chalkiness in indica rice, Field Crops Res.  172 (2015) 1–10.

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