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A single nucleotide polymorphism in the Waxy gene explains a significant component of gel consistency

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Abstract

Gel consistency (GC) is a standard assay used in rice improvement programmes to determine whether rice cultivars/breeding lines of high amylose content are soft or firm textured when cooked. In this study, we show that sequence variation in exon 10 of the Waxy (Wx) gene associates with GC using RILs derived from parents with high amylose content that differ in GC. The association was validated using a diverse set of traditional varieties, selected on the basis of amylose content, from the generation challenge programme. Structural investigations to explain how the mutation leads to differences in GC showed a strong association between GC and the proportion of amylose that leaches. It was shown that cooked rices of hard GC do not change in hardness over 24 h, whereas rices of soft GC retrograde significantly over 24 h. This leads to the conclusion that the mutation on exon 10 of the Wx gene affects the proportion of amylose bound to amylopectin and the proportion able to leach, and these structural differences alter the composition of the gel, which affects the amount of time the gel takes to reach a final hardness. The SNP described here completes the set of markers required to genotype for the current traits of cooking quality, but selecting the allele for soft texture has the negative result of also selecting for retrogradation potential.

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Acknowledgments

NAT is grateful to ADB for her scholarship and to IRRI for enabling this work, and to Dr Genaleen Diaz and Dr Teresita Borromeo from UPLB for discussions. We thank Violeta Bartolome for assisting in the statistical analyses, the staff of the TT Chang GRC for growing the diverse set of traditional varieties, and the staff in the Plant Breeding, Genetics and Biochemistry Division of IRRI for samples of late generation breeding material for quality evaluation over the years. We thank IRRI for funding quality evaluation, and Teodoro Atienza, Leah Villanueva, Dennis Villegas, Juan Alzona and Romulo Aquino from GQNC quality evaluation program for processing the rice samples and measuring gel consistency on the materials.

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Authors and Affiliations

  1. Grain Quality and Nutrition Centre, International Rice Research Institute, DAPO 7777, Manila, Metro Manila, Philippines

    N. A. Tran, V. D. Daygon, A. P. Resurreccion, R. P. Cuevas, H. M. Corpuz & M. A. Fitzgerald

  2. Genetic and Plant Breeding, CuuLong Delta Rice Research Institute, CanTho, ThoiLai, VietNam

    N. A. Tran

  3. University of the Philippines Los Baños, College, Los Baños, 4031, Laguna, Philippines

    N. A. Tran & H. M. Corpuz

  4. Philippine Rice Research Institute, Maligaya, Science City of Muñoz, 3119, Nueva Ecija, Philippines

    H. M. Corpuz

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  1. N. A. Tran
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  2. V. D. Daygon
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  3. A. P. Resurreccion
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  4. R. P. Cuevas
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  5. H. M. Corpuz
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  6. M. A. Fitzgerald
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Corresponding author

Correspondence to M. A. Fitzgerald.

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Communicated by M. Wissuwa.

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Tran, N.A., Daygon, V.D., Resurreccion, A.P. et al. A single nucleotide polymorphism in the Waxy gene explains a significant component of gel consistency. Theor Appl Genet 123, 519–525 (2011). https://doi.org/10.1007/s00122-011-1604-x

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  • DOI: https://doi.org/10.1007/s00122-011-1604-x

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