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Title: Development of new marker protocols that identify Waxy gene DNA sequence variations associated with rice grain quality traits

item Chen, Ming Hsuan

Submitted to: Experiment Station Bulletins
Publication Type: Experiment Station
Publication Acceptance Date: 7/1/2009
Publication Date: 7/1/2009
Citation: Chen, M. 2009. Development of new marker protocols that identify Waxy gene DNA sequence variations associated with rice grain quality traits. Texas Experiment Station Field Day Handout. Available:

Interpretive Summary:

Technical Abstract: Cooked rice texture and processing properties are strongly associated with amylose content. Rice breeders, when selecting for breeding lines with specific end-use properties, often select for their amylose content. However, amylose content and other processing properties, i.e. pasting properties, are known to be affected by environmental factors. Therefore, selecting these quality traits of the breeding lines or germplasm based on their genetics would eliminate ambiguity. Both amylose content and pasting properties have been linked to the Waxy gene. Our previous reports demonstrated the strong association of three DNA sequence variation sites or alleles in the Waxy gene with amylose content and pasting properties. Therefore, one cultivar or breeding line can be selected for its amylose class and pasting properties, i.e. low-amylose, intermediate-amylose, high-amylose, or high-amylose-strong-pasting type, based on its DNA sequence at these three sites of the Waxy gene. These sequence variations differ by one nucleotide at each variation site. Thus, the widely used molecular marker method, that is, the simple-sequence-repeat marker method, in molecular breeding programs cannot be used to genotype or identify the DNA sequences at these sites. Several methods were applied in our previous association studies, most of which required special instruments and techniques and were time-consuming. Therefore, it was essential to develop high-throughput molecular marker protocols for genotyping these Waxy gene DNA sequences at these variation sites that are easy to use and that can use currently available instrumentation found in most of the molecular breeding programs. We have developed three molecular markers called allele-specific PCR co-dominant markers to genotype these three functional alleles or sequence variation sites of the Waxy gene. Each marker contains two DNA-sequence specific primers that can identify the DNA sequences at each of the sequence variation sites, along with one common primer. The assay protocols and allele identification are as simple as, and utilize the same instruments as, those for the commonly used simple-sequence-repeat marker method. The simplicity of these marker protocols suggests that these markers can be easily implemented by breeding programs by using marker assisted selection technology for these important grain quality traits.