PCR Marker Set for Rice Photo-sensitivity Module Prediction
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Solution Overview
Problem
Current molecular markers for rice photo-sensitivity are inadequate for predicting the transgressive photo-sensitivity (TPS) in progenies introduced with the Pigm gene, particularly as they focus on single loci and are not suitable for breeding applications, with high testing costs and limited accuracy in evaluating the combined effect of multiple related loci.
Innovation Solution
Development of a PCR-based molecular marker set, including M80410 for qHd6 and ZLM7-1 for qHd7, which effectively identifies the photo-sensitivity module [qHd6+qHd7] in rice, allowing for accurate prediction of TPS in northern early Geng/japonica rice progenies, with an average accuracy of 91.4% and 100% for Heilongjiang and Jilin breeding materials respectively.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If existing molecular markers for single loci are used, then the testing cost is reduced and operation is simplified, but the accuracy of predicting transgressive photo-sensitivity in Pigm gene progenies is insufficient
Solution Approach 1:
The patent combines multiple molecular markers (RM5436, Se9151, Se9153, and novel markers M80410 and ZLM7-1) into an integrated marker set that simultaneously evaluates multiple loci (qHd6, qHd7, and other photo-sensitivity related loci). This merging approach enables comprehensive prediction of transgressive photo-sensitivity by assessing the combined effect of multiple genetic loci, thereby improving prediction accuracy from single-locus to multi-locus level while maintaining practical applicability in breeding programs.
2Measurement precision
If restricted endonuclease markers (Se9151 and Se9153) are used, then the measurement precision for Ghd7 locus is improved, but the testing cost increases and operation becomes more complex
Solution Approach 1:
The patent segments the photo-sensitivity evaluation into multiple independent locus assessments, each with its own optimized marker. For the Ghd7 locus, it uses the established Se9151 and Se9153 markers, while for qHd6 locus it employs M80410 marker. This segmentation allows breeders to evaluate different loci independently and combine results, improving overall detection accuracy while maintaining operational simplicity through modular assessment approach.
Solution Approach 2:
The patent introduces near-isogenic line Kongyu 131 as an intermediary reference material that carries the Pigm gene in a standardized genetic background. This intermediary enables consistent and reproducible testing across different breeding programs, facilitating accurate comparison and evaluation of photo-sensitivity traits while simplifying the overall testing procedure through standardized reference comparisons.
3Device complexity
If marker RM5436 is used for Ghd7 locus, then the device complexity is reduced, but the reliability of marker-target linkage is insufficient due to prone crossover
Solution Approach 1:
The patent develops and validates multiple copy markers (M80410 for qHd6, and ZLM7-1 for Ghd7) that target specific loci with high reliability. These marker copies are designed to be closely linked to their respective target genes, minimizing crossover events. The use of multiple validated marker copies ensures reliable detection while maintaining system simplicity, as each marker is independently optimized for its specific target locus.
Data Source
AI summary
This invention describes a work including both genetic analysis and development of a marker set for a photo-sensitivity module underlying transgressive photo-sensitivity (TPS) phenomenon found in the breeding improvement of rice blast resistance by the introduction of Pigm gene, belonging to the field of rice molecular genetics and biotechnology breeding. By using bi-parental RIL populations derived from TPS crosses with a Pigm donor as one parent, genetic analysis has been carried out to map the photo-sensitivity module [qHd6+qHd7] under both long-day (LD) and short-day (SD) conditions. With the aid of the molecular marker set proposed by this invention for this module, breeders can predict the degree of TPS in northern early Geng/japonica rice progenies derived from crosses with Pigm donor as one parent when they are doing parental selection or screening progenies carrying Pigm without strong TPS in blast-resistant biotechnology breeding schemes.